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= 048589
(283 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JKE|A Chain A, D-Tyr Trnatyr Deacylase From Escherichia Coli
pdb|1JKE|B Chain B, D-Tyr Trnatyr Deacylase From Escherichia Coli
pdb|1JKE|C Chain C, D-Tyr Trnatyr Deacylase From Escherichia Coli
pdb|1JKE|D Chain D, D-Tyr Trnatyr Deacylase From Escherichia Coli
Length = 145
Score = 31.2 bits (69), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 179 QQDSGSHLA-SEEANDADTDRTLFATFSKGHPITRAE-LFEFFTRR 222
QQ GS L S+ ADT+R + +FSKG RAE L+++F R
Sbjct: 67 QQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVER 112
>pdb|3OKK|B Chain B, Crystal Structure Of S25-39 In Complex With Kdo(2.4)kdo
pdb|3OKL|B Chain B, Crystal Structure Of S25-39 In Complex With Kdo(2.8)kdo
pdb|3OKM|B Chain B, Crystal Structure Of Unliganded S25-39
pdb|3OKN|B Chain B, Crystal Structure Of S25-39 In Complex With
Kdo(2.4)kdo(2.4)kdo
pdb|3OKO|B Chain B, Crystal Structure Of S25-39 In Complex With
Kdo(2.8)kdo(2.4)kdo
Length = 222
Score = 30.8 bits (68), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 60/142 (42%), Gaps = 24/142 (16%)
Query: 70 LKLTDSLRGLYGLALESALCLVCSDQESFTCRDNNLPLMSQVCGRELSLEFVFQNNENAK 129
+KL +S GL + +L L C+ FT D + + Q G+ +LE++ AK
Sbjct: 2 VKLVESGGGL--VQPGGSLRLACA-TSGFTFTDYYMSWVRQPPGK--ALEWLGFIRNKAK 56
Query: 130 AYVTKFVRDVCDRAFIDYDLVLRNNLNNHQVQVLEPAVQLLQPQVNTLRQQDSGSHLASE 189
Y T++ V R I D N Q L Q+NTLR +DS ++
Sbjct: 57 GYTTEYSASVKGRFTISRD--------NSQSS--------LYLQMNTLRAEDSATYYC-- 98
Query: 190 EANDADTDRTLFATFSKGHPIT 211
A D D FA + +G +T
Sbjct: 99 -ARDHDGYYERFAYWGQGTLVT 119
>pdb|3HZY|B Chain B, Crystal Structure Of S73-2 Antibody In Complex With
Antigen Kdo(2.4)kdo(2.4)kdo
Length = 226
Score = 30.8 bits (68), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 51/126 (40%), Gaps = 21/126 (16%)
Query: 70 LKLTDSLRGLYGLALESALCLVCSDQESFTCRDNNLPLMSQVCGRELSLEFVFQNNENAK 129
+KL +S GL + +L L C+ FT D + + Q G+ L +N AK
Sbjct: 2 VKLVESGGGL--VQPGGSLRLSCA-TSGFTFTDYYMSWVRQPPGKALKWLAFIRNK--AK 56
Query: 130 AYVTKFVRDVCDRAFIDYDLVLRNNLNNHQVQVLEPAVQLLQPQVNTLRQQDSGSHLASE 189
Y T++ V R I D N Q L Q+NTLR +DS ++ +
Sbjct: 57 GYTTEYSASVKGRFTISRD--------NSQ--------SFLYLQMNTLRAEDSATYYCAR 100
Query: 190 EANDAD 195
+ N
Sbjct: 101 DINPGS 106
>pdb|3HZK|B Chain B, Crystal Structure Of S73-2 Antibody In Complex With
Antigen Kdo(2.4)kdo
pdb|3HZV|B Chain B, Crystal Structure Of S73-2 Antibody In Complex With
Antigen Kdo(2.8) Kdo(2.4)kdo
Length = 226
Score = 30.8 bits (68), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 53/126 (42%), Gaps = 21/126 (16%)
Query: 70 LKLTDSLRGLYGLALESALCLVCSDQESFTCRDNNLPLMSQVCGRELSLEFVFQNNENAK 129
+KL +S GL + +L L C+ FT D + + Q G+ +LE++ AK
Sbjct: 2 VKLVESGGGL--VQSGGSLRLSCA-TSGFTFTDYYMSWVRQPPGK--ALEWLAFIRNKAK 56
Query: 130 AYVTKFVRDVCDRAFIDYDLVLRNNLNNHQVQVLEPAVQLLQPQVNTLRQQDSGSHLASE 189
Y T++ V R I D N Q L Q+NTLR +DS ++ +
Sbjct: 57 GYTTEYSSSVKGRFTISRD--------NSQ--------SFLYLQMNTLRAEDSATYYCAR 100
Query: 190 EANDAD 195
+ N
Sbjct: 101 DINPGS 106
>pdb|3OKD|B Chain B, Crystal Structure Of S25-39 In Complex With Kdo
pdb|3OKE|B Chain B, Crystal Structure Of S25-39 In Complex With Ko
Length = 222
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 60/142 (42%), Gaps = 24/142 (16%)
Query: 70 LKLTDSLRGLYGLALESALCLVCSDQESFTCRDNNLPLMSQVCGRELSLEFVFQNNENAK 129
+KL +S GL + +L L C+ FT D + + Q G+ +LE++ AK
Sbjct: 2 VKLVESGGGL--VQPGGSLRLACA-TSGFTFTDYYMSWVRQPPGK--ALEWLGFIRNKAK 56
Query: 130 AYVTKFVRDVCDRAFIDYDLVLRNNLNNHQVQVLEPAVQLLQPQVNTLRQQDSGSHLASE 189
Y T++ V R I D N Q L Q+NTLR +DS ++
Sbjct: 57 GYTTEYSASVKGRFTISRD--------NSQSS--------LYLQMNTLRAEDSATYYC-- 98
Query: 190 EANDADTDRTLFATFSKGHPIT 211
A D D FA + +G +T
Sbjct: 99 -ARDHDGYYERFAYWGQGTLVT 119
>pdb|3HZM|B Chain B, Crystal Structure Of S73-2 Antibody In Complex With
Antigen Kdo
Length = 225
Score = 30.8 bits (68), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 53/126 (42%), Gaps = 21/126 (16%)
Query: 70 LKLTDSLRGLYGLALESALCLVCSDQESFTCRDNNLPLMSQVCGRELSLEFVFQNNENAK 129
+KL +S GL + +L L C+ FT D + + Q G+ +LE++ AK
Sbjct: 2 VKLVESGGGL--VQSGGSLRLSCA-TSGFTFTDYYMSWVRQPPGK--ALEWLAFIRNKAK 56
Query: 130 AYVTKFVRDVCDRAFIDYDLVLRNNLNNHQVQVLEPAVQLLQPQVNTLRQQDSGSHLASE 189
Y T++ V R I D N Q L Q+NTLR +DS ++ +
Sbjct: 57 GYTTEYSSSVKGRFTISRD--------NSQ--------SFLYLQMNTLRAEDSATYYCAR 100
Query: 190 EANDAD 195
+ N
Sbjct: 101 DINPGS 106
>pdb|3DUR|B Chain B, Crystal Structure Of Sag173-04
pdb|3DUR|D Chain D, Crystal Structure Of Sag173-04
Length = 121
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 55/126 (43%), Gaps = 21/126 (16%)
Query: 70 LKLTDSLRGLYGLALESALCLVCSDQESFTCRDNNLPLMSQVCGRELSLEFVFQNNENAK 129
++L +S GL + +L L C+ FT D + + Q G+ +LE++ AK
Sbjct: 2 VQLVESGGGL--VQPGGSLRLSCA-TSGFTFTDYYMSWVRQPPGK--ALEWLGFIRNKAK 56
Query: 130 AYVTKFVRDVCDRAFIDYDLVLRNNLNNHQVQVLEPAVQLLQPQVNTLRQQDSGSHLASE 189
Y T++ V R I D N Q +L Q+NTLR +DS ++ +
Sbjct: 57 GYTTEYSASVKGRFSISRD--------NSQ--------SILYLQMNTLRAEDSATYYCAR 100
Query: 190 EANDAD 195
+ AD
Sbjct: 101 DGYYAD 106
>pdb|2RDT|A Chain A, Crystal Structure Of Human Glycolate Oxidase (Go) In
Complex With Cdst
pdb|2RDU|A Chain A, Crystal Structure Of Human Glycolate Oxidase In Complex
With Glyoxylate
pdb|2RDW|A Chain A, Crystal Structure Of Human Glycolate Oxidase In Complex
With Sulfate
Length = 387
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 2 SWITLTVPELQEKYTVSLCHLQQFHYIDREAYAKLVFQ 39
SW T ++ E+ E +L LQ + Y DRE KLV Q
Sbjct: 126 SWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQ 163
>pdb|2W0U|A Chain A, Crystal Structure Of Human Glycolate Oxidase In Complex
With The Inhibitor 5-[(4-Chlorophenyl)sulfanyl]-
1,2,3-Thiadiazole-4-Carboxylate.
pdb|2W0U|B Chain B, Crystal Structure Of Human Glycolate Oxidase In Complex
With The Inhibitor 5-[(4-Chlorophenyl)sulfanyl]-
1,2,3-Thiadiazole-4-Carboxylate.
pdb|2W0U|C Chain C, Crystal Structure Of Human Glycolate Oxidase In Complex
With The Inhibitor 5-[(4-Chlorophenyl)sulfanyl]-
1,2,3-Thiadiazole-4-Carboxylate.
pdb|2W0U|D Chain D, Crystal Structure Of Human Glycolate Oxidase In Complex
With The Inhibitor 5-[(4-Chlorophenyl)sulfanyl]-
1,2,3-Thiadiazole-4-Carboxylate
Length = 370
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 2 SWITLTVPELQEKYTVSLCHLQQFHYIDREAYAKLVFQ 39
SW T ++ E+ E +L LQ + Y DRE KLV Q
Sbjct: 109 SWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQ 146
>pdb|2NZL|A Chain A, Crystal Structure Of Human Hydroxyacid Oxidase 1
Length = 392
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 2 SWITLTVPELQEKYTVSLCHLQQFHYIDREAYAKLVFQ 39
SW T ++ E+ E +L LQ + Y DRE KLV Q
Sbjct: 131 SWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQ 168
>pdb|2ZJB|A Chain A, Crystal Structure Of The Human Dmc1-M200v Polymorphic
Variant
pdb|2ZJB|B Chain B, Crystal Structure Of The Human Dmc1-M200v Polymorphic
Variant
Length = 343
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 12/71 (16%)
Query: 100 CRDNNLPLMSQVCGRELSLEFVFQNNENAKAYVTKFVRDVCDRAFIDYDLVLRNNL---- 155
C LP G ++ +F + EN + +RD+ DR +D+D VL N L
Sbjct: 143 CVTAQLPGAGGYPGGKI----IFIDTENT--FRPDRLRDIADRFNVDHDAVLDNVLYARA 196
Query: 156 --NNHQVQVLE 164
+ HQV++L+
Sbjct: 197 YTSEHQVELLD 207
>pdb|1HR7|B Chain B, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
pdb|1HR7|D Chain D, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
pdb|1HR7|F Chain F, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
pdb|1HR7|H Chain H, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
pdb|1HR8|B Chain B, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
Complexed With Cytochrome C Oxidase Iv Signal Peptide
pdb|1HR8|D Chain D, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
Complexed With Cytochrome C Oxidase Iv Signal Peptide
pdb|1HR8|F Chain F, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
Complexed With Cytochrome C Oxidase Iv Signal Peptide
pdb|1HR8|H Chain H, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
Complexed With Cytochrome C Oxidase Iv Signal Peptide
pdb|1HR9|B Chain B, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
Complexed With Malate Dehydrogenase Signal Peptide
pdb|1HR9|D Chain D, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
Complexed With Malate Dehydrogenase Signal Peptide
pdb|1HR9|F Chain F, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
Complexed With Malate Dehydrogenase Signal Peptide
pdb|1HR9|H Chain H, Yeast Mitochondrial Processing Peptidase Beta-E73q Mutant
Complexed With Malate Dehydrogenase Signal Peptide
Length = 443
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 28/135 (20%), Positives = 52/135 (38%), Gaps = 14/135 (10%)
Query: 113 GRELSLEFV------FQNNENAKAYVTKFVRDVCDRAFIDYDLVLRNNLNNHQVQVLEPA 166
G EL +E + + + EN Y D+ I D++ ++ L+N ++
Sbjct: 68 GIELEIENIGSHLNAYTSRENTVYYAKSLQEDIPKAVDILSDILTKSVLDNSAIERERDV 127
Query: 167 VQLLQPQVNTLRQQDSGSHLASEEANDADTDRTLFATFSKGHPITRAELFEFFTRRY--- 223
+ +V+ + + HL D RT+ ITR +L ++ T+ Y
Sbjct: 128 IIRESEEVDKMYDEVVFDHLHEITYKDQPLGRTILGPIKNIKSITRTDLKDYITKNYKGD 187
Query: 224 -----GEGCVEDIKM 233
G G V+ K+
Sbjct: 188 RMVLAGAGAVDHEKL 202
>pdb|1HR6|B Chain B, Yeast Mitochondrial Processing Peptidase
pdb|1HR6|D Chain D, Yeast Mitochondrial Processing Peptidase
pdb|1HR6|F Chain F, Yeast Mitochondrial Processing Peptidase
pdb|1HR6|H Chain H, Yeast Mitochondrial Processing Peptidase
Length = 443
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 28/135 (20%), Positives = 52/135 (38%), Gaps = 14/135 (10%)
Query: 113 GRELSLEFV------FQNNENAKAYVTKFVRDVCDRAFIDYDLVLRNNLNNHQVQVLEPA 166
G EL +E + + + EN Y D+ I D++ ++ L+N ++
Sbjct: 68 GIELEIENIGSHLNAYTSRENTVYYAKSLQEDIPKAVDILSDILTKSVLDNSAIERERDV 127
Query: 167 VQLLQPQVNTLRQQDSGSHLASEEANDADTDRTLFATFSKGHPITRAELFEFFTRRY--- 223
+ +V+ + + HL D RT+ ITR +L ++ T+ Y
Sbjct: 128 IIRESEEVDKMYDEVVFDHLHEITYKDQPLGRTILGPIKNIKSITRTDLKDYITKNYKGD 187
Query: 224 -----GEGCVEDIKM 233
G G V+ K+
Sbjct: 188 RMVLAGAGAVDHEKL 202
>pdb|3UMC|A Chain A, Crystal Structure Of The L-2-Haloacid Dehalogenase Pa0810
pdb|3UMC|B Chain B, Crystal Structure Of The L-2-Haloacid Dehalogenase Pa0810
pdb|3UMC|C Chain C, Crystal Structure Of The L-2-Haloacid Dehalogenase Pa0810
pdb|3UMC|D Chain D, Crystal Structure Of The L-2-Haloacid Dehalogenase Pa0810
Length = 254
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 35/95 (36%), Gaps = 16/95 (16%)
Query: 21 HLQQFHYIDREAYAKLVFQLALDSHLSKRILAFWNWLETEGFTNFVHESLKLTDSLRGLY 80
HL Q H EA A F LALD L +RI FW H D+L G +
Sbjct: 84 HLDQLHRQSLEALAG-EFGLALDEALLQRITGFW------------HRLRPWPDTLAGXH 130
Query: 81 GLALESALCLVCSDQESF---TCRDNNLPLMSQVC 112
L + L + + + R LP +C
Sbjct: 131 ALKADYWLAALSNGNTALXLDVARHAGLPWDXLLC 165
>pdb|2YQQ|A Chain A, Solution Structure Of The Zf-Hit Domain In Zinc Finger Hit
Domain-Containing Protein 3 (Trip-3)
Length = 56
Score = 28.5 bits (62), Expect = 4.8, Method: Composition-based stats.
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 78 GLYGLALESALCLVCSDQESFTCRDNNLPLMSQVCGRE 115
G GL + +C++C ++ + C +P S VC R+
Sbjct: 4 GSSGLKCSTVVCVICLEKPKYRCPACRVPYCSVVCFRK 41
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
0.324 0.136 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,965,598
Number of Sequences: 62578
Number of extensions: 309180
Number of successful extensions: 852
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 843
Number of HSP's gapped (non-prelim): 23
length of query: 283
length of database: 14,973,337
effective HSP length: 98
effective length of query: 185
effective length of database: 8,840,693
effective search space: 1635528205
effective search space used: 1635528205
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 bits)