RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014874
(416 letters)
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 546 bits (1410), Expect = 0.0
Identities = 176/360 (48%), Positives = 264/360 (73%), Gaps = 2/360 (0%)
Query: 51 EPYLITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQ 110
+P ++ KLE+ + +++L L+DPEV+S+ ++KL++ AEL+ +V YR++K ++
Sbjct: 1 KPSMLDKLEALEERYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAQED 60
Query: 111 LEESRALAKENGNDEEMAEMIASEIKSLSNELIELEEKLKVLLLPSDPLDARNIMLEVRA 170
LEE++ + +E +D EM EM E+K L L ELEE+LK+LLLP DP D +N++LE+RA
Sbjct: 61 LEEAKEMLEE-ESDPEMREMAKEELKELEERLEELEEELKILLLPKDPNDDKNVILEIRA 119
Query: 171 GAGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKY 230
G GGDEA ++AGDL RMY +Y+E+ WK ++S+SE E GG+K V+ EI G+ VYSKLK+
Sbjct: 120 GTGGDEAALFAGDLFRMYSRYAERQGWKVEILSASEGELGGYKEVIAEISGDGVYSKLKF 179
Query: 231 ESGVHRVQRVPQTEAQGRVHTSTATVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNVN 290
ESGVHRVQRVP TE+QGR+HTS ATVA++PEA+EVEV I+PKD+ + T RS GAGGQ+VN
Sbjct: 180 ESGVHRVQRVPATESQGRIHTSAATVAVLPEAEEVEVEINPKDLRIDTFRSSGAGGQHVN 239
Query: 291 KVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQV 350
++A+ + H PTGI + C +ER+Q +NK++A+++LRA+LY+ + ++ Q + R SQV
Sbjct: 240 TTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEAATRKSQV 299
Query: 351 GTGARAEKIRTYNYKDNRVTDHRLKM-NFELTSFLDGNIDNAVQSCAAMEQKELLEELAE 409
G+G R+E+IRTYN+ RVTDHR+ + ++L ++G++D + + A +Q E L L E
Sbjct: 300 GSGDRSERIRTYNFPQGRVTDHRINLTLYKLDEVMEGDLDELIDALIAEDQAEKLAALGE 359
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 484 bits (1248), Expect = e-171
Identities = 178/364 (48%), Positives = 265/364 (72%), Gaps = 4/364 (1%)
Query: 50 AEPYLITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEK 109
+P L+ KLES + +++L L+DPEV+S+P EY+KL++ AEL+ +V YR++K ++
Sbjct: 1 MKPSLLEKLESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQE 60
Query: 110 QLEESRALAKENGNDEEMAEMIASEIKSLSNELIELEEKLKVLLLPSDPLDARNIMLEVR 169
LE+++ + E D EM EM EIK L ++ ELEE+LK+LLLP DP D +NI+LE+R
Sbjct: 61 DLEDAKEMLAEE-KDPEMREMAEEEIKELEAKIEELEEELKILLLPKDPNDDKNIILEIR 119
Query: 170 AGAGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLK 229
AG GGDEA ++AGDL RMY +Y+E WK ++S+SE+E GG+K ++ I G VYS+LK
Sbjct: 120 AGTGGDEAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLK 179
Query: 230 YESGVHRVQRVPQTEAQGRVHTSTATVAIMPEADEV-EVVIDPKDIELTTARSGGAGGQN 288
+ESGVHRVQRVP TE+QGR+HTS ATVA++PE +EV E+ I+PKD+ + T RS GAGGQ+
Sbjct: 180 FESGVHRVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQH 239
Query: 289 VNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLS 348
VN ++A+ + H PTGI + C +ER+Q +NK++A+++LRA+LY+ + ++ Q + ++R S
Sbjct: 240 VNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEASERKS 299
Query: 349 QVGTGARAEKIRTYNYKDNRVTDHRLKM-NFELTSFLD-GNIDNAVQSCAAMEQKELLEE 406
QVG+G R+E+IRTYN+ NRVTDHR+ + ++L ++ G +D + + A +Q E L E
Sbjct: 300 QVGSGDRSERIRTYNFPQNRVTDHRINLTLYKLDEVMEGGKLDEIIDALIAEDQAEQLAE 359
Query: 407 LAES 410
L E
Sbjct: 360 LGEQ 363
>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 = 454 bits (1169), Expect = e-160
Identities = 175/361 (48%), Positives = 266/361 (73%), Gaps = 3/361 (0%)
Query: 50 AEPYLITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEK 109
+P L+ KLES + +++L L+DPEV+S+ + +KL++ ++L+E+V YR+++ ++
Sbjct: 1 MKPSLLEKLESLLERYEELEALLSDPEVISDQDKLRKLSKEYSQLEEIVDCYREYQQAQE 60
Query: 110 QLEESRALAKENGNDEEMAEMIASEIKSLSNELIELEEKLKVLLLPSDPLDARNIMLEVR 169
++E++ + +E+ D EM EM E++ L ++ ELEE+LKVLLLP DP D +N++LE+R
Sbjct: 61 DIKEAKEILEES--DPEMREMAKEELEELEEKIEELEEQLKVLLLPKDPNDEKNVILEIR 118
Query: 170 AGAGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLK 229
AG GGDEA I+AGDL RMY +Y+E WK ++S++E E GG+K V+ EIKG+ VYS+LK
Sbjct: 119 AGTGGDEAAIFAGDLFRMYSRYAESKGWKVEILSANETELGGYKEVIAEIKGDGVYSRLK 178
Query: 230 YESGVHRVQRVPQTEAQGRVHTSTATVAIMPEADEVEVVIDPKDIELTTARSGGAGGQNV 289
+ESGVHRVQRVP TE+QGR+HTS ATVA+MPE +EVEV I+P D+ + T RS GAGGQ+V
Sbjct: 179 FESGVHRVQRVPVTESQGRIHTSAATVAVMPELEEVEVDINPADLRIDTFRSSGAGGQHV 238
Query: 290 NKVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQ 349
N ++A+ + H PTGI + C +ER+Q +NK +A+++LRA+LYE + +QQ + R SQ
Sbjct: 239 NTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQAAQASTRKSQ 298
Query: 350 VGTGARAEKIRTYNYKDNRVTDHRLKMN-FELTSFLDGNIDNAVQSCAAMEQKELLEELA 408
VG+G R+E+IRTYN+ NRVTDHR+ + ++L L+G++D +++ A +Q + L L+
Sbjct: 299 VGSGDRSERIRTYNFPQNRVTDHRINLTLYKLDEVLEGDLDELIEALIAEDQAQQLAALS 358
Query: 409 E 409
E
Sbjct: 359 E 359
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 262 bits (672), Expect = 1e-84
Identities = 118/347 (34%), Positives = 201/347 (57%), Gaps = 21/347 (6%)
Query: 57 KLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEESRA 116
+++ + ++L + DP+ ++ QK+ EL + + ++ ++L++
Sbjct: 24 DVDALKERLEELEAEAEDPDFWNDQERAQKV---TKELSSLKAKLDTLEELRQRLDDLEE 80
Query: 117 LAK--ENGNDEEMAEMIASEIKSLSNELIELEEKLKVLLLPSDPLDARNIMLEVRAGAGG 174
L + E +DEE +E+K+L +L LE L+ LL S DA N +L + AGAGG
Sbjct: 81 LLELAEEEDDEETLAEAEAELKALEKKLAALE--LERLL--SGEYDANNAILTIHAGAGG 136
Query: 175 DEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGV 234
EA WA L+RMY +++E++ +K ++ SE E+ G K+ +IKG Y LK E+GV
Sbjct: 137 TEAQDWASMLLRMYLRWAERHGFKVEVLDYSEGEEAGIKSATFKIKGPYAYGYLKSETGV 196
Query: 235 HRVQRVPQTEAQGRVHTSTATVAIMPEADE-VEVVIDPKDIELTTARSGGAGGQNVNKVE 293
HR+ R+ ++ GR HTS A+V + PE D+ +E+ I+PKD+ + T RS GAGGQ+VNK +
Sbjct: 197 HRLVRISPFDSAGRRHTSFASVEVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTD 256
Query: 294 TAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQR--LSQVG 351
+A+ + H PTGI + C ER+Q QNK+ A+++L+AKLYE+++ ++ + + ++G
Sbjct: 257 SAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRAAEKDALKGEKKEIG 316
Query: 352 TGARAEKIRTYNYKD-NRVTDHRLKMNFELT---SFLDGNIDNAVQS 394
G +IR+Y V D R +E + LDG++D +++
Sbjct: 317 WG---SQIRSYVLHPYQMVKDLR--TGYETGNTQAVLDGDLDGFIEA 358
>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 = 233 bits (596), Expect = 2e-73
Identities = 122/346 (35%), Positives = 198/346 (57%), Gaps = 13/346 (3%)
Query: 54 LITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEE 113
E ++L ++ DP ++ Q + + + L+ V+ T + K+ + L E
Sbjct: 21 GSLDPEKKKARLEELEKEMEDPNFWNDQERAQAVIKERSSLEAVLDTLEELKNSLEDLSE 80
Query: 114 SRALAKENGNDEEMAEMIASEIKSLSNELIELEEKLKVLLLPSDPLDARNIMLEVRAGAG 173
LA E +DEE + +E+K+L +L ELE L+ +L S DA N L ++AGAG
Sbjct: 81 LLELAVEE-DDEETFNELDAELKALEKKLAELE--LRTML--SGEYDANNAYLTIQAGAG 135
Query: 174 GDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESG 233
G EA WA L RMY +++E+ +K +I SE E+ G K+V + IKG Y LK E G
Sbjct: 136 GTEAQDWASMLYRMYLRWAERRGFKVEIIDYSEGEEAGIKSVTILIKGPYAYGYLKSEQG 195
Query: 234 VHRVQRVPQTEAQGRVHTSTATVAIMPEADE-VEVVIDPKDIELTTARSGGAGGQNVNKV 292
VHR+ R+ +A GR HTS A+V +MPE D+ +++ I P+D+ + T R+ GAGGQ+VNK
Sbjct: 196 VHRLVRISPFDANGRRHTSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKT 255
Query: 293 ETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGT 352
++A+ + H PTGI + C +R+Q +NK A+++L+AKLYE+++ ++Q + + +
Sbjct: 256 DSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEMEKEQAEKDAKEGEKSEI 315
Query: 353 GARAEKIRTYNYKD-NRVTDHRLKMNFEL---TSFLDGNIDNAVQS 394
G +IR+Y + V D R +E + LDG+ID +++
Sbjct: 316 GW-GSQIRSYVLHPYSMVKDLR--TGYETGNVQAVLDGDIDQFIEA 358
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 187 bits (476), Expect = 5e-56
Identities = 108/311 (34%), Positives = 179/311 (57%), Gaps = 14/311 (4%)
Query: 85 QKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDEEMAEMIASEIKSLSNELIE 144
Q++ L + + Y ++ + +E + E D+EM + I SE+K++ E+
Sbjct: 14 QEITSEEKYLKDKLDKYNHLRNRIEDIEVLCEMMSEE--DDEMKKEIISEVKNIKEEI-- 69
Query: 145 LEEKLKVLLLPSDPLDARNIMLEVRAGAGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISS 204
++ K+ L S D N +L + +G GG +A W L+RMY +++E+ +K +I
Sbjct: 70 --DRFKIETLLSGEYDRNNAILTLHSGVGGTDAQDWTEMLLRMYTRWAEKKGYKVEIIDL 127
Query: 205 SEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQRVPQTEAQGRVHTSTATVAIMPE-AD 263
E ++ G K+V ++I G Y LK E G+HR+ R+ A G+ TS A+V ++PE D
Sbjct: 128 LEGDEAGIKSVTLKITGEFAYGYLKAEKGIHRLVRISPFNANGKRQTSFASVEVLPELTD 187
Query: 264 EVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRAL 323
+ ++ I +D+++ T R+GGAGGQ+VNK E+A+ + H PTGI + C ER+Q NK A+
Sbjct: 188 DQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAM 247
Query: 324 QLLRAKLYEIKVREQQEKIR--TQRLSQVGTGARAEKIRTYNYKD-NRVTDHRLKM-NFE 379
++L++KL E+K R +EKI T L +G G+ +IR+Y + N V DHR +
Sbjct: 248 KMLKSKLVELKERAHKEKIEDLTGELKDMGWGS---QIRSYVFHPYNLVKDHRTGVETSN 304
Query: 380 LTSFLDGNIDN 390
+ S +DG+IDN
Sbjct: 305 VDSVMDGDIDN 315
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 182 bits (465), Expect = 2e-55
Identities = 84/232 (36%), Positives = 132/232 (56%), Gaps = 10/232 (4%)
Query: 164 IMLEVRAGAGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNR 223
L + AGAGG EA WA L+RMY +++E+ +K ++ +S+ E+ G K+ ++IKG
Sbjct: 1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60
Query: 224 VYSKLKYESGVHRVQRVPQTEAQGRVHTSTATVAIMPEADE-VEVVIDPKDIELTTARSG 282
Y LK E+GVHR+ R+ ++ GR HTS A+V + PE D +E+ I D+ + T R+
Sbjct: 61 AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRAS 120
Query: 283 GAGGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKI 342
GAGGQ+VNK ++A+ L H PTGI + C ER+Q NK+ A ++L+ KLY + ++ ++
Sbjct: 121 GAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQEK 180
Query: 343 ----RTQRLSQVGTGARAEKIRTYNYKDNRVTDHRLKMNFELTS-FLDGNID 389
++L G R+ + Y D R + S LDG+ D
Sbjct: 181 NRERALKKLIGWGNQIRSYVLDPY----QPTKDLRTGVERRNKSKVLDGDKD 228
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 178 bits (452), Expect = 1e-52
Identities = 109/308 (35%), Positives = 177/308 (57%), Gaps = 9/308 (2%)
Query: 85 QKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDEEMAEMIASEIKSLSNELIE 144
Q + L ++V +R+ + + LE + L KE DE++ E + SE+K L E+ E
Sbjct: 14 QAVINEANALKDMVGKFRQLDETFENLEITHELLKEE-YDEDLHEELESEVKGLIQEMNE 72
Query: 145 LEEKLKVLLLPSDPLDARNIMLEVRAGAGGDEAGIWAGDLVRMYQKYSEQNSWKCTLISS 204
E + LL SDP D N +LE+ GAGG E+ W L+RMY +++E+ +K +
Sbjct: 73 YE----LQLLLSDPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRWAEKRGFKVETVDY 128
Query: 205 SEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQRVPQTEAQGRVHTSTATVAIMPE-AD 263
++ G K+V + IKG+ Y LK E GVHR+ R+ ++ GR HTS + ++PE D
Sbjct: 129 LPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFVSCEVVPEFND 188
Query: 264 EVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRAL 323
EVE+ + +D+++ T R+ GAGGQ+VN ++A+ + H PT + C ER+Q++N+ A+
Sbjct: 189 EVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAM 248
Query: 324 QLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEKIRTYNYKD-NRVTDHRLKMNF-ELT 381
++L+AKLY+ K+ EQQ ++ R Q G +IR+Y + + V DHR +
Sbjct: 249 KMLKAKLYQKKLEEQQAELDEIRGEQKEIGW-GSQIRSYVFHPYSLVKDHRTNTEVGNVQ 307
Query: 382 SFLDGNID 389
+ +DG ID
Sbjct: 308 AVMDGEID 315
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 178 bits (452), Expect = 3e-52
Identities = 106/336 (31%), Positives = 188/336 (55%), Gaps = 15/336 (4%)
Query: 71 KLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAK--ENGNDEEMA 128
K DP + ++ E QKL + +LD+ ++ E+ L ++ L E D+ +
Sbjct: 2 KAEDPSLWNDAQEAQKLMRERQQLDDSINGINHL---EQTLNDNIELIAMGEEEGDKSIV 58
Query: 129 EMIASEIKSLSNELIELEEKLKVLLLPSDPLDARNIMLEVRAGAGGDEAGIWAGDLVRMY 188
E I+ L +E+ ++ ++ L S DA + LEV AGAGG E+ WA L+RMY
Sbjct: 59 EDAEKTIRDLKDEI----DRRQIDALLSGEADANDTYLEVHAGAGGTESQDWASMLLRMY 114
Query: 189 QKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQRVPQTEAQGR 248
+++E+ K ++ + E+ G K+ + +KG+ Y LK ESGVHR+ R+ ++ R
Sbjct: 115 TRWAERQGRKVEVLEVHDGEEAGIKSATILVKGHNAYGWLKTESGVHRLVRISPYDSNAR 174
Query: 249 VHTSTATVAIMPEADE-VEVVIDPKDIELTTARSGGAGGQNVNKVETAIDLFHKPTGIRI 307
HTS A++ + P D+ +EV ++ D+ + T RS GAGGQ+VN ++A+ + H PTGI +
Sbjct: 175 RHTSFASIWVYPVIDDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVV 234
Query: 308 FCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEKIRTYNYKDN 367
C +ER+Q +N+++A +LRA+LYE ++++++E S+ G +IR+Y +
Sbjct: 235 QCQQERSQHKNRAKAWSMLRARLYEEELKKREEATNAAAASKTDIGW-GHQIRSYVLQPY 293
Query: 368 R-VTDHRLKM-NFELTSFLDGNIDNAVQSCAAMEQK 401
+ V D R + + LDG+++ ++ AA+ +
Sbjct: 294 QLVKDLRTGVESTNPQDVLDGDLNEFME--AALAHR 327
>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 = 161 bits (411), Expect = 5e-49
Identities = 59/114 (51%), Positives = 80/114 (70%)
Query: 260 PEADEVEVVIDPKDIELTTARSGGAGGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNK 319
P +EVE+ I D+ + T RS G GGQNVNK E+A+ L H PTGI + C EER+Q +N+
Sbjct: 1 PLDEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNR 60
Query: 320 SRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEKIRTYNYKDNRVTDHR 373
+AL+ L+AKLYE ++++++EK + R SQV G R EKIRTYN+ RV DHR
Sbjct: 61 EKALERLKAKLYEAELQKKREKTKPTRASQVRRGDRKEKIRTYNFPQGRVKDHR 114
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 160 bits (406), Expect = 3e-48
Identities = 55/112 (49%), Positives = 75/112 (66%)
Query: 120 ENGNDEEMAEMIASEIKSLSNELIELEEKLKVLLLPSDPLDARNIMLEVRAGAGGDEAGI 179
E +D E+ E E++ L EL ELE++L LLLP DP D +N +LE+RAGAGG EA +
Sbjct: 4 EEEDDPELREEAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTEAQL 63
Query: 180 WAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYE 231
+A DL+RMYQ+Y+E+ WK +I SE E+GG K +EI+G Y LK+E
Sbjct: 64 FAEDLLRMYQRYAERKGWKVEVIDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 165 bits (420), Expect = 5e-48
Identities = 98/279 (35%), Positives = 154/279 (55%), Gaps = 11/279 (3%)
Query: 120 ENGNDEEMAEMIASEIKSLSNELIELEEKLKVLLLPSDPLDARNIMLEVRAGAGGDEAGI 179
E+ DE+ A + +++ + EKL+ + S +D N ++++AGAGG EA
Sbjct: 27 ESEQDEDTALAVIADLDKYQAHV----EKLEFQRMFSGQMDGANAFVDIQAGAGGTEAQD 82
Query: 180 WAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYESGVHRVQR 239
WA L+RMY +++E WK L+ S E G K+ + I+G Y LK E GVHR+ R
Sbjct: 83 WAEILLRMYLRWAESRGWKTELMEVSGGEVAGIKSATVRIEGEYAYGWLKTEIGVHRLVR 142
Query: 240 VPQTEAQGRVHTSTATVAIMPEADE-VEVVIDPKDIELTTARSGGAGGQNVNKVETAIDL 298
++ R HTS +V + PE D+ +E+ I+P D+ RS GAGGQ+VNK E+A+ +
Sbjct: 143 KSPFDSDNRRHTSFTSVFVSPEVDDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRI 202
Query: 299 FHKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKV--REQQEKIRTQRLSQVGTGARA 356
H PT + C R+Q QN+ A+++L AKLYE++V R ++ S +G G+
Sbjct: 203 THIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEVQKRNAEKDALEATKSDIGWGS-- 260
Query: 357 EKIRTYNYKDNRVTDHRLKMNFELTS-FLDGNIDNAVQS 394
+IR Y +R+ D R + T LDG++D V++
Sbjct: 261 -QIRNYVLDQSRIKDLRTGIERSDTQKVLDGDLDEFVEA 298
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 157 bits (399), Expect = 3e-47
Identities = 58/113 (51%), Positives = 77/113 (68%), Gaps = 1/113 (0%)
Query: 120 ENGNDEEMAEMIASEIKSLSNELI-ELEEKLKVLLLPSDPLDARNIMLEVRAGAGGDEAG 178
E D+EM E+ E++ L EL ELEE LK+LLLP DP D +N +LE+RAGAGGDEA
Sbjct: 4 EEEEDDEMRELAEEELEELEAELEEELEELLKLLLLPKDPNDDKNAILEIRAGAGGDEAA 63
Query: 179 IWAGDLVRMYQKYSEQNSWKCTLISSSEAEKGGFKTVVMEIKGNRVYSKLKYE 231
++AGDL+RMY +Y+E+ WK ++ SE E GG K ++I G Y KLK+E
Sbjct: 64 LFAGDLLRMYLRYAERKGWKVEVLDESEGELGGIKEATLKISGEGAYGKLKFE 116
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 68.9 bits (169), Expect = 1e-13
Identities = 25/79 (31%), Positives = 39/79 (49%)
Query: 271 PKDIELTTARSGGAGGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKL 330
+I T RS G GGQ+VNK ++A+ H +GI + ER+Q NK A L+ KL
Sbjct: 106 SDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKL 165
Query: 331 YEIKVREQQEKIRTQRLSQ 349
+ + + +R+
Sbjct: 166 EQQQQEQSAALKSQRRMFH 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 = 65.2 bits (159), Expect = 3e-12
Identities = 30/97 (30%), Positives = 47/97 (48%), Gaps = 3/97 (3%)
Query: 271 PKDIELTTARSGGAGGQNVNKVETAIDLFHKPTGIRIFCTEERTQLQNKSRALQLLRAKL 330
+I T RS G GGQ+VNK E+A+ H +GI + ER+Q NK A LL +L
Sbjct: 105 EDEIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRL 164
Query: 331 YEIKVREQQEKI-RTQRLSQVGTGARAEKIRTYNYKD 366
++++Q R +R + R +R + +
Sbjct: 165 A--DLQQEQAAALRAERRTAHHQIERGNPVRVFKGEL 199
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 61.7 bits (151), Expect = 1e-11
Identities = 31/98 (31%), Positives = 43/98 (43%), Gaps = 28/98 (28%)
Query: 267 VVIDPKDIELTTARSGGAGGQNVNKVETAIDLF---------------------HKPTG- 304
+VI ++E R+ G GGQNVNKV TA++L H+ T
Sbjct: 8 LVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKD 67
Query: 305 --IRIFCTEERTQLQNKSRALQ----LLRAKLYEIKVR 336
I I E R+Q +N+ AL+ L+R L K R
Sbjct: 68 GVIVIKAQEFRSQERNREDALERLVALIREALKPPKKR 105
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 41.5 bits (98), Expect = 7e-04
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 6/90 (6%)
Query: 70 VKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDE---- 125
V + D + + +KL + +L E + R + L E + +E
Sbjct: 31 VHIEDLKEELSNERLRKLRSLLTKLSEALDKLRSYLPKLNPLREEKKKVSVKSLEELIKD 90
Query: 126 --EMAEMIASEIKSLSNELIELEEKLKVLL 153
E E I EIK L E+ ELE ++K L
Sbjct: 91 VEEELEKIEKEIKELEEEISELENEIKELE 120
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 39.3 bits (93), Expect = 0.003
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 14/77 (18%)
Query: 92 AELDEVVSTYRKFKDCEKQLEESRAL----------AKENGNDEE--MAEM--IASEIKS 137
++DE++ + ++ + +LEE +A AK G D E +AE+ + EIK+
Sbjct: 25 LDVDELLELDEERRELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKA 84
Query: 138 LSNELIELEEKLKVLLL 154
L EL ELE +L+ LLL
Sbjct: 85 LEAELDELEAELEELLL 101
>gnl|CDD|215534 PLN02984, PLN02984, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 341
Score = 34.8 bits (80), Expect = 0.075
Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 6/58 (10%)
Query: 213 KTVVMEIKGNRVYSKLKYESGVHRVQRVPQT----EAQG-RVHTSTATVAIMPEADEV 265
KT+ +E+ G++ S L +GV RV R PQ EA G VHT ++ ++I+ + DEV
Sbjct: 180 KTLSLELSGDQKMSYLSESTGVIRVYRYPQCSNEAEAPGMEVHTDSSVISILNQ-DEV 236
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 34.3 bits (79), Expect = 0.12
Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 9/94 (9%)
Query: 67 DLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEE--------SRALA 118
D + +P++V S + +L+++++ + K ++EE S+ +
Sbjct: 3 DRKLLRNNPDLVK-ESLKARGLSVDIDLEKLIALDDERKKLLSEIEELQAKRNELSKQIG 61
Query: 119 KENGNDEEMAEMIASEIKSLSNELIELEEKLKVL 152
K G ++ E I E+K L EL EL LK L
Sbjct: 62 KAKGQKKDKIEEIKKELKELKEELTELSAALKAL 95
>gnl|CDD|217020 pfam02403, Seryl_tRNA_N, Seryl-tRNA synthetase N-terminal domain.
This domain is found associated with the Pfam tRNA
synthetase class II domain (pfam00587) and represents
the N-terminal domain of seryl-tRNA synthetase.
Length = 108
Score = 32.2 bits (74), Expect = 0.12
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 9/69 (13%)
Query: 92 AELDEVVSTYRKFKDCEKQLEE--------SRALAKENGNDEEMAEMIASEIKSLSNELI 143
++DE++ + ++ + +LEE S+ + K E+ +IA E+K L +EL
Sbjct: 26 LDVDELLELDEERRELQVELEELQAERNELSKEIGKAKKKKEDAEALIA-EVKELKDELK 84
Query: 144 ELEEKLKVL 152
LE +L+ L
Sbjct: 85 ALEAELREL 93
>gnl|CDD|223216 COG0138, PurH, AICAR transformylase/IMP cyclohydrolase PurH (only
IMP cyclohydrolase domain in Aful) [Nucleotide transport
and metabolism].
Length = 515
Score = 31.8 bits (73), Expect = 0.66
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 7/49 (14%)
Query: 55 ITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRK 103
T L +AAK KD++V V +P++Y + + + E+ RK
Sbjct: 128 PTMLRAAAKNHKDVTV-------VVDPADYAAVLEELKANGELSLATRK 169
>gnl|CDD|239787 cd04254, AAK_UMPK-PyrH-Ec, UMP kinase (UMPK)-Ec, the
microbial/chloroplast uridine monophosphate kinase
(uridylate kinase) enzyme that catalyzes UMP
phosphorylation and plays a key role in pyrimidine
nucleotide biosynthesis; regulation of this process is
via feed-back control and via gene repression of
carbamoyl phosphate synthetase (the first enzyme of the
pyrimidine biosynthesis pathway). The UMP kinase of E.
coli (Ec) is known to function as a homohexamer, with
GTP and UTP being allosteric effectors. Like other
related enzymes (carbamate kinase, aspartokinase, and
N-acetylglutamate kinase) the E. coli and most bacterial
and chloroplast UMPKs (this CD) have a conserved,
N-terminal, lysine residue proposed to function in the
catalysis of the phosphoryl group transfer, whereas most
archaeal UMPKs appear to lack this residue and the
Pyrococcus furiosus structure has an additional Mg ion
bound to the ATP molecule which is proposed to function
as the catalysis instead. Members of this CD belong to
the Amino Acid Kinase Superfamily (AAK).
Length = 231
Score = 31.3 bits (72), Expect = 0.69
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 116 ALAKENGN--DEEMAEMIASEIKSLSNELIEL 145
ALA ENG D E+ IA EIK + + +E+
Sbjct: 11 ALAGENGFGIDPEVLNRIAREIKEVVDLGVEV 42
>gnl|CDD|238709 cd01421, IMPCH, Inosine monophosphate cyclohydrolase domain. This
is the N-terminal domain in the purine biosynthesis
pathway protein ATIC (purH). The bifunctional ATIC
protein contains a C-terminal ATIC formylase domain
that formylates
5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH
domain then converts the
formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to
inosine monophosphate. This is the final step in de novo
purine production.
Length = 187
Score = 31.0 bits (71), Expect = 0.80
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 55 ITKLESAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRK 103
+ L +AAK +KD++V + +P++YQK+ + + + R+
Sbjct: 125 PSLLRAAAKNYKDVTV-------LVDPADYQKVLEELKSNGSISEETRR 166
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 31.4 bits (72), Expect = 0.80
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 12/85 (14%)
Query: 80 NPSEYQ-KLAQ---SMAELDEVVSTYRKFKDCEKQLEE--------SRALAKENGNDEEM 127
NP + KL + ++D+++ + + ++LEE S+ + + E+
Sbjct: 10 NPDAVREKLKKRGGDALDVDKLLELDEERRKLLRELEELQAERNELSKEIGRALKRGEDD 69
Query: 128 AEMIASEIKSLSNELIELEEKLKVL 152
AE + +E+K L +L ELE L L
Sbjct: 70 AEELIAEVKELKEKLKELEAALDEL 94
>gnl|CDD|234038 TIGR02865, spore_II_E, stage II sporulation protein E. Stage II
sporulation protein E (SpoIIE) is a multiple membrane
spanning protein with two separable functions. It plays
a role in the switch to polar cell division during
sporulation. By means of it protein phosphatase
activity, located in the C-terminal region, it activates
sigma-F. All proteins that score above the trusted
cutoff to this model are found in endospore-forming
Gram-positive bacteria. Surprisingly, a sequence from
the Cyanobacterium-like (and presumably
non-spore-forming) photosynthesizer Heliobacillus
mobilis is homologous, and scores between the trusted
and noise cutoffs [Cellular processes, Sporulation and
germination].
Length = 764
Score = 31.6 bits (72), Expect = 0.94
Identities = 21/99 (21%), Positives = 42/99 (42%), Gaps = 10/99 (10%)
Query: 86 KLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGND-----EEMAEMIASEIK---S 137
K + + +++++ Y + K+LEE R L E E++A+ I EI
Sbjct: 406 KRKELINTTEDILNNYIINEMWRKRLEEGRRLVAEQLKGVAESVEDIAKEINLEIVFHQL 465
Query: 138 LSNELIEL--EEKLKVLLLPSDPLDARNIMLEVRAGAGG 174
L ++I + + + + + NI +E+ A G
Sbjct: 466 LEEKIIRALNKNGIPYEDVLAYNTEGGNIDVELTIAACG 504
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 30.9 bits (70), Expect = 1.5
Identities = 18/68 (26%), Positives = 35/68 (51%)
Query: 85 QKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDEEMAEMIASEIKSLSNELIE 144
++L + L+E+ + ++ E+++EE + E E + ++KSL L +
Sbjct: 274 EELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEK 333
Query: 145 LEEKLKVL 152
LEEKL+ L
Sbjct: 334 LEEKLEKL 341
>gnl|CDD|218681 pfam05667, DUF812, Protein of unknown function (DUF812). This
family consists of several eukaryotic proteins of
unknown function.
Length = 536
Score = 30.9 bits (70), Expect = 1.5
Identities = 28/98 (28%), Positives = 45/98 (45%), Gaps = 5/98 (5%)
Query: 54 LITKLESAAKTWKDLSVKLADPEVVSNPSEYQKL-AQSMAELDEVVSTYRKFKDCEKQLE 112
+LE K K L D E N ++ Q L S L E+ + + ++
Sbjct: 313 ENEELEEEYKIKKRTVELLPDAEN--NVAKLQALVVASSERLLELAQQWEAHR--TPLID 368
Query: 113 ESRALAKENGNDEEMAEMIASEIKSLSNELIELEEKLK 150
E R+L ++N N E+ + EIK L N++ ELE +L+
Sbjct: 369 EYRSLKEKNRNKEDETQRQLDEIKKLRNKIEELESELQ 406
>gnl|CDD|179310 PRK01622, PRK01622, OxaA-like protein precursor; Validated.
Length = 256
Score = 30.1 bits (68), Expect = 2.1
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 85 QKLAQSMAELDEVVSTYRKFKDCEKQLE---ESRALAKENG 122
+K+A ELD++ + + KD EKQ E E L K
Sbjct: 91 EKMAVMKPELDKIQAKLKVTKDLEKQKEYQKEMMELYKSGN 131
>gnl|CDD|214822 smart00798, AICARFT_IMPCHas, AICARFT/IMPCHase bienzyme. This is a
family of bifunctional enzymes catalysing the last two
steps in de novo purine biosynthesis. The bifunctional
enzyme is found in both prokaryotes and eukaryotes. The
second last step is catalysed by
5-aminoimidazole-4-carboxamide ribonucleotide
formyltransferase (AICARFT), this enzyme catalyses the
formylation of AICAR with 10-formyl-tetrahydrofolate to
yield FAICAR and tetrahydrofolate. The last step is
catalysed by IMP (Inosine monophosphate) cyclohydrolase
(IMPCHase), cyclizing FAICAR
(5-formylaminoimidazole-4-carboxamide ribonucleotide) to
IMP.
Length = 311
Score = 30.2 bits (69), Expect = 2.2
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 7/43 (16%)
Query: 61 AAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRK 103
AAK KD++V V +P++Y ++ + + + RK
Sbjct: 1 AAKNHKDVTV-------VVDPADYAEVLEELKANGGLSLETRK 36
>gnl|CDD|215408 PLN02763, PLN02763, hydrolase, hydrolyzing O-glycosyl compounds.
Length = 978
Score = 30.2 bits (68), Expect = 2.6
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 24 RFGGSQSKRNVVFPSLSFRTPKL 46
RF S+ R FPSLSF+ PKL
Sbjct: 18 RFDCSEDARKAAFPSLSFKNPKL 40
>gnl|CDD|168663 PRK06756, PRK06756, flavodoxin; Provisional.
Length = 148
Score = 29.1 bits (65), Expect = 2.6
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 20/63 (31%)
Query: 118 AKENGNDEEMAEMIASEIKSLSNEL-----------IELEEKLKVLL---------LPSD 157
A +GN EEMA+ IA I+ NE+ LE+ ++L LP D
Sbjct: 9 ASMSGNTEEMADHIAGVIRETENEIEVIDIMDSPEASILEQYDGIILGAYTWGDGDLPDD 68
Query: 158 PLD 160
LD
Sbjct: 69 FLD 71
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 29.9 bits (67), Expect = 2.7
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 89 QSMAELDEVVSTYRKFKDCEKQLEE----SRALAKENGNDEEMAEMIASEIKSLSNELIE 144
+++ + E + +++ +++LEE L KE E E + +K L E
Sbjct: 122 KTLQRVPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSR 181
Query: 145 LEEKLKVLL 153
LEE LK L
Sbjct: 182 LEEMLKKLP 190
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 29.3 bits (66), Expect = 2.8
Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 71 KLADPEVVSN------PSEYQKLAQSMAEL-DEVVSTYRKFKDCEKQLE--ESRALAKEN 121
K DPE + SE K Q++A++ RK ++ ++Q + E++A A
Sbjct: 20 KAEDPEKMLEQAIRDMQSELGKARQALAQVIARQKQLERKLEEQKEQAKKLENKARAALT 79
Query: 122 GNDEEMAEMIASEIKSLSNELIELEEKLKVLL 153
+EE+A +EI +L + LE +L
Sbjct: 80 KGNEELAREALAEIATLEKQAEALETQLTQQR 111
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 29.7 bits (66), Expect = 3.5
Identities = 24/108 (22%), Positives = 37/108 (34%), Gaps = 5/108 (4%)
Query: 34 VVFPSLSFRTPKLIC---MAEPYLITKLESAAKTWKDL--SVKLADPEVVSNPSEYQKLA 88
+ P I +A P K E T+ L ++ +P SE K+
Sbjct: 389 SLVAPPGLVAPTEINPSFLASPRKKMKREKLPVTFGALDDTLAWKEPSKEDQTSEDGKML 448
Query: 89 QSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDEEMAEMIASEIK 136
M E ++ K K EK+ EE + N D +A I+
Sbjct: 449 AIMGEAAAALALEPKKKKKEKEGEELQPKLVMNSEDASLASQEGMSIR 496
>gnl|CDD|224755 COG1842, PspA, Phage shock protein A (IM30), suppresses
sigma54-dependent transcription [Transcription / Signal
transduction mechanisms].
Length = 225
Score = 29.2 bits (66), Expect = 3.8
Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 9/91 (9%)
Query: 71 KLADPEVVSN------PSEYQKLAQSMAE-LDEVVSTYRKFKDCEKQLE--ESRALAKEN 121
K DPE + SE K Q++A+ + RK ++ + + E E +A
Sbjct: 21 KAEDPEKMLEQAIRDMESELAKARQALAQAIARQKQLERKLEEAQARAEKLEEKAELALQ 80
Query: 122 GNDEEMAEMIASEIKSLSNELIELEEKLKVL 152
+E++A E +SL + LE +L+
Sbjct: 81 AGNEDLAREALEEKQSLEDLAKALEAELQQA 111
>gnl|CDD|113297 pfam04521, Viral_P18, ssRNA positive strand viral 18kD cysteine
rich protein.
Length = 116
Score = 28.2 bits (63), Expect = 4.0
Identities = 17/59 (28%), Positives = 26/59 (44%)
Query: 300 HKPTGIRIFCTEERTQLQNKSRALQLLRAKLYEIKVREQQEKIRTQRLSQVGTGARAEK 358
H I FC E+ L L L +L +++ RE+Q K + Q L+ A+A
Sbjct: 47 HPELPIDGFCGEKHYGLYESLAQLSDLNLELEKLERREEQLKTQIQVLTAAAKLAKAAV 105
>gnl|CDD|238634 cd01309, Met_dep_hydrolase_C, Metallo-dependent hydrolases,
subgroup C is part of the superfamily of
metallo-dependent hydrolases, a large group of proteins
that show conservation in their 3-dimensional fold (TIM
barrel) and in details of their active site. The vast
majority of the members have a conserved metal binding
site, involving four histidines and one aspartic acid
residue. In the common reaction mechanism, the metal ion
(or ions) deprotonate a water molecule for a
nucleophilic attack on the substrate. The function of
this subgroup is unknown.
Length = 359
Score = 29.2 bits (66), Expect = 4.0
Identities = 16/75 (21%), Positives = 23/75 (30%), Gaps = 18/75 (24%)
Query: 254 ATVAIMPEADEVEVVIDPKDIELTTARSGG-------------AGGQNV----NKVETAI 296
T + P I+P D AR+GG GGQ V +
Sbjct: 55 ETDPVTPHVR-AIDGINPDDEAFKRARAGGVTTVQVLPGSANLIGGQGVVIKTDGGTIED 113
Query: 297 DLFHKPTGIRIFCTE 311
P G+++ E
Sbjct: 114 MFIKAPAGLKMALGE 128
>gnl|CDD|234854 PRK00881, purH, bifunctional
phosphoribosylaminoimidazolecarboxamide
formyltransferase/IMP cyclohydrolase; Provisional.
Length = 513
Score = 29.3 bits (67), Expect = 4.1
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 7/44 (15%)
Query: 60 SAAKTWKDLSVKLADPEVVSNPSEYQKLAQSMAELDEVVSTYRK 103
+AAK KD++V V +P++Y + + + R
Sbjct: 135 AAAKNHKDVAV-------VVDPADYDAVLEELKANGSTTLETRF 171
>gnl|CDD|227334 COG5001, COG5001, Predicted signal transduction protein containing
a membrane domain, an EAL and a GGDEF domain [Signal
transduction mechanisms].
Length = 663
Score = 29.5 bits (66), Expect = 4.3
Identities = 17/92 (18%), Positives = 29/92 (31%), Gaps = 20/92 (21%)
Query: 239 RVPQTEAQGRVHTSTAT-VAIMPE-ADEVEVVIDPKDIELTTARSGGAGGQNVNKVETAI 296
+ P RV + +A P AD E + + D L A+ G G
Sbjct: 336 QAPYDLRGVRVQVGASIGIAPFPSGADTSEQLFERADYALYHAKQNGKGAA--------- 386
Query: 297 DLFHKPTGIRIFCTEERTQLQNKSRALQLLRA 328
+F +++ + Q LR+
Sbjct: 387 ---------VLFDARHEAAIRDMAVVEQALRS 409
>gnl|CDD|183679 PRK12682, PRK12682, transcriptional regulator CysB-like protein;
Reviewed.
Length = 309
Score = 28.8 bits (65), Expect = 5.0
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 109 KQLEESRALAKENGNDEEMAEMIASEIKSLSNELIELEEKLKV 151
+QL R + N N E A+ + + +S +IELEE+L +
Sbjct: 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGI 46
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 29.1 bits (65), Expect = 5.4
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 13/82 (15%)
Query: 82 SEYQKLAQSMAELDEVVSTYRKFK-DCEKQLEE------------SRALAKENGNDEEMA 128
S QK QSM +++ + + + + EKQL E +RA A+ + EE A
Sbjct: 469 SAKQKDKQSMQSMEKRLKSEADSRVNAEKQLAEEKKRKKEEEETAARAAAQAAASREECA 528
Query: 129 EMIASEIKSLSNELIELEEKLK 150
E + + L E+ +LE LK
Sbjct: 529 ESLKQAKQDLEMEIKKLEHDLK 550
>gnl|CDD|235630 PRK05865, PRK05865, hypothetical protein; Provisional.
Length = 854
Score = 28.9 bits (64), Expect = 5.9
Identities = 12/49 (24%), Positives = 18/49 (36%)
Query: 368 RVTDHRLKMNFELTSFLDGNIDNAVQSCAAMEQKELLEELAESVGAPSG 416
R D+ ++ F L G D VQ + + + LL SG
Sbjct: 131 RNVDNWVQRLFALPVLPAGYADRVVQVVHSDDAQRLLVRALLDTVIDSG 179
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 6.1
Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 76 EVVSNPSEYQKLAQSMAELDEVVSTYRKFKDC-EKQLEESRALAKENGNDEEMAEMIASE 134
E+ E ++ + + EL E Y K + E+ L+E R + K EE I
Sbjct: 270 ELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEER 329
Query: 135 IKSLSN---ELIELEEKLKVLL 153
IK L L EL++KLK L
Sbjct: 330 IKELEEKEERLEELKKKLKELE 351
>gnl|CDD|177025 CHL00093, groEL, chaperonin GroEL.
Length = 529
Score = 28.9 bits (65), Expect = 6.6
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 102 RKFKDCEKQLEESRALAK----ENGNDEEMAEMIASEIKSLSNE-LIELEE 147
+ + + +E+ +A+ + GNDEE+ MIA I+ + E +I LEE
Sbjct: 128 SQIAEYARPVEDIQAITQVASISAGNDEEVGSMIADAIEKVGREGVISLEE 178
>gnl|CDD|240178 cd05157, ETNK_euk, Ethanolamine kinase (ETNK) in eukaryotes. ETNK
is part of a larger superfamily that includes the
catalytic domains of other kinases, such as the typical
serine/threonine/tyrosine protein kinases (PKs), RIO
kinases, actin-fragmin kinase (AFK), and
phosphoinositide 3-kinase (PI3K). ETNK catalyzes the
transfer of the gamma-phosphoryl group from CTP to
ethanolamine (Etn), the first step in the CDP-Etn
pathway for the formation of the major phospholipid,
phosphatidylethanolamine (PtdEtn). Unlike ChoK, ETNK
shows specific activity for its substrate, and displays
negligible activity towards N-methylated derivatives of
Etn. The Drosophila ETNK is implicated in development
and neuronal function. Mammals contain two ETNK
proteins, ETNK1 and ETNK2. ETNK1 selectively increases
Etn uptake and phosphorylation, as well as PtdEtn
synthesis. ETNK2 is found primarily in the liver and
reproductive tissues. It plays a critical role in
regulating placental hemostasis to support late
embryonic development. It may also have a role in
testicular maturation.
Length = 235
Score = 28.0 bits (63), Expect = 8.5
Identities = 22/107 (20%), Positives = 40/107 (37%), Gaps = 14/107 (13%)
Query: 74 DPEVVSNPSEYQKLAQSMAELDEVVSTYRKFKDCEKQ------LEESRALAKENGNDEEM 127
+PE + NP Y+ +A+ +A+L + + + + L E
Sbjct: 80 EPEDLRNPKIYRLIARELAKLHSIKPPEAISSPGTPKPILWPTIRKWINLVPTEFKKPEK 139
Query: 128 AEMIASEIK--SLSNELIELEEKLKVLLLP-----SDPLDARNIMLE 167
+ I L +E+ L+E L L P +D L + NI+
Sbjct: 140 FQKKTKAISFEQLRDEISWLKELLSALNSPIVFCHNDLL-SGNIIYN 185
>gnl|CDD|235580 PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase
subunit alpha; Validated.
Length = 319
Score = 28.2 bits (64), Expect = 8.8
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 6/45 (13%)
Query: 105 KDCEKQLEESRALAKENGNDEEMAEMIASEIKSLSNELIELEEKL 149
+ E ++EE RA+A+++ D ++ EI+ L +L EL +K+
Sbjct: 13 AELEAKIEELRAVAEDSDVD------LSEEIERLEKKLEELTKKI 51
>gnl|CDD|204405 pfam10146, zf-C4H2, Zinc finger-containing protein. This is a
family of proteins which appears to have a highly
conserved zinc finger domain at the C terminal end,
described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is
predicted to contain a coiled coil. Members are
annotated as being tumour-associated antigen HCA127 in
humans but this could not confirmed.
Length = 215
Score = 27.9 bits (62), Expect = 8.9
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 82 SEYQKLAQSM-AELDEVVSTYRKFKDCEKQLEESRALAKENGNDEEMAEMIASEIKSLSN 140
E +KL + AE + + S + K+ +K++EE L +E E I ++I +
Sbjct: 11 DELEKLKDEIKAEEEALESEEKHLKEYDKEMEE---LLEEKMQHVEELRQIHADINDMET 67
Query: 141 ELIELEEKLKVLL 153
E+ + + +L+ +
Sbjct: 68 EIKQSKSELERRM 80
>gnl|CDD|203593 pfam07200, Mod_r, Modifier of rudimentary (Mod(r)) protein. This
family represents a conserved region approximately 150
residues long within a number of eukaryotic proteins
that show homology with Drosophila melanogaster Modifier
of rudimentary (Mod(r)) proteins. The N-terminal half of
Mod(r) proteins is acidic, whereas the C-terminal half
is basic, and both of these regions are represented in
this family. Members of this family include the Vps37
subunit of the endosomal sorting complex ESCRT-I, a
complex involved in recruiting transport machinery for
protein sorting at the multivesicular body (MVB). The
yeast ESCRT-I complex consists of three proteins (Vps23,
Vps28 and Vps37). The mammalian homologue of Vps37
interacts with Tsg101 (Pfam: PF05743) through its mod(r)
domain and its function is essential for lysosomal
sorting of EGF receptors.
Length = 150
Score = 27.3 bits (61), Expect = 9.0
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 4/76 (5%)
Query: 82 SEYQKLAQSMAELDEVVSTYRKFKDCEKQLEESRA----LAKENGNDEEMAEMIASEIKS 137
E ++L Q L E V + +D + + A LA+EN E E + ++++
Sbjct: 7 DELKELLQDEDALLEFVLELPQVQDLNLEKDALLAQNESLAEENLEKEPQLEELKAQLRD 66
Query: 138 LSNELIELEEKLKVLL 153
EL +LEEK +
Sbjct: 67 KYEELKKLEEKYEEKK 82
>gnl|CDD|153352 cd07668, BAR_SNX9, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 9. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX9, also known as SH3PX1, is a
cytosolic protein that interacts with proteins
associated with clathrin-coated pits such as
Cdc-42-associated tyrosine kinase 2 (ACK2). It binds
class I polyproline sequences found in dynamin 1/2 and
the WASP/N-WASP actin regulators. SNX9 is localized to
plasma membrane endocytic sites and acts primarily in
clathrin-mediated endocytosis. Its array of interacting
partners suggests that SNX9 functions at the interface
between endocytosis and actin cytoskeletal organization.
BAR domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 210
Score = 27.7 bits (61), Expect = 9.8
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 81 PSEYQKLAQSMAELDEVVSTYRKFKDCEKQLEESRALAKENGNDEEMAEMIASEIKSLSN 140
P EYQK+ +++ L V ST + + + + A+ + EE+A ++A + K +
Sbjct: 47 PKEYQKIGKALQSLATVFST----SGYQGETDLNDAITEAGKTYEEIASLVAEQPKKDLH 102
Query: 141 ELIELEEKLKVLL 153
L+E + K L
Sbjct: 103 FLMETNHEYKGFL 115
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
0.313 0.128 0.351
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,688,146
Number of extensions: 2008056
Number of successful extensions: 2148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2099
Number of HSP's successfully gapped: 137
Length of query: 416
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 317
Effective length of database: 6,546,556
Effective search space: 2075258252
Effective search space used: 2075258252
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (26.9 bits)