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= 044084
(343 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MW8|X Chain X, Crystal Structure Of A Complex Between H365r Mutant Of 67
Kda N-Terminal Fragment Of E. Coli Dna Topoisomerase I
And 5'-Acttcgggatg-3'
pdb|1MW9|X Chain X, Crystal Structure Of H365r Mutant Of 67 Kda N-Terminal
Fragment Of E. Coli Dna Topoisomerase I
Length = 592
Score = 31.6 bits (70), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 12/108 (11%)
Query: 12 KMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKL-DLTPSSTHMYKILCDSL 70
++K+ G +L + ++M A K GD +++ + ++ L +LTP+ H K
Sbjct: 421 RLKARGRILRFDGWTKVMPALRK-GDEDRILPAVNKGDALTLVELTPAQ-HFTKPPA--- 475
Query: 71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELF 118
F ++++++GI PS YAS+I + V+V F
Sbjct: 476 -----RFSEASLVKELEKRGIGR-PSTYASIISTIQDRGYVRVENRRF 517
>pdb|3PWT|A Chain A, Crystal Structure Of Mutant E.Coli Topoisomerase Ia
Length = 596
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 12/108 (11%)
Query: 12 KMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKL-DLTPSSTHMYKILCDSL 70
++K+ G +L + ++M A K GD +++ + ++ L +LTP+ H K
Sbjct: 421 RLKARGRILRFDGWTKVMPALRK-GDEDRILPAVNKGDALTLVELTPAQ-HFTKPPA--- 475
Query: 71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELF 118
F ++++++GI PS YAS+I + V+V F
Sbjct: 476 -----RFSEASLVKELEKRGIGR-PSTYASIISTIQDRGYVRVENRRF 517
>pdb|1ECL|A Chain A, Amino Terminal 67kda Domain Of Escherichia Coli Dna
Topoisomerase I (Residues 2-590 Of Mature Protein)
Cloning Artifact Adds Two Residues To The Amino-Terminus
Which Were Not Observed In The Experimental Electron
Density (Gly-2, Ser-1)
Length = 597
Score = 31.2 bits (69), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 12/108 (11%)
Query: 12 KMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKL-DLTPSSTHMYKILCDSL 70
++K+ G +L + ++M A K GD +++ + ++ L +LTP+ H K
Sbjct: 421 RLKARGRILRFDGWTKVMPALRK-GDEDRILPAVNKGDALTLVELTPAQ-HFTKPPA--- 475
Query: 71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELF 118
F ++++++GI PS YAS+I + V+V F
Sbjct: 476 -----RFSEASLVKELEKRGIGR-PSTYASIISTIQDRGYVRVENRRF 517
>pdb|1CY1|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt
pdb|1CY2|A Chain A, Complex Of E.Coli Dna Topoisomerase I With Tptptp3'
pdb|1CY6|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3' Thymidine
Monophosphate
pdb|1CY7|A Chain A, Complex Of E.coli Dna Topoisomerase I With 5'-thymidine
Monophosphate
pdb|1CY8|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'-Thymidine
Monophosphate And 3'-Thymidine Monophosphate
pdb|1CY0|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3'-5'-Adenosine
Diphosphate
pdb|1CY4|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptptp3'
Length = 599
Score = 31.2 bits (69), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 12/108 (11%)
Query: 12 KMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKL-DLTPSSTHMYKILCDSL 70
++K+ G +L + ++M A K GD +++ + ++ L +LTP+ H K
Sbjct: 423 RLKARGRILRFDGWTKVMPALRK-GDEDRILPAVNKGDALTLVELTPAQ-HFTKPPA--- 477
Query: 71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELF 118
F ++++++GI PS YAS+I + V+V F
Sbjct: 478 -----RFSEASLVKELEKRGIGR-PSTYASIISTIQDRGYVRVENRRF 519
>pdb|3PX7|A Chain A, Crystal Structure Of Covalent Complex Of Topoisomerase 1a
With Substrate
Length = 595
Score = 31.2 bits (69), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 12/108 (11%)
Query: 12 KMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKL-DLTPSSTHMYKILCDSL 70
++K+ G +L + ++M A K GD +++ + ++ L +LTP+ H K
Sbjct: 421 RLKARGRILRFDGWTKVMPALRK-GDEDRILPAVNKGDALTLVELTPAQ-HFTKPPA--- 475
Query: 71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELF 118
F ++++++GI PS YAS+I + V+V F
Sbjct: 476 -----RFSEASLVKELEKRGIGR-PSTYASIISTIQDRGYVRVENRRF 517
>pdb|3KZV|A Chain A, The Crystal Structure Of A Cytoplasmic Protein With
Unknown Function From Saccharomyces Cerevisiae
Length = 254
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 9/104 (8%)
Query: 12 KMKSAGIVLDSGCYCQIMEAFYKIGDSEKVA----ALFLECESRK---LDLTPS--STHM 62
K + +V S C + + + S K A A+ L E R+ + + P T M
Sbjct: 126 KKTNGNVVFVSSDACNMYFSSWGAYGSSKAALNHFAMTLANEERQVKAIAVAPGIVDTDM 185
Query: 63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFA 106
+ +++G S + E LK FR +KE L D SV A++ A
Sbjct: 186 QVNIRENVGPSSMSAEQLKMFRGLKENNQLLDSSVPATVYAKLA 229
>pdb|1FNN|A Chain A, Crystal Structure Of Cdc6p From Pyrobaculum Aerophilum
pdb|1FNN|B Chain B, Crystal Structure Of Cdc6p From Pyrobaculum Aerophilum
Length = 389
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 63 YKILCDSLGKSGRAF-EILKFFRDMKEKGILE 93
YKI+C+ G+ R ++ + D++EKGI+E
Sbjct: 318 YKIVCEEYGERPRVHSQLWSYLNDLREKGIVE 349
>pdb|3UNG|C Chain C, Structure Of The Cmr2 Subunit Of The Crispr Rna Silencing
Complex
pdb|3UR3|C Chain C, Structure Of The Cmr2 Subunit Of The Crispr Rna Silencing
Complex
Length = 693
Score = 28.1 bits (61), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 80 LKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEE 123
LKF + +LE ++Y L+ S+ E KV EE F+++E+
Sbjct: 221 LKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQ 264
>pdb|1G5C|A Chain A, Crystal Structure Of The 'cab' Type Beta Class Carbonic
Anhydrase From Methanobacterium Thermoautotrophicum
pdb|1G5C|B Chain B, Crystal Structure Of The 'cab' Type Beta Class Carbonic
Anhydrase From Methanobacterium Thermoautotrophicum
pdb|1G5C|C Chain C, Crystal Structure Of The 'cab' Type Beta Class Carbonic
Anhydrase From Methanobacterium Thermoautotrophicum
pdb|1G5C|D Chain D, Crystal Structure Of The 'cab' Type Beta Class Carbonic
Anhydrase From Methanobacterium Thermoautotrophicum
pdb|1G5C|E Chain E, Crystal Structure Of The 'cab' Type Beta Class Carbonic
Anhydrase From Methanobacterium Thermoautotrophicum
pdb|1G5C|F Chain F, Crystal Structure Of The 'cab' Type Beta Class Carbonic
Anhydrase From Methanobacterium Thermoautotrophicum
Length = 170
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 13 MKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLD 54
+K+AG ++D G A Y +GD+E + +C +LD
Sbjct: 55 IKNAGNIVDDGVIRSAAVAIYALGDNEIIIVGHTDCGMARLD 96
>pdb|1KT0|A Chain A, Structure Of The Large Fkbp-like Protein, Fkbp51, Involved
In Steroid Receptor Complexes
Length = 457
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 26/61 (42%)
Query: 121 AEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA 180
A EKG+ R E L + +G EK LEV K A L IS C + RR
Sbjct: 349 ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERDRRI 408
Query: 181 Y 181
Y
Sbjct: 409 Y 409
>pdb|4DOZ|A Chain A, Crystal Structure Of Pyrococcus Furiosus Cmr2 (Cas10)
Length = 686
Score = 27.7 bits (60), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 80 LKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEE 123
LKF + +LE ++Y L+ S+ E KV EE F+++E+
Sbjct: 206 LKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQ 249
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
0.322 0.135 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,199,504
Number of Sequences: 62578
Number of extensions: 351383
Number of successful extensions: 885
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 880
Number of HSP's gapped (non-prelim): 11
length of query: 343
length of database: 14,973,337
effective HSP length: 100
effective length of query: 243
effective length of database: 8,715,537
effective search space: 2117875491
effective search space used: 2117875491
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: 52 (24.6 bits)