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= psy9332
         (148 letters)

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

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



>pdb|3TIG|A Chain A, Tubulin Tyrosine Ligase
 pdb|3TII|A Chain A, Tubulin Tyrosine Ligase
 pdb|3TII|B Chain B, Tubulin Tyrosine Ligase
 pdb|3TIN|A Chain A, Tubulin Tyrosine Ligase
          Length = 380

 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 14/28 (50%), Positives = 21/28 (75%)

Query: 49  HCFECYGYDIIIDNQLKPWLIEVNASPS 76
           H F+ +G+D ++D  LK WLIEVN +P+
Sbjct: 313 HSFQLFGFDFMVDKNLKVWLIEVNGAPA 340


>pdb|4I4T|F Chain F, Crystal Structure Of Tubulin-rb3-ttl-zampanolide Complex
 pdb|4I50|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-epothilone A
           Complex
 pdb|4I55|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl Complex
 pdb|4IIJ|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-apo Complex
 pdb|4IHJ|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-adp Complex
          Length = 384

 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 13/26 (50%), Positives = 21/26 (80%)

Query: 51  FECYGYDIIIDNQLKPWLIEVNASPS 76
           F+ +G+D ++D +LK WLIEVN +P+
Sbjct: 312 FQLFGFDFMVDEELKVWLIEVNGAPA 337


>pdb|3V4Z|A Chain A, D-Alanine--D-Alanine Ligase From Yersinia Pestis
 pdb|3V4Z|B Chain B, D-Alanine--D-Alanine Ligase From Yersinia Pestis
          Length = 309

 Score = 27.3 bits (59), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 3/33 (9%)

Query: 49  HCFECYGY---DIIIDNQLKPWLIEVNASPSLT 78
           H  +C G+   D++ D     +L+EVN SP +T
Sbjct: 249 HALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMT 281


>pdb|3QPX|L Chain L, Crystal Structure Of Fab C2507
          Length = 213

 Score = 26.9 bits (58), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 69  IEVNASPSLTCTTVNDRI-LKYKLIDNILNIVMWNKYK 105
           I++  SPSL   +V DR+ L  K   NI N + W + K
Sbjct: 2   IQMTQSPSLLSASVGDRVTLSCKASQNIYNYLNWYQQK 39


>pdb|2B1W|A Chain A, Solution Structure Of The Nod1 Caspase Activating And
           Recruitment Domain
          Length = 127

 Score = 26.6 bits (57), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 9/14 (64%), Positives = 12/14 (85%)

Query: 64  LKPWLIEVNASPSL 77
           L+PWL+E+  SPSL
Sbjct: 89  LRPWLLEIGFSPSL 102


>pdb|4E9M|A Chain A, Nod1 Card Domain With Three Disulfide-clinched,
           Domain-swapped Dimers In The Asymmetric Unit
 pdb|4E9M|B Chain B, Nod1 Card Domain With Three Disulfide-clinched,
           Domain-swapped Dimers In The Asymmetric Unit
 pdb|4E9M|C Chain C, Nod1 Card Domain With Three Disulfide-clinched,
           Domain-swapped Dimers In The Asymmetric Unit
 pdb|4E9M|D Chain D, Nod1 Card Domain With Three Disulfide-clinched,
           Domain-swapped Dimers In The Asymmetric Unit
 pdb|4E9M|E Chain E, Nod1 Card Domain With Three Disulfide-clinched,
           Domain-swapped Dimers In The Asymmetric Unit
 pdb|4E9M|F Chain F, Nod1 Card Domain With Three Disulfide-clinched,
           Domain-swapped Dimers In The Asymmetric Unit
          Length = 144

 Score = 26.2 bits (56), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 9/14 (64%), Positives = 12/14 (85%)

Query: 64  LKPWLIEVNASPSL 77
           L+PWL+E+  SPSL
Sbjct: 106 LRPWLLEIGFSPSL 119


  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    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,246,924
Number of Sequences: 62578
Number of extensions: 151217
Number of successful extensions: 401
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 397
Number of HSP's gapped (non-prelim): 8
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
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: 47 (22.7 bits)