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= psy7895
         (108 letters)

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

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



>pdb|1NVP|D Chain D, Human TfiiaTBPDNA COMPLEX
          Length = 108

 Score =  159 bits (403), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 74/103 (71%), Positives = 90/103 (87%), Gaps = 1/103 (0%)

Query: 2   SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSG 61
           +YQLYRNTTLGN+LQESLDELIQ   ITP LA++VLLQFDK+IN AL  +V++R+ F+ G
Sbjct: 1   AYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFR-G 59

Query: 62  KLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104
            LNTYRFCDNVWTFVL DVEFREV E+ +V+K+KIVACDGK++
Sbjct: 60  SLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNT 102


>pdb|1RM1|B Chain B, Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex
          Length = 122

 Score = 89.7 bits (221), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 48/117 (41%), Positives = 73/117 (62%), Gaps = 15/117 (12%)

Query: 3   YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGK 62
           Y+LYR +T+GN+L ++LD LI  G I  +LAM+VL  FDK +   L    +S+LT K G 
Sbjct: 7   YELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVK-GN 65

Query: 63  LNTYRFCDNVWTFVLTDVE------FREVAE--------IARVNKLKIVACDGKSSD 105
           L+TY FCD+VWTF++ + +       R+ ++        +  V+KL+IVAC+ K S+
Sbjct: 66  LDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE 122


>pdb|1YTF|D Chain D, Yeast TfiiaTBPDNA COMPLEX
 pdb|1NH2|D Chain D, Crystal Structure Of A Yeast TfiiaTBPDNA COMPLEX
          Length = 121

 Score = 89.4 bits (220), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 48/117 (41%), Positives = 73/117 (62%), Gaps = 15/117 (12%)

Query: 3   YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGK 62
           Y+LYR +T+GN+L ++LD LI  G I  +LAM+VL  FDK +   L    +S+LT K G 
Sbjct: 6   YELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVK-GN 64

Query: 63  LNTYRFCDNVWTFVLTDVE------FREVAE--------IARVNKLKIVACDGKSSD 105
           L+TY FCD+VWTF++ + +       R+ ++        +  V+KL+IVAC+ K S+
Sbjct: 65  LDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE 121


>pdb|4F1U|A Chain A, Subatomic Resolution Structure Of A High Affinity
           Periplasmic Phosphate-Binding Protein (Pfluding) Bound
           With Phosphate At Ph 4.5
 pdb|4F1V|A Chain A, Subatomic Resolution Structure Of A High Affinity
           Periplasmic Phosphate-Binding Protein (Pfluding) Bound
           With Phosphate At Ph 8.5
 pdb|4F18|A Chain A, Subatomic Resolution Structure Of A High Affinity
           Periplasmic Phosphate-Binding Protein (Pfluding) Bound
           With Arsenate At Ph 8.5
 pdb|4F19|A Chain A, Subatomic Resolution Structure Of A High Affinity
           Periplasmic Phosphate-Binding Protein (Pfluding) Bound
           With Arsenate At Ph 4.5
          Length = 381

 Score = 26.6 bits (57), Expect = 4.1,   Method: Composition-based stats.
 Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 9   TTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTY 66
           +T  +  Q +  +LIQ     P++   V + F+KS + A+   V+      SG++NT+
Sbjct: 72  STYASAKQPTWGKLIQ----VPSVGTSVAIPFNKSGSAAVDLSVQELCGVFSGRINTW 125


>pdb|2Q9T|A Chain A, High-Resolution Structure Of The Ding Protein From
           Pseudomonas Fluorescens
          Length = 379

 Score = 26.6 bits (57), Expect = 4.1,   Method: Composition-based stats.
 Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 9   TTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTY 66
           +T  +  Q +  +LIQ     P++   V + F+KS + A+   V+      SG++NT+
Sbjct: 72  STYASAKQPTWGKLIQ----VPSVGTSVAIPFNKSGSAAVDLSVQELCGVFSGRINTW 125


  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
   0.319    0.133    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,896,386
Number of Sequences: 62578
Number of extensions: 92857
Number of successful extensions: 274
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 259
Number of HSP's gapped (non-prelim): 15
length of query: 108
length of database: 14,973,337
effective HSP length: 72
effective length of query: 36
effective length of database: 10,467,721
effective search space: 376837956
effective search space used: 376837956
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: 45 (21.9 bits)