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= 009712
(528 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
Length = 428
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 36/80 (45%), Positives = 51/80 (63%)
Query: 19 LTEVYKRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADD 78
L V++RS D+C + + K + ++ SYL +Y Q LN QQL L WRD AR +D
Sbjct: 288 LQVVWQRSRDICLKKFIKPIFTDESYLELYRKQKKHLNTQQLTAFQLLFAWRDKTARRED 347
Query: 79 ESTGYVLPNRTLIEIAKQLP 98
ES GYVLPN +++IA++LP
Sbjct: 348 ESYGYVLPNHMMLKIAEELP 367
>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
Length = 428
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 36/80 (45%), Positives = 51/80 (63%)
Query: 19 LTEVYKRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADD 78
L V++RS D+C + + K + ++ SYL +Y Q LN QQL L WRD AR +D
Sbjct: 288 LQVVWQRSRDICLKKFIKPIFTDESYLELYRKQKKHLNTQQLTAFQLLFAWRDKTARRED 347
Query: 79 ESTGYVLPNRTLIEIAKQLP 98
ES GYVLPN +++IA++LP
Sbjct: 348 ESYGYVLPNHMMLKIAEELP 367
>pdb|2CPR|A Chain A, Solution Structure Of The Hrdc Domain Of Human Exosome
Component 10
Length = 124
Score = 65.1 bits (157), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 30/63 (47%), Positives = 40/63 (63%)
Query: 36 KELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAK 95
K + ++ SYL +Y Q LN QQL L WRD AR +DES GYVLPN +++IA+
Sbjct: 8 KPIFTDESYLELYRKQKKHLNTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAE 67
Query: 96 QLP 98
+LP
Sbjct: 68 ELP 70
>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain
pdb|2HBK|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn
pdb|2HBL|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Amp
pdb|2HBM|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Ump
Length = 410
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 61 AVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMG 120
+V L +WRD+IAR DDES +V+PN+ L + PT + L ++ +
Sbjct: 314 VLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTDVIGVVSLTNGVTEHVRQNAK 373
Query: 121 PVLSIIKNSMQNAAN 135
+ ++I+++++N N
Sbjct: 374 LLANLIRDALRNIKN 388
>pdb|3CYM|A Chain A, Crystal Structure Of Protein Bad_0989 From Bifidobacterium
Adolescentis
Length = 440
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/107 (26%), Positives = 53/107 (49%), Gaps = 19/107 (17%)
Query: 44 YLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAK 103
++H+ + + Q LA+V L RD +AR D + +L + ++IE+AK+ P AA+
Sbjct: 218 WMHVSHITEVMRDRQALAIVRALWTRRDELAREYDIAPTLLLSDSSIIEVAKRKPHNAAQ 277
Query: 104 LRRL-----------------LKSKHSYIERYMGPVLSIIKNSMQNA 133
R + + +++ I+R + P S+ KN +Q+A
Sbjct: 278 FRSIRSINERVRIHTDSEQDKMFERYAPIQRKIKP--SMWKNIIQDA 322
>pdb|2FP8|A Chain A, Structure Of Strictosidine Synthase, The Biosynthetic
Entry To The Monoterpenoid Indole Alkaloid Family
pdb|2FP8|B Chain B, Structure Of Strictosidine Synthase, The Biosynthetic
Entry To The Monoterpenoid Indole Alkaloid Family
pdb|2FP9|A Chain A, Crystal Structure Of Native Strictosidine Synthase
pdb|2FP9|B Chain B, Crystal Structure Of Native Strictosidine Synthase
pdb|2FPC|A Chain A, Structure Of Strictosidine Synthase, The Biosynthetic
Entry To The Monoterpenoid Indole Alkaloid Family
pdb|2FPC|B Chain B, Structure Of Strictosidine Synthase, The Biosynthetic
Entry To The Monoterpenoid Indole Alkaloid Family
pdb|2VAQ|A Chain A, Structure Of Strictosidine Synthase In Complex With
Inhibitor
pdb|2VAQ|B Chain B, Structure Of Strictosidine Synthase In Complex With
Inhibitor
pdb|3V1S|A Chain A, Scaffold Tailoring By A Newly Detected Pictet-Spenglerase
Ac-Tivity Of Strictosidine Synthase (Str1): From The
Common Tryp-Toline Skeleton To The Rare
Piperazino-Indole Framework
pdb|3V1S|B Chain B, Scaffold Tailoring By A Newly Detected Pictet-Spenglerase
Ac-Tivity Of Strictosidine Synthase (Str1): From The
Common Tryp-Toline Skeleton To The Rare
Piperazino-Indole Framework
Length = 322
Score = 32.0 bits (71), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 4/89 (4%)
Query: 25 RSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTG-- 82
R+YD+ L +L + Y H+ + G +A QLA ++ + A D+ TG
Sbjct: 81 RTYDISYNLQNNQLYIVDCYYHLSVVGSEGGHATQLATSVDGVPFKWLYAVTVDQRTGIV 140
Query: 83 YVLPNRTLIEI--AKQLPTTAAKLRRLLK 109
Y TL + +Q+ T+ K RL+K
Sbjct: 141 YFTDVSTLYDDRGVQQIMDTSDKTGRLIK 169
>pdb|2V91|A Chain A, Structure Of Strictosidine Synthase In Complex With
Strictosidine
pdb|2V91|B Chain B, Structure Of Strictosidine Synthase In Complex With
Strictosidine
Length = 302
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 4/89 (4%)
Query: 25 RSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTG-- 82
R+YD+ L +L + Y H+ + G +A QLA ++ + A D+ TG
Sbjct: 72 RTYDISYNLQNNQLYIVDCYYHLSVVGSEGGHATQLATSVDGVPFKWLYAVTVDQRTGIV 131
Query: 83 YVLPNRTLIEI--AKQLPTTAAKLRRLLK 109
Y TL + +Q+ T+ K RL+K
Sbjct: 132 YFTDVSTLYDDRGVQQIMDTSDKTGRLIK 160
>pdb|3E99|A Chain A, Crystal Structure Of The Beta Subunit Of The Benzoate
1,2-dioxygenase (benb, Bmaa0186) From Burkholderia
Mallei Atcc 23344 At 1.90 A Resolution
Length = 164
Score = 30.0 bits (66), Expect = 3.4, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 141 QKLKEERMEVASEETEVLVLDTSSNLKIPNVGRESVDG 178
Q L++ + +E + V DT ++ I NV RES DG
Sbjct: 67 QGLEDRVFRIKTERSSATVPDTRTSHNIANVERESADG 104
>pdb|3JXS|A Chain A, Crystal Structure Of Xg34, An Evolved Xyloglucan Binding
Cbm
pdb|3JXS|B Chain B, Crystal Structure Of Xg34, An Evolved Xyloglucan Binding
Cbm
pdb|3JXS|C Chain C, Crystal Structure Of Xg34, An Evolved Xyloglucan Binding
Cbm
Length = 174
Score = 30.0 bits (66), Expect = 3.8, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 174 ESVDGVDALVGTTMPHPPAYTQLKQEPPKVGSSVAELDRNGLGS 217
E V+G D VG+++ +PP + L+ G+ V + NG+G+
Sbjct: 23 EGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGN 66
>pdb|1K42|A Chain A, The Solution Structure Of The Cbm4-2 Carbohydrate Binding
Module From A Thermostable Rhodothermus Marinus
Xylanase.
pdb|1K45|A Chain A, The Solution Structure Of The Cbm4-2 Carbohydrate Binding
Module From A Thermostable Rhodothermus Marinus Xylanase
Length = 168
Score = 29.6 bits (65), Expect = 4.0, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 174 ESVDGVDALVGTTMPHPPAYTQLKQEPPKVGSSVAELDRNGLGSFAHPGEAIA 226
E V+G D VG+++ +PP + L+ G+ V + NG+G+ EA A
Sbjct: 23 EGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGNNPWDIEATA 75
>pdb|2Y64|A Chain A, Xylopentaose Binding Mutated (X-2 L110f) Cbm4-2
Carbohydrate Binding Module From A Thermostable
Rhodothermus Marinus Xylanase
pdb|2Y6G|A Chain A, Cellopentaose Binding Mutated (X-2 L110f) Cbm4-2
Carbohydrate Binding Module From A Thermostable
Rhodothermus Marinus Xylanase
pdb|2Y6H|A Chain A, X-2 L110f Cbm4-2 Carbohydrate Binding Module From A
Thermostable Rhodothermus Marinus Xylanase
Length = 167
Score = 29.6 bits (65), Expect = 4.2, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 174 ESVDGVDALVGTTMPHPPAYTQLKQEPPKVGSSVAELDRNGLGS 217
E V+G D VG+++ +PP + L+ G+ V + NG+G+
Sbjct: 23 EGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGN 66
>pdb|2Y6J|A Chain A, X-2 Engineered Mutated Cbm4-2 Carbohydrate Binding Module
From A Thermostable Rhodothermus Marinus Xylanase
pdb|2Y6K|A Chain A, Xylotetraose Bound To X-2 Engineered Mutated Cbm4-2
Carbohydrate Binding Module From A Thermostable
Rhodothermus Marinus Xylanase
pdb|2Y6L|A Chain A, Xylopentaose Binding X-2 Engineered Mutated Cbm4-2
Carbohydrate Binding Module From A Thermostable
Rhodothermus Marinus Xylanase
Length = 167
Score = 29.6 bits (65), Expect = 4.5, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 174 ESVDGVDALVGTTMPHPPAYTQLKQEPPKVGSSVAELDRNGLGS 217
E V+G D VG+++ +PP + L+ G+ V + NG+G+
Sbjct: 23 EGVEGWDLNVGSSVTNPPVFEVLETSDAPEGNKVLAVTVNGVGN 66
>pdb|2FJA|A Chain A, Adenosine 5'-Phosphosulfate Reductase In Complex With
Substrate
pdb|2FJA|C Chain C, Adenosine 5'-Phosphosulfate Reductase In Complex With
Substrate
pdb|2FJB|A Chain A, Adenosine-5'-Phosphosulfate Reductase Im Complex With
Products
pdb|2FJB|C Chain C, Adenosine-5'-Phosphosulfate Reductase Im Complex With
Products
pdb|2FJD|A Chain A, Adenosine-5-Phosphosulfate Reductase In Complex With
Sulfite (Covalent Adduct)
pdb|2FJD|C Chain C, Adenosine-5-Phosphosulfate Reductase In Complex With
Sulfite (Covalent Adduct)
pdb|2FJE|A Chain A, Adenosine-5-Phosphosulfate Reductase Oxidized State
pdb|2FJE|C Chain C, Adenosine-5-Phosphosulfate Reductase Oxidized State
Length = 643
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 73 IARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQN 132
++ ADD + Y+LP + L+ + K + AA + + K+ ++R + +L+ +K ++
Sbjct: 501 LSTADDVNPEYILPWQGLVRLQKIMDEYAAGIATIYKTNEKMLQRAL-ELLAFLKEDLEK 559
Query: 133 AA 134
A
Sbjct: 560 LA 561
>pdb|1JNR|A Chain A, Structure Of Adenylylsulfate Reductase From The
Hyperthermophilic Archaeoglobus Fulgidus At 1.6
Resolution
pdb|1JNR|C Chain C, Structure Of Adenylylsulfate Reductase From The
Hyperthermophilic Archaeoglobus Fulgidus At 1.6
Resolution
pdb|1JNZ|A Chain A, Structure Of Adenylylsulfate Reductase From The
Hyperthermophilic Archaeoglobus Fulgidus At 1.6
Resolution
pdb|1JNZ|C Chain C, Structure Of Adenylylsulfate Reductase From The
Hyperthermophilic Archaeoglobus Fulgidus At 1.6
Resolution
Length = 643
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 73 IARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQN 132
++ ADD + Y+LP + L+ + K + AA + + K+ ++R + +L+ +K ++
Sbjct: 501 LSTADDVNPEYILPWQGLVRLQKIMDEYAAGIATIYKTNEKMLQRAL-ELLAFLKEDLEK 559
Query: 133 AA 134
A
Sbjct: 560 LA 561
>pdb|1F0K|A Chain A, The 1.9 Angstrom Crystal Structure Of E. Coli Murg
pdb|1F0K|B Chain B, The 1.9 Angstrom Crystal Structure Of E. Coli Murg
pdb|1NLM|A Chain A, Crystal Structure Of Murg:glcnac Complex
pdb|1NLM|B Chain B, Crystal Structure Of Murg:glcnac Complex
Length = 364
Score = 28.9 bits (63), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 53/247 (21%), Positives = 92/247 (37%), Gaps = 50/247 (20%)
Query: 41 ENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDEST---------GYVLPNRTLI 91
E ++ I GL+G G+ A A + WR ARA ++ GYV L
Sbjct: 57 EIDFIRISGLRGKGIKALIAAPLRIFNAWRQ--ARAIMKAYKPDVVLGMGGYVSGPGGLA 114
Query: 92 EIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNA------ANFEVIAQKLKE 145
+ +P + + + ++ + V+ + NA +V+A L +
Sbjct: 115 AWSLGIPVVLHEQNGIAGLTNKWLAKIATKVMQAFPGAFPNAEVVGNPVRTDVLALPLPQ 174
Query: 146 ERMEVASEETEVLVLDTSSNLKIPNVGRESVDGVDALVGTTMPHPPAYTQLKQEPPKVGS 205
+R+ VLV+ S +I N TMP Q K+G
Sbjct: 175 QRLAGREGPVRVLVVGGSQGARILN--------------QTMP---------QVAAKLGD 211
Query: 206 SVAELDRNGLGS-------FAHPGEAIASENKEATHISTLSSSGQSRDLNACKSPSPRVT 258
SV ++G GS +A G+ ++K I ++++ D+ C+S + V+
Sbjct: 212 SVTIWHQSGKGSQQSVEQAYAEAGQ---PQHKVTEFIDDMAAAYAWADVVVCRSGALTVS 268
Query: 259 EAAVQAL 265
E A L
Sbjct: 269 EIAAAGL 275
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
0.309 0.127 0.348
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,721,580
Number of Sequences: 62578
Number of extensions: 597388
Number of successful extensions: 1203
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1181
Number of HSP's gapped (non-prelim): 43
length of query: 528
length of database: 14,973,337
effective HSP length: 103
effective length of query: 425
effective length of database: 8,527,803
effective search space: 3624316275
effective search space used: 3624316275
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (25.4 bits)