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= psy5032
(193 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4IDQ|A Chain A, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|B Chain B, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|C Chain C, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|D Chain D, Human Atlastin-1 1-446, N440t, Gdpalf4-
Length = 447
Score = 211 bits (538), Expect = 1e-55, Method: Compositional matrix adjust.
Identities = 103/154 (66%), Positives = 126/154 (81%), Gaps = 5/154 (3%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
AFRKGKSFL+DF+LRYM Y +E S DW+G + PL GFSWRGGSER+TTGI +WS +
Sbjct: 76 AFRKGKSFLMDFMLRYM---YNQE--SVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEI 130
Query: 84 YIATLPTGEKAAVILLDTQGTFDSESTVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQH 143
++ P G+K AV+L+DTQGTFDS+ST+RD ATVFALSTM+SSIQ+YNLSQN+QEDDLQH
Sbjct: 131 FLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQH 190
Query: 144 LQLFTEYGRLALADTGTKPFQRLQFLAVNNNNPF 177
LQLFTEYGRLA+ +T KPFQ L FL + + P+
Sbjct: 191 LQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPY 224
>pdb|3Q5E|A Chain A, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|C Chain C, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|E Chain E, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|G Chain G, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
Length = 447
Score = 211 bits (538), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 103/154 (66%), Positives = 126/154 (81%), Gaps = 5/154 (3%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
AFRKGKSFL+DF+LRYM Y +E S DW+G + PL GFSWRGGSER+TTGI +WS +
Sbjct: 75 AFRKGKSFLMDFMLRYM---YNQE--SVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEI 129
Query: 84 YIATLPTGEKAAVILLDTQGTFDSESTVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQH 143
++ P G+K AV+L+DTQGTFDS+ST+RD ATVFALSTM+SSIQ+YNLSQN+QEDDLQH
Sbjct: 130 FLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQH 189
Query: 144 LQLFTEYGRLALADTGTKPFQRLQFLAVNNNNPF 177
LQLFTEYGRLA+ +T KPFQ L FL + + P+
Sbjct: 190 LQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPY 223
>pdb|3QNU|A Chain A, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Hexagonal Form
pdb|3QOF|A Chain A, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|B Chain B, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|C Chain C, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|D Chain D, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
Length = 459
Score = 211 bits (538), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 103/154 (66%), Positives = 126/154 (81%), Gaps = 5/154 (3%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
AFRKGKSFL+DF+LRYM Y +E S DW+G + PL GFSWRGGSER+TTGI +WS +
Sbjct: 87 AFRKGKSFLMDFMLRYM---YNQE--SVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEI 141
Query: 84 YIATLPTGEKAAVILLDTQGTFDSESTVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQH 143
++ P G+K AV+L+DTQGTFDS+ST+RD ATVFALSTM+SSIQ+YNLSQN+QEDDLQH
Sbjct: 142 FLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQH 201
Query: 144 LQLFTEYGRLALADTGTKPFQRLQFLAVNNNNPF 177
LQLFTEYGRLA+ +T KPFQ L FL + + P+
Sbjct: 202 LQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPY 235
>pdb|4IDN|A Chain A, Human Atlastin-1 1-446, C-his6, Gppnhp
pdb|4IDN|B Chain B, Human Atlastin-1 1-446, C-his6, Gppnhp
pdb|4IDO|A Chain A, Human Atlastin-1 1-446, C-his6, Gdpalf4-
pdb|4IDO|B Chain B, Human Atlastin-1 1-446, C-his6, Gdpalf4-
Length = 457
Score = 211 bits (538), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 103/154 (66%), Positives = 126/154 (81%), Gaps = 5/154 (3%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
AFRKGKSFL+DF+LRYM Y +E S DW+G + PL GFSWRGGSER+TTGI +WS +
Sbjct: 75 AFRKGKSFLMDFMLRYM---YNQE--SVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEI 129
Query: 84 YIATLPTGEKAAVILLDTQGTFDSESTVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQH 143
++ P G+K AV+L+DTQGTFDS+ST+RD ATVFALSTM+SSIQ+YNLSQN+QEDDLQH
Sbjct: 130 FLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQH 189
Query: 144 LQLFTEYGRLALADTGTKPFQRLQFLAVNNNNPF 177
LQLFTEYGRLA+ +T KPFQ L FL + + P+
Sbjct: 190 LQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPY 223
>pdb|3Q5D|A Chain A, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 1
Length = 447
Score = 201 bits (510), Expect = 3e-52, Method: Compositional matrix adjust.
Identities = 101/154 (65%), Positives = 120/154 (77%), Gaps = 5/154 (3%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
AFRKGKSFL DF LRY Y +E S DW+G + PL GFSWRGGSER+TTGI +WS +
Sbjct: 75 AFRKGKSFLXDFXLRY---XYNQE--SVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEI 129
Query: 84 YIATLPTGEKAAVILLDTQGTFDSESTVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQH 143
++ P G+K AV+L DTQGTFDS+ST+RD ATVFALST +SSIQ+YNLSQN+QEDDLQH
Sbjct: 130 FLINKPDGKKVAVLLXDTQGTFDSQSTLRDSATVFALSTXISSIQVYNLSQNVQEDDLQH 189
Query: 144 LQLFTEYGRLALADTGTKPFQRLQFLAVNNNNPF 177
LQLFTEYGRLA +T KPFQ L FL + + P+
Sbjct: 190 LQLFTEYGRLAXEETFLKPFQSLIFLVRDWSFPY 223
>pdb|4IDP|A Chain A, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|B Chain B, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|C Chain C, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|D Chain D, Human Atlastin-1 1-446, N440t, Gppnhp
Length = 447
Score = 201 bits (510), Expect = 3e-52, Method: Compositional matrix adjust.
Identities = 101/154 (65%), Positives = 120/154 (77%), Gaps = 5/154 (3%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
AFRKGKSFL DF LRY Y +E S DW+G + PL GFSWRGGSER+TTGI +WS +
Sbjct: 76 AFRKGKSFLXDFXLRY---XYNQE--SVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEI 130
Query: 84 YIATLPTGEKAAVILLDTQGTFDSESTVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQH 143
++ P G+K AV+L DTQGTFDS+ST+RD ATVFALST +SSIQ+YNLSQN+QEDDLQH
Sbjct: 131 FLINKPDGKKVAVLLXDTQGTFDSQSTLRDSATVFALSTXISSIQVYNLSQNVQEDDLQH 190
Query: 144 LQLFTEYGRLALADTGTKPFQRLQFLAVNNNNPF 177
LQLFTEYGRLA +T KPFQ L FL + + P+
Sbjct: 191 LQLFTEYGRLAXEETFLKPFQSLIFLVRDWSFPY 224
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 5/89 (5%)
Query: 62 EGFSWRGGSERDTTGILMWSHVYIATLPTGEKAAVILLDTQGTFDSES-TVRDCATVFAL 120
+GFS + T GI MW + P ++LLDT+G D E ++ + +FAL
Sbjct: 74 KGFSLGSTVQSHTKGIWMWCVPH----PKKPGHILVLLDTEGLGDVEKGDNQNDSWIFAL 129
Query: 121 STMLSSIQIYNLSQNIQEDDLQHLQLFTE 149
+ +LSS +YN I + + L TE
Sbjct: 130 AVLLSSTFVYNSIGTINQQAMDQLYYVTE 158
>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 = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 5/89 (5%)
Query: 62 EGFSWRGGSERDTTGILMWSHVYIATLPTGEKAAVILLDTQGTFDSES-TVRDCATVFAL 120
+GFS + T GI MW + P ++LLDT+G D E ++ + +FAL
Sbjct: 63 KGFSLGSTVQSHTKGIWMWCVPH----PKKPGHILVLLDTEGLGDVEKGDNQNDSWIFAL 118
Query: 121 STMLSSIQIYNLSQNIQEDDLQHLQLFTE 149
+ +LSS +YN I + + L TE
Sbjct: 119 AVLLSSTFVYNSIGTINQQAMDQLYYVTE 147
>pdb|3P0U|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Human
Testicular Receptor 4
pdb|3P0U|B Chain B, Crystal Structure Of The Ligand Binding Domain Of Human
Testicular Receptor 4
Length = 249
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 21/28 (75%), Gaps = 1/28 (3%)
Query: 114 CATVFALSTMLSSIQIYNLSQNIQEDDL 141
CA V +LST+L++I + +L +IQED L
Sbjct: 87 CAQVMSLSTILAAI-VNHLQNSIQEDKL 113
>pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|3IYD|B Chain B, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|3LU0|A Chain A, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|3LU0|B Chain B, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|A Chain A, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|B Chain B, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|F Chain F, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|G Chain G, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 329
Score = 27.7 bits (60), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 96 VILLDTQGTFDSESTVRDCATVFA 119
VI ++T GT D E +R AT+ A
Sbjct: 202 VIEMETNGTIDPEEAIRRAATILA 225
>pdb|1BDF|A Chain A, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
N-Terminal Domain
pdb|1BDF|B Chain B, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
N-Terminal Domain
pdb|1BDF|C Chain C, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
N-Terminal Domain
pdb|1BDF|D Chain D, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
N-Terminal Domain
Length = 235
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 96 VILLDTQGTFDSESTVRDCATVFA 119
VI ++T GT D E +R AT+ A
Sbjct: 202 VIEMETNGTIDPEEAIRRAATILA 225
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 26.6 bits (57), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 123 MLSSIQIYNLSQNIQEDDLQHLQLFTEYGR 152
+LS ++++ + +I +DL HL L +Y R
Sbjct: 207 LLSPLEVHTIFTHISSEDLAHLGLNEQYAR 236
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
0.318 0.133 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,816,190
Number of Sequences: 62578
Number of extensions: 241256
Number of successful extensions: 516
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 499
Number of HSP's gapped (non-prelim): 17
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
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: 49 (23.5 bits)