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= 042424
         (138 letters)

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

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



>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
           Exosome
          Length = 1108

 Score =  119 bits (297), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 55/72 (76%), Positives = 63/72 (87%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT VAEYAIA + ++KQRVIYTS +KALSNQKYREL  EF DVGLMTGD+T++P+A CL
Sbjct: 211 GKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCL 270

Query: 127 VMTTEILRGMLY 138
           VMTTEILR MLY
Sbjct: 271 VMTTEILRSMLY 282


>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
           Processing And Surveillance
 pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
           Processing And Surveillance
          Length = 1010

 Score =  119 bits (297), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 55/72 (76%), Positives = 63/72 (87%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT VAEYAIA + ++KQRVIYTS +KALSNQKYREL  EF DVGLMTGD+T++P+A CL
Sbjct: 113 GKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCL 172

Query: 127 VMTTEILRGMLY 138
           VMTTEILR MLY
Sbjct: 173 VMTTEILRSMLY 184


>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
           Bound To Amppnp
          Length = 997

 Score = 99.0 bits (245), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 48/74 (64%), Positives = 60/74 (81%), Gaps = 2/74 (2%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDV--GLMTGDVTLSPNAS 124
           GKT VAEYAIAMA R+  + IYTS +KALSNQK+R+  + F DV  GL+TGDV ++P+A+
Sbjct: 66  GKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDAN 125

Query: 125 CLVMTTEILRGMLY 138
           CL+MTTEILR MLY
Sbjct: 126 CLIMTTEILRSMLY 139


>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
 pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
          Length = 715

 Score = 33.9 bits (76), Expect = 0.032,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 62  NPVYNGKTAVAEYAI-AMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS 120
           +P  +GKT +AE  I +   ++  + IY + L+AL+N+KY      FKD  L+   V ++
Sbjct: 53  SPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYL----TFKDWELIGFKVAMT 108


>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
           Complex With Unwound Dna
 pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
          Length = 702

 Score = 30.8 bits (68), Expect = 0.26,   Method: Composition-based stats.
 Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 63  PVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGD 116
           P   GKT +AE A+        + +Y   L+AL+ +KY    K  K    +G+ TGD
Sbjct: 48  PTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGD 104


>pdb|1HFE|L Chain L, 1.6 A Resolution Structure Of The Fe-Only Hydrogenase From
           Desulfovibrio Desulfuricans
 pdb|1HFE|M Chain M, 1.6 A Resolution Structure Of The Fe-Only Hydrogenase From
           Desulfovibrio Desulfuricans
          Length = 421

 Score = 26.2 bits (56), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 66  NGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS 120
           NG  A    A  M +  KQ  +YT S+     +KY  L  E K  G+   D TL+
Sbjct: 207 NGALAKTYGAERMKYDPKQ--VYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLT 259


>pdb|1E08|A Chain A, Structural Model Of The [fe]-HydrogenaseCYTOCHROME C553
           Complex Combining Nmr And Soft-Docking
 pdb|1GX7|A Chain A, Best Model Of The Electron Transfer Complex Between
           Cytochrome C3 And [fe]-Hydrogenase
          Length = 371

 Score = 26.2 bits (56), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 66  NGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS 120
           NG  A    A  M +  KQ  +YT S+     +KY  L  E K  G+   D TL+
Sbjct: 181 NGALAKTYGAERMKYDPKQ--VYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLT 233


  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
   0.314    0.127    0.361 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,531,869
Number of Sequences: 62578
Number of extensions: 105702
Number of successful extensions: 159
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 153
Number of HSP's gapped (non-prelim): 10
length of query: 138
length of database: 14,973,337
effective HSP length: 89
effective length of query: 49
effective length of database: 9,403,895
effective search space: 460790855
effective search space used: 460790855
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 46 (22.3 bits)