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= 013725
(437 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3E1Y|A Chain A, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|B Chain B, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|C Chain C, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|D Chain D, Crystal Structure Of Human Erf1ERF3 COMPLEX
Length = 451
Score = 665 bits (1716), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 322/419 (76%), Positives = 360/419 (85%), Gaps = 2/419 (0%)
Query: 3 DGQETDKNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIK 62
D D+N+EIWKIKKLIK+LE+ARGNGTSMISLI+PP+DQISRV KML DEFGTASNIK
Sbjct: 18 DPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIK 77
Query: 63 SRVNRQSVLAAITSAQQRLKLYNKVPPNGLVLYTGTVVTDDGKEKKVTIDFEPFKPINAS 122
SRVNR SVL AITS QQRLKLYNKVPPNGLV+Y GT+VT++GKEKKV IDFEPFKPIN S
Sbjct: 78 SRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTS 137
Query: 123 LYLCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFTVDLPKKHGRG 182
LYLCDNKFHTEAL LL D KFGFIV+DG+G LFGTL GNTREVLHKFTVDLPKKHGRG
Sbjct: 138 LYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRG 197
Query: 183 GQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDM 242
GQSALRFARLRMEKRHNYVRK AE A Q FI + + NV+GL+LAGSADFKTELSQSDM
Sbjct: 198 GQSALRFARLRMEKRHNYVRKVAETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDM 255
Query: 243 FDPRLQAKILNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKY 302
FD RLQ+K+L +VD+SYGGENGFNQAIELS E+LSNVKFIQEK+LIG+YF+EISQDTGKY
Sbjct: 256 FDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKY 315
Query: 303 VFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAA 362
FGV+DTLKALE+GAVEILIV+ENLDI RYVL T E I +L +QE D+S+F D
Sbjct: 316 CFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKE 375
Query: 363 TSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDIR 421
T E E+ E LLEWFAN YK+FG TLE VT+KSQEGSQF +GFGGIGGILRY++D +
Sbjct: 376 TGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQ 434
>pdb|1DT9|A Chain A, The Crystal Structure Of Human Eukaryotic Release Factor
Erf1-Mechanism Of Stop Codon Recognition And
Peptidyl-Trna Hydrolysis
Length = 437
Score = 664 bits (1713), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 322/419 (76%), Positives = 360/419 (85%), Gaps = 2/419 (0%)
Query: 3 DGQETDKNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIK 62
D D+N+EIWKIKKLIK+LE+ARGNGTSMISLI+PP+DQISRV KML DEFGTASNIK
Sbjct: 4 DPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIK 63
Query: 63 SRVNRQSVLAAITSAQQRLKLYNKVPPNGLVLYTGTVVTDDGKEKKVTIDFEPFKPINAS 122
SRVNR SVL AITS QQRLKLYNKVPPNGLV+Y GT+VT++GKEKKV IDFEPFKPIN S
Sbjct: 64 SRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTS 123
Query: 123 LYLCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFTVDLPKKHGRG 182
LYLCDNKFHTEAL LL D KFGFIV+DG+G LFGTL GNTREVLHKFTVDLPKKHGRG
Sbjct: 124 LYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRG 183
Query: 183 GQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDM 242
GQSALRFARLRMEKRHNYVRK AE A Q FI + + NV+GL+LAGSADFKTELSQSDM
Sbjct: 184 GQSALRFARLRMEKRHNYVRKVAETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDM 241
Query: 243 FDPRLQAKILNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKY 302
FD RLQ+K+L +VD+SYGGENGFNQAIELS E+LSNVKFIQEK+LIG+YF+EISQDTGKY
Sbjct: 242 FDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKY 301
Query: 303 VFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAA 362
FGV+DTLKALE+GAVEILIV+ENLDI RYVL T E I +L +QE D+S+F D
Sbjct: 302 CFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKE 361
Query: 363 TSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDIR 421
T E E+ E LLEWFAN YK+FG TLE VT+KSQEGSQF +GFGGIGGILRY++D +
Sbjct: 362 TGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQ 420
>pdb|3J2K|6 Chain 6, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated
Termination Complex
Length = 411
Score = 662 bits (1707), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 320/413 (77%), Positives = 358/413 (86%), Gaps = 2/413 (0%)
Query: 9 KNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIKSRVNRQ 68
+N+EIWKIKKLIK+LE+ARGNGTSMISLI+PP+DQISRV KML DEFGTASNIKSRVNR
Sbjct: 1 RNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRL 60
Query: 69 SVLAAITSAQQRLKLYNKVPPNGLVLYTGTVVTDDGKEKKVTIDFEPFKPINASLYLCDN 128
SVL AITS QQRLKLYNKVPPNGLV+Y GT+VT++GKEKKV IDFEPFKPIN SLYLCDN
Sbjct: 61 SVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDN 120
Query: 129 KFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFTVDLPKKHGRGGQSALR 188
KFHTEAL LL D KFGFIV+DG+G LFGTL GNTREVLHKFTVDLPKKHGRGGQSALR
Sbjct: 121 KFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALR 180
Query: 189 FARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQ 248
FARLRMEKRHNYVRK AE A Q FI + + NV+GL+LAGSADFKTELSQSDMFD RLQ
Sbjct: 181 FARLRMEKRHNYVRKVAETAVQLFI--SGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQ 238
Query: 249 AKILNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDD 308
+K+L +VD+SYGGENGFNQAIELS E+LSNVKFIQEK+LIG+YF+EISQDTGKY FGV+D
Sbjct: 239 SKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGVED 298
Query: 309 TLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELE 368
TLKALE+GAVEILIV+ENLDI RYVL T E I +L +QE D+S+F D T E E
Sbjct: 299 TLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHE 358
Query: 369 VQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDIR 421
+ E LLEWFAN YK+FG TLE VT+KSQEGSQF +GFGGIGGILRY++D +
Sbjct: 359 LIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQ 411
>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 = 553 bits (1425), Expect = e-158, Method: Compositional matrix adjust.
Identities = 272/436 (62%), Positives = 337/436 (77%), Gaps = 8/436 (1%)
Query: 5 QETDKNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIKSR 64
+ +K IEIWKI++L+K L + GNGTSMI+LI+PP +QISR + ML +E+GTASNIKSR
Sbjct: 11 ETAEKAIEIWKIRRLVKQLINCHGNGTSMITLIIPPGEQISRYSNMLAEEYGTASNIKSR 70
Query: 65 VNRQSVLAAITSAQQRLKLYNKVPPNGLVLYTGTVVTDDGKEKKVTIDFEPFKPINASLY 124
VNR SVL+AITS ++RLKLYNKVP NGLV+Y G V+ + K +K+ IDFEPFKPIN S Y
Sbjct: 71 VNRLSVLSAITSTRERLKLYNKVPDNGLVIYCGEVIMEGNKTRKLNIDFEPFKPINTSQY 130
Query: 125 LCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFTVDLPKKHGRGGQ 184
LCDNKFHTEAL ELLESD +FGFIVMDG+ TL+G +SG+ REVL +FTVDLPKKHGRGGQ
Sbjct: 131 LCDNKFHTEALAELLESDQRFGFIVMDGHQTLYGVVSGSAREVLQRFTVDLPKKHGRGGQ 190
Query: 185 SALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFD 244
SALRFARLR EKRHNYVRK AE A Q FI +PNV+G++LAGSADFKTEL QSD+FD
Sbjct: 191 SALRFARLRDEKRHNYVRKVAEGAVQHFI--TDDKPNVAGIVLAGSADFKTELGQSDLFD 248
Query: 245 PRLQAKILNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVF 304
RLQ++I+ VDVSYGG+ GFNQAIEL+A+ LSNVK++QEK+LI ++F+EIS D+GKY F
Sbjct: 249 QRLQSRIIKTVDVSYGGDAGFNQAIELAADTLSNVKYVQEKKLIQRFFDEISLDSGKYCF 308
Query: 305 GVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSN---FRDA 361
GV DT+ AL+ GAVE L+ + +LD+ RY KNS G VI ++ ++QE S D
Sbjct: 309 GVVDTMNALQEGAVETLLCFADLDMIRYEFKNSE-GNPVITYMTKEQEEKDSTNSFLLDK 367
Query: 362 ATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDIR 421
T AE+E+ L EW A YK +G LEFV+++SQEG QF +GFGGIG ++RYQLD+
Sbjct: 368 DTGAEMELVSSMLLSEWLAEHYKDYGANLEFVSDRSQEGMQFVKGFGGIGAVMRYQLDLS 427
Query: 422 SYDELSDDGGVYEDSD 437
D SD+ Y DSD
Sbjct: 428 MLDPESDE--FYSDSD 441
>pdb|2LLX|A Chain A, Solution Structure Of The N-Terminal Domain Of Human
Polypeptide Chain Release Factor Erf1
Length = 150
Score = 242 bits (618), Expect = 3e-64, Method: Compositional matrix adjust.
Identities = 113/137 (82%), Positives = 123/137 (89%)
Query: 3 DGQETDKNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIK 62
D D+N+EIWKIKKLIK+LE+ARGNGTSMISLI+PP+DQISRV KML DEFGTASNIK
Sbjct: 4 DPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIK 63
Query: 63 SRVNRQSVLAAITSAQQRLKLYNKVPPNGLVLYTGTVVTDDGKEKKVTIDFEPFKPINAS 122
SRVNR SVL AITS QQRLKLYNKVPPNGLV+Y GT+VT++GKEKKV IDFEPFKPIN S
Sbjct: 64 SRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTS 123
Query: 123 LYLCDNKFHTEALNELL 139
LYLCDNKFHTEAL LL
Sbjct: 124 LYLCDNKFHTEALTALL 140
>pdb|2LGT|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Qfm(Y)f
Length = 144
Score = 236 bits (603), Expect = 1e-62, Method: Compositional matrix adjust.
Identities = 110/137 (80%), Positives = 121/137 (88%)
Query: 3 DGQETDKNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIK 62
D D+N+EIWKIKKLIK+LE+ARGNGTSMISLI+PP+DQISRV KML DEFGTASNIK
Sbjct: 4 DPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIK 63
Query: 63 SRVNRQSVLAAITSAQQRLKLYNKVPPNGLVLYTGTVVTDDGKEKKVTIDFEPFKPINAS 122
SRVNR SVL AITS QQRLKLYNKVPPNGLV+Y GT+VT++GKEKKV IDFEPFKPIN
Sbjct: 64 SRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINQF 123
Query: 123 LYLCDNKFHTEALNELL 139
+Y CDNKFHTEAL LL
Sbjct: 124 MYFCDNKFHTEALTALL 140
>pdb|2HST|A Chain A, Solution Structure Of The Middle Domain Of Human
Eukaryotic Translation Termination Factor Erf1
Length = 143
Score = 229 bits (585), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 110/138 (79%), Positives = 121/138 (87%), Gaps = 2/138 (1%)
Query: 139 LESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRH 198
L D KFGFIV+DG+G LFGTL GNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRH
Sbjct: 1 LSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRH 60
Query: 199 NYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQAKILNVVDVS 258
NYVRK AE A Q FI+ + NV+GL+LAGSADFKTELSQSDMFD RLQ+K+L +VD+S
Sbjct: 61 NYVRKVAETAVQLFISG--DKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDIS 118
Query: 259 YGGENGFNQAIELSAEIL 276
YGGENGFNQAIELS E+L
Sbjct: 119 YGGENGFNQAIELSTEVL 136
>pdb|2KTU|A Chain A, Human Erf1 C-Domain, "closed" Conformer
pdb|2KTV|A Chain A, Human Erf1 C-Domain, "open" Conformer
Length = 170
Score = 201 bits (512), Expect = 6e-52, Method: Compositional matrix adjust.
Identities = 100/145 (68%), Positives = 117/145 (80%)
Query: 277 SNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKN 336
SNVKFIQEK+LIG+YF+EISQDTGKY FGV+DTLKALE+GAVEILIV+ENLDI RYVL
Sbjct: 1 SNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHC 60
Query: 337 SATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNK 396
T E I +L +QE D+S+F D T E E+ E LLEWFAN YK+FG TLE VT+K
Sbjct: 61 QGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDK 120
Query: 397 SQEGSQFCRGFGGIGGILRYQLDIR 421
SQEGSQF +GFGGIGGILRY++D +
Sbjct: 121 SQEGSQFVKGFGGIGGILRYRVDFQ 145
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 157 bits (397), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 118/422 (27%), Positives = 197/422 (46%), Gaps = 56/422 (13%)
Query: 1 MSDGQ-ETDKNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTAS 59
MS G+ E I ++ +L+K L+ T ++SL +PP +S V +L E+
Sbjct: 1 MSQGRLEERLTISKRELARLLKELKKWSAPATVLLSLYIPPGRPLSDVMTLLRQEYSITD 60
Query: 60 NIKSRVNRQSVLAAITSAQQRLKLYNKVPPNGLVLYTGTVVTDDGKEKKVTIDFEPFKPI 119
NIK + RQ+V A+++A RL++ PPNGLVL+ G D K F P +PI
Sbjct: 61 NIKLKRTRQAVKRALSAAMDRLQMLTSTPPNGLVLFCG---EDMSTGKFECFMFSPPEPI 117
Query: 120 NASLYLCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKFTVDLPKKH 179
Y D +F T+ L +++E ++ G I+++ + G L G EVL + +P KH
Sbjct: 118 RVFYYRTDKRFITDFLEDMVEDNNAIGIIIVERDQATIGLLKGARLEVLKELEGFVPGKH 177
Query: 180 GRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQ 239
GGQS R+ R+ + + +K E A+ + P + + G+I+AG K E +
Sbjct: 178 KMGGQSQRRYERIIEQMVDEFFKKVGEEASNLLV-PLAEKGVLKGVIVAGPGLAKQEFVE 236
Query: 240 SDMFDPRLQAKIL--NVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQ 297
+ D RL+ KIL +VDV+Y G G +A+ + +++ + + ++ +++
Sbjct: 237 GNYLDYRLK-KILAPELVDVAYQGLQGLKEAVMKAEKVVEAQMYRDAVNAMEEFKLHLAK 295
Query: 298 DTGKYVFGVDDTLKALELGAVEILIVWENL-DINRYVLKNSATGEIVIKHLNRDQEADQS 356
TG V+G D ALE+GAV+ L++ E+ D+ +V K ++G VI
Sbjct: 296 GTGMIVYGEKDVEAALEMGAVKTLLIHESREDLEEWVEKAKSSGAQVIV----------- 344
Query: 357 NFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRY 416
V E + EW F + FGG+ GILR+
Sbjct: 345 ------------VPESLAEAEW------------------------FLKTFGGLAGILRF 368
Query: 417 QL 418
++
Sbjct: 369 RI 370
>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 = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 43/164 (26%), Positives = 78/164 (47%), Gaps = 1/164 (0%)
Query: 258 SYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGA 317
+Y E+G ++ + + E L +++ +K + +F+E+ D+GK +G LE+ +
Sbjct: 3 AYTDESGLSELVNAAGEKLQDLELXGQKNAVRDFFKELIADSGKVAYGESQVRANLEINS 62
Query: 318 VEILIVWENLDINRYVLKNSATG-EIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLL 376
V++L++ E+L R K S G E + E + + LEV + T ++
Sbjct: 63 VDVLLLSEDLRAERVTTKCSVCGYENKWTRRWKPGEPAPAAGNCPKCGSSLEVTDVTDIV 122
Query: 377 EWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDI 420
+ F+ + + FV+ EGSQ FGGI ILRY +
Sbjct: 123 DEFSELADKSNAKVVFVSTDFDEGSQLXNAFGGIAAILRYNTGV 166
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 37/52 (71%)
Query: 276 LSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENL 327
L++ K++QE R++ K+++ +++D K +G + LKA ELGA+ L++ ++L
Sbjct: 266 LADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSL 317
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 32/148 (21%), Positives = 59/148 (39%), Gaps = 46/148 (31%)
Query: 273 AEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLDINRY 332
A++LSN + ++K ++ ++ + +D G V+G D T AL++GA+ LI+ + +
Sbjct: 239 AKLLSNERIARDKEIVDEFLVAVKKDMG--VYGRDQTESALQMGALSDLIITDEM----- 291
Query: 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEF 392
FR L + + G +
Sbjct: 292 -------------------------FRTEDGRRSLSIAQTV-------------GTRIHI 313
Query: 393 VTNKSQEGSQFCRGFGGIGGILRYQLDI 420
V+ + G Q + FGG GILRY++ +
Sbjct: 314 VSVSNDPG-QIVKKFGGFAGILRYRVQL 340
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 64/124 (51%), Gaps = 6/124 (4%)
Query: 206 ELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQAKILNVVDVSYGGENGF 265
E+AT+ + Q + ++LAG FK E+S+ + L+ K + + VS G
Sbjct: 192 EIATE--LAEYVKQYDPDAILLAGPGFFKEEVSKK--VNAILKNKKIYIDSVSSATRAGL 247
Query: 266 NQAI--ELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIV 323
++ + ++ +I+++ + + + K E +++ +G++ A+E+GAVE ++V
Sbjct: 248 HEVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLV 307
Query: 324 WENL 327
E+L
Sbjct: 308 IEDL 311
>pdb|3KYH|A Chain A, Saccharomyces Cerevisiae Cet1-Ceg1 Capping Apparatus
pdb|3KYH|B Chain B, Saccharomyces Cerevisiae Cet1-Ceg1 Capping Apparatus
Length = 310
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 15/94 (15%)
Query: 332 YVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKT-SLLEWFANEYKQFGCTL 390
Y+ +S T + K N +Q S R + T+ E+E++ T +LL F N
Sbjct: 222 YIHNDSCTRIDITKVENHNQ---NSKSRQSETTHEVELEINTPALLNAFDN--------- 269
Query: 391 EFVTNKSQEGSQFCRGFGGIGGILRYQLDIRSYD 424
+TN S+E + R F G I+R +L SY+
Sbjct: 270 --ITNDSKEYASLIRTFLNNGTIIRRKLSSLSYE 301
>pdb|1D8H|A Chain A, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With Sulfate And Manganese Ions.
pdb|1D8H|B Chain B, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With Sulfate And Manganese Ions.
pdb|1D8H|C Chain C, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With Sulfate And Manganese Ions.
pdb|1D8I|A Chain A, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With A Sulfate Ion.
pdb|1D8I|B Chain B, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With A Sulfate Ion.
pdb|1D8I|C Chain C, X-Ray Crystal Structure Of Yeast Rna Triphosphatase In
Complex With A Sulfate Ion
Length = 311
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 15/94 (15%)
Query: 332 YVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKT-SLLEWFANEYKQFGCTL 390
Y+ +S T + K N +Q S R + T+ E+E++ T +LL F N
Sbjct: 223 YIHNDSCTRIDITKVENHNQ---NSKSRQSETTHEVELEINTPALLNAFDN--------- 270
Query: 391 EFVTNKSQEGSQFCRGFGGIGGILRYQLDIRSYD 424
+TN S+E + R F G I+R +L SY+
Sbjct: 271 --ITNDSKEYASLIRTFLNNGTIIRRKLSSLSYE 302
>pdb|2BO1|A Chain A, Crystal Structure Of A Hybrid Ribosomal Protein L30e With
Surface Residues From T. Celer, And Core Residues From
Yeast
Length = 101
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 298 DTGKYVFGVDDTLKALELGAVEILIVWENLDINR 331
D+GKY G T+++L++G +++I+ N +R
Sbjct: 13 DSGKYTLGYRKTVQSLKMGGSKLIIIARNTRPDR 46
>pdb|2E1Q|A Chain A, Crystal Structure Of Human Xanthine Oxidoreductase Mutant,
Glu803val
pdb|2E1Q|B Chain B, Crystal Structure Of Human Xanthine Oxidoreductase Mutant,
Glu803val
pdb|2E1Q|C Chain C, Crystal Structure Of Human Xanthine Oxidoreductase Mutant,
Glu803val
pdb|2E1Q|D Chain D, Crystal Structure Of Human Xanthine Oxidoreductase Mutant,
Glu803val
Length = 1333
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 57 TASNIKSRVNRQSVLAAITSAQQRLKLYNKVPPNG 91
TA+++ + +N Q+V AA + +RL+ Y K P+G
Sbjct: 1078 TAASVSADLNGQAVYAACQTILKRLEPYKKKNPSG 1112
>pdb|2CKJ|A Chain A, Human Milk Xanthine Oxidoreductase
pdb|2CKJ|B Chain B, Human Milk Xanthine Oxidoreductase
pdb|2CKJ|C Chain C, Human Milk Xanthine Oxidoreductase
pdb|2CKJ|D Chain D, Human Milk Xanthine Oxidoreductase
Length = 1333
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 57 TASNIKSRVNRQSVLAAITSAQQRLKLYNKVPPNG 91
TA+++ + +N Q+V AA + +RL+ Y K P+G
Sbjct: 1078 TAASVSADLNGQAVYAACQTILKRLEPYKKKNPSG 1112
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
0.316 0.135 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,761,967
Number of Sequences: 62578
Number of extensions: 522963
Number of successful extensions: 1502
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1473
Number of HSP's gapped (non-prelim): 34
length of query: 437
length of database: 14,973,337
effective HSP length: 102
effective length of query: 335
effective length of database: 8,590,381
effective search space: 2877777635
effective search space used: 2877777635
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)