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= 001639
(1039 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H7H|B Chain B, Crystal Structure Of The Human Transcription Elongation
Factor Dsif, Hspt4HSPT5 (176-273)
Length = 106
Score = 89.0 bits (219), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 48/100 (48%), Positives = 68/100 (68%), Gaps = 9/100 (9%)
Query: 181 DPKLWMVKCAIGREREAAVCLMQKCID---KGSELQIRSVIALDHLKNYIYIEADKEAHV 237
DP LW VKC IG ER A+ LM+K I + LQI+SV+A +H+K YIY+EA K+ HV
Sbjct: 5 DPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHV 64
Query: 238 KEACKGLRNI----YSQKVMLVPIREMTDVLAVESKAIDL 273
K+A +G+ N+ ++Q+ +VPI+EMTDVL V + +L
Sbjct: 65 KQAIEGVGNLRLGYWNQQ--MVPIKEMTDVLKVVKEVANL 102
>pdb|2DO3|A Chain A, Solution Structure Of The Third Kow Motif Of Transcription
Elongation Factor Spt5
Length = 69
Score = 54.3 bits (129), Expect = 4e-07, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 42/59 (71%)
Query: 470 SKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSE 528
++EL KYF+ G+HVKV++G G TG++++VE++ +I+ SD T +++V D+ SE
Sbjct: 11 AQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSE 69
>pdb|3P8B|B Chain B, X-Ray Crystal Structure Of Pyrococcus Furiosus
Transcription Elongation Factor Spt45
pdb|3P8B|D Chain D, X-Ray Crystal Structure Of Pyrococcus Furiosus
Transcription Elongation Factor Spt45
Length = 152
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/129 (28%), Positives = 61/129 (47%), Gaps = 2/129 (1%)
Query: 183 KLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACK 242
K++ V+ G+E A + K + L I +++A +K YI++EA + V EA +
Sbjct: 4 KIFAVRVTHGQEETTAKLIYSKV--RTYNLPIYAILAPSRVKGYIFVEAPNKGVVDEAIR 61
Query: 243 GLRNIYSQKVMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQR 302
G+R+ VP +E+ L + L V + G +KG AKVV +D +
Sbjct: 62 GIRHARGVLPGEVPFKEIEHFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDE 121
Query: 303 VTVKLIPRI 311
V V+ I I
Sbjct: 122 VVVQFIDAI 130
>pdb|3QQC|D Chain D, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 163
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/129 (28%), Positives = 61/129 (47%), Gaps = 2/129 (1%)
Query: 183 KLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACK 242
K++ V+ G+E A + K + L I +++A +K YI++EA + V EA +
Sbjct: 4 KIFAVRVTHGQEETTAKLIYSKV--RTYNLPIYAILAPSRVKGYIFVEAPNKGVVDEAIR 61
Query: 243 GLRNIYSQKVMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQR 302
G+R+ VP +E+ L + L V + G +KG AKVV +D +
Sbjct: 62 GIRHARGVLPGEVPFKEIEHFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDE 121
Query: 303 VTVKLIPRI 311
V V+ I I
Sbjct: 122 VVVQFIDAI 130
>pdb|2EXU|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae
Transcription Elongation Factors Spt4-Spt5ngn Domain
Length = 200
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 53/86 (61%), Gaps = 5/86 (5%)
Query: 184 LWMVKCAIGREREAAVCLMQK--CIDKG---SELQIRSVIALDHLKNYIYIEADKEAHVK 238
+W V+C G+E+E L++K +D+ +L+I S+ D+ IYIEA K++ ++
Sbjct: 104 IWGVRCRPGKEKELIRKLLKKKFNLDRAMGKKKLKILSIFQRDNYTGRIYIEAPKQSVIE 163
Query: 239 EACKGLRNIYSQKVMLVPIREMTDVL 264
+ C G+ +IY + +L+P++E+ +L
Sbjct: 164 KFCNGVPDIYISQKLLIPVQELPLLL 189
>pdb|2E70|A Chain A, Solution Structure Of The Fifth Kow Motif Of Human
Transcription Elongation Factor Spt5
Length = 71
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753
+ L+G TV++ GPYKGY G V D + RVEL S + ++VDR ++
Sbjct: 17 NELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 65
>pdb|3LPE|A Chain A, Crystal Structure Of Spt45NGN HETERODIMER COMPLEX FROM
METHANOCOCCUS Jannaschii
pdb|3LPE|C Chain C, Crystal Structure Of Spt45NGN HETERODIMER COMPLEX FROM
METHANOCOCCUS Jannaschii
pdb|3LPE|E Chain E, Crystal Structure Of Spt45NGN HETERODIMER COMPLEX FROM
METHANOCOCCUS Jannaschii
pdb|3LPE|G Chain G, Crystal Structure Of Spt45NGN HETERODIMER COMPLEX FROM
METHANOCOCCUS Jannaschii
Length = 92
Score = 36.2 bits (82), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 178 SVRDPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHV 237
SV ++ V+ +G+E+ A LM +K +L + S++A + LK Y+ +EA+ + V
Sbjct: 6 SVGAHMIFAVRTMVGQEKNIA-GLMASRAEK-EQLDVYSILASESLKGYVLVEAETKGDV 63
Query: 238 KEACKGL 244
+E KG+
Sbjct: 64 EELIKGM 70
>pdb|3EWG|A Chain A, Crystal Structure Of The N-Terminal Domain Of Nusg (Ngn)
From Methanocaldococcus Jannaschii
Length = 91
Score = 35.4 bits (80), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 184 LWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKG 243
++ V+ +G+E+ A LM +K +L + S++A + LK Y+ +EA+ + V+E KG
Sbjct: 2 IFAVRTMVGQEKNIA-GLMASRAEK-EQLDVYSILASESLKGYVLVEAETKGDVEELIKG 59
Query: 244 L 244
+
Sbjct: 60 M 60
>pdb|2E6Z|A Chain A, Solution Structure Of The Second Kow Motif Of Human
Transcription Elongation Factor Spt5
Length = 59
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 425 FMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 475
F GD V V +G+L NL+G + VD + I P+ + L L ++EL K
Sbjct: 8 FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRK 58
>pdb|1U8F|O Chain O, Crystal Structure Of Human Placental Glyceraldehyde-3-
Phosphate Dehydrogenase At 1.75 Resolution
pdb|1U8F|P Chain P, Crystal Structure Of Human Placental Glyceraldehyde-3-
Phosphate Dehydrogenase At 1.75 Resolution
pdb|1U8F|Q Chain Q, Crystal Structure Of Human Placental Glyceraldehyde-3-
Phosphate Dehydrogenase At 1.75 Resolution
pdb|1U8F|R Chain R, Crystal Structure Of Human Placental Glyceraldehyde-3-
Phosphate Dehydrogenase At 1.75 Resolution
Length = 335
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 566 LKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVR-IVEGPCKGKQGPVEHI 624
L G+ R A V + ++ C+LEK + D +K VV+ EGP KG G EH
Sbjct: 228 LTGMAFRVPTANVSVVDLTCRLEKPAKYDD-------IKKVVKQASEGPLKGILGYTEHQ 280
Query: 625 YRGILFIHDRH 635
F D H
Sbjct: 281 VVSSDFNSDTH 291
>pdb|1ZNQ|O Chain O, Crsytal Structure Of Human Liver Gapdh
pdb|1ZNQ|P Chain P, Crsytal Structure Of Human Liver Gapdh
pdb|1ZNQ|R Chain R, Crsytal Structure Of Human Liver Gapdh
pdb|1ZNQ|Q Chain Q, Crsytal Structure Of Human Liver Gapdh
Length = 338
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 566 LKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVR-IVEGPCKGKQGPVEHI 624
L G+ R A V + ++ C+LEK + D +K VV+ EGP KG G EH
Sbjct: 231 LTGMAFRVPTANVSVVDLTCRLEKPAKYDD-------IKKVVKQASEGPLKGILGYTEHQ 283
Query: 625 YRGILFIHDRH 635
F D H
Sbjct: 284 VVSSDFNSDTH 294
>pdb|1HUX|A Chain A, Crystal Structure Of The Acidaminococcus Fermentans (R)-2-
Hydroxyglutaryl-Coa Dehydratase Component A
pdb|1HUX|B Chain B, Crystal Structure Of The Acidaminococcus Fermentans (R)-2-
Hydroxyglutaryl-Coa Dehydratase Component A
Length = 270
Score = 29.6 bits (65), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 981 EIEIVP--PRKTDKIKIMGGPHRGATGKLIGVDGTDGIVK 1018
E E++ + TDKI I+ G HR ++IG+ GIVK
Sbjct: 171 ESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRVGIVK 210
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 0.135 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,716,650
Number of Sequences: 62578
Number of extensions: 1312893
Number of successful extensions: 3117
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 3007
Number of HSP's gapped (non-prelim): 50
length of query: 1039
length of database: 14,973,337
effective HSP length: 109
effective length of query: 930
effective length of database: 8,152,335
effective search space: 7581671550
effective search space used: 7581671550
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: 56 (26.2 bits)