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= 005892
(671 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2B8W|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GmpALF4
pdb|2B8W|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GmpALF4
pdb|2B92|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GdpALF3
pdb|2B92|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GdpALF3
pdb|2BC9|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Non-Hydrolysable Gtp Analogue Gppnhp
pdb|2D4H|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Gmp
pdb|2D4H|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Gmp
Length = 328
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 41 AVVSIMGPQSSGKSTLLNHLFGTNFREMDAFKGRSQTTKGIWMARCAGIEP---CTLIMD 97
VV+I+G +GKS L+N L G + TKGIWM + +++D
Sbjct: 50 VVVAIVGLYRTGKSYLMNKLAGKK-KGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLD 108
Query: 98 LEGTDGRERGEDDTAFEKQSALFALAV 124
EG E+G++ + S +FALAV
Sbjct: 109 TEGLGDVEKGDN----QNDSWIFALAV 131
>pdb|1DG3|A Chain A, Structure Of Human Guanylate Binding Protein-1 In
Nucleotide Free Form
pdb|1F5N|A Chain A, Human Guanylate Binding Protein-1 In Complex With The Gtp
Analogue, Gmppnp
Length = 592
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 34/103 (33%), Positives = 47/103 (45%), Gaps = 24/103 (23%)
Query: 33 LSDCGLSYAVVSIMGPQSSGKSTLLNHLFGTNFREMDAFKGRS------QTTKGIWM--- 83
LS VV+I+G +GKS L+N L G KG S TKGIWM
Sbjct: 31 LSAITQPMVVVAIVGLYRTGKSYLMNKLAGKK-------KGFSLGSTVQSHTKGIWMWCV 83
Query: 84 --ARCAGIEPCTLIMDLEGTDGRERGEDDTAFEKQSALFALAV 124
+ G +++D EG E+G++ + S +FALAV
Sbjct: 84 PHPKKPG--HILVLLDTEGLGDVEKGDN----QNDSWIFALAV 120
>pdb|1PVW|A Chain A, 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M.
Jannaschii
pdb|1PVW|B Chain B, 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M.
Jannaschii
pdb|1PVW|C Chain C, 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M.
Jannaschii
Length = 227
Score = 32.7 bits (73), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 28/120 (23%), Positives = 54/120 (45%), Gaps = 15/120 (12%)
Query: 10 TQLIDGDGTFNVSGIEHFIKEVKLSDCGLSYAVVSIMGPQSSGKSTLLNHLFGTNFREMD 69
T + D D F + + +KE + +D G + +S G TLL G +
Sbjct: 112 TGITDNDRAFTIKKLAELVKEGRFNDFGKEF--------RSPGHVTLLRAAEGL----VK 159
Query: 70 AFKGRSQTTKGIWMARCAGIEPCTLIMDLEGTDGRERGEDDTA-FEKQSALFALAVSDIV 128
+G ++ T + +A A + P T I ++ G DG +++T + ++ L L+ +I+
Sbjct: 160 NRQGHTEMT--VALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEII 217
>pdb|1PVY|A Chain A, 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M.
Jannaschii In Complex With Ribulose 5-Phosphate
pdb|1PVY|B Chain B, 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M.
Jannaschii In Complex With Ribulose 5-Phosphate
pdb|1SNN|A Chain A, 3,4-dihydroxy-2-butanone 4-phosphate Synthase From
Methanococcus Jannaschii
pdb|1SNN|B Chain B, 3,4-dihydroxy-2-butanone 4-phosphate Synthase From
Methanococcus Jannaschii
Length = 227
Score = 32.7 bits (73), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 28/120 (23%), Positives = 54/120 (45%), Gaps = 15/120 (12%)
Query: 10 TQLIDGDGTFNVSGIEHFIKEVKLSDCGLSYAVVSIMGPQSSGKSTLLNHLFGTNFREMD 69
T + D D F + + +KE + +D G + +S G TLL G +
Sbjct: 112 TGITDNDRAFTIKKLAELVKEGRFNDFGKEF--------RSPGSVTLLRAAEGL----VK 159
Query: 70 AFKGRSQTTKGIWMARCAGIEPCTLIMDLEGTDGRERGEDDTA-FEKQSALFALAVSDIV 128
+G ++ T + +A A + P T I ++ G DG +++T + ++ L L+ +I+
Sbjct: 160 NRQGHTEMT--VALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEII 217
>pdb|3CNL|A Chain A, Crystal Structure Of Gnp-Bound Ylqf From T. Maritima
pdb|3CNN|A Chain A, Gtp-Bound Structure Of Tm Ylqf
pdb|3CNO|A Chain A, Gdp-Bound Structue Of Tm Ylqf
Length = 262
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 53/121 (43%), Gaps = 19/121 (15%)
Query: 41 AVVSIMGPQSSGKSTLLNHLFGTNFREMDAFKGRSQTTKGI-WMARCAGIE----PCTLI 95
A V I+G ++GKST++N L G + A G TKGI W + G++ P L
Sbjct: 100 ARVLIVGVPNTGKSTIINKLKGKRASSVGAQPG---ITKGIQWFSLENGVKILDTPGILY 156
Query: 96 MD-----------LEGTDGRERGEDDTAFEKQSALFALAVSDIVLINMWCHDIGREQAAN 144
+ L G+ ER ED FE+ +FA ++ + + D R++
Sbjct: 157 KNIFSEDLAAKLLLVGSLPVERIEDQRIFERAFEIFARSIGIESSFSEFFEDFARKRGLL 216
Query: 145 K 145
K
Sbjct: 217 K 217
>pdb|3OQC|A Chain A, Ubiquitin-Fold Modifier 1 Specific Protease, Ufsp2
pdb|3OQC|B Chain B, Ubiquitin-Fold Modifier 1 Specific Protease, Ufsp2
Length = 481
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 4/46 (8%)
Query: 450 AAKLGELTAIFEAKLNE----SLSGPVEALLDGANNETWPAIRKLL 491
+ LG +T I EA+ E ++S P++A++ A E+W +RKLL
Sbjct: 136 STPLGAVTPILEAENEEHHYINMSLPIDAVVSVAPEESWGKVRKLL 181
>pdb|1L2T|A Chain A, Dimeric Structure Of Mj0796, A Bacterial Abc Transporter
Cassette
pdb|1L2T|B Chain B, Dimeric Structure Of Mj0796, A Bacterial Abc Transporter
Cassette
Length = 235
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/16 (81%), Positives = 14/16 (87%)
Query: 43 VSIMGPQSSGKSTLLN 58
VSIMGP SGKST+LN
Sbjct: 34 VSIMGPSGSGKSTMLN 49
>pdb|3TIF|A Chain A, Dimeric Structure Of A Post-Hydrolysis State Of The
Atp-Binding Cassette Mj0796 Bound To Adp And Pi
pdb|3TIF|B Chain B, Dimeric Structure Of A Post-Hydrolysis State Of The
Atp-Binding Cassette Mj0796 Bound To Adp And Pi
Length = 235
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/16 (81%), Positives = 14/16 (87%)
Query: 43 VSIMGPQSSGKSTLLN 58
VSIMGP SGKST+LN
Sbjct: 34 VSIMGPSGSGKSTMLN 49
>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 = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 510 DMDEETKEKMLASLENYAKGVVEAKAREESGRVLMRMKD 548
D++ +T EK + E Y K +VE+K E+ ++ RMKD
Sbjct: 434 DLETKTLEKFVKGQEAYMKSLVESKGTEDVFKIKNRMKD 472
>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 = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 510 DMDEETKEKMLASLENYAKGVVEAKAREESGRVLMRMKD 548
D++ +T EK + E Y K +VE+K E+ ++ RMKD
Sbjct: 434 DLETKTLEKFVKGQEAYMKSLVESKGTEDVFKIKNRMKD 472
>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 = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 510 DMDEETKEKMLASLENYAKGVVEAKAREESGRVLMRMKD 548
D++ +T EK + E Y K +VE+K E+ ++ RMKD
Sbjct: 434 DLETKTLEKFVKGQEAYMKSLVESKGTEDVFKIKNRMKD 472
>pdb|3R9W|A Chain A, Crystal Structure Of Era In Complex With Mggdpnp And
Nucleotides 1506- 1542 Of 16s Ribosomal Rna
pdb|3R9X|A Chain A, Crystal Structure Of Era In Complex With Mggdpnp,
Nucleotides 1506- 1542 Of 16s Ribosomal Rna, And Ksga
Length = 307
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 38 LSYAVVSIMGPQSSGKSTLLNHLFGT 63
+ V+I+G + GKSTLLN+L GT
Sbjct: 7 MKVGYVAIVGKPNVGKSTLLNNLLGT 32
>pdb|3IEV|A Chain A, Crystal Structure Of Era In Complex With Mggnp And The
3' End Of 16s Rrna
Length = 308
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 38 LSYAVVSIMGPQSSGKSTLLNHLFGT 63
+ V+I+G + GKSTLLN+L GT
Sbjct: 8 MKVGYVAIVGKPNVGKSTLLNNLLGT 33
>pdb|4G1U|C Chain C, X-Ray Structure Of The Bacterial Heme Transporter Hmuuv
From Yersinia Pestis
pdb|4G1U|D Chain D, X-Ray Structure Of The Bacterial Heme Transporter Hmuuv
From Yersinia Pestis
Length = 266
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 26 HFIKEVKLSDCGLSYA---VVSIMGPQSSGKSTLLNHLFG 62
H ++ ++D L A +V+I+GP +GKSTLL L G
Sbjct: 20 HVQQQALINDVSLHIASGEMVAIIGPNGAGKSTLLRLLTG 59
>pdb|4A9A|A Chain A, Structure Of Rbg1 In Complex With Tma46 Dfrp Domain
pdb|4A9A|B Chain B, Structure Of Rbg1 In Complex With Tma46 Dfrp Domain
Length = 376
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 41 AVVSIMGPQSSGKSTLLNHLFGTNFREMDAFKGRSQTTKGIWMARCAGIEPCTLIMDLEG 100
A V +G S GKSTLL+ L GT + T G+ + A I+ L ++G
Sbjct: 73 ASVGFVGFPSVGKSTLLSKLTGTESEAAEYEFTTLVTVPGVIRYKGAKIQMLDLPGIIDG 132
Query: 101 T-DGRERGEDDTAFEKQSALF 120
DGR RG+ A + L
Sbjct: 133 AKDGRGRGKQVIAVARTCNLL 153
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
0.317 0.131 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,360,498
Number of Sequences: 62578
Number of extensions: 712327
Number of successful extensions: 1878
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1866
Number of HSP's gapped (non-prelim): 22
length of query: 671
length of database: 14,973,337
effective HSP length: 105
effective length of query: 566
effective length of database: 8,402,647
effective search space: 4755898202
effective search space used: 4755898202
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)