RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2395
(570 letters)
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 498 bits (1284), Expect = e-175
Identities = 176/302 (58%), Positives = 229/302 (75%), Gaps = 4/302 (1%)
Query: 2 KHLMLSKLEKFSKRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINED 61
K ML KLE +R +EL+ LL+ EV ++ K + K +E++ L PIVE Y YK+ ED
Sbjct: 1 KPSMLDKLEALEERYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAQED 60
Query: 62 IITAKEMLN---DLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAG 118
+ AKEML D EMR A +E+ ++R+ ++E E+K L+LPKD ND +N+ +EIRAG
Sbjct: 61 LEEAKEMLEEESDPEMREMAKEELKELEERLEELEEELKILLLPKDPNDDKNVILEIRAG 120
Query: 119 TGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFE 178
TGGDE+ALF DL RMY R++ER WK EI+S S E+GGYKE+IA I G VYSKLKFE
Sbjct: 121 TGGDEAALFAGDLFRMYSRYAERQGWKVEILSASEGELGGYKEVIAEISGDGVYSKLKFE 180
Query: 179 SGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHIN 238
SGVHRVQRVP TE+QGRIHTSA TVAV+PEA+E+ ++ INP DLRIDT+R+SGAGGQH+N
Sbjct: 181 SGVHRVQRVPATESQGRIHTSAATVAVLPEAEEV-EVEINPKDLRIDTFRSSGAGGQHVN 239
Query: 239 KTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMRRLLI 298
TDSAVRITH+PTGIVV+CQ++RSQHKNKA A+K+L AR+ D++ ++ Q+ A R+ +
Sbjct: 240 TTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEAATRKSQV 299
Query: 299 GS 300
GS
Sbjct: 300 GS 301
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 466 bits (1201), Expect = e-162
Identities = 180/303 (59%), Positives = 229/303 (75%), Gaps = 3/303 (0%)
Query: 1 MKHLMLSKLEKFSKRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINE 60
MK +L KLE +R +EL+ LL+ EV ++ +Y K +E++ L PIVE Y YKK E
Sbjct: 1 MKPSLLEKLESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQE 60
Query: 61 DIITAKEMLN---DLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRA 117
D+ AKEML D EMR A +EI + +I ++E E+K L+LPKD ND +NI +EIRA
Sbjct: 61 DLEDAKEMLAEEKDPEMREMAEEEIKELEAKIEELEEELKILLLPKDPNDDKNIILEIRA 120
Query: 118 GTGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKF 177
GTGGDE+ALF DL RMY R++E WK EI+S S SE+GGYKEIIA I G VYS+LKF
Sbjct: 121 GTGGDEAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLKF 180
Query: 178 ESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHI 237
ESGVHRVQRVP TE+QGRIHTSA TVAV+PE +E+E+I INP DLRIDT+R+SGAGGQH+
Sbjct: 181 ESGVHRVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHV 240
Query: 238 NKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMRRLL 297
N TDSAVRITH+PTGIVV+CQ++RSQHKNKA A+K+L AR+ D++ ++ Q+ A R+
Sbjct: 241 NTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEASERKSQ 300
Query: 298 IGS 300
+GS
Sbjct: 301 VGS 303
>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 = 408 bits (1051), Expect = e-139
Identities = 168/305 (55%), Positives = 230/305 (75%), Gaps = 3/305 (0%)
Query: 1 MKHLMLSKLEKFSKRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINE 60
MK +L KLE +R +EL+ LL+ EV ++ K +E+S L IV+ Y Y++ E
Sbjct: 1 MKPSLLEKLESLLERYEELEALLSDPEVISDQDKLRKLSKEYSQLEEIVDCYREYQQAQE 60
Query: 61 DIITAKEML--NDLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAG 118
DI AKE+L +D EMR A +E+ +++I ++E ++K L+LPKD ND++N+ +EIRAG
Sbjct: 61 DIKEAKEILEESDPEMREMAKEELEELEEKIEELEEQLKVLLLPKDPNDEKNVILEIRAG 120
Query: 119 TGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFE 178
TGGDE+A+F DL RMY R++E WK EI+S + +E+GGYKE+IA I G VYS+LKFE
Sbjct: 121 TGGDEAAIFAGDLFRMYSRYAESKGWKVEILSANETELGGYKEVIAEIKGDGVYSRLKFE 180
Query: 179 SGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHIN 238
SGVHRVQRVP TE+QGRIHTSA TVAV+PE +E+E ++INPADLRIDT+R+SGAGGQH+N
Sbjct: 181 SGVHRVQRVPVTESQGRIHTSAATVAVMPELEEVE-VDINPADLRIDTFRSSGAGGQHVN 239
Query: 239 KTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMRRLLI 298
TDSAVRITH+PTGIVV+CQ++RSQHKNK A+K+L AR+ +++ +QQ+ A R+ +
Sbjct: 240 TTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQAAQASTRKSQV 299
Query: 299 GSVQK 303
GS +
Sbjct: 300 GSGDR 304
>gnl|CDD|236467 PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 275
Score = 299 bits (768), Expect = 2e-98
Identities = 105/260 (40%), Positives = 167/260 (64%), Gaps = 8/260 (3%)
Query: 311 ETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAYIIGKKEFYGLVL 370
+ +LL +V LS +L++N E++L +E+ L+ RR GEP+ YI+G+ EF+GL
Sbjct: 21 DAELLLAHVLGLSRTDLLLNPEEELTPEELERFRALVARRAAGEPLQYILGEAEFWGLDF 80
Query: 371 NITSDVLIPRPETELLVDLIVKKTFEKK-IKLLEMGTGSGAIAIAIAIYSKNKIEIIATD 429
++ VLIPRPETE LV+ ++ K+ +++L++GTGSGAIA+A+A + E+ A D
Sbjct: 81 KVSPGVLIPRPETEELVEWALEALLLKEPLRVLDLGTGSGAIALALAKERPD-AEVTAVD 139
Query: 430 ISKFALKIAKKNAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLN 489
IS AL +A++NAK L ++F++ +W+ L + F++IV+NPPYIP+ DIHL
Sbjct: 140 ISPEALAVARRNAKHGLGA---RVEFLQGDWFEPLPGGR--FDLIVSNPPYIPEADIHLL 194
Query: 490 KGDLR-FEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNLVRKLLFKYG 548
+ ++R EP AL +GL + I++ A +YL G LL+E GY+Q VR LL G
Sbjct: 195 QPEVRDHEPHLALFGGEDGLDFYRRIIEQAPRYLKPGGWLLLEIGYDQGEAVRALLAAAG 254
Query: 549 FSDIKSWRDLSGIERVTQGK 568
F+D+++ +DL+G +RV G+
Sbjct: 255 FADVETRKDLAGRDRVVLGR 274
>gnl|CDD|234248 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase,
release factor-specific. Members of this protein family
are HemK (PrmC), a protein once thought to be involved
in heme biosynthesis but now recognized to be a
protein-glutamine methyltransferase that modifies the
peptide chain release factors. All members of the seed
alignment are encoded next to the release factor 1 gene
(prfA) and confirmed by phylogenetic analysis. SIMBAL
analysis (manuscript in prep.) shows the motif
[LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers
specificity for the release factors rather than for
ribosomal protein L3 [Protein fate, Protein modification
and repair].
Length = 251
Score = 283 bits (727), Expect = 2e-92
Identities = 101/257 (39%), Positives = 162/257 (63%), Gaps = 9/257 (3%)
Query: 311 ETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAYIIGKKEFYGLVL 370
+ +LL +V +L+++ E++L +E+ + L+ RR GEP+AYI+G++EFYGL
Sbjct: 1 DAELLLAHVLGKDRADLLLHPEEELTPEELARFDALLARRAKGEPVAYILGEREFYGLDF 60
Query: 371 NITSDVLIPRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDI 430
++ VLIPRPETE LV+ +++ + +++L++GTGSGAIA+A+A + + A DI
Sbjct: 61 KVSPGVLIPRPETEELVEAALERLKKGPLRVLDLGTGSGAIALALAKERPD-ARVTAVDI 119
Query: 431 SKFALKIAKKNAKK-KLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLN 489
S AL +A+KNA + L ++F++S+W+ L K F++IV+NPPYIP+ DIHL
Sbjct: 120 SPEALAVARKNAARLGLDN----VEFLQSDWFEPLPGGK--FDLIVSNPPYIPEADIHLL 173
Query: 490 KGDLR-FEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNLVRKLLFKYG 548
++R EP AL +GL + I+ A + L G LL+E GY+Q VR L G
Sbjct: 174 DPEVRFHEPRLALFGGEDGLDFYRRIIAQAPRLLKPGGWLLLEIGYDQGEAVRALFEAAG 233
Query: 549 FSDIKSWRDLSGIERVT 565
F+D+++ +DL+G +RV
Sbjct: 234 FADVETRKDLAGKDRVV 250
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 269 bits (689), Expect = 3e-85
Identities = 116/290 (40%), Positives = 174/290 (60%), Gaps = 7/290 (2%)
Query: 8 KLEKFSKRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKE 67
++ +RL+EL+ + N+ + K +E S L ++ ++ +D+ E
Sbjct: 24 DVDALKERLEELEAEAEDPDFWNDQERAQKVTKELSSLKAKLDTLEELRQRLDDLEELLE 83
Query: 68 ML---NDLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDES 124
+ +D E A E+ +K++ +ELE L + D N + I AG GG E+
Sbjct: 84 LAEEEDDEETLAEAEAELKALEKKLAALELER----LLSGEYDANNAILTIHAGAGGTEA 139
Query: 125 ALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFESGVHRV 184
+ + LLRMY+R++ER+ +K E++ S E G K +I G Y LK E+GVHR+
Sbjct: 140 QDWASMLLRMYLRWAERHGFKVEVLDYSEGEEAGIKSATFKIKGPYAYGYLKSETGVHRL 199
Query: 185 QRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAV 244
R+ ++ GR HTS +V V PE D+ +I INP DLRIDTYR+SGAGGQH+NKTDSAV
Sbjct: 200 VRISPFDSAGRRHTSFASVEVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTDSAV 259
Query: 245 RITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMR 294
RITHIPTGIVVQCQN+RSQH+NKA A+K+L A++ + +L ++ + ++
Sbjct: 260 RITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRAAEKDALK 309
>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 = 237 bits (606), Expect = 5e-73
Identities = 120/290 (41%), Positives = 169/290 (58%), Gaps = 7/290 (2%)
Query: 8 KLEKFSKRLKELDFLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKE 67
EK RL+EL+ + N+ + ++E S L +++ K ED+ E
Sbjct: 24 DPEKKKARLEELEKEMEDPNFWNDQERAQAVIKERSSLEAVLDTLEELKNSLEDLSELLE 83
Query: 68 ML---NDLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDES 124
+ +D E N E+ +K++ ++EL + + D N ++ I+AG GG E+
Sbjct: 84 LAVEEDDEETFNELDAELKALEKKLAELELRT----MLSGEYDANNAYLTIQAGAGGTEA 139
Query: 125 ALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFESGVHRV 184
+ + L RMY+R++ER +K EII S E G K + I G Y LK E GVHR+
Sbjct: 140 QDWASMLYRMYLRWAERRGFKVEIIDYSEGEEAGIKSVTILIKGPYAYGYLKSEQGVHRL 199
Query: 185 QRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAV 244
R+ + GR HTS +V V+PE D+ DI I P DLRIDTYRASGAGGQH+NKTDSAV
Sbjct: 200 VRISPFDANGRRHTSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAV 259
Query: 245 RITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAKMR 294
RITHIPTGIVVQCQNDRSQHKNK A+K+L A++ + ++ ++Q+
Sbjct: 260 RITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEMEKEQAEKDAKE 309
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 229 bits (585), Expect = 5e-71
Identities = 93/271 (34%), Positives = 152/271 (56%), Gaps = 10/271 (3%)
Query: 302 QKKSPLNIFETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAYIIG 361
+ +LL ++ +L+ + E +L ++E+ L +L++RR GEP+AYI+G
Sbjct: 15 SAAGGTPNLDAELLLLHLLGKPRDQLLAHPEAELSEEELERLRELLERRAEGEPVAYILG 74
Query: 362 KKEFYGLVLNITSDVLIPRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKN 421
EF GL + VLIPRP+TELLV+ + + ++L++GTGSGAIAIA+A +
Sbjct: 75 SAEFGGLRFKVDEGVLIPRPDTELLVEAALALLLQLDKRILDLGTGSGAIAIALAKEGPD 134
Query: 422 KIEIIATDISKFALKIAKKNAKKKLTKYN-IPIKFIKSNWYNNLQNYKKLFNIIVANPPY 480
E+IA DIS AL +A++NA+ + + + ++S+ + L + F++IV+NPPY
Sbjct: 135 -AEVIAVDISPDALALARENAE----RNGLVRVLVVQSDLFEPL---RGKFDLIVSNPPY 186
Query: 481 IPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNLV 540
IP D L +R+EP+ AL +GL + I+ A L G+L++E G Q V
Sbjct: 187 IPAEDPELLPEVVRYEPLLALVGGGDGLEVYRRILGEAPDILKPGGVLILEIGLTQGEAV 246
Query: 541 RKLLFKYG-FSDIKSWRDLSGIERVTQGKIS 570
+ L G F +++ +DL G +RV K+
Sbjct: 247 KALFEDTGFFEIVETLKDLFGRDRVVLAKLR 277
>gnl|CDD|129627 TIGR00536, hemK_fam, HemK family putative methylases. The gene
hemK from E. coli was found to contribute to heme
biosynthesis and originally suggested to be
protoporphyrinogen oxidase (Medline 95189105).
Functional analysis of the nearest homolog in
Saccharomyces cerevisiae, YNL063w, finds it is not
protoporphyrinogen oxidase and sequence analysis
suggests that HemK homologs have
S-adenosyl-methionine-dependent methyltransferase
activity (Medline 99237242). Homologs are found, usually
in a single copy, in nearly all completed genomes, but
varying somewhat in apparent domain architecture. Both
E. coli and H. influenzae have two members rather than
one. The members from the Mycoplasmas have an additional
C-terminal domain [Protein fate, Protein modification
and repair].
Length = 284
Score = 210 bits (537), Expect = 7e-64
Identities = 98/259 (37%), Positives = 151/259 (58%), Gaps = 8/259 (3%)
Query: 314 ILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAYIIGKKEFYGLVLNIT 373
+LL + L+ ++L E + +L+ RR+ G P+AY++G KEFYGL +
Sbjct: 29 LLLLHDLGRERDLLLAFLTEELTPDEKERIFRLVLRRVKGVPVAYLLGSKEFYGLEFFVN 88
Query: 374 SDVLIPRPETELLVDLIVKKTFEK--KIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDIS 431
VLIPRPETE LV+ + + + +L++GTGSG IA+A+A N E+IA DIS
Sbjct: 89 EHVLIPRPETEELVEKALASLISQNPILHILDLGTGSGCIALALAYEFPNA-EVIAVDIS 147
Query: 432 KFALKIAKKNAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKG 491
AL +A++NA+K + ++FI+SN + L K +IIV+NPPYI + D+
Sbjct: 148 PDALAVAEENAEK--NQLEHRVEFIQSNLFEPLAGQK--IDIIVSNPPYIDEEDLADLPN 203
Query: 492 DLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQ-SNLVRKLLFKYGFS 550
+RFEP+ AL +GL+ +++I++ A YL NG L+ E G Q +L L K+ +
Sbjct: 204 VVRFEPLLALVGGDDGLNILRQIIELAPDYLKPNGFLVCEIGNWQQKSLKELLRIKFTWY 263
Query: 551 DIKSWRDLSGIERVTQGKI 569
D+++ RDL+G ERV G
Sbjct: 264 DVENGRDLNGKERVVLGFY 282
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 207 bits (530), Expect = 2e-63
Identities = 91/186 (48%), Positives = 119/186 (63%)
Query: 111 IFIEIRAGTGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLN 170
++ I AG GG E+ + + LLRMY R++ER +K E++ S E G K +I G N
Sbjct: 1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60
Query: 171 VYSKLKFESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRAS 230
Y LK E+GVHR+ R+ ++ GR HTS +V V PE D +I I DLRIDTYRAS
Sbjct: 61 AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRAS 120
Query: 231 GAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNT 290
GAGGQH+NKTDSAVR+TH+PTGIVV CQN+RSQH NKA A K+L ++ ++
Sbjct: 121 GAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQEK 180
Query: 291 AKMRRL 296
+ R L
Sbjct: 181 NRERAL 186
>gnl|CDD|184930 PRK14966, PRK14966, unknown domain/N5-glutamine
S-adenosyl-L-methionine-dependent methyltransferase
fusion protein; Provisional.
Length = 423
Score = 204 bits (520), Expect = 6e-60
Identities = 107/265 (40%), Positives = 170/265 (64%), Gaps = 8/265 (3%)
Query: 304 KSPLNIFETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAYIIGKK 363
K P N E +LL+Y + + V+L+ +++ + ++L QRR+ GEP+AYI+G +
Sbjct: 161 KLPKN--EARMLLQYASEYTRVQLLTRGGEEMPDEVRQRADRLAQRRLNGEPVAYILGVR 218
Query: 364 EFYGLVLNITSDVLIPRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKI 423
EFYG + +VLIPRPETE LV+ ++ + E ++ ++GTGSGA+A+ +A+ +
Sbjct: 219 EFYGRRFAVNPNVLIPRPETEHLVEAVLARLPENG-RVWDLGTGSGAVAVTVALERPDAF 277
Query: 424 EIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPK 483
+ A+DIS AL+ A+KNA + ++F +W++ + ++IIV+NPPYI
Sbjct: 278 -VRASDISPPALETARKNAADLGAR----VEFAHGSWFDTDMPSEGKWDIIVSNPPYIEN 332
Query: 484 GDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNLVRKL 543
GD HL +GDLRFEP ALTD+S+GLS I+ + + A L + G LL+EHG++Q VR +
Sbjct: 333 GDKHLLQGDLRFEPQIALTDFSDGLSCIRTLAQGAPDRLAEGGFLLLEHGFDQGAAVRGV 392
Query: 544 LFKYGFSDIKSWRDLSGIERVTQGK 568
L + GFS +++ DL+G++RVT GK
Sbjct: 393 LAENGFSGVETLPDLAGLDRVTLGK 417
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 197 bits (502), Expect = 4e-58
Identities = 95/198 (47%), Positives = 129/198 (65%), Gaps = 5/198 (2%)
Query: 104 DKNDKRNIFIEIRAGTGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEII 163
D ND ++E+ AG GG ES + + LLRMY R++ER K E++ E G K
Sbjct: 86 DANDT---YLEVHAGAGGTESQDWASMLLRMYTRWAERQGRKVEVLEVHDGEEAGIKSAT 142
Query: 164 ARIIGLNVYSKLKFESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLR 223
+ G N Y LK ESGVHR+ R+ ++ R HTS ++ V P D+ ++++N +D+R
Sbjct: 143 ILVKGHNAYGWLKTESGVHRLVRISPYDSNARRHTSFASIWVYPVIDDNIEVDVNESDVR 202
Query: 224 IDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKL 283
IDTYR+SGAGGQH+N TDSAVRITHIPTGIVVQCQ +RSQHKN+A A +L AR+ + +L
Sbjct: 203 IDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARLYEEEL 262
Query: 284 --REQQSNTAKMRRLLIG 299
RE+ +N A + IG
Sbjct: 263 KKREEATNAAAASKTDIG 280
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 196 bits (500), Expect = 5e-58
Identities = 104/260 (40%), Positives = 153/260 (58%), Gaps = 6/260 (2%)
Query: 30 NNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITAKEML--NDLEMRNFALDEINLAKK 87
N+IK+ + E +L ++ YN+ + EDI EM+ D EM+ + E+ K+
Sbjct: 8 NDIKEAQEITSEEKYLKDKLDKYNHLRNRIEDIEVLCEMMSEEDDEMKKEIISEVKNIKE 67
Query: 88 RIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESALFVNDLLRMYIRFSERNYWKFE 147
I ++E L + D+ N + + +G GG ++ + LLRMY R++E+ +K E
Sbjct: 68 EIDRFKIET----LLSGEYDRNNAILTLHSGVGGTDAQDWTEMLLRMYTRWAEKKGYKVE 123
Query: 148 IISRSLSEIGGYKEIIARIIGLNVYSKLKFESGVHRVQRVPKTETQGRIHTSACTVAVIP 207
II + G K + +I G Y LK E G+HR+ R+ G+ TS +V V+P
Sbjct: 124 IIDLLEGDEAGIKSVTLKITGEFAYGYLKAEKGIHRLVRISPFNANGKRQTSFASVEVLP 183
Query: 208 EADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHKNK 267
E + +DI I DL+IDTYRA GAGGQH+NKT+SAVRITHIPTGIVVQCQN+RSQH NK
Sbjct: 184 ELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNK 243
Query: 268 AFALKILLARIKDSKLREQQ 287
A+K+L +++ + K R +
Sbjct: 244 ETAMKMLKSKLVELKERAHK 263
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 188 bits (479), Expect = 3e-55
Identities = 98/236 (41%), Positives = 142/236 (60%), Gaps = 16/236 (6%)
Query: 57 KINEDIITAKEMLNDLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIR 116
+ +D TA ++ DL+ ++++ +R+F ++ D N F++I+
Sbjct: 27 ESEQDEDTALAVIADLDKYQAHVEKLEF--QRMFSGQM------------DGANAFVDIQ 72
Query: 117 AGTGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLK 176
AG GG E+ + LLRMY+R++E WK E++ S E+ G K RI G Y LK
Sbjct: 73 AGAGGTEAQDWAEILLRMYLRWAESRGWKTELMEVSGGEVAGIKSATVRIEGEYAYGWLK 132
Query: 177 FESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRIDTYRASGAGGQH 236
E GVHR+ R ++ R HTS +V V PE D+ +I+INPADLR D YR+SGAGGQH
Sbjct: 133 TEIGVHRLVRKSPFDSDNRRHTSFTSVFVSPEVDDNIEIDINPADLRTDVYRSSGAGGQH 192
Query: 237 INKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLREQQSNTAK 292
+NKT+SAVRITHIPT VV CQ RSQH+N+ A+K+L A++ + ++ Q+ N K
Sbjct: 193 VNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEV--QKRNAEK 246
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 169 bits (428), Expect = 1e-47
Identities = 94/214 (43%), Positives = 130/214 (60%), Gaps = 10/214 (4%)
Query: 91 DIELEIKKLI----------LPKDKNDKRNIFIEIRAGTGGDESALFVNDLLRMYIRFSE 140
++E E+K LI L D DK N +E+ G GG ES + + LLRMY R++E
Sbjct: 58 ELESEVKGLIQEMNEYELQLLLSDPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRWAE 117
Query: 141 RNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFESGVHRVQRVPKTETQGRIHTSA 200
+ +K E + + G K + I G N Y LK E GVHR+ R+ ++ GR HTS
Sbjct: 118 KRGFKVETVDYLPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSF 177
Query: 201 CTVAVIPEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQND 260
+ V+PE ++ +I + DL+IDTYRASGAGGQH+N TDSAVRITH PT VV CQ++
Sbjct: 178 VSCEVVPEFNDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSE 237
Query: 261 RSQHKNKAFALKILLARIKDSKLREQQSNTAKMR 294
RSQ KN+ A+K+L A++ KL EQQ+ ++R
Sbjct: 238 RSQIKNREHAMKMLKAKLYQKKLEEQQAELDEIR 271
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 158 bits (403), Expect = 2e-46
Identities = 56/113 (49%), Positives = 73/113 (64%), Gaps = 1/113 (0%)
Query: 67 EMLNDLEMRNFALDEIN-LAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESA 125
E D EMR A +E+ L + ++E +K L+LPKD ND +N +EIRAG GGDE+A
Sbjct: 4 EEEEDDEMRELAEEELEELEAELEEELEELLKLLLLPKDPNDDKNAILEIRAGAGGDEAA 63
Query: 126 LFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFE 178
LF DLLRMY+R++ER WK E++ S E+GG KE +I G Y KLKFE
Sbjct: 64 LFAGDLLRMYLRYAERKGWKVEVLDESEGELGGIKEATLKISGEGAYGKLKFE 116
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 156 bits (396), Expect = 1e-45
Identities = 51/112 (45%), Positives = 67/112 (59%)
Query: 67 EMLNDLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGGDESAL 126
E +D E+R A +E+ +K + ++E E+ L+LP D D +N +EIRAG GG E+ L
Sbjct: 4 EEEDDPELREEAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTEAQL 63
Query: 127 FVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLNVYSKLKFE 178
F DLLRMY R++ER WK E+I S E GG KE I G Y LKFE
Sbjct: 64 FAEDLLRMYQRYAERKGWKVEVIDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115
>gnl|CDD|234958 PRK01544, PRK01544, bifunctional N5-glutamine
S-adenosyl-L-methionine-dependent methyltransferase/tRNA
(m7G46) methyltransferase; Reviewed.
Length = 506
Score = 151 bits (383), Expect = 8e-40
Identities = 101/287 (35%), Positives = 152/287 (52%), Gaps = 43/287 (14%)
Query: 310 FETNILLKYVTRLSDVELIINNEKKLHKQEINILNKLIQRRILGEPIAYIIGKKEFYGLV 369
E ILL++V L+IN +++L++ EI KL++RR+ EPIAYI G KEFY
Sbjct: 26 LEARILLQHVINKPIEYLLINLDEQLNEAEIEAFEKLLERRLKHEPIAYITGVKEFYSRE 85
Query: 370 LNITSDVLIPRPETELLVDLIVKKTFE-------------------------KKIKLLEM 404
+ VLIPR +TE+LVD++ + K + +LE+
Sbjct: 86 FIVNKHVLIPRSDTEVLVDVVFQCHSRESGNPEKKQLNPCFRGNDISSNCNDKFLNILEL 145
Query: 405 GTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIP--IKFIKSNWYN 462
GTGSG IAI++ N +IATDIS A+++AK NA KY + I+ I SNW+
Sbjct: 146 GTGSGCIAISLLCELPNA-NVIATDISLDAIEVAKSNA----IKYEVTDRIQIIHSNWFE 200
Query: 463 NLQNYKKLFNIIVANPPYIPKGDIHLNKGDLRFEPIN-----ALTDYSNGLSSIKEIVKN 517
N++ K F+ IV+NPPYI H K ++ E IN AL +GL + I +N
Sbjct: 201 NIEKQK--FDFIVSNPPYIS----HSEKSEMAIETINYEPSIALFAEEDGLQAYFIIAEN 254
Query: 518 ASKYLVKNGLLLIEHGYNQSNLVRKLLFKYGFSDIKSWRDLSGIERV 564
A ++L NG +++E G+ Q V ++ +G++ ++DL G RV
Sbjct: 255 AKQFLKPNGKIILEIGFKQEEAVTQIFLDHGYNIESVYKDLQGHSRV 301
>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 = 137 bits (348), Expect = 9e-39
Identities = 48/99 (48%), Positives = 73/99 (73%), Gaps = 1/99 (1%)
Query: 207 PEADEIEDININPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHKN 266
P +E+E I I +DLRIDT+R+SG GGQ++NKT+SAVR+TH+PTGIVV+CQ +RSQHKN
Sbjct: 1 PLDEEVE-IEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKN 59
Query: 267 KAFALKILLARIKDSKLREQQSNTAKMRRLLIGSVQKKS 305
+ AL+ L A++ +++L++++ T R + +K
Sbjct: 60 REKALERLKAKLYEAELQKKREKTKPTRASQVRRGDRKE 98
>gnl|CDD|234247 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase,
ribosomal protein L3-specific. Members of this protein
family methylate ribosomal protein L3 on a glutamine
side chain. This family is related to HemK, a
protein-glutamine methyltranferase for peptide chain
release factors [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 284
Score = 109 bits (275), Expect = 1e-26
Identities = 69/220 (31%), Positives = 113/220 (51%), Gaps = 26/220 (11%)
Query: 334 KLHKQEINILNKLIQRRILGE-PIAYIIGKKEFYGLVLNITSDVLIPR-PETELLVD--- 388
+L E + +LI+RRI P+AY+ + F GL + VLIPR P EL+ D
Sbjct: 55 RLTPSEKERILELIERRIEERIPVAYLTNEAWFAGLEFYVDERVLIPRSPIAELIEDGFA 114
Query: 389 -LIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLT 447
+ + ++ +L++ TGSG IAIA A E+ A DIS AL +A+ N ++
Sbjct: 115 PWLEPEPVKR---ILDLCTGSGCIAIACAYAFPEA-EVDAVDISPDALAVAEINIER--- 167
Query: 448 KYNIP--IKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDL----RFEPINAL 501
+ + + I+S+ + L K +++IV+NPPY+ D+ DL EP AL
Sbjct: 168 -HGLEDRVTLIQSDLFAALPGRK--YDLIVSNPPYVDAEDM----ADLPAEYHHEPELAL 220
Query: 502 TDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNLVR 541
+GL ++ I+ A+ +L +NG+L++E G + L
Sbjct: 221 ASGEDGLDLVRRILAEAADHLNENGVLVVEVGNSMEALEE 260
>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 = 106 bits (266), Expect = 2e-26
Identities = 53/205 (25%), Positives = 98/205 (47%), Gaps = 15/205 (7%)
Query: 111 IFIEIRAGTGGDESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGYKEIIARIIGLN 170
I +++ + G E L V L R + + E++ + E+ G + + ++ L+
Sbjct: 1 ILLQLSSAQGPAECCLAVAKALERLTREAAARGVRVEVLEQEPGEVPG--TLRSALVSLD 58
Query: 171 -----VYSKLKFESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRID 225
+ ++E + + P R + V + E ++R +
Sbjct: 59 GEAAAALAD-RWEGTLLWICPSPYRPHHRR---KNWFIGVQRFSASEE---ATEDEIRFE 111
Query: 226 TYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLARIKDSKLRE 285
T R+SG GGQH+NKT+SAVR TH+ +GI V+ Q++RSQH NK A +L R+ D + +
Sbjct: 112 TLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADLQQEQ 171
Query: 286 QQSNTAKMRRLLIGSVQKKSPLNIF 310
+ A+ RR +++ +P+ +F
Sbjct: 172 AAALRAE-RRTAHHQIERGNPVRVF 195
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 106 bits (266), Expect = 2e-26
Identities = 36/94 (38%), Positives = 59/94 (62%), Gaps = 1/94 (1%)
Query: 217 INPADLRIDTYRASGAGGQHINKTDSAVRITHIPTGIVVQCQNDRSQHKNKAFALKILLA 276
++R +T R+SG GGQH+NKTDSAVR TH+ +GI V+ Q++RSQH NK A ++
Sbjct: 104 EQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAW 163
Query: 277 RIKDSKLREQQSNTAKMRRLLIGSVQKKSPLNIF 310
+++ + EQ + RR+ +++ +P +F
Sbjct: 164 KLEQQQQ-EQSAALKSQRRMFHHQIERGNPRRVF 196
>gnl|CDD|236988 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 307
Score = 106 bits (266), Expect = 2e-25
Identities = 69/219 (31%), Positives = 114/219 (52%), Gaps = 28/219 (12%)
Query: 334 KLHKQEINILNKLIQRRILGE--PIAYIIGKKEFYGLVLNITSDVLIPR-PETELLVD-- 388
+L E + +LI+RRI E P AY+ + F GL + VL+PR P EL+ D
Sbjct: 67 RLTPSEKARILELIERRI-NERIPAAYLTNEAWFCGLEFYVDERVLVPRSPIAELIEDGF 125
Query: 389 --LIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKL 446
+ + +L++ TGSG IAIA A + E+ A DIS AL +A+ N +
Sbjct: 126 APWLEDPPVTR---ILDLCTGSGCIAIACAYAFPD-AEVDAVDISPDALAVAEIN----I 177
Query: 447 TKYNIP--IKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDL----RFEPINA 500
++ + + I+S+ + L + +++IV+NPPY+ D+ DL R EP A
Sbjct: 178 ERHGLEDRVTLIESDLFAALPGRR--YDLIVSNPPYVDAEDM----ADLPAEYRHEPELA 231
Query: 501 LTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNL 539
L +GL ++ I+ A YL ++G+L++E G ++ +L
Sbjct: 232 LAAGDDGLDLVRRILAEAPDYLTEDGVLVVEVGNSRVHL 270
>gnl|CDD|234318 TIGR03704, PrmC_rel_meth, putative protein-(glutamine-N5)
methyltransferase, unknown substrate-specific. This
protein family is closely related to two different
families of protein-(glutamine-N5) methyltransferase.
The first is PrmB, which modifies ribosomal protein L3
in some bacteria. The second is PrmC (HemK), which
modifies peptide chain release factors 1 and 2 in most
bacteria and also in eukaryotes. The glutamine side
chain-binding motif NPPY shared by PrmB and PrmC is
N[VAT]PY in this family. The protein substrate is
unknown [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 251
Score = 93.7 bits (233), Expect = 2e-21
Identities = 61/212 (28%), Positives = 103/212 (48%), Gaps = 13/212 (6%)
Query: 343 LNKLIQRRILGEPIAYIIGKKEFYGLVLNITSDVLIPRPETELLVDLIVKKTFEKKIKL- 401
L ++ RR+ G P+ +++G EF GL + + V +PR TE LVD + L
Sbjct: 30 LAAMVDRRVAGLPLEHVLGWAEFCGLRIAVDPGVFVPRRRTEFLVDEAAALARPRSGTLV 89
Query: 402 -LEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKN-AKKKLTKYNIPIKFIKSN 459
+++ GSGA+ A+A + + IE+ A DI A++ A++N A T + + +
Sbjct: 90 VVDLCCGSGAVGAALAA-ALDGIELHAADIDPAAVRCARRNLADAGGTVH-------EGD 141
Query: 460 WYNNL-QNYKKLFNIIVANPPYIPKGDIHLNKGDLRF-EPINALTDYSNGLSSIKEIVKN 517
Y+ L + +I+ AN PY+P I L + R EP AL ++GL ++ +
Sbjct: 142 LYDALPTALRGRVDILAANAPYVPTDAIALMPPEARDHEPRVALDGGADGLDVLRRVAAG 201
Query: 518 ASKYLVKNGLLLIEHGYNQSNLVRKLLFKYGF 549
A +L G LL+E Q+ L + + G
Sbjct: 202 APDWLAPGGHLLVETSERQAPLAVEAFARAGL 233
>gnl|CDD|237872 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 80.7 bits (200), Expect = 1e-17
Identities = 55/181 (30%), Positives = 91/181 (50%), Gaps = 22/181 (12%)
Query: 375 DVLIPRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFA 434
+V P ++ LL + V K K ++LE+GTGSG +AI A KN +++ DI+ +A
Sbjct: 4 EVYEPAEDSFLLAENAVDK---KGDRVLEVGTGSGIVAIVAA---KNGKKVVGVDINPYA 57
Query: 435 LKIAKKNAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDLR 494
++ AK NAK + N ++ I+S+ + + K F++I+ NPPY+P + L
Sbjct: 58 VECAKCNAKLNNIR-NNGVEVIRSDLFEPFRGDK--FDVILFNPPYLPTEEEEEWDDWLN 114
Query: 495 FEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNL-----VRKLLFKYGF 549
+ AL+ +G I + +YL G +L+ QS+L V + L K GF
Sbjct: 115 Y----ALSGGKDGREVIDRFLDEVGRYLKPGGRILLL----QSSLTGEDEVLEYLEKLGF 166
Query: 550 S 550
Sbjct: 167 E 167
>gnl|CDD|203189 pfam05175, MTS, Methyltransferase small domain. This domain is
found in ribosomal RNA small subunit methyltransferase C
as well as other methyltransferases .
Length = 170
Score = 60.7 bits (148), Expect = 8e-11
Identities = 35/150 (23%), Positives = 63/150 (42%), Gaps = 33/150 (22%)
Query: 383 TELLVDLIVKKTFEKKI--KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKK 440
+ LL+ K + K+L++G G G + A+A S +E+ DI+ AL+ A+
Sbjct: 20 SRLLLS-----HLPKPLGGKVLDLGCGYGVLGAALAKRSP-DLEVTMVDINARALESARA 73
Query: 441 NAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDLRFEPINA 500
N + + S+ Y+ ++ F++I++NPP H K
Sbjct: 74 NLAANGLE---NGEVFWSDLYSAVEP--GKFDLIISNPP------FHAGKA--------- 113
Query: 501 LTDYSNGLSSIKEIVKNASKYLVKNGLLLI 530
TDY + + A+++L G L I
Sbjct: 114 -TDYDVA----QRFIAGAARHLKPGGELWI 138
>gnl|CDD|184931 PRK14967, PRK14967, putative methyltransferase; Provisional.
Length = 223
Score = 55.8 bits (135), Expect = 8e-09
Identities = 41/159 (25%), Positives = 76/159 (47%), Gaps = 14/159 (8%)
Query: 375 DVLIPRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFA 434
V P+ +T+LL D + + ++L++ TGSGA+A+A A + + A DIS+ A
Sbjct: 14 GVYRPQEDTQLLADALAAEGLGPGRRVLDLCTGSGALAVAAA--AAGAGSVTAVDISRRA 71
Query: 435 LKIAKKNAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIP-KGDIHLNKGDL 493
++ A+ NA + + + +W ++ F+++V+NPPY+P D ++G
Sbjct: 72 VRSARLNA----LLAGVDVDVRRGDWARAVEFRP--FDVVVSNPPYVPAPPDAPPSRG-- 123
Query: 494 RFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEH 532
P A +G + + + A L G LL+
Sbjct: 124 ---PARAWDAGPDGRAVLDRLCDAAPALLAPGGSLLLVQ 159
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 53.6 bits (129), Expect = 1e-08
Identities = 34/147 (23%), Positives = 65/147 (44%), Gaps = 30/147 (20%)
Query: 395 FEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIK 454
+ IK+L++G G+G + +A E++ DIS+ A++ AK+NAKK Y ++
Sbjct: 1 LKSGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKL--GYE-NVE 57
Query: 455 FIKSNWYN--NLQNYKKLFNIIVANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIK 512
FI+ + LQ F+++++N E +N L D
Sbjct: 58 FIQGDIEELPQLQLEDNSFDVVISN------------------EVLNHLPD-------PD 92
Query: 513 EIVKNASKYLVKNGLLLIEHGYNQSNL 539
++++ + L G+L++ S L
Sbjct: 93 KVLEEIIRVLKPGGVLIVSDPVLLSEL 119
>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
methyltransferases (SAM or AdoMet-MTase), class I;
AdoMet-MTases are enzymes that use
S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
for methyltransfer, creating the product
S-adenosyl-L-homocysteine (AdoHcy). There are at least
five structurally distinct families of AdoMet-MTases,
class I being the largest and most diverse. Within this
class enzymes can be classified by different substrate
specificities (small molecules, lipids, nucleic acids,
etc.) and different target atoms for methylation
(nitrogen, oxygen, carbon, sulfur, etc.).
Length = 107
Score = 51.3 bits (123), Expect = 4e-08
Identities = 26/132 (19%), Positives = 56/132 (42%), Gaps = 29/132 (21%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSN 459
++L++G G+GA+A+A+A + DIS AL++A+K A L ++ +K +
Sbjct: 1 RVLDLGCGTGALALALASG--PGARVTGVDISPVALELARKAAAALLADN---VEVLKGD 55
Query: 460 WYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKNAS 519
+ F++I+++PP + + ++ A
Sbjct: 56 AEELPPEADESFDVIISDPPLHH------------------------LVEDLARFLEEAR 91
Query: 520 KYLVKNGLLLIE 531
+ L G+L++
Sbjct: 92 RLLKPGGVLVLT 103
>gnl|CDD|129628 TIGR00537, hemK_rel_arch, HemK-related putative methylase. The
gene hemK from E. coli was found to contribute to heme
biosynthesis and originally suggested to be
protoporphyrinogen oxidase (Medline 95189105).
Functional analysis of the nearest homolog in
Saccharomyces cerevisiae, YNL063w, finds it is not
protoporphyrinogen oxidase and sequence analysis
suggests that HemK homologs have
S-adenosyl-methionine-dependent methyltransferase
activity (Medline 99237242). Homologs are found, usually
in a single copy, in nearly all completed genomes, but
varying somewhat in apparent domain architecture. This
model represents an archaeal and eukaryotic protein
family that lacks an N-terminal domain found in HemK and
its eubacterial homologs. It is found in a single copy
in the first six completed archaeal and eukaryotic
genomes [Unknown function, Enzymes of unknown
specificity].
Length = 179
Score = 52.9 bits (127), Expect = 4e-08
Identities = 30/107 (28%), Positives = 56/107 (52%), Gaps = 13/107 (12%)
Query: 379 PRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIA 438
P ++ LL + + K +LE+G G+G +AI + I+ TDI+ FA+K
Sbjct: 4 PAEDSLLLEANLREL---KPDDVLEIGAGTGLVAIRL---KGKGKCILTTDINPFAVKEL 57
Query: 439 KKNAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGD 485
++NAK N+ + + ++ + + + F++I+ NPPY+P D
Sbjct: 58 RENAKLN----NVGLDVVMTDLFKGV---RGKFDVILFNPPYLPLED 97
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 50.9 bits (122), Expect = 6e-08
Identities = 19/94 (20%), Positives = 41/94 (43%), Gaps = 3/94 (3%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSN 459
++L+ G GSGA +A A ++ ++ A +A++ + + + +
Sbjct: 3 RVLDPGAGSGAFLLAAARAGP-DARVVGVELDPEAAALARRRLALAGLAPRV--RVVVGD 59
Query: 460 WYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDL 493
L+ F++++ NPPY P+ + DL
Sbjct: 60 ARELLELPDGSFDLVLGNPPYGPRAGDPKDNRDL 93
>gnl|CDD|226608 COG4123, COG4123, Predicted O-methyltransferase [General function
prediction only].
Length = 248
Score = 52.6 bits (127), Expect = 1e-07
Identities = 39/159 (24%), Positives = 77/159 (48%), Gaps = 13/159 (8%)
Query: 397 KKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFI 456
KK ++L++G G+GA+ + +A K +I+ +I + A ++A++N L I+ I
Sbjct: 44 KKGRILDLGAGNGALGLLLA-QRTEKAKIVGVEIQEEAAEMAQRNV--ALNPLEERIQVI 100
Query: 457 KSNWYNNLQNYKKL--FNIIVANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEI 514
+++ F++I+ NPPY +G LN+ LR A+ + L ++++
Sbjct: 101 EAD-IKEFLKALVFASFDLIICNPPYFKQGSR-LNENPLR-----AIARHEITL-DLEDL 152
Query: 515 VKNASKYLVKNGLLLIEHGYNQSNLVRKLLFKYGFSDIK 553
++ A+K L G L H + + +LL Y +
Sbjct: 153 IRAAAKLLKPGGRLAFVHRPERLAEIIELLKSYNLEPKR 191
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 50.2 bits (121), Expect = 2e-07
Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 28/93 (30%)
Query: 214 DININPADLRIDTYRASGAGGQHINKTDSAV-------------------------RITH 248
+ I +L RASG GGQ++NK +AV RIT
Sbjct: 7 RLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRIT- 65
Query: 249 IPTG-IVVQCQNDRSQHKNKAFALKILLARIKD 280
G IV++ Q RSQ +N+ AL+ L+A I++
Sbjct: 66 -KDGVIVIKAQEFRSQERNREDALERLVALIRE 97
>gnl|CDD|225370 COG2813, RsmC, 16S RNA G1207 methylase RsmC [Translation, ribosomal
structure and biogenesis].
Length = 300
Score = 48.4 bits (116), Expect = 4e-06
Identities = 33/150 (22%), Positives = 63/150 (42%), Gaps = 34/150 (22%)
Query: 383 TELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNA 442
+ LL++ + K +L++G G G + + +A S ++ D++ A++ A+KN
Sbjct: 147 SRLLLETLPPDLGGK---VLDLGCGYGVLGLVLAKKSPQA-KLTLVDVNARAVESARKNL 202
Query: 443 KKKLTKYNIP--IKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDLRFEPINA 500
N + SN Y + + F++I++NPP H K
Sbjct: 203 AA-----NGVENTEVWASNLYEPV---EGKFDLIISNPP------FHAGKA--------- 239
Query: 501 LTDYSNGLSSIKEIVKNASKYLVKNGLLLI 530
+S +EI+ A+++L G L I
Sbjct: 240 -VVHSLA----QEIIAAAARHLKPGGELWI 264
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 44.2 bits (105), Expect = 9e-06
Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 397 KKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFI 456
++L++G G+G++AI +A + D+S L++A++NAK L I F+
Sbjct: 1 PGARVLDIGCGTGSLAIELA-RLFPGARVTGVDLSPEMLELARENAKLALGP---RITFV 56
Query: 457 KSNWYNNLQNYKKLFNIIVAN 477
+ + + L + F+ +
Sbjct: 57 QGDAPDALDLLEG-FDAVFIG 76
>gnl|CDD|222287 pfam13649, Methyltransf_25, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 97
Score = 41.2 bits (97), Expect = 1e-04
Identities = 19/94 (20%), Positives = 43/94 (45%), Gaps = 11/94 (11%)
Query: 401 LLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSNW 460
+L++G G+G + A+ + DISK AL++AK+ + K ++F+ ++
Sbjct: 1 ILDLGCGTGRVLRAL--ARAGPSSVTGVDISKEALELAKERLRDK----GPKVRFVVADA 54
Query: 461 YNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDLR 494
+ F++++ + +L+ LR
Sbjct: 55 RDLPFEEGS-FDLVICAGLSLD----YLSPKQLR 83
>gnl|CDD|225136 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
biosynthesis [Coenzyme metabolism].
Length = 238
Score = 42.6 bits (101), Expect = 2e-04
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 386 LVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKK 445
L+ L+ K K+L++ G+G +A+ +A S E++ DIS+ L++A++ KK
Sbjct: 43 LISLLGIK---PGDKVLDVACGTGDMALLLA-KSVGTGEVVGLDISESMLEVAREKLKK- 97
Query: 446 LTKYNIPIKFIKSN 459
K ++F+ +
Sbjct: 98 --KGVQNVEFVVGD 109
>gnl|CDD|216342 pfam01170, UPF0020, Putative RNA methylase family UPF0020. This
domain is probably a methylase. It is associated with
the THUMP domain that also occurs with RNA modification
domains.
Length = 172
Score = 41.5 bits (98), Expect = 3e-04
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 5/75 (6%)
Query: 407 GSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSNWYN-NLQ 465
GSG I I A+ N + +DI ++ A+ NA+ + K L
Sbjct: 38 GSGTILIEAALMGANIAPLYGSDIDWRMVQGARINAE----NAGVGDKIEFVQADAAKLP 93
Query: 466 NYKKLFNIIVANPPY 480
+ IV NPPY
Sbjct: 94 LLNGSVDAIVTNPPY 108
>gnl|CDD|234080 TIGR02987, met_A_Alw26, type II restriction m6 adenine DNA
methyltransferase, Alw26I/Eco31I/Esp3I family. Members
of this family are the m6-adenine DNA methyltransferase
protein, or domain of a fusion protein that also carries
m5 cytosine methyltransferase activity, of type II
restriction systems of the Alw26I/Eco31I/Esp3I family. A
methyltransferase of this family is alway accompanied by
a type II restriction endonuclease from the
Alw26I/Eco31I/Esp3I family (TIGR02986) and by an
adenine-specific modification methyltransferase. Members
of this family are unusual in that regions of similarity
to homologs outside this family are circularly permuted
[DNA metabolism, Restriction/modification].
Length = 524
Score = 43.2 bits (102), Expect = 3e-04
Identities = 41/169 (24%), Positives = 66/169 (39%), Gaps = 30/169 (17%)
Query: 384 ELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKI--------EIIATDISKFAL 435
LV+ I K K K+++ G G + IA + +I I DI K L
Sbjct: 18 ANLVNEIGKNDKSTKTKIIDPCCGDGRL-IAALLKKNEEINYFKEVELNIYFADIDKTLL 76
Query: 436 KIAKKN-AKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDL- 493
K AKK + L + N+ S N+++Y LF+I++ NPPY G + +K +L
Sbjct: 77 KRAKKLLGEFALLEINVINFNSLSYVLLNIESYLDLFDIVITNPPY---GRLKPDKKELT 133
Query: 494 RFEPINALTDYSNGLSSIKEIVKNASKYLVKNGLLLIEHGYNQSNLVRK 542
E + + +K L + S+ +RK
Sbjct: 134 NIETLEYEKY--------IDFLKEFDDLLSRV--------LPYSDPIRK 166
>gnl|CDD|225173 COG2264, PrmA, Ribosomal protein L11 methylase [Translation,
ribosomal structure and biogenesis].
Length = 300
Score = 41.9 bits (99), Expect = 5e-04
Identities = 26/97 (26%), Positives = 47/97 (48%), Gaps = 7/97 (7%)
Query: 381 PETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKK 440
P T L ++ + K + K +L++G GSG +AIA A +++ DI A++ A++
Sbjct: 147 PTTSLCLEALEKLLKKGK-TVLDVGCGSGILAIAAAKL--GAKKVVGVDIDPQAVEAARE 203
Query: 441 NAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVAN 477
NA+ + + K + F++IVAN
Sbjct: 204 NARLNGVELLVQAKG----FLLLEVPENGPFDVIVAN 236
>gnl|CDD|181902 PRK09489, rsmC, 16S ribosomal RNA m2G1207 methyltransferase;
Provisional.
Length = 342
Score = 41.8 bits (99), Expect = 7e-04
Identities = 21/90 (23%), Positives = 47/90 (52%), Gaps = 12/90 (13%)
Query: 394 TFEKKI--KLLEMGTGSGAIAIAIAIYSKN-KIEIIATDISKFALKIAKKNAKKKLTKYN 450
T K+L++G G+G ++ +A + KI + +D+S AL+ ++ L
Sbjct: 191 TLTPHTKGKVLDVGCGAGVLSAVLA--RHSPKIRLTLSDVSAAALESSRAT----LAANG 244
Query: 451 IPIKFIKSNWYNNLQNYKKLFNIIVANPPY 480
+ + SN +++++ F++I++NPP+
Sbjct: 245 LEGEVFASNVFSDIKGR---FDMIISNPPF 271
>gnl|CDD|233645 TIGR01934, MenG_MenH_UbiE, ubiquinone/menaquinone biosynthesis
methyltransferases. This model represents a family of
methyltransferases involved in the biosynthesis of
menaquinone and ubiqinone. Some members such as the UbiE
enzyme from E. coli are believed to act in both
pathways, while others may act in only the menaquinone
pathway. These methyltransferases are members of the
UbiE/CoQ family of methyltransferases (pfam01209) which
also contains ubiquinone methyltransferases and other
methyltransferases. Members of this clade include a wide
distribution of bacteria and eukaryotes, but no archaea.
An outgroup for this clade is provided by the
phosphatidylethanolamine methyltransferase (EC 2.1.1.17)
from Rhodobacter sphaeroides. Note that a number of
non-orthologous genes which are members of pfam03737
have been erroneously annotated as MenG
methyltransferases [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 223
Score = 40.3 bits (95), Expect = 0.001
Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 5/60 (8%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSN 459
K+L++ G+G +AI +A + ++ ++ D S L++AKK ++ L I+FI+++
Sbjct: 42 KVLDVACGTGDLAIELAKSAPDRGKVTGVDFSSEMLEVAKKKSELPL-----NIEFIQAD 96
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 41.0 bits (96), Expect = 0.001
Identities = 37/149 (24%), Positives = 68/149 (45%), Gaps = 10/149 (6%)
Query: 382 ETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKN 441
E+ +V L+++ E +++L+ G AIA K++ +I+A DIS+ +++ +K+
Sbjct: 224 ESSQIVPLLME--LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKH 281
Query: 442 AKK-KLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDLRFEPINA 500
AK+ KL+ I+ ++ + + F+ I+ + P G + LR
Sbjct: 282 AKRLKLS----SIEIKIADAERLTEYVQDTFDRILVDAPCTSLGTARNHPEVLRRVNKED 337
Query: 501 LTDYSNGLSSIKEIVKNASKYLVKNGLLL 529
S IV A K L K G+LL
Sbjct: 338 FKKLS---EIQLRIVSQAWKLLEKGGILL 363
>gnl|CDD|218990 pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA).
This family consists of several Ribosomal protein L11
methyltransferase (EC:2.1.1.-) sequences.
Length = 294
Score = 40.3 bits (95), Expect = 0.001
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSN 459
+L++G GSG +AIA +++ DI A++ AK+NA+ + + +
Sbjct: 163 TVLDVGCGSGILAIAALKL--GAKKVVGVDIDPVAVRAAKENAELNGVEAQLEV------ 214
Query: 460 WYNNLQNYKKLFNIIVAN 477
Y + +++VAN
Sbjct: 215 -YLPGDLPEGKADVVVAN 231
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 40.8 bits (96), Expect = 0.001
Identities = 28/129 (21%), Positives = 54/129 (41%), Gaps = 26/129 (20%)
Query: 406 TGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKK-KLTKYNIPIKFIKSN---WY 461
TG ++ A+ E+ + D+SK AL+ A++NA+ L +FI + W
Sbjct: 228 TGGFSVHAALG----GASEVTSVDLSKRALEWARENAELNGLDG--DRHRFIVGDVFKWL 281
Query: 462 NNLQNYKKLFNIIVANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKNASKY 521
+ + F++I+ +PP + + + +A DY K++ A +
Sbjct: 282 RKAERRGEKFDLIILDPPSFARS---------KKQEFSAQRDY-------KDLNDLALRL 325
Query: 522 LVKNGLLLI 530
L G L+
Sbjct: 326 LAPGGTLVT 334
>gnl|CDD|234786 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed.
Length = 250
Score = 39.7 bits (94), Expect = 0.002
Identities = 34/165 (20%), Positives = 66/165 (40%), Gaps = 54/165 (32%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNK---IEIIATDISKFALKIAKKNAKKKLTKYNIPIKFI 456
+L++G GSG +AIA A K +++A DI A++ A++NA+ N ++
Sbjct: 122 TVLDVGCGSGILAIAAA-----KLGAKKVLAVDIDPQAVEAARENAEL-----N-GVELN 170
Query: 457 KSNWYNNLQNYKKLFNIIVANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVK 516
+L+ ++IVAN I A + + E+
Sbjct: 171 VYLPQGDLK-----ADVIVAN--------------------ILA--------NPLLELAP 197
Query: 517 NASKYLVKNGLLL----IEHGYNQSNLVRKLLFKYGFSDIKSWRD 557
+ ++ L G L+ +E Q++ V + + GF+ +
Sbjct: 198 DLARLLKPGGRLILSGILEE---QADEVLEAYEEAGFTLDEVLER 239
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 37.4 bits (88), Expect = 0.012
Identities = 15/70 (21%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 391 VKKTFEKK-IKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKY 449
+K + K+L++ G+G +AIA+A E++ D S+ L + ++ +
Sbjct: 44 IKWLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGREKLRDLGLSG 103
Query: 450 NIPIKFIKSN 459
N+ F++ +
Sbjct: 104 NVE--FVQGD 111
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 37.2 bits (87), Expect = 0.019
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 404 MGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLT---KYNI 451
G G +AI + ++ E IA +FA ++A+K +KK+T K N+
Sbjct: 139 RILGGGEVAIDTKVITRKGSERIA----RFAFELARKRGRKKVTSVHKANV 185
>gnl|CDD|219760 pfam08242, Methyltransf_12, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 98
Score = 34.7 bits (80), Expect = 0.022
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 402 LEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKK 440
L++G G+G + A+ +E DIS AL+ A +
Sbjct: 1 LDIGCGTGTLLRALLEALPG-LEYTGVDISPAALEAAAE 38
>gnl|CDD|233708 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme,
which is found in biotin biosynthetic gene clusters in
proteobacteria, firmicutes, green-sulfur bacteria,
fusobacterium and bacteroides, is believed to carry out
an enzymatic step prior to the formation of pimeloyl-CoA
(although attribution of this annotation is not
traceable). The enzyme appears related to
methyltransferases by homology [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 240
Score = 36.1 bits (84), Expect = 0.028
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 386 LVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKK 445
L+ L+ +K +L++G G+G + A+ + E IA DIS L AK +
Sbjct: 23 LLALLKEKGIFIPASVLDIGCGTGYLTRALL-KRFPQAEFIANDISAGMLAQAKTKLSEN 81
Query: 446 LT 447
+
Sbjct: 82 VQ 83
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 35.7 bits (83), Expect = 0.029
Identities = 13/45 (28%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKK 444
+L ++G G+G+I I A+ +IA + + AL++ ++NA +
Sbjct: 37 RLWDIGAGTGSITIEWALA-GPSGRVIAIERDEEALELIERNAAR 80
>gnl|CDD|225172 COG2263, COG2263, Predicted RNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 198
Score = 34.6 bits (80), Expect = 0.070
Identities = 22/79 (27%), Positives = 48/79 (60%), Gaps = 10/79 (12%)
Query: 402 LEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSNWY 461
L++G G+G +AI A+ +++ +A DI AL+IA+ NA++ L ++F+ +
Sbjct: 50 LDLGAGTGILAIGAALLGASRV--LAVDIDPEALEIARANAEELLGD----VEFVVA--- 100
Query: 462 NNLQNYKKLFNIIVANPPY 480
++ +++ F+ ++ NPP+
Sbjct: 101 -DVSDFRGKFDTVIMNPPF 118
>gnl|CDD|223194 COG0116, COG0116, Predicted N6-adenine-specific DNA methylase [DNA
replication, recombination, and repair].
Length = 381
Score = 35.4 bits (82), Expect = 0.081
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 412 AIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSNWYNNLQNYKKLF 471
A A K I +DI ++ AK NA + ++ I+F +++ +L+ + +
Sbjct: 244 AEERARRGKELPIIYGSDIDPRHIEGAKANA-RAAGVGDL-IEFKQAD-ATDLKEPLEEY 300
Query: 472 NIIVANPPY 480
++++NPPY
Sbjct: 301 GVVISNPPY 309
>gnl|CDD|225174 COG2265, TrmA, SAM-dependent methyltransferases related to tRNA
(uracil-5-)-methyltransferase [Translation, ribosomal
structure and biogenesis].
Length = 432
Score = 35.4 bits (82), Expect = 0.083
Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 16/86 (18%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPI------ 453
++L++ G G + +A K ++ +IS A++ A++NA N+
Sbjct: 296 RVLDLYCGVGTFGLPLA---KRVKKVHGVEISPEAVEAAQENA-AANGIDNVEFIAGDAE 351
Query: 454 KFIKSNWYNNLQNYKKLFNIIVANPP 479
+F + W + YK +++V +PP
Sbjct: 352 EFTPAWW----EGYK--PDVVVVDPP 371
>gnl|CDD|224271 COG1352, CheR, Methylase of chemotaxis methyl-accepting proteins
[Cell motility and secretion / Signal transduction
mechanisms].
Length = 268
Score = 34.9 bits (81), Expect = 0.089
Identities = 12/65 (18%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 384 ELLVDLIVKKTFEKKIKLLEMGTGSG----AIAIAIAIY----SKNKIEIIATDISKFAL 435
+ ++ +VK+ + I++ +G ++A+ + + +++I+ATDI L
Sbjct: 83 DEVLPELVKRKKGRPIRIWSAACSTGEEPYSLAMLLLEALGKLAGFRVKILATDIDLSVL 142
Query: 436 KIAKK 440
+ A+
Sbjct: 143 EKARA 147
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 32.6 bits (75), Expect = 0.093
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 402 LEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAK 443
L++G G+G +A A+A + + D+S L +A+K A
Sbjct: 1 LDVGCGTGLLAEALA--RRGGARVTGVDLSPEMLALARKRAP 40
>gnl|CDD|225318 COG2520, COG2520, Predicted methyltransferase [General function
prediction only].
Length = 341
Score = 33.8 bits (78), Expect = 0.19
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 390 IVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKK-KLTK 448
+ + E + +L+M G G +I IA K + ++ A DI+ A++ K+N + K+
Sbjct: 182 VAELVKEGET-VLDMFAGVGPFSIPIA--KKGRPKVYAIDINPDAVEYLKENIRLNKVEG 238
Query: 449 YNIPI 453
PI
Sbjct: 239 RVEPI 243
>gnl|CDD|215721 pfam00107, ADH_zinc_N, Zinc-binding dehydrogenase.
Length = 131
Score = 32.7 bits (75), Expect = 0.19
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 405 GTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKK 440
G G A+ +A A+ + +IA D S+ L++AK+
Sbjct: 1 GVGLAAVQLAKALGAA---RVIAVDRSEEKLELAKE 33
>gnl|CDD|216673 pfam01739, CheR, CheR methyltransferase, SAM binding domain. CheR
proteins are part of the chemotaxis signaling mechanism
in bacteria. CheR methylates the chemotaxis receptor at
specific glutamate residues. CheR is an
S-adenosylmethionine- dependent methyltransferase - the
C-terminal domain (this one) binds SAM.
Length = 194
Score = 33.4 bits (77), Expect = 0.21
Identities = 14/63 (22%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 386 LVDLIVKKTFEKKIKLLEMGTGSG----AIAIAIAIYSKN----KIEIIATDISKFALKI 437
++ + + +++++ G SG ++A+ +A N +I+ATDI AL+
Sbjct: 19 VLPELAQARNSRRVRIWSAGCSSGEEPYSLAMLLAETLPNALPWDFKILATDIDLSALEK 78
Query: 438 AKK 440
A+
Sbjct: 79 ARA 81
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 33.5 bits (77), Expect = 0.23
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 376 VLIPRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFAL 435
V I PET L+ L+ + + K+I LE+GT G A+ +A+ + + + +
Sbjct: 40 VPIIDPETGALLRLLARLSGPKRI--LEIGTAIGYSALWMALALPDDGRLTTIERDEERA 97
Query: 436 KIAKKNAKK 444
+IA++N +
Sbjct: 98 EIARENLAE 106
>gnl|CDD|225317 COG2519, GCD14, tRNA(1-methyladenosine) methyltransferase and
related methyltransferases [Translation, ribosomal
structure and biogenesis].
Length = 256
Score = 33.0 bits (76), Expect = 0.29
Identities = 29/105 (27%), Positives = 43/105 (40%), Gaps = 22/105 (20%)
Query: 359 IIGKKEFYGLVLNITSD----VLIPRPETELLV-----------D--LIVKKT--FEKKI 399
+IGK YG V+ VL P PE LL D IV +
Sbjct: 40 VIGKP--YGEVIKSHLGVKFYVLKPTPEDYLLSMKRRTQIIYPKDAGYIVARLGISPGS- 96
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKK 444
++LE GTGSGA+ +A + + +I + K A++N +
Sbjct: 97 RVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARENLSE 141
>gnl|CDD|225139 COG2230, Cfa, Cyclopropane fatty acid synthase and related
methyltransferases [Cell envelope biogenesis, outer
membrane].
Length = 283
Score = 33.4 bits (77), Expect = 0.30
Identities = 24/108 (22%), Positives = 46/108 (42%), Gaps = 16/108 (14%)
Query: 364 EFYGLVLNIT---SDVLIPRPETEL------LVDLIVKK-TFEKKIKLLEMGTGSGAIAI 413
+FY L L+ + S P+ L +DLI++K + + LL++G G G +AI
Sbjct: 29 DFYRLFLDPSMTYSCAYFEDPDMTLEEAQRAKLDLILEKLGLKPGMTLLDIGCGWGGLAI 88
Query: 414 -AIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSNW 460
A Y ++ +S+ L A+K + ++ ++
Sbjct: 89 YAAEEYGVT---VVGVTLSEEQLAYAEKRIAAR--GLEDNVEVRLQDY 131
>gnl|CDD|185082 PRK15128, PRK15128, 23S rRNA m(5)C1962 methyltransferase;
Provisional.
Length = 396
Score = 33.3 bits (76), Expect = 0.36
Identities = 41/161 (25%), Positives = 77/161 (47%), Gaps = 27/161 (16%)
Query: 412 AIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIP-IKFIKSNWYNNLQNYK-- 468
A++ ++++ D S+ AL IA++N +L K ++ +F++ + + L+ Y+
Sbjct: 233 GFAVSALMGGCSQVVSVDTSQEALDIARQNV--ELNKLDLSKAEFVRDDVFKLLRTYRDR 290
Query: 469 -KLFNIIVANPPYIPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKNASKYLVKNGL 527
+ F++IV +PP + NK L + A Y K+I A + L G+
Sbjct: 291 GEKFDVIVMDPPKFVE-----NKSQL----MGACRGY-------KDINMLAIQLLNPGGI 334
Query: 528 LLIEHGYNQSNLVRKLLFKYGFSD--IKSWRDLSGIERVTQ 566
LL ++ S L+ LF+ +D I + RD+ IE+ Q
Sbjct: 335 LLT---FSCSGLMTSDLFQKIIADAAIDAGRDVQFIEQFRQ 372
>gnl|CDD|212120 cd10809, GH38N_AMII_GMII_SfManIII_like, N-terminal catalytic domain
of Golgi alpha-mannosidase II, Spodoptera frugiperda Sf9
alpha-mannosidase III, and similar proteins; glycoside
hydrolase family 38 (GH38). This subfamily is
represented by Golgi alpha-mannosidase II (GMII, also
known as mannosyl-oligosaccharide 1,3- 1,6-alpha
mannosidase, EC 3.2.1.114, Man2A1), a monomeric,
membrane-anchored class II alpha-mannosidase existing in
the Golgi apparatus of eukaryotes. GMII plays a key role
in the N-glycosylation pathway. It catalyzes the
hydrolysis of the terminal both alpha-1,3-linked and
alpha-1,6-linked mannoses from the high-mannose
oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield
GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which
is the committed step of complex N-glycan synthesis.
GMII is activated by zinc or cobalt ions and is strongly
inhibited by swainsonine. Inhibition of GMII provides a
route to block cancer-induced changes in cell surface
oligosaccharide structures. GMII has a pH optimum of
5.5-6.0, which is intermediate between those of acidic
(lysosomal alpha-mannosidase) and neutral (ER/cytosolic
alpha-mannosidase) enzymes. GMII is a retaining glycosyl
hydrolase of family GH38 that employs a two-step
mechanism involving the formation of a covalent glycosyl
enzyme complex; two carboxylic acids positioned within
the active site act in concert: one as a catalytic
nucleophile and the other as a general acid/base
catalyst. This subfamily also includes human
alpha-mannosidase 2x (MX, also known as
mannosyl-oligosaccharide 1,3- 1,6-alpha mannosidase, EC
3.2.1.114, Man2A2). MX is enzymatically and functionally
very similar to GMII, and is thought to also function in
the N-glycosylation pathway. Also found in this
subfamily is class II alpha-mannosidase encoded by
Spodoptera frugiperda Sf9 cell. This alpha-mannosidase
is an integral membrane glycoprotein localized in the
Golgi apparatus. It shows high sequence homology with
mammalian Golgi alpha-mannosidase II(GMII). It can
hydrolyze p-nitrophenyl alpha-D-mannopyranoside
(pNP-alpha-Man), and it is inhibited by swainsonine.
However, the Sf9 enzyme is stimulated by cobalt and can
hydrolyze (Man)5(GlcNAc)2 to (Man)3(GlcNAc)2, but it
cannot hydrolyze GlcNAc(Man)5(GlcNAc)2, which is
distinct from that of GMII. Thus, this enzyme has been
designated as Sf9 alpha-mannosidase III (SfManIII). It
probably functions in an alternate N-glycan processing
pathway in Sf9 cells.
Length = 340
Score = 33.0 bits (76), Expect = 0.36
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 21/100 (21%)
Query: 418 YSKNKIEIIATDISKFALKIAKKNAKK-KLTKYN---IPI----KFIKSN-WYNNLQNYK 468
+ K I ++++ A + + KK +L + N IP+ ++ W NY+
Sbjct: 220 WKKPPQPITDDNVAERAELLLDQYRKKSQLYRSNVVLIPLGDDFRYDSDEEWDAQYDNYQ 279
Query: 469 KLFNIIVANPPYIPKGDIHLNKGDLRFEPINALTDYSNGL 508
KLF+ I +NP +++F L+DY N L
Sbjct: 280 KLFDYINSNPEL---------NVEIQF---GTLSDYFNAL 307
>gnl|CDD|234740 PRK00377, cbiT, cobalt-precorrin-6Y C(15)-methyltransferase;
Provisional.
Length = 198
Score = 32.5 bits (74), Expect = 0.44
Identities = 15/67 (22%), Positives = 35/67 (52%)
Query: 378 IPRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKI 437
IP + E+ + K K +L++G G+G++ + ++ ++ A D + A+ +
Sbjct: 21 IPMTKEEIRALALSKLRLRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINL 80
Query: 438 AKKNAKK 444
++NA+K
Sbjct: 81 TRRNAEK 87
>gnl|CDD|110227 pfam01209, Ubie_methyltran, ubiE/COQ5 methyltransferase family.
Length = 233
Score = 31.3 bits (71), Expect = 0.98
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSN 459
K L++ G+G ++ + + +++ DI++ LK +K AK++ KYN I+F++ N
Sbjct: 50 KFLDVAGGTGDWTFGLSDSAGSSGKVVGLDINENMLKEGEKKAKEE-GKYN--IEFLQGN 106
>gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional.
Length = 241
Score = 31.4 bits (72), Expect = 1.1
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 402 LEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNA 442
L++G G G A +A + ++ D S+ L +AK+ A
Sbjct: 24 LDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAKERA 64
>gnl|CDD|223813 COG0742, COG0742, N6-adenine-specific methylase [DNA replication,
recombination, and repair].
Length = 187
Score = 31.0 bits (71), Expect = 1.2
Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 407 GSGAIAI-AIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSN--WYNN 463
GSGA+ + A+ S+ ++ + + A+KI K+N K + ++++
Sbjct: 53 GSGALGLEAL---SRGAARVVFVEKDRKAVKILKENLK--ALGLEGEARVLRNDALRALK 107
Query: 464 LQNYKKLFNIIVANPPY 480
++ F+++ +PPY
Sbjct: 108 QLGTREPFDLVFLDPPY 124
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 31.2 bits (71), Expect = 1.2
Identities = 18/96 (18%), Positives = 36/96 (37%), Gaps = 9/96 (9%)
Query: 9 LEKFSKRLKELDFLLT---QKEVHNNIKDYCKKVREHSFLYPIVELYNNYKKINEDIITA 65
LE+ ++ L + +E+H ++ Y + + +++ K + E+
Sbjct: 64 LERLLEQKFGLKIVRIGSPAREIHEDVLQYSLEYLLEAKFEQLLKRIRKLKSLLEEKSKL 123
Query: 66 KEMLNDLEMRNFALDEINLAKKRIFDIELEIKKLIL 101
K L EI KK + + I+K IL
Sbjct: 124 KRERRKLR------SEIKKLKKELERLRKSIRKEIL 153
>gnl|CDD|180466 PRK06202, PRK06202, hypothetical protein; Provisional.
Length = 232
Score = 30.7 bits (70), Expect = 1.4
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 401 LLEMGTGSGAIAIAIAIYSKN---KIEIIATDISKFALKIAKKNAKK 444
LL++G G G +AI +A +++ ++E+ A D A+ A+ N ++
Sbjct: 64 LLDIGCGGGDLAIDLARWARRDGLRLEVTAIDPDPRAVAFARANPRR 110
>gnl|CDD|224780 COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 380
Score = 31.2 bits (71), Expect = 1.7
Identities = 12/59 (20%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 385 LLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAK 443
L V ++ ++L+ + +G I A+ + ++++ DIS A+++ K+N +
Sbjct: 40 LSVLVLKAFGKLLPKRVLDALSATGIRGIRYAVETGV-VKVVLNDISPKAVELIKENVR 97
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 30.8 bits (70), Expect = 1.8
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 406 TGSGAIAIAIAIYSKNK-IEIIATDISKFALKIAKK 440
G+G + + A +K +I TD S L++AK+
Sbjct: 141 LGAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKE 176
>gnl|CDD|216840 pfam02005, TRM, N2,N2-dimethylguanosine tRNA methyltransferase.
This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA.
The TRM1 gene of Saccharomyces cerevisiae is necessary
for the N2,N2-dimethylguanosine modification of both
mitochondrial and cytoplasmic tRNAs. The enzyme is found
in both eukaryotes and archaebacteria.
Length = 375
Score = 30.8 bits (70), Expect = 1.9
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 6/96 (6%)
Query: 350 RILGEPIAYIIGKKE--FYGLVLNITSDVLIPRPETELLVDLIVKKTFEKKIKLLEMGTG 407
RIL + K FY + D+ + T + ++ K + I +L+ +
Sbjct: 4 RILVPDKPVTVSSKNPVFYNPRMEFNRDLSV----TVIRQLNLLHKKLGRGIIVLDALSA 59
Query: 408 SGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAK 443
SG AI A+ E+ A DIS A+++ K+N K
Sbjct: 60 SGIRAIRFALEVPGVEEVFANDISPKAVELIKENVK 95
>gnl|CDD|202251 pfam02475, Met_10, Met-10+ like-protein. The methionine-10 mutant
allele of N. crassa codes for a protein of unknown
function. However, homologous proteins have been found
in yeast suggesting this protein may be involved in
methionine biosynthesis, transport and/or utilisation.
Length = 199
Score = 30.4 bits (69), Expect = 2.0
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 402 LEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAK-KKLTKYNIPI 453
++M G G +I IA +SK K + A +++ A+K K+N K K+ PI
Sbjct: 105 VDMFAGIGPFSIPIAKHSKAKR-VYAVELNPEAVKYLKENIKLNKVEGVISPI 156
>gnl|CDD|226413 COG3897, COG3897, Predicted methyltransferase [General function
prediction only].
Length = 218
Score = 30.1 bits (68), Expect = 2.2
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 400 KLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSN 459
++L++G GSG +AIA A E++A DI + + + NA + I F ++
Sbjct: 82 RVLDLGAGSGLVAIAAAR--AGAAEVVAADIDPWLEQAIRLNAA----ANGVSILFTHAD 135
>gnl|CDD|223363 COG0286, HsdM, Type I restriction-modification system
methyltransferase subunit [Defense mechanisms].
Length = 489
Score = 30.8 bits (70), Expect = 2.3
Identities = 27/107 (25%), Positives = 54/107 (50%), Gaps = 8/107 (7%)
Query: 379 PRPETELLVDLIVKKTFEKKIKLLEMGTGSGAIAIAIAIY---SKNKIEIIATDISKFAL 435
PR +EL+V+L+ E + + + GSG + + A Y +++I I +I+
Sbjct: 171 PREVSELIVELL---DPEPRNSIYDPACGSGGMLLQAAKYLKRHQDEIFIYGQEINDTTY 227
Query: 436 KIAKKNAKKKLTKYNIPIKFIK--SNWYNNLQNYKKLFNIIVANPPY 480
++AK N + + I+ SN ++ ++ K F+ ++ANPP+
Sbjct: 228 RLAKMNLILHGIEGDANIRHGDTLSNPKHDDKDDKGKFDFVIANPPF 274
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 30.3 bits (69), Expect = 2.9
Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 7/43 (16%)
Query: 412 AIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLT---KYNI 451
A+ +YS+++IE IA + A ++A+K +KK+T K N+
Sbjct: 153 AVDTKLYSRDEIERIA----RVAFELARKRGRKKVTSVDKANV 191
>gnl|CDD|143473 cd06560, PriL, Archaeal/eukaryotic core primase: Large subunit,
PriL. Primases synthesize the RNA primers required for
DNA replication. Primases are grouped into two classes,
bacteria/bacteriophage and archaeal/eukaryotic. The
proteins in the two classes differ in structure and the
replication apparatus components. The DNA replication
machinery of archaeal organisms contains only the core
primase, a simpler arrangement compared to eukaryotes.
Archaeal/eukaryotic core primase is a heterodimeric
enzyme consisting of a small catalytic subunit (PriS)
and a large subunit (PriL). Although the catalytic
activity resides within PriS, the PriL subunit is
essential for primase function as disruption of the PriL
gene in yeast is lethal. PriL is composed of two
structural domains. Several functions have been proposed
for PriL, such as the stabilization of PriS, involvement
in the initiation of synthesis, the improvement of
primase processivity, and the determination of product
size.
Length = 166
Score = 29.3 bits (66), Expect = 3.1
Identities = 25/118 (21%), Positives = 48/118 (40%), Gaps = 9/118 (7%)
Query: 62 IITAKEMLNDLEMRNFALDEINLAKKRIFDIELEIKKLILPKDKNDKRNIFIEIRAGTGG 121
+ + + + R FA E +A++R+ E I + K + I I G
Sbjct: 48 RVLVAALDDSILTRRFARAEAKIAEERLRKESEEDLLEIAIELGYLKPDELIGIEVGIED 107
Query: 122 DESALFVNDLLRMYIRFSERNYWKFEIISRSLSEIGGY----KEIIARIIGLNVYSKL 175
+ V+D L++ R K+ +++R L GY KE + R++ + +L
Sbjct: 108 LPYKIPVSDYLKLAARLRG---DKWRLVNRILRN--GYVYLTKEELLRLLREAIRERL 160
>gnl|CDD|219622 pfam07891, DUF1666, Protein of unknown function (DUF1666). These
sequences are derived from hypothetical plant proteins
of unknown function. The region in question is
approximately 250 residues long.
Length = 247
Score = 29.8 bits (67), Expect = 3.2
Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 279 KDSKLREQQSNTAKMRRLLIGSVQKKSPLNIFETNILLKYVTRLSDVELIINNEKKLHK- 337
K+ KL+E + + + + + + + IF + I LK V+R+ ++ + + LH
Sbjct: 165 KEKKLKEVLRSGSCILKKFKKNESESDEVLIFFSLIDLKLVSRVLNMSKL--TTEHLHWC 222
Query: 338 ----QEINILNKLIQR 349
+IN +N+ +
Sbjct: 223 QEKLSKINFVNRKLHM 238
>gnl|CDD|232960 TIGR00406, prmA, ribosomal protein L11 methyltransferase.
Ribosomal protein L11 methyltransferase is an
S-adenosyl-L-methionine-dependent methyltransferase
required for the modification of ribosomal protein L11.
This protein is found in bacteria and (with a probable
transit peptide) in Arabidopsis [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 288
Score = 29.8 bits (67), Expect = 4.0
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 396 EKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAK 443
K ++++G GSG ++IA K ++ DI A++ A+KNA+
Sbjct: 158 LKDKNVIDVGCGSGILSIAALKLGAAK--VVGIDIDPLAVESARKNAE 203
>gnl|CDD|233668 TIGR01983, UbiG, ubiquinone biosynthesis O-methyltransferase. This
model represents an O-methyltransferase believed to act
at two points in the ubiquinone biosynthetic pathway in
bacteria (UbiG) and fungi (COQ3). A separate methylase
(MenG/UbiE) catalyzes the single C-methylation step. The
most commonly used names for genes in this family do not
indicate whether this gene is an O-methyl, or C-methyl
transferase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Menaquinone and ubiquinone].
Length = 224
Score = 29.2 bits (66), Expect = 4.8
Identities = 26/114 (22%), Positives = 52/114 (45%), Gaps = 18/114 (15%)
Query: 397 KKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKK-LTKYNIPIKF 455
+++L++G G G ++ +A + + D S+ +++AK +AKK L K I++
Sbjct: 45 FGLRVLDVGCGGGLLSEPLA---RLGANVTGIDASEENIEVAKLHAKKDPLLK----IEY 97
Query: 456 IKSNWYNNLQNYKKLFNII--------VANPPYIPKGDIHLNK--GDLRFEPIN 499
++ + + K F+++ V +P + L K G L F IN
Sbjct: 98 RCTSVEDLAEKGAKSFDVVTCMEVLEHVPDPQAFIRACAQLLKPGGILFFSTIN 151
>gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase. This group
contains arabinose dehydrogenase (AraDH) and related
alcohol dehydrogenases. AraDH is a member of the medium
chain dehydrogenase/reductase family and catalyzes the
NAD(P)-dependent oxidation of D-arabinose and other
pentoses, the initial step in the metabolism of
d-arabinose into 2-oxoglutarate. Like the alcohol
dehydrogenases, AraDH binds a zinc in the catalytic
cleft as well as a distal structural zinc. AraDH forms
homotetramers as a dimer of dimers. AraDH replaces a
conserved catalytic His with replace with Arg, compared
to the canonical ADH site. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 340
Score = 29.5 bits (67), Expect = 4.9
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 405 GTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKN 441
G G A+ I A+ +IA D S+ ALK+A++
Sbjct: 178 GLGHIAVQILRALTP---ATVIAVDRSEEALKLAERL 211
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 29.4 bits (66), Expect = 5.8
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 377 LIPRPETELLVDLIVKKTFEKKIKLLEMGTGSG------AIAIAIAIYSKNKIEIIAT 428
PRPE + + + + + L+E TG+G A+A A K+ II+T
Sbjct: 14 FEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV-IIST 70
>gnl|CDD|176184 cd05281, TDH, Threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via NAD(H)-
dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria) and have 2 tightly bound
zinc atoms per subunit. Sorbitol and aldose reductase
are NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose.
Length = 341
Score = 29.1 bits (66), Expect = 5.8
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 406 TGSGAI---AIAIAIYSKNKIEIIATDISKFALKIAKKN 441
TG G I AIA+A + + +IA+D + + L++AKK
Sbjct: 170 TGCGPIGLMAIAVAKAAGASL-VIASDPNPYRLELAKKM 207
>gnl|CDD|232913 TIGR00308, TRM1, tRNA(guanine-26,N2-N2) methyltransferase. This
enzyme is responsible for two methylations of a
characteristic guanine of most tRNA molecules. The
activity has been demonstrated for eukaryotic and
archaeal proteins, which are active when expressed in E.
coli, a species that lacks this enzyme. At least one
Eubacterium, Aquifex aeolicus, has an ortholog, as do
all completed archaeal genomes [Protein synthesis, tRNA
and rRNA base modification].
Length = 374
Score = 29.4 bits (66), Expect = 5.9
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 379 PRPETELLVDLIVKKTF------EKKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISK 432
PR + + + + F E I + + + SG AI A + E+ A DI+
Sbjct: 20 PRMQFNRDLSVTCIQAFDNLYGKECYINIADALSASGIRAIRYAHEIEGVREVFANDINP 79
Query: 433 FALKIAKKNAK 443
A++ K N +
Sbjct: 80 KAVESIKNNVE 90
>gnl|CDD|176200 cd08238, sorbose_phosphate_red, L-sorbose-1-phosphate reductase.
L-sorbose-1-phosphate reductase, a member of the MDR
family, catalyzes the NADPH-dependent conversion of
l-sorbose 1-phosphate to d-glucitol 6-phosphate in the
metabolism of L-sorbose to (also converts d-fructose
1-phosphate to d-mannitol 6-phosphate). The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability.
Length = 410
Score = 28.9 bits (65), Expect = 6.9
Identities = 20/103 (19%), Positives = 37/103 (35%), Gaps = 12/103 (11%)
Query: 405 GTGS-GAIAIAIAIY-SKNKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSNWYN 462
G G G +AI AI+ ++ TD++ L A++ + I + ++ +
Sbjct: 184 GAGPMGLMAIDYAIHGPIGPSLLVVTDVNDERLARAQRLFPPEAASRGIELLYVNPATID 243
Query: 463 NLQNYKKLFN---------IIVANPPYIPKGDIHLN-KGDLRF 495
+L + V P + + D L G L F
Sbjct: 244 DLHATLMELTGGQGFDDVFVFVPVPELVEEADTLLAPDGCLNF 286
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 29.4 bits (66), Expect = 7.3
Identities = 28/97 (28%), Positives = 43/97 (44%), Gaps = 9/97 (9%)
Query: 421 NKIEIIATDISKFALKIAKKNAKKKLTKYNIPIKFIKSNWYNNLQNYKKLFNIIVANPPY 480
NK I+ DI+ LK KKN + L YNI I+ ++++ N + K+L
Sbjct: 791 NKENKISNDIN--ILKENKKNNQDLLNSYNILIQKLEAHTEKNDEELKQLLQ-------K 841
Query: 481 IPKGDIHLNKGDLRFEPINALTDYSNGLSSIKEIVKN 517
P D +LN +L E N + I+ + KN
Sbjct: 842 FPTEDENLNLKELEKEFNENNQIVDNIIKDIENMNKN 878
>gnl|CDD|237568 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 322
Score = 29.0 bits (65), Expect = 7.6
Identities = 13/48 (27%), Positives = 29/48 (60%)
Query: 397 KKIKLLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKK 444
K +++LE+G G+G A ++ K +++ + S+ +IAK+N ++
Sbjct: 80 KGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVRR 127
>gnl|CDD|236059 PRK07580, PRK07580, Mg-protoporphyrin IX methyl transferase;
Validated.
Length = 230
Score = 28.6 bits (65), Expect = 7.8
Identities = 14/51 (27%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 401 LLEMGTGSGAIAIAIAIYSKNKIEIIATDISKFALKIAKKNAKKKLTKYNI 451
+L+ G G G+++I +A + +++A+DIS ++ A++ A + NI
Sbjct: 67 ILDAGCGVGSLSIPLA---RRGAKVVASDISPQMVEEARERAPEAGLAGNI 114
>gnl|CDD|180054 PRK05396, tdh, L-threonine 3-dehydrogenase; Validated.
Length = 341
Score = 29.0 bits (66), Expect = 7.8
Identities = 12/38 (31%), Positives = 25/38 (65%), Gaps = 4/38 (10%)
Query: 406 TGSGAI---AIAIAIYSKNKIEIIATDISKFALKIAKK 440
TG+G I A A+A + + ++ TD++++ L++A+K
Sbjct: 170 TGAGPIGIMAAAVAKHVGAR-HVVITDVNEYRLELARK 206
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 29.2 bits (66), Expect = 8.4
Identities = 22/70 (31%), Positives = 28/70 (40%), Gaps = 16/70 (22%)
Query: 4 LMLSKLEK-----FSKRLKELD-FLLTQKEVHNNIKDYCKKVREHSFLYPIVELYNNYKK 57
+L LEK F R L+ FLL++ H N K S P + L N Y K
Sbjct: 869 DILRSLEKDLIIEFDSRSAPLEMFLLSRTH-HCNYK---------SPDNPNMYLVNEYNK 918
Query: 58 INEDIITAKE 67
N + I E
Sbjct: 919 NNPEKIEIGE 928
>gnl|CDD|233898 TIGR02500, type_III_yscD, type III secretion apparatus protein,
YscD/HrpQ family. This family represents a conserved
protein of bacterial type III secretion systems. Gene
symbols are variable from species to species. Members
are designated YscD in Yersinia, HrpQ in Pseudomonas
syringae, and EscD in enteropathogenic Escherichia coli.
In the Chlamydiae, this model describes the C-terminal
400 residues of a longer protein [Protein fate, Protein
and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 410
Score = 28.9 bits (65), Expect = 8.4
Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 3/52 (5%)
Query: 174 KLKFESGVHRVQRVPKTETQGRIHTSACTVAVIPEADEIEDININPADLRID 225
KL+ SG HR +P E + T A ++ I L +
Sbjct: 2 KLRVLSGPHRGAELPLPEGNLVLGTDAADCDIVL---SDGGIAAVHVSLHVR 50
>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional.
Length = 670
Score = 28.8 bits (65), Expect = 8.6
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 18/78 (23%)
Query: 305 SPLNIFETNILLKYVTRLSDVELIINNEKKLH--------KQEI-----NILNKLIQR-- 349
+PL +L KY + VEL + E+KL ++E+ LNKL++
Sbjct: 517 TPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKATREEVIEEAKETLNKLLEEFK 576
Query: 350 ---RILGEPIAYIIGKKE 364
+GE +A +G +
Sbjct: 577 KNKDEIGEELAKALGLIK 594
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
0.319 0.138 0.382
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: 29,805,946
Number of extensions: 3109655
Number of successful extensions: 3624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3526
Number of HSP's successfully gapped: 190
Length of query: 570
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 468
Effective length of database: 6,413,494
Effective search space: 3001515192
Effective search space used: 3001515192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.4 bits)