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= 020356
(327 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NN6|H Chain H, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 308
Score = 186 bits (473), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 100/208 (48%), Positives = 133/208 (63%), Gaps = 2/208 (0%)
Query: 9 NQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCG 68
+ ++RL A + L + V GDTI + G ++GHGT + +L A+V G
Sbjct: 15 HMAMEMRLPVARKPLSERLGRDTKKHLVVPGDTI-TTDTGFMRGHGTYMGEEKLIASVAG 73
Query: 69 VVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDG 128
VER+NKLI V+AL+ RY E GDIV+GR+ EV KRWK+E N D++L+LSSMNLP G
Sbjct: 74 SVERVNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGG 133
Query: 129 IQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYL 188
RRR+A DEL MR E DL+ AEV++ DG++ L R+ KYGKL +G L+ V P L
Sbjct: 134 ELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSL 193
Query: 189 VKRRKQHFHHLEEYGIDLIIGCNGYIWI 216
VKR+K HFH L G +I+G NG+IWI
Sbjct: 194 VKRQKTHFHDL-PCGASVILGNNGFIWI 220
>pdb|4IFD|H Chain H, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 361
Score = 169 bits (427), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 110/291 (37%), Positives = 154/291 (52%), Gaps = 33/291 (11%)
Query: 27 SSKSNPNS-CVTVGDTI---PVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRAL 82
+SKS +S VT G+ + P++ ++GHGT ++V G V R+N+L+ V L
Sbjct: 47 ASKSESDSQIVTPGELVTDDPIW----MRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPL 102
Query: 83 RARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMR 142
+ RY PETGD V+GR+ EV KRWK++I Q A+LML S+NLP GI RR++ DEL MR
Sbjct: 103 KGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMR 162
Query: 143 SIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEY 202
S E DL+ AEV+S DGS L R+ KYGKL G V L+ R K H H+L
Sbjct: 163 SFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPG- 221
Query: 203 GIDLIIGCNGYIWIGEHVE---ARDKMVVDQGSNSEQLIAKCDKNSMDL----------- 248
I +++G NGYIW+ + + ARD +NS + + ++ L
Sbjct: 222 NITVVLGVNGYIWLRKTSQMDLARD---TPSANNSSSIKSTGPTGAVSLNPSITRLEEES 278
Query: 249 ------DEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLS 293
DE D + + RQ ICR AN I+ L+ IT + I+ S
Sbjct: 279 SWQIYSDENDPSIS-NNIRQAICRYANVIKALAFCEIGITQQRIVSAYEAS 328
>pdb|2BA0|A Chain A, Archaeal Exosome Core
pdb|2BA0|B Chain B, Archaeal Exosome Core
pdb|2BA0|C Chain C, Archaeal Exosome Core
Length = 229
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 77/183 (42%), Gaps = 40/183 (21%)
Query: 52 GHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEIN 111
G+GT + G++ A + G+ ++ + V L+ RY P GD+VIG + EV W ++I
Sbjct: 19 GYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDIY 78
Query: 112 FTQDAILMLSS-------------MNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS 158
A L +S +++ D I + +D M+ T D +C +R
Sbjct: 79 SPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDRICRPIRF- 136
Query: 159 QGDGSLQLQARNQKYGKLERGQLLTVDPYLVKR---RKQHFHHL--EEYGIDLIIGCNGY 213
G+++ ++P V R +K L E + +++G NG
Sbjct: 137 --------------------GRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGL 176
Query: 214 IWI 216
IW+
Sbjct: 177 IWV 179
>pdb|2Z0S|A Chain A, Crystal Structure Of Putative Exosome Complex Rna-Binding
Protein
Length = 235
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 68/139 (48%), Gaps = 12/139 (8%)
Query: 57 DQKGELAATVCGVVERINK---LIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFT 113
D KG ATV G++ +V+ L+ Y P+ GD+VIG + V W ++IN
Sbjct: 31 DYKGVKRATVVGLLREKGDGGGRAFVK-LKEIYVPQAGDVVIGLIQSVGIMNWFVDINSP 89
Query: 114 QDAILMLSSMNLPDGIQRR-RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQK 172
A+L ++ D + R AVD +M+S+ D + A+V + S L + +
Sbjct: 90 YVAVL-----SVQDFLGRPFNPAVD--DMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGEG 142
Query: 173 YGKLERGQLLTVDPYLVKR 191
G++ RG+++ + P V R
Sbjct: 143 LGRIVRGKIVEISPAKVPR 161
>pdb|4IFD|G Chain G, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 242
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/152 (23%), Positives = 65/152 (42%), Gaps = 24/152 (15%)
Query: 78 YVRALRARYKPETGDIVIGRVIEVVPKRWKLEI-NFTQDAILMLSSMNLPDGIQRRRTAV 136
Y+ RY P D VIG +I +K+ + NF+ + LS M P+ ++ R +
Sbjct: 58 YIDYSSKRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSS--VSLSYMAFPNASKKNRPTL 115
Query: 137 DELNMRSIFTENDLVCAEVRSSQGDGSLQLQ------ARNQKYGKLERGQLLTVDPYLVK 190
DLV A V +++ + +++ R+ +G LE G ++ V+ +
Sbjct: 116 Q---------VGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFAR 166
Query: 191 R--RKQHFHHLEEYG----IDLIIGCNGYIWI 216
+ F L+ ++ IG NG IW+
Sbjct: 167 QLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWV 198
>pdb|2JA9|A Chain A, Structure Of The N-Terminal Deletion Of Yeast Exosome
Component Rrp40
Length = 175
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 63/145 (43%), Gaps = 24/145 (16%)
Query: 85 RYKPETGDIVIGRVIEVVPKRWKLEI-NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRS 143
RY P D VIG +I +K+ + NF+ + LS M P+ ++ R +
Sbjct: 2 RYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSS--VSLSYMAFPNASKKNRPTLQ------ 53
Query: 144 IFTENDLVCAEVRSSQGDGSLQLQ------ARNQKYGKLERGQLLTVDPYLVKR--RKQH 195
DLV A V +++ + +++ R+ +G LE G ++ V+ ++
Sbjct: 54 ---VGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNND 110
Query: 196 FHHLEEYG----IDLIIGCNGYIWI 216
F L+ ++ IG NG IW+
Sbjct: 111 FPLLKVLAAHTKFEVAIGLNGKIWV 135
>pdb|2JEB|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
Length = 251
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 49/217 (22%), Positives = 83/217 (38%), Gaps = 27/217 (12%)
Query: 5 QLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAA 64
++ +Q+QK+ L+ P S V G+ + E I + +
Sbjct: 2 HMNMSQSQKIVLQ--------------PRSIVVPGELLAEGEFQIPWSPYILKINSKYYS 47
Query: 65 TVCGVVERINKLIYVRALRAR-YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSM 123
TV G+ + + V L Y P+ DIVIG V +V W ++I A L S++
Sbjct: 48 TVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNL 107
Query: 124 NLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLT 183
R V E ++R D V A + + L + + G++ G ++
Sbjct: 108 ------LGRSINVGE-DLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVID 160
Query: 184 VDPYLVKR----RKQHFHHL-EEYGIDLIIGCNGYIW 215
+ P V R K + L + G + + NG IW
Sbjct: 161 IMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIW 197
>pdb|2JE6|I Chain I, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|4BA1|I Chain I, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|I Chain I, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 251
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 39/158 (24%), Positives = 64/158 (40%), Gaps = 13/158 (8%)
Query: 64 ATVCGVVERINKLIYVRALRAR-YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSS 122
+TV G+ + + V L Y P+ DIVIG V +V W ++I A L S+
Sbjct: 47 STVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASN 106
Query: 123 MNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLL 182
+ R V E ++R D V A + + L + + G++ G ++
Sbjct: 107 L------LGRSINVGE-DLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVI 159
Query: 183 TVDPYLVKR----RKQHFHHL-EEYGIDLIIGCNGYIW 215
+ P V R K + L + G + + NG IW
Sbjct: 160 DIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIW 197
>pdb|3L7Z|C Chain C, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|F Chain F, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|I Chain I, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 249
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 39/158 (24%), Positives = 64/158 (40%), Gaps = 13/158 (8%)
Query: 64 ATVCGVVERINKLIYVRALRAR-YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSS 122
+TV G+ + + V L Y P+ DIVIG V +V W ++I A L S+
Sbjct: 45 STVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASN 104
Query: 123 MNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLL 182
+ R V E ++R D V A + + L + + G++ G ++
Sbjct: 105 L------LGRSINVGE-DLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVI 157
Query: 183 TVDPYLVKR----RKQHFHHL-EEYGIDLIIGCNGYIW 215
+ P V R K + L + G + + NG IW
Sbjct: 158 DIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIW 195
>pdb|3IC1|A Chain A, Crystal Structure Of Zinc-Bound Succinyl-Diaminopimelate
Desuccinylase From Haemophilus Influenzae
pdb|3IC1|B Chain B, Crystal Structure Of Zinc-Bound Succinyl-Diaminopimelate
Desuccinylase From Haemophilus Influenzae
pdb|3ISZ|A Chain A, Crystal Structure Of Mono-zinc Form Of
Succinyl-diaminopimelate Desuccinylase From Haemophilus
Influenzae
pdb|3ISZ|B Chain B, Crystal Structure Of Mono-zinc Form Of
Succinyl-diaminopimelate Desuccinylase From Haemophilus
Influenzae
Length = 377
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 47 DGILKGHGTSDQKGELAATVCGVVERI 73
DG+L G G +D KG LAA + E +
Sbjct: 90 DGMLYGRGAADMKGSLAAMIVAAEEYV 116
>pdb|4H2K|A Chain A, Crystal Structure Of The Catalytic Domain Of
Succinyl-Diaminopimelate Desuccinylase From Haemophilus
Influenzae
pdb|4H2K|B Chain B, Crystal Structure Of The Catalytic Domain Of
Succinyl-Diaminopimelate Desuccinylase From Haemophilus
Influenzae
Length = 269
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 47 DGILKGHGTSDQKGELAATVCGVVERINKLIYVRA 81
DG+L G G +D KG LAA + E YV+A
Sbjct: 93 DGMLYGRGAADMKGSLAAMIVAAEE------YVKA 121
>pdb|3T68|A Chain A, Crystal Structure Of The Catalytic Domain Of Dape Protein
From V.Cholerea
pdb|3T6M|A Chain A, Crystal Structure Of The Catalytic Domain Of Dape Protein
From V.Cholerea In The Zn Bound Form
Length = 268
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 43 PVYEDGILKGHGTSDQKGELAATVCGV 69
P DG L G G +D KG LA + V
Sbjct: 89 PTVIDGFLHGRGAADMKGSLACMIVAV 115
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 0.135 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,101,116
Number of Sequences: 62578
Number of extensions: 359778
Number of successful extensions: 822
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 811
Number of HSP's gapped (non-prelim): 15
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
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: 52 (24.6 bits)