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= 008633
         (558 letters)

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

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



>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
          Length = 1134

 Score = 38.5 bits (88), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 260 KGKVLFNVMTYNIVISGWSKLGQVVEMERVLKEIVAEGFSPDSLTFSFLIEGLGRAGRID 319
           + + L  +  YN V+ GW++ G   E+  VL  +   G +PD L+++  ++ +GR  +  
Sbjct: 158 QKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDA 217

Query: 320 DAIE-VFDTMKEKG 332
             IE   + M ++G
Sbjct: 218 GTIERCLEQMSQEG 231


>pdb|3LL6|A Chain A, Crystal Structure Of The Human Cyclin G Associated Kinase
           (gak)
 pdb|3LL6|B Chain B, Crystal Structure Of The Human Cyclin G Associated Kinase
           (gak)
          Length = 337

 Score = 37.7 bits (86), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 98/221 (44%), Gaps = 41/221 (18%)

Query: 39  LLSNQKKNMSSLDEHHVLKELSDLFQISSHNSFPNVYKESRSNSVKRIDSSRAVDEFLLP 98
           LLSN+++   +     +++E+  + ++S H   PN+ +   + S+ + +S     EFLL 
Sbjct: 61  LLSNEEEKNRA-----IIQEVCFMKKLSGH---PNIVQFCSAASIGKEESDTGQAEFLLL 112

Query: 99  EERLRGV---FLQKLKGKGVIEDALWNVNVDLSLDVVGKVVNRGNLSGEAMVLFFNWAIK 155
            E  +G    FL+K++ +G            LS D V K+  +   + + M        K
Sbjct: 113 TELCKGQLVEFLKKMESRG-----------PLSCDTVLKIFYQTCRAVQHM-----HRQK 156

Query: 156 HPNVAKDVKSYNVIVKALGRRKFFDF-MCNVLSDMAKEGVNPD----LETLSIVMDSFIR 210
            P + +D+K  N+++   G  K  DF     +S        PD     +  ++V +   R
Sbjct: 157 PPIIHRDLKVENLLLSNQGTIKLCDFGSATTISHY------PDYSWSAQRRALVEEEITR 210

Query: 211 -AGQVYKAIQMLGRLEDF--GLKFDAESLNVVLWCLCQRLH 248
               +Y+  +++    +F  G K D  +L  +L+ LC R H
Sbjct: 211 NTTPMYRTPEIIDLYSNFPIGEKQDIWALGCILYLLCFRQH 251


>pdb|1FFU|A Chain A, Carbon Monoxide Dehydrogenase From Hydrogenophaga
           Pseudoflava Which Lacks The Mo-Pyranopterin Moiety Of
           The Molybdenum Cofactor
 pdb|1FFU|D Chain D, Carbon Monoxide Dehydrogenase From Hydrogenophaga
           Pseudoflava Which Lacks The Mo-Pyranopterin Moiety Of
           The Molybdenum Cofactor
 pdb|1FFV|A Chain A, Carbon Monoxide Dehydrogenase From Hydrogenophaga
           Pseudoflava
 pdb|1FFV|D Chain D, Carbon Monoxide Dehydrogenase From Hydrogenophaga
           Pseudoflava
          Length = 163

 Score = 31.2 bits (69), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 29/58 (50%)

Query: 454 GFGKCGMLLDLWHEMQESGYPSDGEIYEYVIAGLCNIGQLENAVLVMEESLRKGFCPS 511
           GF   GML+  +  +QE+  P++ EI   +   LC     +N V  ++ + RK   PS
Sbjct: 102 GFCTPGMLMRAYRFLQENPNPTEAEIRMGMTGNLCRCTGYQNIVKAVQYAARKLQEPS 159


>pdb|1NA0|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
           Tpr Motif
 pdb|1NA0|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
           Tpr Motif
          Length = 125

 Score = 28.9 bits (63), Expect = 8.1,   Method: Composition-based stats.
 Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 4/88 (4%)

Query: 314 RAGRIDDAIEVFDTMKEKGCGPDTNAYNAVISNYISVGDFDECMKYYKGMSSYNCEP-NM 372
           + G  D+AIE +    E         YN + + Y   GD+DE ++YY+   +   +P N 
Sbjct: 21  KQGDYDEAIEYYQKALELDPNNAEAWYN-LGNAYYKQGDYDEAIEYYQ--KALELDPNNA 77

Query: 373 DTYTRLISGLLKSRKVADALEVFEEMLD 400
           + +  L +   K     +A+E +++ L+
Sbjct: 78  EAWYNLGNAYYKQGDYDEAIEYYQKALE 105


  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
   0.322    0.137    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,342,045
Number of Sequences: 62578
Number of extensions: 616088
Number of successful extensions: 1668
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1662
Number of HSP's gapped (non-prelim): 8
length of query: 558
length of database: 14,973,337
effective HSP length: 104
effective length of query: 454
effective length of database: 8,465,225
effective search space: 3843212150
effective search space used: 3843212150
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: 54 (25.4 bits)