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= 022772
(292 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 219 bits (557), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 100/285 (35%), Positives = 178/285 (62%)
Query: 1 MKILRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAER 60
MK++++N+ +NG G + M P + +D+W YN++ GD + A TVR+V++ A+GS R
Sbjct: 1 MKLIQKNIEKNGSGWITMCPEEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGSR 60
Query: 61 XXXXXXXXXXXXDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSL 120
D+D + + L I+G+ + VK+G++HTL++ELHR F L K+ WD+
Sbjct: 61 VVMKLRILVENMDFDTKAAQLHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAF 120
Query: 121 ALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYES 180
ALD + A +P+ +A++ V++ EGLA+I L+ MTI R RI+ IPRK + Y+
Sbjct: 121 ALDRVDAACNPSRNAEIGAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQK 180
Query: 181 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRI 240
L+KF+++V Q+ DF+ ++ ++ASPGF + ++ A + L+ I+++K++
Sbjct: 181 GLDKFYDSVFQSINSEFDFDKLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKF 240
Query: 241 ILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNML 285
+++H+S+G+ HSL E+L P V + + DTK QE++ L F++++
Sbjct: 241 VILHSSTGHIHSLNEILKDPAVESKLADTKYVQEIRVLNKFYDVM 285
>pdb|2VGM|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-Go Decay.
pdb|3IZQ|0 Chain 0, Structure Of The Dom34-Hbs1-Gdpnp Complex Bound To A
Translating Ribosome
pdb|3J16|A Chain A, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 386
Score = 116 bits (290), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 64/285 (22%), Positives = 134/285 (47%), Gaps = 8/285 (2%)
Query: 4 LRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXX 63
L+++ G + + P D +DL+ Y ++ D + + +K ++ +
Sbjct: 6 LKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKKSTDLV 63
Query: 64 XXXXXXXXXDYDKEGSVLRIRGKNILE-----NEHVKIGAFHTLEIELHRAFVLRKDLWD 118
D+D + L+ +G + + N + +G + + ++ F + K ++
Sbjct: 64 KLKIKVISEDFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFN 123
Query: 119 SLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPA-IAG 177
L++A + +D A V++QEG+AH+ LV S TI + +IE S+P+K +
Sbjct: 124 KFMQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLK 183
Query: 178 YESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENK 237
++ KF++ + A K ++F+ ++ ++ SPGF + AE + I++NK
Sbjct: 184 FDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNK 243
Query: 238 SRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFF 282
+ H S+GY + EVL P + ++DTK ++E+ + +F
Sbjct: 244 GMFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFL 288
>pdb|2VGN|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-go Decay.
pdb|2VGN|B Chain B, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-go Decay
Length = 386
Score = 114 bits (284), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 64/284 (22%), Positives = 132/284 (46%), Gaps = 8/284 (2%)
Query: 4 LRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXX 63
L+++ G + + P D +DL+ Y ++ D + + +K ++ +
Sbjct: 6 LKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKKSTDLV 63
Query: 64 XXXXXXXXXDYDKEGSVLRIRGKNILE-----NEHVKIGAFHTLEIELHRAFVLRKDLWD 118
D+D + L+ +G + + N + +G + + ++ F + K ++
Sbjct: 64 KLKIKVISEDFDXKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFN 123
Query: 119 SLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPA-IAG 177
L++A + +D A V++QEG+AH+ LV S TI + +IE S P+K +
Sbjct: 124 KFXQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSXPKKKRTTDVLK 183
Query: 178 YESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENK 237
++ KF++ + A K ++F+ ++ ++ SPGF + AE + I++NK
Sbjct: 184 FDEKTEKFYKAIYSAXKKDLNFDKLKTIILCSPGFYAKILXDKIFQYAEEEHNKKILDNK 243
Query: 238 SRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDF 281
+ H S+GY + EVL P + ++DTK ++E+ +F
Sbjct: 244 GXFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIXVXDEF 287
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 75.9 bits (185), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 73/278 (26%), Positives = 130/278 (46%), Gaps = 22/278 (7%)
Query: 7 NLVENGP--GSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMAS-GSRDAERXXX 63
++E P G VK++ DDLW Y++I PGD V A T+RK ++ S + E
Sbjct: 2 EILEEKPKEGKVKVKAETLDDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVEVIPV 61
Query: 64 XXXXXXXXXDYDKEGSVLRIRGKNILEN-EHVKIGAFHTLEIELHRAFVLRKDLWDSLAL 122
++ K + +R+ G + + E V +G +HT+ IE ++K W +
Sbjct: 62 FLGVQAEKINFHKFANQVRVTGPIVYASREDVPLGKYHTIAIEQGTVVTIQKPRWKEHHI 121
Query: 123 DTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGY---- 178
+ L +A + A + +V++ +G A + LV R + I SI +H Y
Sbjct: 122 ERLKEAVAASKRARVMIVVIDDGEADMALV-REYGV---EILNSI--RHNLGGKRYNTDR 175
Query: 179 ESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKS 238
ES KFF +V + + + V A++A PGF K+ F++ L ++ P E
Sbjct: 176 ESEEMKFFHDVAKTMEEVMKRENVEKAIVAGPGFVKEDFYKFL------KEKYP--ELAK 227
Query: 239 RIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQ 276
++++ TS + + EV+ V + ++ + A+EVQ
Sbjct: 228 KVVIEDTSVTGRTGIYEVIKRGVVDRVYQENRVAKEVQ 265
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 59/222 (26%), Positives = 97/222 (43%), Gaps = 15/222 (6%)
Query: 1 MKILRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQM-ASGSRDAE 59
M+IL +L +N +++E +D DLW+ N+++ GD V A+T R+V SR+ E
Sbjct: 1 MRILEEDL-KNSTYRIRIESLD--DLWYLRNILSEGDEVSAITFRRVEESADVQRSRERE 57
Query: 60 RXXXXXXXXXXXXDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS 119
R ++ + LRI G I E K G ++ + + + K+ WD
Sbjct: 58 RIPITIRLKVEKIEFQDFDNRLRILGTVIEGPEDTK-GKHQSITVTVDSEISITKE-WDD 115
Query: 120 LALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYE 179
+D L +A D V M E A I L+ ++ T + G G
Sbjct: 116 QHIDLLKEATDEKYVTVYTAVAMDEDEAQIFLI---HPYGIQQVGTVYSGRSGKYAEGNY 172
Query: 180 SALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHL 221
S + +F+ ++ A LK N +I PGF +D+F R+
Sbjct: 173 SEAS-YFDQIVNA-LK----NYSNSIIILGPGFARDRFARYC 208
>pdb|3OBY|A Chain A, Crystal Structure Of Archaeoglobus Fulgidus Pelota Reveals
Inter- Domain Structural Plasticity
pdb|3OBY|B Chain B, Crystal Structure Of Archaeoglobus Fulgidus Pelota Reveals
Inter- Domain Structural Plasticity
Length = 352
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 56/218 (25%), Positives = 95/218 (43%), Gaps = 19/218 (8%)
Query: 1 MKILRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSR-DAE 59
M+I+ NL +N G +K+ P DDLW +I GD V A T R Q + R D E
Sbjct: 1 MQIVEENLRDN-EGEIKLIPETLDDLWHLRFIIEKGDVVFATTKRA--SQSSDKLRSDKE 57
Query: 60 RXXXXXXXXXXXXDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS 119
++ + + LR+ GK + E +HTL I + + + K W
Sbjct: 58 MVTVRLGIEVEKVEFHRFANRLRVSGKIVAGIEE---SGYHTLNITVGKELSIIKK-WKP 113
Query: 120 LALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYE 179
L+ L +A + + ++ ++ ++EG A + + + +E + G G
Sbjct: 114 EQLERLRRAVEDSNRPEIVMLTIEEGYAV------AGVLRQWGVEEIFEERMGYG-KGMG 166
Query: 180 SALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQF 217
+ +FF V A L+ DF + ++A PGF K+ F
Sbjct: 167 DSRKEFFGEV-AAKLESFDFKYL---IVAGPGFAKNDF 200
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 63/273 (23%), Positives = 116/273 (42%), Gaps = 53/273 (19%)
Query: 15 SVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXXXXXXXXXXXDY 74
+VK+ DDLW + ++ D V+A T R V +++ R ++
Sbjct: 32 AVKLHIESEDDLWLLHLILEKDDKVVAKTTRDV-----GLGKESRRIPMTIILKVDYTEF 86
Query: 75 DKEGSVLRIRGKNILEN--EHVKI-GAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADP 131
+ + LRI G I+E+ E I GA HT+ +++ ++ K W+ LD L + A+
Sbjct: 87 QEFTNRLRIHG--IIEDAPERFGIKGAHHTINLDIGDEIIIIKQQWNKYVLDRLKRQANK 144
Query: 132 TASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYES--ALNK----F 185
+ +A+V E L +IP + G I +S LN+
Sbjct: 145 RSRIIIALVDFDEYL------------------IAIPFEQGIKILSEKSLRPLNEEEGII 186
Query: 186 FENVLQ------AFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSR 239
+N L+ ++K D + + ++A PGF K++ +++ I++NK +
Sbjct: 187 EQNALEIATELAEYVKQYDPDAI---LLAGPGFFKEEVS---------KKVNAILKNK-K 233
Query: 240 IILVHTSSGYKHSLREVLDAPNVMNMIKDTKAA 272
I + SS + L EVL + ++ D + A
Sbjct: 234 IYIDSVSSATRAGLHEVLKRDIIDKIMTDYEIA 266
>pdb|3AGJ|B Chain B, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|D Chain D, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|F Chain F, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|H Chain H, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
Length = 358
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 64/288 (22%), Positives = 111/288 (38%), Gaps = 22/288 (7%)
Query: 4 LRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXX 63
+R +++N V++ P +DLW + PGD V T R V GS ER
Sbjct: 3 MRVEVLDNKRRIVRLRPESEEDLWLLRITLRPGDVVRKRTSRDV----PVGSGRKERVVM 58
Query: 64 XXXXXXXXXDYDKEGSVLRIRGKNILENEHVKI-GAFHTLEIELHRAFVLRKDL-WDSLA 121
++ LRI G + + + G H+ + + V+ +D W
Sbjct: 59 TLRIRLDSIEFQPFTGKLRISGIVVEGPDEFGVKGRRHSTAVSIGTWLVVERDKGWSEQE 118
Query: 122 LDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESA 181
L+ L A +A +A V E A +L G M I +P K P+ E
Sbjct: 119 LERL-AAGRARGTAVIAAVDYDE-FALAVLAGHGMKILED-TSARLPGKDDPS---REQE 172
Query: 182 LNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRII 241
+ K+ + + ++ + AVIA PG K + E +R + + ++
Sbjct: 173 VEKYVDRAAKRIVEEAARHRSPIAVIAGPGQLKTS-----VAEKVQRAMPSL-----KVA 222
Query: 242 LVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNVR 289
V TS G +RE L +V ++++ + L++F + R
Sbjct: 223 TVDTSMGGVAGVREALRRESVTRILRELSIVEAEGVLEEFLRRIAKSR 270
>pdb|1X52|A Chain A, Solution Structures Of The C-Terminal Domain Of The Human
Pelota Homolog (Cgi-17)
Length = 124
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 261 NVMNMIKDTKAAQEVQALKDFFNML 285
V + + DTKAA EV+AL DF+ ML
Sbjct: 8 TVASRLSDTKAAGEVKALDDFYKML 32
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
0.322 0.136 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,800,063
Number of Sequences: 62578
Number of extensions: 277832
Number of successful extensions: 537
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 520
Number of HSP's gapped (non-prelim): 9
length of query: 292
length of database: 14,973,337
effective HSP length: 98
effective length of query: 194
effective length of database: 8,840,693
effective search space: 1715094442
effective search space used: 1715094442
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)