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= 040244
(381 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ODJ|A Chain A, Crystal Structure Of The Outer Membrane Protein Oprd From
Pseudomonas Aeruginosa
pdb|2ODJ|B Chain B, Crystal Structure Of The Outer Membrane Protein Oprd From
Pseudomonas Aeruginosa
Length = 428
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 10/85 (11%)
Query: 180 IVSDDNLQINAHFIGTRPEGRTR-----DYTWVQALAVMFDTHTLVIAANRVMHWDDNVD 234
+ SD +L + + T EG+ + + TW A A D HT +A +V H D D
Sbjct: 223 LASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLDAHTFTLAYQKV-HGDQPFD 281
Query: 235 ALSIRLNGEAVDIPTGGDAEWKTNA 259
+ NG GGD+ + N+
Sbjct: 282 YIGFGRNGSGA----GGDSIFLANS 302
>pdb|3SY7|A Chain A, Improved Crystal Structure Of Pseudomonas Aeruginosa Oprd
Length = 428
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 10/85 (11%)
Query: 180 IVSDDNLQINAHFIGTRPEGRTR-----DYTWVQALAVMFDTHTLVIAANRVMHWDDNVD 234
+ SD +L + + T EG+ + + TW A A D HT +A +V H D D
Sbjct: 223 LASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLDAHTFTLAYQKV-HGDQPFD 281
Query: 235 ALSIRLNGEAVDIPTGGDAEWKTNA 259
+ NG GGD+ + N+
Sbjct: 282 YIGFGRNGSGA----GGDSIFLANS 302
>pdb|1RR8|C Chain C, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 360 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 395
>pdb|1R49|A Chain A, Human Topoisomerase I (Topo70) Double Mutant K532rY723F
Length = 592
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 387 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 422
>pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomerase I Dna Complex
Length = 563
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 358 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 393
>pdb|1NH3|A Chain A, Human Topoisomerase I Ara-C Complex
Length = 563
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 358 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 393
>pdb|1A35|A Chain A, Human Topoisomerase IDNA COMPLEX
pdb|1A36|A Chain A, Topoisomerase IDNA COMPLEX
Length = 591
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 386 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 421
>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 = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 387 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 422
>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 = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 387 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 422
>pdb|1A31|A Chain A, Human Reconstituted Dna Topoisomerase I In Covalent
Complex With A 22 Base Pair Dna Duplex
Length = 591
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 386 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 421
>pdb|1RRJ|A Chain A, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 360 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 395
>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 = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 305 PDDDAFAHLETQFKFTNLSDLVEGVLGKTYRPYYVS 340
P+DD F L T +L DL+EG+ K +R Y S
Sbjct: 359 PEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNAS 394
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
0.323 0.138 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,016,166
Number of Sequences: 62578
Number of extensions: 413353
Number of successful extensions: 739
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 728
Number of HSP's gapped (non-prelim): 13
length of query: 381
length of database: 14,973,337
effective HSP length: 101
effective length of query: 280
effective length of database: 8,652,959
effective search space: 2422828520
effective search space used: 2422828520
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)