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= psy5982
(102 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/50 (54%), Positives = 33/50 (66%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKLN+LDPRI+VAW
Sbjct: 482 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAW 531
>pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomerase I Dna Complex
Length = 563
Score = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/50 (54%), Positives = 33/50 (66%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKLN+LDPRI+VAW
Sbjct: 481 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAW 530
>pdb|1RR8|C Chain C, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/50 (54%), Positives = 32/50 (64%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKLN LDPRI+VAW
Sbjct: 483 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNXLDPRITVAW 532
>pdb|1NH3|A Chain A, Human Topoisomerase I Ara-C Complex
Length = 563
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/50 (54%), Positives = 32/50 (64%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKLN LDPRI+VAW
Sbjct: 481 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNXLDPRITVAW 530
>pdb|1R49|A Chain A, Human Topoisomerase I (Topo70) Double Mutant K532rY723F
Length = 592
Score = 55.1 bits (131), Expect = 1e-08, Method: Composition-based stats.
Identities = 27/50 (54%), Positives = 33/50 (66%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKLN+LDPRI+VAW
Sbjct: 510 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAW 559
>pdb|1A35|A Chain A, Human Topoisomerase IDNA COMPLEX
pdb|1A36|A Chain A, Topoisomerase IDNA COMPLEX
Length = 591
Score = 54.7 bits (130), Expect = 1e-08, Method: Composition-based stats.
Identities = 27/50 (54%), Positives = 33/50 (66%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKLN+LDPRI+VAW
Sbjct: 509 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAW 558
>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 = 53.1 bits (126), Expect = 4e-08, Method: Composition-based stats.
Identities = 27/50 (54%), Positives = 32/50 (64%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKLN LDPRI+VAW
Sbjct: 510 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNXLDPRITVAW 559
>pdb|1A31|A Chain A, Human Reconstituted Dna Topoisomerase I In Covalent
Complex With A 22 Base Pair Dna Duplex
Length = 591
Score = 53.1 bits (126), Expect = 4e-08, Method: Composition-based stats.
Identities = 27/50 (54%), Positives = 32/50 (64%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKLN LDPRI+VAW
Sbjct: 509 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNXLDPRITVAW 558
>pdb|1RRJ|A Chain A, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 32/50 (64%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKL+ LDPRI+VAW
Sbjct: 483 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLSXLDPRITVAW 532
>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 = 51.2 bits (121), Expect = 1e-07, Method: Composition-based stats.
Identities = 26/50 (52%), Positives = 32/50 (64%)
Query: 1 MTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNYLDPRISVAW 50
+ + KK A+ R TD+EENK IALGTSKL+ LDPRI+VAW
Sbjct: 510 VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLSXLDPRITVAW 559
>pdb|2B9S|B Chain B, Crystal Structure Of Heterodimeric L. Donovani
Topoisomerase I-Vanadate-Dna Complex
Length = 62
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 22/25 (88%)
Query: 26 KEENKTIALGTSKLNYLDPRISVAW 50
K++NK ++LGTSK+NY+DPRI +W
Sbjct: 7 KDDNKAVSLGTSKINYIDPRIICSW 31
>pdb|2AVP|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr
Superhelix
Length = 70
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 42 LDPRISVAWYNLGFDFY 58
LDPR + AWYNLG +Y
Sbjct: 32 LDPRSAEAWYNLGNAYY 48
>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr
Superhelix (Trigonal Crystal Form)
pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr
Superhelix (Orthorombic Crystal Form)
Length = 136
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 42 LDPRISVAWYNLGFDFYNWSGKTKKVIKV 70
LDPR + AWYNLG +Y G + I+
Sbjct: 30 LDPRSAEAWYNLGNAYYK-QGDYDEAIEY 57
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 42 LDPRISVAWYNLGFDFYNWSGKTKKVIKV 70
LDPR + AWYNLG +Y G + I+
Sbjct: 64 LDPRSAEAWYNLGNAYYK-QGDYDEAIEY 91
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 42 LDPRISVAWYNLGFDFYNWSGKTKKVIKV 70
LDPR + AWYNLG +Y G + I+
Sbjct: 98 LDPRSAEAWYNLGNAYYK-QGDYDEAIEY 125
>pdb|3KD7|A Chain A, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|B Chain B, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|C Chain C, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|D Chain D, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|E Chain E, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
Length = 125
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 42 LDPRISVAWYNLGFDFYNWSGKTKKVIKV 70
LDP + AWYNLG +Y G +K I+
Sbjct: 38 LDPNNASAWYNLGNAYYK-QGDYQKAIEY 65
>pdb|3IC1|A Chain A, Crystal Structure Of Zinc-Bound Succinyl-Diaminopimelate
Desuccinylase From Haemophilus Influenzae
pdb|3IC1|B Chain B, Crystal Structure Of Zinc-Bound Succinyl-Diaminopimelate
Desuccinylase From Haemophilus Influenzae
pdb|3ISZ|A Chain A, Crystal Structure Of Mono-zinc Form Of
Succinyl-diaminopimelate Desuccinylase From Haemophilus
Influenzae
pdb|3ISZ|B Chain B, Crystal Structure Of Mono-zinc Form Of
Succinyl-diaminopimelate Desuccinylase From Haemophilus
Influenzae
Length = 377
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 64 TKKVIKVESFNSLPSQAIKRRIDWDLSGLP 93
T ++IK + L +K RI+W+LSG P
Sbjct: 264 TDEIIKQKVAEMLEKHNLKYRIEWNLSGKP 293
>pdb|1NA3|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
pdb|1NA3|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
Length = 91
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 42 LDPRISVAWYNLGFDFY 58
LDP + AWYNLG +Y
Sbjct: 38 LDPNNAEAWYNLGNAYY 54
>pdb|2B5O|A Chain A, Ferredoxin-nadp Reductase
pdb|2B5O|B Chain B, Ferredoxin-nadp Reductase
Length = 402
Score = 25.8 bits (55), Expect = 5.9, Method: Composition-based stats.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 25 DKEENKTIALGTSKLNYLDP 44
D E+NKT++L +L Y DP
Sbjct: 190 DMEDNKTVSLCVRQLEYQDP 209
>pdb|1NA0|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
pdb|1NA0|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
Length = 125
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 42 LDPRISVAWYNLGFDFY 58
LDP + AWYNLG +Y
Sbjct: 38 LDPNNAEAWYNLGNAYY 54
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 42 LDPRISVAWYNLGFDFY 58
LDP + AWYNLG +Y
Sbjct: 72 LDPNNAEAWYNLGNAYY 88
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
0.314 0.132 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,667,667
Number of Sequences: 62578
Number of extensions: 90859
Number of successful extensions: 167
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 141
Number of HSP's gapped (non-prelim): 26
length of query: 102
length of database: 14,973,337
effective HSP length: 67
effective length of query: 35
effective length of database: 10,780,611
effective search space: 377321385
effective search space used: 377321385
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)