BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 003003
         (858 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3OFU|A Chain A, Crystal Structure Of Cytochrome P450 Cyp101c1
 pdb|3OFU|B Chain B, Crystal Structure Of Cytochrome P450 Cyp101c1
 pdb|3OFU|C Chain C, Crystal Structure Of Cytochrome P450 Cyp101c1
 pdb|3OFU|D Chain D, Crystal Structure Of Cytochrome P450 Cyp101c1
 pdb|3OFU|E Chain E, Crystal Structure Of Cytochrome P450 Cyp101c1
 pdb|3OFU|F Chain F, Crystal Structure Of Cytochrome P450 Cyp101c1
 pdb|3OFT|A Chain A, Crystal Structure Of Cytochrome P450 Cyp101c1
 pdb|3OFT|B Chain B, Crystal Structure Of Cytochrome P450 Cyp101c1
 pdb|3OFT|C Chain C, Crystal Structure Of Cytochrome P450 Cyp101c1
          Length = 396

 Score = 34.3 bits (77), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 47/205 (22%), Positives = 83/205 (40%), Gaps = 27/205 (13%)

Query: 621 PGSVLEILSDVPLDDRKRASNAIGHGKLKNVQVFHKIGNPLNFETLKDTIMNIQNSF--- 677
           P ++   L DVPL+DR R            VQ+    G+ +  E LK    +    F   
Sbjct: 145 PLNIFLTLIDVPLEDRPRLRQL-------GVQLTRPDGS-MTVEQLKQAADDYLWPFIEK 196

Query: 678 ---KDGEELPLSIVV--ISDREWLLGDPSRADKQSAYSLLLAENICNKLGVKVQNLVAEI 732
              + G++L   I+   +  R W + +  R  +   +  L  + +   +G+   +L    
Sbjct: 197 RMAQPGDDLFSRILSEPVGGRPWTVDEARRMCRNLLFGGL--DTVAAMIGMVALHLARHP 254

Query: 733 VDSKLGKQIARNKPSLTYIAAEEIMSLVTAQVVENNELNEVWKD-ILNAEGDEIYVKDIS 791
            D +L     R +P L   AA+E+M       V  N + +V  D +   +GD +Y+  + 
Sbjct: 255 EDQRL----LRERPDLIPAAADELMRRYPTVAVSRNAVADVDADGVTIRKGDLVYLPSVL 310

Query: 792 LYMKEGENPSFFELSERAHLRREVA 816
             +    +P+ FE  E     R +A
Sbjct: 311 HNL----DPASFEAPEEVRFDRGLA 331


>pdb|3V6A|A Chain A, Helical Repeat Structure Of Apoptosis Inhibitor 5 Reveals
           Protein- Protein Interaction Modules
          Length = 474

 Score = 31.2 bits (69), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 72  KTDSSICMNVVDNSSFKFFRMDKKNTPQGYQAQLMIG 108
           +TD S   N+V+N+    F+MD K T  G  +Q++ G
Sbjct: 127 QTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQG 163


>pdb|3U0R|A Chain A, Helical Repeat Structure Of Apoptosis Inhibitor 5 Reveals
           Protein- Protein Interaction Modules
          Length = 507

 Score = 30.8 bits (68), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 72  KTDSSICMNVVDNSSFKFFRMDKKNTPQGYQAQLMIG 108
           +TD S   N+V+N+    F+MD K T  G  +Q++ G
Sbjct: 110 QTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQG 146


>pdb|4H33|A Chain A, Crystal Structure Of A Voltage-gated K+ Channel Pore
           Module In A Closed State In Lipid Membranes, Tetragonal
           Crystal Form
 pdb|4H37|A Chain A, Crystal Structure Of A Voltage-gated K+ Channel Pore
           Domain In A Closed State In Lipid Membranes
 pdb|4H37|B Chain B, Crystal Structure Of A Voltage-gated K+ Channel Pore
           Domain In A Closed State In Lipid Membranes
          Length = 137

 Score = 29.3 bits (64), Expect = 8.8,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 221 ETQSLEDCLWEAWACLISSST---HLKQRTRVERVIGFILAIWGILFYSRLLSTMTEQFR 277
           E  +  D LW  WA + +++     +   T + R++  I+ ++GI F   + ST+T  FR
Sbjct: 40  EINNYPDALW--WAIVTATTVGYGDIVPVTPIGRILASIMMLFGIAFIGMITSTITNFFR 97


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.319    0.135    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,638,146
Number of Sequences: 62578
Number of extensions: 880565
Number of successful extensions: 2069
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2066
Number of HSP's gapped (non-prelim): 8
length of query: 858
length of database: 14,973,337
effective HSP length: 107
effective length of query: 751
effective length of database: 8,277,491
effective search space: 6216395741
effective search space used: 6216395741
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)