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= 029155
(198 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NN6|I Chain I, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 209
Score = 149 bits (377), Expect = 8e-37, Method: Compositional matrix adjust.
Identities = 84/185 (45%), Positives = 113/185 (61%), Gaps = 7/185 (3%)
Query: 13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
PGE L E G G Y +G +++SL G L S P V V
Sbjct: 24 PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 77
Query: 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
+P+ G++V +V+ + +R A I+ VG+ ++ F G IR++DVRATE DKV+++ SFR
Sbjct: 78 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 137
Query: 133 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCPLTGQTEQR 191
PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G MVPISW EMQCP T E R
Sbjct: 138 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFR 197
Query: 192 KVAKV 196
KVA+V
Sbjct: 198 KVARV 202
>pdb|4IFD|I Chain I, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 301
Score = 109 bits (273), Expect = 8e-25, Method: Compositional matrix adjust.
Identities = 66/179 (36%), Positives = 91/179 (50%), Gaps = 36/179 (20%)
Query: 53 PDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAK---------- 102
P + R T + + +P+ G +V+ RVT++ + A+ +I+ V K
Sbjct: 121 PGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRANVEILAVEDKPSPIDSGIGS 180
Query: 103 ------------------------SVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVR 138
+ E F GIIR QDVR+T+ D+V + F+PGDIVR
Sbjct: 181 NGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVR 240
Query: 139 ASVLSLGDARAYFLSTAKNDLGVVSAEST--AGGTMVPISWTEMQCPLTGQTEQRKVAK 195
A VLSLGD Y+L+TA+NDLGVV A + AGG M W M P+TG TE+RK AK
Sbjct: 241 AQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKRKCAK 299
>pdb|1DDG|A Chain A, Crystal Structure Of Sir-Fp60
pdb|1DDG|B Chain B, Crystal Structure Of Sir-Fp60
pdb|1DDI|A Chain A, Crystal Structure Of Sir-Fp60
Length = 374
Score = 34.3 bits (77), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 27/49 (55%)
Query: 87 VMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGD 135
+ T S D V + SV +K +G ++DVR EID D L ++PGD
Sbjct: 1 IHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEIDLGDSGLRYQPGD 49
>pdb|2BA1|A Chain A, Archaeal Exosome Core
pdb|2BA1|B Chain B, Archaeal Exosome Core
pdb|2BA1|C Chain C, Archaeal Exosome Core
pdb|3M7N|A Chain A, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|B Chain B, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|C Chain C, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M85|A Chain A, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|B Chain B, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|C Chain C, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
Length = 179
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 48/191 (25%), Positives = 88/191 (46%), Gaps = 24/191 (12%)
Query: 8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67
M V PG+ +G A E KG V + G ++A++ G L D+ VE
Sbjct: 1 MRFVMPGDRIGSAEEYV--KGEGVYEEGGELFAAVAGKLII-------KDRVAKVE---- 47
Query: 68 KAHGPVPE--PGSVVIARVTKVMTRMASADIMCVGAKSV--REKFSGIIRQQDVRATEID 123
+ P+PE G VV+ RV + +A ++ ++ + GI+ +V +
Sbjct: 48 -SISPIPEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVK 106
Query: 124 KVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQCP 183
++ + + DI++A V +GD LST + ++GV+ A + T + ++CP
Sbjct: 107 EISEAVGYL--DILKARV--IGD--NLRLSTKEEEMGVLRALCSNCKTEMVREGDILKCP 160
Query: 184 LTGQTEQRKVA 194
G+ E+RK++
Sbjct: 161 ECGRVEKRKIS 171
>pdb|2Z0S|A Chain A, Crystal Structure Of Putative Exosome Complex Rna-Binding
Protein
Length = 235
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 37/153 (24%), Positives = 59/153 (38%), Gaps = 21/153 (13%)
Query: 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
+V PGE L + E YV + G+ A++ GLLR + D V +
Sbjct: 11 IVVPGEPLPEEVEASP---PYVIDYKGVKRATVVGLLR------EKGDGGGRAFVKLKEI 61
Query: 70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKV--DM 127
+ VP+ G VVI + V DI + ++ QD + DM
Sbjct: 62 Y--VPQAGDVVIGLIQSVGIMNWFVDI--------NSPYVAVLSVQDFLGRPFNPAVDDM 111
Query: 128 HLSFRPGDIVRASVLSLGDARAYFLSTAKNDLG 160
+ GD ++A V++ R+ L+ LG
Sbjct: 112 QSLLKVGDYIKAKVVAFDKTRSPLLTVQGEGLG 144
>pdb|1SLI|A Chain A, Leech Intramolecular Trans-Sialidase Complexed With Dana
pdb|1SLL|A Chain A, Sialidase L From Leech Macrobdella Decora
pdb|2SLI|A Chain A, Leech Intramolecular Trans-Sialidase Complexed With 2,7-
Anhydro-Neu5ac, The Reaction Product
pdb|3SLI|A Chain A, Leech Intramolecular Trans-Sialidase Complexed With 2,7-
Anhydro-Neu5ac Prepared By Soaking With 3'-Sialyllactose
pdb|4SLI|A Chain A, Leech Intramolecular Trans-Sialidase Complexed With 2-
Propenyl-Neu5ac, An Inactive Substrate Analogue
Length = 679
Score = 28.9 bits (63), Expect = 2.1, Method: Composition-based stats.
Identities = 32/123 (26%), Positives = 51/123 (41%), Gaps = 11/123 (8%)
Query: 62 VEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE 121
V + G K G + P I + KV + A +D + A V I DV +
Sbjct: 153 VTLGGTKRQGKIAYPFGGTIGDI-KVYSN-ALSDEELIQATGVTTYGENIFYAGDVTESN 210
Query: 122 IDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPISWTEMQ 181
++ L+ G +V+S DAR +K+ + + A+ST GG +W+E
Sbjct: 211 YFRIPSLLTLSTG-----TVISAADARYGGTHDSKSKINIAFAKSTDGGN----TWSEPT 261
Query: 182 CPL 184
PL
Sbjct: 262 LPL 264
>pdb|1B9B|A Chain A, Triosephosphate Isomerase Of Thermotoga Maritima
pdb|1B9B|B Chain B, Triosephosphate Isomerase Of Thermotoga Maritima
Length = 255
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 32/133 (24%), Positives = 50/133 (37%), Gaps = 21/133 (15%)
Query: 3 VKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTV 62
VKE E+V+ P L + E+ +G+ + N + Y +SP Q V
Sbjct: 34 VKEFEIVVCPPFTALSEVGEILSGRNIKLGAQN-VFYEDQGAFTGEISPLML---QEIGV 89
Query: 63 E--VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGA---------------KSVR 105
E + GH + + I R K + I+CVG K VR
Sbjct: 90 EYVIVGHSERRRIFKEDDEFINRKVKAVLEKGMTPILCVGETLEEREKGLTFCVVEKQVR 149
Query: 106 EKFSGIIRQQDVR 118
E F G+ +++ R
Sbjct: 150 EGFYGLDKEEAKR 162
>pdb|3I9F|A Chain A, Crystal Structure Of A Putative Type 11 Methyltransferase
From Sulfolobus Solfataricus
pdb|3I9F|B Chain B, Crystal Structure Of A Putative Type 11 Methyltransferase
From Sulfolobus Solfataricus
Length = 170
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 89 TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
T++ DI + K V+EKF +I D + + VD L
Sbjct: 40 TKLYCIDINVIALKEVKEKFDSVITLSDPKEIPDNSVDFIL 80
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
0.315 0.131 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,591,004
Number of Sequences: 62578
Number of extensions: 206990
Number of successful extensions: 554
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 546
Number of HSP's gapped (non-prelim): 11
length of query: 198
length of database: 14,973,337
effective HSP length: 94
effective length of query: 104
effective length of database: 9,091,005
effective search space: 945464520
effective search space used: 945464520
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)