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= 000294
(1711 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 = 70.1 bits (170), Expect = 1e-11, Method: Composition-based stats.
Identities = 34/89 (38%), Positives = 53/89 (59%), Gaps = 2/89 (2%)
Query: 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDI 283
DP +W VKC G ER +A LM+KF+ Q + +QI S A +H+KG+I++EA KQ +
Sbjct: 5 DPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHV 64
Query: 284 NEACKGLSGIY--YSRLAPVPKNEVSHLL 310
+A +G+ + Y VP E++ +L
Sbjct: 65 KQAIEGVGNLRLGYWNQQMVPIKEMTDVL 93
>pdb|2EXU|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae
Transcription Elongation Factors Spt4-Spt5ngn Domain
Length = 200
Score = 57.0 bits (136), Expect = 9e-08, Method: Composition-based stats.
Identities = 33/92 (35%), Positives = 55/92 (59%), Gaps = 2/92 (2%)
Query: 226 TIWKVKCMAGRERQSAFCLMQKFVDL-QSLGSK-MQIISAFAVDHIKGFIFIEADKQCDI 283
TIW V+C G+E++ L++K +L +++G K ++I+S F D+ G I+IEA KQ I
Sbjct: 103 TIWGVRCRPGKEKELIRKLLKKKFNLDRAMGKKKLKILSIFQRDNYTGRIYIEAPKQSVI 162
Query: 284 NEACKGLSGIYYSRLAPVPKNEVSHLLSAQIK 315
+ C G+ IY S+ +P E+ LL ++
Sbjct: 163 EKFCNGVPDIYISQKLLIPVQELPLLLKPNLE 194
>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 = 48.9 bits (115), Expect = 2e-05, Method: Composition-based stats.
Identities = 33/131 (25%), Positives = 60/131 (45%), Gaps = 5/131 (3%)
Query: 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEA 286
I+ V+ G+E +A K + + + I + A +KG+IF+EA + ++EA
Sbjct: 5 IFAVRVTHGQEETTA-----KLIYSKVRTYNLPIYAILAPSRVKGYIFVEAPNKGVVDEA 59
Query: 287 CKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNAR 346
+G+ VP E+ H L + + + G V G +KG A+VV ++ ++
Sbjct: 60 IRGIRHARGVLPGEVPFKEIEHFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESK 119
Query: 347 KRATVKLIPRI 357
V+ I I
Sbjct: 120 DEVVVQFIDAI 130
>pdb|3QQC|D Chain D, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 163
Score = 48.9 bits (115), Expect = 2e-05, Method: Composition-based stats.
Identities = 33/131 (25%), Positives = 60/131 (45%), Gaps = 5/131 (3%)
Query: 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEA 286
I+ V+ G+E +A K + + + I + A +KG+IF+EA + ++EA
Sbjct: 5 IFAVRVTHGQEETTA-----KLIYSKVRTYNLPIYAILAPSRVKGYIFVEAPNKGVVDEA 59
Query: 287 CKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNAR 346
+G+ VP E+ H L + + + G V G +KG A+VV ++ ++
Sbjct: 60 IRGIRHARGVLPGEVPFKEIEHFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESK 119
Query: 347 KRATVKLIPRI 357
V+ I I
Sbjct: 120 DEVVVQFIDAI 130
>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 = 0.31, Method: Composition-based stats.
Identities = 19/89 (21%), Positives = 45/89 (50%), Gaps = 5/89 (5%)
Query: 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEA 286
I+ V+ M G+E+ A + + + ++ + S A + +KG++ +EA+ + D+ E
Sbjct: 2 IFAVRTMVGQEKNIAGLMASR-----AEKEQLDVYSILASESLKGYVLVEAETKGDVEEL 56
Query: 287 CKGLSGIYYSRLAPVPKNEVSHLLSAQIK 315
KG+ + + E+ LL+ +++
Sbjct: 57 IKGMPRVRGIVPGTIAIEEIEPLLTPKLE 85
>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 = 34.7 bits (78), Expect = 0.54, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEA 286
I+ V+ M G+E+ A + + + ++ + S A + +KG++ +EA+ + D+ E
Sbjct: 12 IFAVRTMVGQEKNIAGLMASR-----AEKEQLDVYSILASESLKGYVLVEAETKGDVEEL 66
Query: 287 CKGL 290
KG+
Sbjct: 67 IKGM 70
>pdb|2E70|A Chain A, Solution Structure Of The Fifth Kow Motif Of Human
Transcription Elongation Factor Spt5
Length = 71
Score = 31.6 bits (70), Expect = 3.9, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 709
+GQT+RI GP KGY+ V S V+L S + ++V + L V
Sbjct: 20 IGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTV 67
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
0.308 0.128 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 47,716,449
Number of Sequences: 62578
Number of extensions: 2031843
Number of successful extensions: 3052
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 2873
Number of HSP's gapped (non-prelim): 127
length of query: 1711
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1599
effective length of database: 7,964,601
effective search space: 12735396999
effective search space used: 12735396999
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 58 (26.9 bits)