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= psy10664
         (75 letters)

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

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



>pdb|3VBB|A Chain A, Crystal Structure Of Seryl-Trna Synthetase From Human At
           2.9 Angstroms
 pdb|3VBB|B Chain B, Crystal Structure Of Seryl-Trna Synthetase From Human At
           2.9 Angstroms
 pdb|3VBB|C Chain C, Crystal Structure Of Seryl-Trna Synthetase From Human At
           2.9 Angstroms
 pdb|3VBB|D Chain D, Crystal Structure Of Seryl-Trna Synthetase From Human At
           2.9 Angstroms
 pdb|3VBB|E Chain E, Crystal Structure Of Seryl-Trna Synthetase From Human At
           2.9 Angstroms
 pdb|3VBB|F Chain F, Crystal Structure Of Seryl-Trna Synthetase From Human At
           2.9 Angstroms
          Length = 522

 Score =  112 bits (280), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 51/75 (68%), Positives = 60/75 (80%)

Query: 1   MIDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQ 60
           M+DG + E GA+VAG RGYFLKG  V L+  L+QYAL     +GY P+YTPFFMRKEVMQ
Sbjct: 176 MVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQ 235

Query: 61  EVAQLAQFDEELYKM 75
           EVAQL+QFDEELYK+
Sbjct: 236 EVAQLSQFDEELYKV 250


>pdb|3LSQ|A Chain A, Trypanosoma Brucei Seryl-Trna Synthetase
 pdb|3LSQ|B Chain B, Trypanosoma Brucei Seryl-Trna Synthetase
 pdb|3LSS|A Chain A, Trypanosoma Brucei Seryl-Trna Synthetase In Complex With
           Atp
 pdb|3LSS|B Chain B, Trypanosoma Brucei Seryl-Trna Synthetase In Complex With
           Atp
          Length = 484

 Score = 84.0 bits (206), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 40/69 (57%), Positives = 52/69 (75%)

Query: 7   SEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLA 66
           S+A   +AGGR Y LKG  V LQV LV Y+L   +++GYTP Y PFF+ ++VM EVAQL+
Sbjct: 189 SKAVTSMAGGRSYVLKGGLVQLQVALVSYSLDFLVKRGYTPFYPPFFLNRDVMGEVAQLS 248

Query: 67  QFDEELYKM 75
           QFDEELY++
Sbjct: 249 QFDEELYQV 257


>pdb|3QNE|A Chain A, Candida Albicans Seryl-Trna Synthetase
 pdb|3QO7|A Chain A, Crystal Structure Of The Seryl-Trna Synthetase From
           Candida Albicans
 pdb|3QO8|A Chain A, Crystal Structure Of Seryl-Trna Synthetase From Candida
           Albicans
          Length = 485

 Score = 80.5 bits (197), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/74 (52%), Positives = 46/74 (62%)

Query: 2   IDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQE 61
           +DG D E G  + G RGYFL+   V L   L+ Y LS    KGY PL  P  M KEVM +
Sbjct: 161 LDGYDPERGVRIVGHRGYFLRNYGVFLNQALINYGLSFLSSKGYVPLQAPVMMNKEVMAK 220

Query: 62  VAQLAQFDEELYKM 75
            AQL+QFDEELYK+
Sbjct: 221 TAQLSQFDEELYKV 234


>pdb|3QO5|A Chain A, Crystal Structure Of The Seryl-Trna Synthetase From
           Candida Albicans
          Length = 485

 Score = 77.8 bits (190), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 38/74 (51%), Positives = 45/74 (60%)

Query: 2   IDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQE 61
           +DG D E G  + G RGYFL+   V L   L+ Y L     KGY PL  P  M KEVM +
Sbjct: 161 LDGYDPERGVRIVGHRGYFLRNYGVFLNQALINYGLLFLSSKGYVPLQAPVMMNKEVMAK 220

Query: 62  VAQLAQFDEELYKM 75
            AQL+QFDEELYK+
Sbjct: 221 TAQLSQFDEELYKV 234


>pdb|2DQ0|A Chain A, Crystal Structure Of Seryl-Trna Synthetase From Pyrococcus
           Horikoshii Complexed With A Seryl-Adenylate Analog
 pdb|2DQ0|B Chain B, Crystal Structure Of Seryl-Trna Synthetase From Pyrococcus
           Horikoshii Complexed With A Seryl-Adenylate Analog
 pdb|2ZR2|A Chain A, Crystal Structure Of Seryl-Trna Synthetase From Pyrococcus
           Horikoshii Complexed With Atp
 pdb|2ZR2|B Chain B, Crystal Structure Of Seryl-Trna Synthetase From Pyrococcus
           Horikoshii Complexed With Atp
 pdb|2ZR3|A Chain A, Crystal Structure Of Seryl-Trna Synthetase From Pyrococcus
           Horikoshii
 pdb|2ZR3|B Chain B, Crystal Structure Of Seryl-Trna Synthetase From Pyrococcus
           Horikoshii
          Length = 455

 Score = 55.1 bits (131), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 44/75 (58%)

Query: 1   MIDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQ 60
           ++ G D    A V+G R Y+L    V L + L+++AL + IEKG+TP+  P+ +R+ V +
Sbjct: 168 ILGGADFARAAKVSGSRFYYLLNEIVILDLALIRFALDRLIEKGFTPVIPPYMVRRFVEE 227

Query: 61  EVAQLAQFDEELYKM 75
                  F++ +YK+
Sbjct: 228 GSTSFEDFEDVIYKV 242


>pdb|1WLE|A Chain A, Crystal Structure Of Mammalian Mitochondrial Seryl-Trna
           Synthetase Complexed With Seryl-Adenylate
 pdb|1WLE|B Chain B, Crystal Structure Of Mammalian Mitochondrial Seryl-Trna
           Synthetase Complexed With Seryl-Adenylate
          Length = 501

 Score = 46.6 bits (109), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 20/48 (41%), Positives = 30/48 (62%)

Query: 13  VAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQ 60
           V+G R Y+L+G    LQ GLV + L+K I +G+TP+  P  +R  V +
Sbjct: 206 VSGHRSYYLRGAGALLQHGLVNFTLNKLIHRGFTPMTVPDLLRGVVFE 253


>pdb|2DQ3|A Chain A, Crystal Structure Of Aq_298
 pdb|2DQ3|B Chain B, Crystal Structure Of Aq_298
          Length = 425

 Score = 43.1 bits (100), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/70 (30%), Positives = 38/70 (54%)

Query: 5   VDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQ 64
           +D + GA ++G R   + G    L+  L+ + L    +KGY  +  P  ++ E++    Q
Sbjct: 151 LDFKRGAKLSGSRFTVIAGWGARLERALINFXLDLHTKKGYKEICPPHLVKPEILIGTGQ 210

Query: 65  LAQFDEELYK 74
           L +F+E+LYK
Sbjct: 211 LPKFEEDLYK 220


>pdb|3ERR|A Chain A, Microtubule Binding Domain From Mouse Cytoplasmic Dynein
           As A Fusion With Seryl-Trna Synthetase
 pdb|3ERR|B Chain B, Microtubule Binding Domain From Mouse Cytoplasmic Dynein
           As A Fusion With Seryl-Trna Synthetase
          Length = 536

 Score = 33.1 bits (74), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 26/45 (57%)

Query: 13  VAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKE 57
           V+G R Y LKG     ++ L+++A+     +G+ P+  P + R++
Sbjct: 262 VSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREK 306


>pdb|1SRY|A Chain A, Refined Crystal Structure Of The Seryl-Trna Synthetase
           From Thermus Thermophilus At 2.5 Angstroms Resolution
 pdb|1SRY|B Chain B, Refined Crystal Structure Of The Seryl-Trna Synthetase
           From Thermus Thermophilus At 2.5 Angstroms Resolution
 pdb|1SER|A Chain A, The 2.9 Angstroms Crystal Structure Of T. Thermophilus
           Seryl-Trna Synthetase Complexed With Trna Ser
 pdb|1SER|B Chain B, The 2.9 Angstroms Crystal Structure Of T. Thermophilus
           Seryl-Trna Synthetase Complexed With Trna Ser
 pdb|1SES|A Chain A, Crystal Structures At 2.5 Angstroms Resolution Of
           Seryl-Trna Synthetase Complexed With Two Different
           Analogues Of Seryl-Adenylate
 pdb|1SES|B Chain B, Crystal Structures At 2.5 Angstroms Resolution Of
           Seryl-Trna Synthetase Complexed With Two Different
           Analogues Of Seryl-Adenylate
 pdb|1SET|A Chain A, Crystal Structures At 2.5 Angstroms Resolution Of
           Seryl-Trna Synthetase Complexed With Two Different
           Analogues Of Seryl-Adenylate
 pdb|1SET|B Chain B, Crystal Structures At 2.5 Angstroms Resolution Of
           Seryl-Trna Synthetase Complexed With Two Different
           Analogues Of Seryl-Adenylate
          Length = 421

 Score = 32.3 bits (72), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 13/46 (28%), Positives = 26/46 (56%)

Query: 13  VAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEV 58
           V+G R Y LKG     ++ L+++A+     +G+ P+  P + R++ 
Sbjct: 153 VSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKA 198


>pdb|4ES6|A Chain A, Crystal Structure Of Hemd (pa5259) From Pseudomonas
           Aeruginosa (pao1) At 2.22 A Resolution
          Length = 254

 Score = 26.2 bits (56), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 3/60 (5%)

Query: 6   DSEAGAIVAGGRGYFLKGPAVCLQVGL---VQYALSKWIEKGYTPLYTPFFMRKEVMQEV 62
           D  AG ++A  R   L G  V    GL    Q A + W E G  PL+ P     E+ +E+
Sbjct: 171 DYPAGELLARVRAERLNGLVVSSGQGLQNLYQLAAADWPEIGRLPLFVPSPRVAEMAREL 230


  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
   0.323    0.140    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,355,285
Number of Sequences: 62578
Number of extensions: 78769
Number of successful extensions: 242
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 233
Number of HSP's gapped (non-prelim): 10
length of query: 75
length of database: 14,973,337
effective HSP length: 44
effective length of query: 31
effective length of database: 12,219,905
effective search space: 378817055
effective search space used: 378817055
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: 45 (21.9 bits)