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= 017375
(372 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1U8S|A Chain A, Crystal Structure Of Putative Glycine Cleavage System
Transcriptional Repressor
pdb|1U8S|B Chain B, Crystal Structure Of Putative Glycine Cleavage System
Transcriptional Repressor
Length = 192
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 48 HTAIELTGSDRPGLLSEVSAVLTHLKCNVVSAEVWTHNTRAAALMQVT 95
H I G+DRPG+ +EV ++T CN++ + + LM ++
Sbjct: 6 HLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLIS 53
>pdb|1PHZ|A Chain A, Structure Of Phosphorylated Phenylalanine Hydroxylase
pdb|2PHM|A Chain A, Structure Of Phenylalanine Hydroxylase Dephosphorylated
Length = 429
Score = 32.0 bits (71), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 260 GLKLELCTTDRVGLLSNVTRIFRENSLTVTRAEV-ATKSGKAVNTFYVG-GASGYPVDAK 317
+ L + VG L+ V R+F EN + +T E ++ K F+ PV
Sbjct: 34 AISLIFSLKEEVGALAKVLRLFEENDINLTHIESRPSRLNKDEYEFFTYLDKRTKPVLGS 93
Query: 318 IIDSIRQSIGQTILKVKGNPE 338
II S+R IG T+ ++ + E
Sbjct: 94 IIKSLRNDIGATVHELSRDKE 114
>pdb|1MAB|G Chain G, Rat Liver F1-Atpase
Length = 270
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 177 CYDKDYSVVTITSKDRPKLVFDTVCTLTDMQYVVFHANIDAEGPEAYQEYFIRHI 231
+++ SV++ ++++P F TV +M + +IDA+ + YQEY + +I
Sbjct: 158 IFNQFKSVISYKTEEKPIFSFSTVVAAENMS---IYDDIDADVLQNYQEYNLANI 209
>pdb|2F43|G Chain G, Rat Liver F1-atpase
Length = 273
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 177 CYDKDYSVVTITSKDRPKLVFDTVCTLTDMQYVVFHANIDAEGPEAYQEYFIRHI 231
+++ SV++ ++++P F TV +M + +IDA+ + YQEY + +I
Sbjct: 161 IFNQFKSVISYKTEEKPIFSFSTVVAAENMS---IYDDIDADVLQNYQEYNLANI 212
>pdb|3NRB|A Chain A, Crystal Structure Of A Formyltetrahydrofolate Deformylase
(Puru, Pp_1943) From Pseudomonas Putida Kt2440 At 2.05 A
Resolution
pdb|3NRB|B Chain B, Crystal Structure Of A Formyltetrahydrofolate Deformylase
(Puru, Pp_1943) From Pseudomonas Putida Kt2440 At 2.05 A
Resolution
pdb|3NRB|C Chain C, Crystal Structure Of A Formyltetrahydrofolate Deformylase
(Puru, Pp_1943) From Pseudomonas Putida Kt2440 At 2.05 A
Resolution
pdb|3NRB|D Chain D, Crystal Structure Of A Formyltetrahydrofolate Deformylase
(Puru, Pp_1943) From Pseudomonas Putida Kt2440 At 2.05 A
Resolution
Length = 287
Score = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%)
Query: 51 IELTGSDRPGLLSEVSAVLTHLKCNVVSAEVWTHNTRAAALMQVTDEETGGAISD 105
+ L D PG++SEVS L + N+V AE + + +V+ E ++D
Sbjct: 10 LSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFXRVSVEIPVAGVND 64
>pdb|1A35|A Chain A, Human Topoisomerase IDNA COMPLEX
pdb|1A36|A Chain A, Topoisomerase IDNA COMPLEX
Length = 591
Score = 28.1 bits (61), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 500 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 534
>pdb|1R49|A Chain A, Human Topoisomerase I (Topo70) Double Mutant K532rY723F
Length = 592
Score = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 501 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 535
>pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomerase I Dna Complex
Length = 563
Score = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 472 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 506
>pdb|1SEU|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Indolocarbazole Sa315f And Covalent Complex With A 22
Base Pair Dna Duplex
Length = 592
Score = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 501 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 535
>pdb|1K4S|A Chain A, Human Dna Topoisomerase I In Covalent Complex With A 22
Base Pair Dna Duplex
pdb|1K4T|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Poison Topotecan And Covalent Complex With A 22 Base
Pair Dna Duplex
pdb|1SC7|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Indenoisoquinoline Mj-Ii-38 And Covalent Complex With A
22 Base Pair Dna Duplex
pdb|1T8I|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Poison Camptothecin And Covalent Complex With A 22 Base
Pair Dna Duplex
pdb|1TL8|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Indenoisoquinoline Ai-Iii-52 And Covalent Complex With A
22 Base Pair Dna Duplex
Length = 592
Score = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 501 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 535
>pdb|1A31|A Chain A, Human Reconstituted Dna Topoisomerase I In Covalent
Complex With A 22 Base Pair Dna Duplex
Length = 591
Score = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 500 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 534
>pdb|1NH3|A Chain A, Human Topoisomerase I Ara-C Complex
Length = 563
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 472 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 506
>pdb|1RR8|C Chain C, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 474 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 508
>pdb|1LPQ|A Chain A, Human Dna Topoisomerase I (70 Kda) In Non-Covalent Complex
With A 22 Base Pair Dna Duplex Containing An 8-Oxog
Lesion
Length = 564
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 473 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 507
>pdb|1RRJ|A Chain A, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 236 VKSDAERERVIQCLKAAIERRVSEGLKLELCTTDR 270
V DA+ ++V++ K A++R + +KLE+ TDR
Sbjct: 474 VMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDR 508
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 0.132 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,492,968
Number of Sequences: 62578
Number of extensions: 410228
Number of successful extensions: 1000
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 988
Number of HSP's gapped (non-prelim): 17
length of query: 372
length of database: 14,973,337
effective HSP length: 100
effective length of query: 272
effective length of database: 8,715,537
effective search space: 2370626064
effective search space used: 2370626064
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)