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= 020677
(323 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 = 256 bits (655), Expect = 9e-69, Method: Compositional matrix adjust.
Identities = 122/319 (38%), Positives = 205/319 (64%), Gaps = 2/319 (0%)
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 VKLKLEIKV--VDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSL 118
V +KL I V +D+D + + L I+G+ + VK+G++HTL++ELHR F L K+ WD+
Sbjct: 61 VVMKLRILVENMDFDTKAAQLHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAF 120
Query: 119 ALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYES 178
ALD + A +P+ +A++ V++ EGLA+I L+ MTI R RI+ IPRK + Y+
Sbjct: 121 ALDRVDAACNPSRNAEIGAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQK 180
Query: 179 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRI 238
L+KF+++V Q+ DF+ ++ ++ASPGF + ++ A + L+ I+++K++
Sbjct: 181 GLDKFYDSVFQSINSEFDFDKLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKF 240
Query: 239 ILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVE 298
+++H+S+G+ HSL E+L P V + + DTK QE++ L F++++ D +A YGP HV
Sbjct: 241 VILHSSTGHIHSLNEILKDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVL 300
Query: 299 VAHERMAVQTLLITDDLFR 317
A E A+ LLI+D LFR
Sbjct: 301 KAFELGAIGELLISDSLFR 319
>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 = 144 bits (362), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 83/318 (26%), Positives = 160/318 (50%), Gaps = 10/318 (3%)
Query: 4 LRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQM--ASGSRDAERV 61
L+++ G + + P D +DL+ Y ++ D + + +K ++ A + + V
Sbjct: 6 LKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKKSTDLV 63
Query: 62 KLKLEIKVVDYDKEGSVLRIRGKNILE-----NEHVKIGAFHTLEIELHRAFVLRKDLWD 116
KLK+++ D+D + L+ +G + + N + +G + + ++ F + K ++
Sbjct: 64 KLKIKVISEDFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFN 123
Query: 117 SLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPA-IAG 175
L++A + +D A V++QEG+AH+ LV S TI + +IE S+P+K +
Sbjct: 124 KFMQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLK 183
Query: 176 YESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENK 235
++ KF++ + A K ++F+ ++ ++ SPGF + AE + I++NK
Sbjct: 184 FDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNK 243
Query: 236 SRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPK 295
+ H S+GY + EVL P + ++DTK ++E+ + +F L D +A YG K
Sbjct: 244 GMFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEK 303
Query: 296 HVEVAHERMAVQTLLITD 313
V A E A+ LL+TD
Sbjct: 304 EVVKAAEYGAISYLLLTD 321
>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 = 142 bits (358), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 82/316 (25%), Positives = 154/316 (48%), Gaps = 6/316 (1%)
Query: 4 LRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKL 63
L+++ G + + P D +DL+ Y ++ D ++ A + + VKL
Sbjct: 6 LKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDELIFKKKFTSKLDEAGKKKSTDLVKL 65
Query: 64 KLEIKVVDYDKEGSVLRIRGKNILE-----NEHVKIGAFHTLEIELHRAFVLRKDLWDSL 118
K+++ D+D + L+ +G + + N + +G + + ++ F + K ++
Sbjct: 66 KIKVISEDFDXKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKF 125
Query: 119 ALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPA-IAGYE 177
L++A + +D A V++QEG+AH+ LV S TI + +IE S P+K + ++
Sbjct: 126 XQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSXPKKKRTTDVLKFD 185
Query: 178 SALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSR 237
KF++ + A K ++F+ ++ ++ SPGF + AE + I++NK
Sbjct: 186 EKTEKFYKAIYSAXKKDLNFDKLKTIILCSPGFYAKILXDKIFQYAEEEHNKKILDNKGX 245
Query: 238 IILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHV 297
+ H S+GY + EVL P + ++DTK ++E+ +F L D +A YG K V
Sbjct: 246 FFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIXVXDEFLLHLNKDDDKAWYGEKEV 305
Query: 298 EVAHERMAVQTLLITD 313
A E A+ LL+TD
Sbjct: 306 VKAAEYGAISYLLLTD 321
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 101 bits (251), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 89/323 (27%), Positives = 159/323 (49%), Gaps = 28/323 (8%)
Query: 7 NLVENGP--GSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVK-- 62
++E P G VK++ DDLW Y++I PGD V A T+RK + + S AE+V+
Sbjct: 2 EILEEKPKEGKVKVKAETLDDLWHLYHIIDPGDIVYAKTLRK--QAQRADSLRAEKVEVI 59
Query: 63 ---LKLEIKVVDYDKEGSVLRIRGKNILEN-EHVKIGAFHTLEIELHRAFVLRKDLWDSL 118
L ++ + +++ K + +R+ G + + E V +G +HT+ IE ++K W
Sbjct: 60 PVFLGVQAEKINFHKFANQVRVTGPIVYASREDVPLGKYHTIAIEQGTVVTIQKPRWKEH 119
Query: 119 ALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGY-- 176
++ L +A + A + +V++ +G A + LV R + I SI +H Y
Sbjct: 120 HIERLKEAVAASKRARVMIVVIDDGEADMALV-REYGV---EILNSI--RHNLGGKRYNT 173
Query: 177 --ESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIEN 234
ES KFF +V + + + V A++A PGF K+ F++ L ++ P E
Sbjct: 174 DRESEEMKFFHDVAKTMEEVMKRENVEKAIVAGPGFVKEDFYKFL------KEKYP--EL 225
Query: 235 KSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGP 294
++++ TS + + EV+ V + ++ + A+EVQ ++ + + YG
Sbjct: 226 AKKVVIEDTSVTGRTGIYEVIKRGVVDRVYQENRVAKEVQLVEKVLENIARNNGLVAYGL 285
Query: 295 KHVEVAHERMAVQTLLITDDLFR 317
K VE A AV+TLL+ D+L +
Sbjct: 286 KEVEEAVNYGAVETLLVLDELLK 308
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 81/320 (25%), Positives = 147/320 (45%), Gaps = 30/320 (9%)
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 RVKLKLEIKV--VDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS 117
R+ + + +KV +++ + LRI G I E K G ++ + + + K+ WD
Sbjct: 58 RIPITIRLKVEKIEFQDFDNRLRILGTVIEGPEDTK-GKHQSITVTVDSEISITKE-WDD 115
Query: 118 LALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYE 177
+D L +A D V M E A I L+ ++ T + G G
Sbjct: 116 QHIDLLKEATDEKYVTVYTAVAMDEDEAQIFLI---HPYGIQQVGTVYSGRSGKYAEGNY 172
Query: 178 SALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSR 237
S + +F+ ++ A LK N +I PGF +D+F R+ +R + I +
Sbjct: 173 SEAS-YFDQIVNA-LK----NYSNSIIILGPGFARDRFARY----CAQRGVNVIGSFPAN 222
Query: 238 IILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHV 297
T SG ++ E + + + ++ + + A++ + + +F + D YG
Sbjct: 223 ----RTDSG---AVYEFITSADGAKLLSNERIARDKEIVDEFLVAVKKDM--GVYGRDQT 273
Query: 298 EVAHERMAVQTLLITDDLFR 317
E A + A+ L+ITD++FR
Sbjct: 274 ESALQMGALSDLIITDEMFR 293
>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 = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 81/323 (25%), Positives = 142/323 (43%), Gaps = 38/323 (11%)
Query: 1 MKILRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAER 60
M+I+ NL +N G +K+ P DDLW +I GD V A T R AS S D R
Sbjct: 1 MQIVEENLRDN-EGEIKLIPETLDDLWHLRFIIEKGDVVFATTKR------ASQSSDKLR 53
Query: 61 -------VKLKLEIKVVDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKD 113
V+L +E++ V++ + + LR+ GK + ++ +HTL I + + + K
Sbjct: 54 SDKEMVTVRLGIEVEKVEFHRFANRLRVSGKIVA---GIEESGYHTLNITVGKELSIIKK 110
Query: 114 LWDSLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAI 173
W L+ L +A + + ++ ++ ++EG A + + + +E + G
Sbjct: 111 -WKPEQLERLRRAVEDSNRPEIVMLTIEEGYAV------AGVLRQWGVEEIFEERMGYG- 162
Query: 174 AGYESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIE 233
G + +FF V A L+ DF + ++A PGF K+ F L ++ P E
Sbjct: 163 KGMGDSRKEFFGEV-AAKLESFDF---KYLIVAGPGFAKNDFLDFL------KERYP--E 210
Query: 234 NKSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYG 293
++V SS E+L V ++ + + A+E + + + R YG
Sbjct: 211 MAKNAVVVDVSSVGSRGFIEILKRRVVDKIVGEVRLAEEAEYIDRLLEGIAKGE-RVAYG 269
Query: 294 PKHVEVAHERMAVQTLLITDDLF 316
V AH A++ LL+ D+
Sbjct: 270 LDEVREAHNYRAIEVLLVADEFL 292
>pdb|1X52|A Chain A, Solution Structures Of The C-Terminal Domain Of The Human
Pelota Homolog (Cgi-17)
Length = 124
Score = 72.4 bits (176), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 34/59 (57%), Positives = 44/59 (74%)
Query: 259 NVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFR 317
V + + DTKAA EV+AL DF+ ML ++P RA YG K VE A+E MA+ TLLI+D+LFR
Sbjct: 8 TVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFR 66
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 69.3 bits (168), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 78/319 (24%), Positives = 145/319 (45%), Gaps = 55/319 (17%)
Query: 15 SVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKV--VDY 72
+VK+ DDLW + ++ D V+A T R V +++ R+ + + +KV ++
Sbjct: 32 AVKLHIESEDDLWLLHLILEKDDKVVAKTTRDV-----GLGKESRRIPMTIILKVDYTEF 86
Query: 73 DKEGSVLRIRGKNILEN--EHVKI-GAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADP 129
+ + LRI G I+E+ E I GA HT+ +++ ++ K W+ LD L + A+
Sbjct: 87 QEFTNRLRIHG--IIEDAPERFGIKGAHHTINLDIGDEIIIIKQQWNKYVLDRLKRQANK 144
Query: 130 TASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYES--ALNK----F 183
+ +A+V E L +IP + G I +S LN+
Sbjct: 145 RSRIIIALVDFDEYL------------------IAIPFEQGIKILSEKSLRPLNEEEGII 186
Query: 184 FENVLQ------AFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSR 237
+N L+ ++K D + + ++A PGF K++ + ++ I++NK +
Sbjct: 187 EQNALEIATELAEYVKQYDPDAI---LLAGPGFFKEEVSK---------KVNAILKNK-K 233
Query: 238 IILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHV 297
I + SS + L EVL + ++ D + A + ++ +L P YG + V
Sbjct: 234 IYIDSVSSATRAGLHEVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQV 293
Query: 298 EVAHERMAVQTLLITDDLF 316
+ A E AV+T+L+ +DL
Sbjct: 294 KNAIEMGAVETVLVIEDLL 312
>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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 75/317 (23%), Positives = 128/317 (40%), Gaps = 24/317 (7%)
Query: 4 LRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKL 63
+R +++N V++ P +DLW + PGD V T R V GS ERV +
Sbjct: 3 MRVEVLDNKRRIVRLRPESEEDLWLLRITLRPGDVVRKRTSRDV----PVGSGRKERVVM 58
Query: 64 KLEIKV--VDYDKEGSVLRIRGKNILENEHVKI-GAFHTLEIELHRAFVLRKDL-WDSLA 119
L I++ +++ LRI G + + + G H+ + + V+ +D W
Sbjct: 59 TLRIRLDSIEFQPFTGKLRISGIVVEGPDEFGVKGRRHSTAVSIGTWLVVERDKGWSEQE 118
Query: 120 LDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESA 179
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: 180 LNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRII 239
+ K+ + + ++ + AVIA PG K + E +R + + ++
Sbjct: 173 VEKYVDRAAKRIVEEAARHRSPIAVIAGPGQLKTS-----VAEKVQRAMPSL-----KVA 222
Query: 240 LVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEV 299
V TS G +RE L +V ++++ + L++F + Y P V
Sbjct: 223 TVDTSMGGVAGVREALRRESVTRILRELSIVEAEGVLEEFLRRIAKSRDTVAYTPGEVLA 282
Query: 300 AHERMAVQTLLITDDLF 316
AV T+L+ D L
Sbjct: 283 VARMGAVDTVLLVDTLL 299
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 48/191 (25%), Positives = 86/191 (45%), Gaps = 26/191 (13%)
Query: 135 LAVVLMQEGLAHI-LLVGRSMTITRSRIETSIPRKH---GPAIAGYE----SALNKFFEN 186
+ +++++ A I LL G + + + +E +P KH G + YE +++FF+
Sbjct: 143 IGIIIVERDQATIGLLKGARLEVLKE-LEGFVPGKHKMGGQSQRRYERIIEQMVDEFFKK 201
Query: 187 VLQA----FLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVH 242
V + + + V++ ++A PG K +F L+ +L+ I+ + +
Sbjct: 202 VGEEASNLLVPLAEKGVLKGVIVAGPGLAKQEFVEGNYLDY---RLKKILAPELVDVAYQ 258
Query: 243 TSSGYKHSLREVLDAPNVM--NMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVA 300
G K + V+ A V+ M +D V A+++F L YG K VE A
Sbjct: 259 GLQGLKEA---VMKAEKVVEAQMYRDA-----VNAMEEFKLHLAKGTGMIVYGEKDVEAA 310
Query: 301 HERMAVQTLLI 311
E AV+TLLI
Sbjct: 311 LEMGAVKTLLI 321
>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 = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 41/170 (24%), Positives = 67/170 (39%), Gaps = 28/170 (16%)
Query: 160 RIETSIPRKHGPAIAGYESALN--------------KFFENVLQAFLKHVDFNVVRCAVI 205
R +P+KHG G +SAL K E +Q F+ NV +
Sbjct: 176 RFTVDLPKKHG---RGGQSALRFARLRDEKRHNYVRKVAEGAVQHFITDDKPNVAGIVLA 232
Query: 206 ASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIK 265
S F + L +R Q R I K+ + +G+ ++ D +
Sbjct: 233 GSADFKTELGQSDLF--DQRLQSRII---KTVDVSYGGDAGFNQAIELAADT------LS 281
Query: 266 DTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 315
+ K QE + ++ FF+ ++ D + C+G A + AV+TLL DL
Sbjct: 282 NVKYVQEKKLIQRFFDEISLDSGKYCFGVVDTMNALQEGAVETLLCFADL 331
>pdb|3IR9|A Chain A, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei.
pdb|3IR9|B Chain B, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei
Length = 166
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 248 KHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQ 307
+ L E+++A ++D + + A++DFF L D + YG V E +V
Sbjct: 7 ESGLSELVNAAG--EKLQDLELXGQKNAVRDFFKELIADSGKVAYGESQVRANLEINSVD 64
Query: 308 TLLITDDL 315
LL+++DL
Sbjct: 65 VLLLSEDL 72
>pdb|4DB5|A Chain A, Crystal Structure Of Rabbit Gitrl
Length = 125
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 258 PNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 309
P+ +N I D K L + + DPT + P V++ + A+QTL
Sbjct: 24 PSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTL 75
>pdb|1RWS|A Chain A, Backbone Solution Structure Of Mixed AlphaBETA PROTEIN
PF1061
pdb|1SF0|A Chain A, Backbone Solution Structure Of Mixed AlphaBETA PROTEIN
PF1061
Length = 77
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 26/39 (66%)
Query: 59 ERVKLKLEIKVVDYDKEGSVLRIRGKNILENEHVKIGAF 97
E +K++ ++ V ++ E ++ ++ GK +LE++ VK G F
Sbjct: 29 EGMKVRDILRAVGFNTESAIAKVNGKVVLEDDEVKDGDF 67
>pdb|3AQ8|A Chain A, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Q46e Mutant, Fe(Iii) Form
pdb|3AQ8|B Chain B, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Q46e Mutant, Fe(Iii) Form
Length = 121
Score = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 252 REVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 309
++VL V + K+T E + DF ML P Y K++ AH+ M +Q L
Sbjct: 26 KKVLADERVKHFFKNTDMDHETKQQTDFLTMLLGGPNH--YKGKNMTEAHKGMNLQNL 81
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 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,046,602
Number of Sequences: 62578
Number of extensions: 338442
Number of successful extensions: 851
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 822
Number of HSP's gapped (non-prelim): 17
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
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)