RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 012936
(453 letters)
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 480 bits (1239), Expect = e-169
Identities = 175/365 (47%), Positives = 238/365 (65%), Gaps = 1/365 (0%)
Query: 84 DWKSHAAAIAQSIQVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMG 143
+ + + ++ I+ L L RL L AE P+ W+D A ++++E SL
Sbjct: 4 EISERLKDLDEKLENIRGVLDVDALKERLEELEAEAEDPDFWNDQERAQKVTKELSSLKA 63
Query: 144 KMKEVKAFEQELLEHIDMIKLAREENDTELELESLEALLTMRRKSKEKELDALLSGELDP 203
K+ ++ Q L + ++++LA EE+D E E+ L + +K EL+ LLSGE D
Sbjct: 64 KLDTLEELRQRLDDLEELLELAEEEDDEETLAEAEAELKALEKKLAALELERLLSGEYDA 123
Query: 204 CSCYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDG 263
+ + + AGAGGTE+ DWASM+L+MY WA+R G++V ++D GE AGIK AT K+ G
Sbjct: 124 NNAILTIHAGAGGTEAQDWASMLLRMYLRWAERHGFKVEVLDYSEGEEAGIKSATFKIKG 183
Query: 264 EYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERF 323
YA+GY K+E GVHRLVRISPFDS RRHTSFA+V V P D + ++IN DLRI+ +
Sbjct: 184 PYAYGYLKSETGVHRLVRISPFDSAGRRHTSFASVEVYPEV-DDTIEIEINPKDLRIDTY 242
Query: 324 RSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQA 383
RS GAGGQH N TDSAVRI HIPTGI CQNERSQHQNKASAM +L++++ +LE+ ++A
Sbjct: 243 RSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRA 302
Query: 384 QMNAEHTQSLTDISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLSA 443
+I WG+QIR+YVLHPY+MVKDLRT YE + +VL+GDLDGFI +YL
Sbjct: 303 AEKDALKGEKKEIGWGSQIRSYVLHPYQMVKDLRTGYETGNTQAVLDGDLDGFIEAYLRW 362
Query: 444 SLDKD 448
+
Sbjct: 363 RASQK 367
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 414 bits (1066), Expect = e-143
Identities = 165/364 (45%), Positives = 230/364 (63%), Gaps = 1/364 (0%)
Query: 82 EGDWKSHAAAIAQSIQVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSL 141
+ + + + ++ L + RL L E+ PN W+D A + +E SL
Sbjct: 2 INEVNNRIEDLTSRLDTVRGSLDPEKKKARLEELEKEMEDPNFWNDQERAQAVIKERSSL 61
Query: 142 MGKMKEVKAFEQELLEHIDMIKLAREENDTELELESLEALLTMRRKSKEKELDALLSGEL 201
+ ++ + L + ++++LA EE+D E E L + +K E EL +LSGE
Sbjct: 62 EAVLDTLEELKNSLEDLSELLELAVEEDDEETFNELDAELKALEKKLAELELRTMLSGEY 121
Query: 202 DPCSCYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKV 261
D + Y+ +QAGAGGTE+ DWASM+ +MY WA+RRG++V ++D GE AGIK TI +
Sbjct: 122 DANNAYLTIQAGAGGTEAQDWASMLYRMYLRWAERRGFKVEIIDYSEGEEAGIKSVTILI 181
Query: 262 DGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIE 321
G YA+GY K+E GVHRLVRISPFD+ RRHTSFA+V V+P D ++I DLRI+
Sbjct: 182 KGPYAYGYLKSEQGVHRLVRISPFDANGRRHTSFASVFVMPEV-DDDIDIEIKPEDLRID 240
Query: 322 RFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIAR 381
+R+ GAGGQH N TDSAVRI HIPTGI CQN+RSQH+NK SAM VL++++ +LE+ +
Sbjct: 241 TYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEMEK 300
Query: 382 QAQMNAEHTQSLTDISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYL 441
+ ++I WG+QIR+YVLHPY MVKDLRT YE + +VL+GD+D FI +YL
Sbjct: 301 EQAEKDAKEGEKSEIGWGSQIRSYVLHPYSMVKDLRTGYETGNVQAVLDGDIDQFIEAYL 360
Query: 442 SASL 445
L
Sbjct: 361 KWKL 364
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 358 bits (921), Expect = e-122
Identities = 160/322 (49%), Positives = 221/322 (68%), Gaps = 3/322 (0%)
Query: 122 PNLWDDPVHAGRISREHGSLMGKMKEVKAFEQELLEHIDMIKLAREENDTELELESLEAL 181
P+LW+D A ++ RE L + + EQ L ++I++I + EE D + ++ + +
Sbjct: 6 PSLWNDAQEAQKLMRERQQLDDSINGINHLEQTLNDNIELIAMGEEEGDKSIVEDAEKTI 65
Query: 182 LTMRRKSKEKELDALLSGELDPCSCYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRV 241
++ + +++DALLSGE D Y+EV AGAGGTES DWASM+L+MY WA+R+G +V
Sbjct: 66 RDLKDEIDRRQIDALLSGEADANDTYLEVHAGAGGTESQDWASMLLRMYTRWAERQGRKV 125
Query: 242 TLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVI 301
+++ GE AGIK ATI V G A+G+ K E GVHRLVRISP+DS RRHTSFA++ V
Sbjct: 126 EVLEVHDGEEAGIKSATILVKGHNAYGWLKTESGVHRLVRISPYDSNARRHTSFASIWVY 185
Query: 302 PNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQ 361
P D + V +NESD+RI+ +RS GAGGQH NTTDSAVRI HIPTGI CQ ERSQH+
Sbjct: 186 PVI-DDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHK 244
Query: 362 NKASAMGVLQSRVNQLEI-ARQAQMNAEHTQSLTDISWGNQIRTYVLHPYRMVKDLRTNY 420
N+A A +L++R+ + E+ R+ NA S TDI WG+QIR+YVL PY++VKDLRT
Sbjct: 245 NRAKAWSMLRARLYEEELKKREEATNAAAA-SKTDIGWGHQIRSYVLQPYQLVKDLRTGV 303
Query: 421 EVSDPDSVLEGDLDGFILSYLS 442
E ++P VL+GDL+ F+ + L+
Sbjct: 304 ESTNPQDVLDGDLNEFMEAALA 325
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 336 bits (864), Expect = e-115
Identities = 131/238 (55%), Positives = 164/238 (68%), Gaps = 3/238 (1%)
Query: 206 CYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEY 265
Y+ + AGAGGTE+ DWASM+L+MY WA+R+G++V ++D GE AGIK AT+K+ GE
Sbjct: 1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60
Query: 266 AFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRS 325
A+GY K E GVHRLVRISPFDS RRHTSFA+V V P S ++I + DLRI+ +R+
Sbjct: 61 AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISI-EIEIPDDDLRIDTYRA 119
Query: 326 GGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEI-ARQAQ 384
GAGGQH N TDSAVR+ H+PTGI CQNERSQH NKA A +L+ ++ L R +
Sbjct: 120 SGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQE 179
Query: 385 MNAEHTQSLTDISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLS 442
N E I WGNQIR+YVL PY+ KDLRT E + VL+GD DGFI +YL
Sbjct: 180 KNRERAL-KKLIGWGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDGDKDGFIKAYLK 236
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 322 bits (826), Expect = e-108
Identities = 141/325 (43%), Positives = 211/325 (64%), Gaps = 2/325 (0%)
Query: 119 LNKPNLWDDPVHAGRISREHGSLMGKMKEVKAFEQELLEHIDMIKLAREENDTELELESL 178
+ +PN W+D A I+ E L K+ + + E I+++ E D E++ E +
Sbjct: 1 MQEPNFWNDIKEAQEITSEEKYLKDKLDKYNHLRNRI-EDIEVLCEMMSEEDDEMKKEII 59
Query: 179 EALLTMRRKSKEKELDALLSGELDPCSCYIEVQAGAGGTESMDWASMVLQMYKSWAQRRG 238
+ ++ + +++ LLSGE D + + + +G GGT++ DW M+L+MY WA+++G
Sbjct: 60 SEVKNIKEEIDRFKIETLLSGEYDRNNAILTLHSGVGGTDAQDWTEMLLRMYTRWAEKKG 119
Query: 239 YRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAV 298
Y+V ++D + G+ AGIK T+K+ GE+A+GY KAE G+HRLVRISPF++ +R TSFA+V
Sbjct: 120 YKVEIIDLLEGDEAGIKSVTLKITGEFAYGYLKAEKGIHRLVRISPFNANGKRQTSFASV 179
Query: 299 AVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERS 358
V+P D ++I DL+I+ +R+GGAGGQH N T+SAVRI HIPTGI CQNERS
Sbjct: 180 EVLPELTDDQ-DIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERS 238
Query: 359 QHQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSLTDISWGNQIRTYVLHPYRMVKDLRT 418
QH NK +AM +L+S++ +L+ + + T L D+ WG+QIR+YV HPY +VKD RT
Sbjct: 239 QHSNKETAMKMLKSKLVELKERAHKEKIEDLTGELKDMGWGSQIRSYVFHPYNLVKDHRT 298
Query: 419 NYEVSDPDSVLEGDLDGFILSYLSA 443
E S+ DSV++GD+D FI YL
Sbjct: 299 GVETSNVDSVMDGDIDNFITQYLKG 323
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 273 bits (700), Expect = 3e-89
Identities = 140/293 (47%), Positives = 196/293 (66%), Gaps = 6/293 (2%)
Query: 155 LLEHIDMIKLAREENDTELELESLEALLTMRRKSKEKELDALLSGELDPCSCYIEVQAGA 214
L + +++ LA E D + L + L + ++ E + SG++D + ++++QAGA
Sbjct: 16 LADAGELLDLAESEQDEDTALAVIADLDKYQAHVEKLEFQRMFSGQMDGANAFVDIQAGA 75
Query: 215 GGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEV 274
GGTE+ DWA ++L+MY WA+ RG++ LM+ GE+AGIK AT++++GEYA+G+ K E+
Sbjct: 76 GGTEAQDWAEILLRMYLRWAESRGWKTELMEVSGGEVAGIKSATVRIEGEYAYGWLKTEI 135
Query: 275 GVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHAN 334
GVHRLVR SPFDS RRHTSF +V V P D + + IN +DLR + +RS GAGGQH N
Sbjct: 136 GVHRLVRKSPFDSDNRRHTSFTSVFVSPEV-DDNIEIDINPADLRTDVYRSSGAGGQHVN 194
Query: 335 TTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEI-ARQAQMNA-EHTQS 392
T+SAVRI HIPT CQ RSQHQN+ +AM +L +++ +LE+ R A+ +A E T+S
Sbjct: 195 KTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEVQKRNAEKDALEATKS 254
Query: 393 LTDISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFILSYLSASL 445
DI WG+QIR YVL R +KDLRT E SD VL+GDLD F+ + L A L
Sbjct: 255 --DIGWGSQIRNYVLDQSR-IKDLRTGIERSDTQKVLDGDLDEFVEASLKAGL 304
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 267 bits (684), Expect = 1e-86
Identities = 143/326 (43%), Positives = 205/326 (62%), Gaps = 9/326 (2%)
Query: 124 LWDDPVHAGRISREHGSL---MGKMKEV-KAFEQELLEHIDMIKLAREENDTELELESLE 179
WDD A + E +L +GK +++ + FE + H +L +EE D +L E
Sbjct: 6 FWDDQQGAQAVINEANALKDMVGKFRQLDETFENLEITH----ELLKEEYDEDLHEELES 61
Query: 180 ALLTMRRKSKEKELDALLSGELDPCSCYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGY 239
+ + ++ E EL LLS D + +E+ GAGGTES DW SM+L+MY WA++RG+
Sbjct: 62 EVKGLIQEMNEYELQLLLSDPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRWAEKRGF 121
Query: 240 RVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVA 299
+V +D +PG+ AGIK T+ + G A+GY KAE GVHRLVRISPFDS RRHTSF +
Sbjct: 122 KVETVDYLPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFVSCE 181
Query: 300 VIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQ 359
V+P D +++ DL+I+ +R+ GAGGQH NTTDSAVRI H PT TCQ+ERSQ
Sbjct: 182 VVPEFND-EVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQ 240
Query: 360 HQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSLTDISWGNQIRTYVLHPYRMVKDLRTN 419
+N+ AM +L++++ Q ++ Q E +I WG+QIR+YV HPY +VKD RTN
Sbjct: 241 IKNREHAMKMLKAKLYQKKLEEQQAELDEIRGEQKEIGWGSQIRSYVFHPYSLVKDHRTN 300
Query: 420 YEVSDPDSVLEGDLDGFILSYLSASL 445
EV + +V++G++D FI +YL + +
Sbjct: 301 TEVGNVQAVMDGEIDPFIDAYLRSRI 326
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 255 bits (654), Expect = 2e-81
Identities = 130/341 (38%), Positives = 190/341 (55%), Gaps = 26/341 (7%)
Query: 111 RLNLLSAELNKPNLWDDPVHAGRISREHGSL---MGKMKEVKAFEQELLEHIDMIKLARE 167
R L A L+ P + D ++S+E+ L + +E K +++L E +M++ E
Sbjct: 14 RYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAQEDLEEAKEMLE---E 70
Query: 168 ENDTEL------ELESLEALLTMRRKSKEKELDALL--SGELDPCSCYIEVQAGAGGTES 219
E+D E+ EL+ LE R + E+EL LL D + +E++AG GG E+
Sbjct: 71 ESDPEMREMAKEELKELEE----RLEELEEELKILLLPKDPNDDKNVILEIRAGTGGDEA 126
Query: 220 MDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRL 279
+A + +MY +A+R+G++V ++ GE+ G K ++ G+ + K E GVHR+
Sbjct: 127 ALFAGDLFRMYSRYAERQGWKVEILSASEGELGGYKEVIAEISGDGVYSKLKFESGVHRV 186
Query: 280 VRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSA 339
R+ +S R HTS A VAV+P + + V+IN DLRI+ FRS GAGGQH NTTDSA
Sbjct: 187 QRVPATESQGRIHTSAATVAVLPEAEE--VEVEINPKDLRIDTFRSSGAGGQHVNTTDSA 244
Query: 340 VRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSLTDISWG 399
VRI H+PTGI CQ+ERSQH+NKA AM VL++R+ E + A +S + G
Sbjct: 245 VRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEAATRKSQ--VGSG 302
Query: 400 N---QIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGFI 437
+ +IRTY P V D R N + D V+EGDLD I
Sbjct: 303 DRSERIRTYN-FPQGRVTDHRINLTLYKLDEVMEGDLDELI 342
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 251 bits (643), Expect = 7e-80
Identities = 123/339 (36%), Positives = 183/339 (53%), Gaps = 20/339 (5%)
Query: 111 RLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAFEQELLEHIDMIKLAREEND 170
R L A L+ P + DP ++S+E+ L +++ + +++ + D ++ EE D
Sbjct: 15 RYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAKEMLAEEKD 74
Query: 171 TEL------ELESLEALLTMRRKSKEKELDALLS--GELDPCSCYIEVQAGAGGTESMDW 222
E+ E++ LEA + + E+EL LL D + +E++AG GG E+ +
Sbjct: 75 PEMREMAEEEIKELEAKI----EELEEELKILLLPKDPNDDKNIILEIRAGTGGDEAALF 130
Query: 223 ASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAEVGVHRLVRI 282
A + +MY +A+ +G++V ++ E+ G K + G+ + K E GVHR+ R+
Sbjct: 131 AGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLKFESGVHRVQRV 190
Query: 283 SPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRI 342
+S R HTS A VAV+P + ++IN DLRI+ FRS GAGGQH NTTDSAVRI
Sbjct: 191 PATESQGRIHTSAATVAVLPEV-EEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVRI 249
Query: 343 IHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQMNAEHTQSL---TDISWG 399
H+PTGI CQ+ERSQH+NKA AM VL++R+ E + A +S D S
Sbjct: 250 THLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEASERKSQVGSGDRS-- 307
Query: 400 NQIRTYVLHPYRMVKDLRTNYEVSDPDSVLE-GDLDGFI 437
+IRTY P V D R N + D V+E G LD I
Sbjct: 308 ERIRTYN-FPQNRVTDHRINLTLYKLDEVMEGGKLDEII 345
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 246 bits (631), Expect = 4e-78
Identities = 129/361 (35%), Positives = 193/361 (53%), Gaps = 36/361 (9%)
Query: 91 AIAQSIQVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKA 150
++ + ++ + +R + L A L+ P + D ++S+E+ L +E+
Sbjct: 4 SLLEKLESLLERYE---------ELEALLSDPEVISDQDKLRKLSKEYSQL----EEIVD 50
Query: 151 FEQELLEHIDMIKLAR---EENDTEL------ELESLEALLTMRRKSKEKELDALL--SG 199
+E + + IK A+ EE+D E+ ELE LE + + E++L LL
Sbjct: 51 CYREYQQAQEDIKEAKEILEESDPEMREMAKEELEELEE----KIEELEEQLKVLLLPKD 106
Query: 200 ELDPCSCYIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATI 259
D + +E++AG GG E+ +A + +MY +A+ +G++V ++ E+ G K
Sbjct: 107 PNDEKNVILEIRAGTGGDEAAIFAGDLFRMYSRYAESKGWKVEILSANETELGGYKEVIA 166
Query: 260 KVDGEYAFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLR 319
++ G+ + K E GVHR+ R+ +S R HTS A VAV+P + V IN +DLR
Sbjct: 167 EIKGDGVYSRLKFESGVHRVQRVPVTESQGRIHTSAATVAVMPELEE--VEVDINPADLR 224
Query: 320 IERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEI 379
I+ FRS GAGGQH NTTDSAVRI H+PTGI CQ+ERSQH+NK AM VL++R+ + E
Sbjct: 225 IDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQ 284
Query: 380 ARQAQMNAEHTQSLT---DISWGNQIRTYVLHPYRMVKDLRTNYEVSDPDSVLEGDLDGF 436
+Q A +S D S +IRTY P V D R N + D VLEGDLD
Sbjct: 285 EKQQAAQASTRKSQVGSGDRS--ERIRTYN-FPQNRVTDHRINLTLYKLDEVLEGDLDEL 341
Query: 437 I 437
I
Sbjct: 342 I 342
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 150 bits (380), Expect = 3e-44
Identities = 47/113 (41%), Positives = 67/113 (59%), Gaps = 2/113 (1%)
Query: 306 DSSTHVQINESDLRIERFRSGGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNKAS 365
D ++I ESDLRI+ FRS G GGQ+ N T+SAVR+ H+PTGI CQ ERSQH+N+
Sbjct: 3 DEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREK 62
Query: 366 AMGVLQSRVNQLEIARQAQMNAEHTQSLT-DISWGNQIRTYVLHPYRMVKDLR 417
A+ L++++ + E+ ++ + S +IRTY P VKD R
Sbjct: 63 ALERLKAKLYEAELQKKREKTKPTRASQVRRGDRKEKIRTY-NFPQGRVKDHR 114
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 134 bits (341), Expect = 2e-38
Identities = 47/118 (39%), Positives = 70/118 (59%), Gaps = 9/118 (7%)
Query: 163 KLAREENDTEL------ELESLEALLTMRRKSKEKELDALLSG-ELDPCSCYIEVQAGAG 215
+L EE D E+ ELE LEA L + +E LL D + +E++AGAG
Sbjct: 1 ELLEEEEDDEMRELAEEELEELEAEL--EEELEELLKLLLLPKDPNDDKNAILEIRAGAG 58
Query: 216 GTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAE 273
G E+ +A +L+MY +A+R+G++V ++DE GE+ GIK AT+K+ GE A+G K E
Sbjct: 59 GDEAALFAGDLLRMYLRYAERKGWKVEVLDESEGELGGIKEATLKISGEGAYGKLKFE 116
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 133 bits (338), Expect = 5e-38
Identities = 50/119 (42%), Positives = 74/119 (62%), Gaps = 12/119 (10%)
Query: 163 KLAREENDTEL------ELESLEALLTMRRKSKEKELDALL--SGELDPCSCYIEVQAGA 214
+L EE+D EL ELE LE L + EKEL LL D + +E++AGA
Sbjct: 1 ELLEEEDDPELREEAEEELEELEKEL----EELEKELLNLLLPLDPYDDKNAILEIRAGA 56
Query: 215 GGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDGEYAFGYAKAE 273
GGTE+ +A +L+MY+ +A+R+G++V ++D GE GIK AT++++GE A+GY K E
Sbjct: 57 GGTEAQLFAEDLLRMYQRYAERKGWKVEVIDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115
>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H.
Members of this protein family are bacterial proteins
homologous to peptide chain release factors 1 (RF-1,
product of the prfA gene), and 2 (RF-2, product of the
prfB gene). The member from Escherichia coli K-12,
designated prfH, appears to be a pseudogene. This class
I release factor is always found as the downstream gene
of a two-gene operon [Protein synthesis, Translation
factors].
Length = 200
Score = 123 bits (311), Expect = 3e-33
Identities = 64/200 (32%), Positives = 97/200 (48%), Gaps = 7/200 (3%)
Query: 207 YIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAG-IKRATIKVDGEY 265
+++ + G E + L+ A RG RV ++++ PGE+ G ++ A + +DGE
Sbjct: 2 LLQLSSAQGPAECCLAVAKALERLTREAAARGVRVEVLEQEPGEVPGTLRSALVSLDGEA 61
Query: 266 AFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRS 325
A A G + SP+ RR F V S + E ++R E RS
Sbjct: 62 AAALADRWEGTLLWICPSPYRPHHRRKNWFIGVQRF------SASEEATEDEIRFETLRS 115
Query: 326 GGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQM 385
G GGQH N T+SAVR H+ +GI+ Q+ERSQH NK A +L R+ L+ + A +
Sbjct: 116 SGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADLQQEQAAAL 175
Query: 386 NAEHTQSLTDISWGNQIRTY 405
AE + I GN +R +
Sbjct: 176 RAERRTAHHQIERGNPVRVF 195
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 112 bits (283), Expect = 4e-29
Identities = 56/200 (28%), Positives = 92/200 (46%), Gaps = 7/200 (3%)
Query: 207 YIEVQAGAGGTESMDWASMVLQMYKSWAQRRGYRVTLMDEMPGEIAGIKR-ATIKVDGEY 265
+++ + G E + L+ A R+G RVT+++ G R A + +DG+
Sbjct: 3 LLQLSSAQGPAECCLAVAKALERLLKEAARQGVRVTVLETETGRYPDTLRSALVSLDGDN 62
Query: 266 AFGYAKAEVGVHRLVRISPFDSGKRRHTSFAAVAVIPNSGDSSTHVQINESDLRIERFRS 325
A A++ G + + SP+ R F + S + ++R E RS
Sbjct: 63 AEALAESWCGTIQWICPSPYRPHHGRKNWFVGIGRF------SADEEEQSDEIRFETLRS 116
Query: 326 GGAGGQHANTTDSAVRIIHIPTGITATCQNERSQHQNKASAMGVLQSRVNQLEIARQAQM 385
G GGQH N TDSAVR H+ +GI+ Q+ERSQH NK A ++ ++ Q + + A +
Sbjct: 117 SGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQQQQEQSAAL 176
Query: 386 NAEHTQSLTDISWGNQIRTY 405
++ I GN R +
Sbjct: 177 KSQRRMFHHQIERGNPRRVF 196
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 44.4 bits (106), Expect = 1e-05
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 26/82 (31%)
Query: 311 VQINESDLRIERF-RSGGAGGQHANTTDSAVRII------HIP---------------TG 348
+ I E++L RF R+ G GGQ+ N +AV + +P T
Sbjct: 8 LVIPENELE-WRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITK 66
Query: 349 ---ITATCQNERSQHQNKASAM 367
I Q RSQ +N+ A+
Sbjct: 67 DGVIVIKAQEFRSQERNREDAL 88
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 33.4 bits (77), Expect = 0.15
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 2/68 (2%)
Query: 136 REHGSLMGKMKEVKAFEQELLEHIDMIKLAREENDTELELESLEALLTMRRKSKEKELDA 195
L +++E+K EL I+ +K REE + EL L K + EL+
Sbjct: 69 TRLEKLKKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELKKLKAELEK 128
Query: 196 LLSGELDP 203
+ DP
Sbjct: 129 Y--EKNDP 134
>gnl|CDD|215791 pfam00210, Ferritin, Ferritin-like domain. This family contains
ferritins and other ferritin-like proteins such as
members of the DPS family and bacterioferritins.
Length = 142
Score = 28.4 bits (64), Expect = 3.7
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 137 EHGSLMGKMKEVKAFEQELLEHI-DMIKLAREENDTELELESLEALLTMRRKSKEKELDA 195
E GS++ ++ E+E+ E + ++I+LA EE D + LE L + + E L+A
Sbjct: 77 EFGSVLEALEAALEHEKEVTESLRELIELAEEEGDYATA-DFLEWFLEEQEEH-EWFLEA 134
Query: 196 LLS 198
LL
Sbjct: 135 LLE 137
>gnl|CDD|131662 TIGR02613, mob_myst_B, mobile mystery protein B. Members of this
protein family, which we designate mobile mystery
protein B, are found in mobization-related contexts more
often than not, including within a CRISPR-associated
gene region in Geobacter sulfurreducens PCA, and on
plasmids in Agrobacterium tumefaciens and Coxiella
burnetii, always together with mobile mystery protein A
(TIGR02612), a member of the family of helix-turn-helix
DNA binding proteins (pfam01381). This protein is
encoded by the downstream member of the gene pair and
belongs to the Fic protein family (pfam02661), where Fic
(filamentation induced by cAMP) is a regulator of cell
division. The characteristics of having a two-gene
operon in a varied context and often on plasmids, with
one member affecting cell division and the other able to
bind DNA, suggests similarity to addiction modules.
Length = 186
Score = 28.6 bits (64), Expect = 4.8
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 269 YAKAEVGV---HRLVRISPFDSGKRRHTSFAAVAVIPNSG 305
++ E+ + HRLV I PF +G RH A ++ G
Sbjct: 106 FSPDEIAIRFHHRLVAIHPFPNGNGRHARLATDLLLEQQG 145
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 28.9 bits (65), Expect = 5.5
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 97 QVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGS-LMGKMKEVKAFEQEL 155
+VI +W+ L+ L E NK N V +I++E + L+ + KE+K E
Sbjct: 34 EVIALDKEWRQRQFELDSLRKEFNKLN---KEVAKLKIAKEDATELIAETKELKKEITEK 90
Query: 156 LEHIDMIKLARE 167
+ K A +
Sbjct: 91 EAEVQEAKAALD 102
>gnl|CDD|216919 pfam02181, FH2, Formin Homology 2 Domain.
Length = 372
Score = 28.8 bits (65), Expect = 5.6
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 160 DMIKLAREENDTELELESLEALLTMRRKSKEKELDALLSGELDP 203
++++ E +++ L LE LE LL M +E + G+
Sbjct: 99 EIVQAILEMDESVLGLELLENLLKMAPTKEELKKLKEYKGDPSK 142
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 29.3 bits (66), Expect = 6.1
Identities = 13/53 (24%), Positives = 25/53 (47%)
Query: 144 KMKEVKAFEQELLEHIDMIKLAREENDTELELESLEALLTMRRKSKEKELDAL 196
K+KE+K +++ E+I + + E D E+E + L E+ + L
Sbjct: 281 KVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKEL 333
>gnl|CDD|227453 COG5124, COG5124, Protein predicted to be involved in meiotic
recombination [Cell division and chromosome partitioning
/ General function prediction only].
Length = 209
Score = 28.0 bits (62), Expect = 7.5
Identities = 17/60 (28%), Positives = 26/60 (43%)
Query: 139 GSLMGKMKEVKAFEQELLEHIDMIKLAREENDTELELESLEALLTMRRKSKEKELDALLS 198
L K++EVK E ID K R + TE + L +RK ++ E+ L+
Sbjct: 85 ELLKKKIQEVKQDIATYKEEIDKEKATRRKKFTEGQKNYNREALLEKRKKEQDEIKKKLN 144
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 28.9 bits (65), Expect = 8.3
Identities = 23/92 (25%), Positives = 32/92 (34%), Gaps = 1/92 (1%)
Query: 103 LQWKNLNVRLNLLSAELNKPNLWDDPVHA-GRISREHGSLMGKMKEVKAFEQELLEHIDM 161
+ +NL R + E N P + A SL GK + + E +
Sbjct: 1372 AEIQNLKSRYDPADKENNLPKEILKKIEALLIKQELQLSLEGKDETEVHLSEIFSEEKSL 1431
Query: 162 IKLAREENDTELELESLEALLTMRRKSKEKEL 193
I L R E L SL ALLT + +
Sbjct: 1432 ISLDRNSIYKEEVLSSLSALLTKEKIALLDRK 1463
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 28.4 bits (64), Expect = 8.4
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 8/76 (10%)
Query: 129 VHAGRISREHGSLMGKMKEVKAF--EQELLEHIDMIKLAREENDTELELESLEALLTMRR 186
V A + GS G E++ EL E + +L E + E ELE ++ LL
Sbjct: 308 VKAKEL----GSPAGTKTEIEVGVDFPELKEELK--ELEEELKELEEELEKIKKLLKKLP 361
Query: 187 KSKEKELDALLSGELD 202
K +L +L+
Sbjct: 362 KKARGQLPPEKREQLE 377
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 28.5 bits (64), Expect = 8.5
Identities = 22/103 (21%), Positives = 46/103 (44%), Gaps = 11/103 (10%)
Query: 96 IQVIKKRLQWKNLNVRLNLLSAELNKPNLWDDPVHAGRISREHGSLMGKMKEVKAFEQEL 155
++ + ++L R L E+ L ++ + L +++E++ +EL
Sbjct: 807 RRLDALERELESLEQRRERLEQEIE--ELEEEIEEL---EEKLDELEEELEELEKELEEL 861
Query: 156 LEHIDMIKLAREENDTELELESLEALLTMRRKSKEKELDALLS 198
E ++ +L E+ + E EL+ LE ++ E+EL L S
Sbjct: 862 KEELE--ELEAEKEELEDELKELE----EEKEELEEELRELES 898
>gnl|CDD|227322 COG4989, COG4989, Predicted oxidoreductase [General function
prediction only].
Length = 298
Score = 28.1 bits (63), Expect = 8.8
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 370 LQSRVNQLEIARQAQMNAEHTQSLTD 395
LQSR+ + Q +++ HT L D
Sbjct: 167 LQSRLPFTLVTNQLELSPLHTPMLLD 192
>gnl|CDD|224760 COG1847, Jag, Predicted RNA-binding protein [General function
prediction only].
Length = 208
Score = 28.0 bits (63), Expect = 9.4
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 145 MKEVKAFEQELLEHIDM---IKLAREENDTELELESLEALLTMRRKSKEKELDAL 196
+E K + +ELLE +D I ++ E + +E +A + + K LDAL
Sbjct: 64 AQEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHG--KTLDAL 116
>gnl|CDD|233755 TIGR02165, cas_GSU0054, CRISPR-associated protein GSU0054/csb2,
Dpsyc system. This model represents a CRISPR-associated
protein from the Dpsyc subtype, named for Desulfotalea
psychrophila LSv54. CRISPR systems confer resistance in
prokaryotes to invasive DNA or RNA, including phage and
plasmids. CRISPR-associated proteins typically are found
near CRISPR repeats and other CRISPR-associated
proteins, have low levels of sequence identify, have
sequence relationships that suggest lateral transfer,
and show some sequence similarity to DNA-active proteins
such as helicases and repair proteins [Mobile and
extrachromosomal element functions, Other].
Length = 487
Score = 28.2 bits (63), Expect = 9.9
Identities = 21/95 (22%), Positives = 30/95 (31%), Gaps = 3/95 (3%)
Query: 172 ELELESLEALLTMRRKSKEKELDAL--LSGELDPCSCYIE-VQAGAGGTESMDWASMVLQ 228
E L L R K L L L S Q + + WA++
Sbjct: 327 ADERIWLRRALDGRAGPKLGRLRGLIRLPLVGLGDSPRSLDPQRWPAPSPARIWATVTPV 386
Query: 229 MYKSWAQRRGYRVTLMDEMPGEIAGIKRATIKVDG 263
+ ++RG DE E AG R ++ G
Sbjct: 387 VLPRRPKKRGDGHVFRDEFETEAAGQVRKALRRAG 421
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.131 0.385
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,973,466
Number of extensions: 2208954
Number of successful extensions: 2134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2103
Number of HSP's successfully gapped: 55
Length of query: 453
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 353
Effective length of database: 6,502,202
Effective search space: 2295277306
Effective search space used: 2295277306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.4 bits)