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= psy2395
(570 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 331 bits (849), Expect = 5e-91, Method: Compositional matrix adjust.
Identities = 161/300 (53%), Positives = 221/300 (73%)
Query: 1 MKHLMLSKLEKFSKRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINE 60
MK +++KLE +R +E+ LL + + + + RE++ L + + +++++ E
Sbjct: 1 MKPSIVAKLEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQE 60
Query: 61 DIITAKEMLNDLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTG 120
DI TA+ ML+D EMR A DE+ AK++ +E +++ L+LPKD +D+RN F+E+RAGTG
Sbjct: 61 DIETAQMMLDDPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTG 120
Query: 121 GDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFESG 180
GDE+ALF DL RMY R++E W+ EI+S S E GGYKEIIA+I G VY +LKFESG
Sbjct: 121 GDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESG 180
Query: 181 VHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKT 240
HRVQRVP TE+QGRIHTSACTVAV+PE + E ++NPADLRIDT+R+SGAGGQH+N T
Sbjct: 181 GHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVNTT 240
Query: 241 DSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMRRLLIGS 300
DSA+RITH+PTGIVV+CQ++RSQHKNKA AL +L ARI +++ ++Q A RR L+GS
Sbjct: 241 DSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGS 300
>pdb|2B64|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Subunit, Trnas, Mrna And
Release Factor Rf1 From A Crystal Structure Of The Whole
Ribosomal Complex". The Entire Crystal Structure
Contains One 70s Ribosome, Trnas, Mrna And Release
Factor Rf1 And Is Described In Remark 400.
pdb|3D5A|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5C|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3MR8|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms1.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s).
pdb|3MS0|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms0 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3mrz.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (30s) And 3ms1 (50s)
Length = 354
Score = 243 bits (619), Expect = 3e-64, Method: Compositional matrix adjust.
Identities = 129/306 (42%), Positives = 195/306 (63%), Gaps = 1/306 (0%)
Query: 5 MLSKLEKFSKRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIIT 64
ML KL++ + +EL+ LL+ EV + Y R ++ + ++ L Y+K+ ED+
Sbjct: 1 MLDKLDRLEEEYRELEALLSDPEVLKDKGRYQSLSRRYAEMGEVIGLIREYRKVLEDLEQ 60
Query: 65 AKEMLNDLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDES 124
A+ +L+D E++ A E R +E E+++ +LPKD D+R+ +EIRAGTGG+E+
Sbjct: 61 AESLLDDPELKEMAKAEREALLARKEALEKELERHLLPKDPMDERDAIVEIRAGTGGEEA 120
Query: 125 ALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFESGVHRV 184
ALF DL MY+RF+E ++ E++ +++GG+ +++ + G Y K+ESGVHRV
Sbjct: 121 ALFARDLFNMYLRFAEEMGFETEVLDSHPTDLGGFSKVVFEVRGPGAYGTFKYESGVHRV 180
Query: 185 QRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAV 244
QRVP TETQGRIHTS TVAV+P+A+E ED +N ++RID RASG GGQ +N TDSAV
Sbjct: 181 QRVPVTETQGRIHTSTATVAVLPKAEE-EDFALNMDEIRIDVMRASGPGGQGVNTTDSAV 239
Query: 245 RITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMRRLLIGSVQKK 304
R+ H+PTGI+V CQ+ RSQ KN+ AL IL +R+ + K E+ K R IG+ ++
Sbjct: 240 RVVHLPTGIMVTCQDSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTGERS 299
Query: 305 SPLNIF 310
+ +
Sbjct: 300 EKIRTY 305
>pdb|2FVO|A Chain A, Docking Of The Modified Rf1 X-ray Structure Into The Low
Resolution Cryo-em Map Of E.coli 70s Ribosome Bound With
Rf1
Length = 333
Score = 224 bits (572), Expect = 7e-59, Method: Compositional matrix adjust.
Identities = 106/212 (50%), Positives = 151/212 (71%), Gaps = 3/212 (1%)
Query: 99 LILPKDKNDKRNIFIEIRAGTGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGG 158
+L + +DK +EIR GTGG+E+ALF DL RMY R++ER W E+ +++GG
Sbjct: 78 FLLSPEASDK--AIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGG 135
Query: 159 YKEIIARIIGLNVYSKLKFESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININ 218
+E++ + G N Y LK+ESGVHRVQRVP TE+ GRIHTS TVAV+PE +E +DI I
Sbjct: 136 IREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEE-KDIEIR 194
Query: 219 PADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARI 278
P DL+I+T+RASG GGQ++NKT+SAVRITH+PTGIVV CQN+RSQ++NK AL+IL AR+
Sbjct: 195 PEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARL 254
Query: 279 KDSKLREQQSNTAKMRRLLIGSVQKKSPLNIF 310
+ +++ ++ R+ IG+ ++ + +
Sbjct: 255 YQLQKEQKEREISQKRKSQIGTGERSEKIRTY 286
>pdb|1RQ0|A Chain A, Crystal Structure Of Peptide Releasing Factor 1
pdb|1RQ0|B Chain B, Crystal Structure Of Peptide Releasing Factor 1
pdb|1RQ0|C Chain C, Crystal Structure Of Peptide Releasing Factor 1
Length = 342
Score = 224 bits (572), Expect = 8e-59, Method: Compositional matrix adjust.
Identities = 106/212 (50%), Positives = 151/212 (71%), Gaps = 3/212 (1%)
Query: 99 LILPKDKNDKRNIFIEIRAGTGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGG 158
+L + +DK +EIR GTGG+E+ALF DL RMY R++ER W E+ +++GG
Sbjct: 78 FLLSPEASDK--AIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGG 135
Query: 159 YKEIIARIIGLNVYSKLKFESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININ 218
+E++ + G N Y LK+ESGVHRVQRVP TE+ GRIHTS TVAV+PE +E +DI I
Sbjct: 136 IREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEE-KDIEIR 194
Query: 219 PADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARI 278
P DL+I+T+RASG GGQ++NKT+SAVRITH+PTGIVV CQN+RSQ++NK AL+IL AR+
Sbjct: 195 PEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARL 254
Query: 279 KDSKLREQQSNTAKMRRLLIGSVQKKSPLNIF 310
+ +++ ++ R+ IG+ ++ + +
Sbjct: 255 YQLQKEQKEREISQKRKSQIGTGERSEKIRTY 286
>pdb|1ZBT|A Chain A, Crystal Structure Of Peptide Chain Release Factor 1 (rf-1)
(smu.1085) From Streptococcus Mutans At 2.34 A
Resolution
Length = 371
Score = 222 bits (566), Expect = 4e-58, Method: Compositional matrix adjust.
Identities = 126/313 (40%), Positives = 187/313 (59%), Gaps = 11/313 (3%)
Query: 5 MLSKLEKFSKRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIIT 64
+ +L+ R +EL LL+ +V ++ K + + RE + V +Y YK++ ++I
Sbjct: 15 IYDQLQAVEDRYEELGELLSDPDVVSDTKRFXELSREEANSRETVAVYREYKQVVQNIAD 74
Query: 65 AKEMLNDLE-------MRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRA 117
A+E + D L +AK+ + E +++ L+LPKD ND +NI +EIR
Sbjct: 75 AQEXIKDASGDPELEEXAKEELKNSKVAKE---EYEEKLRFLLLPKDPNDDKNIILEIRG 131
Query: 118 GTGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKF 177
GGDE+ALF DLL Y +++E WKFE+ S + +GG KE++A + G +VYSKLK+
Sbjct: 132 AAGGDEAALFAGDLLNXYQKYAENQGWKFEVXEASANGVGGLKEVVAXVSGQSVYSKLKY 191
Query: 178 ESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHI 237
ESG HRVQRVP TE+QGR+HTS TV V PE E + I+P DLR+D Y ASGAGGQ++
Sbjct: 192 ESGAHRVQRVPVTESQGRVHTSTATVLVXPEV-EEVEYEIDPKDLRVDIYHASGAGGQNV 250
Query: 238 NKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMRRLL 297
NK +AVRI H+PT I V+ Q +R+Q KN+ A KI+ AR+ D + Q R+
Sbjct: 251 NKVATAVRIIHLPTNIKVEXQEERTQQKNRDKAXKIIRARVADHFAQIAQDEQDAERKST 310
Query: 298 IGSVQKKSPLNIF 310
+G+ + + +
Sbjct: 311 VGTGDRSERIRTY 323
>pdb|1MI6|A Chain A, Docking Of The Modified Rf2 X-Ray Structure Into The Low
Resolution Cryo-Em Map Of Rf2 E.Coli 70s Ribosome
Length = 365
Score = 206 bits (524), Expect = 3e-53, Method: Compositional matrix adjust.
Identities = 114/283 (40%), Positives = 177/283 (62%), Gaps = 7/283 (2%)
Query: 14 KRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEML---N 70
+RL+E++ L Q +V N + +E S L +V+ + K+ ED+ E+ +
Sbjct: 32 ERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEAD 91
Query: 71 DLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVND 130
D E N A+ E++ ++++ +LE +++ + D + +++I+AG+GG E+ + +
Sbjct: 92 DEETFNEAVAELDALEEKL--AQLEFRRMF--SGEYDSADCYLDIQAGSGGTEAQDWASM 147
Query: 131 LLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFESGVHRVQRVPKT 190
L RMY+R++E +K EII S E+ G K + +I G Y L+ E+GVHR+ R
Sbjct: 148 LERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPF 207
Query: 191 ETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIP 250
++ GR HTS + V PE D+ DI INPADLRID YRASGAGGQH+N+T+SAVRITHIP
Sbjct: 208 DSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIP 267
Query: 251 TGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKM 293
TGIV QCQNDRSQHKNK A+K + A++ + +++++ + M
Sbjct: 268 TGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAM 310
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 204 bits (519), Expect = 1e-52, Method: Compositional matrix adjust.
Identities = 113/283 (39%), Positives = 176/283 (62%), Gaps = 7/283 (2%)
Query: 14 KRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEML---N 70
+RL+E++ L Q +V N + +E S L +V+ + K+ ED+ E+ +
Sbjct: 32 ERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEAD 91
Query: 71 DLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVND 130
D E N A+ E++ ++++ +LE +++ + D + +++I+AG+GG E+ + +
Sbjct: 92 DEETFNEAVAELDALEEKL--AQLEFRRMF--SGEYDSADCYLDIQAGSGGTEAQDWASM 147
Query: 131 LLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFESGVHRVQRVPKT 190
L RMY+R++E +K EII S E+ G K + +I G Y L+ E+GVHR+ R
Sbjct: 148 LERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPF 207
Query: 191 ETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIP 250
++ GR HTS + V PE D+ DI INPADLRID YR SGAGGQH+N+T+SAVRITHIP
Sbjct: 208 DSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIP 267
Query: 251 TGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKM 293
TGIV QCQNDRSQHKNK A+K + A++ + +++++ + M
Sbjct: 268 TGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNAEKQAM 310
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 199 bits (505), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 112/268 (41%), Positives = 165/268 (61%), Gaps = 7/268 (2%)
Query: 14 KRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEML---N 70
+RL+E++ L Q +V N + +E S L +V+ + K+ ED+ E+ +
Sbjct: 32 ERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQXKQGLEDVSGLLELAVEAD 91
Query: 71 DLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVND 130
D E N A+ E++ ++++ +LE ++ + D + +++I+AG+GG E+ + +
Sbjct: 92 DEETFNEAVAELDALEEKL--AQLEFRRXF--SGEYDSADCYLDIQAGSGGTEAQDWASX 147
Query: 131 LLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFESGVHRVQRVPKT 190
L R Y+R++E +K EII S E+ G K + +I G Y L+ E+GVHR+ R
Sbjct: 148 LERXYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPF 207
Query: 191 ETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIP 250
++ GR HTS + V PE D+ DI INPADLRID YRASGAGGQH+N+T+SAVRITHIP
Sbjct: 208 DSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIP 267
Query: 251 TGIVVQCQNDRSQHKNKAFALKILLARI 278
TGIV QCQNDRSQHKNK A K A++
Sbjct: 268 TGIVTQCQNDRSQHKNKDQAXKQXKAKL 295
>pdb|2B3T|A Chain A, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 276
Score = 166 bits (420), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 89/258 (34%), Positives = 142/258 (55%), Gaps = 6/258 (2%)
Query: 311 ETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAYIIGKKEFYGLVL 370
+ ILL++VT ++ E +L ++ L+ L+ RR GEPIA++ G +EF+ L L
Sbjct: 23 DAEILLEHVTGRGRTFILAFGETQLTDEQCQQLDALLTRRRDGEPIAHLTGVREFWSLPL 82
Query: 371 NITSDVLIPRPETELLVDLIVKKTFEKKIKLLEMGTGSGXXXXXXXXYSKNKIEIIATDI 430
++ LIPRP+TE LV+ + + E+ ++L++GTG+G + EIIA D
Sbjct: 83 FVSPATLIPRPDTECLVEQALARLPEQPCRILDLGTGTGAIALALAS-ERPDCEIIAVD- 140
Query: 431 SXXXXXXXXXXXXXXXXXYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNK 490
NI I ++S+W++ L + F +IV+NPPYI + D HL +
Sbjct: 141 RMPDAVSLAQRNAQHLAIKNIHI--LQSDWFSALAGQQ--FAMIVSNPPYIDEQDPHLQQ 196
Query: 491 GDLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNLVRKLLFKYGFS 550
GD+RFEP+ AL +G++ I I++ + LV G LL+EHG+ Q VR+ G+
Sbjct: 197 GDVRFEPLTALVAADSGMADIVHIIEQSRNALVSGGFLLLEHGWQQGEAVRQAFILAGYH 256
Query: 551 DIKSWRDLSGIERVTQGK 568
D+++ RD ERVT G+
Sbjct: 257 DVETCRDYGDNERVTLGR 274
>pdb|1T43|A Chain A, Crystal Structure Analysis Of E.Coli Protein
(N5)-Glutamine Methyltransferase (Hemk)
Length = 277
Score = 166 bits (420), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 89/258 (34%), Positives = 142/258 (55%), Gaps = 6/258 (2%)
Query: 311 ETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAYIIGKKEFYGLVL 370
+ ILL++VT ++ E +L ++ L+ L+ RR GEPIA++ G +EF+ L L
Sbjct: 23 DAEILLEHVTGRGRTFILAFGETQLTDEQCQQLDALLTRRRDGEPIAHLTGVREFWSLPL 82
Query: 371 NITSDVLIPRPETELLVDLIVKKTFEKKIKLLEMGTGSGXXXXXXXXYSKNKIEIIATDI 430
++ LIPRP+TE LV+ + + E+ ++L++GTG+G + EIIA D
Sbjct: 83 FVSPATLIPRPDTECLVEQALARLPEQPCRILDLGTGTGAIALALAS-ERPDCEIIAVD- 140
Query: 431 SXXXXXXXXXXXXXXXXXYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNK 490
NI I ++S+W++ L + F +IV+NPPYI + D HL +
Sbjct: 141 RMPDAVSLAQRNAQHLAIKNIHI--LQSDWFSALAGQQ--FAMIVSNPPYIDEQDPHLQQ 196
Query: 491 GDLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNLVRKLLFKYGFS 550
GD+RFEP+ AL +G++ I I++ + LV G LL+EHG+ Q VR+ G+
Sbjct: 197 GDVRFEPLTALVAADSGMADIVHIIEQSRNALVSGGFLLLEHGWQQGEAVRQAFILAGYH 256
Query: 551 DIKSWRDLSGIERVTQGK 568
D+++ RD ERVT G+
Sbjct: 257 DVETCRDYGDNERVTLGR 274
>pdb|2WH1|Y Chain Y, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH3|Y Chain Y, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome). This File Contains The
30s Subunit
Length = 351
Score = 145 bits (365), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 102/268 (38%), Positives = 147/268 (54%), Gaps = 13/268 (4%)
Query: 15 RLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEMLNDL-- 72
RLKEL+ L + N+ + K +E + L V + ++ + D+ E++ +L
Sbjct: 20 RLKELERRLEDPSLWNDPEAARKVSQEAARLRRTV---DTFRSLESDLQGLLELMEELPA 76
Query: 73 EMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVNDLL 132
E R E+ A K++ E+ L + ++N + I+ G GG E+ + LL
Sbjct: 77 EEREALKPELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLL 132
Query: 133 RMYIRFSERNYWKFEIISRSLSEIGG--YKEIIARIIGLNVYSKLKFESGVHRVQRVPKT 190
RMY RF+ER ++ E++ + G Y +I+ + G N Y L E+GVHR+ R
Sbjct: 133 RMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVK--GENAYGLLSPEAGVHRLVRPSPF 190
Query: 191 ETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIP 250
+ GR HTS V VIPE DE ++ + P +LRID RASG GGQ +N TDSAVR+ H+P
Sbjct: 191 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 250
Query: 251 TGIVVQCQNDRSQHKNKAFALKILLARI 278
TGI V CQ RSQ KNK ALKIL AR+
Sbjct: 251 TGITVTCQTTRSQIKNKELALKILKARL 278
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 145 bits (365), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 102/268 (38%), Positives = 147/268 (54%), Gaps = 13/268 (4%)
Query: 15 RLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEMLNDL-- 72
RLKEL+ L + N+ + K +E + L V + ++ + D+ E++ +L
Sbjct: 25 RLKELERRLEDPSLWNDPEAARKVSQEAARLRRTV---DTFRSLESDLQGLLELMEELPA 81
Query: 73 EMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVNDLL 132
E R E+ A K++ E+ L + ++N + I+ G GG E+ + LL
Sbjct: 82 EEREALKPELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLL 137
Query: 133 RMYIRFSERNYWKFEIISRSLSEIGG--YKEIIARIIGLNVYSKLKFESGVHRVQRVPKT 190
RMY RF+ER ++ E++ + G Y +I+ + G N Y L E+GVHR+ R
Sbjct: 138 RMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVK--GENAYGLLSPEAGVHRLVRPSPF 195
Query: 191 ETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIP 250
+ GR HTS V VIPE DE ++ + P +LRID RASG GGQ +N TDSAVR+ H+P
Sbjct: 196 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 255
Query: 251 TGIVVQCQNDRSQHKNKAFALKILLARI 278
TGI V CQ RSQ KNK ALKIL AR+
Sbjct: 256 TGITVTCQTTRSQIKNKELALKILKARL 283
>pdb|3F1E|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
70s Ribosome. The Entire Crystal Structure Contains Two
70s Ribosomes As Described In Remark 400.
pdb|3F1G|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400
Length = 378
Score = 144 bits (364), Expect = 9e-35, Method: Compositional matrix adjust.
Identities = 102/268 (38%), Positives = 147/268 (54%), Gaps = 13/268 (4%)
Query: 15 RLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEMLNDL-- 72
RLKEL+ L + N+ + K +E + L V + ++ + D+ E++ +L
Sbjct: 38 RLKELERRLEDPSLWNDPEAARKVSQEAARLRRTV---DTFRSLESDLQGLLELMEELPA 94
Query: 73 EMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVNDLL 132
E R E+ A K++ E+ L + ++N + I+ G GG E+ + LL
Sbjct: 95 EEREALKPELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLL 150
Query: 133 RMYIRFSERNYWKFEIISRSLSEIGG--YKEIIARIIGLNVYSKLKFESGVHRVQRVPKT 190
RMY RF+ER ++ E++ + G Y +I+ + G N Y L E+GVHR+ R
Sbjct: 151 RMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVK--GENAYGLLSPEAGVHRLVRPSPF 208
Query: 191 ETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIP 250
+ GR HTS V VIPE DE ++ + P +LRID RASG GGQ +N TDSAVR+ H+P
Sbjct: 209 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 268
Query: 251 TGIVVQCQNDRSQHKNKAFALKILLARI 278
TGI V CQ RSQ KNK ALKIL AR+
Sbjct: 269 TGITVTCQTTRSQIKNKELALKILKARL 296
>pdb|2B9M|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Ribosomal Subunit, Trnas,
Mrna And Release Factor Rf2 From A Crystal Structure Of
The Whole Ribosomal Complex". The Entire Crystal
Structure Contains One 70s Ribosome, Trnas, Mrna And
Release Factor Rf2 And Is Described In Remark 400
Length = 365
Score = 144 bits (364), Expect = 9e-35, Method: Compositional matrix adjust.
Identities = 102/268 (38%), Positives = 147/268 (54%), Gaps = 13/268 (4%)
Query: 15 RLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEMLNDL-- 72
RLKEL+ L + N+ + K +E + L V + ++ + D+ E++ +L
Sbjct: 25 RLKELERRLEDPSLWNDPEAARKVSQEAARLRRTV---DTFRSLESDLQGLLELMEELPA 81
Query: 73 EMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVNDLL 132
E R E+ A K++ E+ L + ++N + I+ G GG E+ + LL
Sbjct: 82 EEREALKPELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLL 137
Query: 133 RMYIRFSERNYWKFEIISRSLSEIGG--YKEIIARIIGLNVYSKLKFESGVHRVQRVPKT 190
RMY RF+ER ++ E++ + G Y +I+ + G N Y L E+GVHR+ R
Sbjct: 138 RMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVK--GENAYGLLSPEAGVHRLVRPSPF 195
Query: 191 ETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIP 250
+ GR HTS V VIPE DE ++ + P +LRID RASG GGQ +N TDSAVR+ H+P
Sbjct: 196 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 255
Query: 251 TGIVVQCQNDRSQHKNKAFALKILLARI 278
TGI V CQ RSQ KNK ALKIL AR+
Sbjct: 256 TGITVTCQTTRSQIKNKELALKILKARL 283
>pdb|2X9R|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9T|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
Length = 351
Score = 144 bits (364), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 102/268 (38%), Positives = 147/268 (54%), Gaps = 13/268 (4%)
Query: 15 RLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEMLNDL-- 72
RLKEL+ L + N+ + K +E + L V + ++ + D+ E++ +L
Sbjct: 20 RLKELERRLEDPSLWNDPEAARKVSQEAARLRRTV---DTFRSLESDLQGLLELMEELPA 76
Query: 73 EMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVNDLL 132
E R E+ A K++ E+ L + ++N + I+ G GG E+ + LL
Sbjct: 77 EEREALKPELEEAAKKLD----ELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLL 132
Query: 133 RMYIRFSERNYWKFEIISRSLSEIGG--YKEIIARIIGLNVYSKLKFESGVHRVQRVPKT 190
RMY RF+ER ++ E++ + G Y +I+ + G N Y L E+GVHR+ R
Sbjct: 133 RMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVK--GENAYGLLSPEAGVHRLVRPSPF 190
Query: 191 ETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIP 250
+ GR HTS V VIPE DE ++ + P +LRID RASG GGQ +N TDSAVR+ H+P
Sbjct: 191 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 250
Query: 251 TGIVVQCQNDRSQHKNKAFALKILLARI 278
TGI V CQ RSQ KNK ALKIL AR+
Sbjct: 251 TGITVTCQTTRSQIKNKELALKILKARL 278
>pdb|1NV8|A Chain A, N5-Glutamine Methyltransferase, Hemk
pdb|1NV8|B Chain B, N5-Glutamine Methyltransferase, Hemk
pdb|1NV9|A Chain A, Hemk, Apo Structure
Length = 284
Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 73/266 (27%), Positives = 129/266 (48%), Gaps = 22/266 (8%)
Query: 299 GSVQKKSPLNIFETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAY 358
G ++ + ++ E +++ V + +L + + +E IL +L+++R G P+ Y
Sbjct: 25 GKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRIL-ELVEKRASGYPLHY 83
Query: 359 IIGKKEFYGLVLNITSDVLIPRPETELLVDLIVKKTFEKKIK-LLEMGTGSGXXXXXXXX 417
I+G+KEF GL + V +PRPETE LV+L ++ + IK + ++GTGSG
Sbjct: 84 ILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAK 143
Query: 418 YSKNKIEIIATDISXXXXXXXXXXXXXXXXXYNIPIKFIKSNWYNNLQNYKKLF---NII 474
+S + ATD+S F++ + L+ +K+ F +I
Sbjct: 144 FSDAI--VFATDVSSKAVEIARKNAERHGVSDRF---FVRKGEF--LEPFKEKFASIEMI 196
Query: 475 VANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGY 534
++NPPY+ K HL K D+ FEP AL +GL +E +Y ++L+E G
Sbjct: 197 LSNPPYV-KSSAHLPK-DVLFEPPEALFGGEDGLDFYREFF---GRYDTSGKIVLMEIGE 251
Query: 535 NQSNLVRKLLFKYGFSDIKSWRDLSG 560
+Q ++K++ SD +D +G
Sbjct: 252 DQVEELKKIV-----SDTVFLKDSAG 272
>pdb|1SG9|A Chain A, Crystal Structure Of Thermotoga Maritima Protein Hemk, An
N5-Glutamine Methyltransferase
pdb|1SG9|B Chain B, Crystal Structure Of Thermotoga Maritima Protein Hemk, An
N5-Glutamine Methyltransferase
pdb|1SG9|C Chain C, Crystal Structure Of Thermotoga Maritima Protein Hemk, An
N5-Glutamine Methyltransferase
Length = 282
Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 73/266 (27%), Positives = 129/266 (48%), Gaps = 22/266 (8%)
Query: 299 GSVQKKSPLNIFETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAY 358
G ++ + ++ E +++ V + +L + + +E IL +L+++R G P+ Y
Sbjct: 23 GKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRIL-ELVEKRASGYPLHY 81
Query: 359 IIGKKEFYGLVLNITSDVLIPRPETELLVDLIVKKTFEKKIK-LLEMGTGSGXXXXXXXX 417
I+G+KEF GL + V +PRPETE LV+L ++ + IK + ++GTGSG
Sbjct: 82 ILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAK 141
Query: 418 YSKNKIEIIATDISXXXXXXXXXXXXXXXXXYNIPIKFIKSNWYNNLQNYKKLF---NII 474
+S + ATD+S F++ + L+ +K+ F +I
Sbjct: 142 FSDAI--VFATDVSSKAVEIARKNAERHGVSDRF---FVRKGEF--LEPFKEKFASIEMI 194
Query: 475 VANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGY 534
++NPPY+ K HL K D+ FEP AL +GL +E +Y ++L+E G
Sbjct: 195 LSNPPYV-KSSAHLPK-DVLFEPPEALFGGEDGLDFYREFF---GRYDTSGKIVLMEIGE 249
Query: 535 NQSNLVRKLLFKYGFSDIKSWRDLSG 560
+Q ++K++ SD +D +G
Sbjct: 250 DQVEELKKIV-----SDTVFLKDSAG 270
>pdb|4DZR|A Chain A, The Crystal Structure Of Protein-(Glutamine-N5)
Methyltransferase (Release Factor-Specific) From
Alicyclobacillus Acidocaldarius Subsp. Acidocaldarius
Dsm 446
Length = 215
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 53/205 (25%), Positives = 94/205 (45%), Gaps = 16/205 (7%)
Query: 370 LNITSDVLIPRPETELLVDLIVK--KTFEKKIKLLEMGTGSGXXXXXXXXYSKNKIEIIA 427
+ D LIPRP+TE+LV+ ++ K +++++GTGSG + + A
Sbjct: 1 FEVGPDCLIPRPDTEVLVEEAIRFLKRXPSGTRVIDVGTGSGCIAVSIALACPG-VSVTA 59
Query: 428 TDISXXXXXXXXXXXXXXXXXYNIPIKFIKSN---WYNNLQNYKKLFNIIVANPPYIPKG 484
D+S + + + ++ W + ++ IV+NPPYIP G
Sbjct: 60 VDLSXDALAVARRNAER----FGAVVDWAAADGIEWLIERAERGRPWHAIVSNPPYIPTG 115
Query: 485 DIHLNKGDLR-FEPINALTDYSNGLSSIKEIVKNASKYLVKN-GLLLIEHGYNQSNLVRK 542
+I + +R +EP AL +GL + L + + +E G+NQ++ V +
Sbjct: 116 EIDQLEPSVRDYEPRLALDGGEDGLQFYRRXAALPPYVLARGRAGVFLEVGHNQADEVAR 175
Query: 543 LLFKY---GFSDIKSWRDLSGIERV 564
L + GF ++ +DL GI+RV
Sbjct: 176 LFAPWRERGFR-VRKVKDLRGIDRV 199
>pdb|1VQ1|A Chain A, Crystal Structure Of N5-Glutamine Methyltransferase,
Hemk(Ec 2.1.1.-) (Tm0488) From Thermotoga Maritima At
2.80 A Resolution
pdb|1VQ1|B Chain B, Crystal Structure Of N5-Glutamine Methyltransferase,
Hemk(Ec 2.1.1.-) (Tm0488) From Thermotoga Maritima At
2.80 A Resolution
Length = 294
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 73/266 (27%), Positives = 127/266 (47%), Gaps = 22/266 (8%)
Query: 299 GSVQKKSPLNIFETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAY 358
G ++ + ++ E +++ V + +L + + +E IL +L+++R G P+ Y
Sbjct: 35 GKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRIL-ELVEKRASGYPLHY 93
Query: 359 IIGKKEFYGLVLNITSDVLIPRPETELLVDLIVKKTFEKKIK-LLEMGTGSGXXXXXXXX 417
I+G+KEF GL + V +PRPETE LV+L ++ + IK + ++GTGSG
Sbjct: 94 ILGEKEFXGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAK 153
Query: 418 YSKNKIEIIATDISXXXXXXXXXXXXXXXXXYNIPIKFIKSNWYNNLQNYKKLF---NII 474
+S + ATD+S F++ + L+ +K+ F I
Sbjct: 154 FSDAI--VFATDVSSKAVEIARKNAERHGVSDRF---FVRKGEF--LEPFKEKFASIEXI 206
Query: 475 VANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGY 534
++NPPY+ K HL K D+ FEP AL +GL +E +Y ++L E G
Sbjct: 207 LSNPPYV-KSSAHLPK-DVLFEPPEALFGGEDGLDFYREFF---GRYDTSGKIVLXEIGE 261
Query: 535 NQSNLVRKLLFKYGFSDIKSWRDLSG 560
+Q ++K++ SD +D +G
Sbjct: 262 DQVEELKKIV-----SDTVFLKDSAG 282
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 56.6 bits (135), Expect = 4e-08, Method: Composition-based stats.
Identities = 32/96 (33%), Positives = 49/96 (51%), Gaps = 3/96 (3%)
Query: 183 RVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDS 242
R+Q P G +A TV V D + +N ++L + G GGQ NKT +
Sbjct: 12 RLQEKPALLFPG---MAASTVQVAGRKDYPALLPLNESELEEQFVKGHGPGGQATNKTSN 68
Query: 243 AVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARI 278
V + H+P+GIVV+C RS +N+ A K+L ++
Sbjct: 69 CVVLKHVPSGIVVKCHQTRSVDQNRKIARKVLQEKV 104
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 43.1 bits (100), Expect = 4e-04, Method: Composition-based stats.
Identities = 37/120 (30%), Positives = 50/120 (41%), Gaps = 29/120 (24%)
Query: 215 ININPADLRIDTYRASGAGGQHINKTDSA------VRITHIPTG---------------- 252
+ I +L I RA GAGGQH+NKT +A +R + +P
Sbjct: 8 VAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSD 67
Query: 253 --IVVQCQNDRSQHKNKAFALKILLARIKD-----SKLREQQSNTAKMRRLLIGSVQKKS 305
IV++ Q RSQ N+ AL L+A IK+ R + A R L QK S
Sbjct: 68 GVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKARRPTRPTRASKERRLASKAQKSS 127
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 42.0 bits (97), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 53/112 (47%), Gaps = 30/112 (26%)
Query: 215 ININPADLRIDTYRASGAGGQHINKTDSA------VRITHIP--------TG-------- 252
++I +L I RA GAGGQH+NKT SA +R + +P T
Sbjct: 8 VSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLISDD 67
Query: 253 --IVVQCQNDRSQHKNKAFALKILLARIKD------SKLREQQSNTAKMRRL 296
I+++ Q RSQ N+ A+ L+A IK+ S+ + + +K RRL
Sbjct: 68 GVIIIKAQEFRSQELNREAAIARLVAVIKELTAEQKSRRATRPTRASKERRL 119
>pdb|2JVA|A Chain A, Nmr Solution Structure Of Peptidyl-Trna Hydrolase Domain
Protein From Pseudomonas Syringae Pv. Tomato. Northeast
Structural Genomics Consortium Target Psr211
Length = 108
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 24/82 (29%)
Query: 214 DININPADLRIDTYRASGAGGQHINKTDSAVRI------THIPT---------------- 251
++++ A++ + RA GAGGQ++NK SA+ + + +P
Sbjct: 7 NVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITS 66
Query: 252 --GIVVQCQNDRSQHKNKAFAL 271
IV++ Q R+Q +N+A AL
Sbjct: 67 DGVIVLKAQQYRTQEQNRADAL 88
>pdb|3LJ5|A Chain A, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|B Chain B, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|C Chain C, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|D Chain D, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|E Chain E, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|F Chain F, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|G Chain G, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|H Chain H, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|I Chain I, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|J Chain J, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|K Chain K, Full Length Bacteriophage P22 Portal Protein
pdb|3LJ5|L Chain L, Full Length Bacteriophage P22 Portal Protein
Length = 725
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 24/104 (23%), Positives = 52/104 (50%), Gaps = 9/104 (8%)
Query: 252 GIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMRRLLIG-SVQKKSPLNIF 310
G+++Q Q + ++ +N+ +L+I A+++ + Q N A++ + + K+S F
Sbjct: 613 GVLLQGQAELAKAQNQTLSLQIDAAKVE----AQNQLNAARIAEIFNNMDLSKQSEFREF 668
Query: 311 ETNILLKYVTRLSDV----ELIINNEKKLHKQEINILNKLIQRR 350
+ R D EL++ +++ HKQ ++I N L +R
Sbjct: 669 LKTVASFQQDRSEDARANAELLLKGDEQTHKQRMDIANILQSQR 712
>pdb|4A17|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 239
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 515 VKNASKYLVKNGLLLIEHGYNQSNLVRKLLFKYGFSDIKSWR 556
V AS ++K L I GY N + KL++K GF+ + R
Sbjct: 116 VNKASLNMIKRVLPFITFGYPTRNTISKLIYKRGFAKVNGQR 157
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
0.319 0.138 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,659,085
Number of Sequences: 62578
Number of extensions: 647970
Number of successful extensions: 2049
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2014
Number of HSP's gapped (non-prelim): 35
length of query: 570
length of database: 14,973,337
effective HSP length: 104
effective length of query: 466
effective length of database: 8,465,225
effective search space: 3944794850
effective search space used: 3944794850
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)