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= 003897
         (788 letters)

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

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



>pdb|3N29|A Chain A, Crystal Structure Of Carboxynorspermidine Decarboxylase
           Complexed With Norspermidine From Campylobacter Jejuni
 pdb|3N29|B Chain B, Crystal Structure Of Carboxynorspermidine Decarboxylase
           Complexed With Norspermidine From Campylobacter Jejuni
          Length = 418

 Score = 32.7 bits (73), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 31/136 (22%), Positives = 56/136 (41%), Gaps = 17/136 (12%)

Query: 104 WWTTHWVGSNGRDLENETQLVILDNSTDTGRPYVLLLPIVEGPFRAS-LQPGADDYVDVC 162
           W T + V S    +ENE Q+ ILD S++   P  +++P       A  L    ++ +   
Sbjct: 276 WQTGNLVASVVDIIENEKQIAILDTSSEAHMPDTIIMPYTSEVLNARILATRENEKISDL 335

Query: 163 VE-------SGSTKVTGDSFRSVVY---VHLGDDPFKLVKDAMRVVRS------HLGTFK 206
            E       +G+T + GD      +   + +GD    L +    +V++       L    
Sbjct: 336 KENEFAYLLTGNTCLAGDVMGEYAFDKKLKIGDKIVFLDQIHYTIVKNTTFNGIRLPNLM 395

Query: 207 LLDEKTPPPIVDKFGW 222
           LLD K    ++ +F +
Sbjct: 396 LLDHKNELQMIREFSY 411


>pdb|2F9Y|A Chain A, The Crystal Structure Of The Carboxyltransferase Subunit
           Of Acc From Escherichia Coli
          Length = 339

 Score = 31.2 bits (69), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 60/141 (42%), Gaps = 13/141 (9%)

Query: 85  VPIGKLKNIRFMSIF-RFKVWWTTHW--------VGSNGRDLENETQLVILDNSTDTGRP 135
            P G  K +R M +  RFK+   T          VG+  R  ++E     L   +  G P
Sbjct: 156 APEGYRKALRLMQMAERFKMPIITFIDTPGAYPGVGAEERG-QSEAIARNLREMSRLGVP 214

Query: 136 YVLLLPIVEGPFRASLQPGADDYVDVCVESGSTKVTGDSFRSVVYVHLGDDPFKLVKDAM 195
            V  + I EG    +L  G  D V++   S  + ++ +   S+++      P  L  +AM
Sbjct: 215 VVCTV-IGEGGSGGALAIGVGDKVNMLQYSTYSVISPEGCASILWKSADKAP--LAAEAM 271

Query: 196 RVVRSHLGTFKLLDEKTPPPI 216
            ++R  L   KL+D   P P+
Sbjct: 272 GIIRPRLKELKLIDSIIPEPL 292


>pdb|3A5V|A Chain A, Crystal Structure Of Alpha-Galactosidase I From
           Mortierella Vinacea
          Length = 397

 Score = 30.8 bits (68), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 216 IVDKFGWCTWDAFYLTVQPHGVMEGVKGLVDGGCPP---GLVLIDDGWQ 261
           I  + GW TW+ +   V    +++  K +   G        V+IDD WQ
Sbjct: 7   ITPQMGWNTWNKYGCNVDEQLILDAAKAIASSGLKDLGYNYVIIDDCWQ 55


>pdb|1UAS|A Chain A, Crystal Structure Of Rice Alpha-Galactosidase
          Length = 362

 Score = 30.4 bits (67), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 3/51 (5%)

Query: 219 KFGWCTWDAFYLTVQPHGVMEGVKGLVDGGCPP---GLVLIDDGWQSISHD 266
           + GW +W+ FY  +    + E    LV+ G        V IDD W   S D
Sbjct: 10  QMGWNSWNHFYCGINEQIIRETADALVNTGLAKLGYQYVNIDDCWAEYSRD 60


>pdb|2AP3|A Chain A, 1.6 A Crystal Structure Of A Conserved Protein Of Unknown
           Function From Staphylococcus Aureus
          Length = 199

 Score = 30.0 bits (66), Expect = 5.7,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 28/50 (56%)

Query: 392 DQMYEGLHSHLEKVGIDGVKVDVIHLLEILCENYGGRVDLAKAYYKALTA 441
           +Q ++   SH++ +  D  + +V  L ++L E Y    D AKAY KA+ +
Sbjct: 93  EQDFKKAKSHVDNIDNDVKRKEVKQLDDVLKEKYKLHSDYAKAYKKAVNS 142


  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    0.138    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,359,773
Number of Sequences: 62578
Number of extensions: 1230790
Number of successful extensions: 2830
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2827
Number of HSP's gapped (non-prelim): 12
length of query: 788
length of database: 14,973,337
effective HSP length: 107
effective length of query: 681
effective length of database: 8,277,491
effective search space: 5636971371
effective search space used: 5636971371
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)