RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014582
(422 letters)
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 485 bits (1252), Expect = e-172
Identities = 181/359 (50%), Positives = 254/359 (70%), Gaps = 4/359 (1%)
Query: 63 KIMEQRVLAIERRSACLENLVNQPE--ASPAEYSKANKELRKLRDSMHLISELRTKQKEI 120
M ++ A+E R LE L++ PE + + K +KE +L + E + Q+++
Sbjct: 2 PSMLDKLEALEERYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAQEDL 61
Query: 121 DGLKSLIYECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAG 180
+ K ++ E D +M +MA EEL + + L+ L LLPKD D+++ ILE+RAG
Sbjct: 62 EEAKEML-EEESDPEMREMAKEELKELEERLEELEEELKILLLPKDPNDDKNVILEIRAG 120
Query: 181 TGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFE 240
TGG+EA+LFA D+F+MY RY++++GWK E++ +E +L GYKE A ISG GVY KLKFE
Sbjct: 121 TGGDEAALFAGDLFRMYSRYAERQGWKVEILSASEGELGGYKEVIAEISGDGVYSKLKFE 180
Query: 241 SGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANT 300
SG+HRVQRVP TE GR+HTSA +VA+LP+A+EV+V + +DLRIDT+RS G+GGQH NT
Sbjct: 181 SGVHRVQRVPATESQGRIHTSAATVAVLPEAEEVEVEINPKDLRIDTFRSSGAGGQHVNT 240
Query: 301 TNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQIG 360
T+SAVR+TH+PTG+ + QDERSQH NKAKA+KVL A+LY+ ER + + R Q+G
Sbjct: 241 TDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEAATRKSQVG 300
Query: 361 SGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQEMDAIASFG 419
SGDRSERIRTYNFPQGRVTDHR+ +T + + ++MEG+ LD IDAL+ + + + +A+ G
Sbjct: 301 SGDRSERIRTYNFPQGRVTDHRINLTLYKLDEVMEGD-LDELIDALIAEDQAEKLAALG 358
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 454 bits (1170), Expect = e-160
Identities = 178/360 (49%), Positives = 254/360 (70%), Gaps = 4/360 (1%)
Query: 63 KIMEQRVLAIERRSACLENLVNQPE--ASPAEYSKANKELRKLRDSMHLISELRTKQKEI 120
+ +++ ++ R LE L++ PE + P EY K +KE +L + E + Q+++
Sbjct: 3 PSLLEKLESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDL 62
Query: 121 DGLKSLIYECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAG 180
+ K ++ E +D +M +MA EE+ + + L+ L LLPKD D+++ ILE+RAG
Sbjct: 63 EDAKEMLAE-EKDPEMREMAEEEIKELEAKIEELEEELKILLLPKDPNDDKNIILEIRAG 121
Query: 181 TGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFE 240
TGG+EA+LFA D+F+MY RY++ KGWK E++ +ES+L GYKE A+ISG GVY +LKFE
Sbjct: 122 TGGDEAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLKFE 181
Query: 241 SGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEV-DVRLRNEDLRIDTYRSGGSGGQHAN 299
SG+HRVQRVP TE GR+HTSA +VA+LP+ +EV ++ + +DLRIDT+RS G+GGQH N
Sbjct: 182 SGVHRVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHVN 241
Query: 300 TTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQI 359
TT+SAVR+TH+PTG+ + QDERSQH NKAKA+KVL A+LY+ ER + + R Q+
Sbjct: 242 TTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEASERKSQV 301
Query: 360 GSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQEMDAIASFG 419
GSGDRSERIRTYNFPQ RVTDHR+ +T + + ++MEG LD IDAL+ + + + +A G
Sbjct: 302 GSGDRSERIRTYNFPQNRVTDHRINLTLYKLDEVMEGGKLDEIIDALIAEDQAEQLAELG 361
>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 = 400 bits (1029), Expect = e-138
Identities = 171/356 (48%), Positives = 249/356 (69%), Gaps = 5/356 (1%)
Query: 67 QRVLAIERRSACLENLVNQPE--ASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLK 124
+++ ++ R LE L++ PE + + K +KE +L + + E + Q++I K
Sbjct: 7 EKLESLLERYEELEALLSDPEVISDQDKLRKLSKEYSQLEEIVDCYREYQQAQEDIKEAK 66
Query: 125 SLIYECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAGTGGE 184
++ E D +M +MA EEL ++ + L+ L LLPKD DE++ ILE+RAGTGG+
Sbjct: 67 EILEE--SDPEMREMAKEELEELEEKIEELEEQLKVLLLPKDPNDEKNVILEIRAGTGGD 124
Query: 185 EASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIH 244
EA++FA D+F+MY RY++ KGWK E++ E++L GYKE A I G GVY +LKFESG+H
Sbjct: 125 EAAIFAGDLFRMYSRYAESKGWKVEILSANETELGGYKEVIAEIKGDGVYSRLKFESGVH 184
Query: 245 RVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSA 304
RVQRVP+TE GR+HTSA +VA++P+ +EV+V + DLRIDT+RS G+GGQH NTT+SA
Sbjct: 185 RVQRVPVTESQGRIHTSAATVAVMPELEEVEVDINPADLRIDTFRSSGAGGQHVNTTDSA 244
Query: 305 VRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQIGSGDR 364
VR+TH+PTG+ + QDERSQH NK KA+KVL A+LYE E+ + +++ R Q+GSGDR
Sbjct: 245 VRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQAAQASTRKSQVGSGDR 304
Query: 365 SERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQEMDAIASFGS 420
SERIRTYNFPQ RVTDHR+ +T + + +++EG+ LD I+AL+ + + +A+
Sbjct: 305 SERIRTYNFPQNRVTDHRINLTLYKLDEVLEGD-LDELIEALIAEDQAQQLAALSE 359
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 255 bits (654), Expect = 7e-82
Identities = 133/346 (38%), Positives = 199/346 (57%), Gaps = 15/346 (4%)
Query: 71 AIERRSACLENLVNQPE--ASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIY 128
A++ R LE P+ K KEL L+ + + ELR + +++ L L
Sbjct: 27 ALKERLEELEAEAEDPDFWNDQERAQKVTKELSSLKAKLDTLEELRQRLDDLEELLEL-A 85
Query: 129 ECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAGTGGEEASL 188
E +D++ L A EL EK+L +L L+ LL + D + IL + AG GG EA
Sbjct: 86 EEEDDEETLAEAEAELKAL---EKKLAALELERLL-SGEYDANNAILTIHAGAGGTEAQD 141
Query: 189 FAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQR 248
+A + +MY R++++ G+K EV+ +E + G K A+ I G YG LK E+G+HR+ R
Sbjct: 142 WASMLLRMYLRWAERHGFKVEVLDYSEGEEAGIKSATFKIKGPYAYGYLKSETGVHRLVR 201
Query: 249 VPLTEKSGRVHTSAVSVAILPQADE-VDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRV 307
+ + +GR HTS SV + P+ D+ +++ + +DLRIDTYRS G+GGQH N T+SAVR+
Sbjct: 202 ISPFDSAGRRHTSFASVEVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTDSAVRI 261
Query: 308 THIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQ--IGSGDRS 365
THIPTG+ + Q+ERSQH NKA A+K+L AKLYE+E + + L+ E+ IG G
Sbjct: 262 THIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRAAEKDALKGEKKEIGWGS-- 319
Query: 366 ERIRTYNF-PQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQ 410
+IR+Y P V D R G +++G+ LD FI+A L +
Sbjct: 320 -QIRSYVLHPYQMVKDLRTGYETGNTQAVLDGD-LDGFIEAYLRWR 363
>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 = 230 bits (587), Expect = 5e-72
Identities = 120/341 (35%), Positives = 190/341 (55%), Gaps = 11/341 (3%)
Query: 71 AIERRSACLENLVNQPE--ASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIY 128
+ R LE + P KE L + + EL+ +++ L L
Sbjct: 27 KKKARLEELEKEMEDPNFWNDQERAQAVIKERSSLEAVLDTLEELKNSLEDLSELLELAV 86
Query: 129 ECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAGTGGEEASL 188
E +D++ + EL EK+L L L+++L + D + L ++AG GG EA
Sbjct: 87 E-EDDEETFNELDAELKAL---EKKLAELELRTML-SGEYDANNAYLTIQAGAGGTEAQD 141
Query: 189 FAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQR 248
+A +++MY R+++++G+K E++ +E + G K + I G YG LK E G+HR+ R
Sbjct: 142 WASMLYRMYLRWAERRGFKVEIIDYSEGEEAGIKSVTILIKGPYAYGYLKSEQGVHRLVR 201
Query: 249 VPLTEKSGRVHTSAVSVAILPQADE-VDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRV 307
+ + +GR HTS SV ++P+ D+ +D+ ++ EDLRIDTYR+ G+GGQH N T+SAVR+
Sbjct: 202 ISPFDANGRRHTSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRI 261
Query: 308 THIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQIGSGDRSER 367
THIPTG+ + Q++RSQH NK A+KVL AKLYE+E + + E+ G S+
Sbjct: 262 THIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEMEKEQAEKDAKEGEKSEIGWGSQ- 320
Query: 368 IRTYNF-PQGRVTDHRVGITHHAISDMMEGENLDIFIDALL 407
IR+Y P V D R G + +++G ++D FI+A L
Sbjct: 321 IRSYVLHPYSMVKDLRTGYETGNVQAVLDG-DIDQFIEAYL 360
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 198 bits (506), Expect = 2e-60
Identities = 113/318 (35%), Positives = 184/318 (57%), Gaps = 10/318 (3%)
Query: 95 KANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDEEKRL 154
+ E + L+D + + LR + I+ ++ L SE+ D +M E + + ++ +
Sbjct: 15 EITSEEKYLKDKLDKYNHLRNR---IEDIEVLCEMMSEEDD--EMKKEIISEVKNIKEEI 69
Query: 155 QSLLLKSLLPKDDADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVT 214
+++LL + D + IL + +G GG +A + + +MY R+++KKG+K E++ +
Sbjct: 70 DRFKIETLL-SGEYDRNNAILTLHSGVGGTDAQDWTEMLLRMYTRWAEKKGYKVEIIDLL 128
Query: 215 ESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQ-ADE 273
E D G K + I+G YG LK E GIHR+ R+ +G+ TS SV +LP+ D+
Sbjct: 129 EGDEAGIKSVTLKITGEFAYGYLKAEKGIHRLVRISPFNANGKRQTSFASVEVLPELTDD 188
Query: 274 VDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALK 333
D+ +R+EDL+IDTYR+GG+GGQH N T SAVR+THIPTG+ + Q+ERSQH NK A+K
Sbjct: 189 QDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAMK 248
Query: 334 VLCAKLYEMERSRIHLSRSKLRSEQIGSGDRSERIRTYNF-PQGRVTDHRVGITHHAISD 392
+L +KL E+ + R H + + + ++ +IR+Y F P V DHR G+ +
Sbjct: 249 MLKSKLVEL-KERAHKEKIEDLTGELKDMGWGSQIRSYVFHPYNLVKDHRTGVETSNVDS 307
Query: 393 MMEGENLDIFIDALLLQQ 410
+M+G+ +D FI L
Sbjct: 308 VMDGD-IDNFITQYLKGN 324
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 184 bits (469), Expect = 7e-56
Identities = 94/240 (39%), Positives = 144/240 (60%), Gaps = 10/240 (4%)
Query: 173 CILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVG 232
L + AG GG EA +A + +MY R++++KG+K EV+ ++ + G K A+ I G
Sbjct: 1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60
Query: 233 VYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADE-VDVRLRNEDLRIDTYRSG 291
YG LK E+G+HR+ R+ + +GR HTS SV + P+ D +++ + ++DLRIDTYR+
Sbjct: 61 AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRAS 120
Query: 292 GSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSR 351
G+GGQH N T+SAVR+TH+PTG+ + Q+ERSQH+NKA A K+L KLY + + R
Sbjct: 121 GAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQE----KR 176
Query: 352 SKLRSEQIGSGDRSER---IRTYNF-PQGRVTDHRVGITHHAISDMMEGENLDIFIDALL 407
S+ ++ + IR+Y P D R G+ S +++G+ D FI A L
Sbjct: 177 SQEKNRERALKKLIGWGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDGD-KDGFIKAYL 235
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 182 bits (463), Expect = 6e-54
Identities = 117/314 (37%), Positives = 181/314 (57%), Gaps = 16/314 (5%)
Query: 109 LISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAI--DEEKRLQSLLLK------ 160
L+ E + I+G+ L +++ +++ M EE +I D EK ++ L +
Sbjct: 18 LMRERQQLDDSINGINHLEQTLNDNIELIAMGEEEGDKSIVEDAEKTIRDLKDEIDRRQI 77
Query: 161 SLLPKDDADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRG 220
L +AD D LEV AG GG E+ +A + +MY R+++++G K EV+ V + + G
Sbjct: 78 DALLSGEADANDTYLEVHAGAGGTESQDWASMLLRMYTRWAERQGRKVEVLEVHDGEEAG 137
Query: 221 YKEASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADE-VDVRLR 279
K A+ + G YG LK ESG+HR+ R+ + + R HTS S+ + P D+ ++V +
Sbjct: 138 IKSATILVKGHNAYGWLKTESGVHRLVRISPYDSNARRHTSFASIWVYPVIDDNIEVDVN 197
Query: 280 NEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKL 339
D+RIDTYRS G+GGQH NTT+SAVR+THIPTG+ + Q ERSQH N+AKA +L A+L
Sbjct: 198 ESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARL 257
Query: 340 YEME-RSRIHLSRSKLRSE-QIGSGDRSERIRTYNF-PQGRVTDHRVGITHHAISDMMEG 396
YE E + R + + S+ IG G +IR+Y P V D R G+ D+++G
Sbjct: 258 YEEELKKREEATNAAAASKTDIGWG---HQIRSYVLQPYQLVKDLRTGVESTNPQDVLDG 314
Query: 397 ENLDIFIDALLLQQ 410
+L+ F++A L +
Sbjct: 315 -DLNEFMEAALAHR 327
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 179 bits (454), Expect = 8e-53
Identities = 107/250 (42%), Positives = 150/250 (60%), Gaps = 8/250 (3%)
Query: 162 LLPKDDADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGY 221
LL D D+ + ILE+ G GG E+ + + +MY R+++K+G+K E V D G
Sbjct: 77 LLLSDPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRWAEKRGFKVETVDYLPGDEAGI 136
Query: 222 KEASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQ-ADEVDVRLRN 280
K + I G YG LK E G+HR+ R+ + SGR HTS VS ++P+ DEV++ +R
Sbjct: 137 KSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFVSCEVVPEFNDEVEIEVRT 196
Query: 281 EDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLY 340
EDL+IDTYR+ G+GGQH NTT+SAVR+TH PT ++ Q ERSQ N+ A+K+L AKLY
Sbjct: 197 EDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKLY 256
Query: 341 EMERSRIHLSRSKLRSEQ--IGSGDRSERIRTYNF-PQGRVTDHRVGITHHAISDMMEGE 397
+ + ++R EQ IG G +IR+Y F P V DHR + +M+GE
Sbjct: 257 QKKLEEQQAELDEIRGEQKEIGWG---SQIRSYVFHPYSLVKDHRTNTEVGNVQAVMDGE 313
Query: 398 NLDIFIDALL 407
+D FIDA L
Sbjct: 314 -IDPFIDAYL 322
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 175 bits (445), Expect = 1e-51
Identities = 104/302 (34%), Positives = 169/302 (55%), Gaps = 15/302 (4%)
Query: 117 QKEIDGLKSLIYECSEDKDMLDMAT----EELCLAIDEEKRLQSLLLKSL----LPKDDA 168
+K + G+ ++ ++ ++LD+A E+ LA+ + ++ L +
Sbjct: 3 EKTVIGIADVLSGLADAGELLDLAESEQDEDTALAVIADLDKYQAHVEKLEFQRMFSGQM 62
Query: 169 DERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAI 228
D + ++++AG GG EA +A + +MY R+++ +GWK E++ V+ ++ G K A+ I
Sbjct: 63 DGANAFVDIQAGAGGTEAQDWAEILLRMYLRWAESRGWKTELMEVSGGEVAGIKSATVRI 122
Query: 229 SGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADE-VDVRLRNEDLRIDT 287
G YG LK E G+HR+ R + R HTS SV + P+ D+ +++ + DLR D
Sbjct: 123 EGEYAYGWLKTEIGVHRLVRKSPFDSDNRRHTSFTSVFVSPEVDDNIEIDINPADLRTDV 182
Query: 288 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRI 347
YRS G+GGQH N T SAVR+THIPT ++ Q RSQH N+ A+K+L AKLYE+E +
Sbjct: 183 YRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEVQKR 242
Query: 348 HLSRSKLRSEQ--IGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDA 405
+ + L + + IG G +IR Y Q R+ D R GI +++G+ LD F++A
Sbjct: 243 NAEKDALEATKSDIGWG---SQIRNYVLDQSRIKDLRTGIERSDTQKVLDGD-LDEFVEA 298
Query: 406 LL 407
L
Sbjct: 299 SL 300
>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 = 164 bits (417), Expect = 6e-50
Identities = 63/114 (55%), Positives = 80/114 (70%)
Query: 269 PQADEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNK 328
P +EV++ + DLRIDT+RS G GGQ+ N T SAVR+TH+PTG+ + Q+ERSQH N+
Sbjct: 1 PLDEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNR 60
Query: 329 AKALKVLCAKLYEMERSRIHLSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHR 382
KAL+ L AKLYE E + R+ Q+ GDR E+IRTYNFPQGRV DHR
Sbjct: 61 EKALERLKAKLYEAELQKKREKTKPTRASQVRRGDRKEKIRTYNFPQGRVKDHR 114
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 150 bits (381), Expect = 2e-44
Identities = 59/110 (53%), Positives = 80/110 (72%), Gaps = 1/110 (0%)
Query: 132 EDKDMLDMATEELC-LAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAGTGGEEASLFA 190
ED +M ++A EEL L + E+ L+ LL LLPKD D+++ ILE+RAG GG+EA+LFA
Sbjct: 7 EDDEMRELAEEELEELEAELEEELEELLKLLLLPKDPNDDKNAILEIRAGAGGDEAALFA 66
Query: 191 VDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFE 240
D+ +MY RY+++KGWK EV+ +E +L G KEA+ ISG G YGKLKFE
Sbjct: 67 GDLLRMYLRYAERKGWKVEVLDESEGELGGIKEATLKISGEGAYGKLKFE 116
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 139 bits (353), Expect = 2e-40
Identities = 53/112 (47%), Positives = 73/112 (65%)
Query: 129 ECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAGTGGEEASL 188
E +D ++ + A EEL E + L+ LL LLP D D+++ ILE+RAG GG EA L
Sbjct: 4 EEEDDPELREEAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTEAQL 63
Query: 189 FAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFE 240
FA D+ +MY+RY+++KGWK EV+ +E + G KEA+ I G G YG LKFE
Sbjct: 64 FAEDLLRMYQRYAERKGWKVEVIDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 81.6 bits (202), Expect = 5e-18
Identities = 33/79 (41%), Positives = 49/79 (62%), Gaps = 4/79 (5%)
Query: 282 DLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKL-- 339
++R +T RS G GGQH N T+SAVR TH+ +G+++ +Q ERSQH NK A ++ KL
Sbjct: 108 EIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQ 167
Query: 340 YEMERSRIHLSRSKLRSEQ 358
+ E+S +S+ R
Sbjct: 168 QQQEQSAAL--KSQRRMFH 184
>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 = 78.3 bits (193), Expect = 7e-17
Identities = 34/86 (39%), Positives = 55/86 (63%), Gaps = 4/86 (4%)
Query: 282 DLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYE 341
++R +T RS G GGQH N T SAVR TH+ +G+++ +Q ERSQH NK A +L +L +
Sbjct: 107 EIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLAD 166
Query: 342 MERSRIHLSRSKLRSEQIGSGDRSER 367
+++ + + LR+E+ + + ER
Sbjct: 167 LQQEQ----AAALRAERRTAHHQIER 188
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 37.4 bits (88), Expect = 0.003
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 24/85 (28%)
Query: 275 DVRLRNEDLRIDTYRSGGSGGQHANTTNSAV------RVTHIP---------------TG 313
+ + +L R+ G GGQ+ N ++AV + +P T
Sbjct: 7 RLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITK 66
Query: 314 ---MTISIQDERSQHMNKAKALKVL 335
+ I Q+ RSQ N+ AL+ L
Sbjct: 67 DGVIVIKAQEFRSQERNREDALERL 91
>gnl|CDD|166487 PLN02846, PLN02846, digalactosyldiacylglycerol synthase.
Length = 462
Score = 32.1 bits (73), Expect = 0.57
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 9/56 (16%)
Query: 93 YSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAI 148
+SK KEL KL L QKE+ GL+ +Y ED D + A E+L L +
Sbjct: 239 WSKGYKELLKL---------LHKHQKELSGLEVDLYGSGEDSDEVKAAAEKLELDV 285
>gnl|CDD|220410 pfam09798, LCD1, DNA damage checkpoint protein. This is a family
of proteins which regulate checkpoint kinases. In
Schizosaccharomyces pombe this protein is called Rad26
and in Saccharomyces cerevisiae it is called LCD1.
Length = 648
Score = 31.7 bits (72), Expect = 0.87
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 5/72 (6%)
Query: 64 IMEQRVLAIERRSACL---ENLVNQPEASPAEYSKANKELRKLRDSMHLISELRT--KQK 118
++EQR L+ L NL+ +AS +++ + + + EL +
Sbjct: 53 VLEQRGLSANDLRTELSPPSNLLKTSDASHIADESQPNSIKQKKREISPVKELVPLNPNR 112
Query: 119 EIDGLKSLIYEC 130
I KSL +
Sbjct: 113 IIKDDKSLFLDH 124
>gnl|CDD|218704 pfam05701, DUF827, Plant protein of unknown function (DUF827).
This family consists of several plant proteins of
unknown function. Several sequences in this family are
described as being "myosin heavy chain-like".
Length = 484
Score = 30.0 bits (67), Expect = 2.8
Identities = 16/71 (22%), Positives = 38/71 (53%)
Query: 86 PEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELC 145
PE + ++A+ EL L+ + +++ + + KE++ K+ + + +E++ L E L
Sbjct: 227 PEKDLEKLAEASAELESLQKEISIMASVASVLKELEEAKANLEKAAEEEKSLRNLVESLK 286
Query: 146 LAIDEEKRLQS 156
++EEK+
Sbjct: 287 QELEEEKKELE 297
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 29.7 bits (67), Expect = 3.2
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 79 LENLVNQPEASPAEYSKANKELRKLRDSMHL------ISELRTKQKEIDGLKSLIYECS- 131
L+ N+ + + K L+K +S+ L I EL+ K + I+G+K L+
Sbjct: 717 LKVTPNELPKKIERFFEEWKALQKELESLKLKIADQKIDELKDKAETINGVKVLVEVVDA 776
Query: 132 EDKDMLDMATEEL 144
+D L + L
Sbjct: 777 KDMKSLKTMADRL 789
>gnl|CDD|218611 pfam05499, DMAP1, DNA methyltransferase 1-associated protein 1
(DMAP1). DNA methylation can contribute to
transcriptional silencing through several
transcriptionally repressive complexes, which include
methyl-CpG binding domain proteins (MBDs) and histone
deacetylases (HDACs). The chief enzyme that maintains
mammalian DNA methylation, DNMT1, can also establish a
repressive transcription complex. The non-catalytic
amino terminus of DNMT1 binds to HDAC2 and DMAP1 (for
DNMT1 associated protein), and can mediate
transcriptional repression. DMAP1 has intrinsic
transcription repressive activity, and binds to the
transcriptional co-repressor TSG101. DMAP1 is targeted
to replication foci through interaction with the far N
terminus of DNMT1 throughout S phase, whereas HDAC2
joins DNMT1 and DMAP1 only during late S phase,
providing a platform for how histones may become
deacetylated in heterochromatin following replication.
Length = 175
Score = 28.7 bits (64), Expect = 4.2
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 55 EMLSNDLIKIMEQRVLAIERRSACLENLVNQPE-----ASPAEYSKANKELRKLRDSM 107
E L +L KI E R E+++ L+ L+ + S AE K K+L K +
Sbjct: 3 EYLIAELRKI-EARKKEREKKAQDLQKLITAADQQAAGFSTAEARKREKKLPKKKIPQ 59
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 29.4 bits (67), Expect = 4.9
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 80 ENLVNQPEASPAEYSKANKELRKLRDSM--HLISELRTKQKEIDGLKSLIYECSED-KDM 136
E L E E+ + KE+ KLR + L SEL +K +E+ G+K ++ E D ++
Sbjct: 757 EQLPKTVERFFEEWKEQKKEIEKLRKELAELLASELLSKAEEVGGVKVVVEEVDADEDEL 816
Query: 137 LDMATE 142
+A E
Sbjct: 817 RKIANE 822
>gnl|CDD|132951 cd06620, PKc_MAPKK_Byr1_like, Catalytic domain of fungal Byr1-like
dual-specificity MAP kinase kinases. Protein kinases
(PKs), MAP kinase kinase (MAPKK) subfamily, fungal
Byr1-like proteins, catalytic (c) domain. PKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine or tyrosine residues on protein
substrates. The MAPKK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein serine/threonine kinases, protein tyrosine
kinases, RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase. The
mitogen-activated protein (MAP) kinase signaling
pathways are important mediators of cellular responses
to extracellular signals. The pathways involve a triple
kinase core cascade comprising of the MAP kinase (MAPK),
which is phosphorylated and activated by a MAPK kinase
(MAPKK or MKK), which itself is phosphorylated and
activated by a MAPK kinase kinase (MAPKKK or MKKK).
Members of this group include the MAPKKs Byr1 from
Schizosaccharomyces pombe, FUZ7 from Ustilago maydis,
and related proteins. Byr1 phosphorylates its downstream
target, the MAPK Spk1, and is regulated by the MAPKKK
Byr2. The Spk1 cascade is pheromone-responsive and is
essential for sporulation and sexual differentiation in
fission yeast. FUZ7 phosphorylates and activates its
target, the MAPK Crk1, which is required in mating and
virulence in U. maydis.
Length = 284
Score = 29.0 bits (65), Expect = 5.0
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 7/40 (17%)
Query: 278 LRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTIS 317
LRNEDL + G+GG S +V HIPTG ++
Sbjct: 2 LRNEDLETISDLGAGNGG-------SVSKVKHIPTGTVMA 34
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 28.7 bits (64), Expect = 6.0
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 58 SNDLIKIM--EQRVLAIERRS--ACLENLVNQPEASPAEYSKANKELRKL-RDSMHLISE 112
++ L++ + E R ER + L L +Q + Y + EL +L ++ L+ E
Sbjct: 27 ADILLERLDSELRDAEKERDTYKQYLSKLESQNVE-ISNYEALDSELDELKKEEERLLDE 85
Query: 113 LRTKQKEIDGLKSLIYECSEDKDMLDMATEE 143
L +KE D L + E E+K+ L+ +
Sbjct: 86 LEELEKEDDDLDGELVELQEEKEQLENEELQ 116
>gnl|CDD|240440 PTZ00493, PTZ00493, phosphomethylpyrimidine kinase; Provisional.
Length = 321
Score = 28.0 bits (62), Expect = 9.2
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 15/91 (16%)
Query: 128 YECSEDKDMLD-------MATEELCLAIDEEKRLQSLLLKSL-LPKDDADERD------- 172
YEC + LD ELC + E+ + + L KS + ++ A+E +
Sbjct: 148 YECKVILEALDCQMDLSKANMTELCKLVTEKLNINACLFKSCNVGENSAEENEVYAVDHL 207
Query: 173 CILEVRAGTGGEEASLFAVDVFKMYERYSQK 203
CI V + GE+ + A V +Y+ Y +
Sbjct: 208 CIRNVGSYPTGEKQQIDAGGVTYLYDVYKLR 238
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 28.0 bits (62), Expect = 9.5
Identities = 37/190 (19%), Positives = 68/190 (35%), Gaps = 17/190 (8%)
Query: 79 LENLVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECSEDKDMLD 138
++L N P + +++ ++ K+ D + + ++ + K+I L S YE E +D L
Sbjct: 11 TDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISILKKIIDLDSQTYE--EVEDGLL 68
Query: 139 MATEELCLAIDEEKRLQSLLL---KSLLPKDDADERDCILEVRAGTGGEEASLFAVDVFK 195
EL L ++ +S L + LL + D I + A + +
Sbjct: 69 KEIRELLLKAIYIQKEKSDLADRAEKLLRRHRKLLDDRI--AKRPHEKVAARI---ENCH 123
Query: 196 MYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIH-RVQRVPLTEK 254
++ + + SAA S + KLK IH +R P
Sbjct: 124 DAVSRLERNSYSSAA------RRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSS 177
Query: 255 SGRVHTSAVS 264
V + S
Sbjct: 178 KREVSFTLES 187
>gnl|CDD|213060 cd12091, FANCM_ID, insert domain of FANCM helicase and similar
proteins. FANCM and related proteins, like Mph1 and
Fml1, are DNA junction-specific helicases/translocases
that bind to and process perturbed replication forks and
intermediates of homologous recombination. FANCM
contains an N-terminal superfamily 2 helicase (SF2)
domain, although FANCM, in contrast to other members of
this family, does not exhibit DNA helicase activity. The
SF2 helicase domain is comprised of 3 structural
domains, the 2 generally conserved helicase domains and
a helical domain inserted between the two domains. FANCM
is a component of the Fanconi anaemia (FA) core complex.
FA is a rare genetic disease in humans that is
associated with progressive bone marrow failure, a
variety of developmental abnormalities, and a high
incidence of cancer. A key role of this complex is to
monoubiquitination of FANCD2 and FANCI during S-phase
and in response to DNA damage. The role of FANCM during
this process seems to be the recruitment of the complex
to chromatin.
Length = 122
Score = 26.9 bits (60), Expect = 9.7
Identities = 9/41 (21%), Positives = 17/41 (41%)
Query: 76 SACLENLVNQPEASPAEYSKANKELRKLRDSMHLISELRTK 116
+ L + ++ SK+ KEL + L+ EL +
Sbjct: 82 RPFYDYLKEIATETKSKKSKSKKELANNPNFKELMDELEKQ 122
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 0.363
Gapped
Lambda K H
0.267 0.0857 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,160,171
Number of extensions: 2051465
Number of successful extensions: 1891
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1855
Number of HSP's successfully gapped: 74
Length of query: 422
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 323
Effective length of database: 6,546,556
Effective search space: 2114537588
Effective search space used: 2114537588
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: 60 (26.7 bits)