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= 028901
         (202 letters)

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

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



>pdb|1OKC|A Chain A, Structure Of Mitochondrial AdpATP CARRIER IN COMPLEX WITH
           Carboxyatractyloside
 pdb|2C3E|A Chain A, The Bovine Mitochondrial Adp-Atp Carrier
          Length = 297

 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 68/169 (40%), Gaps = 26/169 (15%)

Query: 32  IGGMLSAGTAHLAITPLDVVKVNMQVH--------PIKYSSIASCYTNLLKEQGASAFWR 83
           + G ++A  +  A+ P++ VK+ +QV           +Y  I  C   + KEQG  +FWR
Sbjct: 12  LAGGVAAAISKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWR 71

Query: 84  GSAAKFFGYGAQGGCRFGLYEYFKSLYSSVLGDCXXXXXXXXXXXXXXXXXNVA----LC 139
           G+ A    Y       F   + +K ++   LG                     A    LC
Sbjct: 72  GNLANVIRYFPTQALNFAFKDKYKQIF---LGGVDRHKQFWRYFAGNLASGGAAGATSLC 128

Query: 140 ---PFEAIKVQV-------QAQPHFAKGLADGIPKLYASEGIFGFYRGL 178
              P +  + ++        AQ  F  GL + I K++ S+G+ G Y+G 
Sbjct: 129 FVYPLDFARTRLAADVGKGAAQREFT-GLGNCITKIFKSDGLRGLYQGF 176



 Score = 30.4 bits (67), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 14/64 (21%)

Query: 28  SICAIGGMLSAGTAHLAITPLDVVKVNMQVH------PIKYSSIASCYTNLLKEQGASAF 81
           ++ A+ G++S         P D V+  M +        I Y+    C+  + K++G  AF
Sbjct: 218 TVTAVAGLVS--------YPFDTVRRRMMMQSGRKGADIMYTGTVDCWRKIAKDEGPKAF 269

Query: 82  WRGS 85
           ++G+
Sbjct: 270 FKGA 273


>pdb|2LCK|A Chain A, Structure Of The Mitochondrial Uncoupling Protein 2
           Determined By Nmr Molecular Fragment Replacement
          Length = 303

 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 38/171 (22%), Positives = 62/171 (36%), Gaps = 19/171 (11%)

Query: 32  IGGMLSAGTAHLAITPLDVVKVNMQVH-----------PIKYSSIASCYTNLLKEQGASA 80
           +G   +A  A L   PLD  KV +Q+              +Y  +      +++ +G  +
Sbjct: 6   LGAGTAACIADLITFPLDTAKVRLQIQGESQGLVRTAASAQYRGVLGTILTMVRTEGPRS 65

Query: 81  FWRGSAAKFFGYGAQGGCRFGLYEYFKSLYSSVLGDCXXXXXXXXXXXXXXXXXNVALC- 139
            + G  A      +    R GLY+  K  Y+   G                    VA+  
Sbjct: 66  LYNGLVAGLQRQMSFASVRIGLYDSVKQFYTK--GSEHAGIGSRLLAGSTTGALAVAVAQ 123

Query: 140 PFEAIKVQVQAQPHFAKG-----LADGIPKLYASEGIFGFYRGLIPLLGRN 185
           P + +KV+ QAQ     G       +    +   EGI G ++G  P + RN
Sbjct: 124 PTDVVKVRFQAQARAGGGRRYQSTVEAYKTIAREEGIRGLWKGTSPNVARN 174



 Score = 34.3 bits (77), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 46  TPLDVVKVN-MQVHPIKYSSIASCYTNLLKEQGASAFWRGSAAKFFGYGAQGGCRFGLYE 104
           +P+DVVK   M     +Y S   C   +L+++G  AF++G    F   G+     F  YE
Sbjct: 221 SPVDVVKTRYMNSALGQYHSAGHCALTMLRKEGPRAFYKGFMPSFLRLGSWNVVMFVTYE 280

Query: 105 YFK 107
             K
Sbjct: 281 QLK 283


>pdb|3S25|A Chain A, Crystal Structure Of A Hypothetical 7-Bladed
           Beta-Propeller-Like Protein (Eubrec_1955) From
           Eubacterium Rectale Atcc 33656 At 1.88 A Resolution
          Length = 302

 Score = 28.5 bits (62), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 10/15 (66%), Positives = 13/15 (86%)

Query: 13  IRLRGEEKEKVKGHY 27
           IR+ GEEK+K+K HY
Sbjct: 134 IRIDGEEKKKIKNHY 148


>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
           Synthase Rlud From Escherichia Coli
 pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
          Length = 325

 Score = 26.9 bits (58), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 12/42 (28%), Positives = 21/42 (50%)

Query: 19  EKEKVKGHYSICAIGGMLSAGTAHLAITPLDVVKVNMQVHPI 60
           ++ ++   Y   AIG M + GT    I+     + +M VHP+
Sbjct: 162 QRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM 203


  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
   0.325    0.143    0.448 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,851,767
Number of Sequences: 62578
Number of extensions: 213570
Number of successful extensions: 561
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 549
Number of HSP's gapped (non-prelim): 12
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)