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= 039134
         (339 letters)

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

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



>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader
           (Replication Factor C, Rfc) Bound To The Dna Sliding
           Clamp (Proliferating Cell Nuclear Antigen, Pcna)
          Length = 516

 Score = 31.6 bits (70), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 41/91 (45%), Gaps = 12/91 (13%)

Query: 59  RIICLYGVSGVGKTTL--LVN-------FNSKFSDTRHNFYLVILVK-AVDNKNQQG--R 106
           R   LYG  G+GKTT   LV             SD R    L   VK A+DN +  G  +
Sbjct: 78  RAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFK 137

Query: 107 AEEIFQRLSQRRFALLLDDLRGPINLDEAGV 137
             E  Q L+ + F +++D++ G    D  GV
Sbjct: 138 HNEEAQNLNGKHFVIIMDEVDGMSGGDRGGV 168


>pdb|11AS|A Chain A, Asparagine Synthetase Mutant C51a, C315a Complexed With L-
           Asparagine
 pdb|11AS|B Chain B, Asparagine Synthetase Mutant C51a, C315a Complexed With L-
           Asparagine
 pdb|12AS|A Chain A, Asparagine Synthetase Mutant C51a, C315a Complexed With L-
           Asparagine And Amp
 pdb|12AS|B Chain B, Asparagine Synthetase Mutant C51a, C315a Complexed With L-
           Asparagine And Amp
          Length = 330

 Score = 29.6 bits (65), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 42/99 (42%), Gaps = 7/99 (7%)

Query: 124 DDLRGPINLDEAGVPDQNGSKIVFTTIMEDACNTMGDQIKFKVDYLRRDDDVLNFHPDIL 183
           DD   P  L  AG+   NG  +V+  ++EDA       I+   D L+     L    D L
Sbjct: 219 DDWSTPSELGHAGL---NGDILVWNPVLEDAFELSSMGIRVDADTLKH-QLALTGDEDRL 274

Query: 184 ELAETVADLCRGLPLAHITIGRAMANTRNRMGDLILPRL 222
           EL    A L   +P    TIG  +  +R  M  L LP +
Sbjct: 275 ELEWHQALLRGEMPQ---TIGGGIGQSRLTMLLLQLPHI 310


>pdb|3C98|B Chain B, Revised Structure Of The Munc18a-Syntaxin1 Complex
          Length = 279

 Score = 29.3 bits (64), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 7/47 (14%)

Query: 281 IIDSLIGVCLLEEVQTSFGNYVKM-------HDLLRDLALWIASQDE 320
           I+DS I    L E++T     +K+       HD+  D+A+ + SQ E
Sbjct: 194 IMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGE 240


>pdb|1B64|A Chain A, Solution Structure Of The Guanine Nucleotide Exchange
           Factor Domain From Human Elongation Factor-One Beta,
           Nmr, 20 Structures
          Length = 91

 Score = 29.3 bits (64), Expect = 3.1,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 246 KNQLIRKDELVDLWIGEGLFRGSHNIV-----VARMQGKCII-DSLIGVCLLEEVQTSFG 299
           +  + + +E V     +GL  GS  +V     + ++Q +C++ D  +G  +LEE  T+F 
Sbjct: 18  ETDMAKLEECVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITAFE 77

Query: 300 NYVKMHDL 307
           +YV+  D+
Sbjct: 78  DYVQSMDV 85


>pdb|4AW2|A Chain A, Crystal Structure Of Cdc42 Binding Protein Kinase Alpha
           (Mrck Alpha)
          Length = 437

 Score = 27.7 bits (60), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 52  FEDDFPMRIICLYGVSGVGKTTLLVNFNSKFSDTRHNFYLVILVKAVDNKNQ 103
           F+DD  + ++  Y V G    TLL  F  +  +    FYL  +V A+D+ +Q
Sbjct: 143 FQDDNNLYLVMDYYVGG-DLLTLLSKFEDRLPEEMARFYLAEMVIAIDSVHQ 193


>pdb|3F6K|A Chain A, Crystal Structure Of The Vps10p Domain Of Human
           SortilinNTS3 IN Complex With Neurotensin
          Length = 685

 Score = 27.7 bits (60), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 105 GRAEEIFQRLSQRRFALLLDDLRGPINLDEAGVPDQNGSKIVFTTI 150
           GR  +   +L+      + DDLRG ++L   G  D  G  +V TT 
Sbjct: 10  GRVRDFVAKLANNTHQHVFDDLRGSVSLSWVG--DSTGVILVLTTF 53


  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
   0.324    0.140    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,879,943
Number of Sequences: 62578
Number of extensions: 400481
Number of successful extensions: 1083
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1081
Number of HSP's gapped (non-prelim): 13
length of query: 339
length of database: 14,973,337
effective HSP length: 99
effective length of query: 240
effective length of database: 8,778,115
effective search space: 2106747600
effective search space used: 2106747600
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)