Mercurial > repos > peterjc > blastxml_to_top_descr

diff test-data/blastp_four_human_vs_rhodopsin.xml @ 13:8dc4ba7eba5d draft default tip

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v0.1.2 with Python 3.9 declaration
author peterjc
date Sun, 17 Sep 2023 13:01:56 +0000
parents 98f8431dab44
children
line wrap: on
line diff
--- a/test-data/blastp_four_human_vs_rhodopsin.xml	Wed Jul 30 05:36:52 2014 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin.xml	Sun Sep 17 13:01:56 2023 +0000
@@ -2,10 +2,10 @@
 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastp</BlastOutput_program>
-  <BlastOutput_version>BLASTP 2.2.29+</BlastOutput_version>
+  <BlastOutput_version>BLASTP 2.10.1+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
-  <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>
+  <BlastOutput_query-ID>Q9BS26</BlastOutput_query-ID>
   <BlastOutput_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
   <BlastOutput_query-len>406</BlastOutput_query-len>
   <BlastOutput_param>
@@ -20,7 +20,7 @@
 <BlastOutput_iterations>
 <Iteration>
   <Iteration_iter-num>1</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
+  <Iteration_query-ID>Q9BS26</Iteration_query-ID>
   <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
   <Iteration_query-len>406</Iteration_query-len>
 <Iteration_hits>
@@ -29,8 +29,8 @@
     <Statistics>
       <Statistics_db-num>0</Statistics_db-num>
       <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>30</Statistics_hsp-len>
-      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_hsp-len>42</Statistics_hsp-len>
+      <Statistics_eff-space>657748</Statistics_eff-space>
       <Statistics_kappa>0.041</Statistics_kappa>
       <Statistics_lambda>0.267</Statistics_lambda>
       <Statistics_entropy>0.14</Statistics_entropy>
@@ -40,17 +40,17 @@
 </Iteration>
 <Iteration>
   <Iteration_iter-num>2</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
+  <Iteration_query-ID>Q9NSY1</Iteration_query-ID>
+  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
+  <Iteration_query-len>1161</Iteration_query-len>
 <Iteration_hits>
 </Iteration_hits>
   <Iteration_stat>
     <Statistics>
       <Statistics_db-num>0</Statistics_db-num>
       <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>30</Statistics_hsp-len>
-      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_hsp-len>50</Statistics_hsp-len>
+      <Statistics_eff-space>1954249</Statistics_eff-space>
       <Statistics_kappa>0.041</Statistics_kappa>
       <Statistics_lambda>0.267</Statistics_lambda>
       <Statistics_entropy>0.14</Statistics_entropy>
@@ -60,17 +60,17 @@
 </Iteration>
 <Iteration>
   <Iteration_iter-num>3</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
+  <Iteration_query-ID>P06213</Iteration_query-ID>
+  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
+  <Iteration_query-len>1382</Iteration_query-len>
 <Iteration_hits>
 </Iteration_hits>
   <Iteration_stat>
     <Statistics>
       <Statistics_db-num>0</Statistics_db-num>
       <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>30</Statistics_hsp-len>
-      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_hsp-len>51</Statistics_hsp-len>
+      <Statistics_eff-space>2333243</Statistics_eff-space>
       <Statistics_kappa>0.041</Statistics_kappa>
       <Statistics_lambda>0.267</Statistics_lambda>
       <Statistics_entropy>0.14</Statistics_entropy>
@@ -80,307 +80,7 @@
 </Iteration>
 <Iteration>
   <Iteration_iter-num>4</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>30</Statistics_hsp-len>
-      <Statistics_eff-space>119568</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>5</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>30</Statistics_hsp-len>
-      <Statistics_eff-space>119568</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>6</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>30</Statistics_hsp-len>
-      <Statistics_eff-space>119568</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>7</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>38</Statistics_hsp-len>
-      <Statistics_eff-space>348130</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>8</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>38</Statistics_hsp-len>
-      <Statistics_eff-space>348130</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>9</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>38</Statistics_hsp-len>
-      <Statistics_eff-space>348130</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>10</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>38</Statistics_hsp-len>
-      <Statistics_eff-space>348130</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>11</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>38</Statistics_hsp-len>
-      <Statistics_eff-space>348130</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>12</Iteration_iter-num>
-  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>38</Statistics_hsp-len>
-      <Statistics_eff-space>348130</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>13</Iteration_iter-num>
-  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>39</Statistics_hsp-len>
-      <Statistics_eff-space>414987</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>14</Iteration_iter-num>
-  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>39</Statistics_hsp-len>
-      <Statistics_eff-space>414987</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>15</Iteration_iter-num>
-  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>39</Statistics_hsp-len>
-      <Statistics_eff-space>414987</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>16</Iteration_iter-num>
-  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>39</Statistics_hsp-len>
-      <Statistics_eff-space>414987</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>17</Iteration_iter-num>
-  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>39</Statistics_hsp-len>
-      <Statistics_eff-space>414987</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>18</Iteration_iter-num>
-  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>39</Statistics_hsp-len>
-      <Statistics_eff-space>414987</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>19</Iteration_iter-num>
-  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
+  <Iteration_query-ID>P08100</Iteration_query-ID>
   <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
   <Iteration_query-len>348</Iteration_query-len>
 <Iteration_hits>
@@ -412,74 +112,36 @@
     </Hsp>
   </Hit_hsps>
 </Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>29</Statistics_hsp-len>
-      <Statistics_eff-space>101761</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>20</Iteration_iter-num>
-  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
 <Hit>
-  <Hit_num>1</Hit_num>
-  <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
-  <Hit_def>RecName: Full=Rhodopsin</Hit_def>
-  <Hit_accession>P56514</Hit_accession>
-  <Hit_len>354</Hit_len>
+  <Hit_num>2</Hit_num>
+  <Hit_id>gi|223523|prf||0811197A</Hit_id>
+  <Hit_def>rhodopsin [Bos taurus]</Hit_def>
+  <Hit_accession>0811197A</Hit_accession>
+  <Hit_len>347</Hit_len>
   <Hit_hsps>
     <Hsp>
       <Hsp_num>1</Hsp_num>
-      <Hsp_bit-score>619.002</Hsp_bit-score>
-      <Hsp_score>1595</Hsp_score>
+      <Hsp_bit-score>673.315</Hsp_bit-score>
+      <Hsp_score>1736</Hsp_score>
       <Hsp_evalue>0</Hsp_evalue>
       <Hsp_query-from>1</Hsp_query-from>
-      <Hsp_query-to>341</Hsp_query-to>
+      <Hsp_query-to>348</Hsp_query-to>
       <Hsp_hit-from>1</Hsp_hit-from>
-      <Hsp_hit-to>342</Hsp_hit-to>
+      <Hsp_hit-to>347</Hsp_hit-to>
       <Hsp_query-frame>0</Hsp_query-frame>
       <Hsp_hit-frame>0</Hsp_hit-frame>
-      <Hsp_identity>290</Hsp_identity>
-      <Hsp_positive>322</Hsp_positive>
+      <Hsp_identity>324</Hsp_identity>
+      <Hsp_positive>336</Hsp_positive>
       <Hsp_gaps>1</Hsp_gaps>
-      <Hsp_align-len>342</Hsp_align-len>
-      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>
-      <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>
-      <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE</Hsp_midline>
+      <Hsp_align-len>348</Hsp_align-len>
+      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
+      <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
+      <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
     </Hsp>
   </Hit_hsps>
 </Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>29</Statistics_hsp-len>
-      <Statistics_eff-space>101761</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>21</Iteration_iter-num>
-  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
 <Hit>
-  <Hit_num>1</Hit_num>
+  <Hit_num>3</Hit_num>
   <Hit_id>gi|283855846|gb|ADB45242.1|</Hit_id>
   <Hit_def>rhodopsin [Cynopterus brachyotis]</Hit_def>
   <Hit_accession>ADB45242</Hit_accession>
@@ -506,27 +168,8 @@
     </Hsp>
   </Hit_hsps>
 </Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>29</Statistics_hsp-len>
-      <Statistics_eff-space>101761</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>22</Iteration_iter-num>
-  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
 <Hit>
-  <Hit_num>1</Hit_num>
+  <Hit_num>4</Hit_num>
   <Hit_id>gi|283855823|gb|ADB45229.1|</Hit_id>
   <Hit_def>rhodopsin [Myotis pilosus]</Hit_def>
   <Hit_accession>ADB45229</Hit_accession>
@@ -553,74 +196,36 @@
     </Hsp>
   </Hit_hsps>
 </Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>29</Statistics_hsp-len>
-      <Statistics_eff-space>101761</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>23</Iteration_iter-num>
-  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
 <Hit>
-  <Hit_num>1</Hit_num>
-  <Hit_id>gi|223523|prf||0811197A</Hit_id>
-  <Hit_def>rhodopsin [Bos taurus]</Hit_def>
-  <Hit_accession>0811197A</Hit_accession>
-  <Hit_len>347</Hit_len>
+  <Hit_num>5</Hit_num>
+  <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
+  <Hit_def>RecName: Full=Rhodopsin</Hit_def>
+  <Hit_accession>P56514</Hit_accession>
+  <Hit_len>354</Hit_len>
   <Hit_hsps>
     <Hsp>
       <Hsp_num>1</Hsp_num>
-      <Hsp_bit-score>673.315</Hsp_bit-score>
-      <Hsp_score>1736</Hsp_score>
+      <Hsp_bit-score>619.002</Hsp_bit-score>
+      <Hsp_score>1595</Hsp_score>
       <Hsp_evalue>0</Hsp_evalue>
       <Hsp_query-from>1</Hsp_query-from>
-      <Hsp_query-to>348</Hsp_query-to>
+      <Hsp_query-to>341</Hsp_query-to>
       <Hsp_hit-from>1</Hsp_hit-from>
-      <Hsp_hit-to>347</Hsp_hit-to>
+      <Hsp_hit-to>342</Hsp_hit-to>
       <Hsp_query-frame>0</Hsp_query-frame>
       <Hsp_hit-frame>0</Hsp_hit-frame>
-      <Hsp_identity>324</Hsp_identity>
-      <Hsp_positive>336</Hsp_positive>
+      <Hsp_identity>290</Hsp_identity>
+      <Hsp_positive>322</Hsp_positive>
       <Hsp_gaps>1</Hsp_gaps>
-      <Hsp_align-len>348</Hsp_align-len>
-      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-      <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-      <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
+      <Hsp_align-len>342</Hsp_align-len>
+      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>
+      <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>
+      <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE</Hsp_midline>
     </Hsp>
   </Hit_hsps>
 </Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>29</Statistics_hsp-len>
-      <Statistics_eff-space>101761</Statistics_eff-space>
-      <Statistics_kappa>0.041</Statistics_kappa>
-      <Statistics_lambda>0.267</Statistics_lambda>
-      <Statistics_entropy>0.14</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>24</Iteration_iter-num>
-  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
 <Hit>
-  <Hit_num>1</Hit_num>
+  <Hit_num>6</Hit_num>
   <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id>
   <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def>
   <Hit_accession>BAB21486</Hit_accession>
@@ -652,8 +257,8 @@
     <Statistics>
       <Statistics_db-num>0</Statistics_db-num>
       <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>29</Statistics_hsp-len>
-      <Statistics_eff-space>101761</Statistics_eff-space>
+      <Statistics_hsp-len>41</Statistics_hsp-len>
+      <Statistics_eff-space>556591</Statistics_eff-space>
       <Statistics_kappa>0.041</Statistics_kappa>
       <Statistics_lambda>0.267</Statistics_lambda>
       <Statistics_entropy>0.14</Statistics_entropy>