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= 006742
(633 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 = 258 bits (660), Expect = 6e-69, Method: Compositional matrix adjust.
Identities = 179/483 (37%), Positives = 250/483 (51%), Gaps = 62/483 (12%)
Query: 161 PSTFRLLRVQGLPAWANTSCVSIRD------GDIIVAILSNYMVDIDWLLPACPVLAKIP 214
P F L RV G+ N+ + I+D G ++ + NY D+DWL+ P +
Sbjct: 38 PFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKK 97
Query: 215 HVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTA 272
+L++HG+ H+ + KP N L + L I+FGTHH+K MLL+Y G+R+++HT+
Sbjct: 98 PILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTS 157
Query: 273 NLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDYLSTLKWPEFSANLPAH 328
NLIH DW+ K+QG+W+ +P + D + S E F+ DLI YL P +
Sbjct: 158 NLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWI--- 214
Query: 329 GXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKS- 387
V LI S PG GS WGH +L+ +L++ +S
Sbjct: 215 -------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESW 267
Query: 388 PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEPL-IVWPTVEDVRCSLE 442
P+V QFSS+GSL + KW+ +E E KTP PL +++P+VE+VR SLE
Sbjct: 268 PVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLE 327
Query: 443 GYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARY--NGQKLAWFLL 499
GY AG ++P S Q +++L Y+ KW A +GRS AMPHIKT+ R + K+AWFL+
Sbjct: 328 GYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLV 387
Query: 500 TSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTET 559
TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA F S V + +GS E
Sbjct: 388 TSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------FGLDSFKVKQKFFAGSQEP 441
Query: 560 SQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYTKK-DVYG 618
+ T + Y S+D PW W+ Y K D +G
Sbjct: 442 -------MATFP-----------------VPYDLPPELYGSKDRPWIWNIPYVKAPDTHG 477
Query: 619 QVW 621
+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 = 254 bits (650), Expect = 7e-68, Method: Compositional matrix adjust.
Identities = 177/483 (36%), Positives = 250/483 (51%), Gaps = 62/483 (12%)
Query: 161 PSTFRLLRVQGLPAWANTSCVSIRD------GDIIVAILSNYMVDIDWLLPACPVLAKIP 214
P F L RV G+ N+ + I+D G ++ + NY D+DWL+ P +
Sbjct: 40 PFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKK 99
Query: 215 HVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTA 272
+L++HG+ H+ + KP N L + L I+FGTHH+K MLL+Y G+R+++HT+
Sbjct: 100 PILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTS 159
Query: 273 NLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDYLSTLKWPEFSANLPAH 328
NLIH DW+ K+QG+W+ +P + D + S E F+ +LI YL+ P +
Sbjct: 160 NLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWI--- 216
Query: 329 GXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKS- 387
V LI S PG GS WGH +L+ +L++ +S
Sbjct: 217 -------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESW 269
Query: 388 PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEPL-IVWPTVEDVRCSLE 442
P+V QFSS+GSL + KW+ +E E KTP PL +++P+VE+VR SLE
Sbjct: 270 PVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLE 329
Query: 443 GYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARY--NGQKLAWFLL 499
GY AG ++P S Q +++L Y+ KW A +GRS AMPHIKT+ R + K+AWFL+
Sbjct: 330 GYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLV 389
Query: 500 TSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTET 559
TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA S V + +GS E
Sbjct: 390 TSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------LGLDSFKVKQKFFAGSQEP 443
Query: 560 SQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYTKK-DVYG 618
+ T + Y S+D PW W+ Y K D +G
Sbjct: 444 -------MATFP-----------------VPYDLPPELYGSKDRPWIWNIPYVKAPDTHG 479
Query: 619 QVW 621
+W
Sbjct: 480 NMW 482
>pdb|1JY1|A Chain A, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
(Tdp1)
Length = 464
Score = 241 bits (615), Expect = 1e-63, Method: Compositional matrix adjust.
Identities = 173/483 (35%), Positives = 245/483 (50%), Gaps = 62/483 (12%)
Query: 161 PSTFRLLRVQGLPAWANTSCVSIRD------GDIIVAILSNYMVDIDWLLPACPVLAKIP 214
P F L RV G+ N+ + I+D G ++ + NY D+DWL+ P +
Sbjct: 19 PFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKK 78
Query: 215 HVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTA 272
+L++HG+ H+ + KP N L + L I+FGTHH+K LL+Y G+R+++HT+
Sbjct: 79 PILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKXXLLLYEEGLRVVIHTS 138
Query: 273 NLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDYLSTLKWPEFSANLPAH 328
NLIH DW+ K+QG+W+ +P + D + S E F+ +LI YL+ P +
Sbjct: 139 NLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWI--- 195
Query: 329 GXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKS- 387
V LI S PG GS WGH +L+ +L++ +S
Sbjct: 196 -------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSXPNAESW 248
Query: 388 PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEPL-IVWPTVEDVRCSLE 442
P+V QFSS+GSL + KW+ +E E KTP PL +++P+VE+VR SLE
Sbjct: 249 PVVGQFSSVGSLGADESKWLCSEFKESXLTLGKESKTPGKSSVPLYLIYPSVENVRTSLE 308
Query: 443 GYAAGNAIPSPQKNVDK-DFLKKYWAKWKASHTGRSRAMPHIKTFARY--NGQKLAWFLL 499
GY AG ++P + +K ++L Y+ KW A +GRS A PHIKT+ R + K+AWFL+
Sbjct: 309 GYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAXPHIKTYXRPSPDFSKIAWFLV 368
Query: 500 TSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTET 559
TSANLSKAAWGAL+KN +QL IRSYELGVL LPSA S V + +GS E
Sbjct: 369 TSANLSKAAWGALEKNGTQLXIRSYELGVLFLPSA------LGLDSFKVKQKFFAGSQEP 422
Query: 560 SQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYTKK-DVYG 618
+ Y S+D PW W+ Y K D +G
Sbjct: 423 XATFPVPY------------------------DLPPELYGSKDRPWIWNIPYVKAPDTHG 458
Query: 619 QVW 621
W
Sbjct: 459 NXW 461
>pdb|1Q32|A Chain A, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase
pdb|1Q32|B Chain B, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase
pdb|1Q32|C Chain C, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase
pdb|1Q32|D Chain D, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase
Length = 544
Score = 36.2 bits (82), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 492 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 529
++L W L TSANLS+ AWG + + R+YE GVL
Sbjct: 454 KELEWCLYTSANLSQTAWGTVSRKP-----RNYEAGVL 486
>pdb|3SQ8|A Chain A, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase 1 H432r Mutant (Scan1 Mutant)
pdb|3SQ8|B Chain B, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase 1 H432r Mutant (Scan1 Mutant)
pdb|3SQ8|C Chain C, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase 1 H432r Mutant (Scan1 Mutant)
pdb|3SQ8|D Chain D, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase 1 H432r Mutant (Scan1 Mutant)
Length = 470
Score = 35.8 bits (81), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 492 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 529
++L W L TSANLS+ AWG + + R+YE GVL
Sbjct: 377 KELEWCLYTSANLSQTAWGTVSRKP-----RNYEAGVL 409
>pdb|3SQ5|A Chain A, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H432n Mutant
pdb|3SQ5|B Chain B, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H432n Mutant
pdb|3SQ5|C Chain C, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H432n Mutant
pdb|3SQ5|D Chain D, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H432n Mutant
Length = 470
Score = 35.8 bits (81), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 492 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 529
++L W L TSANLS+ AWG + + R+YE GVL
Sbjct: 377 KELEWCLYTSANLSQTAWGTVSRKP-----RNYEAGVL 409
>pdb|3SQ7|A Chain A, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H432n_glu Mutant
pdb|3SQ7|B Chain B, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H432n_glu Mutant
pdb|3SQ7|C Chain C, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H432n_glu Mutant
pdb|3SQ7|D Chain D, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H432n_glu Mutant
Length = 470
Score = 35.8 bits (81), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 492 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 529
++L W L TSANLS+ AWG + + R+YE GVL
Sbjct: 377 KELEWCLYTSANLSQTAWGTVSRKP-----RNYEAGVL 409
>pdb|3SQ3|A Chain A, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H182a Mutant
pdb|3SQ3|B Chain B, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H182a Mutant
pdb|3SQ3|C Chain C, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H182a Mutant
pdb|3SQ3|D Chain D, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna
Phosphodiesterase H182a Mutant
Length = 470
Score = 35.8 bits (81), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 492 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 529
++L W L TSANLS+ AWG + + R+YE GVL
Sbjct: 377 KELEWCLYTSANLSQTAWGTVSRKP-----RNYEAGVL 409
>pdb|3EYP|A Chain A, Crystal Structure Of Putative Alpha-L-Fucosidase From
Bacteroides Thetaiotaomicron
pdb|3EYP|B Chain B, Crystal Structure Of Putative Alpha-L-Fucosidase From
Bacteroides Thetaiotaomicron
Length = 469
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 28/107 (26%), Positives = 48/107 (44%), Gaps = 11/107 (10%)
Query: 171 GLPAWANTSCVSIRDGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHM 230
G P WA T V+IRD L+ M+D D +PA ++ P H E D ++ +
Sbjct: 217 GDPCWATTDSVAIRDEAQYYKGLNEGMLDGDAYIPAETDVSIRPSWFY-HAEEDSRVKSV 275
Query: 231 KRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHV 277
+ W ++ S G + +LL +P R ++H+ + +H
Sbjct: 276 RE----LWDIY----CTSVG--RNSVLLLNFPPDRRGLIHSTDSLHA 312
>pdb|1ZKL|A Chain A, Multiple Determinants For Inhibitor Selectivity Of Cyclic
Nucleotide Phosphodiesterases
Length = 353
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 481 PHIKTFARYNGQKLAWFLLTSANLSKAAWGALQK--NNSQLMIRSYELGVLILPSAKR 536
P +AR++ +L+ +L L+KA+W LQ+ ++S+ ++EL +LP R
Sbjct: 294 PLFTEWARFSNTRLSQTMLGHVGLNKASWKGLQREQSSSEDTDAAFELNSQLLPQENR 351
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: 19,224,868
Number of Sequences: 62578
Number of extensions: 778522
Number of successful extensions: 1768
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1734
Number of HSP's gapped (non-prelim): 20
length of query: 633
length of database: 14,973,337
effective HSP length: 105
effective length of query: 528
effective length of database: 8,402,647
effective search space: 4436597616
effective search space used: 4436597616
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)