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= 042331
(378 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 = 309 bits (792), Expect = 2e-84, Method: Compositional matrix adjust.
Identities = 150/370 (40%), Positives = 238/370 (64%)
Query: 1 MRIVRKDLIPNGPGSVKMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTKSGGKDAER 60
M++++K++ NG G + M P + +D+W YN++ GD + A TVR+VV+ +G R
Sbjct: 1 MKLIQKNIEKNGSGWITMCPEEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGSR 60
Query: 61 VKLKLEIKVEALDYDKEGSALRISGKNILENEHVKIGAFHSLEIELHRPFVLTKDVWDSV 120
V +KL I VE +D+D + + L I G+ + VK+G++H+L++ELHR F L K+ WD+
Sbjct: 61 VVMKLRILVENMDFDTKAAQLHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAF 120
Query: 121 ALDTLHQASDSAATADLAVVLMQEGLANIFLVGRSMTITRSRIETSIPRKHGPAVARYES 180
ALD + A + + A++ V++ EGLANI L+ MTI R RI+ IPRK + Y+
Sbjct: 121 ALDRVDAACNPSRNAEIGAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQK 180
Query: 181 ALNKFFDSVLHAFLKHVDFNVVRCAVIASPGFTKDQFHRYLLLEAERTQLRPIIANKSRI 240
L+KF+DSV + DF+ ++ ++ASPGF + Y+ A + L+ I+ +K++
Sbjct: 181 GLDKFYDSVFQSINSEFDFDKLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKF 240
Query: 241 VIVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYGPKHVE 300
VI+H+S+G+ HSL E+L V + + +TK QE++VL +F+++++ D +A YGP HV
Sbjct: 241 VILHSSTGHIHSLNEILKDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVL 300
Query: 301 VAHERMAVQTLLITDDLFRNFEIATRKKYVDLVNSVKDSGGTAHIFSSMHFSGEQLGQLT 360
A E A+ LLI+D LFR+ +IATRKK+V LV VK+ +IFSS+H SG+QL L+
Sbjct: 301 KAFELGAIGELLISDSLFRSSDIATRKKWVSLVEGVKEINCPVYIFSSLHESGKQLDLLS 360
Query: 361 GVAAILRFPL 370
G+AAIL +P+
Sbjct: 361 GIAAILTYPV 370
>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 = 208 bits (530), Expect = 4e-54, Method: Compositional matrix adjust.
Identities = 118/383 (30%), Positives = 210/383 (54%), Gaps = 10/383 (2%)
Query: 1 MRIV--RKDLIPNGPGSVKMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTKSGGKDA 58
M+++ +KD G + ++P D +DL+ Y +V+ D + + +K + GK
Sbjct: 1 MKVISLKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKK 58
Query: 59 ERVKLKLEIKVEALDYDKEGSALRISGKNILE-----NEHVKIGAFHSLEIELHRPFVLT 113
+KL+IKV + D+D + L+ G + + N + +G + S ++ PF +
Sbjct: 59 STDLVKLKIKVISEDFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTII 118
Query: 114 KDVWDSVALDTLHQASDSAATADLAVVLMQEGLANIFLVGRSMTITRSRIETSIPRKHGP 173
K ++ L++A + +D A V++QEG+A++ LV S TI + +IE S+P+K
Sbjct: 119 KQNFNKFMQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRT 178
Query: 174 A-VARYESALNKFFDSVLHAFLKHVDFNVVRCAVIASPGFTKDQFHRYLLLEAERTQLRP 232
V +++ KF+ ++ A K ++F+ ++ ++ SPGF + AE +
Sbjct: 179 TDVLKFDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKK 238
Query: 233 IIANKSRIVIVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRA 292
I+ NK I H S+GY + EVL + +++TK ++E+ V+ EF L+ D +A
Sbjct: 239 ILDNKGMFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKA 298
Query: 293 CYGPKHVEVAHERMAVQTLLITDDLFRNFEIATRKKYVDLVNSVKDSGGTAHIFSSMHFS 352
YG K V A E A+ LL+TD + + IA R++Y+ L++SV+ +GG A + S++H
Sbjct: 299 WYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLMDSVESNGGKALVLSTLHSL 358
Query: 353 GEQLGQLTGVAAILRFPLPDLED 375
GE+L QLTG+A IL++PLPDL++
Sbjct: 359 GEELDQLTGIACILKYPLPDLDE 381
>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 = 206 bits (523), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 117/378 (30%), Positives = 204/378 (53%), Gaps = 8/378 (2%)
Query: 4 VRKDLIPNGPGSVKMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTKSGGKDAERVKL 63
++KD G + ++P D +DL+ Y +V+ D + + +K + GK +
Sbjct: 6 LKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKKSTDLV 63
Query: 64 KLEIKVEALDYDKEGSALRISGKNILE-----NEHVKIGAFHSLEIELHRPFVLTKDVWD 118
KL+IKV + D+D + L+ G + + N + +G + S ++ PF + K ++
Sbjct: 64 KLKIKVISEDFDXKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFN 123
Query: 119 SVALDTLHQASDSAATADLAVVLMQEGLANIFLVGRSMTITRSRIETSIPRKHGPA-VAR 177
L++A + +D A V++QEG+A++ LV S TI + +IE S P+K V +
Sbjct: 124 KFXQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSXPKKKRTTDVLK 183
Query: 178 YESALNKFFDSVLHAFLKHVDFNVVRCAVIASPGFTKDQFHRYLLLEAERTQLRPIIANK 237
++ KF+ ++ A K ++F+ ++ ++ SPGF + AE + I+ NK
Sbjct: 184 FDEKTEKFYKAIYSAXKKDLNFDKLKTIILCSPGFYAKILXDKIFQYAEEEHNKKILDNK 243
Query: 238 SRIVIVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYGPK 297
I H S+GY + EVL + +++TK ++E+ V EF L+ D +A YG K
Sbjct: 244 GXFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIXVXDEFLLHLNKDDDKAWYGEK 303
Query: 298 HVEVAHERMAVQTLLITDDLFRNFEIATRKKYVDLVNSVKDSGGTAHIFSSMHFSGEQLG 357
V A E A+ LL+TD + + IA R++Y+ L +SV+ +GG A + S++H GE+L
Sbjct: 304 EVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLXDSVESNGGKALVLSTLHSLGEELD 363
Query: 358 QLTGVAAILRFPLPDLED 375
QLTG+A IL++PLPDL++
Sbjct: 364 QLTGIACILKYPLPDLDE 381
>pdb|1X52|A Chain A, Solution Structures Of The C-Terminal Domain Of The Human
Pelota Homolog (Cgi-17)
Length = 124
Score = 140 bits (353), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 67/113 (59%), Positives = 88/113 (77%)
Query: 259 ASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 318
+ V + + +TKAA EVK L +F+ ML ++P RA YG K VE A+E MA+ TLLI+D+LF
Sbjct: 6 SGTVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELF 65
Query: 319 RNFEIATRKKYVDLVNSVKDSGGTAHIFSSMHFSGEQLGQLTGVAAILRFPLP 371
R+ ++ATR +YV LV+SVK++ GT IFSS+H SGEQL QLTGVAAILRFP+P
Sbjct: 66 RHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVP 118
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 134 bits (338), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 106/361 (29%), Positives = 187/361 (51%), Gaps = 23/361 (6%)
Query: 14 GSVKMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTKS-GGKDAERVKLKLEIKVEAL 72
G VK+ DDLW Y++++ GD V A T+RK ++ S + E + + L ++ E +
Sbjct: 11 GKVKVKAETLDDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVEVIPVFLGVQAEKI 70
Query: 73 DYDKEGSALRISGKNILEN-EHVKIGAFHSLEIELHRPFVLTKDVWDSVALDTLHQASDS 131
++ K + +R++G + + E V +G +H++ IE + K W ++ L +A +
Sbjct: 71 NFHKFANQVRVTGPIVYASREDVPLGKYHTIAIEQGTVVTIQKPRWKEHHIERLKEAVAA 130
Query: 132 AATADLAVVLMQEGLANIFLVGRSMTITRSRIETSIPRKHGPAVARY----ESALNKFFD 187
+ A + +V++ +G A++ LV R + I SI +H RY ES KFF
Sbjct: 131 SKRARVMIVVIDDGEADMALV-REYGV---EILNSI--RHNLGGKRYNTDRESEEMKFFH 184
Query: 188 SVLHAFLKHVDFNVVRCAVIASPGFTKDQFHRYLLLEAERTQLRPIIANKSRIVIVHTSS 247
V + + V A++A PGF K+ F+++L + P +A K +VI TS
Sbjct: 185 DVAKTMEEVMKRENVEKAIVAGPGFVKEDFYKFL------KEKYPELAKK--VVIEDTSV 236
Query: 248 GYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYGPKHVEVAHERMA 307
+ + EV+ V + +E + A+EV+++++ ++ + YG K VE A A
Sbjct: 237 TGRTGIYEVIKRGVVDRVYQENRVAKEVQLVEKVLENIARNNGLVAYGLKEVEEAVNYGA 296
Query: 308 VQTLLITDDLFRNFEIATRKKYVDLVNSVKDSGGTAHIFSSMHFSGEQLGQLTGVAAILR 367
V+TLL+ D+L + R+K +L+++V+ S G + SS H GE+L L G+AA+LR
Sbjct: 297 VETLLVLDELLKG---ELREKVEELMDAVRYSRGEVVVVSSEHEGGEKLKALGGLAALLR 353
Query: 368 F 368
F
Sbjct: 354 F 354
>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 = 109 bits (273), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 105/379 (27%), Positives = 182/379 (48%), Gaps = 38/379 (10%)
Query: 1 MRIVRKDLIPNGPGSVKMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTKSGGK---D 57
M+IV ++L N G +K+IP DDLW ++ GD V A T R ++S K D
Sbjct: 1 MQIVEENLRDN-EGEIKLIPETLDDLWHLRFIIEKGDVVFATTKR----ASQSSDKLRSD 55
Query: 58 AERVKLKLEIKVEALDYDKEGSALRISGKNILENEHVKIGAFHSLEIELHRPFVLTKDVW 117
E V ++L I+VE +++ + + LR+SGK + E +H+L I + + + K W
Sbjct: 56 KEMVTVRLGIEVEKVEFHRFANRLRVSGKIVAGIEE---SGYHTLNITVGKELSIIKK-W 111
Query: 118 DSVALDTLHQASDSAATADLAVVLMQEGLANIFLVGRSMTITRSRIETSIPRKHGPAVAR 177
L+ L +A + + ++ ++ ++EG A + + + +E + G
Sbjct: 112 KPEQLERLRRAVEDSNRPEIVMLTIEEGYAV------AGVLRQWGVEEIFEERMGYGKGM 165
Query: 178 YESALNKFFDSVLHAFLKHVDFNVVRCAVIASPGFTKDQFHRYLLLEAERTQLRPIIANK 237
+S +FF V A L+ DF + ++A PGF K+ F +L + P +A
Sbjct: 166 GDSR-KEFFGEV-AAKLESFDFKYL---IVAGPGFAKNDFLDFL------KERYPEMAKN 214
Query: 238 SRIVIVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYGPK 297
+ +V V + E+L V ++ E + A+E + + ++ R YG
Sbjct: 215 AVVVDVSSVG--SRGFIEILKRRVVDKIVGEVRLAEEAEYIDRLLEGIAKGE-RVAYGLD 271
Query: 298 HVEVAHERMAVQTLLITDDLFRNFEIATRKKY-VD-LVNSVKDSGGTAHIFSSMHFSGEQ 355
V AH A++ LL+ D+ F + R+K+ VD L+ V++SGG I S+ G++
Sbjct: 272 EVREAHNYRAIEVLLVADE----FLLEEREKWDVDGLLREVEESGGKVVIMSTEFEPGKR 327
Query: 356 LGQLTGVAAILRFPLPDLE 374
L L G+AA+LRF + LE
Sbjct: 328 LMSLGGIAALLRFNVKGLE 346
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 105 bits (263), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 103/373 (27%), Positives = 174/373 (46%), Gaps = 42/373 (11%)
Query: 1 MRIVRKDLIPNGPGSVKMIPVDS-DDLWFAYNLVNAGDSVLAVTVRKVVRQTK-SGGKDA 58
MRI+ +DL S I ++S DDLW+ N+++ GD V A+T R+V ++
Sbjct: 1 MRILEEDL----KNSTYRIRIESLDDLWYLRNILSEGDEVSAITFRRVEESADVQRSRER 56
Query: 59 ERVKLKLEIKVEALDYDKEGSALRISGKNILENEHVKIGAFHSLEIELHRPFVLTKDVWD 118
ER+ + + +KVE +++ + LRI G I E K G S+ + + +TK+ WD
Sbjct: 57 ERIPITIRLKVEKIEFQDFDNRLRILGTVIEGPEDTK-GKHQSITVTVDSEISITKE-WD 114
Query: 119 SVALDTLHQASDSAATADLAVVLMQEGLANIFLVGRSMTITRSRIETSIPRKHGP-AVAR 177
+D L +A+D V M E A IFL+ ++ T + G A
Sbjct: 115 DQHIDLLKEATDEKYVTVYTAVAMDEDEAQIFLI---HPYGIQQVGTVYSGRSGKYAEGN 171
Query: 178 YESALNKFFDSVLHAFLKHVDFNVVRCAVIASPGFTKDQFHRYLLLEAER--TQLRPIIA 235
Y A +FD +++A LK N +I PGF +D+F RY A+R + A
Sbjct: 172 YSEA--SYFDQIVNA-LK----NYSNSIIILGPGFARDRFARYC---AQRGVNVIGSFPA 221
Query: 236 NKSRIVIVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYG 295
N+ T SG ++ E + +++ L+ + A++ +++ EF + D YG
Sbjct: 222 NR-------TDSG---AVYEFITSADGAKLLSNERIARDKEIVDEFLVAVKKDM--GVYG 269
Query: 296 PKHVEVAHERMAVQTLLITDDLFRNFEIATRKKYVDLVNSVKDSGGTAHIFSSMHFSGEQ 355
E A + A+ L+ITD++FR ++ + + +V G HI S + G+
Sbjct: 270 RDQTESALQMGALSDLIITDEMFRT---EDGRRSLSIAQTV---GTRIHIVSVSNDPGQI 323
Query: 356 LGQLTGVAAILRF 368
+ + G A ILR+
Sbjct: 324 VKKFGGFAGILRY 336
>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 = 96.3 bits (238), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 101/370 (27%), Positives = 160/370 (43%), Gaps = 22/370 (5%)
Query: 4 VRKDLIPNGPGSVKMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTKSGGKDAERVKL 63
+R +++ N V++ P +DLW + GD V T R V SG K ERV +
Sbjct: 3 MRVEVLDNKRRIVRLRPESEEDLWLLRITLRPGDVVRKRTSRDV--PVGSGRK--ERVVM 58
Query: 64 KLEIKVEALDYDKEGSALRISGKNILENEHVKI-GAFHSLEIELHRPFVLTKDV-WDSVA 121
L I+++++++ LRISG + + + G HS + + V+ +D W
Sbjct: 59 TLRIRLDSIEFQPFTGKLRISGIVVEGPDEFGVKGRRHSTAVSIGTWLVVERDKGWSEQE 118
Query: 122 LDTLHQASDSAATADLAVVLMQEGLANIFLVGRSMTITRSRIETSIPRKHGPAVARYESA 181
L+ L A + TA +A V E A L G M I +P K P+ E
Sbjct: 119 LERL-AAGRARGTAVIAAVDYDE-FALAVLAGHGMKILED-TSARLPGKDDPS---REQE 172
Query: 182 LNKFFDSVLHAFLKHVDFNVVRCAVIASPGFTKDQFHRYLLLEAERTQLRPIIANKSRIV 241
+ K+ D ++ + AVIA PG K AE+ Q R + + K +
Sbjct: 173 VEKYVDRAAKRIVEEAARHRSPIAVIAGPGQLKTSV-------AEKVQ-RAMPSLK--VA 222
Query: 242 IVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYGPKHVEV 301
V TS G +RE L +V +++E + VL+EF ++ Y P V
Sbjct: 223 TVDTSMGGVAGVREALRRESVTRILRELSIVEAEGVLEEFLRRIAKSRDTVAYTPGEVLA 282
Query: 302 AHERMAVQTLLITDDLFRNFEIATRKKYVDLVNSVKDSGGTAHIFSSMHFSGEQLGQLTG 361
AV T+L+ D L + + A R+ + + V+ GG I +GE+L G
Sbjct: 283 VARMGAVDTVLLVDTLLHSPDDAVREAVDEALRLVESMGGRVIIIPGDSPAGERLVSFGG 342
Query: 362 VAAILRFPLP 371
V A+LR+P+P
Sbjct: 343 VIALLRYPVP 352
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 85.5 bits (210), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 92/365 (25%), Positives = 172/365 (47%), Gaps = 46/365 (12%)
Query: 15 SVKMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTKSGGKDAERVKLKLEIKVEALDY 74
+VK+ DDLW + ++ D V+A T R V GK++ R+ + + +KV+ ++
Sbjct: 32 AVKLHIESEDDLWLLHLILEKDDKVVAKTTRDV-----GLGKESRRIPMTIILKVDYTEF 86
Query: 75 DKEGSALRISGKNILEN--EHVKI-GAFHSLEIELHRPFVLTKDVWDSVALDTLHQASDS 131
+ + LRI G I+E+ E I GA H++ +++ ++ K W+ LD L + ++
Sbjct: 87 QEFTNRLRIHG--IIEDAPERFGIKGAHHTINLDIGDEIIIIKQQWNKYVLDRLKRQANK 144
Query: 132 AATADLAVVLMQEGLANI-FLVGRSMTITRS----RIETSIPRKHGPAVARYESALNKFF 186
+ +A+V E L I F G + +S E I ++ +A
Sbjct: 145 RSRIIIALVDFDEYLIAIPFEQGIKILSEKSLRPLNEEEGIIEQNALEIA---------- 194
Query: 187 DSVLHAFLKHVDFNVVRCAVIASPGFTKDQFHRYLLLEAERTQLRPIIANKSRIVIVHTS 246
+ L ++K D + + ++A PGF K++ + ++ I+ NK +I I S
Sbjct: 195 -TELAEYVKQYDPDAI---LLAGPGFFKEEVSK---------KVNAILKNK-KIYIDSVS 240
Query: 247 SGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYGPKHVEVAHERM 306
S + L EVL + ++ + + A K +++ +L+ P YG + V+ A E
Sbjct: 241 SATRAGLHEVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMG 300
Query: 307 AVQTLLITDDLFRNFEIATRKKYVDLVNSVKDSGGTAHIF---SSMHFSGEQLGQLTGVA 363
AV+T+L+ +DL + E R ++ +++ G + S ++F +L LTG+
Sbjct: 301 AVETVLVIEDLLSSDE-QERLTIERMLEDIENKRGEVILVPKESPIYF---ELKNLTGIL 356
Query: 364 AILRF 368
AILRF
Sbjct: 357 AILRF 361
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 61/248 (24%), Positives = 99/248 (39%), Gaps = 38/248 (15%)
Query: 137 LAVVLMQEGLANIFLVGRSMTITRSRIETSIPRKH---GPAVARYESALNKFFDSVLHAF 193
+ +++++ A I L+ + +E +P KH G + RYE + + D F
Sbjct: 143 IGIIIVERDQATIGLLKGARLEVLKELEGFVPGKHKMGGQSQRRYERIIEQMVDE----F 198
Query: 194 LKHV------------DFNVVRCAVIASPGFTKDQFHRYLLLEAERTQLRPIIANKSRIV 241
K V + V++ ++A PG K +F L+ +L+ I+A + V
Sbjct: 199 FKKVGEEASNLLVPLAEKGVLKGVIVAGPGLAKQEFVEGNYLD---YRLKKILAPELVDV 255
Query: 242 IVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRACYGPKHVEV 301
G K + V+ A V ++ V ++EF L+ YG K VE
Sbjct: 256 AYQGLQGLKEA---VMKAEKV---VEAQMYRDAVNAMEEFKLHLAKGTGMIVYGEKDVEA 309
Query: 302 AHERMAVQTLLITDDLFRNFEIATRKKYVDLVNSVKDSGGTAHIFSSMHFSGEQ-LGQLT 360
A E AV+TLLI + +R+ + V K SG + E L
Sbjct: 310 ALEMGAVKTLLIHE---------SREDLEEWVEKAKSSGAQVIVVPESLAEAEWFLKTFG 360
Query: 361 GVAAILRF 368
G+A ILRF
Sbjct: 361 GLAGILRF 368
>pdb|3E20|C Chain C, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|B Chain B, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|H Chain H, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|K Chain K, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
Length = 441
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 59/221 (26%), Positives = 91/221 (41%), Gaps = 44/221 (19%)
Query: 162 RIETSIPRKHGPAVARYESALN--KFFDSVLHAFLKHV-----------DFNVVRCAVIA 208
R +P+KHG +SAL + D H +++ V D V V+A
Sbjct: 176 RFTVDLPKKHGRGG---QSALRFARLRDEKRHNYVRKVAEGAVQHFITDDKPNVAGIVLA 232
Query: 209 SPGFTKDQFHRYLLLEAERTQLRPIIANKSRIVIVHTSSGYKHSLREVLDA-SNVMNLIK 267
K + + L + +R Q R I K+ V +G+ ++ D SNV
Sbjct: 233 GSADFKTELGQSDLFD-QRLQSRII---KTVDVSYGGDAGFNQAIELAADTLSNV----- 283
Query: 268 ETKAAQEVKVLKEFFNMLSNDPTRACYGPKHVEVAHERMAVQTLLITDDL------FRNF 321
K QE K+++ FF+ +S D + C+G A + AV+TLL DL F+N
Sbjct: 284 --KYVQEKKLIQRFFDEISLDSGKYCFGVVDTMNALQEGAVETLLCFADLDMIRYEFKNS 341
Query: 322 E-------IATRKKYVDLVNSV---KDSGGTAHIFSSMHFS 352
E + ++ D NS KD+G + SSM S
Sbjct: 342 EGNPVITYMTKEQEEKDSTNSFLLDKDTGAEMELVSSMLLS 382
>pdb|1XDF|A Chain A, Crystal Structure Of Pathogenesis-Related Protein
Llpr-10.2a From Yellow Lupine
pdb|1XDF|B Chain B, Crystal Structure Of Pathogenesis-Related Protein
Llpr-10.2a From Yellow Lupine
Length = 157
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 17 KMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTK----SGGKDAERVKLKLEIKVEAL 72
K+ VD +L + Y++V G L T+ K+ +TK + G +V +K+E K +A
Sbjct: 69 KIEAVDEANLRYNYSIV--GGVGLPDTIEKISFETKLVEGANGGSIGKVTIKIETKGDAQ 126
Query: 73 DYDKEGSALRISG 85
++EG A + G
Sbjct: 127 PNEEEGKAAKARG 139
>pdb|2QIM|A Chain A, Crystal Structure Of Pathogenesis-Related Protein
Llpr-10.2b From Yellow Lupine In Complex With Cytokinin
pdb|3E85|A Chain A, Crystal Structure Of Pathogenesis-Related Protein
Llpr-10.2b From Yellow Lupine In Complex With
Diphenylurea
Length = 158
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 17 KMIPVDSDDLWFAYNLVNAGDSVLAVTVRKVVRQTK----SGGKDAERVKLKLEIKVEAL 72
K+ +D +L + Y++V G L T+ K+ +TK + G +V +K+E K +A
Sbjct: 70 KIEAIDEANLGYNYSIV--GGVGLPDTIEKISFETKLVEGANGGSIGKVTIKIETKGDAQ 127
Query: 73 DYDKEGSALRISG 85
++EG A + G
Sbjct: 128 PNEEEGKAAKARG 140
>pdb|2NWT|A Chain A, Nmr Structure Of Protein Upf0165 Protein Af_2212 From
Archaeoglobus Fulgidus; Northeast Structural Genomics
Consortium Target Gr83
pdb|2NWT|B Chain B, Nmr Structure Of Protein Upf0165 Protein Af_2212 From
Archaeoglobus Fulgidus; Northeast Structural Genomics
Consortium Target Gr83
Length = 69
Score = 29.3 bits (64), Expect = 4.2, Method: Composition-based stats.
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 56 KDAERVKLKLEIKVEALD 73
K+ ERVK+KLE+KVE +D
Sbjct: 23 KEGERVKIKLELKVEPID 40
>pdb|3TXX|A Chain A, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|B Chain B, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|C Chain C, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|D Chain D, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|E Chain E, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|F Chain F, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|G Chain G, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|H Chain H, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|I Chain I, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|J Chain J, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|K Chain K, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
pdb|3TXX|L Chain L, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis
Length = 359
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 221 LLLEAERTQLRPIIANKSRIVIVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKE 280
L+ ER +AN + I +++ S Y H +E+ D ++ + E K ++ KV+
Sbjct: 120 LMARVERHHSIVDLANCATIPVINGMSDYNHPTQELGDLCTMVEHLPEGKKLEDCKVV-- 177
Query: 281 FFNMLSNDPTRACY 294
D T+ C+
Sbjct: 178 ----FVGDATQVCF 187
>pdb|4A8T|A Chain A, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis Lacking Its C-Terminal Helix, With
Bound N5-(Phosphonoacetyl)-L-Ornithine
Length = 339
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 221 LLLEAERTQLRPIIANKSRIVIVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKE 280
L+ ER +AN + I +++ S Y H +E+ D ++ + E K ++ KV+
Sbjct: 122 LMARVERHHSIVDLANCATIPVINGMSDYNHPTQELGDLCTMVEHLPEGKKLEDCKVV-- 179
Query: 281 FFNMLSNDPTRACY 294
D T+ C+
Sbjct: 180 ----FVGDATQVCF 189
>pdb|4A8H|A Chain A, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis With
N-(Phosphonoacetyl)-Putrescine
pdb|4A8H|B Chain B, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis With
N-(Phosphonoacetyl)-Putrescine
pdb|4A8P|A Chain A, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis With
N5-(Phosphonoacetyl)-L-Ornithine
pdb|4A8P|B Chain B, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis With
N5-(Phosphonoacetyl)-L-Ornithine
pdb|4A8P|C Chain C, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis With
N5-(Phosphonoacetyl)-L-Ornithine
pdb|4A8P|D Chain D, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis With
N5-(Phosphonoacetyl)-L-Ornithine
pdb|4A8P|E Chain E, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis With
N5-(Phosphonoacetyl)-L-Ornithine
pdb|4A8P|F Chain F, Crystal Structure Of Putrescine Transcarbamylase From
Enterococcus Faecalis With
N5-(Phosphonoacetyl)-L-Ornithine
Length = 355
Score = 28.5 bits (62), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 234 IANKSRIVIVHTSSGYKHSLREVLDASNVMNLIKETKAAQEVKVLKEFFNMLSNDPTRAC 293
+AN + I +++ S Y H +E+ D ++ + E K ++ KV+ D T+ C
Sbjct: 113 LANCATIPVINGMSDYNHPTQELGDLCTMVEHLPEGKKLEDCKVV------FVGDATQVC 166
Query: 294 Y 294
+
Sbjct: 167 F 167
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
0.320 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: 10,512,764
Number of Sequences: 62578
Number of extensions: 399349
Number of successful extensions: 1037
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1002
Number of HSP's gapped (non-prelim): 18
length of query: 378
length of database: 14,973,337
effective HSP length: 100
effective length of query: 278
effective length of database: 8,715,537
effective search space: 2422919286
effective search space used: 2422919286
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)