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= psy17307
(342 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 = 221 bits (563), Expect = 4e-58, Method: Compositional matrix adjust.
Identities = 126/308 (40%), Positives = 175/308 (56%), Gaps = 50/308 (16%)
Query: 85 KESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXXRVRTMLTISVESIDFDTQACV 144
+E EDMWH YN++ GD ++AST+R+V RV L I VE++DFDT+A
Sbjct: 21 EEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGSRVVMKLRILVENMDFDTKAAQ 80
Query: 145 LRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAV 204
L +KGR + + VKMG+YHTLDLEL+R F L K EWD+ AL+R++ ACN + A++ AV
Sbjct: 81 LHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAFALDRVDAACNPSRNAEIGAV 140
Query: 205 MMQEGLANIMLITASMSLVRTKIETNIPRKRRDNKDLLKE-------------------- 244
++ EGLANI LIT M+++R +I+ IPRKRR + ++
Sbjct: 141 VLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQKGLDKFYDSVFQSINSEFDFD 200
Query: 245 ------LLSPITTVE---------AVKMDNKVLLENKSKFLLVHSSSAFKHSLKEILADP 289
L SP AVK+D K ++++K+KF+++HSS+ HSL EIL DP
Sbjct: 201 KLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKFVILHSSTGHIHSLNEILKDP 260
Query: 290 TVTSKMQDTKAL---------------DPSRAFYGYRHVSAANESQAIDTLLIADCLFRN 334
V SK+ DTK + D +A+YG HV A E AI LLI+D LFR+
Sbjct: 261 AVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSLFRS 320
Query: 335 SDLNERKK 342
SD+ RKK
Sbjct: 321 SDIATRKK 328
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 40/92 (43%), Positives = 56/92 (60%), Gaps = 1/92 (1%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQXXXXXXXXXXX 60
MKL+ KNI +K+ SG + + PEE EDMWH YN++ GD ++AST+R+V
Sbjct: 1 MKLIQKNI-EKNGSGWITMCPEEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGS 59
Query: 61 RVRTMLTISVESIDFDTQACVLRLKESEDMWH 92
RV L I VE++DFDT+A L +K +H
Sbjct: 60 RVVMKLRILVENMDFDTKAAQLHIKGRTTEYH 91
>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 = 105 bits (261), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 88/335 (26%), Positives = 149/335 (44%), Gaps = 62/335 (18%)
Query: 65 MLTISVESIDFDTQACVLRL--KESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXX 122
M IS++ F+ V+ L ++ ED++ Y ++ + D + +K
Sbjct: 1 MKVISLKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDELIFK--KKFTSKLDEAGKKK 58
Query: 123 XRVRTMLTISVESIDFDTQACVLRLKGRNIQE-----NQYVKMGAYHTLDLELNRKFELS 177
L I V S DFD + L+ KG + + N + +G Y + L+ F +
Sbjct: 59 STDLVKLKIKVISEDFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTII 118
Query: 178 KPEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRD 237
K ++ + + ACNIE +D AAV++QEG+A++ L+T+S ++++ KIE ++P+K+R
Sbjct: 119 KQNFNKFMQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRT 178
Query: 238 -------------------------NKDLLKE--LLSPITTVEAVKMD----------NK 260
N D LK L SP + MD NK
Sbjct: 179 TDVLKFDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSP-GFYAKILMDKIFQYAEEEHNK 237
Query: 261 VLLENKSKFLLVHSSSAFKHSLKEILADPTVTSKMQDTKA---------------LDPSR 305
+L+NK F + H S+ + + E+L +P SK+QDTK D +
Sbjct: 238 KILDNKGMFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDK 297
Query: 306 AFYGYRHVSAANESQAIDTLLIADCLFRNSDLNER 340
A+YG + V A E AI LL+ D + + ++ +R
Sbjct: 298 AWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQR 332
>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 = 103 bits (258), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 86/331 (25%), Positives = 147/331 (44%), Gaps = 60/331 (18%)
Query: 68 ISVESIDFDTQACVLRL--KESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXXRV 125
IS++ F+ V+ L ++ ED++ Y ++ + D + +K
Sbjct: 4 ISLKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDELIFK--KKFTSKLDEAGKKKSTD 61
Query: 126 RTMLTISVESIDFDTQACVLRLKGRNIQE-----NQYVKMGAYHTLDLELNRKFELSKPE 180
L I V S DFD + L+ KG + + N + +G Y + L+ F + K
Sbjct: 62 LVKLKIKVISEDFDXKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQN 121
Query: 181 WDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRD--- 237
++ + + ACNIE +D AAV++QEG+A++ L+T+S ++++ KIE + P+K+R
Sbjct: 122 FNKFXQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSXPKKKRTTDV 181
Query: 238 ----------------------NKDLLKE--LLSPITTVE---------AVKMDNKVLLE 264
N D LK L SP + A + NK +L+
Sbjct: 182 LKFDEKTEKFYKAIYSAXKKDLNFDKLKTIILCSPGFYAKILXDKIFQYAEEEHNKKILD 241
Query: 265 NKSKFLLVHSSSAFKHSLKEILADPTVTSKMQDTKA---------------LDPSRAFYG 309
NK F + H S+ + + E+L +P SK+QDTK D +A+YG
Sbjct: 242 NKGXFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIXVXDEFLLHLNKDDDKAWYG 301
Query: 310 YRHVSAANESQAIDTLLIADCLFRNSDLNER 340
+ V A E AI LL+ D + + ++ +R
Sbjct: 302 EKEVVKAAEYGAISYLLLTDKVLHSDNIAQR 332
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 71/150 (47%), Gaps = 2/150 (1%)
Query: 88 EDMWHAYNLITEGDSVRASTIRK-VQXXXXXXXXXXXRVRTMLTISVESIDFDTQACVLR 146
+D+WH Y++I GD V A T+RK Q + L + E I+F A +R
Sbjct: 21 DDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVEVIPVFLGVQAEKINFHKFANQVR 80
Query: 147 LKGRNIQENQY-VKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVM 205
+ G + ++ V +G YHT+ +E + KP W +ER++ A K A V V+
Sbjct: 81 VTGPIVYASREDVPLGKYHTIAIEQGTVVTIQKPRWKEHHIERLKEAVAASKRARVMIVV 140
Query: 206 MQEGLANIMLITASMSLVRTKIETNIPRKR 235
+ +G A++ L+ + I N+ KR
Sbjct: 141 IDDGEADMALVREYGVEILNSIRHNLGGKR 170
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 8 INDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRK-VQXXXXXXXXXXXRVRTML 66
+ +K K G V + E +D+WH Y++I GD V A T+RK Q + L
Sbjct: 4 LEEKPKEGKVKVKAETLDDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVEVIPVFL 63
Query: 67 TISVESIDFDTQACVLRL 84
+ E I+F A +R+
Sbjct: 64 GVQAEKINFHKFANQVRV 81
>pdb|1X52|A Chain A, Solution Structures Of The C-Terminal Domain Of The Human
Pelota Homolog (Cgi-17)
Length = 124
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 39/68 (57%), Gaps = 15/68 (22%)
Query: 290 TVTSKMQDTKAL---------------DPSRAFYGYRHVSAANESQAIDTLLIADCLFRN 334
TV S++ DTKA +P RAFYG + V ANE+ AIDTLLI+D LFR+
Sbjct: 8 TVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRH 67
Query: 335 SDLNERKK 342
D+ R +
Sbjct: 68 QDVATRSR 75
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 69/136 (50%), Gaps = 3/136 (2%)
Query: 82 LRLKESEDMWHAYNLITEGDSVRASTIRKVQXXX-XXXXXXXXRVRTMLTISVESIDFDT 140
+R++ +D+W+ N+++EGD V A T R+V+ R+ + + VE I+F
Sbjct: 15 IRIESLDDLWYLRNILSEGDEVSAITFRRVEESADVQRSRERERIPITIRLKVEKIEFQD 74
Query: 141 QACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTAD 200
LR+ G I+ + K G + ++ + ++ + ++K EWD ++ ++ A + +
Sbjct: 75 FDNRLRILGTVIEGPEDTK-GKHQSITVTVDSEISITK-EWDDQHIDLLKEATDEKYVTV 132
Query: 201 VAAVMMQEGLANIMLI 216
AV M E A I LI
Sbjct: 133 YTAVAMDEDEAQIFLI 148
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 22 EESEDMWHAYNLIAEGDSVRASTIRKVQXXX-XXXXXXXXRVRTMLTISVESIDF 75
E +D+W+ N+++EGD V A T R+V+ R+ + + VE I+F
Sbjct: 18 ESLDDLWYLRNILSEGDEVSAITFRRVEESADVQRSRERERIPITIRLKVEKIEF 72
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 76/306 (24%), Positives = 124/306 (40%), Gaps = 48/306 (15%)
Query: 73 IDFDT--QACVLRLKESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXXRVRTMLT 130
++FD QA L ++ +D+W + ++ + D V A T R V R+ +
Sbjct: 24 LEFDEKRQAVKLHIESEDDLWLLHLILEKDDKVVAKTTRDV-----GLGKESRRIPMTII 78
Query: 131 ISVESIDFDTQACVLRLKG--RNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALER 188
+ V+ +F LR+ G + E +K GA+HT++L++ + + K +W+ L+R
Sbjct: 79 LKVDYTEFQEFTNRLRIHGIIEDAPERFGIK-GAHHTINLDIGDEIIIIKQQWNKYVLDR 137
Query: 189 IEVACNIEKTADVAAVMMQEGLANIML-----ITASMSLVRTKIETNIPR---------- 233
++ N +A V E L I I + SL E I
Sbjct: 138 LKRQANKRSRIIIALVDFDEYLIAIPFEQGIKILSEKSLRPLNEEEGIIEQNALEIATEL 197
Query: 234 ----KRRDNKDLLKELLSPITTVEAVKMDNKVLLENKSKFLLVHSSSAFKHSLKEILADP 289
K+ D +L L P E V +L+NK K + SSA + L E+L
Sbjct: 198 AEYVKQYDPDAIL--LAGPGFFKEEVSKKVNAILKNK-KIYIDSVSSATRAGLHEVLKRD 254
Query: 290 TVTSKMQD----------TKALD-----PSRAFYGYRHVSAANESQAIDTLLIADCLFRN 334
+ M D KA++ P YG V A E A++T+L+ + L +
Sbjct: 255 IIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLVIEDLL-S 313
Query: 335 SDLNER 340
SD ER
Sbjct: 314 SDEQER 319
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/141 (29%), Positives = 63/141 (44%), Gaps = 22/141 (15%)
Query: 88 EDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXXRVRTMLTISVESIDFDTQACVLRL 147
+D+WH +I +GD V A+T R Q V L I VE ++F A LR+
Sbjct: 23 DDLWHLRFIIEKGDVVFATTKRASQSSDKLRSDKEM-VTVRLGIEVEKVEFHRFANRLRV 81
Query: 148 KGR---NIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIE-----------VAC 193
G+ I+E+ YHTL++ + ++ + K +W LER+ V
Sbjct: 82 SGKIVAGIEES------GYHTLNITVGKELSIIK-KWKPEQLERLRRAVEDSNRPEIVML 134
Query: 194 NIEKTADVAAVMMQEGLANIM 214
IE+ VA V+ Q G+ I
Sbjct: 135 TIEEGYAVAGVLRQWGVEEIF 155
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 3/84 (3%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQXXXXXXXXXXX 60
M++V +N+ +D G + L+PE +D+WH +I +GD V A+T R Q
Sbjct: 1 MQIVEENL--RDNEGEIKLIPETLDDLWHLRFIIEKGDVVFATTKRASQSSDKLRSDKEM 58
Query: 61 RVRTMLTISVESIDFDTQACVLRL 84
V L I VE ++F A LR+
Sbjct: 59 -VTVRLGIEVEKVEFHRFANRLRV 81
>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 = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 59/137 (43%), Gaps = 7/137 (5%)
Query: 70 VESIDFDTQACVLRLKESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXXRVRTML 129
VE +D + LR + ED+W + GD VR T R V RV L
Sbjct: 5 VEVLDNKRRIVRLRPESEEDLWLLRITLRPGDVVRKRTSRDVP----VGSGRKERVVMTL 60
Query: 130 TISVESIDFDTQACVLRLKGRNIQ-ENQYVKMGAYHTLDLELNRKFELSKPE-WDSIALE 187
I ++SI+F LR+ G ++ +++ G H+ + + + + + W LE
Sbjct: 61 RIRLDSIEFQPFTGKLRISGIVVEGPDEFGVKGRRHSTAVSIGTWLVVERDKGWSEQELE 120
Query: 188 RIEVACNIEKTADVAAV 204
R+ A TA +AAV
Sbjct: 121 RL-AAGRARGTAVIAAV 136
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 12 DKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQXXXXXXXXXXXRVRTMLTISVE 71
+K +V L PE ED+W + GD VR T R V RV L I ++
Sbjct: 10 NKRRIVRLRPESEEDLWLLRITLRPGDVVRKRTSRDVP----VGSGRKERVVMTLRIRLD 65
Query: 72 SIDFDTQACVLRL 84
SI+F LR+
Sbjct: 66 SIEFQPFTGKLRI 78
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 233 RKRRDNKDLLKELLSPITTVEAVKMDNKVLLENKSKFLLVHSSSAFKHSLKEILAD--PT 290
+KRRD ++L + L + A KMD +L+ FL H + + EI D PT
Sbjct: 21 KKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPT 80
Query: 291 VTSKMQDTKAL 301
S + T+ +
Sbjct: 81 FLSNEEFTQLM 91
>pdb|3N72|A Chain A, Crystal Structure Of Aha-1 From Plasmodium Falciparum,
Pfc0270w
pdb|3N72|B Chain B, Crystal Structure Of Aha-1 From Plasmodium Falciparum,
Pfc0270w
Length = 164
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 129 LTISVESIDFDTQACVLRLKGRNIQENQY-VKMGAYHTLDLELNRKFELSK--PEWDSIA 185
LTI +++ ACV KG+ I +Y +K ++ E F S P++ + +
Sbjct: 44 LTIYFDNLQVSGNACVSIRKGKQINSFEYIIKFEWLYSKKKEGKDYFGGSVEIPDFSTFS 103
Query: 186 LERIEVACNIEKT 198
LE + A NIE+T
Sbjct: 104 LEENDYAINIERT 116
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
0.317 0.130 0.355
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,769,227
Number of Sequences: 62578
Number of extensions: 246631
Number of successful extensions: 658
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 633
Number of HSP's gapped (non-prelim): 25
length of query: 342
length of database: 14,973,337
effective HSP length: 100
effective length of query: 242
effective length of database: 8,715,537
effective search space: 2109159954
effective search space used: 2109159954
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)