RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16898
(324 letters)
>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 = 202 bits (517), Expect = 6e-65
Identities = 81/206 (39%), Positives = 122/206 (59%), Gaps = 24/206 (11%)
Query: 62 SSFTSVGHIVHCNLREELIEHKFIIGRVLLDKVPSCETVVNKAHTIDNTYRNFQMELLAG 121
SSF +G IV N+ EEL+ +K +IG +L K + V+ K + +R ++E++AG
Sbjct: 1 SSFDIIGDIVILNIPEELMPYKKVIGEAILKKTK-VKAVLRKVGIVTGEFRTRRLEVIAG 59
Query: 122 KDCMVTMHKENGCTFKMDFSKVYWNSRLSTEHERVTKEVREGDLVLDVFAGVGPFSIPAA 181
+D T+HKENGC FK+D SKVY++ RL E ER+ K V+EG++V+D+FAG+GPFSIP A
Sbjct: 60 EDRTETIHKENGCRFKIDVSKVYFSPRLIGERERIAKLVKEGEVVVDMFAGIGPFSIPIA 119
Query: 182 R--RGAIVAANDLNPDSYAWLQASIRLNERQVKTPISATQKDARDFLQTDARAHLVRWSQ 239
+ + V A +LNP++ +L+ +I+LN +V+ IS D RD +
Sbjct: 120 KHSKAKRVYAVELNPEAVKYLKENIKLN--KVEGVISPILGDVRDVILEG---------- 167
Query: 240 SEGNSTGGTAVARVIMNLPATAVEYV 265
RVIMNLP +A E++
Sbjct: 168 ---------VADRVIMNLPKSAHEFL 184
>gnl|CDD|225318 COG2520, COG2520, Predicted methyltransferase [General function
prediction only].
Length = 341
Score = 196 bits (501), Expect = 1e-60
Identities = 93/328 (28%), Positives = 151/328 (46%), Gaps = 58/328 (17%)
Query: 19 NVKVLENAKLTAKDFTHAEVLLTYD-------------------NFSAEDILKAILPDNV 59
+L+ +D + + + + N + ++IL LP+ V
Sbjct: 22 AAGLLDKDYKIDRDGDYLLIPVKDEANAILEVVVLEEEPVRRRSNENLKEILSDRLPEEV 81
Query: 60 A----MSSFTSVGHIVHCNLREELIEHKFIIGRVLLDKVPSCETVVNKAHTIDNTYRNFQ 115
SSF +G I ++ +EL +K I +L + V+ K + +R +
Sbjct: 82 LRELVPSSFDIIGDIAILSIPDELEPYKREIAEAILRVHGKVKAVLLKEGPVAGEFRVPR 141
Query: 116 MELLAGKDCMVTMHKENGCTFKMDFSKVYWNSRLSTEHERVTKEVREGDLVLDVFAGVGP 175
+E+LAG+ T+H+ENGC FK+D +KVY++ RLSTE RV + V+EG+ VLD+FAGVGP
Sbjct: 142 LEVLAGERRTETIHRENGCRFKVDVAKVYFSPRLSTERARVAELVKEGETVLDMFAGVGP 201
Query: 176 FSIPAARRGAI-VAANDLNPDSYAWLQASIRLNERQVKTPISATQKDARDFLQTDARAHL 234
FSIP A++G V A D+NPD+ +L+ +IRLN +V+ + DAR+ A
Sbjct: 202 FSIPIAKKGRPKVYAIDINPDAVEYLKENIRLN--KVEGRVEPILGDAREVAPELGVA-- 257
Query: 235 VRWSQSEGNSTGGTAVARVIMNLPATAVEYVRYLKVLTRE-------EFGKLSRPPVLYL 287
R+IM LP +A E++ L ++ EF
Sbjct: 258 ----------------DRIIMGLPKSAHEFLPLALELLKDGGIIHYYEFVPEDDIEERPE 301
Query: 288 Y-------CFLPKMDLETKKKIKSYDPS 308
K+++ +++KSY P
Sbjct: 302 KRIKSAARKGGYKVEVLKVRRVKSYSPG 329
>gnl|CDD|225174 COG2265, TrmA, SAM-dependent methyltransferases related to tRNA
(uracil-5-)-methyltransferase [Translation, ribosomal
structure and biogenesis].
Length = 432
Score = 42.7 bits (101), Expect = 1e-04
Identities = 37/167 (22%), Positives = 63/167 (37%), Gaps = 46/167 (27%)
Query: 159 EVREGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIRLNERQVKTPISAT 218
E+ G+ VLD++ GVG F +P A+R V +++P++ Q + N
Sbjct: 290 ELAGGERVLDLYCGVGTFGLPLAKRVKKVHGVEISPEAVEAAQENAAAN----------- 338
Query: 219 QKDARDFLQTDARAHLVRWSQSEGNSTGGTAVARVIMNLPAT--AVEYVRYLKVLTREEF 276
D +F+ DA W + V+++ P E ++ L
Sbjct: 339 GIDNVEFIAGDAEEFTPAWWEGYKPDV-------VVVDPPRAGADREVLKQLA------- 384
Query: 277 GKLSRPPVLYLYCFLPKMDLETKKKIKSYDPSYATLIRGIRRLSSDG 323
KL ++Y+ S +P ATL R + L+S G
Sbjct: 385 -KLKPKRIVYV----------------SCNP--ATLARDLAILASTG 412
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 39.3 bits (92), Expect = 4e-04
Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 163 GDLVLDVFAGVGPFSIPAARRGAI--VAANDLNPDSYAWLQASIRLNERQVKTPISATQK 220
GD VLD AG G F + AAR G V +L+P++ A A RL + +
Sbjct: 1 GDRVLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAAL--ARRRLALAGLAPRVRVVVG 58
Query: 221 DARDFLQ-TDARAHLV 235
DAR+ L+ D LV
Sbjct: 59 DARELLELPDGSFDLV 74
>gnl|CDD|236059 PRK07580, PRK07580, Mg-protoporphyrin IX methyl transferase;
Validated.
Length = 230
Score = 40.6 bits (96), Expect = 4e-04
Identities = 17/29 (58%), Positives = 21/29 (72%)
Query: 166 VLDVFAGVGPFSIPAARRGAIVAANDLNP 194
+LD GVG SIP ARRGA V A+D++P
Sbjct: 67 ILDAGCGVGSLSIPLARRGAKVVASDISP 95
>gnl|CDD|225137 COG2227, UbiG,
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol
methylase [Coenzyme metabolism].
Length = 243
Score = 40.4 bits (95), Expect = 6e-04
Identities = 18/46 (39%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 161 REGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDS--YAWLQASI 204
G VLDV G G S P AR GA V D + A L A
Sbjct: 58 LPGLRVLDVGCGGGILSEPLARLGASVTGIDASEKPIEVAKLHALE 103
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 40.0 bits (94), Expect = 0.001
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 162 EGDLVLDVFAGVGPFSIPAARRGAI-VAANDLNPDSYAWLQASIRLNERQVKTPISATQK 220
G VL++F+ G FS+ AA GA V + DL+ + W + + LN
Sbjct: 217 AGKRVLNLFSYTGGFSVHAALGGASEVTSVDLSKRALEWARENAELNGLDGD-RHRFIVG 275
Query: 221 DARDFLQTDAR 231
D +L+ R
Sbjct: 276 DVFKWLRKAER 286
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 37.3 bits (87), Expect = 0.001
Identities = 22/76 (28%), Positives = 31/76 (40%), Gaps = 5/76 (6%)
Query: 162 EGDLVLDVFAGVGPFSIPAAR--RGAIVAANDLNPDSYAWLQASIRLNERQVKTPISATQ 219
G VLD+ G G +I AR GA V DL+P+ + + + + I+ Q
Sbjct: 1 PGARVLDIGCGTGSLAIELARLFPGARVTGVDLSPEMLELARENA---KLALGPRITFVQ 57
Query: 220 KDARDFLQTDARAHLV 235
DA D L V
Sbjct: 58 GDAPDALDLLEGFDAV 73
>gnl|CDD|129571 TIGR00479, rumA, 23S rRNA (uracil-5-)-methyltransferase RumA. This
protein family was first proposed to be RNA
methyltransferases by homology to the TrmA family. The
member from E. coli has now been shown to act as the 23S
RNA methyltransferase for the conserved U1939. The gene
is now designated rumA and was previously designated
ygcA [Protein synthesis, tRNA and rRNA base
modification].
Length = 431
Score = 39.4 bits (92), Expect = 0.002
Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 12/86 (13%)
Query: 159 EVREGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIRLNERQVKTPISAT 218
E++ +LV+D + GVG F++P A++ V ++ P+S Q + LN
Sbjct: 289 ELQGEELVVDAYCGVGTFTLPLAKQAKSVVGIEVVPESVEKAQQNAELN----------- 337
Query: 219 QKDARDFLQTDARAHLVRWSQSEGNS 244
+FL L + G
Sbjct: 338 GIANVEFLAGTLETVLPKQPW-AGQI 362
>gnl|CDD|226562 COG4076, COG4076, Predicted RNA methylase [General function
prediction only].
Length = 252
Score = 38.3 bits (89), Expect = 0.003
Identities = 18/94 (19%), Positives = 32/94 (34%), Gaps = 8/94 (8%)
Query: 137 KMDFSKVYWNSRLSTEHERVTK-----EVREGDLVLDVFAGVGPFSIPAARRGAIVAAND 191
+ ++ L + ER+ D D+ AG G S+ AA V A +
Sbjct: 2 EFRLLVDSYHLDLLRDVERLAVFTSAIAEVAEDTFADLGAGSGILSVVAAHAAERVIAIE 61
Query: 192 LNPDSYAWLQASIRLNERQVKTPISATQKDARDF 225
+P + ++ + DARD+
Sbjct: 62 KDPKRARLAEENLHVPG---DVNWEVVVGDARDY 92
>gnl|CDD|233687 TIGR02021, BchM-ChlM, magnesium protoporphyrin O-methyltransferase.
This model represents the
S-adenosylmethionine-dependent O-methyltransferase
responsible for methylation of magnesium protoporphyrin
IX. This step is essentiasl for the biosynthesis of both
chlorophyll and bacteriochlorophyll. This model
encompasses two closely related clades, from
cyanobacteria (and plants) where it is called ChlM and
other photosynthetic bacteria where it is known as BchM
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 219
Score = 37.1 bits (86), Expect = 0.007
Identities = 38/146 (26%), Positives = 59/146 (40%), Gaps = 10/146 (6%)
Query: 154 ERVTKEVREGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPD--SYAWLQASIRLNERQV 211
+ + K+ +G VLD G G SI A+RGAIV A D++ A +A R V
Sbjct: 47 DWLPKDPLKGKRVLDAGCGTGLLSIELAKRGAIVKAVDISEQMVQMARNRAQGRDVAGNV 106
Query: 212 KTPISATQKDARDFLQTDARAHLVRWSQSEGNST----GGTAVARVIMNL-PATAVEYVR 266
+ ++ +F L+ + S+ RVI P TA ++
Sbjct: 107 EFEVNDLLSLCGEFDIVVCMDVLIHYPASDMAKALGHLASLTKERVIFTFAPKTA--WLA 164
Query: 267 YLKVLTREEFGKLSRPPVLYLYCFLP 292
+LK++ E F SR YL+
Sbjct: 165 FLKMIG-ELFPGSSRATSAYLHPMTD 189
>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 = 34.7 bits (80), Expect = 0.012
Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 166 VLDVFAGVGPFSIPAARRGAI-VAANDLNPDSYAWLQASIRLNERQVKTPISATQKDARD 224
VLD+ G G ++ A V D++P + + + + DA +
Sbjct: 2 VLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAALLADNVEVLKG---DAEE 58
Query: 225 FL 226
Sbjct: 59 LP 60
>gnl|CDD|237291 PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed.
Length = 443
Score = 36.7 bits (86), Expect = 0.015
Identities = 14/29 (48%), Positives = 21/29 (72%)
Query: 159 EVREGDLVLDVFAGVGPFSIPAARRGAIV 187
+ + GD VLD+F G+G F++P AR+ A V
Sbjct: 294 DPQPGDRVLDLFCGLGNFTLPLARQAAEV 322
>gnl|CDD|224657 COG1743, COG1743, Adenine-specific DNA methylase containing a
Zn-ribbon [DNA replication, recombination, and repair].
Length = 875
Score = 36.7 bits (85), Expect = 0.015
Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 148 RLSTEHERVTKEVREGDLVLDVFAGVGPFSIP--AARRGAIVAANDLNPDSYAWLQASI 204
RL+ + + EG +LD FAG G SIP A R G V A +LNP +Y +L+A +
Sbjct: 76 RLNPRWPQPIETPFEGPKLLDPFAGGG--SIPLEALRLGLEVVAVELNPVAYLFLKAVL 132
>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 = 35.2 bits (81), Expect = 0.019
Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 12/70 (17%)
Query: 160 VREGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIRLNERQVKTPISATQ 219
+ D VL++ AG G +I +G + D+NP + L+ + +LN +
Sbjct: 17 ELKPDDVLEIGAGTGLVAIRLKGKGKCILTTDINPFAVKELRENAKLNNVGL-------- 68
Query: 220 KDARDFLQTD 229
D + TD
Sbjct: 69 ----DVVMTD 74
>gnl|CDD|215319 PLN02585, PLN02585, magnesium protoporphyrin IX methyltransferase.
Length = 315
Score = 36.0 bits (83), Expect = 0.021
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 162 EGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIRLNERQV-KTPISATQK 220
G V D G G +IP A GAIV+A+D++ A +A R E P +
Sbjct: 144 AGVTVCDAGCGTGSLAIPLALEGAIVSASDISAAMVA--EAERRAKEALAALPPEVLPKF 201
Query: 221 DARDFLQTDARAHLV 235
+A D + V
Sbjct: 202 EANDLESLSGKYDTV 216
>gnl|CDD|223971 COG1041, COG1041, Predicted DNA modification methylase [DNA
replication, recombination, and repair].
Length = 347
Score = 35.8 bits (83), Expect = 0.024
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 159 EVREGDLVLDVFAGVGPFSIPAARRGAIVAANDL 192
V+ G+LVLD F G G I A GA V +D+
Sbjct: 194 RVKRGELVLDPFCGTGGILIEAGLMGARVIGSDI 227
>gnl|CDD|237872 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 34.9 bits (81), Expect = 0.026
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 160 VREGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQA--SIRLNE 208
++GD VL+V G G +I AA+ G V D+NP YA A + +LN
Sbjct: 21 DKKGDRVLEVGTGSGIVAIVAAKNGKKVVGVDINP--YAVECAKCNAKLNN 69
>gnl|CDD|225319 COG2521, COG2521, Predicted archaeal methyltransferase [General
function prediction only].
Length = 287
Score = 34.3 bits (79), Expect = 0.070
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 160 VREGDLVLDVFAGVGPFSIPAARRGAI 186
V+ G+ VLD G+G +I A RGAI
Sbjct: 132 VKRGERVLDTCTGLGYTAIEALERGAI 158
>gnl|CDD|233303 TIGR01177, TIGR01177, TIGR01177 family protein. This family is
found exclusively in the Archaea [Hypothetical proteins,
Conserved].
Length = 329
Score = 34.0 bits (78), Expect = 0.082
Identities = 17/33 (51%), Positives = 18/33 (54%)
Query: 160 VREGDLVLDVFAGVGPFSIPAARRGAIVAANDL 192
V EGD VLD F G G F I A GA V D+
Sbjct: 180 VTEGDRVLDPFCGTGGFLIEAGLMGAKVIGCDI 212
>gnl|CDD|233415 TIGR01444, fkbM_fam, methyltransferase, FkbM family. Members of
this family are characterized by two well-conserved
short regions separated by a variable in both sequence
and length. The first of the two regions is found in a
large number of proteins outside this subfamily, a
number of which have been characterized as
methyltransferases. One member of the present family,
FkbM, was shown to be required for a specific
methylation in the biosynthesis of the immunosuppressant
FK506 in Streptomyces strain MA6548.
Length = 144
Score = 31.5 bits (72), Expect = 0.28
Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 166 VLDVFAGVGPFSIPAARRGA--IVAANDLNPDSYAWLQASIRLNERQ 210
V+DV A +G FS+ AR+GA V A + PD+Y L+ +++LN
Sbjct: 2 VIDVGANIGDFSLYFARKGAEGRVIAFEPLPDAYEILEENVKLNNLP 48
>gnl|CDD|131869 TIGR02822, adh_fam_2, zinc-binding alcohol dehydrogenase family
protein. Members of this model form a distinct subset
of the larger family of oxidoreductases that includes
zinc-binding alcohol dehydrogenases and NADPH:quinone
reductases (pfam00107). The gene neighborhood of members
of this family is not conserved and it appears that no
members are characterized. The sequence of the family
includes 6 invariant cysteine residues and one invariant
histidine. It appears that no member is characterized
[Energy metabolism, Fermentation].
Length = 329
Score = 32.6 bits (74), Expect = 0.28
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 12/74 (16%)
Query: 169 VFAGVGPFSIPAAR---RGAIVAA-----NDLNPDSYAWLQASIRLNERQVKTPISATQK 220
+FA G PA RG ++A D P +Y Q + ERQ+++ S T+
Sbjct: 229 LFAPAGGLVPPALEALDRGGVLAVAGIHLTDTPPLNY---QRHL-FYERQIRSVTSNTRA 284
Query: 221 DARDFLQTDARAHL 234
DAR+FL+ A+ +
Sbjct: 285 DAREFLELAAQHGV 298
>gnl|CDD|176258 cd08298, CAD2, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
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 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. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. 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.
Length = 329
Score = 31.8 bits (73), Expect = 0.46
Identities = 14/69 (20%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 169 VFAGVG---PFSIPAARRGAIVAANDLNPDSYAWLQASIRLNERQVKTPISATQKDARDF 225
+FA VG P ++ A ++G V ++ + E+ +++ + T++D +F
Sbjct: 231 IFAPVGALVPAALRAVKKGGRVVLAGIHMSDIPAFDYELLWGEKTIRSVANLTRQDGEEF 290
Query: 226 LQTDARAHL 234
L+ A +
Sbjct: 291 LKLAAEIPI 299
>gnl|CDD|235286 PRK04338, PRK04338, N(2),N(2)-dimethylguanosine tRNA
methyltransferase; Provisional.
Length = 382
Score = 31.4 bits (72), Expect = 0.54
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 166 VLDVFAGVGPFSIPAARRGAI--VAANDLNPDSYAWLQASIRLNERQVKTPISATQKDAR 223
VLD + G I A + V ND+NPD+ ++ ++ LN KDA
Sbjct: 61 VLDALSASGIRGIRYALETGVEKVTLNDINPDAVELIKKNLELNG---LENEKVFNKDAN 117
Query: 224 DFLQTDARAHLV 235
L + + +V
Sbjct: 118 ALLHEERKFDVV 129
>gnl|CDD|216870 pfam02086, MethyltransfD12, D12 class N6 adenine-specific DNA
methyltransferase.
Length = 254
Score = 31.2 bits (71), Expect = 0.64
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 168 DVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIRLN 207
+ FAG G A +RG V ND+N D +A I+ N
Sbjct: 26 EPFAGGGAVFFEAKKRGKKVLINDINEDLINLYKALIKNN 65
>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 = 30.7 bits (70), Expect = 0.72
Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 5/87 (5%)
Query: 148 RLSTEHERVTKEVR--EGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIR 205
RL + + K + G VLDV G G S P AR GA V D + ++ A +
Sbjct: 29 RLDYIRDTIRKNKKPLFGLRVLDVGCGGGLLSEPLARLGANVTGIDASEENIE--VAKLH 86
Query: 206 LNERQVKTPISATQKDARDFLQTDARA 232
+ + I D + A++
Sbjct: 87 AKKDPLLK-IEYRCTSVEDLAEKGAKS 112
>gnl|CDD|226413 COG3897, COG3897, Predicted methyltransferase [General function
prediction only].
Length = 218
Score = 30.5 bits (69), Expect = 0.95
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 166 VLDVFAGVGPFSIPAARRGAI-VAANDLNPDSYAWLQASIRLNERQVKTPISATQKDA 222
VLD+ AG G +I AAR GA V A D++P WL+ +IRLN I T D
Sbjct: 83 VLDLGAGSGLVAIAAARAGAAEVVAADIDP----WLEQAIRLNAAANGVSILFTHADL 136
>gnl|CDD|220246 pfam09445, Methyltransf_15, RNA cap guanine-N2 methyltransferase.
RNA cap guanine-N2 methyltransferases such as
Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2
catalyze methylation of the exocyclic N2 amine of
7-methylguanosine.
Length = 165
Score = 29.6 bits (67), Expect = 1.5
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 163 GDLVLDVFAGVGPFSIPAARRGAIVAANDLNPD 195
++LDVF G G +I A V D+NP+
Sbjct: 1 ARIILDVFCGAGGNTIQFANVFCSVIGIDINPE 33
>gnl|CDD|224780 COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 380
Score = 30.0 bits (68), Expect = 1.5
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 166 VLDVFAGVGPFSIPAARRGAIVA--ANDLNPDSYAWLQASIRLNE 208
VLD + G I A +V ND++P + ++ ++RLN
Sbjct: 56 VLDALSATGIRGIRYAVETGVVKVVLNDISPKAVELIKENVRLNS 100
>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 = 29.9 bits (68), Expect = 1.7
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 160 VREGDLVLDVFAGVGPFSIPAARRGAI-VAANDLNP 194
V+ G+ VLDV G G +I A + GA V D++P
Sbjct: 158 VKPGETVLDVGCGSGILAIAALKLGAKKVVGVDIDP 193
>gnl|CDD|223813 COG0742, COG0742, N6-adenine-specific methylase [DNA replication,
recombination, and repair].
Length = 187
Score = 29.1 bits (66), Expect = 1.9
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 162 EGDLVLDVFAGVGPFSIPAARRGA 185
EG VLD+FAG G + A RGA
Sbjct: 43 EGARVLDLFAGSGALGLEALSRGA 66
>gnl|CDD|222171 pfam13489, Methyltransf_23, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 154
Score = 29.0 bits (65), Expect = 1.9
Identities = 13/49 (26%), Positives = 20/49 (40%)
Query: 148 RLSTEHERVTKEVREGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDS 196
L+ R+ ++ G VLD+ G G RG V D +P +
Sbjct: 8 FLARLLARLLPRLKPGGRVLDIGCGTGILLRLLRERGFDVTGVDPSPAA 56
>gnl|CDD|225776 COG3236, COG3236, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 162
Score = 29.0 bits (65), Expect = 2.0
Identities = 16/60 (26%), Positives = 22/60 (36%), Gaps = 4/60 (6%)
Query: 1 MTLHFYKVIQKFEDFGEFN---VKVLENAKLTAKD-FTHAEVLLTYDNFSAEDILKAILP 56
++FY + F F +KV TA+ F + L D E IL A P
Sbjct: 15 TYIYFYSTSDPYGCFSNFAPWPIKVDGKTWPTAEHYFQAQKFLEFLDPAYREAILAARSP 74
>gnl|CDD|233021 TIGR00555, panK_eukar, pantothenate kinase,
eukaryotic/staphyloccocal type. This model describes a
eukaryotic form of pantothenate kinase, characterized
from the fungus Aspergillus nidulans and with similar
forms known in several other eukaryotes. It also
includes forms from several Gram-positive bacteria
suggested to have originated from the eukaryotic form by
lateral transfer. It differs in a number of biochemical
properties (such as inhibition by acetyl-CoA) from most
bacterial CoaA and lacks sequence similarity. This
enzyme is the key regulatory step in the biosynthesis of
coenzyme A (CoA) [Biosynthesis of cofactors, prosthetic
groups, and carriers, Pantothenate and coenzyme A].
Length = 296
Score = 29.7 bits (67), Expect = 2.2
Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 5/73 (6%)
Query: 28 LTAKDFTHAEVLLTYDNFSAEDILKAILPDNVAMSSFTSVGHIVHCNLREELIEHKFIIG 87
LTA F +FS EDI ++L + + ++G I + I+ IG
Sbjct: 201 LTASSFGKVLSKHLDQSFSPEDIAASLL---GLIGN--NIGQIAYLCALRYNIDRIVFIG 255
Query: 88 RVLLDKVPSCETV 100
L + + +
Sbjct: 256 SFLRNNQLLMKVL 268
>gnl|CDD|225173 COG2264, PrmA, Ribosomal protein L11 methylase [Translation,
ribosomal structure and biogenesis].
Length = 300
Score = 29.6 bits (67), Expect = 2.3
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 160 VREGDLVLDVFAGVGPFSIPAARRGAI-VAANDLNPDSYAWLQAS---IRLNERQVKTPI 215
+++G VLDV G G +I AA+ GA V D+ D A ++A+ RLN V+ +
Sbjct: 160 LKKGKTVLDVGCGSGILAIAAAKLGAKKVVGVDI--DPQA-VEAARENARLN--GVELLV 214
Query: 216 SATQKDARDFLQ 227
A + +
Sbjct: 215 QAKGFLLLEVPE 226
>gnl|CDD|173170 PRK14707, PRK14707, hypothetical protein; Provisional.
Length = 2710
Score = 29.8 bits (66), Expect = 2.6
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 10/69 (14%)
Query: 194 PDSYAWLQASIRLNERQVKTPISATQKDARDFLQ----TDARAHLVRWSQSEGNSTGGTA 249
PD+ A A+ L ERQ++ P D RD L+ T+A L +W + + +A
Sbjct: 764 PDNQACAAAANTLAERQLREP------DVRDVLKPREMTNALNALSKWPDTPACAAAASA 817
Query: 250 VARVIMNLP 258
+A + + P
Sbjct: 818 LAARVADDP 826
>gnl|CDD|202698 pfam03602, Cons_hypoth95, Conserved hypothetical protein 95.
Length = 183
Score = 28.8 bits (65), Expect = 2.8
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 166 VLDVFAGVGPFSIPAARRGA 185
VLD+FAG G + A RGA
Sbjct: 47 VLDLFAGSGALGLEALSRGA 66
>gnl|CDD|225139 COG2230, Cfa, Cyclopropane fatty acid synthase and related
methyltransferases [Cell envelope biogenesis, outer
membrane].
Length = 283
Score = 29.1 bits (66), Expect = 3.2
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 160 VREGDLVLDVFAGVGPFSIPAARR-GAIVAANDLNPDSYAWLQASIRLNERQVKTPISAT 218
++ G +LD+ G G +I AA G V L+ + A+ + I R ++ +
Sbjct: 70 LKPGMTLLDIGCGWGGLAIYAAEEYGVTVVGVTLSEEQLAYAEKRIA--ARGLEDNVEVR 127
Query: 219 QKDARDF 225
+D RDF
Sbjct: 128 LQDYRDF 134
>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 = 28.4 bits (64), Expect = 3.3
Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 159 EVREGDLVLDVFAGVGPFSIPAARRGAIVAAN---DLNPDSYAWLQASIRLNERQ--VKT 213
+ GD +LD G G I AA GA +A D++ +Q + R+N V
Sbjct: 25 GWKPGDPLLDPMCGSGTILIEAALMGANIAPLYGSDIDWRM---VQGA-RINAENAGVGD 80
Query: 214 PISATQKDARDF 225
I Q DA
Sbjct: 81 KIEFVQADAAKL 92
>gnl|CDD|218716 pfam05721, PhyH, Phytanoyl-CoA dioxygenase (PhyH). This family is
made up of several eukaryotic phytanoyl-CoA dioxygenase
(PhyH) proteins, ectoine hydroxylases and a number of
bacterial deoxygenases. PhyH is a peroxisomal enzyme
catalyzing the first step of phytanic acid
alpha-oxidation. PhyH deficiency causes Refsum's disease
(RD) which is an inherited neurological syndrome
biochemically characterized by the accumulation of
phytanic acid in plasma and tissues.
Length = 213
Score = 28.6 bits (64), Expect = 3.9
Identities = 14/82 (17%), Positives = 21/82 (25%), Gaps = 21/82 (25%)
Query: 124 CMVTMHKENGCTF------------------KMDFSKVYWNSRLSTEHERVTKEVREGDL 165
+ +ENGC + E V ++ GD
Sbjct: 132 ALDDATEENGCLRFIPGSHKWEVGDLTRRLPYDPGHLNDDEAPKYDEEPAVPVPMKAGDA 191
Query: 166 VL---DVFAGVGPFSIPAARRG 184
VL + G G +RR
Sbjct: 192 VLFHPRLLHGSGANRSDKSRRA 213
>gnl|CDD|225136 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
biosynthesis [Coenzyme metabolism].
Length = 238
Score = 28.8 bits (65), Expect = 3.9
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 13/69 (18%)
Query: 139 DFSKVY--WNSRLSTEHERVTKE-------VREGDLVLDVFAGVGPFSIPAARR---GAI 186
+K Y N +S R+ + ++ GD VLDV G G ++ A+ G +
Sbjct: 19 KVAKKYDLMNDLMSFGLHRLWRRALISLLGIKPGDKVLDVACGTGDMALLLAKSVGTGEV 78
Query: 187 VAANDLNPD 195
V D++
Sbjct: 79 VGL-DISES 86
>gnl|CDD|114667 pfam05958, tRNA_U5-meth_tr, tRNA (Uracil-5-)-methyltransferase.
This family consists of (Uracil-5-)-methyltransferases
EC:2.1.1.35 from bacteria, archaea and eukaryotes. A
5-methyluridine (m(5)U) residue at position 54 is a
conserved feature of bacterial and eukaryotic tRNAs. The
methylation of U54 is catalyzed by the
tRNA(m5U54)methyltransferase, which in Saccharomyces
cerevisiae is encoded by the nonessential TRM2 gene. It
is thought that tRNA modification enzymes might have a
role in tRNA maturation not necessarily linked to their
known catalytic activity.
Length = 353
Score = 28.9 bits (65), Expect = 4.1
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 161 REGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIRLN 207
+GDL L+++ G G FS+ A+ V A ++ S Q +I N
Sbjct: 197 SKGDL-LELYCGNGNFSLALAQNFRRVLATEIAKPSVNAAQYNIAAN 242
>gnl|CDD|131198 TIGR02143, trmA_only, tRNA (uracil-5-)-methyltransferase. This
family consists exclusively of proteins believed to act
as tRNA (uracil-5-)-methyltransferase. All members of
far are proteobacterial. The seed alignment was taken
directly from pfam05958 in Pfam 12.0, but higher cutoffs
are used to select only functionally equivalent
proteins. Homologous proteins excluded by the higher
cutoff scores of this model include other uracil
methyltransferases, such as RumA, active on rRNA
[Protein synthesis, tRNA and rRNA base modification].
Length = 353
Score = 28.9 bits (65), Expect = 4.1
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 161 REGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIRLN 207
+GDL L+++ G G FS+ A+ V A ++ S Q +I N
Sbjct: 197 SKGDL-LELYCGNGNFSLALAQNFRRVLATEIAKPSVNAAQYNIAAN 242
>gnl|CDD|238192 cd00315, Cyt_C5_DNA_methylase, Cytosine-C5 specific DNA methylases;
Methyl transfer reactions play an important role in many
aspects of biology. Cytosine-specific DNA methylases are
found both in prokaryotes and eukaryotes. DNA
methylation, or the covalent addition of a methyl group
to cytosine within the context of the CpG dinucleotide,
has profound effects on the mammalian genome. These
effects include transcriptional repression via
inhibition of transcription factor binding or the
recruitment of methyl-binding proteins and their
associated chromatin remodeling factors, X chromosome
inactivation, imprinting and the suppression of
parasitic DNA sequences. DNA methylation is also
essential for proper embryonic development and is an
important player in both DNA repair and genome
stability.
Length = 275
Score = 28.7 bits (65), Expect = 4.2
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 166 VLDVFAGVGPFSIPAARRGA-IVAANDLNPDSYAW 199
V+D+FAG+G F + + G IVAAN+++ A
Sbjct: 3 VIDLFAGIGGFRLGLEKAGFEIVAANEIDK--SAA 35
>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 = 28.5 bits (64), Expect = 5.5
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 158 KEVREGDLVLDVFAGVGPFSI------PAARRGAIVAANDLNPDSYAWLQASIRLNERQV 211
K++ G +VLD + G +I P V AND++P + ++ +++LNE V
Sbjct: 45 KKLGRGIIVLDALSASGIRAIRFALEVPGVEE---VFANDISPKAVELIKENVKLNE--V 99
Query: 212 KTPISATQKDARDFL 226
+ + DA +
Sbjct: 100 ENIVVINGDDANMLM 114
>gnl|CDD|225172 COG2263, COG2263, Predicted RNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 198
Score = 28.0 bits (63), Expect = 5.7
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 162 EGDLVLDVFAGVGPFSIPAARRGA-IVAANDLNPDS 196
EG VLD+ AG G +I AA GA V A D++P++
Sbjct: 45 EGKTVLDLGAGTGILAIGAALLGASRVLAVDIDPEA 80
>gnl|CDD|215900 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.
Length = 254
Score = 28.0 bits (63), Expect = 5.7
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 159 EVREGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAWLQASIRLNER 209
++E D VL++ G G + A+R V A +++P LQ + L+
Sbjct: 26 NLQESDTVLEIGPGKGALTTELAKRAKQVVAIEIDPRLAKRLQEKLALHPN 76
>gnl|CDD|184931 PRK14967, PRK14967, putative methyltransferase; Provisional.
Length = 223
Score = 28.1 bits (63), Expect = 6.0
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 166 VLDVFAGVGPFSIPAARRGAI-VAANDLNPDS--YAWLQASIR 205
VLD+ G G ++ AA GA V A D++ + A L A +
Sbjct: 40 VLDLCTGSGALAVAAAAAGAGSVTAVDISRRAVRSARLNALLA 82
>gnl|CDD|227133 COG4796, HofQ, Type II secretory pathway, component HofQ
[Intracellular trafficking and secretion].
Length = 709
Score = 28.2 bits (63), Expect = 7.4
Identities = 20/98 (20%), Positives = 31/98 (31%), Gaps = 12/98 (12%)
Query: 140 FSKVYWNSRLSTEHERVTKEVREGDLVLDVFAGVGPFSIPAARRGAIVAANDLNPDSYAW 199
+K S S +R T E + G P A A +A N A+
Sbjct: 93 ENKRARRSLQSLPRDRQTAAELEEAELA-----SGTGFSPLAASVAALAPNPAIRAQ-AY 146
Query: 200 LQASIRLNERQVKTPISATQKD-ARDFLQTDARAHLVR 236
Q SI+ + + A DF + + + R
Sbjct: 147 RQQSIKQ-----SSQSTGANSPRAIDFARRKPISLVFR 179
>gnl|CDD|213903 TIGR04290, meth_Rta_06860, methyltransferase, Rta_06860 family.
Members of this family are methyltransferases that mark
a widely distributed large conserved gene neighborhood
of unknown function. It appears most common in soil and
rhizosphere bacteria.
Length = 226
Score = 27.7 bits (62), Expect = 7.5
Identities = 19/57 (33%), Positives = 22/57 (38%), Gaps = 6/57 (10%)
Query: 139 DFSKVYWNSRLSTEHERVTKEVREGDLVLDVFAGVGPFSIPAARRGAI-VAANDLNP 194
DF W E E G VLD+ G +SI RRGA V D +P
Sbjct: 31 DFPAFKWR-----EFAHAIPEDLSGWSVLDIGCNAGFYSIEMKRRGAGRVLGIDSDP 82
>gnl|CDD|223348 COG0270, Dcm, Site-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 328
Score = 27.8 bits (62), Expect = 8.1
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 166 VLDVFAGVGPFSIPAARRGA-IVAANDLNPDSYAWLQASIRLNERQVKT-PISATQKDAR 223
V+D+FAG+G S+ G IV AN+++P + A+ + N + D
Sbjct: 6 VIDLFAGIGGLSLGFEEAGFEIVFANEIDPPA----VATYKANFPHGDIILGDIKELDGE 61
Query: 224 DFLQTDARA 232
++D
Sbjct: 62 ALRKSDVDV 70
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
0.321 0.135 0.395
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,464,377
Number of extensions: 1569477
Number of successful extensions: 1529
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1519
Number of HSP's successfully gapped: 70
Length of query: 324
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 227
Effective length of database: 6,635,264
Effective search space: 1506204928
Effective search space used: 1506204928
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 (21.9 bits)
S2: 59 (26.6 bits)