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= 014613
(421 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EFC|A Chain A, Ara7-GdpATVPS9A
pdb|2EFC|C Chain C, Ara7-GdpATVPS9A
pdb|2EFD|A Chain A, Ara7ATVPS9A
pdb|2EFD|C Chain C, Ara7ATVPS9A
pdb|2EFE|A Chain A, Ara7-Gdpnh2ATVPS9A
pdb|2EFE|C Chain C, Ara7-Gdpnh2ATVPS9A
pdb|4G01|A Chain A, Ara7-gdp-ca2+/vps9a
Length = 267
Score = 350 bits (899), Expect = 6e-97, Method: Compositional matrix adjust.
Identities = 163/209 (77%), Positives = 187/209 (89%)
Query: 1 MEAAFRAHPLWAGCSEEELDSAGEGLEKYVMTKLFTRVFASIPDDVKTDEQLSEKIALVQ 60
MEAAFRAHPLW+GCSEEELDSAG+GLEKYVMTKLFTRVFAS ++V DE+L +K++LVQ
Sbjct: 59 MEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLFQKMSLVQ 118
Query: 61 QFVRPENLDIKASFQNETSWLLAQKELQKINMYKAPRDKLVCILNCCKVXXXXXXXXXXX 120
QF+ PENLDI+ +FQNE+SWLLAQKELQKINMYKAPRDKLVCILNCCKV
Sbjct: 119 QFISPENLDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIA 178
Query: 121 XXENPPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRQSRLVGEAAYFFTNMLSAESF 180
EN PGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRR+S+LVGEAAYFFTN+LSAESF
Sbjct: 179 SNENAPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESF 238
Query: 181 ISNIDAQALSMEESEFERNMESAQALLSG 209
ISNIDA+++S++E+EFE+NMESA+A +SG
Sbjct: 239 ISNIDAKSISLDEAEFEKNMESARARISG 267
>pdb|2EFH|A Chain A, Ara7-GdpATVPS9A(D185N)
pdb|2EFH|C Chain C, Ara7-GdpATVPS9A(D185N)
Length = 267
Score = 349 bits (895), Expect = 2e-96, Method: Compositional matrix adjust.
Identities = 162/209 (77%), Positives = 187/209 (89%)
Query: 1 MEAAFRAHPLWAGCSEEELDSAGEGLEKYVMTKLFTRVFASIPDDVKTDEQLSEKIALVQ 60
MEAAFRAHPLW+GCSEEELDSAG+GLEKYVMTKLFTRVFAS ++V DE+L +K++LVQ
Sbjct: 59 MEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLFQKMSLVQ 118
Query: 61 QFVRPENLDIKASFQNETSWLLAQKELQKINMYKAPRDKLVCILNCCKVXXXXXXXXXXX 120
QF+ PENLDI+ +FQNE+SWLLAQKELQKINMYKAPRDKLVCILNCCKV
Sbjct: 119 QFISPENLDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIA 178
Query: 121 XXENPPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRQSRLVGEAAYFFTNMLSAESF 180
EN PGA+EFLPVLIYVTIKANPPQLHSNLLYIQRYRR+S+LVGEAAYFFTN+LSAESF
Sbjct: 179 SNENAPGANEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESF 238
Query: 181 ISNIDAQALSMEESEFERNMESAQALLSG 209
ISNIDA+++S++E+EFE+NMESA+A +SG
Sbjct: 239 ISNIDAKSISLDEAEFEKNMESARARISG 267
>pdb|2OT3|A Chain A, Crystal Structure Of Rabex-5 Vps9 Domain In Complex With
Nucleotide Free Rab21
Length = 274
Score = 115 bits (287), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 70/193 (36%), Positives = 102/193 (52%), Gaps = 18/193 (9%)
Query: 17 EELDSAGEGLEKYVMTKLFTRVFAS-IPDDVKTDEQLSEKIALV-----QQFVRPENLDI 70
E ++ + +EKY+MT+L+ VF DD K D + ++I + Q P N DI
Sbjct: 79 ERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQMLCVPVNEDI 138
Query: 71 KASFQNETSWLLAQKELQKINM--YKAPRDKLVCILNCCKVXXXXXXXXXXXXXENPPGA 128
E S ++ + I M + PRDKL CI C K P A
Sbjct: 139 P-----EVSDMVVKAITDIIEMDSKRVPRDKLACITKCSK----HIFNAIKITKNEPASA 189
Query: 129 DEFLPVLIYVTIKANPPQLHSNLLYIQRYRRQSRLV-GEAAYFFTNMLSAESFISNIDAQ 187
D+FLP LIY+ +K NPP+L SN+ YI R+ SRL+ GE Y+FTN+ A +FI +DAQ
Sbjct: 190 DDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQ 249
Query: 188 ALSMEESEFERNM 200
+L++ + +F+R M
Sbjct: 250 SLNLSQEDFDRYM 262
>pdb|1TXU|A Chain A, Crystal Structure Of The Vps9 Domain Of Rabex-5
Length = 273
Score = 108 bits (271), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 65/189 (34%), Positives = 99/189 (52%), Gaps = 14/189 (7%)
Query: 17 EELDSAGEGLEKYVMTKLFTRVFAS-IPDDVKTDEQLSEKIALV-----QQFVRPENLDI 70
E ++ + +EKY+ T+L+ VF DD K D + ++I + Q P N DI
Sbjct: 81 ERVEKIXDQIEKYIXTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQXLCVPVNEDI 140
Query: 71 KASFQNETSWLLAQKELQKINMYKAPRDKLVCILNCCKVXXXXXXXXXXXXXENPPGADE 130
+ + A ++ + + + PRDKL CI C K P AD+
Sbjct: 141 P---EVSDXVVKAITDIIEXDSKRVPRDKLACITKCSK----HIFNAIKITKNEPASADD 193
Query: 131 FLPVLIYVTIKANPPQLHSNLLYIQRYRRQSRL-VGEAAYFFTNMLSAESFISNIDAQAL 189
FLP LIY+ +K NPP+L SN+ YI R+ SRL GE Y+FTN+ A +FI +DAQ+L
Sbjct: 194 FLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLXTGEDGYYFTNLCCAVAFIEKLDAQSL 253
Query: 190 SMEESEFER 198
++ + +F+R
Sbjct: 254 NLSQEDFDR 262
>pdb|4FPV|A Chain A, Crystal Structure Of D. Rerio Tdp2 Complexed With Single
Strand Dna Product
pdb|4FPV|B Chain B, Crystal Structure Of D. Rerio Tdp2 Complexed With Single
Strand Dna Product
Length = 257
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 14/66 (21%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 170 FFTNMLSAESFISNIDAQALSMEESEFERNMESAQALLSG-----LSADMDGLSNQNDES 224
+FT ++ +S + ++++ + ++ RN+ AQ SG +++ ++ NQ+ E
Sbjct: 75 YFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQKLYLMTSHLESCKNQSQER 134
Query: 225 EGQISV 230
Q+ V
Sbjct: 135 TKQLRV 140
>pdb|4F1H|A Chain A, Crystal Structure Of Tdp2 From Danio Rerio Complexed With
A Single Strand Dna
Length = 250
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 14/66 (21%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 170 FFTNMLSAESFISNIDAQALSMEESEFERNMESAQALLSG-----LSADMDGLSNQNDES 224
+FT ++ +S + ++++ + ++ RN+ AQ SG +++ ++ NQ+ E
Sbjct: 68 YFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQKLYLMTSHLESCKNQSQER 127
Query: 225 EGQISV 230
Q+ V
Sbjct: 128 TKQLRV 133
>pdb|4F1H|B Chain B, Crystal Structure Of Tdp2 From Danio Rerio Complexed With
A Single Strand Dna
Length = 251
Score = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/66 (21%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 170 FFTNMLSAESFISNIDAQALSMEESEFERNMESAQALLSG-----LSADMDGLSNQNDES 224
+FT ++ +S + ++++ + ++ RN+ AQ SG +++ ++ NQ+ E
Sbjct: 69 YFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQKLYLMTSHLESCKNQSQER 128
Query: 225 EGQISV 230
Q+ V
Sbjct: 129 TKQLRV 134
>pdb|2X6F|A Chain A, The Crystal Structure Of The Drosophila Class Iii
Pi3-Kinase Vps34 In Complex With 3-Methyladenine
pdb|2X6F|B Chain B, The Crystal Structure Of The Drosophila Class Iii
Pi3-Kinase Vps34 In Complex With 3-Methyladenine
pdb|2X6H|A Chain A, The Crystal Structure Of The Drosophila Class Iii
Pi3-Kinase Vps34
pdb|2X6H|B Chain B, The Crystal Structure Of The Drosophila Class Iii
Pi3-Kinase Vps34
pdb|2X6I|A Chain A, The Crystal Structure Of The Drosophila Class Iii
Pi3-kinase Vps34 In Complex With Pik-90
pdb|2X6I|B Chain B, The Crystal Structure Of The Drosophila Class Iii
Pi3-kinase Vps34 In Complex With Pik-90
pdb|2X6J|A Chain A, The Crystal Structure Of The Drosophila Class Iii
Pi3-Kinase Vps34 In Complex With Pik-93
pdb|2X6J|B Chain B, The Crystal Structure Of The Drosophila Class Iii
Pi3-Kinase Vps34 In Complex With Pik-93
pdb|2X6K|A Chain A, The Crystal Structure Of The Drosophila Class Iii
Pi3-Kinase Vps34 In Complex With Pi-103
pdb|2X6K|B Chain B, The Crystal Structure Of The Drosophila Class Iii
Pi3-Kinase Vps34 In Complex With Pi-103
Length = 696
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 44 DDVKTDEQLSEKIALVQQFVRPENLDIKAS 73
DD++ D+ + + I L+ + +R ENLD+K +
Sbjct: 448 DDLRQDQLILQMITLMDKLLRRENLDLKLT 477
>pdb|3LS8|A Chain A, Crystal Structure Of Human Pik3c3 In Complex With 3-[4-(4-
Morpholinyl)thieno[3,2-D]pyrimidin-2-Yl]-Phenol
pdb|3LS8|B Chain B, Crystal Structure Of Human Pik3c3 In Complex With 3-[4-(4-
Morpholinyl)thieno[3,2-D]pyrimidin-2-Yl]-Phenol
Length = 614
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 22/30 (73%)
Query: 44 DDVKTDEQLSEKIALVQQFVRPENLDIKAS 73
DD++ D+ + + I+L+ + +R ENLD+K +
Sbjct: 374 DDLRQDQLILQIISLMDKLLRKENLDLKLT 403
>pdb|3IHY|A Chain A, Human Pik3c3 Crystal Structure
pdb|3IHY|B Chain B, Human Pik3c3 Crystal Structure
pdb|3IHY|C Chain C, Human Pik3c3 Crystal Structure
pdb|3IHY|D Chain D, Human Pik3c3 Crystal Structure
pdb|3IHY|E Chain E, Human Pik3c3 Crystal Structure
Length = 600
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 22/30 (73%)
Query: 44 DDVKTDEQLSEKIALVQQFVRPENLDIKAS 73
DD++ D+ + + I+L+ + +R ENLD+K +
Sbjct: 360 DDLRQDQLILQIISLMDKLLRKENLDLKLT 389
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
0.310 0.127 0.347
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,357,040
Number of Sequences: 62578
Number of extensions: 358937
Number of successful extensions: 685
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 670
Number of HSP's gapped (non-prelim): 14
length of query: 421
length of database: 14,973,337
effective HSP length: 101
effective length of query: 320
effective length of database: 8,652,959
effective search space: 2768946880
effective search space used: 2768946880
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)