RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15742
(342 letters)
>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 = 146 bits (370), Expect = 5e-43
Identities = 61/129 (47%), Positives = 81/129 (62%), Gaps = 7/129 (5%)
Query: 192 VVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 251
+++D FCG GGNTIQFA V VI IDI+P L AQHNA VYGVS +I FI GD+F L
Sbjct: 3 IILDVFCGAGGNTIQFANVFCSVIGIDINPEHLACAQHNAEVYGVSDRIWFILGDWFELL 62
Query: 252 PSLQG-----DVVFLSPPWGGPEYARSS-FSIDNIFPEQGGGRRLFQVARGISPNVGYYL 305
L+ D VFLSPPWGGP Y R + + ++ + G +L + + IS N+ +L
Sbjct: 63 AKLKFGKIPYDCVFLSPPWGGPSYKRQNVYDLEKKL-KPYGLYQLLKESTEISKNIILFL 121
Query: 306 PRTSDVFEI 314
PR SD+ ++
Sbjct: 122 PRNSDLNQL 130
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 60.1 bits (146), Expect = 2e-11
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 190 SDVVIDGFCGCGGNTIQFAAVCQK--VISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF 247
D V+D G G + A V+ +++DP LA+ ++ G++ +++ + GD
Sbjct: 1 GDRVLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAALARRRLALAGLAPRVRVVVGDA 60
Query: 248 FALAPSLQG--DVVFLSPPWG 266
L G D+V +PP+G
Sbjct: 61 RELLELPDGSFDLVLGNPPYG 81
>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 = 55.0 bits (133), Expect = 3e-09
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 185 SRCKASDVVIDGFCGCGGNTIQFAAVCQKVISI---DIDPAKLRLAQHNASVYGVSHKIQ 241
+ K D ++D CG G I+ A + + + DID ++ A+ NA GV KI+
Sbjct: 24 AGWKPGDPLLDPMCGSGTILIEAALMGANIAPLYGSDIDWRMVQGARINAENAGVGDKIE 83
Query: 242 FIQGDFFAL-APSLQGDVVFLSPPWG 266
F+Q D L + D + +PP+G
Sbjct: 84 FVQADAAKLPLLNGSVDAIVTNPPYG 109
>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 = 50.9 bits (122), Expect = 3e-08
Identities = 25/102 (24%), Positives = 41/102 (40%), Gaps = 5/102 (4%)
Query: 193 VIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 251
V+D CG G + A +V +DI P L LA+ A+ ++ ++ ++GD L
Sbjct: 2 VLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAA-ALLADNVEVLKGDAEELP 60
Query: 252 PSLQG--DVVFLSPPWGGPEYARSSFSIDNIFPEQGGGRRLF 291
P DV+ PP + F ++ G L
Sbjct: 61 PEADESFDVIISDPPLHHLVEDLARF-LEEARRLLKPGGVLV 101
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 49.2 bits (118), Expect = 1e-07
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 198 CGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQ 255
CG G I+ A + +V +D+ P L LA+ NA + +I F+QGD L+
Sbjct: 10 CGTGSLAIELARLFPGARVTGVDLSPEMLELARENAK-LALGPRITFVQGDAPDALDLLE 68
Query: 256 G-DVVFLS 262
G D VF+
Sbjct: 69 GFDAVFIG 76
>gnl|CDD|225174 COG2265, TrmA, SAM-dependent methyltransferases related to tRNA
(uracil-5-)-methyltransferase [Translation, ribosomal
structure and biogenesis].
Length = 432
Score = 48.9 bits (117), Expect = 2e-06
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 191 DVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 250
+ V+D +CG G + A +KV ++I P + AQ NA+ G+ ++FI GD
Sbjct: 295 ERVLDLYCGVGTFGLPLAKRVKKVHGVEISPEAVEAAQENAAANGID-NVEFIAGDAEEF 353
Query: 251 APSLQG----DVVFLSPP 264
P+ DVV + PP
Sbjct: 354 TPAWWEGYKPDVVVVDPP 371
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 47.7 bits (114), Expect = 3e-06
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 4/89 (4%)
Query: 179 VAQHIASRCKASDVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGV 236
V +A + ++D G G I A +VI++DI P L LA+ NA G+
Sbjct: 100 VEAALALLLQLDKRILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARENAERNGL 159
Query: 237 SHKIQFIQGDFFALAPSLQGDVVFLSPPW 265
++ +Q D F + D++ +PP+
Sbjct: 160 -VRVLVVQSDLFE-PLRGKFDLIVSNPPY 186
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 47.7 bits (114), Expect = 4e-06
Identities = 27/101 (26%), Positives = 45/101 (44%), Gaps = 13/101 (12%)
Query: 189 ASDVVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLAQHNASVYGVS-HKIQFIQG 245
A V++ F GG ++ AA+ +V S+D+ L A+ NA + G+ + +FI G
Sbjct: 217 AGKRVLNLFSYTGGFSV-HAALGGASEVTSVDLSKRALEWARENAELNGLDGDRHRFIVG 275
Query: 246 DFFALAPSLQG-----DVVFLSPPWGGPEYARSSFSIDNIF 281
D F + D++ L P P +ARS +
Sbjct: 276 DVFKWLRKAERRGEKFDLIILDP----PSFARSKKQEFSAQ 312
>gnl|CDD|223194 COG0116, COG0116, Predicted N6-adenine-specific DNA methylase [DNA
replication, recombination, and repair].
Length = 381
Score = 46.5 bits (111), Expect = 1e-05
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 211 CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSL-QGDVVFLSPPWG 266
+ DIDP + A+ NA GV I+F Q D L L + VV +PP+G
Sbjct: 254 LPIIYGSDIDPRHIEGAKANARAAGVGDLIEFKQADATDLKEPLEEYGVVISNPPYG 310
>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 = 45.0 bits (107), Expect = 2e-05
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 193 VIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 250
++D G G + A +VI++DI P L +A+ NA + H+++FIQ + F
Sbjct: 118 ILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAEENAEKNQLEHRVEFIQSNLFEP 177
Query: 251 APSLQGDVVFLSPPW 265
+ D++ +PP+
Sbjct: 178 LAGQKIDIIVSNPPY 192
>gnl|CDD|237872 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 44.1 bits (105), Expect = 2e-05
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 188 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSH-KIQFIQGD 246
K D V++ G G I A +KV+ +DI+P + A+ NA + + + ++ I+ D
Sbjct: 22 KKGDRVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNNGVEVIRSD 81
Query: 247 FFALAPSLQGDVVFLSPP 264
F + DV+ +PP
Sbjct: 82 LFEPFRGDKFDVILFNPP 99
>gnl|CDD|225318 COG2520, COG2520, Predicted methyltransferase [General function
prediction only].
Length = 341
Score = 45.0 bits (107), Expect = 3e-05
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 2/90 (2%)
Query: 183 IASRCKASDVVIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQ 241
+A K + V+D F G G +I A KV +IDI+P + + N + V +++
Sbjct: 182 VAELVKEGETVLDMFAGVGPFSIPIAKKGRPKVYAIDINPDAVEYLKENIRLNKVEGRVE 241
Query: 242 FIQGDFFALAP-SLQGDVVFLSPPWGGPEY 270
I GD +AP D + + P E+
Sbjct: 242 PILGDAREVAPELGVADRIIMGLPKSAHEF 271
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 43.8 bits (104), Expect = 3e-05
Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 25/102 (24%)
Query: 191 DVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFF 248
D + D G G TI++A +VI+I+ D L L + NA+ +GV + ++ ++GD
Sbjct: 36 DRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELIERNAARFGVDN-LEVVEGD-- 92
Query: 249 ALAPSLQGDVVFLSPPWGGPEYARSSFSIDNIFPEQGGGRRL 290
PE S D IF GGG +
Sbjct: 93 ------------------APEALPDLPSPDAIF--IGGGGNI 114
>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 = 44.4 bits (106), Expect = 3e-05
Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 213 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLSPP 264
+V ++DI P L +A+ NA+ G+ ++F+Q D+F P + D++ +PP
Sbjct: 113 RVTAVDISPEALAVARKNAARLGLD-NVEFLQSDWFEPLPGGKFDLIVSNPP 163
>gnl|CDD|222287 pfam13649, Methyltransf_25, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 97
Score = 41.2 bits (97), Expect = 6e-05
Identities = 25/106 (23%), Positives = 38/106 (35%), Gaps = 15/106 (14%)
Query: 193 VIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 251
++D CG G A A V +DI L LA+ G K++F+ D L
Sbjct: 1 ILDLGCGTGRVLRALARAGPSSVTGVDISKEALELAKERLRDKG--PKVRFVVADARDL- 57
Query: 252 PSLQG--DVVFLSPPWGGPEYARSSFSIDNIFPEQGGGRRLFQVAR 295
P +G D+V G S + + R ++ R
Sbjct: 58 PFEEGSFDLVIC---AGLSLDYLSPKQLRALL------REAARLLR 94
>gnl|CDD|236467 PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 275
Score = 42.8 bits (102), Expect = 1e-04
Identities = 19/53 (35%), Positives = 35/53 (66%), Gaps = 3/53 (5%)
Query: 213 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLS-PP 264
+V ++DI P L +A+ NA +G+ +++F+QGD+F P + D++ +S PP
Sbjct: 134 EVTAVDISPEALAVARRNA-KHGLGARVEFLQGDWFEPLPGGRFDLI-VSNPP 184
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. 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. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. 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 an
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.
Length = 363
Score = 42.1 bits (100), Expect = 2e-04
Identities = 25/93 (26%), Positives = 37/93 (39%), Gaps = 19/93 (20%)
Query: 192 VVIDGFCGCGG---NTIQFAAVC--QKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
VI GCGG N IQ A + ++I++D P KL LA+ +G +H + + D
Sbjct: 187 AVI----GCGGVGLNAIQGARIAGASRIIAVDPVPEKLELAR----RFGATHTVNASEDD 238
Query: 247 FFALAPSLQG----DVVFLSPPWGGPEYARSSF 275
L D F + G R +
Sbjct: 239 AVEAVRDLTDGRGADYAFEAV--GRAATIRQAL 269
>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 = 41.3 bits (97), Expect = 4e-04
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 191 DVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 250
++V+D +CG G T+ A + V+ I++ P + AQ NA + G+++ ++F+ G +
Sbjct: 294 ELVVDAYCGVGTFTLPLAKQAKSVVGIEVVPESVEKAQQNAELNGIAN-VEFLAGTLETV 352
Query: 251 APSL-----QGDVVFLSPPWGG 267
P DV+ L PP G
Sbjct: 353 LPKQPWAGQIPDVLLLDPPRKG 374
>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 = 40.0 bits (94), Expect = 7e-04
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 4/85 (4%)
Query: 183 IASRCKASDVVIDGFCGCGGNTIQFAAVCQK---VISIDIDPAKLRLAQHNASVYGVSHK 239
IA K +VV+D F G G +I A K V +++++P ++ + N + V
Sbjct: 94 IAKLVKEGEVVVDMFAGIGPFSIP-IAKHSKAKRVYAVELNPEAVKYLKENIKLNKVEGV 152
Query: 240 IQFIQGDFFALAPSLQGDVVFLSPP 264
I I GD + D V ++ P
Sbjct: 153 ISPILGDVRDVILEGVADRVIMNLP 177
>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 = 39.5 bits (92), Expect = 0.001
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 191 DVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 250
D V++ G G I+ + +++ DI+P ++ + NA + V + + D L
Sbjct: 21 DDVLEIGAGTGLVAIRLKGKGKCILTTDINPFAVKELRENAKLNNVG--LDVVMTD---L 75
Query: 251 APSLQG--DVVFLSPPW 265
++G DV+ +PP+
Sbjct: 76 FKGVRGKFDVILFNPPY 92
>gnl|CDD|240367 PTZ00338, PTZ00338, dimethyladenosine transferase-like protein;
Provisional.
Length = 294
Score = 39.6 bits (93), Expect = 0.001
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 179 VAQHI--ASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGV 236
V I + K +D V++ G G T + + +KVI+I+IDP + + +
Sbjct: 24 VLDKIVEKAAIKPTDTVLEIGPGTGNLTEKLLQLAKKVIAIEIDPRMVAELKKRFQNSPL 83
Query: 237 SHKIQFIQGDF 247
+ K++ I+GD
Sbjct: 84 ASKLEVIEGDA 94
>gnl|CDD|236981 PRK11783, rlmL, 23S rRNA m(2)G2445 methyltransferase; Provisional.
Length = 702
Score = 40.2 bits (95), Expect = 0.001
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 218 DIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGD---VVFLSPPWG 266
DIDP ++ A+ NA GV+ I F D L L +V +PP+G
Sbjct: 263 DIDPRVIQAARKNARRAGVAELITFEVKDVADLKNPLPKGPTGLVISNPPYG 314
>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 = 39.0 bits (91), Expect = 0.002
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 193 VIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 250
V+D CG G +I+ A V ++DI +++A++ A V+ ++F D +L
Sbjct: 59 VLDAGCGTGLLSIELAKRGAIVKAVDISEQMVQMARNRAQGRDVAGNVEFEVNDLLSL 116
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 37.8 bits (88), Expect = 0.002
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 188 KASDVVIDGFCGCGGNTIQFAA-VCQ--KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 244
K+ V+D CG G T A + +V+ IDI + A+ NA G ++FIQ
Sbjct: 2 KSGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKLGYE-NVEFIQ 60
Query: 245 GDFFAL 250
GD L
Sbjct: 61 GDIEEL 66
>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 = 38.6 bits (91), Expect = 0.003
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 213 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLSPP 264
+V ++DI P L +A+ N +G+ ++ IQ D FA P + D++ +PP
Sbjct: 147 EVDAVDISPDALAVAEINIERHGLEDRVTLIQSDLFAALPGRKYDLIVSNPP 198
>gnl|CDD|233303 TIGR01177, TIGR01177, TIGR01177 family protein. This family is
found exclusively in the Archaea [Hypothetical proteins,
Conserved].
Length = 329
Score = 38.6 bits (90), Expect = 0.003
Identities = 28/83 (33%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 185 SRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 244
+R D V+D FCG GG I+ + KVI DID + A+ N YG+ +
Sbjct: 178 ARVTEGDRVLDPFCGTGGFLIEAGLMGAKVIGCDIDWKMVAGARINLEHYGIE-DFFVKR 236
Query: 245 GDFFALA-PSLQGDVVFLSPPWG 266
GD L S D + PP+G
Sbjct: 237 GDATKLPLSSESVDAIATDPPYG 259
>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 = 37.8 bits (88), Expect = 0.005
Identities = 26/85 (30%), Positives = 39/85 (45%), Gaps = 7/85 (8%)
Query: 180 AQHIASRCKASDVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVS 237
A +A + VV+D CG G AA ++ + DIDPA +R A+ N +
Sbjct: 77 AAALARPRSGTLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCARRNLA----D 132
Query: 238 HKIQFIQGDFF-ALAPSLQGDVVFL 261
+GD + AL +L+G V L
Sbjct: 133 AGGTVHEGDLYDALPTALRGRVDIL 157
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. 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 have 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 = 338
Score = 38.0 bits (89), Expect = 0.006
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 192 VVIDGFCGCGGNTIQFAAVCQ-KVISIDIDPAKLRLA-QHNASVYGVSHKIQFIQGDFFA 249
V++ G G G N +Q A VI++DI KL LA + A V + + D A
Sbjct: 169 VLVIGLGGLGLNAVQIAKAMGAAVIAVDIKEEKLELAKELGAD--EVLNSLDDSPKDKKA 226
Query: 250 LAPSLQGDVVF 260
DV+F
Sbjct: 227 AGLGGGFDVIF 237
>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 = 37.5 bits (87), Expect = 0.007
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 191 DVVIDGFCGCGGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 244
VID GCG + AA+ KV+ IDIDP + A+ NA + VS ++Q
Sbjct: 161 KNVID--VGCGSGILSIAALKLGAAKVVGIDIDPLAVESARKNAELNQVSDRLQVKL 215
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 36.9 bits (86), Expect = 0.007
Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 204 TIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
+ A ++ +I+ D + +A+ N + GV +I+ + G
Sbjct: 74 ALWMALALPDDGRLTTIERDEERAEIARENLAEAGVDDRIELLLGG 119
>gnl|CDD|234740 PRK00377, cbiT, cobalt-precorrin-6Y C(15)-methyltransferase;
Provisional.
Length = 198
Score = 36.7 bits (85), Expect = 0.008
Identities = 24/89 (26%), Positives = 46/89 (51%), Gaps = 8/89 (8%)
Query: 186 RCKASDVVIDGFCGCGGNTIQFAAVC---QKVISIDIDPAKLRLAQHNASVYGVSHKIQF 242
R + D+++D CG G T++ + + KV ++D D + L + NA +GV + I
Sbjct: 37 RLRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAEKFGVLNNIVL 96
Query: 243 IQGDFFALAPSL--QGDVVFLSPPWGGPE 269
I+G+ + ++ + D +F+ GG E
Sbjct: 97 IKGEAPEILFTINEKFDRIFIG---GGSE 122
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 37.0 bits (86), Expect = 0.010
Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 14/107 (13%)
Query: 169 DGWYSVTPEKVAQHIASRC---KASDVVIDGFC-GCGGNTIQFAAVCQ----KVISIDID 220
+G V ++ +Q + + K + V+D C GG T A + + V+++D+
Sbjct: 135 EGLIYVQ-DEASQ-LPALVLDPKPGERVLD-LCAAPGGKTTHLAELMENEGAIVVAVDVS 191
Query: 221 PAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQG---DVVFLSPP 264
P +L+ + N GV + I + G D + L P
Sbjct: 192 PKRLKRLRENLKRLGVRNVIVVNKDARRLAELLPGGEKFDRILLDAP 238
>gnl|CDD|222236 pfam13578, Methyltransf_24, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 105
Score = 34.9 bits (81), Expect = 0.012
Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 198 CGCGGNTIQFAAVCQ-----KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAP 252
G +T+ A + ++ SID P A N G++ +++ ++GD
Sbjct: 5 VYSGVSTLWLAQALKDNGLGRLYSIDPWPG--AEAGANLRKAGLADRVRLLRGDSLEALA 62
Query: 253 SLQG---DVVFL 261
L D++F+
Sbjct: 63 RLPDGSIDLLFI 74
>gnl|CDD|225172 COG2263, COG2263, Predicted RNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 198
Score = 36.1 bits (84), Expect = 0.013
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 192 VVIDGFCGCGGNTIQFAAV-CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 250
V+D G G I A + +V+++DIDP L +A+ NA ++F+ D
Sbjct: 48 TVLDLGAGTGILAIGAALLGASRVLAVDIDPEALEIARANAEELLG--DVEFVVAD--VS 103
Query: 251 APSLQGDVVFLSPPWG 266
+ D V ++PP+G
Sbjct: 104 DFRGKFDTVIMNPPFG 119
>gnl|CDD|223109 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation)
[Translation, ribosomal structure and biogenesis].
Length = 259
Score = 36.4 bits (85), Expect = 0.014
Identities = 22/92 (23%), Positives = 33/92 (35%), Gaps = 7/92 (7%)
Query: 177 EKVAQHI--ASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVY 234
+ V I A+ D V++ G G T +V +I+ID RLA+ +
Sbjct: 16 KNVIDKIVEAANISPGDNVLEIGPGLGALTEPLLERAARVTAIEIDR---RLAEVLKERF 72
Query: 235 GVSHKIQFIQGDF--FALAPSLQGDVVFLSPP 264
+ I GD F Q V + P
Sbjct: 73 APYDNLTVINGDALKFDFPSLAQPYKVVANLP 104
>gnl|CDD|226608 COG4123, COG4123, Predicted O-methyltransferase [General function
prediction only].
Length = 248
Score = 36.1 bits (84), Expect = 0.014
Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 193 VIDGFCGCGGNTIQFAAVCQK--VISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 250
++D G G + A +K ++ ++I +AQ N ++ + +IQ I+ D
Sbjct: 48 ILDLGAGNGALGLLLAQRTEKAKIVGVEIQEEAAEMAQRNVALNPLEERIQVIEADIKEF 107
Query: 251 APSLQG---DVVFLSPP 264
+L D++ +PP
Sbjct: 108 LKALVFASFDLIICNPP 124
>gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases.
Length = 169
Score = 35.6 bits (83), Expect = 0.016
Identities = 31/115 (26%), Positives = 47/115 (40%), Gaps = 16/115 (13%)
Query: 188 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF 247
+ D V++ G G T + ++V +I+IDP RLA + + + I GD
Sbjct: 12 RPGDTVLEIGPGKGALTEELLERAKRVTAIEIDP---RLAPRLREKFAAADNLTVIHGDA 68
Query: 248 --FALAPSLQGDVVFLSPPWGGPEYARSSFSIDNIFPEQGGGRR---LFQ--VAR 295
F L P LQ V + P Y S+ + + E R + Q VAR
Sbjct: 69 LKFDL-PKLQPYKVVGNLP-----YNISTPILFKLLEEPPAFRDAVLMVQKEVAR 117
>gnl|CDD|182918 PRK11036, PRK11036, putative S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 255
Score = 36.1 bits (84), Expect = 0.016
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 193 VIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 244
V+D G G I+ A + +VI D+ ++ A+ A GVS +QFI
Sbjct: 48 VLDAGGGEGQTAIKLAELGHQVILCDLSAEMIQRAKQAAEAKGVSDNMQFIH 99
>gnl|CDD|131140 TIGR02085, meth_trns_rumB, 23S rRNA (uracil-5-)-methyltransferase
RumB. This family consists of RNA methyltransferases
designated RumB, formerly YbjF. Members act on 23S rRNA
U747 and the equivalent position in other
proteobacterial species. This family is homologous to
the other 23S rRNA methyltransferase RumA and to the
tRNA methyltransferase TrmA [Protein synthesis, tRNA and
rRNA base modification].
Length = 374
Score = 36.4 bits (84), Expect = 0.017
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 195 DGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF--FALAP 252
D FCG GG + A ++ I+I+ + AQ +A + G+ + + F D FA A
Sbjct: 239 DLFCGVGGFGLHCAGPDTQLTGIEIESEAIACAQQSAQMLGLDN-LSFAALDSAKFATAQ 297
Query: 253 SLQGDVVFLSPP 264
++V ++PP
Sbjct: 298 MSAPELVLVNPP 309
>gnl|CDD|223971 COG1041, COG1041, Predicted DNA modification methylase [DNA
replication, recombination, and repair].
Length = 347
Score = 36.2 bits (84), Expect = 0.021
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 185 SRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVS 237
+R K ++V+D FCG GG I+ + +VI DID +R A+ N YG+
Sbjct: 193 ARVKRGELVLDPFCGTGGILIEAGLMGARVIGSDIDERMVRGAKINLEYYGIE 245
>gnl|CDD|236988 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 307
Score = 35.5 bits (83), Expect = 0.026
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 217 IDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLSPP 264
+DI P L +A+ N +G+ ++ I+ D FA P + D++ +PP
Sbjct: 163 VDISPDALAVAEINIERHGLEDRVTLIESDLFAALPGRRYDLIVSNPP 210
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 35.7 bits (83), Expect = 0.030
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 190 SDVVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLA 227
V + G G G IQ A ++I++DI+P KL LA
Sbjct: 187 DTVAVFGLGGVGLAAIQGAKAAGAGRIIAVDINPEKLELA 226
>gnl|CDD|223813 COG0742, COG0742, N6-adenine-specific methylase [DNA replication,
recombination, and repair].
Length = 187
Score = 34.5 bits (80), Expect = 0.034
Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 193 VIDGFCGCGGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 249
V+D F G G + A+ + +V+ ++ D +++ + N G+ + + ++ D
Sbjct: 47 VLDLFAGSGA--LGLEALSRGAARVVFVEKDRKAVKILKENLKALGLEGEARVLRNDALR 104
Query: 250 LAPSLQG----DVVFLSPP 264
L D+VFL PP
Sbjct: 105 ALKQLGTREPFDLVFLDPP 123
>gnl|CDD|218365 pfam04989, CmcI, Cephalosporin hydroxylase. Members of this family
are about 220 amino acids long. The CmcI protein is
presumed to represent the cephalosporin-7--hydroxylase.
However this has not been experimentally verified.
Length = 206
Score = 34.5 bits (80), Expect = 0.037
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 14/55 (25%)
Query: 201 GGNTIQFAAVCQ------KVISIDIDPAKLRLAQHN---ASVYGVSHKIQFIQGD 246
GG+ + FA++ + KV+ IDID + +HN + ++ +I IQG
Sbjct: 44 GGSALFFASMLELLGSDGKVLGIDID-----IREHNRPAIEAHPMASRITLIQGS 93
>gnl|CDD|233880 TIGR02469, CbiT, precorrin-6Y C5,15-methyltransferase
(decarboxylating), CbiT subunit. This model recognizes
the CbiT methylase which is responsible, in part (along
with CbiE), for methylating precorrin-6y (or
cobalt-precorrin-6y) at both the 5 and 15 positions as
well as the concomitant decarbozylation at C-12. In many
organisms, this protein is fused to the CbiE subunit.
The fused protein, when found in organisms catalyzing
the oxidative version of the cobalamin biosynthesis
pathway, is called CobL [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 124
Score = 33.5 bits (77), Expect = 0.039
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 186 RCKASDVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVS 237
R + DV+ D G G TI+ A + +V +I+ +P L L + N +GVS
Sbjct: 16 RLRPGDVLWDIGAGTGSVTIEAARLVPNGRVYAIERNPEALDLIERNLRRFGVS 69
>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 = 34.9 bits (81), Expect = 0.046
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 10/77 (12%)
Query: 188 KASDVVIDGFCGCGGNTIQFAAV---CQKVISIDIDPAKLRLAQHNASVYGVSHKIQ-FI 243
K + V+D GCG + AA+ +KV+ +DIDP +R A+ NA + GV +++ ++
Sbjct: 159 KPGETVLD--VGCGSGILAIAALKLGAKKVVGVDIDPVAVRAAKENAELNGVEAQLEVYL 216
Query: 244 QGDFFALAPSLQGDVVF 260
GD P + DVV
Sbjct: 217 PGD----LPEGKADVVV 229
>gnl|CDD|202698 pfam03602, Cons_hypoth95, Conserved hypothetical protein 95.
Length = 183
Score = 34.2 bits (79), Expect = 0.047
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 10/80 (12%)
Query: 193 VIDGFCGCGGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 249
V+D F G G ++ A+ + V+ ++ D + + N G+ + ++ D
Sbjct: 47 VLDLFAGSGALGLE--ALSRGAASVVFVEKDKKAVATLKENLEALGLEGETAVLRNDAAR 104
Query: 250 LAPSLQG-----DVVFLSPP 264
L G D+VFL PP
Sbjct: 105 ALLRLAGKGPPFDLVFLDPP 124
>gnl|CDD|234958 PRK01544, PRK01544, bifunctional N5-glutamine
S-adenosyl-L-methionine-dependent methyltransferase/tRNA
(m7G46) methyltransferase; Reviewed.
Length = 506
Score = 34.8 bits (80), Expect = 0.053
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 199 GCGGNTIQFAAVCQ----KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSL 254
G G I + +C+ VI+ DI + +A+ NA Y V+ +IQ I ++F
Sbjct: 146 GTGSGCIAISLLCELPNANVIATDISLDAIEVAKSNAIKYEVTDRIQIIHSNWFENIEKQ 205
Query: 255 QGDVVFLSPPW 265
+ D + +PP+
Sbjct: 206 KFDFIVSNPPY 216
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 32.6 bits (75), Expect = 0.057
Identities = 19/67 (28%), Positives = 24/67 (35%), Gaps = 9/67 (13%)
Query: 198 CGCGGNTIQFAAVCQK-VISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL-APSLQ 255
CG G A V +D+ P L LA+ +F+ GD L P
Sbjct: 5 CGTGLLAEALARRGGARVTGVDLSPEMLALARKR-------APRKFVVGDAEDLPFPDES 57
Query: 256 GDVVFLS 262
DVV S
Sbjct: 58 FDVVVSS 64
>gnl|CDD|225317 COG2519, GCD14, tRNA(1-methyladenosine) methyltransferase and
related methyltransferases [Translation, ribosomal
structure and biogenesis].
Length = 256
Score = 34.2 bits (79), Expect = 0.073
Identities = 26/95 (27%), Positives = 38/95 (40%), Gaps = 7/95 (7%)
Query: 178 KVAQHIASRCKAS--DVVIDGFCGCGGNTIQFA-AVCQ--KVISIDIDPAKLRLAQHNAS 232
K A +I +R S V++ G G T A AV V + +I + A+ N S
Sbjct: 81 KDAGYIVARLGISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARENLS 140
Query: 233 VYGVSHKIQFIQGDFFALAPSLQGDVVFLS--PPW 265
+G+ ++ GD D VFL PW
Sbjct: 141 EFGLGDRVTLKLGDVREGIDEEDVDAVFLDLPDPW 175
>gnl|CDD|215900 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.
Length = 254
Score = 33.8 bits (78), Expect = 0.095
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 190 SDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 249
SD V++ G G T + A ++V++I+IDP + Q +++ ++ + DF
Sbjct: 30 SDTVLEIGPGKGALTTELAKRAKQVVAIEIDPRLAKRLQEKLALH---PNVEVVHQDFLK 86
Query: 250 LA-PSLQGDVVF 260
+ P +V
Sbjct: 87 FSFPKDDPFLVV 98
>gnl|CDD|237007 PRK11873, arsM, arsenite S-adenosylmethyltransferase; Reviewed.
Length = 272
Score = 33.8 bits (78), Expect = 0.11
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 188 KASDVVIDGFCGCGGNTIQFAAVCQ-----KVISIDIDPAKLRLAQHNASVYGVSHKIQF 242
K + V+D G GG F A + KVI +D+ P L A+ NA G ++ ++F
Sbjct: 76 KPGETVLD--LGSGGGFDCFLAARRVGPTGKVIGVDMTPEMLAKARANARKAGYTN-VEF 132
Query: 243 IQGD 246
G+
Sbjct: 133 RLGE 136
>gnl|CDD|176222 cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This
group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family. 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 includes
various 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 = 337
Score = 32.9 bits (76), Expect = 0.18
Identities = 28/99 (28%), Positives = 35/99 (35%), Gaps = 20/99 (20%)
Query: 174 VTPEKVAQHIASR--CKASD--VVIDGFCGCGG---NTIQFA-AVCQKVISIDIDPAKLR 225
V P + H R A D +V+ G G IQ A A +VI +DID +L
Sbjct: 142 VEPLAIGAHAVRRAGVTAGDTVLVV----GAGPIGLGVIQVAKARGARVIVVDIDDERLE 197
Query: 226 LAQHNASVYGVSHKIQFIQGDFFALAPSLQG----DVVF 260
A+ G I D A L DVV
Sbjct: 198 FARE----LGADDTINVGDEDVAARLRELTDGEGADVVI 232
>gnl|CDD|182371 PRK10309, PRK10309, galactitol-1-phosphate dehydrogenase;
Provisional.
Length = 347
Score = 32.9 bits (75), Expect = 0.19
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 180 AQHIASRCKASDVVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLAQ 228
A H+A C+ +V+I G G IQ A + V +IDI+ KL LA+
Sbjct: 152 AFHLAQGCEGKNVIIIGAGTIGLLAIQCAVALGAKSVTAIDINSEKLALAK 202
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 32.4 bits (75), Expect = 0.23
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 11/77 (14%)
Query: 181 QHIASR---CKASDV-----VIDGFCGCGGNTIQFAAVCQK---VISIDIDPAKLRLAQH 229
H R K V V+D CG G I A K V+ +D L + +
Sbjct: 35 LHRVWRRKTIKWLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGRE 94
Query: 230 NASVYGVSHKIQFIQGD 246
G+S ++F+QGD
Sbjct: 95 KLRDLGLSGNVEFVQGD 111
>gnl|CDD|225173 COG2264, PrmA, Ribosomal protein L11 methylase [Translation,
ribosomal structure and biogenesis].
Length = 300
Score = 32.7 bits (75), Expect = 0.25
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 193 VIDGFCGCGGNTIQFAAV---CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 249
V+D GCG + AA +KV+ +DIDP + A+ NA + GV +Q
Sbjct: 166 VLD--VGCGSGILAIAAAKLGAKKVVGVDIDPQAVEAARENARLNGVELLVQAKGFLLLE 223
Query: 250 LAPSLQGDVVF 260
+ + DV+
Sbjct: 224 VPENGPFDVIV 234
>gnl|CDD|217121 pfam02582, DUF155, Uncharacterized ACR, YagE family COG1723.
Length = 174
Score = 31.7 bits (73), Expect = 0.26
Identities = 24/98 (24%), Positives = 33/98 (33%), Gaps = 17/98 (17%)
Query: 46 ITYKLSTLSGCAQKVLFNILEDV--AYQETLNTLPSEFGSQRKKKRRRKKRS-------- 95
+ KL+ AQ V ++ E+ E+ LP E K RK+
Sbjct: 69 LLDKLAISHALAQSVKLSVFEEQVDNLLESTEPLPEELAKTGKLNLSRKELLKLIGELLS 128
Query: 96 --FELNYQEDLGDLENVPEEIWANPYLNKYYQQ--RYL 129
+N DL D P+ W P L Y YL
Sbjct: 129 LRHRINLYSDLLD---TPDFFWDEPELEPLYLALREYL 163
>gnl|CDD|184931 PRK14967, PRK14967, putative methyltransferase; Provisional.
Length = 223
Score = 32.3 bits (74), Expect = 0.26
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 193 VIDGFCGCGGNTIQFAAV-CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 251
V+D G G + AA V ++DI +R A+ NA + G + +GD+
Sbjct: 40 VLDLCTGSGALAVAAAAAGAGSVTAVDISRRAVRSARLNALLAG--VDVDVRRGDWARAV 97
Query: 252 PSLQGDVVFLSPPW 265
DVV +PP+
Sbjct: 98 EFRPFDVVVSNPPY 111
>gnl|CDD|226413 COG3897, COG3897, Predicted methyltransferase [General function
prediction only].
Length = 218
Score = 32.4 bits (74), Expect = 0.26
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 205 IQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPS----LQGDVVF 260
A +V++ DIDP + + NA+ GVS I F D P+ L GD+ +
Sbjct: 96 AAARAGAAEVVAADIDPWLEQAIRLNAAANGVS--ILFTHADLIGSPPAFDLLLAGDLFY 153
>gnl|CDD|218767 pfam05827, ATP-synt_S1, Vacuolar ATP synthase subunit S1 (ATP6S1).
This family consists of eukaryotic vacuolar ATP synthase
subunit S1 proteins.
Length = 277
Score = 32.4 bits (74), Expect = 0.27
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 140 MDEESWYSVTPEKVAQHIASRCKASDVVIDGWYSVTPEKVA 180
+ E W +++A+++ +C AS +ID + E
Sbjct: 89 NEVEGWLE--LKQLAEYLKKKCGASVEIIDVSDNKEHELNE 127
Score = 30.0 bits (68), Expect = 1.6
Identities = 8/34 (23%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 163 ASDVVIDGWYSVTPEKVAQHIASRCKASDVVIDG 196
++GW +++A+++ +C AS +ID
Sbjct: 86 YVVNEVEGWLE--LKQLAEYLKKKCGASVEIIDV 117
>gnl|CDD|181601 PRK08978, PRK08978, acetolactate synthase 2 catalytic subunit;
Reviewed.
Length = 548
Score = 32.9 bits (76), Expect = 0.28
Identities = 21/46 (45%), Positives = 25/46 (54%), Gaps = 15/46 (32%)
Query: 213 KVISIDIDPA---KLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQ 255
KVI +DIDPA KLR A V+ +QGD AL P+LQ
Sbjct: 289 KVIHLDIDPAEINKLRQAH-------VA-----LQGDLNALLPALQ 322
>gnl|CDD|184643 PRK14354, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 458
Score = 32.5 bits (75), Expect = 0.29
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 288 RRLFQVARGISPNVG---YYLPRTSDVFEIFHDSGKK 321
+ LF+ + IS + YYL DV EI + G+K
Sbjct: 178 KALFEALKKISNDNAQGEYYLT---DVIEILKNEGEK 211
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the characteristic
catalytic and structural zinc sites of the
zinc-dependent alcohol dehydrogenases. 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 = 345
Score = 32.2 bits (74), Expect = 0.35
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 4/34 (11%)
Query: 199 GCGG---NTIQFA-AVCQKVISIDIDPAKLRLAQ 228
GCGG + + A A+ +VI++DID KL LA+
Sbjct: 173 GCGGVGLSAVMIASALGARVIAVDIDDDKLELAR 206
>gnl|CDD|132245 TIGR03201, dearomat_had, 6-hydroxycyclohex-1-ene-1-carbonyl-CoA
dehydrogenase. Members of this protein family are
6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase, an
enzyme in the anaerobic metabolism of aromatic enzymes
by way of benzoyl-CoA, as seen in Thauera aromatica,
Geobacter metallireducens, and Azoarcus sp. The
experimentally characterized form from T. aromatica uses
only NAD+, not NADP+. Note that Rhodopseudomonas
palustris uses a different pathway to perform a similar
degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Length = 349
Score = 32.2 bits (73), Expect = 0.35
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 192 VVIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRL 226
V++ G G GG +Q A A+ V++IDIDP KL +
Sbjct: 170 VIVIGAGGVGGYMVQTAKAMGAAVVAIDIDPEKLEM 205
>gnl|CDD|185082 PRK15128, PRK15128, 23S rRNA m(5)C1962 methyltransferase;
Provisional.
Length = 396
Score = 32.1 bits (73), Expect = 0.42
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 211 CQKVISIDIDPAKLRLAQHNASVYGVS-HKIQFIQGDFFALAPSL--QG---DVVFLSPP 264
C +V+S+D L +A+ N + + K +F++ D F L + +G DV+ + PP
Sbjct: 243 CSQVVSVDTSQEALDIARQNVELNKLDLSKAEFVRDDVFKLLRTYRDRGEKFDVIVMDPP 302
>gnl|CDD|218278 pfam04816, DUF633, Family of unknown function (DUF633). This
family of proteins are uncharacterized have no known
function.
Length = 204
Score = 31.5 bits (72), Expect = 0.44
Identities = 10/46 (21%), Positives = 20/46 (43%)
Query: 210 VCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQ 255
+ I+ +++ L A +N G++ +I GD A+ L
Sbjct: 20 LASFAIAGEVNKGPLESAVNNVKKNGLTERIDVRLGDGLAVLEELD 65
>gnl|CDD|233085 TIGR00675, dcm, DNA-methyltransferase (dcm). All proteins in this
family for which functions are known are DNA-cytosine
methyltransferases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 315
Score = 31.5 bits (72), Expect = 0.52
Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 8/70 (11%)
Query: 193 VIDGFCGCGGNTIQF-AAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 251
ID F G GG + F A + V + +ID + Y + + GD ++
Sbjct: 1 FIDLFAGIGGIRLGFEQAGFKCVFASEIDK-------YAQKTYEANFGNKVPFGDITKIS 53
Query: 252 PSLQGDVVFL 261
PS D L
Sbjct: 54 PSDIPDFDIL 63
>gnl|CDD|176202 cd08240, 6_hydroxyhexanoate_dh_like, 6-hydroxyhexanoate
dehydrogenase. 6-hydroxyhexanoate dehydrogenase, an
enzyme of the zinc-dependent alcohol dehydrogenase-like
family of medium chain dehydrogenases/reductases
catalyzes the conversion of 6-hydroxyhexanoate and
NAD(+) to 6-oxohexanoate + NADH and H+.
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 = 350
Score = 31.4 bits (72), Expect = 0.63
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 192 VVIDGFCGCGGNTIQFA-AVCQK-VISIDIDPAKLRLAQ 228
VVI G G G + A+ +I +DID AKL A+
Sbjct: 179 VVIIGAGGLGLMALALLKALGPANIIVVDIDEAKLEAAK 217
>gnl|CDD|223348 COG0270, Dcm, Site-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 328
Score = 31.2 bits (71), Expect = 0.64
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 13/78 (16%)
Query: 193 VIDGFCGCGGNTIQFAAVCQKVI-SIDIDPAKLRLAQHNASVYGVSHK-IQFIQGDFFAL 250
VID F G GG ++ F +++ + +IDP + + N I GD L
Sbjct: 6 VIDLFAGIGGLSLGFEEAGFEIVFANEIDPPAVATYKAN-------FPHGDIILGDIKEL 58
Query: 251 APS----LQGDVVFLSPP 264
DV+ PP
Sbjct: 59 DGEALRKSDVDVLIGGPP 76
>gnl|CDD|176257 cd08297, CAD3, 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 = 341
Score = 31.4 bits (72), Expect = 0.68
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 185 SRCKASDVVIDGFCGCGGN----TIQFA-AVCQKVISIDIDPAKLRLA 227
+ K D V G GG +Q+A A+ +VI+ID+ KL LA
Sbjct: 161 AGLKPGDWV--VISGAGGGLGHLGVQYAKAMGLRVIAIDVGDEKLELA 206
>gnl|CDD|215812 pfam00239, Resolvase, Resolvase, N terminal domain. The N-terminal
domain of the resolvase family (this family) contains
the active site and the dimer interface. The extended
arm at the C-terminus of this domain connects to the
C-terminal helix-turn-helix domain of resolvase - see
pfam02796.
Length = 139
Score = 30.2 bits (69), Expect = 0.73
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 11/95 (11%)
Query: 4 KKVLEDVAYQDILITYKLSTLSGCAQKVLFNILEDVAYQDI-LITYKLST-LSGCAQKVL 61
+++LED+ D L+ KL L G + + L ++E++ + + L++ S A ++L
Sbjct: 49 QRLLEDLREGDTLVVTKLDRL-GRSLRDLLELVEELREKGVRLVSLDEGIDTSTPAGRLL 107
Query: 62 FNILEDVAYQETLNTLPSEFGSQRKK--KRRRKKR 94
IL +A E E S+R K K R
Sbjct: 108 LTILAALAEFE------RELISERTKAGLAAAKAR 136
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 31.0 bits (71), Expect = 0.78
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 192 VVIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRLAQ 228
V + G G G +Q+A A+ +VI+I KL LA+
Sbjct: 170 VAVVGAGGLGHMAVQYAKAMGAEVIAITRSEEKLELAK 207
>gnl|CDD|234786 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed.
Length = 250
Score = 30.9 bits (71), Expect = 0.78
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 211 CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
+KV+++DIDP + A+ NA + GV + QGD
Sbjct: 142 AKKVLAVDIDPQAVEAARENAELNGVELNVYLPQGD 177
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 31.2 bits (71), Expect = 0.81
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 213 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLSPPWGG 267
++ ++D P KL + +AS G++ I+ I+GD + +P Q D + L P G
Sbjct: 277 QITAVDRYPQKLEKIRSHASALGIT-IIETIEGDARSFSPEEQPDAILLDAPCTG 330
>gnl|CDD|131865 TIGR02818, adh_III_F_hyde, S-(hydroxymethyl)glutathione
dehydrogenase/class III alcohol dehydrogenase. The
members of this protein family show dual function.
First, they remove formaldehyde, a toxic metabolite, by
acting as S-(hydroxymethyl)glutathione dehydrogenase
(1.1.1.284). S-(hydroxymethyl)glutathione can form
spontaneously from formaldehyde and glutathione, and so
this enzyme previously was designated
glutathione-dependent formaldehyde dehydrogenase. These
same proteins are also designated alcohol dehydrogenase
(EC 1.1.1.1) of class III, for activities that do not
require glutathione; they tend to show poor activity for
ethanol among their various substrate alcohols [Cellular
processes, Detoxification, Energy metabolism,
Fermentation].
Length = 368
Score = 31.0 bits (70), Expect = 1.00
Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 2/87 (2%)
Query: 144 SWYSVTPEKVAQHIASRCKASDVVIDGWYSVTPEKVAQHIASRCKASDVVIDGFCGCGGN 203
S Y+V PE I +V + G T + A + V + G G G +
Sbjct: 141 SEYTVVPEISLAKINPAAPLEEVCLLGCGVTTGIGAVLNTAKVEEGDTVAVFGLGGIGLS 200
Query: 204 TIQFA--AVCQKVISIDIDPAKLRLAQ 228
IQ A A ++I+IDI+PAK LA+
Sbjct: 201 VIQGARMAKASRIIAIDINPAKFELAK 227
>gnl|CDD|201880 pfam01596, Methyltransf_3, O-methyltransferase. Members of this
family are O-methyltransferases. The family includes
catechol o-methyltransferase, caffeoyl-CoA
O-methyltransferase and a family of bacterial
O-methyltransferases that may be involved in antibiotic
production.
Length = 204
Score = 30.0 bits (68), Expect = 1.3
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 213 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
K+ + DIDP + GV+ KI F GD
Sbjct: 71 KITACDIDPEAYEIGLPFIQKAGVADKISFRLGD 104
>gnl|CDD|215721 pfam00107, ADH_zinc_N, Zinc-binding dehydrogenase.
Length = 131
Score = 28.8 bits (65), Expect = 1.7
Identities = 18/80 (22%), Positives = 27/80 (33%), Gaps = 6/80 (7%)
Query: 201 GGNTIQFAAV--CQKVISIDIDPAKLRLA-QHNASVYGVSHKIQFIQGDFFALAPSLQGD 257
G +Q A +VI++D KL LA + A F++ L D
Sbjct: 3 GLAAVQLAKALGAARVIAVDRSEEKLELAKELGADHVINYRDEDFVE-RVRELTGGRGVD 61
Query: 258 VVFLSPPWGGPEYARSSFSI 277
VV G P + +
Sbjct: 62 VVIDCV--GAPATLEQALEL 79
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. 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.
Length = 277
Score = 29.9 bits (68), Expect = 1.7
Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 9/59 (15%)
Query: 204 TIQFAAV--CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVF 260
Q A ++V+ +D D A+ LA+ V+ G A DVV
Sbjct: 113 AAQLAKAAGAREVVGVDPDAARRELAEALGPADPVAADTADEIGGRGA-------DVVI 164
>gnl|CDD|181354 PRK08287, PRK08287, cobalt-precorrin-6Y C(15)-methyltransferase;
Validated.
Length = 187
Score = 29.2 bits (66), Expect = 2.1
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 14/76 (18%)
Query: 193 VIDGFCGCGGNTIQFAAVCQ----KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFF 248
+ID G G +I+ A Q +V +I+ +P LRL + N +G I I G
Sbjct: 35 LIDVGAGTGSVSIE--AALQFPSLQVTAIERNPDALRLIKENRQRFGC-GNIDIIPG--- 88
Query: 249 ALAP---SLQGDVVFL 261
AP + D +F+
Sbjct: 89 -EAPIELPGKADAIFI 103
>gnl|CDD|226562 COG4076, COG4076, Predicted RNA methylase [General function
prediction only].
Length = 252
Score = 29.5 bits (66), Expect = 2.2
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 183 IASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQF 242
IA A D D G G ++ A ++VI+I+ DP + RLA+ N V G + +
Sbjct: 28 IAEV--AEDTFADLGAGSGILSVVAAHAAERVIAIEKDPKRARLAEENLHVPGDVN-WEV 84
Query: 243 IQGD 246
+ GD
Sbjct: 85 VVGD 88
>gnl|CDD|236059 PRK07580, PRK07580, Mg-protoporphyrin IX methyl transferase;
Validated.
Length = 230
Score = 29.4 bits (67), Expect = 2.2
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 193 VIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
++D CG G +I A KV++ DI P + A+ A G++ I F GD
Sbjct: 67 ILDAGCGVGSLSIPLARRGAKVVASDISPQMVEEARERAPEAGLAGNITFEVGD 120
>gnl|CDD|218185 pfam04634, DUF600, Protein of unknown function, DUF600. This
conserved region is found in several uncharacterized
proteins from Gram positive bacteria.
Length = 147
Score = 28.8 bits (65), Expect = 2.2
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 91 RKKRSFELNYQEDLGDLENVPEEIWANPYLNKYYQQRYLYWSRYDEGILMDEESWYSVT 149
S E Y D+ D NV E+ ++ K+ + L+ +E ++E W S+T
Sbjct: 41 YTPGSDEPIYSHDIPDKYNVSEDE----FMEKWNELYDLFEELREEFKENNQEPWTSLT 95
>gnl|CDD|237852 PRK14896, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Provisional.
Length = 258
Score = 29.1 bits (66), Expect = 2.6
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 191 DVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
D V++ G G T + A +KV +I++DP RLA+ + ++ I+GD
Sbjct: 31 DPVLEIGPGKGALTDELAKRAKKVYAIELDP---RLAEFLRDDEIAAGNVEIIEGD 83
>gnl|CDD|188504 TIGR03989, Rxyl_3153, oxidoreductase, Rxyl_3153 family. This model
describes a clade within the family pfam00107 of
zinc-binding dehydrogenases. The family pfam00107
contains class III alcohol dehydrogenases, including
enzymes designated S-(hydroxymethyl)glutathione
dehydrogenase and NAD/mycothiol-dependent formaldehyde
dehydrogenase. Members of the current family occur only
in species that contain the very small protein
mycofactocin (TIGR03969), a possible cofactor precursor,
and radical SAM protein TIGR03962. We name this family
for Rxyl_3153, where the lone member of the family
co-clusters with these markers in Rubrobacter
xylanophilus [Unknown function, Enzymes of unknown
specificity].
Length = 369
Score = 29.2 bits (66), Expect = 3.2
Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 12/76 (15%)
Query: 167 VIDGWYSVTPEKVAQHIASRCKASDVVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKL 224
V GW S A +IA VV+ G G G N +Q AAV +KVI++D K
Sbjct: 170 VPTGWGS------AVNIADVRPGDTVVVMGIGGVGINAVQGAAVAGARKVIAVDPVEFKR 223
Query: 225 RLAQHNASVYGVSHKI 240
A +G +H
Sbjct: 224 EQALK----FGATHAF 235
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. 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. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 29.1 bits (66), Expect = 3.5
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 12/57 (21%)
Query: 180 AQHIASRCKASDVVIDGFCGCGGNTI-----QFAAV--CQKVISIDIDPAKLRLAQH 229
A +A VV+ G G TI Q+ + ++VI++DID KL +A+
Sbjct: 151 AVRLAGITLGDTVVV---IGAG--TIGLLAIQWLKILGAKRVIAVDIDDEKLAVARE 202
>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 = 3.5
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 8/55 (14%)
Query: 193 VIDGFCGCGGNTIQFAAVCQKVI-SIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
VID F G GG + +++ + +ID + + N + I+GD
Sbjct: 3 VIDLFAGIGGFRLGLEKAGFEIVAANEIDKSAAETYEAN-------FPNKLIEGD 50
>gnl|CDD|180780 PRK06965, PRK06965, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 587
Score = 29.0 bits (65), Expect = 3.9
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 202 GNTIQFAAVCQKVISIDIDPAKL 224
GN FA+ +K+I IDIDP+ +
Sbjct: 304 GNPAHFASRPRKIIHIDIDPSSI 326
>gnl|CDD|132492 TIGR03451, mycoS_dep_FDH, S-(hydroxymethyl)mycothiol dehydrogenase.
Members of this protein family are mycothiol-dependent
formaldehyde dehydrogenase (EC 1.2.1.66). This protein
is found, so far, only in the Actinobacteria
(Mycobacterium sp., Streptomyces sp., Corynebacterium
sp., and related species), where mycothione replaces
glutathione [Cellular processes, Detoxification].
Length = 358
Score = 29.0 bits (65), Expect = 4.0
Identities = 28/93 (30%), Positives = 40/93 (43%), Gaps = 18/93 (19%)
Query: 192 VVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLAQH-------NASVYGVSHKIQF 242
V + G G G I AA+ K+I++DID KL A+ N+S I+
Sbjct: 180 VAVIGCGGVGDAAIAGAALAGASKIIAVDIDDRKLEWAREFGATHTVNSSGTDPVEAIRA 239
Query: 243 IQGDFFALAPSLQGDVVFLSPPWGGPEYARSSF 275
+ G F A DVV + G PE + +F
Sbjct: 240 LTGGFGA-------DVVIDAV--GRPETYKQAF 263
>gnl|CDD|215417 PLN02781, PLN02781, Probable caffeoyl-CoA O-methyltransferase.
Length = 234
Score = 28.6 bits (64), Expect = 4.0
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 213 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
++ +IDID + GV HKI FIQ D
Sbjct: 95 RITAIDIDKEAYEVGLEFIKKAGVDHKINFIQSD 128
>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl
alcohol dehydrogenase is similar to liver alcohol
dehydrogenase, but has some amino acid substitutions
near the active site, which may determine the enzyme's
specificity of oxidizing aromatic substrates. Also
known as aryl-alcohol dehydrogenases, they catalyze the
conversion of an aromatic alcohol + NAD+ to an aromatic
aldehyde + NADH + H+. 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 = 365
Score = 29.0 bits (66), Expect = 4.1
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 13/51 (25%)
Query: 186 RCKASD-VVIDGFCGCGGNTIQFAAV-------CQKVISIDIDPAKLRLAQ 228
+ + + + F G G + AAV C +I++DI ++L LA+
Sbjct: 183 KPRPGSSIAV--F-GAGA--VGLAAVMAAKIAGCTTIIAVDIVDSRLELAK 228
>gnl|CDD|233025 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
RsmB. This protein is also known as sun protein. The
reading frame was originally interpreted as two reading
frames, fmu and fmv. The recombinant protein from E.
coli was shown to methylate only C967 of small subunit
(16S) ribosomal RNA and to produce only m5C at that
position. The seed alignment is built from bacterial
sequences only. Eukaryotic homologs include Nop2, a
protein required for processing pre-rRNA, that is likely
also a rRNA methyltransferase, although the fine
specificity may differ. Cutoff scores are set to avoid
treating archaeal and eukaroytic homologs automatically
as functionally equivalent, although they may have very
similar roles [Protein synthesis, tRNA and rRNA base
modification].
Length = 426
Score = 28.7 bits (64), Expect = 4.4
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 7/83 (8%)
Query: 169 DGWYSVTPEK---VAQHIASRCKASDVVIDGFCGCGGNTIQFAAVCQK--VISIDIDPAK 223
+GW +V VA +A + + ++D GG T + + V+++DI +
Sbjct: 217 EGWVTVQDASAQWVATWLAP--QNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHR 274
Query: 224 LRLAQHNASVYGVSHKIQFIQGD 246
L+ N G++ K + GD
Sbjct: 275 LKRVYENLKRLGLTIKAETKDGD 297
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
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 have 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 = 367
Score = 28.9 bits (65), Expect = 4.4
Identities = 22/103 (21%), Positives = 37/103 (35%), Gaps = 6/103 (5%)
Query: 146 YSVTPEKVAQHIASRCKASDVVIDGWYSVTPEKVAQHIASRCKASDVVIDGFCGCGGNTI 205
Y+V P + ++ + G T +H A V + G G G + I
Sbjct: 145 YAVVPATALAPLPESLDYTESAVLGCAGFTAYGALKHAADVRPGETVAVIGVGGVGSSAI 204
Query: 206 QFAAV--CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 246
Q A +I++D+ KL A G +H + + D
Sbjct: 205 QLAKAFGASPIIAVDVRDEKLA----KAKELGATHTVNAAKED 243
>gnl|CDD|163691 cd08060, MPN_UPF0172, Mov34/MPN/PAD-1 family: UPF0172 family of
unknown function includes neighbor of COX4 (Noc4p).
This family includes Noc4p (neighbor of COX4; neighbor
of Cytochrome c Oxidase 4; nucleolar complex associated
4 homolog) which belongs to the family of unknown
function, UPF0172, with MPN/JAMM-like domains. Proteins
in this family are homologs of the NOC4 gene which is
conserved in eukaryotic members including human, dog,
mouse, rat, chicken, zebrafish, fruit fly, mosquito,
S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa,
A.thaliana, and rice. NOC4 highly expressed in the
pancreas and moderately in liver, heart, lung, kidney,
brain, skeletal muscle, and placenta. This nucleolar
protein forms a complex with Nop14p that mediates
maturation and nuclear export of 40S ribosomal subunits.
This family of eukaryotic MPN-like domains lacks the key
residues that coordinate a metal ion and therefore does
not show catalytic isopeptidase activity.
Length = 182
Score = 28.0 bits (63), Expect = 4.6
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 12/53 (22%)
Query: 156 HIASRCKASDVVIDGWY-----------SVTPEKVAQHIASRCK-ASDVVIDG 196
+ + CK+S +VI G+Y S +K+A IA A +++D
Sbjct: 60 LVDAYCKSSGLVIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDN 112
>gnl|CDD|237291 PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed.
Length = 443
Score = 28.6 bits (65), Expect = 4.7
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 6/82 (7%)
Query: 188 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF 247
+ D V+D FCG G T+ A +V+ ++ A + A+ NA G+ + F +
Sbjct: 296 QPGDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARRNGL-DNVTFYHANL 354
Query: 248 FALAPS----LQG-DVVFLSPP 264
L G D V L PP
Sbjct: 355 EEDFTDQPWALGGFDKVLLDPP 376
>gnl|CDD|176182 cd05279, Zn_ADH1, Liver alcohol dehydrogenase and related
zinc-dependent alcohol dehydrogenases.
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. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48), 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. 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 an
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.
Length = 365
Score = 28.6 bits (64), Expect = 5.1
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 189 ASDVVIDGFCGCGGNTIQFAAVC--QKVISIDIDPAKLRLAQ 228
S + G G G + I ++I++DI+ K A+
Sbjct: 184 GSTCAVFGLGGVGLSVIMGCKAAGASRIIAVDINKDKFEKAK 225
>gnl|CDD|235675 PRK06025, PRK06025, acetyl-CoA acetyltransferase; Provisional.
Length = 417
Score = 28.6 bits (64), Expect = 5.1
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 188 KASDVVIDGFCGCGGNTIQFAA 209
KAS V +D FCG G ++ AA
Sbjct: 82 KASGVTLDRFCGGGITSVNLAA 103
>gnl|CDD|233115 TIGR00755, ksgA, dimethyladenosine transferase. In both E. coli
and Saccharomyces cerevisiae, this protein is
responsible for the dimethylation of two adjacent
adenosine residues in a conserved hairpin of 16S rRNA in
bacteria, 18S rRNA in eukaryotes. This adjacent
dimethylation is the only rRNA modification shared by
bacteria and eukaryotes. A single member of this family
is present in each of the first 20 completed microbial
genomes. This protein is essential in yeast, but not in
E. coli, where its deletion leads to resistance to the
antibiotic kasugamycin. Alternate name:
S-adenosylmethionine--6-N',N'-adenosyl (rRNA)
dimethyltransferase [Protein synthesis, tRNA and rRNA
base modification].
Length = 253
Score = 28.4 bits (64), Expect = 5.7
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 188 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF 247
DVV++ G G T +KV +I+ID RLA+ + + ++ I+GD
Sbjct: 28 LEGDVVLEIGPGLGALTEPLLKRAKKVTAIEIDR---RLAERLRKLLSLYENLEIIEGDA 84
>gnl|CDD|211976 TIGR04253, mesacon_CoA_iso, mesaconyl-CoA isomerase. Members of
this protein family belong by homology to the family of
CoA transferases. However, the characterized member from
Chloroflexus aurantiacus appears to perform an
intramolecular transfer, making it an isomerase. The
enzyme converts mesaconyl-C1-CoA to mesaconyl-C4-CoA as
part of the bicyclic 3-hydroxyproprionate pathway for
carbon fixation.
Length = 403
Score = 28.4 bits (63), Expect = 5.8
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 235 GVSHKIQFIQGDFFALAP-------SLQGDVVFLSPPWGGPEYARSSFSID 278
G+ H ++ ++G F AP L DV+ P GG +Y R ++D
Sbjct: 1 GILHGLRVVEGSAFVAAPLGGMTLAQLGADVIRFDPIGGGLDYKRWPLTLD 51
>gnl|CDD|181842 PRK09422, PRK09422, ethanol-active
dehydrogenase/acetaldehyde-active reductase;
Provisional.
Length = 338
Score = 28.5 bits (64), Expect = 5.9
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 192 VVIDGFCGCGGNTIQFA--AVCQKVISIDIDPAKLRLAQHN 230
+ I G G G +Q+A KVI++DI+ KL LA+
Sbjct: 166 IAIYGAGGLGNLALQYAKNVFNAKVIAVDINDDKLALAKEV 206
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 28.0 bits (63), Expect = 6.3
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 12/37 (32%)
Query: 213 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 249
K++++DI P K + F+QGD
Sbjct: 72 KIVAVDILPMKPI------------PGVIFLQGDITD 96
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 28.2 bits (64), Expect = 6.4
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 9/50 (18%)
Query: 188 KASDVVIDGFCGC---GGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNA 231
K D V+D C GG T A + + KV+++DI KL+L + NA
Sbjct: 249 KGGDTVLDA---CAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENA 295
>gnl|CDD|225729 COG3188, FimD, P pilus assembly protein, porin PapC [Cell motility
and secretion / Intracellular trafficking and
secretion].
Length = 835
Score = 28.4 bits (64), Expect = 6.5
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 11/64 (17%)
Query: 70 YQETLNTLPSEFGSQRKKKRRRKKRSFELNYQEDLGDLENVPEEIWANPYLNKYYQQRYL 129
+ L++ + S + RK+ F N + LG + + YL+ YQ
Sbjct: 471 LSDALDSR-DDDYSDYNDLQYRKRSRFSANISQSLGS-------GYGSLYLSGSYQD--- 519
Query: 130 YWSR 133
YW+
Sbjct: 520 YWNA 523
>gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.
Members identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the zinc
dependent/medium chain alcohol dehydrogenase family.
FDH converts formaldehyde and NAD(P) to formate and
NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. 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. 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 have 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.
Length = 368
Score = 28.0 bits (63), Expect = 7.2
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 188 KASDVVIDGFCGCGGNTIQFA--AVCQKVISIDIDPAKLRLAQH 229
S V + G G IQ A A ++I IDI+P K LA+
Sbjct: 186 PGSTVAVFGLGAVGLAVIQGAKAAGASRIIGIDINPDKFELAKK 229
>gnl|CDD|217008 pfam02384, N6_Mtase, N-6 DNA Methylase. Restriction-modification
(R-M) systems protect a bacterial cell against invasion
of foreign DNA by endonucleolytic cleavage of DNA that
lacks a site specific modification. The R-M system is a
complex containing three polypeptides: M (this family),
S (pfam01420), and R. This family consists of N-6
adenine-specific DNA methylase EC:2.1.1.72 from Type I
and Type IC restriction systems. These methylases have
the same sequence specificity as their corresponding
restriction enzymes.
Length = 312
Score = 28.0 bits (63), Expect = 8.2
Identities = 32/126 (25%), Positives = 52/126 (41%), Gaps = 15/126 (11%)
Query: 175 TPEKVAQHIASRCKASD--VVIDGFCGCGGNTIQFAAVCQKV------ISI---DIDPAK 223
TP +V++ I + + D CG GG IQ + ISI +++P
Sbjct: 30 TPREVSKLIVELLEPKPGESIYDPACGSGGFLIQADKFVKSHDGDTNDISIYGQELNPTT 89
Query: 224 LRLAQHNASVYGVSHKIQFIQGDFFALAP----SLQGDVVFLSPPWGGPEYARSSFSIDN 279
RLA+ N ++G+ + I+ L+P + DVV +PP+ A + D
Sbjct: 90 YRLARMNMILHGIEYNDFGIRHGDTLLSPKFEEDKKFDVVVANPPFNQKWDANDNLENDP 149
Query: 280 IFPEQG 285
F G
Sbjct: 150 RFRAYG 155
>gnl|CDD|177639 PHA03411, PHA03411, putative methyltransferase; Provisional.
Length = 279
Score = 27.8 bits (61), Expect = 8.4
Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 8/94 (8%)
Query: 175 TPEKVAQHIASRCKASDVVIDGFCGCGGNTIQFAAVC--QKVISIDIDPAKLRLAQHNAS 232
TPE +A + V+D G G + C +K++ ++++P R+ +
Sbjct: 50 TPEGLAWDFTIDAHCTGKVLDLCAGIGRLSFCMLHRCKPEKIVCVELNPEFARIGKR--- 106
Query: 233 VYGVSHKIQFIQGDFFALAPSLQGDVVFLSPPWG 266
+ + ++I D F + + DVV +PP+G
Sbjct: 107 ---LLPEAEWITSDVFEFESNEKFDVVISNPPFG 137
>gnl|CDD|234556 TIGR04345, ovoA_Cterm, putative 4-mercaptohistidine
N1-methyltranferase. Ovothiol A is
N1-methyl-4-mercaptohistidine. In the absence of
S-adenosylmethione, a methyl donor, the intermediate
produced is 4-mercaptohistidine. In both Erwinia
tasmaniensis and Trypanosoma cruzi, a protein occurs
with 5-histidylcysteine sulfoxide synthase activity, but
these two enzymes and most homologs share an additional
C-terminal methyltransferase domain. Thus OvoA may be a
bifunctional enzyme with 5-histidylcysteine sulfoxide
synthase and 4-mercaptohistidine N1-methyltranferase
activity. This model describes C-terminal putative
4-mercaptohistidine N1-methyltranferase domain
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Glutathione and analogs].
Length = 242
Score = 27.6 bits (62), Expect = 8.5
Identities = 25/116 (21%), Positives = 38/116 (32%), Gaps = 29/116 (25%)
Query: 176 PEKVAQHI--ASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQH---- 229
P K+A+ R K+ +D C G + + A +V ID +R A
Sbjct: 26 PVKLAELALAQFRNKSRKRALDIGCAVGRASFELARYFDEVDGIDFSARFIRPAVALKER 85
Query: 230 -------------------NASVYG---VSHKIQFIQGDFFALAPSLQG-DVVFLS 262
S G V ++ F QGD L P G D++ +
Sbjct: 86 GSLRYALKEEGELVSFKEVTLSDLGLDEVRDRVSFFQGDACNLKPHFTGYDLILAA 141
>gnl|CDD|225258 COG2384, COG2384, Predicted SAM-dependent methyltransferase
[General function prediction only].
Length = 226
Score = 27.6 bits (62), Expect = 8.6
Identities = 9/40 (22%), Positives = 15/40 (37%)
Query: 210 VCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 249
++ ++ P L A N +S +I GD A
Sbjct: 39 PASTAVAGEVVPGPLESAIRNVKKNNLSERIDVRLGDGLA 78
>gnl|CDD|218754 pfam05795, Plasmodium_Vir, Plasmodium vivax Vir protein. This
family consists of several Vir proteins specific to
Plasmodium vivax. The vir genes are present at about
600-1,000 copies per haploid genome and encode proteins
that are immunovariant in natural infections, indicating
that they may have a functional role in establishing
chronic infection through antigenic variation.
Length = 348
Score = 27.5 bits (61), Expect = 9.6
Identities = 11/44 (25%), Positives = 18/44 (40%)
Query: 81 FGSQRKKKRRRKKRSFELNYQEDLGDLENVPEEIWANPYLNKYY 124
GS +KK RKK+ N +E+ E + ++Y
Sbjct: 299 LGSWLRKKLGRKKKIMNNNNEEEYELELYAYESENPSLNSSRYN 342
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 0.136 0.408
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,827,762
Number of extensions: 1757819
Number of successful extensions: 1778
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1756
Number of HSP's successfully gapped: 121
Length of query: 342
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 244
Effective length of database: 6,590,910
Effective search space: 1608182040
Effective search space used: 1608182040
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 (21.8 bits)
S2: 59 (26.3 bits)