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= 021563
(311 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 = 234 bits (596), Expect = 7e-62, Method: Compositional matrix adjust.
Identities = 111/302 (36%), Positives = 185/302 (61%)
Query: 4 MEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXXXXXXXXXXXDYDKE 63
M P + +D+W YN++ GD + A TVR+V++ A+GS R D+D +
Sbjct: 18 MCPEEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGSRVVMKLRILVENMDFDTK 77
Query: 64 GSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADL 123
+ L I+G+ + VK+G++HTL++ELHR F L K+ WD+ ALD + A +P+ +A++
Sbjct: 78 AAQLHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAFALDRVDAACNPSRNAEI 137
Query: 124 AVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHV 183
V++ EGLA+I L+ MTI R RI+ IPRK + Y+ L+KF+++V Q+
Sbjct: 138 GAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQKGLDKFYDSVFQSINSEF 197
Query: 184 DFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVL 243
DF+ ++ ++ASPGF + ++ A + L+ I+++K++ +++H+S+G+ HSL E+L
Sbjct: 198 DFDKLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKFVILHSSTGHIHSLNEIL 257
Query: 244 DAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 303
P V + + DTK QE++ L F++++ D +A YGP HV A E A+ LLI+D L
Sbjct: 258 KDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSL 317
Query: 304 FR 305
FR
Sbjct: 318 FR 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 = 132 bits (333), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 76/302 (25%), Positives = 144/302 (47%), Gaps = 8/302 (2%)
Query: 6 PVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXXXXXXXXXXXDYDKEGS 65
P D +DL+ Y ++ D + + +K ++ + D+D +
Sbjct: 22 PEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKKSTDLVKLKIKVISEDFDMKDE 79
Query: 66 VLRIRGKNILE-----NEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTAS 120
L+ +G + + N + +G + + ++ F + K ++ L++A +
Sbjct: 80 YLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFMQKLLNEACNIEYK 139
Query: 121 ADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPA-IAGYESALNKFFENVLQAF 179
+D A V++QEG+AH+ LV S TI + +IE S+P+K + ++ KF++ + A
Sbjct: 140 SDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLKFDEKTEKFYKAIYSAM 199
Query: 180 LKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSL 239
K ++F+ ++ ++ SPGF + AE + I++NK + H S+GY +
Sbjct: 200 KKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCSTGYLQGI 259
Query: 240 REVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLI 299
EVL P + ++DTK ++E+ + +F L D +A YG K V A E A+ LL+
Sbjct: 260 NEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLL 319
Query: 300 TD 301
TD
Sbjct: 320 TD 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 = 131 bits (329), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 76/302 (25%), Positives = 142/302 (47%), Gaps = 8/302 (2%)
Query: 6 PVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXXXXXXXXXXXDYDKEGS 65
P D +DL+ Y ++ D + + +K ++ + D+D +
Sbjct: 22 PEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKKSTDLVKLKIKVISEDFDXKDE 79
Query: 66 VLRIRGKNILE-----NEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTAS 120
L+ +G + + N + +G + + ++ F + K ++ L++A +
Sbjct: 80 YLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFXQKLLNEACNIEYK 139
Query: 121 ADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPA-IAGYESALNKFFENVLQAF 179
+D A V++QEG+AH+ LV S TI + +IE S P+K + ++ KF++ + A
Sbjct: 140 SDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSXPKKKRTTDVLKFDEKTEKFYKAIYSAX 199
Query: 180 LKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSL 239
K ++F+ ++ ++ SPGF + AE + I++NK + H S+GY +
Sbjct: 200 KKDLNFDKLKTIILCSPGFYAKILXDKIFQYAEEEHNKKILDNKGXFFIAHCSTGYLQGI 259
Query: 240 REVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLI 299
EVL P + ++DTK ++E+ +F L D +A YG K V A E A+ LL+
Sbjct: 260 NEVLKNPLYASKLQDTKYSKEIXVXDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLL 319
Query: 300 TD 301
TD
Sbjct: 320 TD 321
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 92.4 bits (228), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 81/302 (26%), Positives = 142/302 (47%), Gaps = 20/302 (6%)
Query: 10 DDLWFAYNLIAPGDSVMAVTVRKVLRQMAS-GSRDAERXXXXXXXXXXXXDYDKEGSVLR 68
DDLW Y++I PGD V A T+RK ++ S + E ++ K + +R
Sbjct: 21 DDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVEVIPVFLGVQAEKINFHKFANQVR 80
Query: 69 IRGKNILEN-EHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVL 127
+ G + + E V +G +HT+ IE ++K W ++ L +A + A + +V+
Sbjct: 81 VTGPIVYASREDVPLGKYHTIAIEQGTVVTIQKPRWKEHHIERLKEAVAASKRARVMIVV 140
Query: 128 MQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGY----ESALNKFFENVLQAFLKHV 183
+ +G A + LV R + I SI +H Y ES KFF +V + + +
Sbjct: 141 IDDGEADMALV-REYGV---EILNSI--RHNLGGKRYNTDRESEEMKFFHDVAKTMEEVM 194
Query: 184 DFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVL 243
V A++A PGF K+ F++ L ++ P E ++++ TS + + EV+
Sbjct: 195 KRENVEKAIVAGPGFVKEDFYKFL------KEKYP--ELAKKVVIEDTSVTGRTGIYEVI 246
Query: 244 DAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 303
V + ++ + A+EVQ ++ + + YG K VE A AV+TLL+ D+L
Sbjct: 247 KRGVVDRVYQENRVAKEVQLVEKVLENIARNNGLVAYGLKEVEEAVNYGAVETLLVLDEL 306
Query: 304 FR 305
+
Sbjct: 307 LK 308
>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: 247 NVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFR 305
V + + DTKAA EV+AL DF+ ML ++P RA YG K VE A+E MA+ TLLI+D+LFR
Sbjct: 8 TVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFR 66
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 73/297 (24%), Positives = 127/297 (42%), Gaps = 25/297 (8%)
Query: 10 DDLWFAYNLIAPGDSVMAVTVRKVLRQM-ASGSRDAERXXXXXXXXXXXXDYDKEGSVLR 68
DDLW+ N+++ GD V A+T R+V SR+ ER ++ + LR
Sbjct: 21 DDLWYLRNILSEGDEVSAITFRRVEESADVQRSRERERIPITIRLKVEKIEFQDFDNRLR 80
Query: 69 IRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLM 128
I G I E K G ++ + + + K+ WD +D L +A D V M
Sbjct: 81 ILGTVIEGPEDTK-GKHQSITVTVDSEISITKE-WDDQHIDLLKEATDEKYVTVYTAVAM 138
Query: 129 QEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVDFNVV 188
E A I L+ ++ T + G G S + +F+ ++ A LK N
Sbjct: 139 DEDEAQIFLI---HPYGIQQVGTVYSGRSGKYAEGNYSEAS-YFDQIVNA-LK----NYS 189
Query: 189 RCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNV 248
+I PGF +D+F R+ +R + I + T SG ++ E + + +
Sbjct: 190 NSIIILGPGFARDRFARY----CAQRGVNVIGSFPAN----RTDSG---AVYEFITSADG 238
Query: 249 MNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFR 305
++ + + A++ + + +F + D YG E A + A+ L+ITD++FR
Sbjct: 239 AKLLSNERIARDKEIVDEFLVAVKKDM--GVYGRDQTESALQMGALSDLIITDEMFR 293
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 74/311 (23%), Positives = 135/311 (43%), Gaps = 53/311 (17%)
Query: 9 SDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXXXXXXXXXXXDYDKEGSVLR 68
DDLW + ++ D V+A T R V +++ R ++ + + LR
Sbjct: 40 EDDLWLLHLILEKDDKVVAKTTRDV-----GLGKESRRIPMTIILKVDYTEFQEFTNRLR 94
Query: 69 IRGKNILEN--EHVKI-GAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAV 125
I G I+E+ E I GA HT+ +++ ++ K W+ LD L + A+ + +A+
Sbjct: 95 IHG--IIEDAPERFGIKGAHHTINLDIGDEIIIIKQQWNKYVLDRLKRQANKRSRIIIAL 152
Query: 126 VLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYES--ALNK----FFENVLQ-- 177
V E L +IP + G I +S LN+ +N L+
Sbjct: 153 VDFDEYL------------------IAIPFEQGIKILSEKSLRPLNEEEGIIEQNALEIA 194
Query: 178 ----AFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSS 233
++K D + + ++A PGF K++ + ++ I++NK +I + SS
Sbjct: 195 TELAEYVKQYDPDAI---LLAGPGFFKEEVSK---------KVNAILKNK-KIYIDSVSS 241
Query: 234 GYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMA 293
+ L EVL + ++ D + A + ++ +L P YG + V+ A E A
Sbjct: 242 ATRAGLHEVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGA 301
Query: 294 VQTLLITDDLF 304
V+T+L+ +DL
Sbjct: 302 VETVLVIEDLL 312
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 70/300 (23%), Positives = 121/300 (40%), Gaps = 27/300 (9%)
Query: 6 PVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSR-DAERXXXXXXXXXXXXDYDKEG 64
P DDLW +I GD V A T R Q + R D E ++ +
Sbjct: 19 PETLDDLWHLRFIIEKGDVVFATTKRA--SQSSDKLRSDKEMVTVRLGIEVEKVEFHRFA 76
Query: 65 SVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLA 124
+ LR+ GK + E +HTL I + + + K W L+ L +A + + ++
Sbjct: 77 NRLRVSGKIVAGIEE---SGYHTLNITVGKELSIIKK-WKPEQLERLRRAVEDSNRPEIV 132
Query: 125 VVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVD 184
++ ++EG A + + + +E + G G + +FF V A L+ D
Sbjct: 133 MLTIEEGYAV------AGVLRQWGVEEIFEERMGYG-KGMGDSRKEFFGEV-AAKLESFD 184
Query: 185 FNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLD 244
F + ++A PGF K+ F L ++ P E ++V SS E+L
Sbjct: 185 F---KYLIVAGPGFAKNDFLDFL------KERYP--EMAKNAVVVDVSSVGSRGFIEILK 233
Query: 245 APNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 304
V ++ + + A+E + + + R YG V AH A++ LL+ D+
Sbjct: 234 RRVVDKIVGEVRLAEEAEYIDRLLEGIAKGE-RVAYGLDEVREAHNYRAIEVLLVADEFL 292
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 69/303 (22%), Positives = 113/303 (37%), Gaps = 22/303 (7%)
Query: 4 MEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERXXXXXXXXXXXXDYDKE 63
+ P +DLW + PGD V T R V GS ER ++
Sbjct: 17 LRPESEEDLWLLRITLRPGDVVRKRTSRDV----PVGSGRKERVVMTLRIRLDSIEFQPF 72
Query: 64 GSVLRIRGKNILENEHVKI-GAFHTLEIELHRAFVLRKDL-WDSLALDTLHQAADPTASA 121
LRI G + + + G H+ + + V+ +D W L+ L A +A
Sbjct: 73 TGKLRISGIVVEGPDEFGVKGRRHSTAVSIGTWLVVERDKGWSEQELERL-AAGRARGTA 131
Query: 122 DLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLK 181
+A V E A +L G M I +P K P+ E + K+ + + ++
Sbjct: 132 VIAAVDYDE-FALAVLAGHGMKILED-TSARLPGKDDPS---REQEVEKYVDRAAKRIVE 186
Query: 182 HVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLRE 241
+ AVIA PG K + E +R + + ++ V TS G +RE
Sbjct: 187 EAARHRSPIAVIAGPGQLKTS-----VAEKVQRAMPSL-----KVATVDTSMGGVAGVRE 236
Query: 242 VLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITD 301
L +V ++++ + L++F + Y P V AV T+L+ D
Sbjct: 237 ALRRESVTRILRELSIVEAEGVLEEFLRRIAKSRDTVAYTPGEVLAVARMGAVDTVLLVD 296
Query: 302 DLF 304
L
Sbjct: 297 TLL 299
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 48/191 (25%), Positives = 86/191 (45%), Gaps = 26/191 (13%)
Query: 123 LAVVLMQEGLAHI-LLVGRSMTITRSRIETSIPRKH---GPAIAGYE----SALNKFFEN 174
+ +++++ A I LL G + + + +E +P KH G + YE +++FF+
Sbjct: 143 IGIIIVERDQATIGLLKGARLEVLKE-LEGFVPGKHKMGGQSQRRYERIIEQMVDEFFKK 201
Query: 175 VLQA----FLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVH 230
V + + + V++ ++A PG K +F L+ +L+ I+ + +
Sbjct: 202 VGEEASNLLVPLAEKGVLKGVIVAGPGLAKQEFVEGNYLDY---RLKKILAPELVDVAYQ 258
Query: 231 TSSGYKHSLREVLDAPNVM--NMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVA 288
G K + V+ A V+ M +D V A+++F L YG K VE A
Sbjct: 259 GLQGLKEA---VMKAEKVVEAQMYRDA-----VNAMEEFKLHLAKGTGMIVYGEKDVEAA 310
Query: 289 HERMAVQTLLI 299
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 = 0.025, Method: Compositional matrix adjust.
Identities = 41/170 (24%), Positives = 67/170 (39%), Gaps = 28/170 (16%)
Query: 148 RIETSIPRKHGPAIAGYESALN--------------KFFENVLQAFLKHVDFNVVRCAVI 193
R +P+KHG G +SAL K E +Q F+ NV +
Sbjct: 176 RFTVDLPKKHG---RGGQSALRFARLRDEKRHNYVRKVAEGAVQHFITDDKPNVAGIVLA 232
Query: 194 ASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIK 253
S F + L +R Q R I K+ + +G+ ++ D +
Sbjct: 233 GSADFKTELGQSDLF--DQRLQSRII---KTVDVSYGGDAGFNQAIELAADT------LS 281
Query: 254 DTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 303
+ 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 = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 236 KHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQ 295
+ L E+++A ++D + + A++DFF L D + YG V E +V
Sbjct: 7 ESGLSELVNAAG--EKLQDLELXGQKNAVRDFFKELIADSGKVAYGESQVRANLEINSVD 64
Query: 296 TLLITDDL 303
LL+++DL
Sbjct: 65 VLLLSEDL 72
>pdb|4DB5|A Chain A, Crystal Structure Of Rabbit Gitrl
Length = 125
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 246 PNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 297
P+ +N I D K L + + DPT + P V++ + A+QTL
Sbjct: 24 PSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTL 75
>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 = 6.6, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 240 REVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 297
++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 0.135 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,295,916
Number of Sequences: 62578
Number of extensions: 293643
Number of successful extensions: 535
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 514
Number of HSP's gapped (non-prelim): 16
length of query: 311
length of database: 14,973,337
effective HSP length: 99
effective length of query: 212
effective length of database: 8,778,115
effective search space: 1860960380
effective search space used: 1860960380
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)