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= 009833
(524 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 = 162 bits (409), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 143/502 (28%), Positives = 223/502 (44%), Gaps = 78/502 (15%)
Query: 30 IMAATGGLMFGYDVGVSGGVTAMPHFLKKFFPVVYRRTQQGDDSNYCKYDNQGLQLFTSS 89
++A GGL+FGYD V G + V+ Q +S N L +S
Sbjct: 15 LVATLGGLLFGYDTAVISGTV-------ESLNTVFVAPQNLSESA----ANSLLGFCVAS 63
Query: 90 LYLAGLTATFFASYXXXXXXXXXXXXIAGI-FFIAGVAF-------------NVAAQNLA 135
+ + Y IA + FFI+GV N LA
Sbjct: 64 ALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLA 123
Query: 136 ----MLIVGRILLGCGVGFANQAVPLFLSEIAPTRIRGGLNILFQLNVTIGILFANLVNY 191
++ RI+ G GVG A+ P++++E+AP IRG L Q + G L VNY
Sbjct: 124 GYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNY 183
Query: 192 -----GTSHIKSQWGWRISLGLAGIPAALLTVGSLLVTDTPNSLIERGRFEEGKAVLRKI 246
G + + GWR IPA L + V ++P L+ RG+ E+ + +LRKI
Sbjct: 184 FIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKI 243
Query: 247 RGTDKIEPEFLELVEASRIAKEVKHPFRNLLKRRNR------PQLVIAVALQIFQQCTGI 300
G A++ +E+KH + K R +VI V L IFQQ GI
Sbjct: 244 MGNTL----------ATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGI 293
Query: 301 NAIMFYAPVLFKTLGFGGSASLYSTVITGAVNVLSTLVSIYSVDKVGRRMLLLEAGIQMF 360
N +++YAP +FKTLG +L T+I G +N+ T+++I +VDK GR+ L
Sbjct: 294 NVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPL--------- 344
Query: 361 LSQTVIAIILGIKVKDHSEDLHTGFAVLVVIMICTF-ISAFAWSWGPLGWLIPSETFPLE 419
Q + A+ + I + +T +V ++ F ++AFA SWGP+ W++ SE FP
Sbjct: 345 --QIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNA 402
Query: 420 TRSAGQSVTVCVNLLFTFVIAQAFLSM------LCHFKFGIFLFFSGWV-----LIMSCF 468
R ++ V L + ++ F M + HF G FS W+ ++ + F
Sbjct: 403 IRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNG----FSYWIYGCMGVLAALF 458
Query: 469 VFFLLPETKNVPIEEMTERVWK 490
++ +PETK +EE+ E +W+
Sbjct: 459 MWKFVPETKGKTLEEL-EALWE 479
>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 = 1.1, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 231 IERGRFEEGKAVLRKIRGTDKIEPEFLELV---EASRIAKEVK------HPFRNLLKRRN 281
++RGR EE + D+ PE + L E S++A++VK +PF +L
Sbjct: 30 MKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELA 89
Query: 282 RPQLVIAVALQIFQ 295
+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 = 1.1, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 231 IERGRFEEGKAVLRKIRGTDKIEPEFLELV---EASRIAKEVK------HPFRNLLKRRN 281
++RGR EE + D+ PE + L E S++A++VK +PF +L
Sbjct: 30 MKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELA 89
Query: 282 RPQLVIAVALQIFQ 295
+P + + + +++Q
Sbjct: 90 KPSVAMDILNRVYQ 103
>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 = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 465 MSCFVFFLLPET---------KNVPI-EEMTERVWKQHWLWKNFMVDDGFDDDEPKKNGH 514
MSC + PE K +P+ E E+++ ++ + +DDDE K G
Sbjct: 74 MSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNYDDDEKKVTGG 133
Query: 515 RNGF 518
RNG+
Sbjct: 134 RNGY 137
>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 = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 477 KNVPIE-EMTERVWKQHWLWKNFMVDDGFDDDEPKKNGHRNGF 518
K +PIE E ++ ++ + + +DDDE K G RNG+
Sbjct: 107 KGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGY 149
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 477 KNVPIE-EMTERVWKQHWLWKNFMVDDGFDDDEPKKNGHRNGF 518
K +PIE E ++ ++ + + +DDDE K G RNG+
Sbjct: 96 KGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGY 138
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 477 KNVPIE-EMTERVWKQHWLWKNFMVDDGFDDDEPKKNGHRNGF 518
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 = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 477 KNVPIE-EMTERVWKQHWLWKNFMVDDGFDDDEPKKNGHRNGF 518
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
0.327 0.142 0.436
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,545,117
Number of Sequences: 62578
Number of extensions: 572827
Number of successful extensions: 1463
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: 1456
Number of HSP's gapped (non-prelim): 14
length of query: 524
length of database: 14,973,337
effective HSP length: 103
effective length of query: 421
effective length of database: 8,527,803
effective search space: 3590205063
effective search space used: 3590205063
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: 54 (25.4 bits)