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= 015442
         (406 letters)

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

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



>pdb|1RM1|C Chain C, Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex
          Length = 286

 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 34/45 (75%)

Query: 362 QHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 406
           ++L+L  +DKVTRTK+RWKC+LKDG++ IN  D  F KA  E ++
Sbjct: 241 ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEW 285



 Score = 41.2 bits (95), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 31/51 (60%)

Query: 1  MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51
          M+ +    VY  ++E V+++VR++F N G  E  L +L+ IW+ K+ +  V
Sbjct: 1  MSNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKV 51


>pdb|1YTF|C Chain C, Yeast TfiiaTBPDNA COMPLEX
 pdb|1NH2|C Chain C, Crystal Structure Of A Yeast TfiiaTBPDNA COMPLEX
          Length = 79

 Score = 54.3 bits (129), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 24/45 (53%), Positives = 34/45 (75%)

Query: 362 QHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 406
           ++L+L  +DKVTRTK+RWKC+LKDG++ IN  D  F KA  E ++
Sbjct: 34  ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEW 78


>pdb|1NVP|C Chain C, Human TfiiaTBPDNA COMPLEX
          Length = 76

 Score = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 21/47 (44%), Positives = 39/47 (82%)

Query: 360 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 406
           +T+++V+ Q+DK+ R+K++WK  LKDGIM++N +D +F+KA G+ ++
Sbjct: 30  DTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW 76


>pdb|1NVP|B Chain B, Human TfiiaTBPDNA COMPLEX
          Length = 57

 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 32/44 (72%)

Query: 9  VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct: 12 LYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 55


>pdb|1YTF|B Chain B, Yeast TfiiaTBPDNA COMPLEX
 pdb|1NH2|B Chain B, Crystal Structure Of A Yeast TfiiaTBPDNA COMPLEX
          Length = 53

 Score = 37.4 bits (85), Expect = 0.017,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 28/43 (65%)

Query: 9  VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51
          VY  ++E V+++VR++F N G  E  L +L+ IW+ K+ +  V
Sbjct: 8  VYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKV 50


>pdb|1V10|A Chain A, Structure Of Rigidoporus Lignosus Laccase From
           Hemihedrally Twinned Crystals
          Length = 521

 Score = 29.3 bits (64), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 18/35 (51%)

Query: 198 GTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNI 232
           G SHQPLT D  T+ AG+R      A    G Y I
Sbjct: 251 GVSHQPLTVDSLTIFAGQRYSVVVEANQAVGNYWI 285


>pdb|1X5F|A Chain A, The Solution Structure Of The First Fibronectin Type Iii
           Domain Of Human Neogenin
          Length = 120

 Score = 28.9 bits (63), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 254 PGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVN 313
           P     + +A R++ A+L S+         P  DP+ D L+    Y  +G+  E   + N
Sbjct: 11  PATTGPLPSAPRDVVASLVSTRFIKLTWRTPASDPHGDNLTYSVFYTKEGIARE--RVEN 68

Query: 314 TPAPNDIQAS 323
           T  P ++Q +
Sbjct: 69  TSHPGEMQVT 78


  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
   0.313    0.132    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,121,739
Number of Sequences: 62578
Number of extensions: 368520
Number of successful extensions: 579
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 572
Number of HSP's gapped (non-prelim): 8
length of query: 406
length of database: 14,973,337
effective HSP length: 101
effective length of query: 305
effective length of database: 8,652,959
effective search space: 2639152495
effective search space used: 2639152495
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)