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= 030413
(177 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W4S|A Chain A, Crystal Structure Of The Proximal Bah Domain Of Polybromo
Length = 174
Score = 65.1 bits (157), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 40/121 (33%), Positives = 60/121 (49%), Gaps = 3/121 (2%)
Query: 28 NKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGA 87
N + VGD V + P++ P++ IE++ D+ + W+YRP E+ +
Sbjct: 24 NSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNETFHLATRKFLE 83
Query: 88 KELFLSDHYDVQSAHTIEGKCIVHSFKNYTKL--ENVGAED-YYCRFEYKAASGGFTQTE 144
KE+F SD+Y+ I GKC+V K Y KL EN ED Y C Y A + F + +
Sbjct: 84 KEVFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDEDVYVCESRYSAKTKSFKKIK 143
Query: 145 L 145
L
Sbjct: 144 L 144
>pdb|3PTA|A Chain A, Crystal Structure Of Human Dnmt1(646-1600) In Complex With
Dna
Length = 956
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAK 88
+ + VGDCV + P D+ KP Y+AR+ + D+ N W+ +++ G
Sbjct: 111 ETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATS--DPL 168
Query: 89 ELFLSDHYDVQSAHTIEGKCIV 110
ELFL D + I K V
Sbjct: 169 ELFLVDECEDMQLSYIHSKVKV 190
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 49/111 (44%), Gaps = 13/111 (11%)
Query: 43 DTGKPPYVARIEKI----ESDARNN---VKVRVRWYYRPEESLGGRRQFHGA--KELFLS 93
D +P + RI++I +S+ R N +K+RV +YRPE + + A L+ S
Sbjct: 342 DAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWS 401
Query: 94 DHYDVQSAHTIEGKCIVHSFKNYTKLENV----GAEDYYCRFEYKAASGGF 140
D V ++G+C V ++ + V G +Y Y A S F
Sbjct: 402 DEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSF 452
>pdb|3SWR|A Chain A, Structure Of Human Dnmt1 (601-1600) In Complex With
Sinefungin
Length = 1002
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAK 88
+ + VGDCV + P D+ KP Y+AR+ + D+ N W+ +++ G
Sbjct: 157 ETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATS--DPL 214
Query: 89 ELFLSDHYDVQSAHTIEGKCIV 110
ELFL D + I K V
Sbjct: 215 ELFLVDECEDMQLSYIHSKVKV 236
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 49/111 (44%), Gaps = 13/111 (11%)
Query: 43 DTGKPPYVARIEKI----ESDARNN---VKVRVRWYYRPEESLGGRRQFHGA--KELFLS 93
D +P + RI++I +S+ R N +K+RV +YRPE + + A L+ S
Sbjct: 388 DAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWS 447
Query: 94 DHYDVQSAHTIEGKCIVHSFKNYTKLENV----GAEDYYCRFEYKAASGGF 140
D V ++G+C V ++ + V G +Y Y A S F
Sbjct: 448 DEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSF 498
>pdb|3PT9|A Chain A, Crystal Structure Of Mouse Dnmt1(731-1602) In The Free
State
pdb|4DA4|A Chain A, Structure Of Mouse Dnmt1 (731-1602) Bound To
Hemimethylated Cpg Dna
pdb|4DA4|B Chain B, Structure Of Mouse Dnmt1 (731-1602) Bound To
Hemimethylated Cpg Dna
Length = 873
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 7 GIPTKTKTGKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKV 66
G P K + + + +I +++ VGDCV + P D+ KP Y+AR+ + D +
Sbjct: 9 GQPMKIEENRTYYQKVSI--DEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMF 66
Query: 67 RVRWY 71
W+
Sbjct: 67 HAHWF 71
>pdb|3PT6|A Chain A, Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With
Dna
pdb|3PT6|B Chain B, Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With
Dna
Length = 954
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 7 GIPTKTKTGKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKV 66
G P K + + + +I +++ VGDCV + P D+ KP Y+AR+ + D +
Sbjct: 90 GQPMKIEENRTYYQKVSI--DEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMF 147
Query: 67 RVRWY 71
W+
Sbjct: 148 HAHWF 152
>pdb|3AV4|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1
pdb|3AV5|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adohcy
pdb|3AV6|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adomet
Length = 1330
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 7 GIPTKTKTGKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKV 66
G P K + + + +I +++ VGDCV + P D+ KP Y+AR+ + D +
Sbjct: 448 GQPMKIEENRTYYQKVSI--DEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMF 505
Query: 67 RVRWY 71
W+
Sbjct: 506 HAHWF 510
>pdb|3T8S|A Chain A, Apo And Insp3-Bound Crystal Structures Of The
Ligand-Binding Domain Of An Insp3 Receptor
pdb|3T8S|B Chain B, Apo And Insp3-Bound Crystal Structures Of The
Ligand-Binding Domain Of An Insp3 Receptor
Length = 585
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 14/86 (16%)
Query: 22 YTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVK-----------VRVRW 70
Y +R V +GD V++ P + G+P + + + +++ N V + ++W
Sbjct: 165 YKLRSIGDSVVIGDKVVLNPVNAGQPLHASSHQLVDNPGCNEVNSVNCNTSWKIVLFMKW 224
Query: 71 YYRPEESLGGR---RQFHGAKELFLS 93
++ L G R FH +E FL+
Sbjct: 225 SDNKDDILKGGDVVRLFHAEQEKFLT 250
>pdb|3UJ0|A Chain A, Crystal Structure Of The Inositol 1,4,5-Trisphosphate
Receptor With Ligand Bound Form.
pdb|3UJ0|B Chain B, Crystal Structure Of The Inositol 1,4,5-Trisphosphate
Receptor With Ligand Bound Form.
pdb|3UJ4|A Chain A, Crystal Structure Of The Apo-Inositol 1,4,5-Trisphosphate
Receptor
pdb|3UJ4|B Chain B, Crystal Structure Of The Apo-Inositol 1,4,5-Trisphosphate
Receptor
Length = 604
Score = 31.2 bits (69), Expect = 0.31, Method: Composition-based stats.
Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 14/86 (16%)
Query: 22 YTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVK-----------VRVRW 70
Y +R V +GD V++ P + G+P + + + +++ N V + ++W
Sbjct: 167 YKLRSIGDSVVIGDKVVLNPVNAGQPLHASSHQLVDNPGANEVNSVNANTSWKIVLFMKW 226
Query: 71 YYRPEESLGGR---RQFHGAKELFLS 93
++ L G R FH +E FL+
Sbjct: 227 SDNKDDILKGGDVVRLFHAEQEKFLT 252
>pdb|1XZZ|A Chain A, Crystal Structure Of The Ligand Binding Suppressor Domain
Of Type 1 Inositol 1,4,5-trisphosphate Receptor
Length = 246
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 23/43 (53%)
Query: 22 YTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNV 64
Y +R V +GD V++ P + G+P + + + +++ N V
Sbjct: 182 YKLRSIGDSVVIGDKVVLNPVNAGQPLHASSHQLVDNPGCNEV 224
>pdb|2P2V|A Chain A, Crystal Structure Analysis Of Monofunctional Alpha-2,3-
Sialyltransferase Cst-I From Campylobacter Jejuni
pdb|2P56|A Chain A, Crystal Structure Of Alpha-2,3-Sialyltransferase From
Campylobacter Jejuni In Apo Form
Length = 288
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 82 RQFHGAKELFLSDHYDVQSAHT-------IEGKCIVHSFKNYTKLENVGAE 125
+Q+H AK+L L + Y++++ IE +H F N+ +G E
Sbjct: 75 QQYHTAKQLILKNEYEIKNIFCSTFNLPFIESNDFLHQFYNFFPDAKLGYE 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
0.321 0.136 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,449,513
Number of Sequences: 62578
Number of extensions: 221375
Number of successful extensions: 350
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 337
Number of HSP's gapped (non-prelim): 13
length of query: 177
length of database: 14,973,337
effective HSP length: 92
effective length of query: 85
effective length of database: 9,216,161
effective search space: 783373685
effective search space used: 783373685
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)