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= psy3185
         (298 letters)

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

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



>pdb|3MI6|A Chain A, Crystal Structure Of The Alpha-Galactosidase From
           Lactobacil Brevis, Northeast Structural Genomics
           Consortium Target Lbr
 pdb|3MI6|B Chain B, Crystal Structure Of The Alpha-Galactosidase From
           Lactobacil Brevis, Northeast Structural Genomics
           Consortium Target Lbr
 pdb|3MI6|C Chain C, Crystal Structure Of The Alpha-Galactosidase From
           Lactobacil Brevis, Northeast Structural Genomics
           Consortium Target Lbr
 pdb|3MI6|D Chain D, Crystal Structure Of The Alpha-Galactosidase From
           Lactobacil Brevis, Northeast Structural Genomics
           Consortium Target Lbr
          Length = 745

 Score = 29.3 bits (64), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 41/96 (42%), Gaps = 15/96 (15%)

Query: 6   NEQYLESLP-------EKHQKLLSKYKDHLNDLKSCIDKNYEII---KLIIKDVGVMFEN 55
            +Q L +LP       +  Q L+  + D +  L   +D NY I     +I+K     F N
Sbjct: 113 GKQRLANLPSTFDDTDDDAQTLVVSFNDRITGL--ALDLNYSIFPHQDVIVK--SAKFTN 168

Query: 56  VPSSEPIKLISPLPNSTDLEKVQTTLKQFVRDWSEE 91
            PSSE + L   L +  DL      L QF   W+ E
Sbjct: 169 -PSSEKLVLNRALSSQLDLPDANYDLIQFSGTWARE 203


>pdb|3CXM|A Chain A, Leishmania Naiffi Uracil-Dna Glycosylase In Complex With
           5-Bromouracil
          Length = 268

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 23/104 (22%)

Query: 5   RNEQYLESLPEKHQKLLSKYKDHLNDLKSCIDKNYEIIKL-------IIKDVGVMFENVP 57
           R E++L+   EK + +L    D  N   SC  +  +++ L       + +  G+ F  +P
Sbjct: 59  RIERFLDEEKEKGRVILPPAADIFNAFNSCPFRGLKVVLLGQDPYHDLHQAHGLCFSVLP 118

Query: 58  SSEPIKLISPLPNS---------TDLEKVQTTLKQFVRDWSEEG 92
                    PLP S         TD+   Q     +++ WSE+G
Sbjct: 119 EV-------PLPPSLRNIYKELTTDIAGFQAPKHGYLQSWSEQG 155


>pdb|2YQC|A Chain A, Crystal Structure Of Uridine-Diphospho-N-Acetylglucosamine
           Pyrophosphorylase From Candida Albicans, In The Apo-Like
           Form
 pdb|2YQH|A Chain A, Crystal Structure Of Uridine-Diphospho-N-Acetylglucosamine
           Pyrophosphorylase From Candida Albicans, In The
           Substrate-Binding Form
 pdb|2YQH|B Chain B, Crystal Structure Of Uridine-Diphospho-N-Acetylglucosamine
           Pyrophosphorylase From Candida Albicans, In The
           Substrate-Binding Form
 pdb|2YQJ|A Chain A, Crystal Structure Of Uridine-Diphospho-N-Acetylglucosamine
           Pyrophosphorylase From Candida Albicans, In The
           Reaction-Completed Form
 pdb|2YQJ|B Chain B, Crystal Structure Of Uridine-Diphospho-N-Acetylglucosamine
           Pyrophosphorylase From Candida Albicans, In The
           Reaction-Completed Form
 pdb|2YQS|A Chain A, Crystal Structure Of Uridine-Diphospho-N-Acetylglucosamine
           Pyrophosphorylase From Candida Albicans, In The
           Product-Binding Form
          Length = 486

 Score = 28.5 bits (62), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 31/141 (21%), Positives = 55/141 (39%), Gaps = 17/141 (12%)

Query: 1   MKVKRNEQYLESLPEKHQKLLSKYKDHLNDLKSCIDKNYEIIKLIIKDVGVMFENVPSSE 60
           M VK  +Q ++S  + +Q  L +Y D L      ID+  E I  +              E
Sbjct: 1   MTVKSQQQIIDSFKQANQDQLFQYYDSL-----TIDQQQEFIDQL----------STIEE 45

Query: 61  PIKLISPLPNSTDLEKVQTTLKQFVRDWSEEGSEERKTCYEPIISEILARFPPETINPKD 120
           P KLIS +  +    +  +T + F +  +E+ +       +  I +       + I   +
Sbjct: 46  PAKLISTVEQAIQFSQTNSTSRNFTQLPNEQTASTLDLSKD--ILQNWTELGLKAIGNGE 103

Query: 121 VNILVPGAGLGRLAFEIARRG 141
           V +L+   G G      A +G
Sbjct: 104 VAVLLMAGGQGTRLGSSAPKG 124


>pdb|1PVL|A Chain A, Structure Of The Panton-Valentine Leucocidin F Component
           From Staphylococcus Aureus
          Length = 301

 Score = 28.1 bits (61), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 22/49 (44%)

Query: 192 VTFPDINTSDYNDDCDFSMAAGDFLQVYVHPNKWDCVATCFFIDCANNI 240
           +TF  I    Y+ D     AAG+    Y  PN  D +++ F+     NI
Sbjct: 36  LTFNFIKDKSYDKDTLILKAAGNIYSGYTKPNPKDTISSQFYWGSKYNI 84


  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
   0.320    0.138    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,480,737
Number of Sequences: 62578
Number of extensions: 402315
Number of successful extensions: 1196
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1191
Number of HSP's gapped (non-prelim): 19
length of query: 298
length of database: 14,973,337
effective HSP length: 98
effective length of query: 200
effective length of database: 8,840,693
effective search space: 1768138600
effective search space used: 1768138600
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: 51 (24.3 bits)