RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020135
(330 letters)
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 356 bits (916), Expect = e-123
Identities = 131/265 (49%), Positives = 185/265 (69%), Gaps = 3/265 (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 TNSAVRVTHIPTGMTISIQDERSQH 325
T+SAVR+TH+PTG+ + QDERSQH
Sbjct: 241 TDSAVRITHLPTGIVVECQDERSQH 265
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 330 bits (848), Expect = e-112
Identities = 130/270 (48%), Positives = 189/270 (70%), Gaps = 4/270 (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 TTNSAVRVTHIPTGMTISIQDERSQHMVKD 329
TT+SAVR+TH+PTG+ + QDERSQH K
Sbjct: 242 TTDSAVRITHLPTGIVVECQDERSQHKNKA 271
>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 = 292 bits (750), Expect = 1e-97
Identities = 128/265 (48%), Positives = 184/265 (69%), Gaps = 4/265 (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 VRVTHIPTGMTISIQDERSQHMVKD 329
VR+TH+PTG+ + QDERSQH KD
Sbjct: 245 VRITHLPTGIVVECQDERSQHKNKD 269
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 203 bits (520), Expect = 5e-63
Identities = 103/263 (39%), Positives = 154/263 (58%), Gaps = 8/263 (3%)
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 THIPTGMTISIQDERSQHMVKDS 330
THIPTG+ + Q+ERSQH K S
Sbjct: 262 THIPTGIVVQCQNERSQHQNKAS 284
>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 = 185 bits (472), Expect = 5e-56
Identities = 94/263 (35%), Positives = 150/263 (57%), Gaps = 8/263 (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 THIPTGMTISIQDERSQHMVKDS 330
THIPTG+ + Q++RSQH KDS
Sbjct: 262 THIPTGIVVQCQNDRSQHKNKDS 284
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 163 bits (415), Expect = 5e-48
Identities = 88/237 (37%), Positives = 143/237 (60%), Gaps = 7/237 (2%)
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 VDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMVKDS 330
D+ +R+EDL+IDTYR+GG+GGQH N T SAVR+THIPTG+ + Q+ERSQH K++
Sbjct: 189 QDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKET 245
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 150 bits (381), Expect = 2e-45
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|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 153 bits (390), Expect = 3e-45
Identities = 69/154 (44%), Positives = 105/154 (68%), Gaps = 1/154 (0%)
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 GSGGQHANTTNSAVRVTHIPTGMTISIQDERSQH 325
G+GGQH N T+SAVR+TH+PTG+ + Q+ERSQH
Sbjct: 121 GAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQH 154
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 151 bits (384), Expect = 2e-43
Identities = 88/226 (38%), Positives = 134/226 (59%), Gaps = 9/226 (3%)
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 NEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQH 325
D+RIDTYRS G+GGQH NTT+SAVR+THIPTG+ + Q ERSQH
Sbjct: 198 ESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQH 243
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 139 bits (354), Expect = 2e-41
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|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 144 bits (364), Expect = 1e-40
Identities = 75/164 (45%), Positives = 105/164 (64%), Gaps = 1/164 (0%)
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 EDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQ 324
EDL+IDTYR+ G+GGQH NTT+SAVR+TH PT ++ Q ERSQ
Sbjct: 197 EDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQ 240
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 137 bits (347), Expect = 3e-38
Identities = 76/223 (34%), Positives = 126/223 (56%), Gaps = 9/223 (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 YRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMVKDS 330
YRS G+GGQH N T SAVR+THIPT ++ Q RSQH +D+
Sbjct: 183 YRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDN 225
>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 = 91.9 bits (229), Expect = 4e-23
Identities = 32/61 (52%), Positives = 45/61 (73%)
Query: 269 PQADEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMVK 328
P +EV++ + DLRIDT+RS G GGQ+ N T SAVR+TH+PTG+ + Q+ERSQH +
Sbjct: 1 PLDEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNR 60
Query: 329 D 329
+
Sbjct: 61 E 61
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 71.6 bits (176), Expect = 7e-15
Identities = 24/44 (54%), Positives = 34/44 (77%)
Query: 282 DLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQH 325
++R +T RS G GGQH N T+SAVR TH+ +G+++ +Q ERSQH
Sbjct: 108 EIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQH 151
>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 = 71.7 bits (176), Expect = 8e-15
Identities = 24/44 (54%), Positives = 33/44 (75%)
Query: 282 DLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQH 325
++R +T RS G GGQH N T SAVR TH+ +G+++ +Q ERSQH
Sbjct: 107 EIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQH 150
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 34.0 bits (79), Expect = 0.034
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 275 DVRLRNEDLRIDTYRSGGSGGQHANTTNSAV 305
+ + +L R+ G GGQ+ N ++AV
Sbjct: 7 RLVIPENELEWRFIRASGPGGQNVNKVSTAV 37
>gnl|CDD|166487 PLN02846, PLN02846, digalactosyldiacylglycerol synthase.
Length = 462
Score = 32.1 bits (73), Expect = 0.43
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 = 0.59
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|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 = 30.0 bits (68), Expect = 2.2
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|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 = 29.6 bits (66), Expect = 2.5
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|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 = 3.3
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 = 3.5
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 = 3.6
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 = 4.6
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|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 = 27.3 bits (61), Expect = 6.0
Identities = 9/41 (21%), Positives = 17/41 (41%)
Query: 76 SACLENLVNQPEASPAEYSKANKELRKLRDSMHLISELRTK 116
+ L + ++ SK+ KEL + L+ EL +
Sbjct: 82 RPFYDYLKEIATETKSKKSKSKKELANNPNFKELMDELEKQ 122
>gnl|CDD|240440 PTZ00493, PTZ00493, phosphomethylpyrimidine kinase; Provisional.
Length = 321
Score = 28.0 bits (62), Expect = 6.8
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|226999 COG4652, COG4652, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 657
Score = 28.1 bits (63), Expect = 7.6
Identities = 8/40 (20%), Positives = 16/40 (40%)
Query: 94 SKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECSED 133
SK++ R + S + S ++ + LK + S
Sbjct: 102 SKSSLLTRDILGSYLIKSGHTDVEELSNVLKKKGGQTSLV 141
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 27.6 bits (61), Expect = 7.9
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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 28.1 bits (63), Expect = 7.9
Identities = 24/112 (21%), Positives = 44/112 (39%), Gaps = 9/112 (8%)
Query: 55 EMLSNDLIKIMEQRVLAIERRSACLENLVNQPEASPAEYSKANKELRKLRDSMH------ 108
E L + + + IE + L + E E +A + L L +
Sbjct: 764 EEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRR 823
Query: 109 --LISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDE-EKRLQSL 157
L E+ ++EI+ L+ + E E+ + L+ EEL ++E E + L
Sbjct: 824 ERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEEL 875
>gnl|CDD|218778 pfam05852, DUF848, Gammaherpesvirus protein of unknown function
(DUF848). This family consists of several
uncharacterized proteins from the Gammaherpesvirinae.
Length = 146
Score = 26.9 bits (60), Expect = 9.3
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 12/103 (11%)
Query: 91 AEYSKANKELR---KLRDSMHLI-------SELRTKQKEIDGLKSLIYECSEDKDMLDMA 140
A++ K LR LR L +E+R K+KE+ LK + E + L
Sbjct: 38 AQFQDTQKSLRSHQSLRQERELKNKVSSLETEIREKKKELSLLKKFDRKKVERAEALTDR 97
Query: 141 TEELCLAIDEE-KRLQSLLLKSL-LPKDDADERDCILEVRAGT 181
EEL ++ E +RL++ + L ++ + D I R
Sbjct: 98 VEELKEELEFELERLEAAGGEQEELSGEEEEPEDTITRWRLEA 140
>gnl|CDD|185763 cd09240, BRO1_Alix, Protein-interacting, N-terminal, Bro1-like
domain of mammalian Alix and related domains. This
family contains the N-terminal, Bro1-like domain of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), also called apoptosis-linked gene-2
interacting protein 1 (AIP1). It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure. Bro1-like
domains bind components of the ESCRT-III complex: CHMP4,
in the case of Alix. The Alix Bro1-like domain can also
bind human immunodeficiency virus type 1 (HIV-1)
nucleocapsid and Rab5-specfic GAP (RabGAP5, also known
as Rab-GAPLP). In addition to this Bro1-like domain,
Alix has a middle V-shaped (V) domain. The Alix V-domain
is a dimerization domain, and carries a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the superfamily. Alix
also has a C-terminal proline-rich region (PRR) that
binds multiple partners including Tsg101 (tumor
susceptibility gene 101, a component of ESCRT-1) and the
apoptotic protein ALG-2.
Length = 346
Score = 27.6 bits (62), Expect = 10.0
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 79 LENLVN---QPEASPAEYSKANKELRKLRDS 106
LE + A+Y +A KEL KLR++
Sbjct: 20 LEKFIKNTYSSGEEQADYKEAIKELNKLRNN 50
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
0.315 0.130 0.360
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: 16,427,446
Number of extensions: 1577019
Number of successful extensions: 1515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1485
Number of HSP's successfully gapped: 81
Length of query: 330
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 233
Effective length of database: 6,635,264
Effective search space: 1546016512
Effective search space used: 1546016512
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: 59 (26.3 bits)