--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rps_test.tab	Mon Mar 04 19:55:52 2024 +0000
@@ -0,0 +1,105 @@
+#query_id	query_length	cdd_id	hit_id	evalue	startQ	endQ	frame	description	superkingdom
+ds2020-267_120	339	pfam01333	gnl|CDD|366578	0.000848733	197	325	-3	pfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal.  This is a sub-family of cytochrome C. See pfam00034.	Eukaryota(19);Bacteria(1)
+ds2020-267_374	242	pfam00124	gnl|CDD|365890	5.09126e-07	21	125	3	pfam00124, Photo_RC, Photosynthetic reaction centre protein.  	Bacteria(9);Eukaryota(6);Viruses(4);unclassified sequences(1)
+ds2020-267_471	230	pfam00201	gnl|CDD|278624	3.12575e-07	46	210	1	pfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase.  	Eukaryota(20)
+ds2020-267_710	213	pfam01127	gnl|CDD|366480	0.000723904	46	210	1	pfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase transmembrane subunit.  This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.	Bacteria(20)
+ds2020-267_692	214	pfam00680	gnl|CDD|366242	4.79875e-05	70	180	1	pfam00680, RdRP_1, RNA dependent RNA polymerase.  	Viruses(20)
+ds2020-267_817	208	pfam05656	gnl|CDD|377540	3.45664e-06	86	190	-1	pfam05656, DUF805, Protein of unknown function (DUF805).  This family consists of several bacterial proteins of unknown function.	Bacteria(17);unclassified sequences(2);Archaea(1)
+ds2020-267_98	379	pfam16203	gnl|CDD|374428	1.33948e-30	131	280	-1	pfam16203, ERCC3_RAD25_C, ERCC3/RAD25/XPB C-terminal helicase.  This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases.	Bacteria(11);Eukaryota(6);Archaea(2);unclassified sequences(1)
+ds2020-267_21	858	pfam00680	gnl|CDD|366242	8.36679e-11	295	729	-1	pfam00680, RdRP_1, RNA dependent RNA polymerase.  	Viruses(20)
+ds2020-267_261	260	pfam01051	gnl|CDD|376444	1.77523e-19	26	217	-2	pfam01051, Rep_3, Initiator Replication protein.  This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene.	Bacteria(19);unclassified sequences(1)
+ds2020-267_773	210	pfam01641	gnl|CDD|376583	5.23903e-34	16	174	1	pfam01641, SelR, SelR domain.  Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.	Bacteria(18);Archaea(1);unclassified sequences(1)
+ds2020-267_287	256	pfam00115	gnl|CDD|376293	2.8946e-26	13	237	1	pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I.  	Eukaryota(18);Bacteria(2)
+ds2020-267_139	320	pfam05860	gnl|CDD|368641	1.34887e-13	167	298	2	pfam05860, Haemagg_act, haemagglutination activity domain.  This domain is suggested to be a carbohydrate- dependent haemagglutination activity site. It is found in a range of haemagglutinins and haemolysins.	Bacteria(20)
+ds2020-267_763	211	pfam00557	gnl|CDD|376349	0.000231782	167	298	2	pfam00557, Peptidase_M24, Metallopeptidase family M24.  This family contains metallopeptidases. It also contains non-peptidase homologs such as the N terminal domain of Spt16 which is a histone H3-H4 binding module.	Bacteria(18);Archaea(2)
+ds2020-267_571	221	pfam00501	gnl|CDD|366135	2.61467e-07	34	201	1	pfam00501, AMP-binding, AMP-binding enzyme.  	Bacteria(17);Eukaryota(2);unclassified sequences(1)
+ds2020-267_565	222	pfam03950	gnl|CDD|377172	9.52435e-10	53	184	-3	pfam03950, tRNA-synt_1c_C, tRNA synthetases class I (E and Q), anti-codon binding domain.  Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).	Bacteria(16);Archaea(3);Eukaryota(1)
+ds2020-267_427	235	pfam03154	gnl|CDD|367360	0.000552392	53	184	-3	pfam03154, Atrophin-1, Atrophin-1 family.  Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.	Eukaryota(20)
+ds2020-267_4	2297	pfam00680	gnl|CDD|366242	4.43825e-05	995	1510	-2	pfam00680, RdRP_1, RNA dependent RNA polymerase.  	Viruses(20)
+ds2020-267_16	1165	pfam00680	gnl|CDD|366242	8.1737e-06	707	1042	-1	pfam00680, RdRP_1, RNA dependent RNA polymerase.  	Viruses(20)
+ds2020-267_438	234	pfam00078	gnl|CDD|365856	0.000870142	707	1042	-1	pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA polymerase).  A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.	Eukaryota(16);Viruses(4)
+ds2020-267_370	242	pfam00146	gnl|CDD|376297	2.41391e-10	22	111	1	pfam00146, NADHdh, NADH dehydrogenase.  	Bacteria(14);Eukaryota(3);Archaea(2);unclassified sequences(1)
+ds2020-267_278	258	pfam00012	gnl|CDD|365808	4.1355e-19	50	232	2	pfam00012, HSP70, Hsp70 protein.  Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.	Bacteria(15);Eukaryota(4);Viruses(1)
+ds2020-267_364	243	pfam00216	gnl|CDD|365952	1.5507e-10	134	241	-3	pfam00216, Bac_DNA_binding, Bacterial DNA-binding protein.  	Bacteria(19);unclassified sequences(1)
+ds2020-267_558	222	pfam03737	gnl|CDD|377116	4.93695e-13	57	179	-2	pfam03737, RraA-like, Aldolase/RraA.  Members of this family include regulator of ribonuclease E activity A (RraA) and 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy- 4-hydroxy-2-oxoadipate (CHA) aldolase, also known as RraA-like protein. RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing. RraA-like proteins seem to contain aldolase and/or decarboxylase activity either in place of or in addition to the RNase E inhibitor functions.	Bacteria(19);unclassified sequences(1)
+ds2020-267_218	274	pfam01348	gnl|CDD|279664	1.66328e-05	51	257	3	pfam01348, Intron_maturas2, Type II intron maturase.  Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X.	Eukaryota(15);Bacteria(5)
+ds2020-267_363	243	pfam00416	gnl|CDD|366086	2.02528e-05	15	134	-2	pfam00416, Ribosomal_S13, Ribosomal protein S13/S18.  This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.	Bacteria(16);Archaea(3);Eukaryota(1)
+ds2020-267_746	211	pfam01490	gnl|CDD|279788	0.000177299	15	134	-2	pfam01490, Aa_trans, Transmembrane amino acid transporter protein.  This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases.	Eukaryota(20)
+ds2020-267_145	315	pfam02626	gnl|CDD|376868	3.97676e-05	140	256	-3	pfam02626, CT_A_B, Carboxyltransferase domain, subdomain A and B.  Urea carboxylase (UC) catalyzes a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the A and B subdomains of the CT domain. This domain covers the whole length of KipA (kinase A) from Bacillus subtilis. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity.	Bacteria(19);unclassified sequences(1)
+ds2020-267_637	217	pfam07026	gnl|CDD|284449	1.36077e-13	47	172	2	pfam07026, DUF1317, Protein of unknown function (DUF1317).  This family consists of several hypothetical bacterial and phage proteins of around 60 residues in length. The function of this family is unknown.	Bacteria(20)
+ds2020-267_557	222	pfam00421	gnl|CDD|366090	3.32623e-20	12	200	-2	pfam00421, PSII, Photosystem II protein.  	Eukaryota(13);Bacteria(7)
+ds2020-267_117	344	pfam00252	gnl|CDD|376306	7.27175e-23	107	295	2	pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.  	Bacteria(16);Archaea(3);Eukaryota(1)
+ds2020-267_352	245	pfam00946	gnl|CDD|366381	3.23548e-05	1	141	1	pfam00946, Mononeg_RNA_pol, Mononegavirales RNA dependent RNA polymerase.  Members of the Mononegavirales including the Paramyxoviridae, like other non-segmented negative strand RNA viruses, have an RNA-dependent RNA polymerase composed of two subunits, a large protein L and a phosphoprotein P. This is a protein family of the L protein. The L protein confers the RNA polymerase activity on the complex. The P protein acts as a transcription factor.	Viruses(20)
+ds2020-267_97	380	pfam04879	gnl|CDD|368171	1.9903e-08	125	274	-2	pfam04879, Molybdop_Fe4S4, Molybdopterin oxidoreductase Fe4S4 domain.  This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of Structure 1aa6 is an Fe4S4 cluster just below the protein surface.	Bacteria(19);unclassified sequences(1)
+ds2020-267_2	2436	pfam02123	gnl|CDD|280316	2.17343e-21	184	1476	1	pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.	Viruses(19);unclassified sequences(1)
+ds2020-267_595	219	pfam02123	gnl|CDD|280316	5.90575e-11	13	210	1	pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.	Viruses(19);unclassified sequences(1)
+ds2020-267_622	217	pfam01370	gnl|CDD|366597	1.5719e-08	50	172	2	pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.  This family of proteins utilize NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions.	Bacteria(17);unclassified sequences(2);Archaea(1)
+ds2020-267_214	276	pfam00070	gnl|CDD|365851	1.70856e-05	135	254	3	pfam00070, Pyr_redox, Pyridine nucleotide-disulphide oxidoreductase.  This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Eukaryota(12);Bacteria(5);unclassified sequences(2);Archaea(1)
+ds2020-267_610	218	pfam17759	gnl|CDD|380005	1.47034e-13	25	195	1	pfam17759, tRNA_synthFbeta, Phenylalanyl tRNA synthetase beta chain CLM domain.  This domain corresponds to the catalytic like domain (CLM) in the beta chain of phe tRNA synthetase.	Bacteria(17);Archaea(2);unclassified sequences(1)
+ds2020-267_94	386	pfam01347	gnl|CDD|366585	0.000224462	25	195	1	pfam01347, Vitellogenin_N, Lipoprotein amino terminal region.  This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.	Eukaryota(20)
+ds2020-267_323	250	pfam00227	gnl|CDD|365960	5.8155e-09	10	150	-2	pfam00227, Proteasome, Proteasome subunit.  The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologs vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria. The second is call beta-proteobacteria proteasome homolog (BPH).	Eukaryota(8);Bacteria(7);Archaea(5)
+ds2020-267_168	298	pfam13546	gnl|CDD|379252	0.000766911	10	150	-2	pfam13546, DDE_5, DDE superfamily endonuclease.  This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.	Bacteria(18);unclassified sequences(2)
+ds2020-267_636	217	pfam13812	gnl|CDD|316342	0.000111468	16	123	-2	pfam13812, PPR_3, Pentatricopeptide repeat domain.  This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.	Eukaryota(20)
+ds2020-267_486	228	pfam17035	gnl|CDD|374956	5.12677e-09	108	203	3	pfam17035, BET, Bromodomain extra-terminal - transcription regulation.  The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins.	Eukaryota(20)
+ds2020-267_599	219	pfam05717	gnl|CDD|377551	3.2952e-06	28	147	1	pfam05717, TnpB_IS66, IS66 Orf2 like protein.  This protein is found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition.	Bacteria(19);unclassified sequences(1)
+ds2020-267_837	207	pfam04061	gnl|CDD|367791	2.43363e-18	1	159	1	pfam04061, ORMDL, ORMDL family.  Evidence form suggests that ORMDLs are involved in protein folding in the ER. Orm proteins have been identified as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. This novel and conserved protein complex, has been termed the SPOTS complex (serine palmitoyltransferase, Orm1/2, Tsc3, and Sac1).	Eukaryota(20)
+ds2020-267_516	225	pfam00115	gnl|CDD|376293	0.000272517	1	159	1	pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I.  	Eukaryota(18);Bacteria(2)
+ds2020-267_529	224	pfam00510	gnl|CDD|366140	6.14777e-23	35	211	2	pfam00510, COX3, Cytochrome c oxidase subunit III.  	Bacteria(15);Eukaryota(3);unclassified sequences(1);Archaea(1)
+ds2020-267_230	268	pfam00115	gnl|CDD|376293	1.95663e-15	81	236	-3	pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I.  	Eukaryota(18);Bacteria(2)
+ds2020-267_444	233	pfam00680	gnl|CDD|366242	0.00060937	81	236	-3	pfam00680, RdRP_1, RNA dependent RNA polymerase.  	Viruses(20)
+ds2020-267_336	248	pfam00113	gnl|CDD|365883	4.23282e-13	15	116	-1	pfam00113, Enolase_C, Enolase, C-terminal TIM barrel domain.  	Bacteria(17);Archaea(2);unclassified sequences(1)
+ds2020-267_365	243	pfam13041	gnl|CDD|372443	0.000129396	15	116	-1	pfam13041, PPR_2, PPR repeat family.  This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.	Eukaryota(20)
+ds2020-267_75	425	pfam00005	gnl|CDD|365804	4.26261e-07	129	275	-1	pfam00005, ABC_tran, ABC transporter.  ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide as in CFTR, or belong in different polypeptide chains.	Bacteria(19);unclassified sequences(1)
+ds2020-267_8	1703	pfam00680	gnl|CDD|366242	2.85682e-13	685	1458	-3	pfam00680, RdRP_1, RNA dependent RNA polymerase.  	Viruses(20)
+ds2020-267_114	347	pfam00471	gnl|CDD|376336	8.05888e-12	132	302	3	pfam00471, Ribosomal_L33, Ribosomal protein L33.  	Bacteria(20)
+ds2020-267_589	219	pfam12161	gnl|CDD|378823	0.0004347	132	302	3	pfam12161, HsdM_N, HsdM N-terminal domain.  This domain is found at the N-terminus of the methylase subunit of Type I DNA methyltransferases. This domain family is found in bacteria and archaea, and is typically between 123 and 138 amino acids in length. The family is found in association with pfam02384. Mutations in this region of EcoKI methyltransferase abolish the normally strong preference of this system for methylating hemimethylated substrate. The structure of this domain has been shown to be all alpha-helical.	Bacteria(20)
+ds2020-267_206	279	pfam03947	gnl|CDD|377170	2.63457e-16	155	265	2	pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal domain.  	Bacteria(15);Archaea(4);Eukaryota(1)
+ds2020-267_316	251	pfam02123	gnl|CDD|280316	3.50628e-08	28	228	-3	pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.	Viruses(19);unclassified sequences(1)
+ds2020-267_697	214	pfam00378	gnl|CDD|334046	5.08319e-08	45	170	-3	pfam00378, ECH_1, Enoyl-CoA hydratase/isomerase.  This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase.	Bacteria(17);unclassified sequences(2);Archaea(1)
+ds2020-267_318	251	pfam00252	gnl|CDD|376306	5.63854e-12	78	206	-1	pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.  	Bacteria(16);Archaea(3);Eukaryota(1)
+ds2020-267_20	893	pfam02874	gnl|CDD|367225	7.30466e-19	126	329	3	pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain.  This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.	Bacteria(17);Eukaryota(2);Archaea(1)
+ds2020-267_329	249	pfam13173	gnl|CDD|379049	4.80752e-08	106	249	1	pfam13173, AAA_14, AAA domain.  This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.	Bacteria(19);Archaea(1)
+ds2020-267_130	330	pfam00680	gnl|CDD|366242	7.64962e-05	124	282	1	pfam00680, RdRP_1, RNA dependent RNA polymerase.  	Viruses(20)
+ds2020-267_280	257	pfam01788	gnl|CDD|366811	2.47901e-09	132	224	-1	pfam01788, PsbJ, PsbJ.  This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. In Synechocystis sp. PCC 6803 PsbJ regulates the number of photosystem II centers in thylakoid membranes, it is a predicted 4kDa protein with one membrane spanning domain.	Eukaryota(17);Bacteria(3)
+ds2020-267_100	376	pfam00401	gnl|CDD|366077	8.90041e-05	87	218	-3	pfam00401, ATP-synt_DE, ATP synthase, Delta/Epsilon chain, long alpha-helix domain.  Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213).	Bacteria(18);unclassified sequences(2)
+ds2020-267_436	234	pfam00155	gnl|CDD|365910	0.000283584	87	218	-3	pfam00155, Aminotran_1_2, Aminotransferase class I and II.  	Bacteria(19);Archaea(1)
+ds2020-267_210	276	pfam17919	gnl|CDD|375430	6.42624e-11	52	237	1	pfam17919, RT_RNaseH_2, RNase H-like domain found in reverse transcriptase.  	Eukaryota(20)
+ds2020-267_58	476	pfam03641	gnl|CDD|367590	7.19579e-14	142	315	-3	pfam03641, Lysine_decarbox, Possible lysine decarboxylase.  The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear.	Bacteria(17);Eukaryota(2);unclassified sequences(1)
+ds2020-267_466	230	pfam00072	gnl|CDD|333815	5.42419e-08	50	208	2	pfam00072, Response_reg, Response regulator receiver domain.  This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Bacteria(20)
+ds2020-267_118	343	pfam00421	gnl|CDD|366090	7.68219e-41	92	337	-1	pfam00421, PSII, Photosystem II protein.  	Eukaryota(13);Bacteria(7)
+ds2020-267_643	216	pfam00078	gnl|CDD|365856	0.000675747	92	337	-1	pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA polymerase).  A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.	Eukaryota(16);Viruses(4)
+ds2020-267_5	2029	pfam00680	gnl|CDD|366242	0.000288253	92	337	-1	pfam00680, RdRP_1, RNA dependent RNA polymerase.  	Viruses(20)
+ds2020-267_506	226	pfam05173	gnl|CDD|377479	2.45773e-17	93	215	-3	pfam05173, DapB_C, Dihydrodipicolinate reductase, C-terminus.  Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain.	Bacteria(19);unclassified sequences(1)
+ds2020-267_315	251	pfam13426	gnl|CDD|379177	0.000472059	32	241	2	pfam13426, PAS_9, PAS domain.  	Bacteria(19);unclassified sequences(1)
+ds2020-267_227	272	pfam00873	gnl|CDD|334294	2.32215e-15	36	245	-1	pfam00873, ACR_tran, AcrB/AcrD/AcrF family.  Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer membrane channel TolC. The structure shows the AcrB forms a homotrimer.	Bacteria(20)
+ds2020-267_639	216	pfam00033	gnl|CDD|306530	3.68894e-05	2	118	2	pfam00033, Cytochrome_B, Cytochrome b/b6/petB.  	Eukaryota(16);Bacteria(4)
+ds2020-267_407	239	pfam00177	gnl|CDD|365924	1.14399e-06	28	126	1	pfam00177, Ribosomal_S7, Ribosomal protein S7p/S5e.  This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.	Bacteria(16);Archaea(3);Eukaryota(1)
+ds2020-267_457	231	pfam00481	gnl|CDD|366121	0.000499491	28	126	1	pfam00481, PP2C, Protein phosphatase 2C.  Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase.	Eukaryota(20)
+ds2020-267_402	239	pfam06122	gnl|CDD|368759	0.000851192	28	126	1	pfam06122, TraH, Conjugative relaxosome accessory transposon protein.  The TraH protein is thought to be a relaxosome accessory component, also necessary for transfer but not for H-pilus synthesis within the conjugative transposon.	Bacteria(20)
+ds2020-267_369	243	pfam12137	gnl|CDD|378818	6.51052e-05	137	217	-3	pfam12137, RapA_C, RNA polymerase recycling family C-terminal.  This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with pfam00271, pfam00176. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement.	Bacteria(19);unclassified sequences(1)
+ds2020-267_750	211	pfam02391	gnl|CDD|376774	1.24642e-05	28	114	-2	pfam02391, MoaE, MoaE protein.  This family contains the MoaE protein that is involved in biosynthesis of molybdopterin. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.	Bacteria(17);Archaea(2);unclassified sequences(1)
+ds2020-267_428	235	pfam00164	gnl|CDD|333891	1.04166e-24	3	182	3	pfam00164, Ribosom_S12_S23, Ribosomal protein S12/S23.  This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.	Bacteria(16);Archaea(3);Eukaryota(1)
+ds2020-267_203	281	pfam03040	gnl|CDD|367312	1.76794e-22	121	231	-3	pfam03040, CemA, CemA family.  Members of this family are probable integral membrane proteins. Their molecular function is unknown. CemA proteins are found in the inner envelope membrane of chloroplasts but not in the thylakoid membrane. A cyanobacterial member of this family has been implicated in CO2 transport, but is probably not a CO2 transporter itself. They are predicted to be haem-binding however this has not been proven experimentally.	Eukaryota(20)
+ds2020-267_33	680	pfam04157	gnl|CDD|367847	4.86455e-13	342	494	-1	pfam04157, EAP30, EAP30/Vps36 family.  This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity.	Eukaryota(17);Archaea(3)
+ds2020-267_6	1860	pfam02123	gnl|CDD|280316	1.35634e-17	1147	1764	-1	pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.	Viruses(19);unclassified sequences(1)
+ds2020-267_555	222	pfam00124	gnl|CDD|365890	7.71427e-08	48	203	3	pfam00124, Photo_RC, Photosynthetic reaction centre protein.  	Bacteria(9);Eukaryota(6);Viruses(4);unclassified sequences(1)
+ds2020-267_550	223	pfam05694	gnl|CDD|377548	0.00097637	48	203	3	pfam05694, SBP56, 56kDa selenium binding protein (SBP56).  This family consists of several eukaryotic selenium binding proteins as well as three sequences from archaea. The exact function of this protein is unknown although it is thought that SBP56 participates in late stages of intra-Golgi protein transport. The Lotus japonicus homolog of SBP56, LjSBP is thought to have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport.	Bacteria(12);Eukaryota(8)
+ds2020-267_65	462	pfam13406	gnl|CDD|372592	4.82338e-27	145	360	-1	pfam13406, SLT_2, Transglycosylase SLT domain.  This family is related to the SLT domain pfam01464.	Bacteria(19);unclassified sequences(1)
+ds2020-267_729	212	pfam01405	gnl|CDD|279713	5.43744e-05	19	99	-3	pfam01405, PsbT, Photosystem II reaction centre T protein.  The exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The Chlamydomonas reinhardtii psbT protein appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity under adverse growth conditions.	Eukaryota(17);Bacteria(3)
+ds2020-267_404	239	pfam00361	gnl|CDD|366050	3.50341e-05	70	219	1	pfam00361, Proton_antipo_M, Proton-conducting membrane transporter.  This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla.	Bacteria(16);Eukaryota(2);Archaea(1);unclassified sequences(1)
+ds2020-267_312	252	pfam00585	gnl|CDD|278982	1.52007e-05	29	166	2	pfam00585, Thr_dehydrat_C, C-terminal regulatory domain of Threonine dehydratase.  Threonine dehydratases pfam00291 all contain a carboxy terminal region. This region may have a regulatory role. Some members contain two copies of this region. This family is homologous to the pfam01842 domain.	Bacteria(19);unclassified sequences(1)
+ds2020-267_176	291	pfam01235	gnl|CDD|376500	1.13408e-29	115	243	1	pfam01235, Na_Ala_symp, Sodium:alanine symporter family.  	Bacteria(19);unclassified sequences(1)
+ds2020-267_388	241	pfam02123	gnl|CDD|280316	6.16383e-08	35	214	-1	pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.	Viruses(19);unclassified sequences(1)
+ds2020-267_669	215	pfam17862	gnl|CDD|380037	4.46873e-06	33	122	-1	pfam17862, AAA_lid_3, AAA+ lid domain.  This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Eukaryota(9);Bacteria(8);Archaea(3)
+ds2020-267_187	287	pfam02673	gnl|CDD|376891	3.59766e-13	7	156	1	pfam02673, BacA, Bacitracin resistance protein BacA.  Bacitracin resistance protein (BacA) is a putative undecaprenol kinase. BacA confers resistance to bacitracin, probably by phosphorylation of undecaprenol. More recent studies show that BacA has undecaprenyl pyrophosphate phosphatase activity. Undecaprenyl phosphate is a key lipid intermediate involved in the synthesis of various bacterial cell wall polymers. Bacitracin, a mixture of related cyclic polypeptide antibiotics, is used to treat surface tissue infections. Its primary mode of action is the inhibition of bacterial cell wall synthesis through sequestration of the essential carrier lipid undecaprenyl pyrophosphate, C55-PP, resulting in the loss of cell integrity and lysis. The characteristic phosphatase sequence-motif in this family is likely to be the PGxSRSGG, compared with the PSGH of the PAP family of phosphatases.	Bacteria(19);unclassified sequences(1)
+ds2020-267_641	216	pfam00804	gnl|CDD|366315	9.72957e-23	23	187	-3	pfam00804, Syntaxin, Syntaxin.  Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteristic of and conserved in all syntaxins (pfam05739), and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A it is found as three alpha-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role. The function of syntaxins is determined by their localization. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors.	Eukaryota(20)
+ds2020-267_597	219	pfam00421	gnl|CDD|366090	8.10522e-27	22	207	1	pfam00421, PSII, Photosystem II protein.  	Eukaryota(13);Bacteria(7)
+ds2020-267_268	259	pfam02123	gnl|CDD|280316	3.22949e-21	18	251	3	pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.	Viruses(19);unclassified sequences(1)
+ds2020-267_719	213	pfam00072	gnl|CDD|333815	9.1657e-13	45	185	-2	pfam00072, Response_reg, Response regulator receiver domain.  This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Bacteria(20)
+ds2020-267_811	208	pfam07991	gnl|CDD|285265	1.80927e-08	20	190	-1	pfam07991, IlvN, Acetohydroxy acid isomeroreductase, NADPH-binding domain.  Acetohydroxy acid isomeroreductase catalyzes the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine. This N-terminal region of the enzyme carries the binding-site for NADPH. The active-site for enzymatic activity lies in the C-terminal part, IlvC, pfam01450.	Bacteria(16);Archaea(2);unclassified sequences(2)
+ds2020-267_642	216	pfam02874	gnl|CDD|367225	0.000376273	20	190	-1	pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain.  This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.	Bacteria(17);Eukaryota(2);Archaea(1)
+ds2020-267_504	226	pfam01578	gnl|CDD|307628	0.000112784	20	190	-1	pfam01578, Cytochrom_C_asm, Cytochrome C assembly protein.  This family consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium, CcmC from E. coli and Paracoccus denitrificans and orf240 from wheat mitochondria. The members of this family are probably integral membrane proteins with six predicted transmembrane helices. It has been proposed that members of this family comprise a membrane component of an ABC (ATP binding cassette) transporter complex. It is also proposed that this transporter is necessary for transport of some component needed for cytochrome c assembly. One member CycK contains a putative heme-binding motif, orf240 also contains a putative heme-binding motif and is a proposed ABC transporter with c-type heme as its proposed substrate. However it seems unlikely that all members of this family transport heme nor c-type apocytochromes because CcmC in the putative CcmABC transporter transports neither. CcmF forms a working module with CcmH and CcmI, CcmFHI, and itself is unlikely to bind haem directly.	Bacteria(19);Archaea(1)
+ds2020-267_274	258	pfam03713	gnl|CDD|367619	9.45376e-09	24	173	-2	pfam03713, DUF305, Domain of unknown function (DUF305).  Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1. This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important. This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha helices.	Bacteria(18);unclassified sequences(2)
+ds2020-267_42	575	pfam00283	gnl|CDD|365999	2.95472e-07	325	411	1	pfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits.  	Eukaryota(18);Bacteria(2)
+ds2020-267_283	257	pfam13041	gnl|CDD|372443	3.148e-06	13	114	1	pfam13041, PPR_2, PPR repeat family.  This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.	Eukaryota(20)
+ds2020-267_685	214	pfam09334	gnl|CDD|370442	1.80219e-14	16	117	-2	pfam09334, tRNA-synt_1g, tRNA synthetases class I (M).  This family includes methionyl tRNA synthetases.	Bacteria(17);Archaea(2);unclassified sequences(1)