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= psy15420
         (187 letters)

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

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



>pdb|1Z63|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
           With Dsdna
 pdb|1Z63|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
           With Dsdna
          Length = 500

 Score = 27.7 bits (60), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 64/152 (42%), Gaps = 18/152 (11%)

Query: 44  KLQDNMRIRTEVAAILRQYKLNNVQNQYNAEEQATRQNLENEKSLLYDHMXXXXXXXXXX 103
           KL+D   I T  A +LR  +L  V+ +Y   ++A  QN++N ++ ++  +          
Sbjct: 125 KLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEA--QNIKNPQTKIFKAVKELKSKYRIA 182

Query: 104 XXXD--RNSVDINADLW----FFEHNKRGSNQNPLSSKRGP--KGFNRMKSRRKAVTVSG 155
                  N VD   DLW    F      GS     S    P  KG N  K   KA+    
Sbjct: 183 LTGTPIENKVD---DLWSIXTFLNPGLLGSYSEFKSKFATPIKKGDNXAKEELKAII--S 237

Query: 156 PYIVYMLR-DEEIIEDWTIIKKAMSQRKCDLT 186
           P+I+   + D+ II D  +  K  +   C+LT
Sbjct: 238 PFILRRTKYDKAIIND--LPDKIETNVYCNLT 267


>pdb|1BJ4|A Chain A, Recombinant Serine Hydroxymethyltransferase (human)
          Length = 470

 Score = 27.7 bits (60), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 53  TEVAAILRQYKLNNVQNQYNAEEQATRQNLENEKSLL 89
           T VAA L+++K     ++Y A  QA R+ +E+  SL 
Sbjct: 429 TGVAATLKEFKERLAGDKYQAAVQALREEVESFASLF 465


>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
          Length = 500

 Score = 27.3 bits (59), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 64/152 (42%), Gaps = 18/152 (11%)

Query: 44  KLQDNMRIRTEVAAILRQYKLNNVQNQYNAEEQATRQNLENEKSLLYDHMXXXXXXXXXX 103
           KL+D   I T  A +LR  +L  V+ +Y   ++A  QN++N ++ ++  +          
Sbjct: 125 KLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEA--QNIKNPQTKIFKAVKELKSKYRIA 182

Query: 104 XXXD--RNSVDINADLW----FFEHNKRGSNQNPLSSKRGP--KGFNRMKSRRKAVTVSG 155
                  N VD   DLW    F      GS     S    P  KG N  K   KA+    
Sbjct: 183 LTGTPIENKVD---DLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAII--S 237

Query: 156 PYIVYMLR-DEEIIEDWTIIKKAMSQRKCDLT 186
           P+I+   + D+ II D  +  K  +   C+LT
Sbjct: 238 PFILRRTKYDKAIIND--LPDKIETNVYCNLT 267


>pdb|2XRY|A Chain A, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
           Methanosarcina Mazei
 pdb|2XRZ|A Chain A, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
           Methanosarcina Mazei In Complex With Intact Cpd-Lesion
 pdb|2XRZ|B Chain B, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
           Methanosarcina Mazei In Complex With Intact Cpd-Lesion
          Length = 482

 Score = 26.6 bits (57), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 10/50 (20%)

Query: 125 RGSNQNPLSSKRGPKGFNRMKSRRKAVTVSGPYIVYMLRDEEIIEDWTII 174
           RGS+ NP           R+++ +      GP + +M RD+   ++W ++
Sbjct: 17  RGSHMNP----------KRIRALKSGKQGDGPVVYWMSRDQRAEDNWALL 56


  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
   0.317    0.133    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,553,608
Number of Sequences: 62578
Number of extensions: 148651
Number of successful extensions: 315
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: 313
Number of HSP's gapped (non-prelim): 8
length of query: 187
length of database: 14,973,337
effective HSP length: 93
effective length of query: 94
effective length of database: 9,153,583
effective search space: 860436802
effective search space used: 860436802
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)