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= 003225
(838 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 = 62.0 bits (149), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 49/66 (74%), Gaps = 6/66 (9%)
Query: 11 LQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNI----YSQKVMLVPIREMTDVLAVE 66
LQI+SV+A +H+K YIY+EA K+ HVK+A +G+ N+ ++Q+ +VPI+EMTDVL V
Sbjct: 39 LQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGYWNQQ--MVPIKEMTDVLKVV 96
Query: 67 SKAIDL 72
+ +L
Sbjct: 97 KEVANL 102
>pdb|2DO3|A Chain A, Solution Structure Of The Third Kow Motif Of Transcription
Elongation Factor Spt5
Length = 69
Score = 54.7 bits (130), Expect = 2e-07, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 42/59 (71%)
Query: 269 SKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSE 327
++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 = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 49/100 (49%)
Query: 11 LQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVLAVESKAI 70
L I +++A +K YI++EA + V EA +G+R+ VP +E+ L +
Sbjct: 31 LPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPGEVPFKEIEHFLEEKPAVS 90
Query: 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 110
L V + G +KG AKVV +D + V V+ I I
Sbjct: 91 GLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAI 130
>pdb|3QQC|D Chain D, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 163
Score = 46.6 bits (109), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 49/100 (49%)
Query: 11 LQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVLAVESKAI 70
L I +++A +K YI++EA + V EA +G+R+ VP +E+ L +
Sbjct: 31 LPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPGEVPFKEIEHFLEEKPAVS 90
Query: 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 110
L V + G +KG AKVV +D + V V+ I I
Sbjct: 91 GLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAI 130
>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: 504 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552
+ L+G TV++ GPYKGY G V D + RVEL S + ++VDR ++
Sbjct: 17 NELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 65
>pdb|2EXU|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae
Transcription Elongation Factors Spt4-Spt5ngn Domain
Length = 200
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 36/54 (66%)
Query: 10 ELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVL 63
+L+I S+ D+ IYIEA K++ +++ C G+ +IY + +L+P++E+ +L
Sbjct: 136 KLKILSIFQRDNYTGRIYIEAPKQSVIEKFCNGVPDIYISQKLLIPVQELPLLL 189
>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 = 1.1, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 224 FMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 274
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 = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 365 LKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIV-EGPCKGKQGPVEHI 423
L G+ R A V + ++ C+LEK + D +K VV+ EGP KG G EH
Sbjct: 228 LTGMAFRVPTANVSVVDLTCRLEKPAKYDD-------IKKVVKQASEGPLKGILGYTEHQ 280
Query: 424 YRGILFIHDRH 434
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 = 2.3, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 365 LKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIV-EGPCKGKQGPVEHI 423
L G+ R A V + ++ C+LEK + D +K VV+ EGP KG G EH
Sbjct: 231 LTGMAFRVPTANVSVVDLTCRLEKPAKYDD-------IKKVVKQASEGPLKGILGYTEHQ 283
Query: 424 YRGILFIHDRH 434
F D H
Sbjct: 284 VVSSDFNSDTH 294
>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 = 31.2 bits (69), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 10 ELQIRSVIALDHLKNYIYIEADKEAHVKEACKGL 43
+L + S++A + LK Y+ +EA+ + V+E KG+
Sbjct: 37 QLDVYSILASESLKGYVLVEAETKGDVEELIKGM 70
>pdb|3EWG|A Chain A, Crystal Structure Of The N-Terminal Domain Of Nusg (Ngn)
From Methanocaldococcus Jannaschii
Length = 91
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 10 ELQIRSVIALDHLKNYIYIEADKEAHVKEACKGL 43
+L + S++A + LK Y+ +EA+ + V+E KG+
Sbjct: 27 QLDVYSILASESLKGYVLVEAETKGDVEELIKGM 60
>pdb|2OX8|A Chain A, Human Scavenger Receptor C-Type Lectin Carbohydrate-
Recognition Domain.
pdb|2OX8|B Chain B, Human Scavenger Receptor C-Type Lectin Carbohydrate-
Recognition Domain.
pdb|2OX8|C Chain C, Human Scavenger Receptor C-Type Lectin Carbohydrate-
Recognition Domain.
pdb|2OX8|D Chain D, Human Scavenger Receptor C-Type Lectin Carbohydrate-
Recognition Domain
Length = 140
Score = 30.0 bits (66), Expect = 5.0, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 600 GMRTPMRDRAWNPYTPMSPPRDNWEDGNPGSWG 632
G+ R+ W SP NW+ G P +WG
Sbjct: 65 GLTDSERENEWKWLDGTSPDYKNWKAGQPDNWG 97
>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 = 7.2, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 780 EIEIVP--PRKTDKIKIMGGPHRGATGKLIGVDGTDGIVK 817
E E++ + TDKI I+ G HR ++IG+ GIVK
Sbjct: 171 ESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRVGIVK 210
>pdb|3J21|U Chain U, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 121
Score = 29.6 bits (65), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 49 QKVMLVPI-REMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 104
QK+M P+ RE+ + V + + + VR+ G+YKG KVV+VD R R+ V
Sbjct: 24 QKLMSAPLSRELREKYKVRNLPVRVG--DKVRIMRGDYKGHEGKVVEVDLKRYRIYV 78
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 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,013,995
Number of Sequences: 62578
Number of extensions: 1169598
Number of successful extensions: 2843
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2734
Number of HSP's gapped (non-prelim): 54
length of query: 838
length of database: 14,973,337
effective HSP length: 107
effective length of query: 731
effective length of database: 8,277,491
effective search space: 6050845921
effective search space used: 6050845921
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)