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= 030121
(182 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3O65|A Chain A, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|C Chain C, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|E Chain E, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|G Chain G, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
Length = 191
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 47/181 (25%), Positives = 75/181 (41%), Gaps = 24/181 (13%)
Query: 8 IYHERQKLQFCLLHSLNNLFQQEGAFTRASLNEIAEKL------VLDYPNKQTWTPLSVV 61
I+HE+Q+ C H LNNL Q E F+ L IA +L + L+ +
Sbjct: 5 IFHEKQEGFLCAQHCLNNLLQGE-YFSPVELASIAHQLDEEERXRXAEGGVTSEEYLAFL 63
Query: 62 FKPHHNAL-TGNYDINVLIAALEGRGKSVVWHDRRNEASAIDLDGGENCLMGIVINVPVT 120
+P N TG + I V+ AL+ G ++ H E + +D P+
Sbjct: 64 QQPSENXDDTGFFSIQVISNALKFWGLEII-HFNNPEYQKLGID-------------PIN 109
Query: 121 RYAGLWK-SRHWVALRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDYIIGLGGEVLLVKN 179
+ + +HW +RK W+NL+S P+ D+ + FL + V +VK
Sbjct: 110 ERSFICNYKQHWFTIRKFGKHWFNLNSLLAGPELISDTC-LANFLARLQQQAYSVFVVKG 168
Query: 180 D 180
D
Sbjct: 169 D 169
>pdb|2AGA|A Chain A, De-Ubiquitinating Function Of Ataxin-3: Insights From The
Solution Structure Of The Josephin Domain
Length = 190
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/184 (24%), Positives = 77/184 (41%), Gaps = 28/184 (15%)
Query: 7 KIYHERQKLQFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHH 66
I+HE+Q+ C H LNNL Q E F+ L+ IA +L D + V + +
Sbjct: 8 SIFHEKQEGSLCAQHCLNNLLQGE-YFSPVELSSIAHQL--DEEERMRMAEGGVTSEDYR 64
Query: 67 NAL---------TGNYDINVLIAALEGRGKSVVWHDRRNEASAIDLDGGENCLMGIVINV 117
L +G + I V+ AL+ G ++ + E + +D
Sbjct: 65 TFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNS-PEYQRLRID------------- 110
Query: 118 PVTRYAGLWKSR-HWVALRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDYIIGLGGEVLL 176
P+ + + + HW +RK+ W+NL+S P+ D+ + FL + G + +
Sbjct: 111 PINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTY-LALFLAQLQQEGYSIFV 169
Query: 177 VKND 180
VK D
Sbjct: 170 VKGD 173
>pdb|2JRI|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3 In
Complex With Ubiquitin Molecule.
pdb|1YZB|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3
Length = 182
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/184 (24%), Positives = 77/184 (41%), Gaps = 28/184 (15%)
Query: 7 KIYHERQKLQFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHH 66
I+HE+Q+ C H LNNL Q E F+ L+ IA +L D + V + +
Sbjct: 3 SIFHEKQEGSLCAQHCLNNLLQGE-YFSPVELSSIAHQL--DEEERMRMAEGGVTSEDYR 59
Query: 67 NAL---------TGNYDINVLIAALEGRGKSVVWHDRRNEASAIDLDGGENCLMGIVINV 117
L +G + I V+ AL+ G ++ + E + +D
Sbjct: 60 TFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNS-PEYQRLRID------------- 105
Query: 118 PVTRYAGLWKSR-HWVALRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDYIIGLGGEVLL 176
P+ + + + HW +RK+ W+NL+S P+ D+ + FL + G + +
Sbjct: 106 PINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTY-LALFLAQLQQEGYSIFV 164
Query: 177 VKND 180
VK D
Sbjct: 165 VKGD 168
>pdb|2DOS|A Chain A, Structural Basis For The Recognition Of Lys48-Linked
Polyubiquitin Chain By The Josephin Domain Of Ataxin-3,
A Putative Deubiquitinating Enzyme
Length = 176
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/184 (24%), Positives = 77/184 (41%), Gaps = 28/184 (15%)
Query: 7 KIYHERQKLQFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHH 66
I+HE+Q+ C H LNNL Q E F+ L+ IA +L D + V + +
Sbjct: 8 SIFHEKQEGSLCAQHCLNNLLQGE-YFSPVELSSIAHQL--DEEERMRMAEGGVTSEDYR 64
Query: 67 NAL---------TGNYDINVLIAALEGRGKSVVWHDRRNEASAIDLDGGENCLMGIVINV 117
L +G + I V+ AL+ G ++ + E + +D
Sbjct: 65 TFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNSP-EYQRLRID------------- 110
Query: 118 PVTRYAGLWKSR-HWVALRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDYIIGLGGEVLL 176
P+ + + + HW +RK+ W+NL+S P+ D+ + FL + G + +
Sbjct: 111 PINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTY-LALFLAQLQQEGYSIFV 169
Query: 177 VKND 180
VK D
Sbjct: 170 VKGD 173
>pdb|3D40|A Chain A, Crystal Structure Of Fosfomycin Resistance Kinase Foma
From Streptomyces Wedmorensis Complexed With Diphosphate
pdb|3D41|A Chain A, Crystal Structure Of Fosfomycin Resistance Kinase Foma
From Streptomyces Wedmorensis Complexed With Mgamppnp
And Fosfomycin
pdb|3QUN|A Chain A, Crystal Structure Of Fosfomycin Resistance Kinase Foma
From Streptomyces Wedmorensis Complexed With Mgatp
pdb|3QUO|A Chain A, Crystal Structure Of Fosfomycin Resistance Kinase Foma
From Streptomyces Wedmorensis Complexed With Atp And
Fosfomycin
pdb|3QUR|A Chain A, Crystal Structure Of Fosfomycin Resistance Kinase Foma
From Streptomyces Wedmorensis Complexed With Mgadp And
Fosfomycin Monophosphate
pdb|3QVF|A Chain A, Crystal Structure Of Fosfomycin Resistance Kinase Foma
From Streptomyces Wedmorensis Complexed With Mgadp And
Fosfomycin Vanadate
pdb|3QVH|A Chain A, Crystal Structure Of Fosfomycin Resistance Kinase Foma
From Streptomyces Wedmorensis Complexed With Adp
Length = 286
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 68 ALTGNYDINVLIAALEGRGKSVVWHDRRNEASAIDLDGGENCLMGIVINVPVTRYAGLWK 127
A + + VL+ +EGR + V D + D GG+ L + P YA LW
Sbjct: 166 AFSSDRVPEVLLPMVEGRLRVVTLTD--VDGIVTDGAGGDTILPEVDARSPEQAYAALWG 223
Query: 128 SRHWVA 133
S W A
Sbjct: 224 SSEWDA 229
>pdb|2J3V|A Chain A, Crystal Structure Of The Enzymatic Component C2-I Of The
C2- Toxin From Clostridium Botulinum At Ph 3.0
Length = 431
Score = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 132 VALRKIDGVWYNLDSDF-----HAPQCFKDSKEVREFLD 165
+A R++DG+ ++L SDF + D +++ EF+D
Sbjct: 296 IAYRRVDGIPFDLPSDFSFDKKENGEIIADKQKLNEFID 334
>pdb|2J3Z|A Chain A, Crystal Structure Of The Enzymatic Component C2-i Of The
C2-toxin From Clostridium Botulinum At Ph 6.1
pdb|2J3Z|B Chain B, Crystal Structure Of The Enzymatic Component C2-i Of The
C2-toxin From Clostridium Botulinum At Ph 6.1
pdb|2J3Z|C Chain C, Crystal Structure Of The Enzymatic Component C2-i Of The
C2-toxin From Clostridium Botulinum At Ph 6.1
pdb|2J3Z|D Chain D, Crystal Structure Of The Enzymatic Component C2-i Of The
C2-toxin From Clostridium Botulinum At Ph 6.1
pdb|2J3Z|E Chain E, Crystal Structure Of The Enzymatic Component C2-i Of The
C2-toxin From Clostridium Botulinum At Ph 6.1
pdb|2J3Z|F Chain F, Crystal Structure Of The Enzymatic Component C2-i Of The
C2-toxin From Clostridium Botulinum At Ph 6.1
Length = 431
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 132 VALRKIDGVWYNLDSDF-----HAPQCFKDSKEVREFLD 165
+A R++DG+ ++L SDF + D +++ EF+D
Sbjct: 296 IAYRRVDGIPFDLPSDFSFDKKENGEIIADKQKLNEFID 334
>pdb|2J3X|A Chain A, Crystal Structure Of The Enzymatic Component C2-I Of The
C2-Toxin From Clostridium Botulinum At Ph 3.0
(Mut-S361r)
Length = 431
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 132 VALRKIDGVWYNLDSDF-----HAPQCFKDSKEVREFLD 165
+A R++DG+ ++L SDF + D +++ EF+D
Sbjct: 296 IAYRRVDGIPFDLPSDFSFDKKENGEIIADKQKLNEFID 334
>pdb|1E2R|A Chain A, Cytochrome Cd1 Nitrite Reductase, Reduced And Cyanide
Bound
pdb|1E2R|B Chain B, Cytochrome Cd1 Nitrite Reductase, Reduced And Cyanide
Bound
Length = 567
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 37/149 (24%), Positives = 55/149 (36%), Gaps = 22/149 (14%)
Query: 37 SLNEIAEKLVLDYP--NKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHDR 94
++ E + L++DY N T +S H L G++ I A R K VV +
Sbjct: 315 NVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSH--RYFITAANARNKLVVIDTK 372
Query: 95 RNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHW----VALRKIDGVWYNLDSDFHA 150
+ AI+ GG+ G N + +W + H VAL D + H
Sbjct: 373 EGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVAL-------IGTDPEGHP 425
Query: 151 PQCFKDSKEVREFLDYIIGLGGEVLLVKN 179
+K LD LGG L +K
Sbjct: 426 DNAWK-------ILDSFPALGGGSLFIKT 447
>pdb|1AOF|A Chain A, Cytochrome Cd1 Nitrite Reductase, Reduced Form
pdb|1AOF|B Chain B, Cytochrome Cd1 Nitrite Reductase, Reduced Form
pdb|1AOM|A Chain A, Substrate And Product Bound To Cytochrome Cd1 Nitrite
Reductase
pdb|1AOM|B Chain B, Substrate And Product Bound To Cytochrome Cd1 Nitrite
Reductase
pdb|1AOQ|A Chain A, Cytochrome Cd1 Nitrite Reductase With Substrate And
Product Bound
pdb|1AOQ|B Chain B, Cytochrome Cd1 Nitrite Reductase With Substrate And
Product Bound
pdb|1QKS|A Chain A, Cytochrome Cd1 Nitrite Reductase, Oxidised Form
pdb|1QKS|B Chain B, Cytochrome Cd1 Nitrite Reductase, Oxidised Form
Length = 567
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 37/149 (24%), Positives = 55/149 (36%), Gaps = 22/149 (14%)
Query: 37 SLNEIAEKLVLDYP--NKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHDR 94
++ E + L++DY N T +S H L G++ I A R K VV +
Sbjct: 315 NVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSH--RYFITAANARNKLVVIDTK 372
Query: 95 RNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHW----VALRKIDGVWYNLDSDFHA 150
+ AI+ GG+ G N + +W + H VAL D + H
Sbjct: 373 EGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVAL-------IGTDPEGHP 425
Query: 151 PQCFKDSKEVREFLDYIIGLGGEVLLVKN 179
+K LD LGG L +K
Sbjct: 426 DNAWK-------ILDSFPALGGGSLFIKT 447
>pdb|3H7J|A Chain A, Crystal Structure Of Bacb, An Enzyme Involved In Bacilysin
Synthesis, In Monoclinic Form
pdb|3H7J|B Chain B, Crystal Structure Of Bacb, An Enzyme Involved In Bacilysin
Synthesis, In Monoclinic Form
pdb|3H7Y|A Chain A, Crystal Structure Of Bacb, An Enzyme Involved In Bacilysin
Synthesis, In Tetragonal Form
pdb|3H7Y|B Chain B, Crystal Structure Of Bacb, An Enzyme Involved In Bacilysin
Synthesis, In Tetragonal Form
Length = 243
Score = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 75 INVLIAALEGRGKSVVWHDRRNEASAIDLDGG 106
+ +++A + G G + +H RNE I + GG
Sbjct: 145 VEIMLAKIPGNGGEMPFHKHRNEQIGICIGGG 176
>pdb|1DY7|A Chain A, Cytochrome Cd1 Nitrite Reductase, Co Complex
pdb|1DY7|B Chain B, Cytochrome Cd1 Nitrite Reductase, Co Complex
pdb|1HJ3|A Chain A, Cytochrome Cd1 Nitrite Reductase, Dioxygen Complex
pdb|1HJ3|B Chain B, Cytochrome Cd1 Nitrite Reductase, Dioxygen Complex
pdb|1HJ4|A Chain A, Cytochrome Cd1 Nitrite Reductase, X-Ray Reduced Dioxygen
Complex
pdb|1HJ4|B Chain B, Cytochrome Cd1 Nitrite Reductase, X-Ray Reduced Dioxygen
Complex
pdb|1HJ5|A Chain A, Cytochrome Cd1 Nitrite Reductase, Reoxidised Enzyme
pdb|1HJ5|B Chain B, Cytochrome Cd1 Nitrite Reductase, Reoxidised Enzyme
pdb|1H9X|A Chain A, Cytochrome Cd1 Nitrite Reductase, Reduced Form
pdb|1H9X|B Chain B, Cytochrome Cd1 Nitrite Reductase, Reduced Form
pdb|1H9Y|A Chain A, Cytochrome Cd1 Nitrite Reductase, Reduced Form Complexed
To Cn
pdb|1H9Y|B Chain B, Cytochrome Cd1 Nitrite Reductase, Reduced Form Complexed
To Cn
pdb|1HCM|A Chain A, Cytochrome Cd1 Nitrite Reductase, Oxidised From From
Tetragonal Crystals
pdb|1HCM|B Chain B, Cytochrome Cd1 Nitrite Reductase, Oxidised From From
Tetragonal Crystals
Length = 567
Score = 26.6 bits (57), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 30/119 (25%), Positives = 42/119 (35%), Gaps = 20/119 (16%)
Query: 65 HHNALTGNYDINVLIAALEGRGKSVVWHDRRNEASAIDLDGGENCLMGIVINVPVTRYAG 124
H L G++ I A R K VV + + AI+ GG+ G N +
Sbjct: 345 HDGGLDGSH--RYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGP 402
Query: 125 LWKSRHW----VALRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDYIIGLGGEVLLVKN 179
+W + H VAL D + H +K LD LGG L +K
Sbjct: 403 VWATSHMGDDSVAL-------IGTDPEGHPDNAWK-------ILDSFPALGGGSLFIKT 447
>pdb|1GQ1|A Chain A, Cytochrome Cd1 Nitrite Reductase, Y25s Mutant, Oxidised
Form
pdb|1GQ1|B Chain B, Cytochrome Cd1 Nitrite Reductase, Y25s Mutant, Oxidised
Form
Length = 567
Score = 26.6 bits (57), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 30/119 (25%), Positives = 42/119 (35%), Gaps = 20/119 (16%)
Query: 65 HHNALTGNYDINVLIAALEGRGKSVVWHDRRNEASAIDLDGGENCLMGIVINVPVTRYAG 124
H L G++ I A R K VV + + AI+ GG+ G N +
Sbjct: 345 HDGGLDGSH--RYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGP 402
Query: 125 LWKSRHW----VALRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDYIIGLGGEVLLVKN 179
+W + H VAL D + H +K LD LGG L +K
Sbjct: 403 VWATSHMGDDSVAL-------IGTDPEGHPDNAWK-------ILDSFPALGGGSLFIKT 447
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
0.321 0.138 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,886,762
Number of Sequences: 62578
Number of extensions: 242128
Number of successful extensions: 561
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 551
Number of HSP's gapped (non-prelim): 17
length of query: 182
length of database: 14,973,337
effective HSP length: 93
effective length of query: 89
effective length of database: 9,153,583
effective search space: 814668887
effective search space used: 814668887
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)