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= 041357
(169 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3DOM|A Chain A, Crystal Structure Of The Complex Between Tfb5 And The
C-Terminal Domain Of Tfb2
pdb|3DOM|C Chain C, Crystal Structure Of The Complex Between Tfb5 And The
C-Terminal Domain Of Tfb2
Length = 108
Score = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 44/83 (53%)
Query: 83 PRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLW 142
P + + +P V DQIRLW+ +L+RV T Y +F + + YA+D LLW
Sbjct: 19 PNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLW 78
Query: 143 EDSKKMRLVVNAEIHMHMREFLR 165
+D KK + ++ E + + +F +
Sbjct: 79 KDDKKKKFFISKEGNSQVLDFAK 101
>pdb|3DGP|A Chain A, Crystal Structure Of The Complex Between Tfb5 And The
C-Terminal Domain Of Tfb2
Length = 80
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 95 NVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNA 154
V DQIRLW+ +L+RV T Y +F + + YA+D LLW+D KK + ++
Sbjct: 3 TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62
Query: 155 EIHMHMREFLR 165
E + + +F +
Sbjct: 63 EGNSQVLDFAK 73
>pdb|1E7P|A Chain A, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|1E7P|D Chain D, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|2BS3|A Chain A, Glu C180-> Gln Variant Quinol:fumarate Reductase From
Wolinella Succinogenes
pdb|2BS3|D Chain D, Glu C180-> Gln Variant Quinol:fumarate Reductase From
Wolinella Succinogenes
pdb|2BS4|A Chain A, Glu C180-> Ile Variant Quinol:fumarate Reductase From
Wolinella Succinogenes
pdb|2BS4|D Chain D, Glu C180-> Ile Variant Quinol:fumarate Reductase From
Wolinella Succinogenes
pdb|1E7P|G Chain G, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|1E7P|J Chain J, Quinol:fumarate Reductase From Wolinella Succinogenes
Length = 656
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 64 ESLYNAFEN-GITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFP 122
E LY +N GI ++ +A+P + + VP + + + + L+R E+ AH +++P
Sbjct: 495 EELYKKSKNVGIKNKRLHANPELEEAY-RVPMMLKVALCVAKGALDRTESRGAHNREDYP 553
Query: 123 SRD 125
RD
Sbjct: 554 KRD 556
>pdb|1QLB|A Chain A, Respiratory Complex Ii-Like Fumarate Reductase From
Wolinella Succinogenes
pdb|1QLB|D Chain D, Respiratory Complex Ii-Like Fumarate Reductase From
Wolinella Succinogenes
Length = 656
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 64 ESLYNAFEN-GITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFP 122
E LY +N GI ++ +A+P + + VP + + + + L+R E+ AH +++P
Sbjct: 495 EELYKKSKNVGIKNKRLHANPELEEAY-RVPMMLKVALCVAKGALDRTESRGAHNREDYP 553
Query: 123 SRD 125
RD
Sbjct: 554 KRD 556
>pdb|2BS2|A Chain A, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|2BS2|D Chain D, Quinol:fumarate Reductase From Wolinella Succinogenes
Length = 660
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 64 ESLYNAFEN-GITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFP 122
E LY +N GI ++ +A+P + + VP + + + + L+R E+ AH +++P
Sbjct: 495 EELYKKSKNVGIKNKRLHANPELEEAY-RVPMMLKVALCVAKGALDRTESRGAHNREDYP 553
Query: 123 SRD 125
RD
Sbjct: 554 KRD 556
>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWJ|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWK|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWK|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWL|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3MWL|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3NBF|A Chain A, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|B Chain B, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|C Chain C, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|D Chain D, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NEJ|A Chain A, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
pdb|3NEJ|B Chain B, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
Length = 207
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 43 LRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRL 102
L++ S++ P+L V A+ + Y +Q+ A R AD + + P D +R
Sbjct: 86 LQVASELTAVAPHLKVVAVYGGTGYG--------KQKEALLRGADAVVATPGRALDYLRQ 137
Query: 103 WESDLNRVETTPAHYYDEF 121
DL+RVE DE
Sbjct: 138 GVLDLSRVEVAVLDEADEM 156
>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1
pdb|2GXS|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXS|B Chain B, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXU|A Chain A, Hera N-Terminal Domain In Complex With Orthophosphate,
Crystal Form 1
Length = 207
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 43 LRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRL 102
L++ S++ P+L V A+ + Y +Q+ A R AD + + P D +R
Sbjct: 86 LQVASELTAVAPHLKVVAVYGGTGYG--------KQKEALLRGADAVVATPGRALDYLRQ 137
Query: 103 WESDLNRVETTPAHYYDEF 121
DL+RVE DE
Sbjct: 138 GVLDLSRVEVAVLDEADEM 156
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
0.320 0.134 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,133,078
Number of Sequences: 62578
Number of extensions: 196450
Number of successful extensions: 407
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 405
Number of HSP's gapped (non-prelim): 8
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)