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= 012002
(473 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 160 bits (406), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 116/376 (30%), Positives = 185/376 (49%), Gaps = 49/376 (13%)
Query: 87 IVGRILLGCGVGFANQAVPLFLSEIAPTRIRGGLNILFQLNVTIGILFANLVNY-----G 141
++ RI+ G GVG A+ P++++E+AP IRG L Q + G L VNY G
Sbjct: 130 VIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSG 189
Query: 142 TSHIKSQWGWRISLGLAGIPAALLTVGSLLVTDTPNSLIERGRFEEGKAVLRKIRGTDKI 201
+ + GWR IPA L + V ++P L+ RG+ E+ + +LRKI G
Sbjct: 190 DASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTL- 248
Query: 202 EPEFLELVEASRIAKEVKHPFRNLLKRRNR------PQLVIAVALQIFQQCTGINAIMFY 255
A++ +E+KH + K R +VI V L IFQQ GIN +++Y
Sbjct: 249 ---------ATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYY 299
Query: 256 APVLFKTLGFGGSASLYSTVITGAVNVLSTLVSIYSVDKVGRRMLLLEAGIQMFLSQTVI 315
AP +FKTLG +L T+I G +N+ T+++I +VDK GR+ L Q +
Sbjct: 300 APEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPL-----------QIIG 348
Query: 316 AIILGIKVKDHSEDLHTGFAVLVVIMICTF-ISAFAWSWGPLGWLIPSETFPLETRSAGQ 374
A+ + I + +T +V ++ F ++AFA SWGP+ W++ SE FP R
Sbjct: 349 ALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKAL 408
Query: 375 SVTVCVNLLFTFVIAQAFLSM------LCHFKFGIFLFFSGWV-----LIMSCFVFFLLP 423
++ V L + ++ F M + HF G FS W+ ++ + F++ +P
Sbjct: 409 AIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNG----FSYWIYGCMGVLAALFMWKFVP 464
Query: 424 ETKNVPIEEMTERVWK 439
ETK +EE+ E +W+
Sbjct: 465 ETKGKTLEEL-EALWE 479
>pdb|1ZXM|A Chain A, Human Topo Iia Atpase/amp-pnp
pdb|1ZXM|B Chain B, Human Topo Iia Atpase/amp-pnp
pdb|1ZXN|A Chain A, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|B Chain B, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|C Chain C, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|D Chain D, Human Dna Topoisomerase Iia AtpaseADP
Length = 400
Score = 32.0 bits (71), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 414 MSCFVFFLLPET---------KNVPI-EEMTERVWKQHWLWKNFMVDDGFDDDEPKKNGH 463
MSC + PE K +P+ E E+++ ++ + +DDDE K G
Sbjct: 74 MSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNYDDDEKKVTGG 133
Query: 464 RNGF 467
RNG+
Sbjct: 134 RNGY 137
>pdb|1Y2Q|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi
pdb|2HKZ|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
L-Serine
pdb|2HL0|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'- Aminoadenosine
pdb|2HL2|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With An
Analog Of Seryladenylate
pdb|2HL2|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With An
Analog Of Seryladenylate
Length = 143
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 180 IERGRFEEGKAVLRKIRGTDKIEPEFLELV---EASRIAKEVK------HPFRNLLKRRN 230
++RGR EE + D+ PE + L E S++A++VK +PF +L
Sbjct: 30 MKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELA 89
Query: 231 RPQLVIAVALQIFQ 244
+P + + + +++Q
Sbjct: 90 KPSVAMDILNRVYQ 103
>pdb|2HL1|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'- Aminoadenosine
pdb|2HL1|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'- Aminoadenosine
pdb|3PD2|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'-Aminoadenosine
pdb|3PD2|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'-Aminoadenosine
pdb|3PD3|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Threonyl-3'-Aminoadenosine
pdb|3PD3|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Threonyl-3'-Aminoadenosine
pdb|3PD4|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Glycyl-3'-Aminoadenosine
pdb|3PD4|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Glycyl-3'-Aminoadenosine
pdb|3PD5|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With An
Analog Of Threonyl- Adenylate
pdb|3PD5|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With An
Analog Of Threonyl- Adenylate
Length = 147
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 180 IERGRFEEGKAVLRKIRGTDKIEPEFLELV---EASRIAKEVK------HPFRNLLKRRN 230
++RGR EE + D+ PE + L E S++A++VK +PF +L
Sbjct: 30 MKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELA 89
Query: 231 RPQLVIAVALQIFQ 244
+P + + + +++Q
Sbjct: 90 KPSVAMDILNRVYQ 103
>pdb|1QZR|A Chain A, Crystal Structure Of The Atpase Region Of Saccharomyces
Cerevisiae Topoisomerase Ii Bound To Icrf-187
(Dexrazoxane)
pdb|1QZR|B Chain B, Crystal Structure Of The Atpase Region Of Saccharomyces
Cerevisiae Topoisomerase Ii Bound To Icrf-187
(Dexrazoxane)
Length = 418
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 426 KNVPIE-EMTERVWKQHWLWKNFMVDDGFDDDEPKKNGHRNGF 467
K +PIE E ++ ++ + + +DDDE K G RNG+
Sbjct: 107 KGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGY 149
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 426 KNVPIE-EMTERVWKQHWLWKNFMVDDGFDDDEPKKNGHRNGF 467
K +PIE E ++ ++ + + +DDDE K G RNG+
Sbjct: 96 KGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGY 138
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 426 KNVPIE-EMTERVWKQHWLWKNFMVDDGFDDDEPKKNGHRNGF 467
K +PIE E ++ ++ + + +DDDE K G RNG+
Sbjct: 96 KGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGY 138
>pdb|1PVG|A Chain A, Crystal Structure Of The Atpase Region Of Saccharomyces
Cerevisiae Topoisomerase Ii
pdb|1PVG|B Chain B, Crystal Structure Of The Atpase Region Of Saccharomyces
Cerevisiae Topoisomerase Ii
Length = 418
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 426 KNVPIE-EMTERVWKQHWLWKNFMVDDGFDDDEPKKNGHRNGF 467
K +PIE E ++ ++ + + +DDDE K G RNG+
Sbjct: 107 KGIPIEIHNKENIYIPEXIFGHLLTSSNYDDDEKKVTGGRNGY 149
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
0.328 0.142 0.437
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,868,029
Number of Sequences: 62578
Number of extensions: 495226
Number of successful extensions: 1259
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1253
Number of HSP's gapped (non-prelim): 13
length of query: 473
length of database: 14,973,337
effective HSP length: 102
effective length of query: 371
effective length of database: 8,590,381
effective search space: 3187031351
effective search space used: 3187031351
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)