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= 028759
         (204 letters)

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

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



>pdb|1NMN|A Chain A, Structure Of Yqgf From Escherichia Coli, A Hypothetical
           Protein
 pdb|1NMN|B Chain B, Structure Of Yqgf From Escherichia Coli, A Hypothetical
           Protein
          Length = 138

 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 65/133 (48%), Gaps = 6/133 (4%)

Query: 63  GFSLGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119
           G  L  D G    G+A+ +      RPL  +K +    +  ++E   +E + DE I+GLP
Sbjct: 3   GTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLP 62

Query: 120 KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQT 179
            + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + 
Sbjct: 63  LNMDGTEQPLTARARKFANRIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKG 119

Query: 180 KTDAYAAVVRQES 192
           K D+ +AV+  ES
Sbjct: 120 KVDSASAVIILES 132


>pdb|1OVQ|A Chain A, Solution Structure Of The Hypothetical Protein Yqgf From
           Escherichia Coli
          Length = 138

 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 65/133 (48%), Gaps = 6/133 (4%)

Query: 63  GFSLGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119
           G  L  D G    G+A+ +      RPL  +K +    +  ++E   +E + DE I+GLP
Sbjct: 3   GTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLP 62

Query: 120 KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQT 179
            + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + 
Sbjct: 63  LNMDGTEQPLTARARKFANRIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKG 119

Query: 180 KTDAYAAVVRQES 192
           K D+ +AV+  ES
Sbjct: 120 KVDSASAVIILES 132


>pdb|1NU0|A Chain A, Structure Of The Double Mutant (L6m; F134m, Semet Form) Of
           Yqgf From Escherichia Coli, A Hypothetical Protein
 pdb|1NU0|B Chain B, Structure Of The Double Mutant (L6m; F134m, Semet Form) Of
           Yqgf From Escherichia Coli, A Hypothetical Protein
          Length = 138

 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 66/132 (50%), Gaps = 11/132 (8%)

Query: 62  GGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLPK 120
           G  S+GV +G   TG A       RPL  +K +    +  ++E   +E + DE I+GLP 
Sbjct: 11  GTKSIGVAVGQRITGTA-------RPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPL 63

Query: 121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTK 180
           + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + K
Sbjct: 64  NXDGTEQPLTARARKFANRIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKGK 120

Query: 181 TDAYAAVVRQES 192
            D+ +AV+  ES
Sbjct: 121 VDSASAVIILES 132


>pdb|1VHX|A Chain A, Crystal Structure Of Putative Holliday Junction Resolvase
 pdb|1VHX|B Chain B, Crystal Structure Of Putative Holliday Junction Resolvase
          Length = 150

 Score = 40.0 bits (92), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 35/127 (27%), Positives = 60/127 (47%), Gaps = 8/127 (6%)

Query: 66  LGVDLGLSRTGLALSK--GFCVRPLTVLKL---RGEKLELQLLEIAQREETDEFIIGLPK 120
           LG+DLG    G+ALS   G+  + +  +K+    G+    +L E+ +    D+ ++G PK
Sbjct: 6   LGLDLGTKTLGVALSDEXGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPK 65

Query: 121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTK 180
           + +G+  P+    ++ A    V        V L DE  T+  A   +I   +S+  R+  
Sbjct: 66  NXNGTVGPRGEASQTFA---KVLETTYNVPVVLWDERLTTXAAEKXLIAADVSRQKRKKV 122

Query: 181 TDAYAAV 187
            D  AAV
Sbjct: 123 IDKXAAV 129


>pdb|1IV0|A Chain A, Solution Structure Of The Yqgf-Family Protein (N-Terminal
           Fragment)
          Length = 98

 Score = 33.5 bits (75), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 34/102 (33%), Positives = 51/102 (50%), Gaps = 19/102 (18%)

Query: 68  VDLGLSRTGLALS---------KGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGL 118
           +D+G +R GLA+          +G+ VR     K   E +E  LL+  +RE   + ++GL
Sbjct: 6   LDVGEARIGLAVGEEGVPLASGRGYLVR-----KTLEEDVE-ALLDFVRREGLGKLVVGL 59

Query: 119 PKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTS 160
           P   D  E+ Q+ KV  +    A+RA  RG  V L DE  T+
Sbjct: 60  PLRTDLKESAQAGKVLPLVE--ALRA--RGVEVELWDERFTT 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
   0.321    0.136    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,428,694
Number of Sequences: 62578
Number of extensions: 205226
Number of successful extensions: 383
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 374
Number of HSP's gapped (non-prelim): 8
length of query: 204
length of database: 14,973,337
effective HSP length: 94
effective length of query: 110
effective length of database: 9,091,005
effective search space: 1000010550
effective search space used: 1000010550
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)