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= 026458
(238 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NN6|G Chain G, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 289
Score = 156 bits (395), Expect = 7e-39, Method: Compositional matrix adjust.
Identities = 83/221 (37%), Positives = 130/221 (58%), Gaps = 8/221 (3%)
Query: 22 LDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNK------YWVESSQKRYVPCVE 75
L+ + + + G GLR+ D + V K G+LR +P YWV+S QKRYVP
Sbjct: 69 LNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKG 128
Query: 76 DTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM 135
D V+GIV D F VD+ G A L L+FEG T+RN P ++G L+Y + V AN M
Sbjct: 129 DHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDM 188
Query: 136 NPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL 194
PE+ C D+ G+A G++ +DG +F+ + GL R LL +P C +++E+GK EI G+
Sbjct: 189 EPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLL-APDCEIIQEVGKLYPLEIVFGM 247
Query: 195 NGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
NGR+WV A++ ++++N + E +++ Q+K + +L +
Sbjct: 248 NGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAE 288
>pdb|4IFD|G Chain G, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 242
Score = 110 bits (274), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 61/196 (31%), Positives = 106/196 (54%), Gaps = 13/196 (6%)
Query: 32 IKLGGGLRQECD----SVSVIKAGKLRFSKPNK-----YWVESSQKRYVPCVEDTVLGIV 82
+KLG G+ CD + + G L S K +++ S KRY+P V D V+G++
Sbjct: 21 VKLGPGIY--CDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVI 78
Query: 83 VDCKADNFFVDIRGPTIAF-LPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141
+ +D++ V ++ + + L +AF +++N P ++G L+Y RV A + E+ C
Sbjct: 79 IGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIEC 138
Query: 142 TDAS-GKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWV 200
D++ G+ A FG+L+DG + + + +R LL + P+L+ L FE+A+GLNG++WV
Sbjct: 139 FDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWV 198
Query: 201 NAESPSTVVLVSNAIM 216
E S + IM
Sbjct: 199 KCEELSNTLACYRTIM 214
>pdb|2JA9|A Chain A, Structure Of The N-Terminal Deletion Of Yeast Exosome
Component Rrp40
Length = 175
Score = 104 bits (260), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 50/151 (33%), Positives = 88/151 (58%), Gaps = 2/151 (1%)
Query: 68 KRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAF-LPVLAFEGGTRRNIPKFEIGSLLYV 126
KRY+P V D V+G+++ +D++ V ++ + + L +AF +++N P ++G L+Y
Sbjct: 1 KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60
Query: 127 RVVKANPGMNPELSCTDAS-GKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQ 185
RV A + E+ C D++ G+ A FG+L+DG + + + +R LL + P+L+ L
Sbjct: 61 RVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAH 120
Query: 186 LSFEIAVGLNGRVWVNAESPSTVVLVSNAIM 216
FE+A+GLNG++WV E S + IM
Sbjct: 121 TKFEVAIGLNGKIWVKCEELSNTLACYRTIM 151
>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 = 55.1 bits (131), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 43/171 (25%), Positives = 76/171 (44%), Gaps = 15/171 (8%)
Query: 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPK--FEIGSLLYV 126
RY P V D V+GI+ + A+ + VDI P AFLPV P +IG +
Sbjct: 52 RYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIA 111
Query: 127 RVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQL 186
+V+ +P M L+ D + FG + + + R++ + +++ L +L
Sbjct: 112 KVLNIDPKMKVTLTMKDRICRPIRFGRI----VAINPARVPRVIGKKGS--MIKLLKSEL 165
Query: 187 SFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
+I VG NG +WVN + + E++ ++Q+ + L R+
Sbjct: 166 DVQIVVGQNGLIWVNGDRRKVSIA-------EEAIYLIEQEAHTEGLTDRV 209
>pdb|2JEB|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
Length = 251
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 81/177 (45%), Gaps = 20/177 (11%)
Query: 70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT-------RRNIPKFEIGS 122
Y P + D V+G+V D + + VDI+ P A+LP G + RR + ++G
Sbjct: 70 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYL---DVGD 126
Query: 123 LLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFET-STGLSRMLLSSPTCPVLEE 181
+ R+ + ++P LS K + G + +G + + + R++ + + + E
Sbjct: 127 YVIARIENFDRSIDPVLSV-----KGKDLGRVSNGIVIDIMPVKVPRVIGKNKS--MYET 179
Query: 182 LGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
L + I V NGR+W S + ++ AI E+ S + K + D++ Q I+
Sbjct: 180 LTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHI--KGLTDRIKQFIE 234
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 81/177 (45%), Gaps = 20/177 (11%)
Query: 70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT-------RRNIPKFEIGS 122
Y P + D V+G+V D + + VDI+ P A+LP G + RR + ++G
Sbjct: 68 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYL---DVGD 124
Query: 123 LLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFET-STGLSRMLLSSPTCPVLEE 181
+ R+ + ++P LS K + G + +G + + + R++ + + + E
Sbjct: 125 YVIARIENFDRSIDPVLSV-----KGKDLGRVSNGIVIDIMPVKVPRVIGKNKS--MYET 177
Query: 182 LGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
L + I V NGR+W S + ++ AI E+ S + K + D++ Q I+
Sbjct: 178 LTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHI--KGLTDRIKQFIE 232
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 81/177 (45%), Gaps = 20/177 (11%)
Query: 70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT-------RRNIPKFEIGS 122
Y P + D V+G+V D + + VDI+ P A+LP G + RR + ++G
Sbjct: 70 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYL---DVGD 126
Query: 123 LLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFET-STGLSRMLLSSPTCPVLEE 181
+ R+ + ++P LS K + G + +G + + + R++ + + + E
Sbjct: 127 YVIARIENFDRSIDPVLSV-----KGKDLGRVSNGIVIDIMPVKVPRVIGKNKS--MYET 179
Query: 182 LGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
L + I V NGR+W S + ++ AI E+ S + K + D++ Q I+
Sbjct: 180 LTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHI--KGLTDRIKQFIE 234
>pdb|2Z0S|A Chain A, Crystal Structure Of Putative Exosome Complex Rna-Binding
Protein
Length = 235
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 55/238 (23%), Positives = 96/238 (40%), Gaps = 44/238 (18%)
Query: 6 STANLVDKIVVPGD-----------VVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLR 54
S L +IVVPG+ V+D + T+ G LR++ D G
Sbjct: 3 SERQLAGRIVVPGEPLPEEVEASPPYVIDYKGVKRATVV--GLLREKGD------GGGRA 54
Query: 55 FSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRN 114
F K + YVP D V+G++ N+FVDI P +A L V F G R
Sbjct: 55 FVKLKEI--------YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLG--RPF 104
Query: 115 IPK-------FEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLS 167
P ++G + +VV + +P L+ + G + G + E S
Sbjct: 105 NPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTV-----QGEGLGRIVRGKIVEISPAKV 159
Query: 168 RMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNA--ESPSTVVLVSNAIMNSESLSA 223
++ +L+ L ++ +I V NGR+ + E + +++ I++ E+ ++
Sbjct: 160 PRVIGRKMS-MLKTLEEKTECKIFVARNGRIHLECPNEDLEAIAVMAIKIIDEEAYTS 216
>pdb|3G5V|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 213
Score = 33.9 bits (76), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 44/106 (41%), Gaps = 12/106 (11%)
Query: 65 SSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTI----AFLPVLAFEGGTRRNIPKFEI 120
S RY P ++ + I D ++ FF+ + TI + V A R P +
Sbjct: 55 SGNTRYNPSLKSRI-SITRDTSSNQFFLQLNSVTIEDTATYYCVTA-----GRGFPYWGQ 108
Query: 121 GSLLYVRVVKANPGMNPELS--CTDASGKAAEFGLLKDGYMFETST 164
G+L+ V K P L+ C D +G + G L GY E+ T
Sbjct: 109 GTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVT 154
>pdb|3G5X|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
pdb|3G5X|D Chain D, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 216
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 43/106 (40%), Gaps = 12/106 (11%)
Query: 65 SSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTI----AFLPVLAFEGGTRRNIPKFEI 120
S RY P ++ + I D + FF+ + TI + V A R P +
Sbjct: 55 SGNTRYNPSLKSRI-SITRDTSKNQFFLQLNSVTIEDTATYYCVTA-----GRGFPYWGQ 108
Query: 121 GSLLYVRVVKANPGMNPELS--CTDASGKAAEFGLLKDGYMFETST 164
G+L+ V K P L+ C D +G + G L GY E+ T
Sbjct: 109 GTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVT 154
>pdb|3G5Z|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 217
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 28/104 (26%), Positives = 42/104 (40%), Gaps = 8/104 (7%)
Query: 65 SSQKRYVPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFEGGTRRNIPKFEIGS 122
S RY P ++ + I D ++ FF+ + P A G R P + G+
Sbjct: 55 SGNTRYNPSLKSRI-SITRDTSSNQFFLQLNSVTPEDTATYYCATAG---RGFPYWGQGT 110
Query: 123 LLYVRVVKANPGMNPELS--CTDASGKAAEFGLLKDGYMFETST 164
L+ V K P L+ C D +G + G L GY E+ T
Sbjct: 111 LVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVT 154
>pdb|3G5Y|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 216
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 4/99 (4%)
Query: 65 SSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLL 124
S+ RY P ++ + I D + FF+ + T+ + R P + G+L+
Sbjct: 55 SANTRYNPSLKSRI-SITRDTSKNQFFLQLNSVTVEDTATY-YCATAGRGFPYWGQGTLV 112
Query: 125 YVRVVKAN-PGMNPELS-CTDASGKAAEFGLLKDGYMFE 161
V K P + P C D +G + G L GY E
Sbjct: 113 TVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPE 151
>pdb|4IFD|H Chain H, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 361
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 37/165 (22%), Positives = 65/165 (39%), Gaps = 19/165 (11%)
Query: 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPV--LAFEGGTRRNIPKFEIGSLLYV 126
RY P D V+G + + + VDI G A L + + GG R K E L
Sbjct: 105 RYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRR--KSESDELQMR 162
Query: 127 RVVKANPGMNPELSCTDASGKAA------EFGLLKDGYMFETSTGL-SRMLLSSPTCPVL 179
+K +N E+ G A+ ++G L++G + + L R + P
Sbjct: 163 SFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPG- 221
Query: 180 EELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAV 224
+ + +G+NG +W+ S + + + NS S+ +
Sbjct: 222 -------NITVVLGVNGYIWLRKTSQMDLARDTPSANNSSSIKST 259
>pdb|3R3J|A Chain A, Kinetic And Structural Characterization Of Plasmodium
Falciparum Glutamate Dehydrogenase 2
pdb|3R3J|B Chain B, Kinetic And Structural Characterization Of Plasmodium
Falciparum Glutamate Dehydrogenase 2
pdb|3R3J|C Chain C, Kinetic And Structural Characterization Of Plasmodium
Falciparum Glutamate Dehydrogenase 2
pdb|3R3J|D Chain D, Kinetic And Structural Characterization Of Plasmodium
Falciparum Glutamate Dehydrogenase 2
pdb|3R3J|E Chain E, Kinetic And Structural Characterization Of Plasmodium
Falciparum Glutamate Dehydrogenase 2
pdb|3R3J|F Chain F, Kinetic And Structural Characterization Of Plasmodium
Falciparum Glutamate Dehydrogenase 2
Length = 456
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGK-------LRFSKPNKYW 62
LV+K++ G +VL +S ++ G +++ + + IK + L++SK KY+
Sbjct: 254 LVEKLIEKGAIVLTMSDSNGYILEPNGFTKEQLNYIMDIKNNQRLRLKEYLKYSKTAKYF 313
Query: 63 VESSQKRYVPC 73
E+ + +PC
Sbjct: 314 -ENQKPWNIPC 323
>pdb|1HH2|P Chain P, Crystal Structure Of Nusa From Thermotoga Maritima
Length = 344
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 8/95 (8%)
Query: 48 IKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF 107
I+ GKL P K W+ + + V+ ++ +V K V R P
Sbjct: 152 IRIGKLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVI------ 205
Query: 108 EGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCT 142
G + IP+ E G ++ ++ + PG+ +++
Sbjct: 206 -GLMKLEIPEVENG-IVEIKAIAREPGVRTKVAVA 238
>pdb|1L2F|A Chain A, Crystal Structure Of Nusa From Thermotoga Maritima: A
Structure-Based Role Of The N-Terminal Domain
Length = 369
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 8/95 (8%)
Query: 48 IKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF 107
I+ GKL P K W+ + + V+ ++ +V K V R P
Sbjct: 177 IRIGKLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVI------ 230
Query: 108 EGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCT 142
G + IP+ E G ++ ++ + PG+ +++
Sbjct: 231 -GLXKLEIPEVENG-IVEIKAIAREPGVRTKVAVA 263
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 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,591,019
Number of Sequences: 62578
Number of extensions: 257889
Number of successful extensions: 893
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 873
Number of HSP's gapped (non-prelim): 20
length of query: 238
length of database: 14,973,337
effective HSP length: 96
effective length of query: 142
effective length of database: 8,965,849
effective search space: 1273150558
effective search space used: 1273150558
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: 50 (23.9 bits)