RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13204
(189 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 (371), Expect = 3e-45
Identities = 62/129 (48%), Positives = 81/129 (62%), Gaps = 7/129 (5%)
Query: 66 VVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 125
+++D FCG GGNTIQFA V VI IDI+P L AQHNA VYGVS +I FI GD+F L
Sbjct: 3 IILDVFCGAGGNTIQFANVFCSVIGIDINPEHLACAQHNAEVYGVSDRIWFILGDWFELL 62
Query: 126 PSLQG-----DVVFLSPPWGGPEYARSS-FSIDNIFPEQGGGRRLFQVARGISPNVGYYL 179
L+ D VFLSPPWGGP Y R + + ++ + G +L + + IS N+ +L
Sbjct: 63 AKLKFGKIPYDCVFLSPPWGGPSYKRQNVYDLEKKL-KPYGLYQLLKESTEISKNIILFL 121
Query: 180 PRTSDVFEL 188
PR SD+ +L
Sbjct: 122 PRNSDLNQL 130
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 56.3 bits (136), Expect = 9e-11
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 64 SDVVIDGFCGCGGNTIQFAAVCQK--VISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF 121
D V+D G G + A V+ +++DP LA+ ++ G++ +++ + GD
Sbjct: 1 GDRVLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAALARRRLALAGLAPRVRVVVGDA 60
Query: 122 FALAPSLQG--DVVFLSPPWG 140
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 = 8e-10
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 59 SRCKASDVVIDGFCGCGGNTIQFAAVCQKVISI---DIDPAKLRLAQHNASVYGVSHKIQ 115
+ K D ++D CG G I+ A + + + DID ++ A+ NA GV KI+
Sbjct: 24 AGWKPGDPLLDPMCGSGTILIEAALMGANIAPLYGSDIDWRMVQGARINAENAGVGDKIE 83
Query: 116 FIQGDFFAL-APSLQGDVVFLSPPWG 140
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 = 48.6 bits (116), Expect = 6e-08
Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 5/102 (4%)
Query: 67 VIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 125
V+D CG G + A +V +DI P L LA+ A ++ ++ ++GD L
Sbjct: 2 VLDLGCGTGALALALASGPGARVTGVDISPVALELARKAA-AALLADNVEVLKGDAEELP 60
Query: 126 PSLQG--DVVFLSPPWGGPEYARSSFSIDNIFPEQGGGRRLF 165
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 = 46.9 bits (112), Expect = 2e-07
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 72 CGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQ 129
CG G I+ A + +V +D+ P L LA+ NA + +I F+QGD L+
Sbjct: 10 CGTGSLAIELARLFPGARVTGVDLSPEMLELARENAK-LALGPRITFVQGDAPDALDLLE 68
Query: 130 G-DVVFLS 136
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 = 49.2 bits (118), Expect = 3e-07
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 65 DVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 124
+ V+D +CG G + A +KV ++I P + AQ NA+ G+ ++FI GD
Sbjct: 295 ERVLDLYCGVGTFGLPLAKRVKKVHGVEISPEAVEAAQENAAANGID-NVEFIAGDAEEF 353
Query: 125 APSLQG----DVVFLSPP 138
P+ DVV + PP
Sbjct: 354 TPAWWEGYKPDVVVVDPP 371
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 48.1 bits (115), Expect = 6e-07
Identities = 27/101 (26%), Positives = 45/101 (44%), Gaps = 13/101 (12%)
Query: 63 ASDVVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLAQHNASVYGVS-HKIQFIQG 119
A V++ F GG ++ AA+ +V S+D+ L A+ NA + G+ + +FI G
Sbjct: 217 AGKRVLNLFSYTGGFSV-HAALGGASEVTSVDLSKRALEWARENAELNGLDGDRHRFIVG 275
Query: 120 DFFALAPSLQG-----DVVFLSPPWGGPEYARSSFSIDNIF 155
D F + D++ L P P +ARS +
Sbjct: 276 DVFKWLRKAERRGEKFDLIILDP----PSFARSKKQEFSAQ 312
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 47.3 bits (113), Expect = 1e-06
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 4/89 (4%)
Query: 53 VAQHIASRCKASDVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGV 110
V +A + ++D G G I A +VI++DI P L LA+ NA G+
Sbjct: 100 VEAALALLLQLDKRILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARENAERNGL 159
Query: 111 SHKIQFIQGDFFALAPSLQGDVVFLSPPW 139
++ +Q D F + D++ +PP+
Sbjct: 160 -VRVLVVQSDLFE-PLRGKFDLIVSNPPY 186
>gnl|CDD|223194 COG0116, COG0116, Predicted N6-adenine-specific DNA methylase [DNA
replication, recombination, and repair].
Length = 381
Score = 46.9 bits (112), Expect = 2e-06
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 85 CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSL-QGDVVFLSPPWG 140
+ DIDP + A+ NA GV I+F Q D L L + VV +PP+G
Sbjct: 254 LPIIYGSDIDPRHIEGAKANARAAGVGDLIEFKQADATDLKEPLEEYGVVISNPPYG 310
>gnl|CDD|225318 COG2520, COG2520, Predicted methyltransferase [General function
prediction only].
Length = 341
Score = 46.6 bits (111), Expect = 2e-06
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 2/90 (2%)
Query: 57 IASRCKASDVVIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQ 115
+A K + V+D F G G +I A KV +IDI+P + + N + V +++
Sbjct: 182 VAELVKEGETVLDMFAGVGPFSIPIAKKGRPKVYAIDINPDAVEYLKENIRLNKVEGRVE 241
Query: 116 FIQGDFFALAP-SLQGDVVFLSPPWGGPEY 144
I GD +AP D + + P E+
Sbjct: 242 PILGDAREVAPELGVADRIIMGLPKSAHEF 271
>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 = 45.8 bits (109), Expect = 3e-06
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 67 VIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 124
++D G G + A +VI++DI P L +A+ NA + H+++FIQ + F
Sbjct: 118 ILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAEENAEKNQLEHRVEFIQSNLFEP 177
Query: 125 APSLQGDVVFLSPPW 139
+ D++ +PP+
Sbjct: 178 LAGQKIDIIVSNPPY 192
>gnl|CDD|237872 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 43.7 bits (104), Expect = 9e-06
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 62 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSH-KIQFIQGD 120
K D V++ G G I A +KV+ +DI+P + A+ NA + + + ++ I+ D
Sbjct: 22 KKGDRVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNNGVEVIRSD 81
Query: 121 FFALAPSLQGDVVFLSPP 138
F + DV+ +PP
Sbjct: 82 LFEPFRGDKFDVILFNPP 99
>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 = 44.0 bits (105), Expect = 1e-05
Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 87 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLSPP 138
+V ++DI P L +A+ NA+ G+ ++F+Q D+F P + D++ +PP
Sbjct: 113 RVTAVDISPEALAVARKNAARLGLD-NVEFLQSDWFEPLPGGKFDLIVSNPP 163
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 43.0 bits (102), Expect = 2e-05
Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 25/102 (24%)
Query: 65 DVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFF 122
D + D G G TI++A +VI+I+ D L L + NA+ +GV + ++ ++GD
Sbjct: 36 DRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELIERNAARFGVDN-LEVVEGD-- 92
Query: 123 ALAPSLQGDVVFLSPPWGGPEYARSSFSIDNIFPEQGGGRRL 164
PE S D IF GGG +
Sbjct: 93 ------------------APEALPDLPSPDAIF--IGGGGNI 114
>gnl|CDD|236467 PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 275
Score = 42.5 bits (101), Expect = 4e-05
Identities = 19/53 (35%), Positives = 35/53 (66%), Gaps = 3/53 (5%)
Query: 87 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLS-PP 138
+V ++DI P L +A+ NA +G+ +++F+QGD+F P + D++ +S PP
Sbjct: 134 EVTAVDISPEALAVARRNA-KHGLGARVEFLQGDWFEPLPGGRFDLI-VSNPP 184
>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 = 42.1 bits (99), Expect = 6e-05
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 65 DVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 124
++V+D +CG G T+ A + V+ I++ P + AQ NA + G+++ ++F+ G +
Sbjct: 294 ELVVDAYCGVGTFTLPLAKQAKSVVGIEVVPESVEKAQQNAELNGIAN-VEFLAGTLETV 352
Query: 125 APSL-----QGDVVFLSPPWGG 141
P DV+ L PP G
Sbjct: 353 LPKQPWAGQIPDVLLLDPPRKG 374
>gnl|CDD|222287 pfam13649, Methyltransf_25, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 97
Score = 39.3 bits (92), Expect = 1e-04
Identities = 25/106 (23%), Positives = 38/106 (35%), Gaps = 15/106 (14%)
Query: 67 VIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 125
++D CG G A A V +DI L LA+ G K++F+ D L
Sbjct: 1 ILDLGCGTGRVLRALARAGPSSVTGVDISKEALELAKERLRDKG--PKVRFVVADARDL- 57
Query: 126 PSLQG--DVVFLSPPWGGPEYARSSFSIDNIFPEQGGGRRLFQVAR 169
P +G D+V G S + + R ++ R
Sbjct: 58 PFEEGSFDLVIC---AGLSLDYLSPKQLRALL------REAARLLR 94
>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 = 40.8 bits (96), Expect = 1e-04
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 4/85 (4%)
Query: 57 IASRCKASDVVIDGFCGCGGNTIQFAAVCQK---VISIDIDPAKLRLAQHNASVYGVSHK 113
IA K +VV+D F G G +I A K V +++++P ++ + N + V
Sbjct: 94 IAKLVKEGEVVVDMFAGIGPFSIP-IAKHSKAKRVYAVELNPEAVKYLKENIKLNKVEGV 152
Query: 114 IQFIQGDFFALAPSLQGDVVFLSPP 138
I I GD + D V ++ P
Sbjct: 153 ISPILGDVRDVILEGVADRVIMNLP 177
>gnl|CDD|240367 PTZ00338, PTZ00338, dimethyladenosine transferase-like protein;
Provisional.
Length = 294
Score = 40.0 bits (94), Expect = 3e-04
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 53 VAQHI--ASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGV 110
V I + K +D V++ G G T + + +KVI+I+IDP + + +
Sbjct: 24 VLDKIVEKAAIKPTDTVLEIGPGTGNLTEKLLQLAKKVIAIEIDPRMVAELKKRFQNSPL 83
Query: 111 SHKIQFIQGDF 121
+ 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 = 4e-04
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 92 DIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGD---VVFLSPPWG 140
DIDP ++ A+ NA GV+ I F D L L +V +PP+G
Sbjct: 263 DIDPRVIQAARKNARRAGVAELITFEVKDVADLKNPLPKGPTGLVISNPPYG 314
>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 = 39.8 bits (94), Expect = 4e-04
Identities = 25/93 (26%), Positives = 37/93 (39%), Gaps = 19/93 (20%)
Query: 66 VVIDGFCGCGG---NTIQFAAVC--QKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
VI GCGG N IQ A + ++I++D P KL LA+ +G +H + + D
Sbjct: 187 AVI----GCGGVGLNAIQGARIAGASRIIAVDPVPEKLELAR----RFGATHTVNASEDD 238
Query: 121 FFALAPSLQG----DVVFLSPPWGGPEYARSSF 149
L D F + G R +
Sbjct: 239 AVEAVRDLTDGRGADYAFEAV--GRAATIRQAL 269
>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 = 39.1 bits (91), Expect = 4e-04
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 65 DVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 124
D V++ G G I+ + +++ DI+P ++ + NA + V + + D L
Sbjct: 21 DDVLEIGAGTGLVAIRLKGKGKCILTTDINPFAVKELRENAKLNNVG--LDVVMTD---L 75
Query: 125 APSLQG--DVVFLSPPW 139
++G DV+ +PP+
Sbjct: 76 FKGVRGKFDVILFNPPY 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 = 39.0 bits (91), Expect = 5e-04
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 67 VIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 124
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 = 38.2 bits (89), Expect = 7e-04
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 62 KASDVVIDGFCGCGGNTIQFAA-VCQ--KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 118
K+ V+D CG G T A + +V+ IDI + A+ NA G ++FIQ
Sbjct: 2 KSGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKLGYE-NVEFIQ 60
Query: 119 GDFFAL 124
GD L
Sbjct: 61 GDIEEL 66
>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 = 0.001
Identities = 28/83 (33%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 59 SRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 118
+R D V+D FCG GG I+ + KVI DID + A+ N YG+ +
Sbjct: 178 ARVTEGDRVLDPFCGTGGFLIEAGLMGAKVIGCDIDWKMVAGARINLEHYGIE-DFFVKR 236
Query: 119 GDFFALA-PSLQGDVVFLSPPWG 140
GD L S D + PP+G
Sbjct: 237 GDATKLPLSSESVDAIATDPPYG 259
>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 = 38.3 bits (90), Expect = 0.001
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 87 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLSPP 138
+V ++DI P L +A+ N +G+ ++ IQ D FA P + D++ +PP
Sbjct: 147 EVDAVDISPDALAVAEINIERHGLEDRVTLIQSDLFAALPGRKYDLIVSNPP 198
>gnl|CDD|234740 PRK00377, cbiT, cobalt-precorrin-6Y C(15)-methyltransferase;
Provisional.
Length = 198
Score = 37.5 bits (87), Expect = 0.002
Identities = 24/89 (26%), Positives = 46/89 (51%), Gaps = 8/89 (8%)
Query: 60 RCKASDVVIDGFCGCGGNTIQFAAVC---QKVISIDIDPAKLRLAQHNASVYGVSHKIQF 116
R + D+++D CG G T++ + + KV ++D D + L + NA +GV + I
Sbjct: 37 RLRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAEKFGVLNNIVL 96
Query: 117 IQGDFFALAPSL--QGDVVFLSPPWGGPE 143
I+G+ + ++ + D +F+ GG E
Sbjct: 97 IKGEAPEILFTINEKFDRIFIG---GGSE 122
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 36.9 bits (86), Expect = 0.003
Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 78 TIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
+ A ++ +I+ D + +A+ N + GV +I+ + G
Sbjct: 74 ALWMALALPDDGRLTTIERDEERAEIARENLAEAGVDDRIELLLGG 119
>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 = 37.1 bits (86), Expect = 0.003
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 65 DVVIDGFCGCGGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 118
VID GCG + AA+ KV+ IDIDP + A+ NA + VS ++Q
Sbjct: 161 KNVID--VGCGSGILSIAALKLGAAKVVGIDIDPLAVESARKNAELNQVSDRLQVKL 215
>gnl|CDD|223971 COG1041, COG1041, Predicted DNA modification methylase [DNA
replication, recombination, and repair].
Length = 347
Score = 37.0 bits (86), Expect = 0.004
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 59 SRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVS 111
+R K ++V+D FCG GG I+ + +VI DID +R A+ N YG+
Sbjct: 193 ARVKRGELVLDPFCGTGGILIEAGLMGARVIGSDIDERMVRGAKINLEYYGIE 245
>gnl|CDD|226608 COG4123, COG4123, Predicted O-methyltransferase [General function
prediction only].
Length = 248
Score = 36.5 bits (85), Expect = 0.004
Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 67 VIDGFCGCGGNTIQFAAVCQK--VISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 124
++D G G + A +K ++ ++I +AQ N ++ + +IQ I+ D
Sbjct: 48 ILDLGAGNGALGLLLAQRTEKAKIVGVEIQEEAAEMAQRNVALNPLEERIQVIEADIKEF 107
Query: 125 APSLQG---DVVFLSPP 138
+L D++ +PP
Sbjct: 108 LKALVFASFDLIICNPP 124
>gnl|CDD|223109 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation)
[Translation, ribosomal structure and biogenesis].
Length = 259
Score = 36.4 bits (85), Expect = 0.004
Identities = 22/92 (23%), Positives = 33/92 (35%), Gaps = 7/92 (7%)
Query: 51 EKVAQHI--ASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVY 108
+ V I A+ D V++ G G T +V +I+ID RLA+ +
Sbjct: 16 KNVIDKIVEAANISPGDNVLEIGPGLGALTEPLLERAARVTAIEIDR---RLAEVLKERF 72
Query: 109 GVSHKIQFIQGDF--FALAPSLQGDVVFLSPP 138
+ I GD F Q V + P
Sbjct: 73 APYDNLTVINGDALKFDFPSLAQPYKVVANLP 104
>gnl|CDD|182918 PRK11036, PRK11036, putative S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 255
Score = 36.5 bits (85), Expect = 0.004
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 67 VIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 118
V+D G G I+ A + +VI D+ ++ A+ A GVS +QFI
Sbjct: 48 VLDAGGGEGQTAIKLAELGHQVILCDLSAEMIQRAKQAAEAKGVSDNMQFIH 99
>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 = 36.5 bits (85), Expect = 0.004
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 66 VVIDGFCGCGGNTIQFAAVCQ-KVISIDIDPAKLRLA-QHNASVYGVSHKIQFIQGDFFA 123
V++ G G G N +Q A VI++DI KL LA + A V + + D A
Sbjct: 169 VLVIGLGGLGLNAVQIAKAMGAAVIAVDIKEEKLELAKELGAD--EVLNSLDDSPKDKKA 226
Query: 124 LAPSLQGDVVF 134
DV+F
Sbjct: 227 AGLGGGFDVIF 237
>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 = 36.7 bits (85), Expect = 0.004
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 69 DGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF--FALAP 126
D FCG GG + A ++ I+I+ + AQ +A + G+ + + F D FA A
Sbjct: 239 DLFCGVGGFGLHCAGPDTQLTGIEIESEAIACAQQSAQMLGLDN-LSFAALDSAKFATAQ 297
Query: 127 SLQGDVVFLSPP 138
++V ++PP
Sbjct: 298 MSAPELVLVNPP 309
>gnl|CDD|225172 COG2263, COG2263, Predicted RNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 198
Score = 36.1 bits (84), Expect = 0.005
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 66 VVIDGFCGCGGNTIQFAAV-CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL 124
V+D G G I A + +V+++DIDP L +A+ NA ++F+ D
Sbjct: 48 TVLDLGAGTGILAIGAALLGASRVLAVDIDPEALEIARANAEELLG--DVEFVVAD--VS 103
Query: 125 APSLQGDVVFLSPPWG 140
+ D V ++PP+G
Sbjct: 104 DFRGKFDTVIMNPPFG 119
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 36.2 bits (84), Expect = 0.006
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 9/85 (10%)
Query: 62 KASDVVIDGFC-GCGGNTIQFAAVCQ----KVISIDIDPAKLRLAQHNASVYGVSHKIQF 116
K + V+D C GG T A + + V+++D+ P +L+ + N GV + I
Sbjct: 155 KPGERVLD-LCAAPGGKTTHLAELMENEGAIVVAVDVSPKRLKRLRENLKRLGVRNVIVV 213
Query: 117 IQGDFFALAPSLQG---DVVFLSPP 138
+ G D + L P
Sbjct: 214 NKDARRLAELLPGGEKFDRILLDAP 238
>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 = 35.9 bits (83), Expect = 0.007
Identities = 26/85 (30%), Positives = 39/85 (45%), Gaps = 7/85 (8%)
Query: 54 AQHIASRCKASDVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVS 111
A +A + VV+D CG G AA ++ + DIDPA +R A+ N +
Sbjct: 77 AAALARPRSGTLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCARRNLA----D 132
Query: 112 HKIQFIQGDFF-ALAPSLQGDVVFL 135
+GD + AL +L+G V L
Sbjct: 133 AGGTVHEGDLYDALPTALRGRVDIL 157
>gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases.
Length = 169
Score = 35.2 bits (82), Expect = 0.008
Identities = 31/115 (26%), Positives = 47/115 (40%), Gaps = 16/115 (13%)
Query: 62 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF 121
+ D V++ G G T + ++V +I+IDP RLA + + + I GD
Sbjct: 12 RPGDTVLEIGPGKGALTEELLERAKRVTAIEIDP---RLAPRLREKFAAADNLTVIHGDA 68
Query: 122 --FALAPSLQGDVVFLSPPWGGPEYARSSFSIDNIFPEQGGGRR---LFQ--VAR 169
F L P LQ V + P Y S+ + + E R + Q VAR
Sbjct: 69 LKFDL-PKLQPYKVVGNLP-----YNISTPILFKLLEEPPAFRDAVLMVQKEVAR 117
>gnl|CDD|234958 PRK01544, PRK01544, bifunctional N5-glutamine
S-adenosyl-L-methionine-dependent methyltransferase/tRNA
(m7G46) methyltransferase; Reviewed.
Length = 506
Score = 35.6 bits (82), Expect = 0.009
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 73 GCGGNTIQFAAVCQ----KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSL 128
G G I + +C+ VI+ DI + +A+ NA Y V+ +IQ I ++F
Sbjct: 146 GTGSGCIAISLLCELPNANVIATDISLDAIEVAKSNAIKYEVTDRIQIIHSNWFENIEKQ 205
Query: 129 QGDVVFLSPPW 139
+ D + +PP+
Sbjct: 206 KFDFIVSNPPY 216
>gnl|CDD|236988 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 307
Score = 35.1 bits (82), Expect = 0.012
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 91 IDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLSPP 138
+DI P L +A+ N +G+ ++ I+ D FA P + D++ +PP
Sbjct: 163 VDISPDALAVAEINIERHGLEDRVTLIESDLFAALPGRRYDLIVSNPP 210
>gnl|CDD|223813 COG0742, COG0742, N6-adenine-specific methylase [DNA replication,
recombination, and repair].
Length = 187
Score = 34.9 bits (81), Expect = 0.013
Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 67 VIDGFCGCGGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 123
V+D F G G + A+ + +V+ ++ D +++ + N G+ + + ++ D
Sbjct: 47 VLDLFAGSGA--LGLEALSRGAARVVFVEKDRKAVKILKENLKALGLEGEARVLRNDALR 104
Query: 124 LAPSLQG----DVVFLSPP 138
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 = 0.014
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 14/55 (25%)
Query: 75 GGNTIQFAAVCQ------KVISIDIDPAKLRLAQHN---ASVYGVSHKIQFIQGD 120
GG+ + FA++ + KV+ IDID + +HN + ++ +I IQG
Sbjct: 44 GGSALFFASMLELLGSDGKVLGIDID-----IREHNRPAIEAHPMASRITLIQGS 93
>gnl|CDD|202698 pfam03602, Cons_hypoth95, Conserved hypothetical protein 95.
Length = 183
Score = 34.2 bits (79), Expect = 0.020
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 10/80 (12%)
Query: 67 VIDGFCGCGGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 123
V+D F G G ++ A+ + V+ ++ D + + N G+ + ++ D
Sbjct: 47 VLDLFAGSGALGLE--ALSRGAASVVFVEKDKKAVATLKENLEALGLEGETAVLRNDAAR 104
Query: 124 LAPSLQG-----DVVFLSPP 138
L G D+VFL PP
Sbjct: 105 ALLRLAGKGPPFDLVFLDPP 124
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 34.5 bits (80), Expect = 0.021
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 64 SDVVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLA 101
V + G G G IQ A ++I++DI+P KL LA
Sbjct: 187 DTVAVFGLGGVGLAAIQGAKAAGAGRIIAVDINPEKLELA 226
>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 = 0.021
Identities = 26/95 (27%), Positives = 38/95 (40%), Gaps = 7/95 (7%)
Query: 52 KVAQHIASRCKAS--DVVIDGFCGCGGNTIQFA-AVCQ--KVISIDIDPAKLRLAQHNAS 106
K A +I +R S V++ G G T A AV V + +I + A+ N S
Sbjct: 81 KDAGYIVARLGISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARENLS 140
Query: 107 VYGVSHKIQFIQGDFFALAPSLQGDVVFLS--PPW 139
+G+ ++ GD D VFL PW
Sbjct: 141 EFGLGDRVTLKLGDVREGIDEEDVDAVFLDLPDPW 175
>gnl|CDD|222236 pfam13578, Methyltransf_24, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 105
Score = 33.0 bits (76), Expect = 0.023
Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 72 CGCGGNTIQFAAVCQ-----KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAP 126
G +T+ A + ++ SID P A N G++ +++ ++GD
Sbjct: 5 VYSGVSTLWLAQALKDNGLGRLYSIDPWPG--AEAGANLRKAGLADRVRLLRGDSLEALA 62
Query: 127 SLQG---DVVFL 135
L D++F+
Sbjct: 63 RLPDGSIDLLFI 74
>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 = 34.1 bits (79), Expect = 0.025
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 10/77 (12%)
Query: 62 KASDVVIDGFCGCGGNTIQFAAV---CQKVISIDIDPAKLRLAQHNASVYGVSHKIQ-FI 117
K + V+D GCG + AA+ +KV+ +DIDP +R A+ NA + GV +++ ++
Sbjct: 159 KPGETVLD--VGCGSGILAIAALKLGAKKVVGVDIDPVAVRAAKENAELNGVEAQLEVYL 216
Query: 118 QGDFFALAPSLQGDVVF 134
GD P + DVV
Sbjct: 217 PGD----LPEGKADVVV 229
>gnl|CDD|215900 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.
Length = 254
Score = 34.2 bits (79), Expect = 0.026
Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 6/87 (6%)
Query: 51 EKVAQHIASRCKA--SDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVY 108
KV I + SD V++ G G T + A ++V++I+IDP + Q +++
Sbjct: 15 PKVINRIVDKANLQESDTVLEIGPGKGALTTELAKRAKQVVAIEIDPRLAKRLQEKLALH 74
Query: 109 GVSHKIQFIQGDFFALA-PSLQGDVVF 134
++ + DF + P +V
Sbjct: 75 ---PNVEVVHQDFLKFSFPKDDPFLVV 98
>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 = 33.1 bits (76), Expect = 0.029
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 60 RCKASDVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQHNASVYGVS 111
R + DV+ D G G TI+ A + +V +I+ +P L L + N +GVS
Sbjct: 16 RLRPGDVLWDIGAGTGSVTIEAARLVPNGRVYAIERNPEALDLIERNLRRFGVS 69
>gnl|CDD|237007 PRK11873, arsM, arsenite S-adenosylmethyltransferase; Reviewed.
Length = 272
Score = 33.0 bits (76), Expect = 0.064
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 62 KASDVVIDGFCGCGGNTIQFAAVCQ-----KVISIDIDPAKLRLAQHNASVYGVSHKIQF 116
K + V+D G GG F A + KVI +D+ P L A+ NA G ++ ++F
Sbjct: 76 KPGETVLD--LGSGGGFDCFLAARRVGPTGKVIGVDMTPEMLAKARANARKAGYTN-VEF 132
Query: 117 IQGD 120
G+
Sbjct: 133 RLGE 136
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 31.5 bits (72), Expect = 0.074
Identities = 19/67 (28%), Positives = 24/67 (35%), Gaps = 9/67 (13%)
Query: 72 CGCGGNTIQFAAVCQK-VISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFAL-APSLQ 129
CG G A V +D+ P L LA+ +F+ GD L P
Sbjct: 5 CGTGLLAEALARRGGARVTGVDLSPEMLALARKR-------APRKFVVGDAEDLPFPDES 57
Query: 130 GDVVFLS 136
DVV S
Sbjct: 58 FDVVVSS 64
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 32.4 bits (75), Expect = 0.083
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 11/77 (14%)
Query: 55 QHIASR---CKASDV-----VIDGFCGCGGNTIQFAAVCQK---VISIDIDPAKLRLAQH 103
H R K V V+D CG G I A K V+ +D L + +
Sbjct: 35 LHRVWRRKTIKWLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGRE 94
Query: 104 NASVYGVSHKIQFIQGD 120
G+S ++F+QGD
Sbjct: 95 KLRDLGLSGNVEFVQGD 111
>gnl|CDD|182371 PRK10309, PRK10309, galactitol-1-phosphate dehydrogenase;
Provisional.
Length = 347
Score = 32.5 bits (74), Expect = 0.093
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 54 AQHIASRCKASDVVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLAQ 102
A H+A C+ +V+I G G IQ A + V +IDI+ KL LA+
Sbjct: 152 AFHLAQGCEGKNVIIIGAGTIGLLAIQCAVALGAKSVTAIDINSEKLALAK 202
>gnl|CDD|218278 pfam04816, DUF633, Family of unknown function (DUF633). This
family of proteins are uncharacterized have no known
function.
Length = 204
Score = 32.3 bits (74), Expect = 0.099
Identities = 10/46 (21%), Positives = 20/46 (43%)
Query: 84 VCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQ 129
+ I+ +++ L A +N G++ +I GD A+ L
Sbjct: 20 LASFAIAGEVNKGPLESAVNNVKKNGLTERIDVRLGDGLAVLEELD 65
>gnl|CDD|225173 COG2264, PrmA, Ribosomal protein L11 methylase [Translation,
ribosomal structure and biogenesis].
Length = 300
Score = 32.3 bits (74), Expect = 0.11
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 67 VIDGFCGCGGNTIQFAAV---CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 123
V+D GCG + AA +KV+ +DIDP + A+ NA + GV +Q
Sbjct: 166 VLD--VGCGSGILAIAAAKLGAKKVVGVDIDPQAVEAARENARLNGVELLVQAKGFLLLE 223
Query: 124 LAPSLQGDVVF 134
+ + DV+
Sbjct: 224 VPENGPFDVIV 234
>gnl|CDD|185082 PRK15128, PRK15128, 23S rRNA m(5)C1962 methyltransferase;
Provisional.
Length = 396
Score = 32.1 bits (73), Expect = 0.14
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 85 CQKVISIDIDPAKLRLAQHNASVYGVS-HKIQFIQGDFFALAPSL--QG---DVVFLSPP 138
C +V+S+D L +A+ N + + K +F++ D F L + +G DV+ + PP
Sbjct: 243 CSQVVSVDTSQEALDIARQNVELNKLDLSKAEFVRDDVFKLLRTYRDRGEKFDVIVMDPP 302
>gnl|CDD|223348 COG0270, Dcm, Site-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 328
Score = 32.0 bits (73), Expect = 0.16
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 13/78 (16%)
Query: 67 VIDGFCGCGGNTIQFAAVCQKVI-SIDIDPAKLRLAQHNASVYGVSHK-IQFIQGDFFAL 124
VID F G GG ++ F +++ + +IDP + + N I GD L
Sbjct: 6 VIDLFAGIGGLSLGFEEAGFEIVFANEIDPPAVATYKAN-------FPHGDIILGDIKEL 58
Query: 125 APS----LQGDVVFLSPP 138
DV+ PP
Sbjct: 59 DGEALRKSDVDVLIGGPP 76
>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 = 31.8 bits (73), Expect = 0.17
Identities = 28/99 (28%), Positives = 35/99 (35%), Gaps = 20/99 (20%)
Query: 48 VTPEKVAQHIASR--CKASD--VVIDGFCGCGG---NTIQFA-AVCQKVISIDIDPAKLR 99
V P + H R A D +V+ G G IQ A A +VI +DID +L
Sbjct: 142 VEPLAIGAHAVRRAGVTAGDTVLVV----GAGPIGLGVIQVAKARGARVIVVDIDDERLE 197
Query: 100 LAQHNASVYGVSHKIQFIQGDFFALAPSLQG----DVVF 134
A+ G I D A L DVV
Sbjct: 198 FARE----LGADDTINVGDEDVAARLRELTDGEGADVVI 232
>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 = 31.9 bits (73), Expect = 0.18
Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 8/70 (11%)
Query: 67 VIDGFCGCGGNTIQF-AAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 125
ID F G GG + F A + V + +ID + Y + + GD ++
Sbjct: 1 FIDLFAGIGGIRLGFEQAGFKCVFASEIDK-------YAQKTYEANFGNKVPFGDITKIS 53
Query: 126 PSLQGDVVFL 135
PS D L
Sbjct: 54 PSDIPDFDIL 63
>gnl|CDD|181601 PRK08978, PRK08978, acetolactate synthase 2 catalytic subunit;
Reviewed.
Length = 548
Score = 31.8 bits (73), Expect = 0.19
Identities = 21/46 (45%), Positives = 25/46 (54%), Gaps = 15/46 (32%)
Query: 87 KVISIDIDPA---KLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQ 129
KVI +DIDPA KLR A V+ +QGD AL P+LQ
Sbjct: 289 KVIHLDIDPAEINKLRQAH-------VA-----LQGDLNALLPALQ 322
>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 = 31.8 bits (72), Expect = 0.20
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 66 VVIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRL 100
V++ G G GG +Q A A+ V++IDIDP KL +
Sbjct: 170 VIVIGAGGVGGYMVQTAKAMGAAVVAIDIDPEKLEM 205
>gnl|CDD|226413 COG3897, COG3897, Predicted methyltransferase [General function
prediction only].
Length = 218
Score = 31.2 bits (71), Expect = 0.24
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 79 IQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPS----LQGDVVF 134
A +V++ DIDP + + NA+ GVS I F D P+ L GD+ +
Sbjct: 96 AAARAGAAEVVAADIDPWLEQAIRLNAAANGVS--ILFTHADLIGSPPAFDLLLAGDLFY 153
>gnl|CDD|184931 PRK14967, PRK14967, putative methyltransferase; Provisional.
Length = 223
Score = 30.8 bits (70), Expect = 0.29
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 67 VIDGFCGCGGNTIQFAAV-CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALA 125
V+D G G + AA V ++DI +R A+ NA + G + +GD+
Sbjct: 40 VLDLCTGSGALAVAAAAAGAGSVTAVDISRRAVRSARLNALLAG--VDVDVRRGDWARAV 97
Query: 126 PSLQGDVVFLSPPW 139
DVV +PP+
Sbjct: 98 EFRPFDVVVSNPPY 111
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 31.2 bits (71), Expect = 0.29
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 87 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVFLSPPWGG 141
++ ++D P KL + +AS G++ I+ I+GD + +P Q D + L P G
Sbjct: 277 QITAVDRYPQKLEKIRSHASALGIT-IIETIEGDARSFSPEEQPDAILLDAPCTG 330
>gnl|CDD|129245 TIGR00139, h_aconitase, homoaconitase. Homoaconitase is known only
as a fungal enzyme from two species, where it is part of
an unusual lysine biosynthesis pathway. Because This
model is based on just two sequences from a narrow
taxonomic range, it may not recognize distant orthologs,
should any exist. Homoaconitase, aconitase, and
3-isopropylmalate dehydratase have similar overall
structures, but 3-isopropylmalate dehydratase is split
into large (leuC) and small (leuD) chains in eubacteria.
Several pairs of archaeal proteins resemble leuC and
leuD over their lengths but are even closer to the
respective domains of homoaconitase, and their identity
is uncertain [Amino acid biosynthesis, Aspartate
family].
Length = 712
Score = 31.2 bits (70), Expect = 0.32
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 18/79 (22%)
Query: 31 ELTLADADNDATESWY--------SVTPEKVAQ--------HIASRCKASDVVIDGF-CG 73
EL DADN T+ Y V EK+AQ ++ D+++ GF G
Sbjct: 534 ELVFCDADNINTDGIYPGKYTYQDDVPKEKMAQVCMENYDAEFRTKAHEGDILVSGFNFG 593
Query: 74 CGGNTIQFA-AVCQKVISI 91
CG + Q A A+ K I++
Sbjct: 594 CGSSREQAATAILAKGINL 612
>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 = 31.0 bits (71), Expect = 0.33
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 4/34 (11%)
Query: 73 GCGG---NTIQFA-AVCQKVISIDIDPAKLRLAQ 102
GCGG + + A A+ +VI++DID KL LA+
Sbjct: 173 GCGGVGLSAVMIASALGARVIAVDIDDDKLELAR 206
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 31.0 bits (71), Expect = 0.34
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 66 VVIDGFCGCGGNTIQFA-AVCQKVISIDIDPAKLRLAQ 102
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 = 30.5 bits (70), Expect = 0.37
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 85 CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
+KV+++DIDP + A+ NA + GV + QGD
Sbjct: 142 AKKVLAVDIDPQAVEAARENAELNGVELNVYLPQGD 177
>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 = 30.7 bits (70), Expect = 0.43
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 66 VVIDGFCGCGGNTIQFA-AVCQK-VISIDIDPAKLRLAQ 102
VVI G G G + A+ +I +DID AKL A+
Sbjct: 179 VVIIGAGGLGLMALALLKALGPANIIVVDIDEAKLEAAK 217
>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 = 30.6 bits (70), Expect = 0.43
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 59 SRCKASDVVIDGFCGCGGN----TIQFA-AVCQKVISIDIDPAKLRLA 101
+ K D V G GG +Q+A A+ +VI+ID+ KL LA
Sbjct: 161 AGLKPGDWV--VISGAGGGLGHLGVQYAKAMGLRVIAIDVGDEKLELA 206
>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 = 0.51
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 87 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
K+ + DIDP + GV+ KI F GD
Sbjct: 71 KITACDIDPEAYEIGLPFIQKAGVADKISFRLGD 104
>gnl|CDD|226562 COG4076, COG4076, Predicted RNA methylase [General function
prediction only].
Length = 252
Score = 29.9 bits (67), Expect = 0.75
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 57 IASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQF 116
IA A D D G G ++ A ++VI+I+ DP + RLA+ N V G + +
Sbjct: 28 IAEV--AEDTFADLGAGSGILSVVAAHAAERVIAIEKDPKRARLAEENLHVPGDVN-WEV 84
Query: 117 IQGD 120
+ GD
Sbjct: 85 VVGD 88
>gnl|CDD|237852 PRK14896, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Provisional.
Length = 258
Score = 29.5 bits (67), Expect = 0.81
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 65 DVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
D V++ G G T + A +KV +I++DP RLA+ + ++ I+GD
Sbjct: 31 DPVLEIGPGKGALTDELAKRAKKVYAIELDP---RLAEFLRDDEIAAGNVEIIEGD 83
>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 = 29.8 bits (67), Expect = 0.89
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 62 KASDVVIDGFCGCGGNTIQFA--AVCQKVISIDIDPAKLRLAQ 102
+ V + G G G + IQ A A ++I+IDI+PAK LA+
Sbjct: 185 EGDTVAVFGLGGIGLSVIQGARMAKASRIIAIDINPAKFELAK 227
>gnl|CDD|236059 PRK07580, PRK07580, Mg-protoporphyrin IX methyl transferase;
Validated.
Length = 230
Score = 29.4 bits (67), Expect = 0.94
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 67 VIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
++D CG G +I A KV++ DI P + A+ A G++ I F GD
Sbjct: 67 ILDAGCGVGSLSIPLARRGAKVVASDISPQMVEEARERAPEAGLAGNITFEVGD 120
>gnl|CDD|181354 PRK08287, PRK08287, cobalt-precorrin-6Y C(15)-methyltransferase;
Validated.
Length = 187
Score = 28.8 bits (65), Expect = 1.1
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 14/76 (18%)
Query: 67 VIDGFCGCGGNTIQFAAVCQ----KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFF 122
+ID G G +I+ A Q +V +I+ +P LRL + N +G I I G
Sbjct: 35 LIDVGAGTGSVSIE--AALQFPSLQVTAIERNPDALRLIKENRQRFGC-GNIDIIPG--- 88
Query: 123 ALAP---SLQGDVVFL 135
AP + D +F+
Sbjct: 89 -EAPIELPGKADAIFI 103
>gnl|CDD|215417 PLN02781, PLN02781, Probable caffeoyl-CoA O-methyltransferase.
Length = 234
Score = 29.0 bits (65), Expect = 1.2
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 87 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
++ +IDID + GV HKI FIQ D
Sbjct: 95 RITAIDIDKEAYEVGLEFIKKAGVDHKINFIQSD 128
>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 = 29.1 bits (66), Expect = 1.3
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 8/55 (14%)
Query: 67 VIDGFCGCGGNTIQFAAVCQKVI-SIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
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 = 29.4 bits (66), Expect = 1.4
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 76 GNTIQFAAVCQKVISIDIDPAKL 98
GN FA+ +K+I IDIDP+ +
Sbjct: 304 GNPAHFASRPRKIIHIDIDPSSI 326
>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 = 28.8 bits (65), Expect = 1.4
Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 9/59 (15%)
Query: 78 TIQFAAV--CQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFALAPSLQGDVVF 134
Q A ++V+ +D D A+ LA+ V+ G A DVV
Sbjct: 113 AAQLAKAAGAREVVGVDPDAARRELAEALGPADPVAADTADEIGGRGA-------DVVI 164
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 29.0 bits (66), Expect = 1.4
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 9/50 (18%)
Query: 62 KASDVVIDGFCGC---GGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNA 105
K D V+D C GG T A + + KV+++DI KL+L + NA
Sbjct: 249 KGGDTVLDA---CAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENA 295
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 28.3 bits (64), Expect = 1.8
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 12/37 (32%)
Query: 87 KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 123
K++++DI P K + F+QGD
Sbjct: 72 KIVAVDILPMKPI------------PGVIFLQGDITD 96
>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 = 1.9
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 62 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF 121
DVV++ G G T +KV +I+ID RLA+ + + ++ I+GD
Sbjct: 28 LEGDVVLEIGPGLGALTEPLLKRAKKVTAIEIDR---RLAERLRKLLSLYENLEIIEGDA 84
>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 = 28.7 bits (65), Expect = 2.0
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 12/57 (21%)
Query: 54 AQHIASRCKASDVVIDGFCGCGGNTI-----QFAAV--CQKVISIDIDPAKLRLAQH 103
A +A VV+ G G TI Q+ + ++VI++DID KL +A+
Sbjct: 151 AVRLAGITLGDTVVV---IGAG--TIGLLAIQWLKILGAKRVIAVDIDDEKLAVARE 202
>gnl|CDD|225258 COG2384, COG2384, Predicted SAM-dependent methyltransferase
[General function prediction only].
Length = 226
Score = 28.4 bits (64), Expect = 2.1
Identities = 9/40 (22%), Positives = 15/40 (37%)
Query: 84 VCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDFFA 123
++ ++ P L A N +S +I GD A
Sbjct: 39 PASTAVAGEVVPGPLESAIRNVKKNNLSERIDVRLGDGLA 78
>gnl|CDD|215721 pfam00107, ADH_zinc_N, Zinc-binding dehydrogenase.
Length = 131
Score = 27.7 bits (62), Expect = 2.2
Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 4/63 (6%)
Query: 75 GGNTIQFAAV--CQKVISIDIDPAKLRLA-QHNASVYGVSHKIQFIQGDFFALAPSLQGD 131
G +Q A +VI++D KL LA + A F++ L D
Sbjct: 3 GLAAVQLAKALGAARVIAVDRSEEKLELAKELGADHVINYRDEDFVE-RVRELTGGRGVD 61
Query: 132 VVF 134
VV
Sbjct: 62 VVI 64
>gnl|CDD|237291 PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed.
Length = 443
Score = 28.6 bits (65), Expect = 2.2
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 6/82 (7%)
Query: 62 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGDF 121
+ D V+D FCG G T+ A +V+ ++ A + A+ NA G+ + F +
Sbjct: 296 QPGDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARRNGL-DNVTFYHANL 354
Query: 122 FALAPS----LQG-DVVFLSPP 138
L G D V L PP
Sbjct: 355 EEDFTDQPWALGGFDKVLLDPP 376
>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 = 28.4 bits (64), Expect = 2.2
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 65 DVVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLAQHNASVYGVSHKI 114
VV+ G G G N +Q AAV +KVI++D K A +G +H
Sbjct: 188 TVVVMGIGGVGINAVQGAAVAGARKVIAVDPVEFKREQALK----FGATHAF 235
>gnl|CDD|177639 PHA03411, PHA03411, putative methyltransferase; Provisional.
Length = 279
Score = 28.1 bits (62), Expect = 2.3
Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 8/94 (8%)
Query: 49 TPEKVAQHIASRCKASDVVIDGFCGCGGNTIQFAAVC--QKVISIDIDPAKLRLAQHNAS 106
TPE +A + V+D G G + C +K++ ++++P R+ +
Sbjct: 50 TPEGLAWDFTIDAHCTGKVLDLCAGIGRLSFCMLHRCKPEKIVCVELNPEFARIGKR--- 106
Query: 107 VYGVSHKIQFIQGDFFALAPSLQGDVVFLSPPWG 140
+ + ++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 = 28.0 bits (63), Expect = 2.8
Identities = 25/116 (21%), Positives = 38/116 (32%), Gaps = 29/116 (25%)
Query: 50 PEKVAQHI--ASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQH---- 103
P K+A+ R K+ +D C G + + A +V ID +R A
Sbjct: 26 PVKLAELALAQFRNKSRKRALDIGCAVGRASFELARYFDEVDGIDFSARFIRPAVALKER 85
Query: 104 -------------------NASVYG---VSHKIQFIQGDFFALAPSLQG-DVVFLS 136
S G V ++ F QGD L P G D++ +
Sbjct: 86 GSLRYALKEEGELVSFKEVTLSDLGLDEVRDRVSFFQGDACNLKPHFTGYDLILAA 141
>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 = 28.1 bits (63), Expect = 3.0
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 42 TESWYSVTPEKVAQHIASRCKASDVVIDG 70
E W +++A+++ +C AS +ID
Sbjct: 91 VEGWLE--LKQLAEYLKKKCGASVEIIDV 117
>gnl|CDD|235675 PRK06025, PRK06025, acetyl-CoA acetyltransferase; Provisional.
Length = 417
Score = 28.2 bits (63), Expect = 3.1
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 62 KASDVVIDGFCGCGGNTIQFAA 83
KAS V +D FCG G ++ AA
Sbjct: 82 KASGVTLDRFCGGGITSVNLAA 103
>gnl|CDD|225319 COG2521, COG2521, Predicted archaeal methyltransferase [General
function prediction only].
Length = 287
Score = 27.8 bits (62), Expect = 3.2
Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 5/84 (5%)
Query: 60 RCKASDVVIDGFCGCGGNTIQ-FAAVCQKVISIDIDPAKLRLAQHNASVYGV-SHKIQFI 117
+ K + V+D G G I+ VI+++ DP L LA+ N + I+ I
Sbjct: 131 KVKRGERVLDTCTGLGYTAIEALERGAIHVITVEKDPNVLELAKLNPWSRELFEIAIKII 190
Query: 118 QGDFFALAPSLQG---DVVFLSPP 138
GD + + D + PP
Sbjct: 191 LGDAYEVVKDFDDESFDAIIHDPP 214
>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 = 3.2
Identities = 32/126 (25%), Positives = 52/126 (41%), Gaps = 15/126 (11%)
Query: 49 TPEKVAQHIASRCKASD--VVIDGFCGCGGNTIQFAAVCQKV------ISI---DIDPAK 97
TP +V++ I + + D CG GG IQ + ISI +++P
Sbjct: 30 TPREVSKLIVELLEPKPGESIYDPACGSGGFLIQADKFVKSHDGDTNDISIYGQELNPTT 89
Query: 98 LRLAQHNASVYGVSHKIQFIQGDFFALAP----SLQGDVVFLSPPWGGPEYARSSFSIDN 153
RLA+ N ++G+ + I+ L+P + DVV +PP+ A + D
Sbjct: 90 YRLARMNMILHGIEYNDFGIRHGDTLLSPKFEEDKKFDVVVANPPFNQKWDANDNLENDP 149
Query: 154 IFPEQG 159
F G
Sbjct: 150 RFRAYG 155
>gnl|CDD|181842 PRK09422, PRK09422, ethanol-active
dehydrogenase/acetaldehyde-active reductase;
Provisional.
Length = 338
Score = 28.1 bits (63), Expect = 3.3
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 66 VVIDGFCGCGGNTIQFA--AVCQKVISIDIDPAKLRLAQHN 104
+ I G G G +Q+A KVI++DI+ KL LA+
Sbjct: 166 IAIYGAGGLGNLALQYAKNVFNAKVIAVDINDDKLALAKEV 206
>gnl|CDD|215522 PLN02968, PLN02968, Probable N-acetyl-gamma-glutamyl-phosphate
reductase.
Length = 381
Score = 27.9 bits (62), Expect = 3.6
Identities = 36/139 (25%), Positives = 48/139 (34%), Gaps = 34/139 (24%)
Query: 25 TGLE---------YFELTLADADNDATESWYSVTPEKVAQHIASRCKASDVVIDG----F 71
TG E FE+T+ AD A +S+ SV P + Q + + D F
Sbjct: 50 TGAEVRRLLANHPDFEITVMTADRKAGQSFGSVFPHLITQDLPNLVAVKDADFSDVDAVF 109
Query: 72 CGC--GGNTIQFAAVCQKVISIDIDPAKLRLAQHN--ASVYGVSHKIQFIQGDFFALAPS 127
C C G T + K + I A RL YG H+ AP
Sbjct: 110 C-CLPHGTTQEIIKALPKDLKIVDLSADFRLRDIAEYEEWYGHPHR-----------APE 157
Query: 128 LQGDVVFLSPPWGGPEYAR 146
LQ + V+ G E R
Sbjct: 158 LQKEAVY-----GLTELQR 171
>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 = 28.0 bits (62), Expect = 3.6
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 109 GVSHKIQFIQGDFFALAP-------SLQGDVVFLSPPWGGPEYARSSFSID 152
G+ H ++ ++G F AP L DV+ P GG +Y R ++D
Sbjct: 1 GILHGLRVVEGSAFVAAPLGGMTLAQLGADVIRFDPIGGGLDYKRWPLTLD 51
>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 = 27.8 bits (62), Expect = 3.6
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 63 ASDVVIDGFCGCGGNTIQFAAVC--QKVISIDIDPAKLRLAQ 102
S + G G G + I ++I++DI+ K A+
Sbjct: 184 GSTCAVFGLGGVGLSVIMGCKAAGASRIIAVDINKDKFEKAK 225
>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 = 27.6 bits (62), Expect = 3.8
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 62 KASDVVIDGFCGCGGNTIQFA--AVCQKVISIDIDPAKLRLAQH 103
S V + G G IQ A A ++I IDI+P K LA+
Sbjct: 186 PGSTVAVFGLGAVGLAVIQGAKAAGASRIIGIDINPDKFELAKK 229
>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 = 27.5 bits (61), Expect = 4.4
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 9/67 (13%)
Query: 66 VVIDGFCGCGGNTIQFAAV--CQKVISIDIDPAKLRLAQH-------NASVYGVSHKIQF 116
V + G G G I AA+ K+I++DID KL A+ N+S I+
Sbjct: 180 VAVIGCGGVGDAAIAGAALAGASKIIAVDIDDRKLEWAREFGATHTVNSSGTDPVEAIRA 239
Query: 117 IQGDFFA 123
+ G F A
Sbjct: 240 LTGGFGA 246
>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 = 27.5 bits (62), Expect = 4.9
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 9/37 (24%)
Query: 73 GCGGNTIQFAAV-------CQKVISIDIDPAKLRLAQ 102
G G + AAV C +I++DI ++L LA+
Sbjct: 194 GAGA--VGLAAVMAAKIAGCTTIIAVDIVDSRLELAK 228
>gnl|CDD|183921 PRK13255, PRK13255, thiopurine S-methyltransferase; Reviewed.
Length = 218
Score = 27.1 bits (61), Expect = 5.0
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 114 IQFIQGDFFALAPSLQGDV 132
I GDFFAL + DV
Sbjct: 99 ITIYCGDFFALTAADLADV 117
>gnl|CDD|235766 PRK06276, PRK06276, acetolactate synthase catalytic subunit;
Reviewed.
Length = 586
Score = 27.4 bits (61), Expect = 5.0
Identities = 21/53 (39%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 46 YSVTPEKVAQHIASRCKASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKL 98
YSVT V IA C+ SD G+ FA K+I IDIDPA++
Sbjct: 265 YSVTESDVL--IAIGCRFSDRTT-------GDISSFAPNA-KIIHIDIDPAEI 307
>gnl|CDD|216568 pfam01555, N6_N4_Mtase, DNA methylase. Members of this family are
DNA methylases. The family contains both N-4
cytosine-specific DNA methylases and N-6
Adenine-specific DNA methylases.
Length = 219
Score = 27.0 bits (60), Expect = 5.0
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 50 PEKVAQ-HIASRCKASDVVIDGFCGCGGNTIQFAAVCQ--KVISIDIDPAKLRLAQ 102
PE + + I + D+V+D F G G T AA I I+I+ + +A+
Sbjct: 165 PEALLERLILASTNPGDIVLDPFAGSG--TTGAAAKELGRNFIGIEIEEEYVEIAK 218
>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 = 27.1 bits (60), Expect = 6.4
Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 7/83 (8%)
Query: 43 ESWYSVTPEK---VAQHIASRCKASDVVIDGFCGCGGNTIQFAAVCQK--VISIDIDPAK 97
E W +V VA +A + + ++D GG T + + V+++DI +
Sbjct: 217 EGWVTVQDASAQWVATWLAP--QNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHR 274
Query: 98 LRLAQHNASVYGVSHKIQFIQGD 120
L+ N G++ K + GD
Sbjct: 275 LKRVYENLKRLGLTIKAETKDGD 297
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, 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 = 330
Score = 26.9 bits (60), Expect = 7.1
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 66 VVIDGFCGCGGNTIQFAAVC-QKVISIDIDPAKLRLA 101
V + G G G +Q+A + ++I P K LA
Sbjct: 166 VAVLGIGGLGHLAVQYARAMGFETVAITRSPDKRELA 202
>gnl|CDD|213871 TIGR03840, TMPT_Se_Te, thiopurine S-methyltransferase, Se/Te
detoxification family. Members of this family are
thiopurine S-methyltransferase from a branch in which at
least some member proteins can perform selenium
methylation as a means to detoxify selenium, or perform
a related detoxification of tellurium. Note that the EC
number definition does not specify a particular
thiopurine, but rather represents a class of activity.
Length = 213
Score = 26.7 bits (60), Expect = 7.2
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 111 SHKIQFIQGDFFALAPSLQGDV 132
+ I+ GDFFAL + G V
Sbjct: 93 AGNIEIFCGDFFALTAADLGPV 114
>gnl|CDD|225927 COG3392, COG3392, Adenine-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 330
Score = 26.7 bits (59), Expect = 7.5
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 118 QGDFFALAPSLQGDVVFLSPPWGGPEYARSSFSIDNI 154
Q D L + GD+++L PP+ +Y+ + ++ I
Sbjct: 192 QEDANELIKKISGDILYLDPPYNARQYSANYHLLETI 228
>gnl|CDD|234597 PRK00050, PRK00050, 16S rRNA m(4)C1402 methyltranserfase;
Provisional.
Length = 296
Score = 26.6 bits (60), Expect = 8.1
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 62 KASDVVIDGFCGCGGNTIQFAAVCQ---KVISIDIDPAKLRLAQHNASVYGVSHKIQFIQ 118
K + +DG G GG++ ++I+ID DP + A+ +G + +
Sbjct: 18 KPDGIYVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAKDRLKPFG---RFTLVH 74
Query: 119 GDFFALAPSLQGDV 132
G+F L L +
Sbjct: 75 GNFSNLKEVLAEGL 88
>gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This model
describes a protein family of unknown function, about
690 residues in length, in which some members show
C-terminal sequence similarity to pfam05362, which is
the Lon protease C-terminal proteolytic domain, from
MEROPS family S16. However, the annotated catalytic
sites of E. coli Lon protease are not conserved in
members of this family. Members have a motif
GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif
GxxGxGK[ST] [Hypothetical proteins, Conserved].
Length = 675
Score = 26.7 bits (59), Expect = 8.4
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 26 GLEYFELTLADADNDATESWYSVTPEK 52
G E+F++ + DN++ E ++ PE+
Sbjct: 456 GFEFFDVNFSYIDNESLEEFFVSVPEQ 482
>gnl|CDD|117519 pfam08952, DUF1866, Domain of unknown function (DUF1866). This
domain, found in Synaptojanin, has no known function.
Length = 145
Score = 26.2 bits (58), Expect = 8.8
Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 11/47 (23%)
Query: 1 MSLKLQTLDWIKNLSD-----------VLDTVNNSTGLEYFELTLAD 36
++++L++ DWIK L + V T N++ E +L + +
Sbjct: 98 LNIRLKSPDWIKALEEEISLCTLEMIPVSPTANSTLLEEDTDLAVPE 144
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 26.4 bits (59), Expect = 9.0
Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 1/59 (1%)
Query: 62 KASDVVIDGFCGCGGNTIQFAAVCQKVISIDIDPAKLRLAQHNASVYGVSHKIQFIQGD 120
K D V++ G G A + +V+SI+ A+ N G + GD
Sbjct: 71 KPGDRVLEIGTGSGYQAAVLARLVGRVVSIERIEELAEQARRNLETLGY-ENVTVRHGD 128
>gnl|CDD|234494 TIGR04191, YphP_YqiW, bacillithiol system oxidoreductase,
YphP/YqiW family. This protein family is one of
several observed in species that express bacillithiol,
an analog of glutathione and mycothiol. Rather than
being involved in bacillithiol biosynthesis, members
are likely to act in bacillithiol-dependent processes.
Length = 136
Score = 26.0 bits (58), Expect = 9.6
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 49 TPEKVAQHIASRCKASDVVIDGFCGCGG 76
T E V + + + + VV++ CGC
Sbjct: 23 TAEDVDEAMENAEGTTLVVVNSVCGCAA 50
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.137 0.419
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: 9,696,000
Number of extensions: 889244
Number of successful extensions: 891
Number of sequences better than 10.0: 1
Number of HSP's gapped: 871
Number of HSP's successfully gapped: 126
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
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: 56 (25.2 bits)