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= 004393
(756 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FJI|1 Chain 1, Crystal Structure Of The C-Terminal Domain Of The Exocyst
Subunit Sec6p
pdb|2FJI|2 Chain 2, Crystal Structure Of The C-Terminal Domain Of The Exocyst
Subunit Sec6p
Length = 399
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 65/366 (17%), Positives = 148/366 (40%), Gaps = 47/366 (12%)
Query: 397 DPLMNSYVERMQATTKKWYLNILDAD------KVQPPKRTEDGKLYTPAAVDLFRILGEQ 450
+ L Y+ + +W N+ A+ + PP DG L+ F++ +Q
Sbjct: 10 ETLFKDYLNLIVVKMTEWIGNLEKAEFDVFLERSTPPHSDSDGLLFLDGTKTCFQMFTQQ 69
Query: 451 VQI------------VRENSTDIMLYRIALAIIQVMIDFQXXXXXXXXXXXXXIGLEP-- 496
V++ V E +D++ R I ++ + + + P
Sbjct: 70 VEVAAGTNQAKILVGVVERFSDLLTKRQKNWISKISEEIKKQINYNHKYDIDPESITPED 129
Query: 497 ---------LCAMINNNLRCYDLAMELSTSTMEALPPNYAEQV--NFEDACKGFLEVTKE 545
L A+ N+ ++ D A+ +S+ + + Y +Q+ + E GF EV +
Sbjct: 130 ECPGGLVEYLIAVSNDQMKAADYAVAISSKYGKLVSKVYEKQITNHLEGTLDGFAEVAQC 189
Query: 546 AVRHTLNVIFEDPGVEQLLVKLYQKEWSDGQVTEYLTATFGDYFMDVKMFIEERSFRRFV 605
+ + ++F+D + + +++ K W G + + T +Y +D+K + F F+
Sbjct: 190 SSLGLITLMFDD--LRKPYQEIFSKTWYMGSQAQQIADTLDEYLLDIKPQMNSVLFVNFI 247
Query: 606 EACLEETIVIYI-----DHLLTQKNYIRELTIERLRVDEEVITDFFREYISINK-----V 655
+ + ETI+ ++ +H KN +E ++ D E+ F + + N+ +
Sbjct: 248 DNVIGETIIKFLTALSFEHSFKNKN---NKFLEAMKRDFEIFYQLFVKVLDGNESKDTLI 304
Query: 656 ENRVRILTDLRELASANSVDAFALIYTNILEHQPDCPPEVVERLVALRDGIPRKDAKEVL 715
++ +L S +D+ I+ LE D +++ ++ R + + K+++
Sbjct: 305 TQNFTVMEFFMDL-SCEPIDSILDIWQKYLEVYWDSRIDLLVGILKCRKDVSSSERKKIV 363
Query: 716 QECKEI 721
Q+ E+
Sbjct: 364 QQATEM 369
>pdb|2OVJ|A Chain A, The Crystal Structure Of The Human Rac Gtpase Activating
Protein 1 (Racgap1) Mgcracgap
Length = 201
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 31/163 (19%), Positives = 66/163 (40%), Gaps = 8/163 (4%)
Query: 34 MKADYIARQQANDSQLSTMVAEQIEQ---AQTGLESLALSEQMISQLRENFISIERYCQE 90
M AD++++ + +IEQ +TGL ++ ++ + +L+E F+ ++
Sbjct: 5 MLADFVSQTSPMIPSIVVHCVNEIEQRGLTETGLYRISGCDRTVKELKEKFLRVKTV--- 61
Query: 91 CQTLIENHDQIKLLSNARNNLSTTLKDVEGMMSISVEAAEAKDSLGDDKELINTYERLTA 150
L+ D I + + + LK+ ++ EA + +D + Y+ +
Sbjct: 62 --PLLSKVDDIHAICSLLKDFLRNLKEPLLTFRLNRAFMEAAEITDEDNSIAAMYQAVGE 119
Query: 151 LDGKRRFALAAAESHKEEVGRLREYFEDVDQIWETFEKTLWGY 193
L R LA H + V + DV + + F T+ +
Sbjct: 120 LPQANRDTLAFLMIHLQRVAQSPHTKMDVANLAKVFGPTIVAH 162
>pdb|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 179
Score = 30.0 bits (66), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 659 VRILTDLRELASANSVDAFALIYT------NILEHQPDCPPEVVERLVALRDGIPRKDAK 712
VR+ D REL + LI + N E + P V++ L +L G + K
Sbjct: 32 VRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYISEVK 91
Query: 713 EVLQECKEI 721
EVLQECK +
Sbjct: 92 EVLQECKTV 100
>pdb|3QKR|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
pdb|3QKS|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
Length = 203
Score = 29.6 bits (65), Expect = 7.1, Method: Composition-based stats.
Identities = 29/128 (22%), Positives = 60/128 (46%), Gaps = 10/128 (7%)
Query: 541 EVTKEAVRHT-LNVIFEDPGVEQLLVKLYQKEWSDGQVTEYLTATFGDYFMDVKMFIEER 599
E TK R T +++IFE G + + + + K +S G++ ++ K E
Sbjct: 60 EFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEW----KHVTEPS 115
Query: 600 SFRRFVEACLEETIVIYIDHLLTQKNYIRELTIERLRVDEEVITDFFREYISINKVENRV 659
S + + A +E+ I ++ YIR+ I+ + +E RE ++++K E
Sbjct: 116 S--KAISAFMEKLIPY---NIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFETAY 170
Query: 660 RILTDLRE 667
+ L++L++
Sbjct: 171 KKLSELKK 178
>pdb|2H5G|A Chain A, Crystal Structure Of Human Pyrroline-5-carboxylate
Synthetase
pdb|2H5G|B Chain B, Crystal Structure Of Human Pyrroline-5-carboxylate
Synthetase
Length = 463
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 651 SINKVENRVRILTDLRELASANSVDAFALIYTNILEHQPDCPPEVVERLVALRDGIPRKD 710
S+ +V R RI +L EL L+ I E +PDC P+V +A +G+ K
Sbjct: 118 SVGRVLRRTRIAKNL-ELEQVTVPIGVLLV---IFESRPDCLPQVAALAIASGNGLLLKG 173
Query: 711 AKE 713
KE
Sbjct: 174 GKE 176
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 0.135 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,107,624
Number of Sequences: 62578
Number of extensions: 733293
Number of successful extensions: 2106
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2104
Number of HSP's gapped (non-prelim): 12
length of query: 756
length of database: 14,973,337
effective HSP length: 106
effective length of query: 650
effective length of database: 8,340,069
effective search space: 5421044850
effective search space used: 5421044850
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: 55 (25.8 bits)