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= 014978
         (415 letters)

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

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



>pdb|3E4B|A Chain A, Crystal Structure Of Algk From Pseudomonas Fluorescens
           Wcs374r
 pdb|3E4B|B Chain B, Crystal Structure Of Algk From Pseudomonas Fluorescens
           Wcs374r
 pdb|3E4B|C Chain C, Crystal Structure Of Algk From Pseudomonas Fluorescens
           Wcs374r
 pdb|3E4B|D Chain D, Crystal Structure Of Algk From Pseudomonas Fluorescens
           Wcs374r
          Length = 452

 Score = 33.5 bits (75), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 38/177 (21%), Positives = 69/177 (38%), Gaps = 10/177 (5%)

Query: 142 KTKIDPDWISYSTLTSLYIKMELPEKAATTLKEME----KRTCRKNRVAYSSLLSLYTNM 197
           K  ++   I Y  L ++Y K + PE+ A  LK+ME    + T    RV   + +     +
Sbjct: 169 KAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATL 228

Query: 198 GYKDEVLRIWKKMMSLFAKMNDAEYTCVISSLVKLGEFEKAENIYDEWESISGTGDPRVP 257
           G  DE  +  + ++   A    A +  +   L    E    E +    ++      PR  
Sbjct: 229 GTPDE--KTAQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAE 286

Query: 258 NILLAAYINRN----QLEMAESFYNRLVTKGIKPCYTTWELLTWGYLKKGQMEKVLE 310
            +L   Y          + AE+ + + V + +   Y   ++   GYL K   +K L+
Sbjct: 287 LLLGKLYYEGKWVPADAKAAEAHFEKAVGREVAADYYLGQIYRRGYLGKVYPQKALD 343


>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
           (Trigonal Crystal Form)
 pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
           (Orthorombic Crystal Form)
          Length = 136

 Score = 30.4 bits (67), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 30/134 (22%), Positives = 61/134 (45%), Gaps = 9/134 (6%)

Query: 186 AYSSLLSLYTNMGYKDEVLRIWKKMMSLFAKMNDAEYTCVISSLVKLGEFEKAENIYDEW 245
           A+ +L + Y   G  DE +  ++K + L  +  +A Y  + ++  K G++++A   Y + 
Sbjct: 3   AWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYN-LGNAYYKQGDYDEAIEYYQKA 61

Query: 246 ESISGTGDPRVPNI---LLAAYINRNQLEMAESFYNRLVTKGIKPCYTTWELLTWGYLKK 302
             +    DPR       L  AY  +   + A  +Y + +    +     W  L   Y K+
Sbjct: 62  LEL----DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSA-EAWYNLGNAYYKQ 116

Query: 303 GQMEKVLECFKKAI 316
           G  ++ +E ++KA+
Sbjct: 117 GDYDEAIEYYQKAL 130


>pdb|2KLO|A Chain A, Structure Of The Cdt1 C-Terminal Domain
          Length = 138

 Score = 29.6 bits (65), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 8/62 (12%)

Query: 300 LKKGQMEKVLECFKKAIGSVRKWVPDHRLITAAYNKLEEQGDIDGAEHLLVTLRNAGHVS 359
           L  G+MEK L    + +     W+  HR+ T  Y KL++  D+ G     +T R A HV 
Sbjct: 83  LSPGEMEKHLVLLAELLPD---WLSLHRIRTDTYVKLDKAVDLAG-----LTARLAHHVH 134

Query: 360 TE 361
            E
Sbjct: 135 AE 136


>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C-
           Terminal Aaa-Atpase Domain
          Length = 274

 Score = 28.9 bits (63), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 13/49 (26%), Positives = 30/49 (61%), Gaps = 2/49 (4%)

Query: 85  HMLNLYISNGQLDKVPQMLQELKKNTSPDVVTYNLWLAACASQNDKETA 133
            +LN+Y+  G+ ++  + + +  KN++P V+ ++   A C  ++D+ET 
Sbjct: 79  ELLNMYV--GESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETG 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
   0.316    0.130    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,818,727
Number of Sequences: 62578
Number of extensions: 470326
Number of successful extensions: 1328
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1323
Number of HSP's gapped (non-prelim): 23
length of query: 415
length of database: 14,973,337
effective HSP length: 101
effective length of query: 314
effective length of database: 8,652,959
effective search space: 2717029126
effective search space used: 2717029126
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)