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= 006900
(626 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QZQ|A Chain A, Human Tyrosyl Dna Phosphodiesterase
pdb|1QZQ|B Chain B, Human Tyrosyl Dna Phosphodiesterase
Length = 483
Score = 237 bits (605), Expect = 1e-62, Method: Compositional matrix adjust.
Identities = 168/483 (34%), Positives = 240/483 (49%), Gaps = 69/483 (14%)
Query: 161 PSTFRLLRVQGLPAWANTSCVSIRDVIQ---GDIIVAILSNYMVDIDWLLPACPVLAKIP 217
P F L RV G+ N+ + I+D++ G ++ + NY D+DWL+ P +
Sbjct: 38 PFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKK 97
Query: 218 HVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTA 275
+L++HG+ H+ + KP N L + L I+FGTHH+K MLL+Y G+R+++HT+
Sbjct: 98 PILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTS 157
Query: 276 NLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDYLSTLKWPEFSANLPAH 331
NLIH DW+ K+QG+W+ +P + D + S E F+ DLI YL P +
Sbjct: 158 NLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWI--- 214
Query: 332 GXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKS- 390
V LI S PG GS WGH +L+ +L++ +S
Sbjct: 215 -------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESW 267
Query: 391 PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEPL-IVWPTVEDVRCSLE 445
P+V QFSS+GSL + KW+ +E E KTP PL +++P+VE+VR SLE
Sbjct: 268 PVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLE 327
Query: 446 GYAAGNAIPSPQKNVDK-DFLKKYWAKWKASHTGRSRAMPHIKTFAR------------Y 492
GY AG ++P + +K ++L Y+ KW A +GRS AMPHIKT+ R
Sbjct: 328 GYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLV 387
Query: 493 NGQKLAKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTET 552
L+KAAWGAL+KN +QLMIRSYELGVL LPSA F S V + +GS E
Sbjct: 388 TSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------FGLDSFKVKQKFFAGSQEP 441
Query: 553 SQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYTKK-DVYG 611
+ T + Y S+D PW W+ Y K D +G
Sbjct: 442 -------MATFP-----------------VPYDLPPELYGSKDRPWIWNIPYVKAPDTHG 477
Query: 612 QVW 614
+W
Sbjct: 478 NMW 480
>pdb|1MU7|A Chain A, Crystal Structure Of A Human Tyrosyl-dna Phosphodiesterase
(tdp1)- Tungstate Complex
pdb|1MU7|B Chain B, Crystal Structure Of A Human Tyrosyl-dna Phosphodiesterase
(tdp1)- Tungstate Complex
pdb|1MU9|A Chain A, Crystal Structure Of A Human Tyrosyl-Dna Phosphodiesterase
(Tdp1)- Vanadate Complex
pdb|1MU9|B Chain B, Crystal Structure Of A Human Tyrosyl-Dna Phosphodiesterase
(Tdp1)- Vanadate Complex
pdb|1NOP|A Chain A, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
(Tdp1) In Complex With Vanadate, Dna And A Human
Topoisomerase I-Derived Peptide
pdb|1NOP|B Chain B, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
(Tdp1) In Complex With Vanadate, Dna And A Human
Topoisomerase I-Derived Peptide
pdb|1RFF|A Chain A, Crystal Structure Of Human Tyrosyl-dna Phosphodiesterase
Complexed With Vanadate, Octapeptide Klnyydpr, And
Tetranucleotide Agtt.
pdb|1RFF|B Chain B, Crystal Structure Of Human Tyrosyl-dna Phosphodiesterase
Complexed With Vanadate, Octapeptide Klnyydpr, And
Tetranucleotide Agtt.
pdb|1RFI|A Chain A, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
Complexed With Vanadate, Pentapeptide Klnyk, And
Tetranucleotide Agtc
pdb|1RFI|B Chain B, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
Complexed With Vanadate, Pentapeptide Klnyk, And
Tetranucleotide Agtc
pdb|1RG1|A Chain A, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
Complexed With Vanadate, Octopamine, And Tetranucleotide
Agtt
pdb|1RG1|B Chain B, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
Complexed With Vanadate, Octopamine, And Tetranucleotide
Agtt
pdb|1RG2|A Chain A, Crystal Structure Of Human Tyrosyl-dna Phosphodiesterase
Complexed With Vanadate, Octopamine, And Tetranucleotide
Agta
pdb|1RG2|B Chain B, Crystal Structure Of Human Tyrosyl-dna Phosphodiesterase
Complexed With Vanadate, Octopamine, And Tetranucleotide
Agta
pdb|1RGT|A Chain A, Crystal Structure Of Human Tyrosyl-dna Phosphodiesterase
Complexed With Vanadate, Octopamine, And Tetranucleotide
Agtc
pdb|1RGT|B Chain B, Crystal Structure Of Human Tyrosyl-dna Phosphodiesterase
Complexed With Vanadate, Octopamine, And Tetranucleotide
Agtc
pdb|1RGU|A Chain A, The Crystal Structure Of Human Tyrosyl-dna
Phosphodiesterase Complexed With Vanadate, Octopamine,
And Tetranucleotide Agtg
pdb|1RGU|B Chain B, The Crystal Structure Of Human Tyrosyl-dna
Phosphodiesterase Complexed With Vanadate, Octopamine,
And Tetranucleotide Agtg
pdb|1RH0|A Chain A, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
Complexed With Vanadate, Octopamine And Trinucleotide
Gtt
pdb|1RH0|B Chain B, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
Complexed With Vanadate, Octopamine And Trinucleotide
Gtt
Length = 485
Score = 234 bits (598), Expect = 9e-62, Method: Compositional matrix adjust.
Identities = 167/483 (34%), Positives = 240/483 (49%), Gaps = 69/483 (14%)
Query: 161 PSTFRLLRVQGLPAWANTSCVSIRDVIQ---GDIIVAILSNYMVDIDWLLPACPVLAKIP 217
P F L RV G+ N+ + I+D++ G ++ + NY D+DWL+ P +
Sbjct: 40 PFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKK 99
Query: 218 HVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTA 275
+L++HG+ H+ + KP N L + L I+FGTHH+K MLL+Y G+R+++HT+
Sbjct: 100 PILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTS 159
Query: 276 NLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDYLSTLKWPEFSANLPAH 331
NLIH DW+ K+QG+W+ +P + D + S E F+ +LI YL+ P +
Sbjct: 160 NLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWI--- 216
Query: 332 GXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKS- 390
V LI S PG GS WGH +L+ +L++ +S
Sbjct: 217 -------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESW 269
Query: 391 PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEPL-IVWPTVEDVRCSLE 445
P+V QFSS+GSL + KW+ +E E KTP PL +++P+VE+VR SLE
Sbjct: 270 PVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLE 329
Query: 446 GYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFAR------------Y 492
GY AG ++P S Q +++L Y+ KW A +GRS AMPHIKT+ R
Sbjct: 330 GYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLV 389
Query: 493 NGQKLAKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTET 552
L+KAAWGAL+KN +QLMIRSYELGVL LPSA S V + +GS E
Sbjct: 390 TSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------LGLDSFKVKQKFFAGSQEP 443
Query: 553 SQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYTKK-DVYG 611
+ T + Y S+D PW W+ Y K D +G
Sbjct: 444 -------MATFP-----------------VPYDLPPELYGSKDRPWIWNIPYVKAPDTHG 479
Query: 612 QVW 614
+W
Sbjct: 480 NMW 482
>pdb|1JY1|A Chain A, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
(Tdp1)
Length = 464
Score = 220 bits (561), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 163/483 (33%), Positives = 235/483 (48%), Gaps = 69/483 (14%)
Query: 161 PSTFRLLRVQGLPAWANTSCVSIRDVIQ---GDIIVAILSNYMVDIDWLLPACPVLAKIP 217
P F L RV G+ N+ + I+D++ G ++ + NY D+DWL+ P +
Sbjct: 19 PFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKK 78
Query: 218 HVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTA 275
+L++HG+ H+ + KP N L + L I+FGTHH+K LL+Y G+R+++HT+
Sbjct: 79 PILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKXXLLLYEEGLRVVIHTS 138
Query: 276 NLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDYLSTLKWPEFSANLPAH 331
NLIH DW+ K+QG+W+ +P + D + S E F+ +LI YL+ P +
Sbjct: 139 NLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWI--- 195
Query: 332 GXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKS- 390
V LI S PG GS WGH +L+ +L++ +S
Sbjct: 196 -------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSXPNAESW 248
Query: 391 PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEPL-IVWPTVEDVRCSLE 445
P+V QFSS+GSL + KW+ +E E KTP PL +++P+VE+VR SLE
Sbjct: 249 PVVGQFSSVGSLGADESKWLCSEFKESXLTLGKESKTPGKSSVPLYLIYPSVENVRTSLE 308
Query: 446 GYAAGNAIPSPQKNVDK-DFLKKYWAKWKASHTGRSRAMPHIKTFAR------------Y 492
GY AG ++P + +K ++L Y+ KW A +GRS A PHIKT+ R
Sbjct: 309 GYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAXPHIKTYXRPSPDFSKIAWFLV 368
Query: 493 NGQKLAKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTET 552
L+KAAWGAL+KN +QL IRSYELGVL LPSA S V + +GS E
Sbjct: 369 TSANLSKAAWGALEKNGTQLXIRSYELGVLFLPSA------LGLDSFKVKQKFFAGSQEP 422
Query: 553 SQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYTKK-DVYG 611
+ Y S+D PW W+ Y K D +G
Sbjct: 423 XATFPVPY------------------------DLPPELYGSKDRPWIWNIPYVKAPDTHG 458
Query: 612 QVW 614
W
Sbjct: 459 NXW 461
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 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,015,627
Number of Sequences: 62578
Number of extensions: 772769
Number of successful extensions: 1733
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1709
Number of HSP's gapped (non-prelim): 8
length of query: 626
length of database: 14,973,337
effective HSP length: 105
effective length of query: 521
effective length of database: 8,402,647
effective search space: 4377779087
effective search space used: 4377779087
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: 54 (25.4 bits)