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= 013742
(437 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 = 241 bits (614), Expect = 8e-64, Method: Compositional matrix adjust.
Identities = 167/439 (38%), Positives = 231/439 (52%), Gaps = 56/439 (12%)
Query: 3 DIDWLLPACPVLAKIPHVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKA 60
D+DWL+ P + +L++HG+ H+ + KP N L + L I+FGTHH+K
Sbjct: 82 DVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKM 141
Query: 61 MLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDY 116
MLL+Y G+R+++HT+NLIH DW+ K+QG+W+ +P + D + S E F+ DLI Y
Sbjct: 142 MLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISY 201
Query: 117 LSTLKWPEFSANLPAHGXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLR 176
L P + V LI S PG GS WGH +L+
Sbjct: 202 LMAYNAPSLKEWIDV----------IHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLK 251
Query: 177 TVLQECTFEKGFKKS-PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEP 231
+L++ +S P+V QFSS+GSL + KW+ +E E KTP P
Sbjct: 252 KLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVP 311
Query: 232 L-IVWPTVEDVRCSLEGYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKT 289
L +++P+VE+VR SLEGY AG ++P S Q +++L Y+ KW A +GRS AMPHIKT
Sbjct: 312 LYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKT 371
Query: 290 FARY--NGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSC 347
+ R + K+AWFL+TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA F
Sbjct: 372 YMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------FGL 425
Query: 348 TSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDV 407
S V + +GS E + T + Y S+D
Sbjct: 426 DSFKVKQKFFAGSQEP-------MATFP-----------------VPYDLPPELYGSKDR 461
Query: 408 PWSWDKRYTKK-DVYGQVW 425
PW W+ Y K D +G +W
Sbjct: 462 PWIWNIPYVKAPDTHGNMW 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 = 238 bits (606), Expect = 7e-63, Method: Compositional matrix adjust.
Identities = 165/439 (37%), Positives = 231/439 (52%), Gaps = 56/439 (12%)
Query: 3 DIDWLLPACPVLAKIPHVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKA 60
D+DWL+ P + +L++HG+ H+ + KP N L + L I+FGTHH+K
Sbjct: 84 DVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKM 143
Query: 61 MLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDY 116
MLL+Y G+R+++HT+NLIH DW+ K+QG+W+ +P + D + S E F+ +LI Y
Sbjct: 144 MLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISY 203
Query: 117 LSTLKWPEFSANLPAHGXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLR 176
L+ P + V LI S PG GS WGH +L+
Sbjct: 204 LTAYNAPSLKEWIDV----------IHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLK 253
Query: 177 TVLQECTFEKGFKKS-PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEP 231
+L++ +S P+V QFSS+GSL + KW+ +E E KTP P
Sbjct: 254 KLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVP 313
Query: 232 L-IVWPTVEDVRCSLEGYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKT 289
L +++P+VE+VR SLEGY AG ++P S Q +++L Y+ KW A +GRS AMPHIKT
Sbjct: 314 LYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKT 373
Query: 290 FARY--NGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSC 347
+ R + K+AWFL+TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA
Sbjct: 374 YMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------LGL 427
Query: 348 TSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDV 407
S V + +GS E + T + Y S+D
Sbjct: 428 DSFKVKQKFFAGSQEP-------MATFP-----------------VPYDLPPELYGSKDR 463
Query: 408 PWSWDKRYTKK-DVYGQVW 425
PW W+ Y K D +G +W
Sbjct: 464 PWIWNIPYVKAPDTHGNMW 482
>pdb|1JY1|A Chain A, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase
(Tdp1)
Length = 464
Score = 224 bits (570), Expect = 1e-58, Method: Compositional matrix adjust.
Identities = 162/439 (36%), Positives = 226/439 (51%), Gaps = 56/439 (12%)
Query: 3 DIDWLLPACPVLAKIPHVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKA 60
D+DWL+ P + +L++HG+ H+ + KP N L + L I+FGTHH+K
Sbjct: 63 DVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKX 122
Query: 61 MLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDY 116
LL+Y G+R+++HT+NLIH DW+ K+QG+W+ +P + D + S E F+ +LI Y
Sbjct: 123 XLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISY 182
Query: 117 LSTLKWPEFSANLPAHGXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLR 176
L+ P + V LI S PG GS WGH +L+
Sbjct: 183 LTAYNAPSLKEWIDV----------IHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLK 232
Query: 177 TVLQECTFEKGFKKS-PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEP 231
+L++ +S P+V QFSS+GSL + KW+ +E E KTP P
Sbjct: 233 KLLKDHASSXPNAESWPVVGQFSSVGSLGADESKWLCSEFKESXLTLGKESKTPGKSSVP 292
Query: 232 L-IVWPTVEDVRCSLEGYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKT 289
L +++P+VE+VR SLEGY AG ++P S Q +++L Y+ KW A +GRS A PHIKT
Sbjct: 293 LYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAXPHIKT 352
Query: 290 FARY--NGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSC 347
+ R + K+AWFL+TSANLSKAAWGAL+KN +QL IRSYELGVL LPSA
Sbjct: 353 YXRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLXIRSYELGVLFLPSA------LGL 406
Query: 348 TSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDV 407
S V + +GS E + Y S+D
Sbjct: 407 DSFKVKQKFFAGSQEPXATFPVPY------------------------DLPPELYGSKDR 442
Query: 408 PWSWDKRYTKK-DVYGQVW 425
PW W+ Y K D +G W
Sbjct: 443 PWIWNIPYVKAPDTHGNXW 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 = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 296 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 333
++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 = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 296 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 333
++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 = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 296 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 333
++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 = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 296 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 333
++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 = 35.4 bits (80), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 296 QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVL 333
++L W L TSANLS+ AWG + + R+YE GVL
Sbjct: 377 KELEWCLYTSANLSQTAWGTVSRKP-----RNYEAGVL 409
>pdb|1ZKL|A Chain A, Multiple Determinants For Inhibitor Selectivity Of Cyclic
Nucleotide Phosphodiesterases
Length = 353
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 285 PHIKTFARYNGQKLAWFLLTSANLSKAAWGALQK--NNSQLMIRSYELGVLILPSAKR 340
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
0.318 0.133 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,109,204
Number of Sequences: 62578
Number of extensions: 509564
Number of successful extensions: 1143
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1109
Number of HSP's gapped (non-prelim): 17
length of query: 437
length of database: 14,973,337
effective HSP length: 102
effective length of query: 335
effective length of database: 8,590,381
effective search space: 2877777635
effective search space used: 2877777635
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)