RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020225
(329 letters)
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 212 bits (541), Expect = 4e-66
Identities = 111/336 (33%), Positives = 178/336 (52%), Gaps = 25/336 (7%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
+ W+D ++ +V +L+ ++ L++LR + ++ + + +LAE E D A
Sbjct: 43 DFWNDQERAQKVTKELSSLKAKLDTLEELRQRLDDLEELLELAEEED-DEETLAEAEAEL 101
Query: 66 LDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRG 125
+ K L E+ +LL G D A +TI AG+ G + WA LL MY+RWA++ G++
Sbjct: 102 KALEKKLAALELERLLSGEYDANNAILTIHAGAGGTEAQDWASMLLRMYLRWAERHGFKV 161
Query: 126 RVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNG-----SFPHEATL 177
V+D + G+KSAT + + YA+GYL ETG H L+ F + SF
Sbjct: 162 EVLDYSEGEEAGIKSATFKIKGPYAYGYLKSETGVHRLVRISPFDSAGRRHTSF------ 215
Query: 178 ACVDVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAK--PAACIQHIPTGIAVQS 232
A V+V P ++ + +++I+ +DL + S S G Q + K A I HIPTGI VQ
Sbjct: 216 ASVEVYPE-VDDTIEIEINPKDLRIDTYRS-SGAGG-QHVNKTDSAVRITHIPTGIVVQC 272
Query: 233 LGERNHFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNI-WQRETRRYVSHPYKL 291
ER+ NK A+ LKAKL + E+ + + + I W + R YV HPY++
Sbjct: 273 QNERSQHQNKASAMKMLKAKLYELELEKRAAEKDAL-KGEKKEIGWGSQIRSYVLHPYQM 331
Query: 292 VQDVKTGIQLPDFNSVLDGNIKPFIEAHINSRRSSD 327
V+D++TG + + +VLDG++ FIEA++ R S
Sbjct: 332 VKDLRTGYETGNTQAVLDGDLDGFIEAYLRWRASQK 367
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 178 bits (454), Expect = 2e-53
Identities = 102/324 (31%), Positives = 164/324 (50%), Gaps = 9/324 (2%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
N W+D ++ V+ + + V++ L++L+ E+ + +LA E D F
Sbjct: 43 NFWNDQERAQAVIKERSSLEAVLDTLEELKNSLEDLSELLELAV-EEDDEETFNELDAEL 101
Query: 66 LDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRG 125
+ K L + E+ +L G D A +TI+AG+ G + WA L MY+RWA++ G++
Sbjct: 102 KALEKKLAELELRTMLSGEYDANNAYLTIQAGAGGTEAQDWASMLYRMYLRWAERRGFKV 161
Query: 126 RVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACVDV 182
++D + G+KS TI + YA+GYL E G H L+ F H + A V V
Sbjct: 162 EIIDYSEGEEAGIKSVTILIKGPYAYGYLKSEQGVHRLVRISPFDANGRRH-TSFASVFV 220
Query: 183 VPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERNHF 239
+P + D++I EDL + + G+ + A I HIPTGI VQ +R+
Sbjct: 221 MPEVDDDI-DIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQH 279
Query: 240 ANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGI 299
NK A+ LKAKL + E+ + + E W + R YV HPY +V+D++TG
Sbjct: 280 KNKDSAMKVLKAKLYELEMEKEQAEKDAKEGEKSEIGWGSQIRSYVLHPYSMVKDLRTGY 339
Query: 300 QLPDFNSVLDGNIKPFIEAHINSR 323
+ + +VLDG+I FIEA++ +
Sbjct: 340 ETGNVQAVLDGDIDQFIEAYLKWK 363
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 161 bits (408), Expect = 6e-47
Identities = 99/325 (30%), Positives = 168/325 (51%), Gaps = 14/325 (4%)
Query: 6 NLWDDPTKSNEVLVK---LADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAY 62
N W+D ++ E+ + L D L N L++ + E+ +++ ++ E D + K
Sbjct: 5 NFWNDIKEAQEITSEEKYLKDKLDKYNHLRN---RIEDIEVLCEMMSEE--DDEMKKEII 59
Query: 63 RASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEG 122
++ + +D++++ LL G D A +T+ +G G + W E LL MY RWA+K+G
Sbjct: 60 SEVKNIKEEIDRFKIETLLSGEYDRNNAILTLHSGVGGTDAQDWTEMLLRMYTRWAEKKG 119
Query: 123 YRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFP--NGSFPHEATLACV 180
Y+ ++D G+KS T++ E+A+GYL E G H L+ N + + + A V
Sbjct: 120 YKVEIIDLLEGDEAGIKSVTLKITGEFAYGYLKAEKGIHRLVRISPFNANGKRQTSFASV 179
Query: 181 DVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERN 237
+V+P L D++I EDL + + G+ + + A I HIPTGI VQ ER+
Sbjct: 180 EVLPE-LTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERS 238
Query: 238 HFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKT 297
+NK A+ LK+KL+ + + + E W + R YV HPY LV+D +T
Sbjct: 239 QHSNKETAMKMLKSKLVELKERAHKEKIEDLTGELKDMGWGSQIRSYVFHPYNLVKDHRT 298
Query: 298 GIQLPDFNSVLDGNIKPFIEAHINS 322
G++ + +SV+DG+I FI ++
Sbjct: 299 GVETSNVDSVMDGDIDNFITQYLKG 323
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 142 bits (360), Expect = 8e-40
Identities = 95/335 (28%), Positives = 164/335 (48%), Gaps = 31/335 (9%)
Query: 6 NLWDDPTKSNEVL---VKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAY 62
+LW+D ++ +++ +L DS +N + L + + + E E D + + A
Sbjct: 7 SLWNDAQEAQKLMRERQQLDDS---INGINHLEQTLNDNIELIAMGEEEG-DKSIVEDAE 62
Query: 63 RASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEG 122
+ D+ +D+ ++ LL G D + + AG+ G + WA LL MY RWA+++G
Sbjct: 63 KTIRDLKDEIDRRQIDALLSGEADANDTYLEVHAGAGGTESQDWASMLLRMYTRWAERQG 122
Query: 123 YRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINF-PNGSFPHEAT-LACV 180
+ V++ + G+KSATI + A+G+L E+G H L+ P S T A +
Sbjct: 123 RKVEVLEVHDGEEAGIKSATILVKGHNAYGWLKTESGVHRLVRISPYDSNARRHTSFASI 182
Query: 181 DVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERN 237
V P+ ++ + ++ +++ D+ + S G+ + A I HIPTGI VQ ER+
Sbjct: 183 WVYPV-IDDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERS 241
Query: 238 HFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNI---------WQRETRRYVSHP 288
N+ KA + L+A+L KRE N W + R YV P
Sbjct: 242 QHKNRAKAWSMLRARLY---------EEELKKREEATNAAAASKTDIGWGHQIRSYVLQP 292
Query: 289 YKLVQDVKTGIQLPDFNSVLDGNIKPFIEAHINSR 323
Y+LV+D++TG++ + VLDG++ F+EA + R
Sbjct: 293 YQLVKDLRTGVESTNPQDVLDGDLNEFMEAALAHR 327
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 141 bits (357), Expect = 1e-39
Identities = 101/332 (30%), Positives = 157/332 (47%), Gaps = 27/332 (8%)
Query: 7 LWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASL 66
WDD + V+ + NALKD+ K + + + E I + L K Y L
Sbjct: 6 FWDDQQGAQAVINE-------ANALKDMVGKFRQ---LDETFENLEITHELLKEEYDEDL 55
Query: 67 ------DVSKL---LDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRW 117
+V L +++YE+ LL P D A + + G+ G + W LL MY RW
Sbjct: 56 HEELESEVKGLIQEMNEYELQLLLSDPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRW 115
Query: 118 ADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHE 174
A+K G++ VD G+KS T+ + A+GYL E G H L+ F + H
Sbjct: 116 AEKRGFKVETVDYLPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHT 175
Query: 175 ATLACVDVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQ 231
+ ++C +VVP F ++++ EDL + + G+ + A I H PT V
Sbjct: 176 SFVSC-EVVPEF-NDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVT 233
Query: 232 SLGERNHFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKL 291
ER+ N+ A+ LKAKL E+ + + I+ E W + R YV HPY L
Sbjct: 234 CQSERSQIKNREHAMKMLKAKLYQKKLEEQQAELDEIRGEQKEIGWGSQIRSYVFHPYSL 293
Query: 292 VQDVKTGIQLPDFNSVLDGNIKPFIEAHINSR 323
V+D +T ++ + +V+DG I PFI+A++ SR
Sbjct: 294 VKDHRTNTEVGNVQAVMDGEIDPFIDAYLRSR 325
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 131 bits (331), Expect = 2e-36
Identities = 82/240 (34%), Positives = 127/240 (52%), Gaps = 8/240 (3%)
Query: 90 ASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEY 149
A +TI AG+ G + WA LL MY RWA+++G++ V+D + G+KSAT++ + E
Sbjct: 1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60
Query: 150 AFGYLSGETGAHCLI-NFPNGSFPHEAT-LACVDVVPLFLETSPDLQISDEDLLFSS--P 205
A+GYL ETG H L+ P S T A V+V P S +++I D+DL +
Sbjct: 61 AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDI-SIEIEIPDDDLRIDTYRA 119
Query: 206 SLPGERQSIAK--PAACIQHIPTGIAVQSLGERNHFANKMKALNRLKAKLLVIVGEQGVS 263
S G Q + K A + H+PTGI V ER+ NK A LK KL ++ E+
Sbjct: 120 SGAGG-QHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQ 178
Query: 264 NVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQLPDFNSVLDGNIKPFIEAHINSR 323
+ + + W + R YV PY+ +D++TG++ + + VLDG+ FI+A++
Sbjct: 179 EKNRERALKKLIGWGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDGDKDGFIKAYLKWD 238
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 120 bits (303), Expect = 7e-32
Identities = 87/304 (28%), Positives = 149/304 (49%), Gaps = 12/304 (3%)
Query: 26 KVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKL-LDQYEMSKLLRGP 84
K V + D+ +A + LAE E + A A LD + +++ E ++ G
Sbjct: 4 KTVIGIADVLSGLADAGELLDLAESEQDEDTA--LAVIADLDKYQAHVEKLEFQRMFSGQ 61
Query: 85 NDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIE 144
D A V I+AG+ G + WAE LL MY+RWA+ G++ +++ + G+KSAT+
Sbjct: 62 MDGANAFVDIQAGAGGTEAQDWAEILLRMYLRWAESRGWKTELMEVSGGEVAGIKSATVR 121
Query: 145 FEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACVDVVPLFLETSPDLQISDEDL- 200
E EYA+G+L E G H L+ F + + H + V V P ++ + ++ I+ DL
Sbjct: 122 IEGEYAYGWLKTEIGVHRLVRKSPFDSDNRRH-TSFTSVFVSPE-VDDNIEIDINPADLR 179
Query: 201 --LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERNHFANKMKALNRLKAKLLVIVG 258
++ S G+ + + A I HIPT V R+ N+ A+ L AKL +
Sbjct: 180 TDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEV 239
Query: 259 EQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQLPDFNSVLDGNIKPFIEA 318
++ + ++ W + R YV + ++D++TGI+ D VLDG++ F+EA
Sbjct: 240 QKRNAEKDALEATKSDIGWGSQIRNYVLDQSR-IKDLRTGIERSDTQKVLDGDLDEFVEA 298
Query: 319 HINS 322
+ +
Sbjct: 299 SLKA 302
>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 = 93.2 bits (232), Expect = 2e-21
Identities = 81/333 (24%), Positives = 144/333 (43%), Gaps = 31/333 (9%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVV---NALKDLRYKAEEAKLIAQ--------LAEMEAID 54
+ D K ++ + + ++V + + +EAK I + +A+ E
Sbjct: 27 EVISDQDKLRKLSKEYSQLEEIVDCYREYQQAQEDIKEAKEILEESDPEMREMAKEELE- 85
Query: 55 YGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMY 114
+ +L +Q ++ L + PND + + I+AG+ G I+A L MY
Sbjct: 86 --------ELEEKIEELEEQLKVLLLPKDPNDEKNVILEIRAGTGGDEAAIFAGDLFRMY 137
Query: 115 VRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFP----NGS 170
R+A+ +G++ ++ + GG K E + + + L E+G H + P G
Sbjct: 138 SRYAESKGWKVEILSANETELGGYKEVIAEIKGDGVYSRLKFESGVHRVQRVPVTESQGR 197
Query: 171 FPHEATLACVDVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTG 227
H + A V V+P E D I+ DL F S G+ + A I H+PTG
Sbjct: 198 I-HTSA-ATVAVMPELEEVEVD--INPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPTG 253
Query: 228 IAVQSLGERNHFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSH 287
I V+ ER+ NK KA+ L+A+L E+ + + ++ + + + E R +
Sbjct: 254 IVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQAAQASTRKSQVGSGDRSERIRTYNF 313
Query: 288 PYKLVQDVKTGIQLPDFNSVLDGNIKPFIEAHI 320
P V D + + L + VL+G++ IEA I
Sbjct: 314 PQNRVTDHRINLTLYKLDEVLEGDLDELIEALI 346
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 80.7 bits (200), Expect = 6e-19
Identities = 39/113 (34%), Positives = 62/113 (54%), Gaps = 4/113 (3%)
Query: 49 EMEAIDYGLFKRAYRASLDVSKLLDQYEM----SKLLRGPNDVEGASVTIKAGSNGICPE 104
E D L + A ++ K L++ E L P D + A + I+AG+ G +
Sbjct: 3 LEEEDDPELREEAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTEAQ 62
Query: 105 IWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGE 157
++AE LL MY R+A+++G++ V+D + GG+K AT+E E E A+GYL E
Sbjct: 63 LFAEDLLRMYQRYAERKGWKVEVIDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 78.7 bits (195), Expect = 3e-18
Identities = 37/122 (30%), Positives = 65/122 (53%), Gaps = 10/122 (8%)
Query: 37 KAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRG-PNDVEGASVTIK 95
+ EE + +LAE E ++ + L++ LL PND + A + I+
Sbjct: 4 EEEEDDEMRELAEEEL---------EELEAELEEELEELLKLLLLPKDPNDDKNAILEIR 54
Query: 96 AGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLS 155
AG+ G ++A LL MY+R+A+++G++ V+D+ + GG+K AT++ E A+G L
Sbjct: 55 AGAGGDEAALFAGDLLRMYLRYAERKGWKVEVLDESEGELGGIKEATLKISGEGAYGKLK 114
Query: 156 GE 157
E
Sbjct: 115 FE 116
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 67.6 bits (166), Expect = 1e-12
Identities = 53/179 (29%), Positives = 86/179 (48%), Gaps = 14/179 (7%)
Query: 84 PNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATI 143
PND + + I+AG+ G ++A L MY R+A+ +G++ ++ + GG K
Sbjct: 108 PNDDKNIILEIRAGTGGDEAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIA 167
Query: 144 EFEFEYAFGYLSGETGAHCLINFP----NGSFPHEATLACVDVVPLFLETSPDLQISDED 199
+ + L E+G H + P G H + A V V+P +E +++I+ +D
Sbjct: 168 SISGKGVYSRLKFESGVHRVQRVPATESQGRI-HTSA-ATVAVLPE-VEEVEEIEINPKD 224
Query: 200 L---LFSSPSLPGERQSIAK--PAACIQHIPTGIAVQSLGERNHFANKMKALNRLKAKL 253
L F S G Q + A I H+PTGI V+ ER+ NK KA+ L+A+L
Sbjct: 225 LRIDTFRSSGAGG--QHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARL 281
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 55.9 bits (136), Expect = 7e-09
Identities = 73/267 (27%), Positives = 119/267 (44%), Gaps = 59/267 (22%)
Query: 16 EVLVKLADSLKVVNALKDLRYKAEEAKLIAQ---------LAEMEAIDYGLFKRAYRASL 66
E +V+ K A +DL EEAK + + +A+ E + L
Sbjct: 45 EPIVEAYREYK--QAQEDL----EEAKEMLEEESDPEMREMAKEEL-------KELEERL 91
Query: 67 DVSKLLDQYEMSKLL--RGPNDVEGASVTIKAGSNGICPE--IWAEQLLNMYVRWADKEG 122
+ L++ E+ LL + PND + + I+AG+ G E ++A L MY R+A+++G
Sbjct: 92 EE---LEE-ELKILLLPKDPNDDKNVILEIRAGTGG--DEAALFAGDLFRMYSRYAERQG 145
Query: 123 YRGRVVDKCCCKN----GGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEA--- 175
++ ++ + GG K E + + L E+G H + P E+
Sbjct: 146 WKVEILSA----SEGELGGYKEVIAEISGDGVYSKLKFESGVHRVQRVPAT----ESQGR 197
Query: 176 --TLAC-VDVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAK--PAACIQHIPTG 227
T A V V+P E +++I+ +DL F S S G Q + A I H+PTG
Sbjct: 198 IHTSAATVAVLPEAEEV--EVEINPKDLRIDTFRS-SGAGG-QHVNTTDSAVRITHLPTG 253
Query: 228 IAVQSLGERNHFANKMKALNRLKAKLL 254
I V+ ER+ NK KA+ L+A+L
Sbjct: 254 IVVECQDERSQHKNKAKAMKVLRARLY 280
>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 = 44.1 bits (105), Expect = 7e-06
Identities = 31/110 (28%), Positives = 51/110 (46%), Gaps = 7/110 (6%)
Query: 190 SPDLQISDEDLL--FSSPSLPGERQSIAKPAACIQ--HIPTGIAVQSLGERNHFANKMKA 245
+++I + DL S PG Q++ K + ++ H+PTGI V+ ER+ N+ KA
Sbjct: 5 EVEIEIPESDLRIDTFRSSGPGG-QNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREKA 63
Query: 246 LNRLKAKLLVIVGEQGVSNVSCIKREAIVNI-WQRETRRYVSHPYKLVQD 294
L RLKAKL ++ + + + + R Y P V+D
Sbjct: 64 LERLKAKLYEAELQKKREKTKPTRASQVRRGDRKEKIRTYN-FPQGRVKD 112
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 35.8 bits (83), Expect = 0.014
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 223 HIPTGIAVQSLGERNHFANKMKALNRLKAKL 253
H+ +GI+V+ ER+ ANK A + KL
Sbjct: 135 HLASGISVKVQSERSQHANKRLARLLIAWKL 165
>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 = 34.0 bits (78), Expect = 0.059
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 223 HIPTGIAVQSLGERNHFANKMKALNRLKAKL 253
H+ +GI+V+ ER+ ANK A L +L
Sbjct: 134 HLASGISVKVQSERSQHANKRLATLLLAVRL 164
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 32.7 bits (75), Expect = 0.25
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 13 KSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLL 72
K + LV + + +V D Y E AK + +L +++ LF + + L VS LL
Sbjct: 609 KKQDQLVVVDQDMPLVTETSDEVYAEEIAKRLEELKQLQQPILVLFN-SKKHLLAVSDLL 667
Query: 73 DQYEMSKLLRGPN 85
DQ+++S L + N
Sbjct: 668 DQWQVSHLAQEKN 680
>gnl|CDD|238414 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic domain.
Cre-like recombinases belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their catalytic domain and the overall reaction
mechanism. The bacteriophage P1 Cre recombinase
maintains the circular phage replicon in a monomeric
state by catalyzing a site-specific recombination
between two loxP sites. The catalytic core domain of
Cre recombinase is linked to a more divergent helical
N-terminal domain, which interacts primarily with the
DNA major groove proximal to the crossover region.
Length = 287
Score = 31.2 bits (71), Expect = 0.71
Identities = 27/119 (22%), Positives = 39/119 (32%), Gaps = 18/119 (15%)
Query: 16 EVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKL-LDQ 74
E L KL L + L+DLR A + L GL +R+ L L
Sbjct: 98 EDLDKLRSLLDESDTLRDLRDLA-----LLLLGF-----AGLLRRSELVRLRWEDLTFTD 147
Query: 75 YEMSKLL--RGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWAD-KEGYRGRVVDK 130
+ R D G V CP + L ++ A +G R +D+
Sbjct: 148 GGGLLVTLRRSKTDQSGLGVLKLIPPLTTCP----VRALERWLEAARIPKGPLFRRIDR 202
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 30.5 bits (70), Expect = 1.3
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 18/68 (26%)
Query: 42 KLIAQLAEMEA-IDY-----------GLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEG 89
+L+ LA +EA ID+ + ++ ++ LL ++LR EG
Sbjct: 161 ELLELLALVEAAIDFPEEDIEFLSDEKILEKLEELIAELEALLASARQGEILR-----EG 215
Query: 90 ASVTIKAG 97
V I AG
Sbjct: 216 LKVVI-AG 222
>gnl|CDD|234570 PRK00009, PRK00009, phosphoenolpyruvate carboxylase; Reviewed.
Length = 911
Score = 29.7 bits (68), Expect = 2.8
Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 8/39 (20%)
Query: 180 VDVVPLFLETSPDLQISD---EDLLFSSPSLPGERQSIA 215
+ VVPLF ET DL+ + LL SLP R IA
Sbjct: 523 LPVVPLF-ETIEDLRNAADVMRQLL----SLPWYRGLIA 556
>gnl|CDD|226908 COG4531, ZnuA, ABC-type Zn2+ transport system, periplasmic
component/surface adhesin [Inorganic ion transport and
metabolism].
Length = 318
Score = 29.3 bits (66), Expect = 3.1
Identities = 12/49 (24%), Positives = 21/49 (42%)
Query: 4 NYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEA 52
+ +LW P + V +A L ++ +Y A AQLA ++
Sbjct: 150 DMHLWLSPAIAKAVAAAIAKKLAELDPQNAAKYDANLKDFEAQLAALDK 198
>gnl|CDD|224958 COG2047, COG2047, Uncharacterized protein (ATP-grasp superfamily)
[General function prediction only].
Length = 258
Score = 28.9 bits (65), Expect = 3.7
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 10 DPTKSNEVLVKLADSLKVVNALKDLRYKAEE-AKLIAQLAEMEA 52
DP + VL L L + ++ L +A+E ++I +L EME
Sbjct: 197 DPKAAKAVLEVLCKMLGIEIDMEALEERAKEMEEIIEKLKEMEE 240
>gnl|CDD|176714 cd09012, Glo_EDI_BRP_like_24, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 124
Score = 27.9 bits (63), Expect = 3.8
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 10 DPTKSNEVLVKL-ADSLKVVNALKDLRYKAEEA 41
D KS EVL+ L ADS + V+ L + KA A
Sbjct: 63 DTKKSTEVLISLSADSREEVDELVE---KALAA 92
>gnl|CDD|132757 cd07072, NR_LBD_DHR38_like, Ligand binding domain of DHR38_like
proteins, members of the nuclear receptor superfamily.
The ligand binding domain of nuclear receptor DHR38_like
proteins: DHR38 is a member of the steroid receptor
superfamily in Drosophila. DHR38 interacts with the USP
component of the ecdysone receptor complex, suggesting
that DHR38 might modulate ecdysone-triggered signals in
the fly, in addition to the ECR/USP pathway. At least
four differentially expressed mRNA isoforms have been
detected during development. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, DHR38 has a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 239
Score = 28.6 bits (64), Expect = 3.9
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 180 VDVVPLFLETSP---DLQISDEDLLFSSPSL 207
+DV+ F E P DL D++LLF S SL
Sbjct: 55 IDVIKTFAEKIPGFPDLCKEDQELLFQSASL 85
>gnl|CDD|173712 cd05622, STKc_ROCK1, Catalytic domain of the Protein
Serine/Threonine Kinase, Rho-associated coiled-coil
containing protein kinase 1. Serine/Threonine Kinases
(STKs), ROCK subfamily, ROCK1 (or ROK-beta) isoform,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The ROCK subfamily is
part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. ROCK contains an N-terminal
extension, a catalytic kinase domain, and a C-terminal
extension, which contains a coiled-coil region
encompassing a Rho-binding domain (RBD) and a
pleckstrin homology (PH) domain. ROCK is auto-inhibited
by the RBD and PH domain interacting with the catalytic
domain, and is activated via interaction with Rho
GTPases. ROCK1 is preferentially expressed in the
liver, lung, spleen, testes, and kidney. It mediates
signaling from Rho to the actin cytoskeleton. It is
implicated in the development of cardiac fibrosis,
cardiomyocyte apoptosis, and hyperglycemia. Mice
deficient with ROCK1 display eyelids open at birth
(EOB) and omphalocele phenotypes due to the
disorganization of actin filaments in the eyelids and
the umbilical ring.
Length = 371
Score = 28.8 bits (64), Expect = 4.3
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 28 VNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSK 79
+N ++DLR KAE+ +++ + + L + + KLL ++EM K
Sbjct: 32 INKIRDLRMKAEDYEVVKVIGRGAFGEVQLVRHKSTRKVYAMKLLSKFEMIK 83
>gnl|CDD|132356 TIGR03313, Se_sel_red_Mo, probable selenate reductase,
molybdenum-binding subunit. Our comparative genomics
suggests this protein family to be a subunit of a
selenium-dependent molybdenum hydroxylase, although the
substrate is not specified. This protein is suggested by
Bebien, et al., to be the molybdenum-binding subunit of
a molydbopterin-containing selenate reductase. Xi, et
al, however, show that mutation of this gene in E. coli
conferred sensitivity to adenine, suggesting a defect in
purine interconversion. This finding, plus homology of
nearby genes in a 23-gene purine catabolism region in E.
coli to xanthine dehydrogase subunits suggests xanthine
dehydrogenase activity.
Length = 951
Score = 28.8 bits (64), Expect = 5.1
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 155 SGETGAHCLINFPNGSFPHEATLACV 180
+ G H +INFP GS P + A V
Sbjct: 332 ADPRGEHMIINFPIGSRPRKNIAASV 357
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 28.6 bits (65), Expect = 5.1
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 227 GIAVQ-SLGERNHFANKMKALNRLKAKLLVIVGEQ 260
GI V+ G R + K ++ A+ ++I+GE
Sbjct: 345 GIRVELDYGGRK-LKKQFKYADKSGARFVLILGED 378
>gnl|CDD|219855 pfam08463, EcoEI_R_C, EcoEI R protein C-terminal. The restriction
enzyme EcoEI recognises 5'-GAGN(7)ATGC-3' and is
composed of the three proteins R, M, and S. The domain
described here is found at the C-terminus of the R
protein (HsdR) which is required for both nuclease and
ATPase activity.
Length = 162
Score = 27.6 bits (62), Expect = 5.6
Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 7 LWDDPTKSNEVLVKLADSLKVVNALKDLR-----YKAEEAKLIAQLAEMEAIDYGLFKRA 61
LW++P + E L +L + L L Y+ A L + + +D L R
Sbjct: 27 LWNNPPLTREDLKELEEKLIDDEELFSEERLQEAYEDIAADLFDLIRHLVGLDAPLLTRE 86
Query: 62 YRASLDVSKLLDQY 75
R SK L ++
Sbjct: 87 ERVEAAFSKFLAEH 100
>gnl|CDD|185285 PRK15387, PRK15387, E3 ubiquitin-protein ligase SspH2; Provisional.
Length = 788
Score = 28.2 bits (62), Expect = 7.0
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 29 NALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
N +KD +KA+ + +AQLAE EA+ F A A+
Sbjct: 541 NFIKDAGFKAQISSWLAQLAEDEALRANTFAMATEAT 577
>gnl|CDD|177970 PLN02336, PLN02336, phosphoethanolamine N-methyltransferase.
Length = 475
Score = 28.2 bits (63), Expect = 7.6
Identities = 17/38 (44%), Positives = 19/38 (50%), Gaps = 9/38 (23%)
Query: 168 NGSFPHEATLACVDVVPLFLETSPDLQISDE--DLLFS 203
NG + C DV TSPDL ISD DL+FS
Sbjct: 79 NGHY-KNVKFMCADV------TSPDLNISDGSVDLIFS 109
>gnl|CDD|238436 cd00859, HisRS_anticodon, HisRS Histidyl-anticodon binding domain.
HisRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only.
Length = 91
Score = 26.3 bits (59), Expect = 8.4
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 239 FANKMKALNRLKAKLLVIVGEQGVSN 264
+ K +R A+ VI+GE ++
Sbjct: 40 LKKQFKYADRSGARFAVILGEDELAA 65
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 28.0 bits (62), Expect = 9.5
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 191 PDLQI----SDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERNH--FANKMK 244
P ++I ++ D + S S GE + + +I TGI + L R+ F N
Sbjct: 196 PQIRIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETGILDEVLRHRSTIVFTNSRG 255
Query: 245 ALNRLKAKL 253
+L A+L
Sbjct: 256 LAEKLTARL 264
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
0.318 0.135 0.398
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: 16,564,885
Number of extensions: 1580036
Number of successful extensions: 1268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1241
Number of HSP's successfully gapped: 40
Length of query: 329
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 232
Effective length of database: 6,635,264
Effective search space: 1539381248
Effective search space used: 1539381248
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 (21.7 bits)
S2: 59 (26.3 bits)