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= psy10828
         (245 letters)

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

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



>pdb|3F9V|A Chain A, Crystal Structure Of A Near Full-Length Archaeal Mcm:
           Functional Insights For An Aaa+ Hexameric Helicase
          Length = 595

 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 49/157 (31%), Positives = 75/157 (47%), Gaps = 11/157 (7%)

Query: 94  CHSALWWAKEISFPQAGLVCKLNTRCSIIAACNPK-GHYDPNIPISVNIAIASPXXXXXX 152
            H A+   + +S  +AG+V KLN R ++IAA NPK G Y    P+S NI +         
Sbjct: 411 IHEAME-QQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILSRFD 469

Query: 153 XXXXXXXXKSEQWDKMVSNYILFGKRLGPSSNQATSLWDVEKLQAYF-YLIKGLRPQMTL 211
                     EQ D+ ++NYIL       S     ++ D++ L+ Y  Y  K + P++T 
Sbjct: 470 LIFILKDQPGEQ-DRELANYILDVH----SGKSTKNIIDIDTLRKYIAYARKYVTPKITS 524

Query: 212 EANRILTRYYQAQRKADMR---NAARTTVRLLESLIR 245
           EA  ++T ++   RK       +    T R LE+LIR
Sbjct: 525 EAKNLITDFFVEMRKKSSETPDSPILITPRQLEALIR 561


>pdb|3F8T|A Chain A, Crystal Structure Analysis Of A Full-Length Mcm Homolog
           From Methanopyrus Kandleri
          Length = 506

 Score = 27.3 bits (59), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 10/24 (41%), Positives = 16/24 (66%)

Query: 115 LNTRCSIIAACNPKGHYDPNIPIS 138
           LN RC+++AA NP   +  + PI+
Sbjct: 336 LNARCAVLAAINPGEQWPSDPPIA 359


  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    0.132    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,654,450
Number of Sequences: 62578
Number of extensions: 242638
Number of successful extensions: 368
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 366
Number of HSP's gapped (non-prelim): 2
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
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: 50 (23.9 bits)