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= 025587
(250 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ICP|A Chain A, Crystal Structure Of Udp-Galactose 4-Epimerase
pdb|3KO8|A Chain A, Crystal Structure Of Udp-Galactose 4-Epimerase
Length = 312
Score = 34.7 bits (78), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 60/137 (43%), Gaps = 22/137 (16%)
Query: 84 SGGHAVIGFYLAKELLGSGHEVTIMTVGDENSDKMKKPPFNRFNEI-VSAGGKTVWGDPA 142
+GG IG +L +L+ G+EV ++ +N ++ N E+ V WG
Sbjct: 6 TGGAGFIGSHLVDKLVELGYEVVVV----DNLSSGRREFVNPSAELHVRDLKDYSWG--- 58
Query: 143 EVGNVVGGVTF------DVVLDNN------GKNLDAVRPVADWAKSSGVKQFLFISSAGI 190
+ G V F +V L +N+ A V +WA+ +GV+ +F SS+ +
Sbjct: 59 --AGIKGDVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTV 116
Query: 191 YKPADEPPHVEGDVVKP 207
Y AD P E + KP
Sbjct: 117 YGDADVIPTPEEEPYKP 133
>pdb|3AW9|A Chain A, Structure Of Udp-Galactose 4-Epimerase Mutant
pdb|3AW9|B Chain B, Structure Of Udp-Galactose 4-Epimerase Mutant
pdb|3AW9|C Chain C, Structure Of Udp-Galactose 4-Epimerase Mutant
Length = 308
Score = 34.3 bits (77), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 34/127 (26%), Positives = 59/127 (46%), Gaps = 6/127 (4%)
Query: 84 SGGHAVIGFYLAKELLGSGHEVTIMTVGDEN---SDKMKKPPFNRFNEIVSAGGKTVWGD 140
+GG IG +L +L+ G+EV ++ + + S ++ ++ G V+
Sbjct: 6 TGGAGFIGSHLVDKLVELGYEVVVVDIVQRDTGGSAELHVRDLKDYSWGAGIKGDVVFHF 65
Query: 141 PAEVGNVVGGVTFDVVLDNNGKNLDAVRPVADWAKSSGVKQFLFISSAGIYKPADEPPHV 200
A V T +V N +N+ A V +WA+ +GV+ +F SS+ +Y AD P
Sbjct: 66 AAN-PEVRLSTTEPIVHFN--ENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTP 122
Query: 201 EGDVVKP 207
E + KP
Sbjct: 123 EEEPYKP 129
>pdb|3VPS|A Chain A, Structure Of A Novel Nad Dependent-Ndp-Hexosamine
5,6-Dehydratase, Tuna, Involved In Tunicamycin
Biosynthesis
pdb|3VPS|B Chain B, Structure Of A Novel Nad Dependent-Ndp-Hexosamine
5,6-Dehydratase, Tuna, Involved In Tunicamycin
Biosynthesis
Length = 321
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 11/50 (22%)
Query: 74 KKKVLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGDENSDKMKKPPF 123
K ++LI +GG IG +LA+ L+ SG EVT++ D ++ PP
Sbjct: 7 KHRILI----TGGAGFIGGHLARALVASGEEVTVL-------DDLRVPPM 45
>pdb|3SZF|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase H198a
Variant From Acidithiobacillus Ferrooxidans In Complex
With Bound Trisulfide And Decylubiquinone
Length = 437
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 77 VLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGD 112
V+I+ +GG Y KE LGSGHEVT+++ D
Sbjct: 7 VVILGAGTGGMPAA--YEMKEALGSGHEVTLISAND 40
>pdb|3T2Y|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase
His132ala Variant From Acidithiobacillus Ferrooxidans
With Bound Disulfide
Length = 434
Score = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 77 VLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGD 112
V+I+ +GG Y KE LGSGHEVT+++ D
Sbjct: 4 VVILGAGTGGMPAA--YEMKEALGSGHEVTLISAND 37
>pdb|3SY4|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase
Ser126ala Variant From Acidithiobacillus Ferrooxidans
pdb|3SYI|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase
Ser126ala Variant From Acidithiobacillus Ferrooxidans
Using 7.0 Kev Diffraction Data
Length = 437
Score = 30.8 bits (68), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 77 VLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGD 112
V+I+ +GG Y KE LGSGHEVT+++ D
Sbjct: 7 VVILGAGTGGMPAA--YEMKEALGSGHEVTLISAND 40
>pdb|3KPK|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase From
Acidithiobacillus Ferrooxidans, C160a Mutant
Length = 434
Score = 30.8 bits (68), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 77 VLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGD 112
V+I+ +GG Y KE LGSGHEVT+++ D
Sbjct: 4 VVILGAGTGGMPAA--YEMKEALGSGHEVTLISAND 37
>pdb|3SXI|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase
Cys128ala Variant From Acidithiobacillus Ferrooxidans
Complexed With Decylubiquinone
pdb|3T14|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase
Cys128ala Variant From Acidithiobacillus Ferrooxidans
With Bound Disulfide
pdb|3T2K|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase
Cys128ala Variant From Acidithiobacillus Ferrooxidans
With Bound Trisulfane
Length = 437
Score = 30.8 bits (68), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 77 VLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGD 112
V+I+ +GG Y KE LGSGHEVT+++ D
Sbjct: 7 VVILGAGTGGMPAA--YEMKEALGSGHEVTLISAND 40
>pdb|3SX6|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase
Cys356ala Variant From Acidithiobacillus Ferrooxidans
Complexed With Decylubiquinone
Length = 437
Score = 30.8 bits (68), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 77 VLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGD 112
V+I+ +GG Y KE LGSGHEVT+++ D
Sbjct: 7 VVILGAGTGGMPAA--YEMKEALGSGHEVTLISAND 40
>pdb|3T2Z|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase From
Acidithiobacillus Ferrooxidans
pdb|3T2Z|B Chain B, Crystal Structure Of Sulfide:quinone Oxidoreductase From
Acidithiobacillus Ferrooxidans
pdb|3T31|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase From
Acidithiobacillus Ferrooxidans In Complex With
Decylubiquinone
pdb|3SZ0|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase From
Acidithiobacillus Ferrooxidans In Complex With Sodium
Selenide
pdb|3SZC|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase From
Acidithiobacillus Ferrooxidans In Complex With Gold (I)
Cyanide
pdb|3T0K|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase From
Acidithiobacillus Ferrooxidans With Bound Trisulfide And
Decylubiquinone
Length = 437
Score = 30.8 bits (68), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 77 VLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGD 112
V+I+ +GG Y KE LGSGHEVT+++ D
Sbjct: 7 VVILGAGTGGMPAA--YEMKEALGSGHEVTLISAND 40
>pdb|3SZW|A Chain A, Crystal Structure Of Sulfide:quinone Oxidoreductase
Cys128ser Variant From Acidithiobacillus Ferrooxidans In
Complex With Decylubiquinone
Length = 437
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 77 VLIVNTNSGGHAVIGFYLAKELLGSGHEVTIMTVGD 112
V+I+ +GG Y KE LGSGHEVT+++ D
Sbjct: 7 VVILGAGTGGMPAA--YEMKEALGSGHEVTLISAND 40
>pdb|4ID9|A Chain A, Crystal Structure Of A Short-Chain DehydrogenaseREDUCTASE
SUPERFAMILY Protein From Agrobacterium Tumefaciens
(Target Efi-506441) With Bound Nad, Monoclinic Form 1
pdb|4ID9|B Chain B, Crystal Structure Of A Short-Chain DehydrogenaseREDUCTASE
SUPERFAMILY Protein From Agrobacterium Tumefaciens
(Target Efi-506441) With Bound Nad, Monoclinic Form 1
pdb|4IDG|A Chain A, Crystal Structure Of A Short-Chain DehydrogenaseREDUCTASE
SUPERFAMILY Protein From Agrobacterium Tumefaciens
(Target Efi-506441) With Bound Nad, Monoclinic Form 2
pdb|4IDG|B Chain B, Crystal Structure Of A Short-Chain DehydrogenaseREDUCTASE
SUPERFAMILY Protein From Agrobacterium Tumefaciens
(Target Efi-506441) With Bound Nad, Monoclinic Form 2
Length = 347
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 163 NLDAVRPVADWAKSSGVKQFLFISSAGIYKPADEP 197
N++ R + D A ++GV++F+F SS +Y P + P
Sbjct: 102 NVEGTRRLLDAASAAGVRRFVFASSGEVY-PENRP 135
>pdb|4EF7|A Chain A, Udp-Xylose Synthase
pdb|4EF7|B Chain B, Udp-Xylose Synthase
pdb|4GLL|A Chain A, Crystal Structure Of Human Udp-Xylose Synthase.
pdb|4GLL|B Chain B, Crystal Structure Of Human Udp-Xylose Synthase
Length = 337
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 4/36 (11%)
Query: 73 EKKKVLIVNTNSGGHAVIGFYLAKELLGSGHEVTIM 108
++K++LI +GG +G +L +L+ GHEVT++
Sbjct: 4 DRKRILI----TGGAGFVGSHLTDKLMMDGHEVTVV 35
>pdb|1S68|A Chain A, Structure And Mechanism Of Rna Ligase
Length = 249
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 44/89 (49%), Gaps = 4/89 (4%)
Query: 153 FDVVLDNNGKNLDAVRPVADWAKSSGVKQFLFISSAGIYKP---ADEPPHVEGDVVKPDA 209
++++L N ++ AV+ + + + + F + GI K D+ +V +V ++
Sbjct: 68 YEIILKNYADSIKAVQDIMETSAVVSYQVFGEFAGPGIQKNVDYCDKDFYVFDIIVTTES 127
Query: 210 GHVQ-VEKYISENFSNWASFRPQYMIGSG 237
G V V+ Y+ E+F N F+ ++G G
Sbjct: 128 GDVTYVDDYMMESFCNTFKFKMAPLLGRG 156
>pdb|1AK0|A Chain A, P1 Nuclease In Complex With A Substrate Analog
Length = 270
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 23/50 (46%)
Query: 196 EPPHVEGDVVKPDAGHVQVEKYISENFSNWASFRPQYMIGSGNNKDCEEW 245
+P H E V + +V + Y S+W ++ PQ +IG D E W
Sbjct: 123 QPLHDEAYAVGGNKINVTFDGYHDNLHSDWDTYMPQKLIGGHALSDAESW 172
>pdb|2HVQ|A Chain A, Structure Of Adenylated Full-length T4 Rna Ligase 2
Length = 335
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 44/89 (49%), Gaps = 4/89 (4%)
Query: 153 FDVVLDNNGKNLDAVRPVADWAKSSGVKQFLFISSAGIYKPAD---EPPHVEGDVVKPDA 209
++++L N ++ AV+ + + + + F + GI K D + +V +V ++
Sbjct: 69 YEIILKNYADSIKAVQDIMETSAVVSYQVFGEFAGPGIQKNVDYGDKDFYVFDIIVTTES 128
Query: 210 GHVQ-VEKYISENFSNWASFRPQYMIGSG 237
G V V+ Y+ E+F N F+ ++G G
Sbjct: 129 GDVTYVDDYMMESFCNTFKFKMAPLLGRG 157
>pdb|2HVR|A Chain A, Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated
Nucleic Acid Duplex Containing A 3'-Deoxyribonucleotide
At The Nick
pdb|2HVR|B Chain B, Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated
Nucleic Acid Duplex Containing A 3'-Deoxyribonucleotide
At The Nick
pdb|2HVS|A Chain A, Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated
Nucleic Acid Duplex Containing A 2'-Deoxyribonucleotide
At The Nick
pdb|2HVS|B Chain B, Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated
Nucleic Acid Duplex Containing A 2'-Deoxyribonucleotide
At The Nick
Length = 335
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 44/89 (49%), Gaps = 4/89 (4%)
Query: 153 FDVVLDNNGKNLDAVRPVADWAKSSGVKQFLFISSAGIYKPAD---EPPHVEGDVVKPDA 209
++++L N ++ AV+ + + + + F + GI K D + +V +V ++
Sbjct: 69 YEIILKNYADSIKAVQDIMETSAVVSYQVFGEFAGPGIQKNVDYGDKDFYVFDIIVTTES 128
Query: 210 GHVQ-VEKYISENFSNWASFRPQYMIGSG 237
G V V+ Y+ E+F N F+ ++G G
Sbjct: 129 GDVTYVDDYMMESFCNTFKFKMAPLLGRG 157
>pdb|2B69|A Chain A, Crystal Structure Of Human Udp-Glucoronic Acid
Decarboxylase
Length = 343
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 73 EKKKVLIVNTNSGGHAVIGFYLAKELLGSGHEVTIM 108
++K++LI +GG +G +L +L GHEVT++
Sbjct: 26 DRKRILI----TGGAGFVGSHLTDKLXXDGHEVTVV 57
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
0.314 0.132 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,726,376
Number of Sequences: 62578
Number of extensions: 301425
Number of successful extensions: 625
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 607
Number of HSP's gapped (non-prelim): 26
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)