RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1134
(149 letters)
>gnl|CDD|240367 PTZ00338, PTZ00338, dimethyladenosine transferase-like protein;
Provisional.
Length = 294
Score = 124 bits (314), Expect = 8e-36
Identities = 45/61 (73%), Positives = 53/61 (86%)
Query: 22 IQFNKDFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEID 81
+ FNK FGQHILKNPL++ IV+K AI+PTDTVLEIGPGTGN+T K+L+ AKKVIA EID
Sbjct: 8 MVFNKKFGQHILKNPLVLDKIVEKAAIKPTDTVLEIGPGTGNLTEKLLQLAKKVIAIEID 67
Query: 82 P 82
P
Sbjct: 68 P 68
Score = 58.9 bits (143), Expect = 4e-11
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 100 QEVPTDFDIKTLIDTVLNEINFADKRARTMDLDDFVLLLATFNKHGIHF 148
+ + K I +L + +KR+ +D+DDF+ LL FNK GIHF
Sbjct: 245 KVPVSLEPFKEFIAEILEDSGMFEKRSVKLDIDDFLKLLLAFNKKGIHF 293
>gnl|CDD|223109 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation)
[Translation, ribosomal structure and biogenesis].
Length = 259
Score = 86.1 bits (214), Expect = 2e-21
Identities = 28/63 (44%), Positives = 37/63 (58%)
Query: 22 IQFNKDFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEID 81
+ NK GQ+ L + +I IV+ I P D VLEIGPG G +T +LE+A +V A EID
Sbjct: 2 FRPNKRLGQNFLIDKNVIDKIVEAANISPGDNVLEIGPGLGALTEPLLERAARVTAIEID 61
Query: 82 PSC 84
Sbjct: 62 RRL 64
>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 = 81.9 bits (203), Expect = 9e-20
Identities = 27/66 (40%), Positives = 37/66 (56%)
Query: 22 IQFNKDFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEID 81
+ K GQ+ L + +IQ IV+ + D VLEIGPG G +T +L++AKKV A EID
Sbjct: 1 FRPRKSLGQNFLIDESVIQKIVEAANVLEGDVVLEIGPGLGALTEPLLKRAKKVTAIEID 60
Query: 82 PSCKSY 87
Sbjct: 61 RRLAER 66
>gnl|CDD|234708 PRK00274, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Reviewed.
Length = 272
Score = 80.5 bits (200), Expect = 3e-19
Identities = 28/63 (44%), Positives = 36/63 (57%)
Query: 22 IQFNKDFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEID 81
+ K GQ+ L + I+ IVD +P D VLEIGPG G +T +LE+A KV A EID
Sbjct: 14 HRAKKSLGQNFLIDENILDKIVDAAGPQPGDNVLEIGPGLGALTEPLLERAAKVTAVEID 73
Query: 82 PSC 84
Sbjct: 74 RDL 76
>gnl|CDD|215900 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.
Length = 254
Score = 77.3 bits (191), Expect = 4e-18
Identities = 29/60 (48%), Positives = 44/60 (73%)
Query: 23 QFNKDFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDP 82
+ + +GQ+ L NP +I IVDK ++ +DTVLEIGPG G +T ++ ++AK+V+A EIDP
Sbjct: 2 KGRRKYGQNFLTNPKVINRIVDKANLQESDTVLEIGPGKGALTTELAKRAKQVVAIEIDP 61
>gnl|CDD|237852 PRK14896, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Provisional.
Length = 258
Score = 73.0 bits (180), Expect = 2e-16
Identities = 26/63 (41%), Positives = 37/63 (58%)
Query: 25 NKDFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDPSC 84
NK GQH L + ++ IV+ D VLEIGPG G +T ++ ++AKKV A E+DP
Sbjct: 4 NKKLGQHFLIDDRVVDRIVEYAEDTDGDPVLEIGPGKGALTDELAKRAKKVYAIELDPRL 63
Query: 85 KSY 87
+
Sbjct: 64 AEF 66
>gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases.
Length = 169
Score = 71.0 bits (175), Expect = 3e-16
Identities = 26/47 (55%), Positives = 33/47 (70%)
Query: 38 IIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDPSC 84
+I IV +RP DTVLEIGPG G +T ++LE+AK+V A EIDP
Sbjct: 1 VIDKIVRAANLRPGDTVLEIGPGKGALTEELLERAKRVTAIEIDPRL 47
>gnl|CDD|237872 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 41.4 bits (98), Expect = 3e-05
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 37 LIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDP 82
L+ ++ VDK D VLE+G G+G + + + KKV+ +I+P
Sbjct: 14 LLAENAVDK----KGDRVLEVGTGSGIVAIVAAKNGKKVVGVDINP 55
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 37.6 bits (88), Expect = 8e-04
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 27 DFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDP 82
GQ I P ++ ++ ++P D VLEIG G+G + +V++ E
Sbjct: 50 GCGQTISA-PHMVARMLQLLELKPGDRVLEIGTGSGYQAAVLARLVGRVVSIERIE 104
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 34.9 bits (81), Expect = 0.006
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 24 FNKDFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQ--AKKVIACEID 81
F +D G + K + ++ K RP D + +IG GTG++T++ + +VIA E D
Sbjct: 9 FERDEGGPMTKEEIRALTL-SKLRPRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIERD 67
Query: 82 P 82
Sbjct: 68 E 68
>gnl|CDD|225136 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
biosynthesis [Coenzyme metabolism].
Length = 238
Score = 34.9 bits (81), Expect = 0.007
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 28 FGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAK--KVIACEIDPS 83
FG H L ++++ I+P D VL++ GTG+M + + + +V+ +I S
Sbjct: 33 FGLHRLWR----RALISLLGIKPGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISES 86
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This
family contains methyltransferase domains.
Length = 117
Score = 33.9 bits (78), Expect = 0.008
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 52 DTVLEIGPGTGNMTVKILEQAKK--VIACEIDP 82
D VL+ G G+G + V+ E+DP
Sbjct: 2 DRVLDPGAGSGAFLLAAARAGPDARVVGVELDP 34
>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 = 32.4 bits (74), Expect = 0.022
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 53 TVLEIGPGTGNMTVKILEQ-AKKVIACEIDP 82
VL++G GTG + + + +V +I P
Sbjct: 1 RVLDLGCGTGALALALASGPGARVTGVDISP 31
>gnl|CDD|223498 COG0421, SpeE, Spermidine synthase [Amino acid transport and
metabolism].
Length = 282
Score = 33.5 bits (77), Expect = 0.027
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 54 VLEIGPGTGNMT---VKILEQAKKVIACEIDPS----CKSYFPSL 91
VL IG G G +K L + + EIDP+ + Y P
Sbjct: 80 VLIIGGGDGGTLREVLKHLPVER-ITMVEIDPAVIELARKYLPEP 123
>gnl|CDD|222171 pfam13489, Methyltransf_23, Methyltransferase domain. This
family appears to be a methyltransferase domain.
Length = 154
Score = 32.8 bits (75), Expect = 0.030
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 47 AIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDPSCKSYFPSLYYFRN 96
++P VL+IG GTG + + E+ V +DPS + +
Sbjct: 19 RLKPGGRVLDIGCGTGILLRLLRERGFDVTG--VDPSPAAVLIFSLFDAP 66
>gnl|CDD|226562 COG4076, COG4076, Predicted RNA methylase [General function
prediction only].
Length = 252
Score = 33.0 bits (75), Expect = 0.039
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 52 DTVLEIGPGTGNMTVKILEQAKKVIACEIDP 82
DT ++G G+G ++V A++VIA E DP
Sbjct: 34 DTFADLGAGSGILSVVAAHAAERVIAIEKDP 64
>gnl|CDD|225317 COG2519, GCD14, tRNA(1-methyladenosine) methyltransferase and
related methyltransferases [Translation, ribosomal
structure and biogenesis].
Length = 256
Score = 32.7 bits (75), Expect = 0.047
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 8/64 (12%)
Query: 27 DFGQHILKNPLIIQS-----IVDKGAIRPTDTVLEIGPGTGNMTVKILEQAK---KVIAC 78
D+ + + II IV + I P VLE G G+G +T + V
Sbjct: 66 DYLLSMKRRTQIIYPKDAGYIVARLGISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTY 125
Query: 79 EIDP 82
EI
Sbjct: 126 EIRE 129
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 31.9 bits (73), Expect = 0.098
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 39 IQSIVDKGAIRPTDTVLEIGPGT-GNMTVKILEQA-KKVIACEIDPS 83
++ G ++P DTVL +G G G + ++ + A +VI +
Sbjct: 123 YHALRRAGVLKPGDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSDE 169
>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 = 31.4 bits (71), Expect = 0.10
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 49 RPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDP 82
D VLEIG GTG + +++ + K ++ +I+P
Sbjct: 18 LKPDDVLEIGAGTGLVAIRLKGKGKCILTTDINP 51
>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 = 30.8 bits (70), Expect = 0.12
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 42 IVDKGAIRPTDTVLEIGPGTGNMTVKILEQAK--KVIACEIDP 82
+ K +RP D + +IG GTG++T++ +V A E +P
Sbjct: 11 TLSKLRLRPGDVLWDIGAGTGSVTIEAARLVPNGRVYAIERNP 53
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 30.4 bits (69), Expect = 0.13
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 50 PTDTVLEIGPGTGNMTVKILEQAK--KVIACEIDPSC 84
P VL+IG GTG++ +++ +V ++ P
Sbjct: 1 PGARVLDIGCGTGSLAIELARLFPGARVTGVDLSPEM 37
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish 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 GroES-like catalytic
domain. 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 = 343
Score = 31.0 bits (71), Expect = 0.19
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 45 KGAIRPTDTVLEIGPG-TGNMTVKI--LEQAKKVIACEIDP 82
K I+P DTVL IG G G + + A+KVI +++
Sbjct: 160 KAGIKPGDTVLVIGAGPIGLLHAMLAKASGARKVIVSDLNE 200
>gnl|CDD|226472 COG3963, COG3963, Phospholipid N-methyltransferase [Lipid
metabolism].
Length = 194
Score = 30.8 bits (70), Expect = 0.20
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 54 VLEIGPGTGNMTVKILEQAKK---VIACEIDP 82
VLE+GPGTG +T IL + + + A E P
Sbjct: 52 VLELGPGTGVITKAILSRGVRPESLTAIEYSP 83
>gnl|CDD|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. 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. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. 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.
Length = 347
Score = 31.1 bits (71), Expect = 0.20
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 48 IRPTDTVLEIGPG-TGNMTVKI--LEQAKKVIACEIDPSC 84
I+P TV IG G G V L A ++IA + +P
Sbjct: 165 IKPGSTVAVIGAGPVGLCAVAGARLLGAARIIAVDSNPER 204
>gnl|CDD|176196 cd08234, threonine_DH_like, L-threonine dehydrogenase. L-threonine
dehydrogenase (TDH) catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine,
via NAD(H)-dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and have 2 tightly
bound zinc atoms per subunit. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Length = 334
Score = 30.6 bits (70), Expect = 0.24
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 43 VDKGAIRPTDTVLEIGPG-TGNMTVKILEQ--AKKVIACEIDPS 83
+D I+P D+VL G G G + ++L+ A +V E +
Sbjct: 152 LDLLGIKPGDSVLVFGAGPIGLLLAQLLKLNGASRVTVAEPNEE 195
>gnl|CDD|176219 cd08258, Zn_ADH4, Alcohol dehydrogenases of the MDR family. This
group shares the zinc coordination sites of the
zinc-dependent 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 an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. 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 = 306
Score = 30.4 bits (69), Expect = 0.31
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 40 QSIVDKGAIRPTDTVLEIGPGT 61
++ ++ IRP DTV+ GPG
Sbjct: 154 HAVAERSGIRPGDTVVVFGPGP 175
>gnl|CDD|225173 COG2264, PrmA, Ribosomal protein L11 methylase [Translation,
ribosomal structure and biogenesis].
Length = 300
Score = 30.0 bits (68), Expect = 0.37
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 48 IRPTDTVLEIGPGTGNMTVKILEQ-AKKVIACEIDP 82
++ TVL++G G+G + + + AKKV+ +IDP
Sbjct: 160 LKKGKTVLDVGCGSGILAIAAAKLGAKKVVGVDIDP 195
>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 = 29.9 bits (68), Expect = 0.37
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 40 QSIVDKGAIRPTDTVLEIGPG--TGNMTVKILEQAKKVIACEIDPS 83
++V G ++P +TVL IG G N VIA +I
Sbjct: 155 HAVVRAGEVKPGETVLVIGLGGLGLNAVQIAKAMGAAVIAVDIKEE 200
>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 = 0.38
Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 41 SIVDKGAIRPTDTVLEIGPGT-GNMTVKILEQ--AKKVIACEIDPS 83
+ V R + V +G G G + ++ + A++V+ + D +
Sbjct: 88 NGVRDAEPRLGERVAVVGLGLVGLLAAQLAKAAGAREVVGVDPDAA 133
>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 = 29.8 bits (68), Expect = 0.39
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 42 IVDKGAIRPTDTVLEIGPGTGNMTVKILEQAK--KVIACEIDPS 83
V + + DTVL +G G + V + +A+ +VI +ID
Sbjct: 151 AVRRAGVTAGDTVLVVGAGPIGLGVIQVAKARGARVIVVDIDDE 194
>gnl|CDD|233645 TIGR01934, MenG_MenH_UbiE, ubiquinone/menaquinone biosynthesis
methyltransferases. This model represents a family of
methyltransferases involved in the biosynthesis of
menaquinone and ubiqinone. Some members such as the
UbiE enzyme from E. coli are believed to act in both
pathways, while others may act in only the menaquinone
pathway. These methyltransferases are members of the
UbiE/CoQ family of methyltransferases (pfam01209) which
also contains ubiquinone methyltransferases and other
methyltransferases. Members of this clade include a
wide distribution of bacteria and eukaryotes, but no
archaea. An outgroup for this clade is provided by the
phosphatidylethanolamine methyltransferase (EC
2.1.1.17) from Rhodobacter sphaeroides. Note that a
number of non-orthologous genes which are members of
pfam03737 have been erroneously annotated as MenG
methyltransferases [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 223
Score = 29.9 bits (68), Expect = 0.39
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 28 FGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACE-IDPS 83
FG H L + V + VL++ GTG++ +++ + A +D S
Sbjct: 21 FGLHRLWR----RRAVKLIGVFKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDFS 73
>gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional.
Length = 241
Score = 29.9 bits (68), Expect = 0.45
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 47 AIRPTDTVLEIGPGTGNMTVKILEQ---AKKVIACEIDPS 83
A++P D VL++G G GN ++ + +V+ ID S
Sbjct: 16 AVQPGDRVLDVGCGPGNDARELARRVGPEGRVVG--IDRS 53
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 29.7 bits (68), Expect = 0.45
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 28 FGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKK---VIACEIDPS 83
FG H + + + +RP D VL++ GTG++ + + + K V+ D S
Sbjct: 33 FGLHRVWR----RKTIKWLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGL--DFS 85
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 29.7 bits (67), Expect = 0.54
Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 26/91 (28%)
Query: 45 KGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDPSCKSYFPSLYYFRNLCLQEVPT 104
KG I + TV N+ + E KKV+ DP RNL +++PT
Sbjct: 9 KGGIGKSTTV-------CNIAAALAESGKKVLVVGCDPKADCT-------RNLVGEKIPT 54
Query: 105 DFDIKTLIDTVLNEINFADKRARTMDLDDFV 135
D+ +K + L+D +
Sbjct: 55 VLDV------------LREKGIDNLGLEDII 73
>gnl|CDD|232960 TIGR00406, prmA, ribosomal protein L11 methyltransferase.
Ribosomal protein L11 methyltransferase is an
S-adenosyl-L-methionine-dependent methyltransferase
required for the modification of ribosomal protein L11.
This protein is found in bacteria and (with a probable
transit peptide) in Arabidopsis [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 288
Score = 29.0 bits (65), Expect = 0.78
Identities = 11/34 (32%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 50 PTDTVLEIGPGTGNMTVKILEQ-AKKVIACEIDP 82
V+++G G+G +++ L+ A KV+ +IDP
Sbjct: 159 KDKNVIDVGCGSGILSIAALKLGAAKVVGIDIDP 192
>gnl|CDD|234740 PRK00377, cbiT, cobalt-precorrin-6Y C(15)-methyltransferase;
Provisional.
Length = 198
Score = 29.0 bits (65), Expect = 0.79
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 3/41 (7%)
Query: 45 KGAIRPTDTVLEIGPGTGNMTVK---ILEQAKKVIACEIDP 82
K +R D +L+IG GTG++TV+ ++ + KV A + D
Sbjct: 35 KLRLRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDE 75
>gnl|CDD|219760 pfam08242, Methyltransf_12, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 98
Score = 27.7 bits (62), Expect = 0.99
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 55 LEIGPGTGNMTVKILEQAK--KVIACEIDPS 83
L+IG GTG + +LE + +I P+
Sbjct: 1 LDIGCGTGTLLRALLEALPGLEYTGVDISPA 31
>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 = 29.0 bits (65), Expect = 1.1
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 35 NPLIIQSIVDKG----AIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDP 82
N + +VD+ ++ + V++ G G T+ + +QAK V+ E+ P
Sbjct: 273 NSGQNEKLVDRALEALELQGEELVVDAYCGVGTFTLPLAKQAKSVVGIEVVP 324
>gnl|CDD|234649 PRK00121, trmB, tRNA (guanine-N(7)-)-methyltransferase; Reviewed.
Length = 202
Score = 27.8 bits (63), Expect = 1.7
Identities = 12/37 (32%), Positives = 13/37 (35%), Gaps = 8/37 (21%)
Query: 49 RPTDTVLEIGPGTGNMTVKILEQAKK-----VIACEI 80
LEIG G G V E AK I E+
Sbjct: 39 NDAPIHLEIGFGKGEFLV---EMAKANPDINFIGIEV 72
>gnl|CDD|226504 COG4017, COG4017, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 254
Score = 27.9 bits (62), Expect = 2.0
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 61 TGNMTVKILEQAKKVIACEIDPSCKSYFPSLYYFRNLCLQEVPTDFDIKTLIDT 114
TGN T ++L +A KV +I P + + P+ FRNL L+ + + D+ ++D
Sbjct: 56 TGNYTAQMLSKADKVTVVDIHPFMRGFLPNNVKFRNL-LKFIRGEVDL--IVDL 106
>gnl|CDD|176228 cd08267, MDR1, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent 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. 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 = 319
Score = 28.0 bits (63), Expect = 2.2
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 40 QSIVDKGAIRPTDTVLEIGP--GTGNMTVKILEQAKKVIACEIDPSC 84
Q++ D G ++P VL G G G V+I K + + C
Sbjct: 133 QALRDAGKVKPGQRVLINGASGGVGTFAVQIA----KALGAHVTGVC 175
>gnl|CDD|234492 TIGR04188, methyltr_grsp, methyltransferase, ATP-grasp peptide
maturase system. Members of this protein family are
predicted SAM-dependent methyltransferases that
regularly occur in the context of a putative peptide
modification ATP-grasp enzyme (TIGR04187, related to
enzymes of microviridin maturation) and a putative
ribosomal peptide modification target (TIGR04186).
Length = 363
Score = 27.3 bits (61), Expect = 2.8
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 48 IRPTDTVLEIGPGTGNMTVKILEQ--AKKVIACEIDP 82
+ VLEIG GTG + + V + E+DP
Sbjct: 105 VEDGHRVLEIGTGTGYSAALLCHRLGDDNVTSVEVDP 141
>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 = 27.2 bits (61), Expect = 3.0
Identities = 15/36 (41%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 48 IRPTDTVLEIGPGTGNMTVKILE-QAKKVIACEIDP 82
++P +TVL++G G+G + + L+ AKKV+ +IDP
Sbjct: 158 VKPGETVLDVGCGSGILAIAALKLGAKKVVGVDIDP 193
>gnl|CDD|225174 COG2265, TrmA, SAM-dependent methyltransferases related to tRNA
(uracil-5-)-methyltransferase [Translation, ribosomal
structure and biogenesis].
Length = 432
Score = 27.3 bits (61), Expect = 3.3
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 49 RPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDPS 83
+ VL++ G G + + ++ KKV EI P
Sbjct: 292 AGGERVLDLYCGVGTFGLPLAKRVKKVHGVEISPE 326
>gnl|CDD|176188 cd05285, sorbitol_DH, Sorbitol dehydrogenase. 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. Aldose reductase catalyzes
the NADP(H)-dependent conversion of glucose to sorbital,
and SDH uses NAD(H) in the conversion of sorbitol to
fructose. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. 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.
Length = 343
Score = 27.1 bits (61), Expect = 3.8
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 43 VDKGAIRPTDTVLEIGPGT-GNMTVKILE--QAKKVIACEIDPS 83
+ +RP DTVL G G G +T + + A KV+ +IDPS
Sbjct: 155 CRRAGVRPGDTVLVFGAGPIGLLTAAVAKAFGATKVVVTDIDPS 198
>gnl|CDD|226413 COG3897, COG3897, Predicted methyltransferase [General function
prediction only].
Length = 218
Score = 27.0 bits (60), Expect = 3.9
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 15/57 (26%)
Query: 31 HILKNPLIIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQ---AKKVIACEIDPSC 84
+I +P +++ K VL++G G+G V I A +V+A +IDP
Sbjct: 70 YIDDHP---ETVRGK-------RVLDLGAGSG--LVAIAAARAGAAEVVAADIDPWL 114
>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 = 26.8 bits (60), Expect = 4.5
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 43 VDKGAIRPTDTVLEIGPGT-GNMTVK--ILEQAKKVIACEIDP 82
V I DTV+ IG GT G + ++ + AK+VIA +ID
Sbjct: 152 VRLAGITLGDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDD 194
>gnl|CDD|118234 pfam09702, Cas_Csa5, CRISPR-associated protein (Cas_Csa5). CRISPR
is a term for Clustered, Regularly Interspaced Short
Palindromic Repeats. A number of protein families appear
only in association with these repeats and are
designated Cas (CRISPR-Associated) proteins. This entry
represents a minor family of Cas proteins found in
various species of Sulfolobus and Pyrococcus (all
archaeal). It is found with two different CRISPR loci in
Sulfolobus solfataricus.
Length = 105
Score = 26.0 bits (57), Expect = 4.7
Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 25/89 (28%)
Query: 38 IIQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQAKKVIACEIDPSCKSYFPSLYYFRNL 97
I++S +++G IR E ++ IA + +Y Y
Sbjct: 33 IVRSGIERGEIRLQTG----------------ENGRRYIAVKEGEKDGNYIVVGY----- 71
Query: 98 CLQEVPTDFDIKTLIDTVLNEINFADKRA 126
+P+D D++ ++ V +I +A K
Sbjct: 72 ----LPSDEDVEQFLEDVERDIYYARKVG 96
>gnl|CDD|173766 cd08226, PK_STRAD_beta, Pseudokinase domain of STE20-related kinase
adapter protein beta. Protein Kinase family,
STE20-related kinase adapter protein (STRAD) beta
subfamily, pseudokinase domain. The STRAD-beta subfamily
is part of a larger superfamily that includes the
catalytic domains of serine/threonine kinases (STKs),
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. The pseudokinase domain shows similarity to
protein kinases but lacks crucial residues for catalytic
activity. STRAD forms a complex with the scaffolding
protein MO25, and the STK, LKB1, resulting in the
activation of the kinase. In the complex, LKB1
phosphorylates and activates adenosine
monophosphate-activated protein kinases (AMPKs), which
regulate cell energy metabolism and cell polarity. LKB1
is a tumor suppressor linked to the rare inherited
disease, Peutz-Jeghers syndrome, which is characterized
by a predisposition to benign polyps and
hyperpigmentation of the buccal mucosa. There are two
forms of STRAD, alpha and beta, that complex with LKB1
and MO25. STRAD-beta is also referred to as ALS2CR2
(Amyotrophic lateral sclerosis 2 chromosomal region
candidate gene 2 protein), since the human gene encoding
it is located within the juvenile ALS2 critical region
on chromosome 2q33-q34. It is not linked to the
development of ALS2.
Length = 328
Score = 26.9 bits (59), Expect = 5.0
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 82 PSCKSYFPSLYYFRNLCLQEVP 103
PS K++ P+ LCLQ+ P
Sbjct: 275 PSSKTFSPAFQNLVELCLQQDP 296
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 26.5 bits (59), Expect = 5.0
Identities = 7/33 (21%), Positives = 12/33 (36%), Gaps = 3/33 (9%)
Query: 54 VLEIGPGTGNMTVKILEQAK---KVIACEIDPS 83
+LEIG G + + ++ E D
Sbjct: 63 ILEIGTAIGYSALWMALALPDDGRLTTIERDEE 95
>gnl|CDD|131751 TIGR02704, carboxysome_B, carboxysome peptide B. This model
distinguishes one of two closely related paralogs
encoded by nearby genes in the carboxysome operons of a
number of cyanobacteria and chemoautotrophic bacteria.
More distantly related proteins, also belonging to Pfam
family pfam03319, participate in other types of shell
such as the ethanolamine degradation organelle [Central
intermediary metabolism, One-carbon metabolism].
Length = 80
Score = 25.6 bits (56), Expect = 5.0
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 59 PGTGNMTVKILEQAKKVIACEIDP 82
PG N ++++L AK I+ +DP
Sbjct: 17 PGLKNASLRVLRDAKGKISVAVDP 40
>gnl|CDD|149273 pfam08123, DOT1, Histone methylation protein DOT1. The DOT1
domain regulates gene expression by methylating histone
H3. H3 methylation by DOT1 has been shown to be
required for the DNA damage checkpoint in yeast.
Length = 205
Score = 26.5 bits (59), Expect = 5.1
Identities = 22/99 (22%), Positives = 42/99 (42%), Gaps = 14/99 (14%)
Query: 3 LPNVDKLNYYVCRTVWKICIQFNKDFGQHILKNPLIIQSIVDKGAIRPTDTVLEIGPGTG 62
P+ +KLN+Y + N+ +G+ P + ++DK + P D +++G G G
Sbjct: 6 SPDANKLNHYKAFS--------NEVYGE---LLPEFLSDVLDKCNLGPQDVFVDLGSGVG 54
Query: 63 NMTVKILEQA--KKVIACEIDPSCKSYFPSLY-YFRNLC 98
N ++ + K CEI + + F+ C
Sbjct: 55 NCVLQAALEFGCKLSFGCEIMDNASNLAELQDEEFKKRC 93
>gnl|CDD|217715 pfam03759, PRONE, PRONE (Plant-specific Rop nucleotide exchanger).
This is a functional guanine exchange factor (GEF) of
plant Rho GTPase.
Length = 360
Score = 26.6 bits (59), Expect = 5.2
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 22 IQFNKDFGQHIL 33
IQ+NKD GQ IL
Sbjct: 317 IQYNKDVGQAIL 328
>gnl|CDD|233708 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme,
which is found in biotin biosynthetic gene clusters in
proteobacteria, firmicutes, green-sulfur bacteria,
fusobacterium and bacteroides, is believed to carry out
an enzymatic step prior to the formation of
pimeloyl-CoA (although attribution of this annotation
is not traceable). The enzyme appears related to
methyltransferases by homology [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 240
Score = 26.5 bits (59), Expect = 5.5
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 39 IQSIVDKGAIRPTDTVLEIGPGTGNMTVKILEQ 71
+ + +KG P +VL+IG GTG +T +L++
Sbjct: 24 LALLKEKGIFIPA-SVLDIGCGTGYLTRALLKR 55
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 25.7 bits (57), Expect = 5.8
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 55 LEIGPGTGNMTVKILE-QAKKVIACEIDP 82
L++G GTG + + +V ++ P
Sbjct: 1 LDVGCGTGLLAEALARRGGARVTGVDLSP 29
>gnl|CDD|213237 cd03270, ABC_UvrA_I, ATP-binding cassette domain I of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 226
Score = 26.5 bits (59), Expect = 6.3
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 44 DKGAIRPTDTVLEIGPGTG 62
D+ IR D V++IGPG G
Sbjct: 198 DEDTIRAADHVIDIGPGAG 216
>gnl|CDD|232976 TIGR00438, rrmJ, cell division protein FtsJ. Methylates the 23S
rRNA. Previously known as cell division protein ftsJ.//
Trusted cutoff too high? [SS 10/1/04] [Protein
synthesis, tRNA and rRNA base modification].
Length = 188
Score = 26.3 bits (58), Expect = 6.5
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 48 IRPTDTVLEIG--PGTGNMTVKILEQAKK--VIACEIDP 82
I+P DTVL++G PG G V + + K VIA ++ P
Sbjct: 30 IKPGDTVLDLGAAPG-GWSQVAVEQVGGKGRVIAVDLQP 67
>gnl|CDD|177970 PLN02336, PLN02336, phosphoethanolamine N-methyltransferase.
Length = 475
Score = 26.6 bits (59), Expect = 6.8
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 53 TVLEIGPGTGNMTVKILEQAKKVIA 77
+VLE+G G G T ++ ++A +VIA
Sbjct: 40 SVLELGAGIGRFTGELAKKAGQVIA 64
>gnl|CDD|146898 pfam04490, Pox_T4_C, Poxvirus T4 protein, C terminus. This
family of poxvirus proteins are thought to be retained
in the endoplasmic reticulum. M-T4 of myxoma virus is
thought to protect infected lymphocytes from apoptosis
and modulate the inflammatory response to virus
infection.
Length = 149
Score = 25.9 bits (57), Expect = 6.8
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 76 IACEIDPSCKSYFPSLYYFRNLC 98
I +ID SC + S Y RN C
Sbjct: 71 ITIKIDTSCIKHLSSNYSVRNEC 93
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 26.5 bits (58), Expect = 6.9
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 95 RNLCLQEVPTDFDI 108
RNL LQ +P DFDI
Sbjct: 467 RNLFLQHLPQDFDI 480
>gnl|CDD|180961 PRK07402, PRK07402, precorrin-6B methylase; Provisional.
Length = 196
Score = 26.1 bits (58), Expect = 7.0
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 47 AIRPT-DTVL-EIGPGTGNMTVKI--LEQAKKVIACEIDP 82
+R D+VL +IG GTG + V+ L +VIA E D
Sbjct: 35 QLRLEPDSVLWDIGAGTGTIPVEAGLLCPKGRVIAIERDE 74
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
0.326 0.142 0.436
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: 7,693,785
Number of extensions: 690307
Number of successful extensions: 944
Number of sequences better than 10.0: 1
Number of HSP's gapped: 942
Number of HSP's successfully gapped: 86
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.4 bits)