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= 007132
         (617 letters)

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

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



>pdb|3VMV|A Chain A, Crystal Structure Of Pectate Lyase Bsp165pela From
           Bacillus Sp. N165
 pdb|3VMW|A Chain A, Crystal Structure Of Pectate Lyase Bsp165pela From
           Bacillus Sp. N165 In Complex With Trigalacturonate
          Length = 326

 Score = 34.7 bits (78), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 42/206 (20%), Positives = 81/206 (39%), Gaps = 32/206 (15%)

Query: 285 NRTLENGPFREVVVSLDGEVVGAIWPFSVIYTGGISPLFWAPITGIGSFDLPSYDIEITP 344
           NR+  N P   + + ++G +     P S+I               + +    +++I+   
Sbjct: 37  NRSRSNNPDEPLTIYVNGTITQGNSPQSLI--------------DVKNHRGKAHEIKNIS 82

Query: 345 FLGNILDGEIHKFGFSVTNALNVWLIDANLHLWLDSRSTKTEGKVLKKNVMPLRVSLHAD 404
            +G   +GE    G  ++NA N+ + + ++H   +   T  E     KNV       +++
Sbjct: 83  IIGVGTNGEFDGIGIRLSNAHNIIIQNVSIHHVREGEGTAIEVTDDSKNVWIDHNEFYSE 142

Query: 405 FEG------LDGTFLTNVSRSISATGQIRSSYGEITTSWIQNFSYSNSMLISKNENLQII 458
           F G       DG  L ++ R+             IT SW +  ++  +ML+   +N  + 
Sbjct: 143 FPGNGDSDYYDG--LVDMKRNAEY----------ITVSWNKFENHWKTMLVGHTDNASLA 190

Query: 459 DQMIHFHDTYSQSSHKVYPLRLSIDV 484
              I +H  Y  + +   PL    DV
Sbjct: 191 PDKITYHHNYFNNLNSRVPLIRYADV 216


>pdb|3ATY|A Chain A, Crystal Structure Of Tcoye
 pdb|3ATY|B Chain B, Crystal Structure Of Tcoye
 pdb|3ATZ|A Chain A, Crystal Structure Of Tcoye With Phba
 pdb|3ATZ|B Chain B, Crystal Structure Of Tcoye With Phba
 pdb|3ATZ|C Chain C, Crystal Structure Of Tcoye With Phba
 pdb|3ATZ|D Chain D, Crystal Structure Of Tcoye With Phba
          Length = 379

 Score = 33.9 bits (76), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 16/56 (28%), Positives = 30/56 (53%)

Query: 174 VDSTYTGVYHVNITIHFYPAEGNLNDRKHDLDSLASRFYSNADLILPISRNLPMND 229
           V  +Y+GV   N+   F  A+  + + K D  +  ++F +N DL+    +N P+N+
Sbjct: 302 VRGSYSGVKISNLRYDFEEADQQIREGKVDAVAFGAKFIANPDLVERAQQNWPLNE 357


>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
 pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
          Length = 1724

 Score = 31.2 bits (69), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 23/93 (24%), Positives = 39/93 (41%), Gaps = 9/93 (9%)

Query: 63   PKTKPCSYPILSHDFGYTYGQPPVLTNYTPPSHC-TTHRLSKIVLDFEATCKGTQFDRIF 121
            P  +P    +    F  ++ Q  +L+   P  H  T H   K V+ F  + K T+     
Sbjct: 1115 PNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTR----- 1169

Query: 122  GIWLGGVELLRSCTAEPTRTGIVWSVEKDITRY 154
               L  +++L +C A+  R   +   EKD+  Y
Sbjct: 1170 ---LTAIDILTTCAADIQRQRFLHCTEKDLIPY 1199


>pdb|4F91|B Chain B, Brr2 Helicase Region
          Length = 1724

 Score = 31.2 bits (69), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 23/93 (24%), Positives = 39/93 (41%), Gaps = 9/93 (9%)

Query: 63   PKTKPCSYPILSHDFGYTYGQPPVLTNYTPPSHC-TTHRLSKIVLDFEATCKGTQFDRIF 121
            P  +P    +    F  ++ Q  +L+   P  H  T H   K V+ F  + K T+     
Sbjct: 1115 PNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTR----- 1169

Query: 122  GIWLGGVELLRSCTAEPTRTGIVWSVEKDITRY 154
               L  +++L +C A+  R   +   EKD+  Y
Sbjct: 1170 ---LTAIDILTTCAADIQRQRFLHCTEKDLIPY 1199


>pdb|3BBO|J Chain J, Homology Model For The Spinach Chloroplast 50s Subunit
           Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
          Length = 197

 Score = 30.4 bits (67), Expect = 2.7,   Method: Composition-based stats.
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 428 SSYGEITTSWIQNFSYSNSMLISKNENLQIIDQMIHFHDTYSQSSHKVYPLRLSIDVLDK 487
           +S   ++ SW  +  +S+S     NE L++ ++  +F     + + K+  + L  DV D 
Sbjct: 2   ASSTALSLSWSSSPCWSHSFNGGANETLKVSERRFNFEVVSQKKAKKLRKVILKEDVTDL 61

Query: 488 GNRSFLQLTNVTLGYY 503
           G +   QL +V  G++
Sbjct: 62  GKQG--QLLDVKAGFF 75


  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    0.136    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,684,740
Number of Sequences: 62578
Number of extensions: 804736
Number of successful extensions: 1660
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1657
Number of HSP's gapped (non-prelim): 9
length of query: 617
length of database: 14,973,337
effective HSP length: 105
effective length of query: 512
effective length of database: 8,402,647
effective search space: 4302155264
effective search space used: 4302155264
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: 54 (25.4 bits)