RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7830
(364 letters)
>gnl|CDD|216320 pfam01135, PCMT, Protein-L-isoaspartate(D-aspartate)
O-methyltransferase (PCMT).
Length = 210
Score = 109 bits (275), Expect = 2e-28
Identities = 65/209 (31%), Positives = 95/209 (45%), Gaps = 17/209 (8%)
Query: 61 RSYADFLEGLKERKLLNHPRVEEAFYAVRRADFINVKPK-FGFCDIPYAFANQVVMEPPS 119
+E LK ++ +V EA AV R +F+ K + + DIP + + P
Sbjct: 1 NRNEALIENLKNYGVIASDKVAEAMLAVDREEFVPESFKSYAYEDIPLSIGYGQTISAPH 60
Query: 120 YIARCLEQLVDHLQNGSRVLDIGSGQGY-------MATAKEWLSSVRQLLLPETLNNSLK 172
A LE L L+ G RVL+IGSG GY M + S+ + PE + + +
Sbjct: 61 MHAMMLELL--ELKPGMRVLEIGSGSGYLTACFARMVGEVGLVVSIEHI--PELVEIARR 116
Query: 173 NIKISRPDLLQSKTLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIVA 232
N++ + + ++ D R G E PYD I GA E+ + ++ QLK GR+V
Sbjct: 117 NLEKLGLENVI-----VVVGDGRQGWPEFAPYDAIHVGAAAPEIPEALIDQLKEGGRLVI 171
Query: 233 PVGNVWRQNLSVIDKGPDGSISSKILRRV 261
PVG Q L DK DGS+ K L V
Sbjct: 172 PVGPNGNQVLQQFDKRNDGSVVIKDLEGV 200
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 95.0 bits (237), Expect = 4e-23
Identities = 61/198 (30%), Positives = 90/198 (45%), Gaps = 15/198 (7%)
Query: 66 FLEGLKERKLLNHPRVEEAFYAVRRADFINVKPK-FGFCDIPYAFANQVVMEPPSYIARC 124
+E L+ + + RV +AF AV R F+ K + D + P +AR
Sbjct: 6 LVERLRTEGITD-ERVLKAFLAVPRELFVPAAYKHLAYEDRALPIGCGQTISAPHMVARM 64
Query: 125 LEQLVDHLQNGSRVLDIGSGQGYMA--TAK--EWLSSVRQLLLPETLNNSLKNIKISRPD 180
L+ L L+ G RVL+IG+G GY A A+ + S+ + E + +N++
Sbjct: 65 LQLL--ELKPGDRVLEIGTGSGYQAAVLARLVGRVVSIE--RIEELAEQARRNLE----- 115
Query: 181 LLQSKTLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIVAPVGNVWRQ 240
L + + D G E PYD I A EV + +L QLKP GR+V PVG+ Q
Sbjct: 116 TLGYENVTVRHGDGSKGWPEEAPYDRIIVTAAAPEVPEALLDQLKPGGRLVIPVGSGPAQ 175
Query: 241 NLSVIDKGPDGSISSKIL 258
L I K DG+ + L
Sbjct: 176 RLLRITKDGDGNFERRDL 193
>gnl|CDD|178974 PRK00312, pcm, protein-L-isoaspartate O-methyltransferase;
Reviewed.
Length = 212
Score = 77.9 bits (193), Expect = 8e-17
Identities = 53/207 (25%), Positives = 76/207 (36%), Gaps = 57/207 (27%)
Query: 78 HPRVEEAFYAVRRADFINVKPKFGFCDIPYAFANQV------------VMEPPSYIARCL 125
RV EA A R F+ P AF ++ + P +AR
Sbjct: 23 DERVLEAIEATPRELFV-----------PEAFKHKAYENRALPIGCGQTISQPYMVARMT 71
Query: 126 EQLVDHLQNGSRVLDIGSGQGYMATA--------------KEWLSSVRQLLLPETLNNSL 171
E L L+ G RVL+IG+G GY A K ++ L + L L
Sbjct: 72 ELL--ELKPGDRVLEIGTGSGYQAAVLAHLVRRVFSVERIKTLQWEAKRRL--KQLG--L 125
Query: 172 KNIKISRPDLLQSKTLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIV 231
N+ + D G P+D I A E+ + +L QLK G +V
Sbjct: 126 HNVSV-------------RHGDGWKGWPAYAPFDRILVTAAAPEIPRALLEQLKEGGILV 172
Query: 232 APVGNVWRQNLSVIDKGPDGSISSKIL 258
APVG +Q L+ + K G ++L
Sbjct: 173 APVGGEEQQLLTRVRKR-GGRFEREVL 198
>gnl|CDD|232816 TIGR00080, pimt, protein-L-isoaspartate(D-aspartate)
O-methyltransferase. This is an all-kingdom (but not
all species) full-length ortholog enzyme for repairing
aging proteins. Among the prokaryotes, the gene name is
pcm. Among eukaryotes, pimt [Protein fate, Protein
modification and repair].
Length = 215
Score = 74.1 bits (182), Expect = 2e-15
Identities = 51/201 (25%), Positives = 85/201 (42%), Gaps = 15/201 (7%)
Query: 67 LEGLKERKLLNHPRVEEAFYAVRRADFINVKPK-FGFCDIPYAFANQVVMEPPSYIARCL 125
++ L + RV +A +V R +F+ K + + D P + P +A
Sbjct: 11 IDKLINEGYIKSKRVIDALLSVPREEFVPEHFKEYAYVDTPLEIGYGQTISAPHMVAMMT 70
Query: 126 EQLVDHLQNGSRVLDIGSGQGYMATAKEWLSSVRQLL-----LPETLNNSLKNIKISRPD 180
E L L+ G +VL+IG+G GY A + L+ +PE + + ++
Sbjct: 71 ELL--ELKPGMKVLEIGTGSGYQAAVLAEIVGRDGLVVSIERIPELAEKAERRLRK---- 124
Query: 181 LLQSKTLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIVAPVGNVWRQ 240
L + I+ D G PYD I+ A ++ + ++ QLK G +V PVG + Q
Sbjct: 125 -LGLDNVIVIVGDGTQGWEPLAPYDRIYVTAAGPKIPEALIDQLKEGGILVMPVGE-YLQ 182
Query: 241 NLSVIDKGPDGSISSKILRRV 261
L +K G I K + V
Sbjct: 183 VLKRAEK-RGGEIIIKDVEPV 202
>gnl|CDD|184409 PRK13942, PRK13942, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 212
Score = 68.5 bits (168), Expect = 2e-13
Identities = 55/205 (26%), Positives = 88/205 (42%), Gaps = 21/205 (10%)
Query: 67 LEGLKERKLLNHPRVEEAFYAVRRADFINVKPK----FGFCDIPYAFANQVVMEPPSYIA 122
+E L + +V +A V R F+ P+ + + D P + +A
Sbjct: 10 IEELIREGYIKSKKVIDALLKVPRHLFV---PEYLEEYAYVDTPLEIGYGQTISAIHMVA 66
Query: 123 RCLEQLVDHLQNGSRVLDIGSGQGYMATAKEWLSSVRQLL-----LPETLNNSLKNIKIS 177
E L L+ G +VL+IG+G GY A + + +PE + K +K
Sbjct: 67 IMCELL--DLKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIERIPELAEKAKKTLK-- 122
Query: 178 RPDLLQSKTLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIVAPVGNV 237
L +E I+ D G+ E PYD I+ A ++ K ++ QLK G +V PVG+
Sbjct: 123 ---KLGYDNVEVIVGDGTLGYEENAPYDRIYVTAAGPDIPKPLIEQLKDGGIMVIPVGS- 178
Query: 238 WRQNLSVIDKGPDGSISSKILRRVS 262
+ Q L ++K G I K L V+
Sbjct: 179 YSQELIRVEKDN-GKIIKKKLGEVA 202
>gnl|CDD|234563 TIGR04364, methyltran_FxLD, methyltransferase, FxLD system.
Members of this family resemble occur regularly in the
vicinity of lantibiotic biosynthesis enzymes and their
probable target, the FxLD family of putative ribosomal
natural product precursor (TIGR04363). Members resemble
protein-L-isoaspartate O-methyltransferase (TIGR00080)
and a predicted methyltranserase, TIGR04188, of another
putative peptide modification system.
Length = 394
Score = 67.4 bits (165), Expect = 2e-12
Identities = 56/189 (29%), Positives = 74/189 (39%), Gaps = 43/189 (22%)
Query: 70 LKERKLLNHPRVEEAFYAVRRADFINVKPKFGFCDIPYAFANQVV------------MEP 117
L+E ++ PRVE AF V R F P + YA VV +
Sbjct: 12 LREDGVIRSPRVEAAFRTVPRHLFAPGAP----LEKAYAANRAVVTKRDEDGAALSSVSA 67
Query: 118 PSYIARCLEQLVDHLQNGSRVLDIGSGQGYMATAKEWLSSVRQLLLPETLNNS--LKNIK 175
P A LEQ ++ G RVL+IGSG GY A LL E + S + +
Sbjct: 68 PHIQAMMLEQA--GVEPGMRVLEIGSG-GYNAA-----------LLAELVGPSGEVTTVD 113
Query: 176 ISRPDLLQS----------KTLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLK 225
I D+ + +L DA G E PYD I G ++ L QL
Sbjct: 114 ID-EDVTDRARACLAAAGYPQVTVVLADAEAGVPELAPYDRIIVTVGAWDIPPAWLDQLA 172
Query: 226 PNGRIVAPV 234
P GR+V P+
Sbjct: 173 PGGRLVVPL 181
>gnl|CDD|237568 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 322
Score = 64.5 bits (157), Expect = 1e-11
Identities = 50/181 (27%), Positives = 79/181 (43%), Gaps = 24/181 (13%)
Query: 80 RVEEAFYAVRRADFINVK--PKFGFCDI---------PYAFANQVVMEPPSYIARCLEQL 128
+ +AF V R +F+ + + DI Y+ ++Q PS +A +E
Sbjct: 22 HIAKAFLEVPREEFLTKSYPLSYVYEDIVLVSYDDGEEYSTSSQ-----PSLMALFME-- 74
Query: 129 VDHLQNGSRVLDIGSGQGYMATAKEWLSSVRQLLLPETLNNSLKNIKISRPDLLQSKTLE 188
L G RVL+IG G GY A + + L++ + + I L + +
Sbjct: 75 WVGLDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVRRLGIENVI 134
Query: 189 FILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIVAPVGNVWRQNLSVIDKG 248
F+ D +G E PYDVIF G EV +T +QLK GR++ P+ NL + +
Sbjct: 135 FVCGDGYYGVPEFAPYDVIFVTVGVDEVPETWFTQLKEGGRVIVPI------NLKLSRRQ 188
Query: 249 P 249
P
Sbjct: 189 P 189
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 52.3 bits (126), Expect = 1e-08
Identities = 32/107 (29%), Positives = 44/107 (41%), Gaps = 16/107 (14%)
Query: 135 GSRVLDIGSGQGYMATAKEWLSSVRQLLL------PETLNNSLKNIKISRPDLLQSKTLE 188
G+RVLDIG G G + A E + PE L + +N K L +
Sbjct: 2 GARVLDIGCGTGSL--AIELARLFPGARVTGVDLSPEMLELARENAK-----LALGPRIT 54
Query: 189 FILKDARWGHAEGGPYDVIFFGAGT---TEVSKTILSQLKPNGRIVA 232
F+ DA +D +F G G E+ + S LKP GR+V
Sbjct: 55 FVQGDAPDALDLLEGFDAVFIGGGGGDLLELLDALASLLKPGGRLVL 101
>gnl|CDD|140001 PRK13944, PRK13944, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 205
Score = 46.0 bits (109), Expect = 7e-06
Identities = 48/194 (24%), Positives = 85/194 (43%), Gaps = 18/194 (9%)
Query: 67 LEGLKERKLLNHPRVEEAFYAVRRADFINVKPKF---GFCDIPYA-FANQVVMEPPSYIA 122
+E L ++ RV++A +V R +F V P++ + D P FA + P
Sbjct: 6 VEELVREGIIKSERVKKAMLSVPREEF--VMPEYRMMAYEDRPLPLFAGATISAPHMVAM 63
Query: 123 RCLEQLVDHLQNGSRVLDIGSGQGYMAT----AKEWLSSVRQL-LLPETLNNSLKNIKIS 177
C +L++ + G ++L++G+G GY A A E V + ++ E + +NI+
Sbjct: 64 MC--ELIEP-RPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEIVKELAIYAAQNIE-- 118
Query: 178 RPDLLQSKTLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIVAPVGNV 237
L +E D + G + P+D I A + + ++ QLK G +V PV
Sbjct: 119 --RLGYWGVVEVYHGDGKRGLEKHAPFDAIIVTAAASTIPSALVRQLKDGGVLVIPVEEG 176
Query: 238 WRQNLSVIDKGPDG 251
Q L + K +
Sbjct: 177 VGQVLYKVVKRGEK 190
>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 = 45.4 bits (108), Expect = 2e-05
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 24/128 (18%)
Query: 118 PSYIARCLEQLVDHLQNGSRVLDIGSGQGYMATAKEWLSSVRQLLLPETLN-NSLKNIKI 176
PS +AR LE L +++G RVL+IG+G GY A LL L +++ ++++
Sbjct: 93 PSLVARMLEAL--DVEDGHRVLEIGTGTGYSAA-----------LLCHRLGDDNVTSVEV 139
Query: 177 SRPDLLQSK---------TLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPN 227
P L + D GH PYD I V L Q +P
Sbjct: 140 D-PGLAARAASALAAAGYAPTVVTGDGLLGHPPRAPYDRIIATCAVRRVPPAWLRQTRPG 198
Query: 228 GRIVAPVG 235
G I+ +
Sbjct: 199 GVILTTLS 206
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 36.6 bits (85), Expect = 0.006
Identities = 27/115 (23%), Positives = 48/115 (41%), Gaps = 19/115 (16%)
Query: 132 LQNGSRVLDIGSGQGYMAT--AKEWLSSVRQLLL---PETLNNSLKNIKISRPDLLQSKT 186
L++G +VLD+G G GY+ A++ + + E + + +N K L +
Sbjct: 1 LKSGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKK-----LGYEN 55
Query: 187 LEFILKDAR---WGHAEGGPYDVIFF------GAGTTEVSKTILSQLKPNGRIVA 232
+EFI D E +DV+ +V + I+ LKP G ++
Sbjct: 56 VEFIQGDIEELPQLQLEDNSFDVVISNEVLNHLPDPDKVLEEIIRVLKPGGVLIV 110
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 35.7 bits (83), Expect = 0.017
Identities = 26/112 (23%), Positives = 42/112 (37%), Gaps = 21/112 (18%)
Query: 132 LQNGSRVLDIGSGQGYMATAKEWLSSVRQL------LLPETLNNSLKN---IKISRPDLL 182
+ G R+ DIG+G G + EW + E L +N + +++
Sbjct: 32 PRPGDRLWDIGAGTGSITI--EWALAGPSGRVIAIERDEEALELIERNAARFGVDNLEVV 89
Query: 183 QSKTLEFILKDARWGHAEGGPYDVIFFGAG--TTEVSKTILSQLKPNGRIVA 232
+ E + D IF G G E+ + +LKP GR+VA
Sbjct: 90 EGDAPEALPDLPS--------PDAIFIGGGGNIEEILEAAWERLKPGGRLVA 133
>gnl|CDD|222171 pfam13489, Methyltransf_23, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 154
Score = 34.0 bits (78), Expect = 0.052
Identities = 32/125 (25%), Positives = 46/125 (36%), Gaps = 33/125 (26%)
Query: 118 PSYIARCLEQLVDHLQNGSRVLDIGSGQGYMAT-AKEWLSSVRQLLLPETLNNSLKNIKI 176
++AR L +L+ L+ G RVLDIG G G + +E V +
Sbjct: 6 ERFLARLLARLLPRLKPGGRVLDIGCGTGILLRLLRERGFDVTGV--------------- 50
Query: 177 SRPDLLQSKTLEFILKDARWGHAEGGPYDVIFFGAGTTEVS----------KTILSQLKP 226
D + L F L DA G YD+I EV + + LKP
Sbjct: 51 ---DPSPAAVLIFSLFDAPDPAVLAGKYDLITA----FEVLEHLPDPPALLQQLRELLKP 103
Query: 227 NGRIV 231
G ++
Sbjct: 104 GGVLL 108
>gnl|CDD|225173 COG2264, PrmA, Ribosomal protein L11 methylase [Translation,
ribosomal structure and biogenesis].
Length = 300
Score = 34.2 bits (79), Expect = 0.094
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 124 CLEQLVDHLQNGSRVLDIGSGQGYMATA 151
CLE L L+ G VLD+G G G +A A
Sbjct: 152 CLEALEKLLKKGKTVLDVGCGSGILAIA 179
>gnl|CDD|234786 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed.
Length = 250
Score = 33.6 bits (78), Expect = 0.12
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 124 CLEQLVDHLQNGSRVLDIGSGQG 146
CLE L + G VLD+G G G
Sbjct: 109 CLEALEKLVLPGKTVLDVGCGSG 131
>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 = 33.4 bits (77), Expect = 0.14
Identities = 13/38 (34%), Positives = 15/38 (39%)
Query: 194 ARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIV 231
GG DV+ G E L L+P GRIV
Sbjct: 192 EELRLTGGGGADVVIDAVGGPETLAQALRLLRPGGRIV 229
>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 = 33.4 bits (77), Expect = 0.15
Identities = 26/113 (23%), Positives = 45/113 (39%), Gaps = 16/113 (14%)
Query: 127 QLVDHLQNG-----SRVLDIGSGQGYMATAKEWLSSVRQLLLPETLNNSLKNIKISRPDL 181
+L+ L+ + VLDIG G GY+ + L Q E + N + +++
Sbjct: 22 RLLALLKEKGIFIPASVLDIGCGTGYL--TRALLKRFPQA---EFIANDISAGMLAQAKT 76
Query: 182 LQSKTLEFILKDARWGHAEGGPYDVIFFGAGT------TEVSKTILSQLKPNG 228
S+ ++FI DA E +D+I ++ + LKP G
Sbjct: 77 KLSENVQFICGDAEKLPLEDSSFDLIVSNLALQWCDDLSQALSELARVLKPGG 129
>gnl|CDD|225139 COG2230, Cfa, Cyclopropane fatty acid synthase and related
methyltransferases [Cell envelope biogenesis, outer
membrane].
Length = 283
Score = 31.8 bits (73), Expect = 0.44
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 131 HLQNGSRVLDIGSGQGYMA 149
L+ G +LDIG G G +A
Sbjct: 69 GLKPGMTLLDIGCGWGGLA 87
>gnl|CDD|176130 cd08439, PBP2_LrhA_like, The C-terminal substrate domain of
LysR-like regulator LrhA (LysR homologue A) and that of
closely related homologs, contains the type 2
periplasmic binding fold. This CD represents the LrhA
subfamily of LysR-like bacterial transcriptional
regulators, including LrhA, HexA, PecT, and DgdR. LrhA
is involved in control of the transcription of
flagellar, motility, and chemotaxis genes by regulating
the synthesis and concentration of FlhD(2)C(2), the
master regulator for the expression of flagellar and
chemotaxis genes. The LrhA protein has strong homology
to HexA and PecT from plant pathogenic bacteria, in
which HexA and PecT act as repressors of motility and of
virulence factors, such as exoenzymes required for lytic
reactions. DgdR also shares similar characteristics to
those of LrhA, HexA and PecT. The topology of this
substrate-binding domain is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 185
Score = 30.8 bits (70), Expect = 0.82
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 248 GPDGSISSKILRRVSSDFLCNLEYQLHPDVFPQPLNTSAEDT 289
P S+ ILRR + + C Y L P P PL E T
Sbjct: 57 HPPPGASATILRRSPTVWYCAAGYILAPGE-PLPLALLDEPT 97
>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 = 31.1 bits (71), Expect = 0.85
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 124 CLEQLVDHLQNGSRVLDIGSGQGYMATA 151
CLE L ++ G VLD+G G G +A A
Sbjct: 150 CLEALESLVKPGETVLDVGCGSGILAIA 177
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 29.7 bits (67), Expect = 0.86
Identities = 23/117 (19%), Positives = 38/117 (32%), Gaps = 23/117 (19%)
Query: 135 GSRVLDIGSGQGYMAT-AKEWLSSVRQLLL---PETLNNSLKNIKISRPDLLQSKTLEFI 190
G RVLD G+G G A R + + PE + + + ++ + +
Sbjct: 1 GDRVLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAALARRRLALAGLA----PRVRVV 56
Query: 191 LKDAR-WGHAEGGPYDVIFF--------------GAGTTEVSKTILSQLKPNGRIVA 232
+ DAR G +D++ L LKP G +V
Sbjct: 57 VGDARELLELPDGSFDLVLGNPPYGPRAGDPKDNRDLYDRFLAAALRLLKPGGVLVV 113
>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 = 31.0 bits (70), Expect = 0.96
Identities = 32/113 (28%), Positives = 49/113 (43%), Gaps = 16/113 (14%)
Query: 124 CLEQLVDHLQNGSRVLDIGSGQGYMATAKEWL---SSVRQLLLPETLNNSLKNIKISR-P 179
CLE L D V+D+G G G ++ A L V + P + ++ KN ++++
Sbjct: 149 CLEWLEDLDLKDKNVIDVGCGSGILSIAALKLGAAKVVGIDIDPLAVESARKNAELNQVS 208
Query: 180 DLLQSKTLEFILKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQ----LKPNG 228
D LQ K L ++ + G DVI EV K + Q +KP G
Sbjct: 209 DRLQVK-LIYLEQ------PIEGKADVIVANI-LAEVIKELYPQFSRLVKPGG 253
>gnl|CDD|234637 PRK00107, gidB, 16S rRNA methyltransferase GidB; Reviewed.
Length = 187
Score = 30.1 bits (69), Expect = 1.0
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 127 QLVDHLQNGSRVLDIGSGQG 146
+ +L G RVLD+GSG G
Sbjct: 38 AIAPYLPGGERVLDVGSGAG 57
>gnl|CDD|152787 pfam12352, V-SNARE_C, Snare region anchored in the vesicle membrane
C-terminus. Within the SNARE proteins interactions in
the C-terminal half of the SNARE helix are critical to
the driving of membrane fusion; whereas interactions in
the N-terminal half of the SNARE domain are important
for promoting priming or docking of the vesicle
pfam05008.
Length = 66
Score = 28.3 bits (64), Expect = 1.2
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 125 LEQLVDHLQNGSRVLD--IGSGQGYMATAKEWLSSVRQLLLP--ETLNNSLKNIKISR 178
L + D L+N R+ D I GQ + L S R+ L L+N+ + S
Sbjct: 3 LLREHDRLKNSHRIADETISIGQAILED----LHSQRETLKRARNKLHNTDNRLGKSN 56
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 30.7 bits (70), Expect = 1.3
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 194 ARWGHAEGGPYDVIFFGAGTTE----VSKTILSQLKPNGRIV 231
AR+ +A+ D I F GTTE V++ + LKP IV
Sbjct: 76 ARFLNAD--SSDEIVFTRGTTEALNLVARGLGRSLKPGDEIV 115
>gnl|CDD|203189 pfam05175, MTS, Methyltransferase small domain. This domain is
found in ribosomal RNA small subunit methyltransferase C
as well as other methyltransferases .
Length = 170
Score = 29.8 bits (68), Expect = 1.4
Identities = 36/137 (26%), Positives = 51/137 (37%), Gaps = 51/137 (37%)
Query: 128 LVDHLQN--GSRVLDIGSGQGYMAT--AKEW--------------LSSVRQLLLPETL-N 168
L+ HL G +VLD+G G G + AK L S R L
Sbjct: 23 LLSHLPKPLGGKVLDLGCGYGVLGAALAKRSPDLEVTMVDINARALESAR-----ANLAA 77
Query: 169 NSLKNIKISRPDLLQSKTLEFILKDARWGHAEGGPYDVIF----FGAG---TTEVSKTIL 221
N L+N ++ DL + E G +D+I F AG +V++ +
Sbjct: 78 NGLENGEVFWSDLYSA--------------VEPGKFDLIISNPPFHAGKATDYDVAQRFI 123
Query: 222 SQ----LKPNGR--IVA 232
+ LKP G IVA
Sbjct: 124 AGAARHLKPGGELWIVA 140
>gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional.
Length = 241
Score = 29.9 bits (68), Expect = 1.9
Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 119 SYIARCLEQLVDHLQNGSRVLDIGSGQG 146
Y AR E L +Q G RVLD+G G G
Sbjct: 6 RYRARTFELL--AVQPGDRVLDVGCGPG 31
>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 = 28.8 bits (65), Expect = 1.9
Identities = 27/114 (23%), Positives = 44/114 (38%), Gaps = 19/114 (16%)
Query: 132 LQNGSRVLDIGSGQGYMATAKEWLSSVRQLLL------PETLNNSLKNIKISRPDLLQSK 185
L+ G + DIG+G G + E V + PE L+ +N++ R +
Sbjct: 17 LRPGDVLWDIGAGTGSVTI--EAARLVPNGRVYAIERNPEALDLIERNLR--RFGV---S 69
Query: 186 TLEFILKDARWG-HAEGGPYDVIFFGAGTTEVSKTIL----SQLKPNGRIVAPV 234
+ + DA D +F G + + IL +L+P GRIV
Sbjct: 70 NIVIVEGDAPEAPEDLLPDPDAVFVGGSGGLL-QEILEAVERRLRPGGRIVLNA 122
>gnl|CDD|117364 pfam08794, Lipoprot_C, Lipoprotein GNA1870 C terminal like.
GNA1870 is a surface exposed lipoprotein in Neisseria
meningitidis that and is a potent antigen of
Meningococcus. The structure of the C terminal domain
consists of an anti-parallel beta barrel overlaid by a
short alpha helical region.
Length = 155
Score = 29.2 bits (65), Expect = 2.2
Identities = 21/67 (31%), Positives = 27/67 (40%), Gaps = 5/67 (7%)
Query: 151 AKEWLSSVRQLLLPETLNNSLKNIKISRPDLLQSKTLEFILKDARWGHAEGGPYDVIFFG 210
AK+ + L PE LN L I +PD K I + AE G Y + FG
Sbjct: 74 AKQGHGKIEHLKSPE-LNVDLAAADI-KPD---EKRHAVISGSVLYNQAEKGSYSLGIFG 128
Query: 211 AGTTEVS 217
EV+
Sbjct: 129 GRAQEVA 135
>gnl|CDD|216988 pfam02353, CMAS, Mycolic acid cyclopropane synthetase. This family
consist of Cyclopropane-fatty-acyl-phospholipid synthase
or CFA synthase EC:2.1.1.79 this enzyme catalyze the
reaction: S-adenosyl-L-methionine + phospholipid
olefinic fatty acid <=> S-adenosyl-L-homocysteine +
phospholipid cyclopropane fatty acid.
Length = 273
Score = 29.6 bits (67), Expect = 2.2
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 125 LEQLVDHLQNGSRVLDIGSGQGYMA 149
L++L L+ G +LDIG G G +
Sbjct: 55 LDKL--GLKPGMTLLDIGCGWGGLM 77
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 29.2 bits (66), Expect = 3.1
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 191 LKDARWGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIV 231
+ G DV+ G + L+ L P GR+V
Sbjct: 199 FVEQVRELTGGKGVDVVLDTVGGDTFAA-SLAALAPGGRLV 238
>gnl|CDD|165783 PLN00218, PLN00218, predicted protein; Provisional.
Length = 151
Score = 28.4 bits (63), Expect = 3.2
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 5 GRPLKIERCVLAVFFILVSRGQGWKPDPGM-PIEPPPDLRSEMYDEDN 51
G +ERCV++ FF+++S W D M + P LR E D +
Sbjct: 82 GSSWVVERCVISFFFLILSLRGRWSLDRKMCKRKACPSLRGERRDSSS 129
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 29.7 bits (68), Expect = 3.3
Identities = 25/100 (25%), Positives = 35/100 (35%), Gaps = 35/100 (35%)
Query: 11 ERCVLAVFFILVSRGQGWKPDPGMPIEPPPDLRSEMYDEDNENEENFFYTRSYADFL--- 67
ERC + V P +P P PD +E D+L
Sbjct: 266 ERCNVEV----------RLGKPFLPRFPTPDGETE------------------EDYLRKE 297
Query: 68 --EGLKERKLLNHPRVEEAFYAVRRADF-INVKPKFGFCD 104
EGL+ER L EE V R ++ ++V + GF
Sbjct: 298 AKEGLEER-LAFLFPDEERPEYVERLEYELDVIIQMGFPG 336
>gnl|CDD|222287 pfam13649, Methyltransf_25, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 97
Score = 27.3 bits (61), Expect = 3.9
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 138 VLDI--GSGQGYMATAKEWLSSVRQLLL---PETLNNSLKNIKISRPDLLQSKTLEFILK 192
+LD+ G+G+ A A+ SSV + E L + + ++ P + F++
Sbjct: 1 ILDLGCGTGRVLRALARAGPSSV--TGVDISKEALELAKERLRDKGPKV------RFVVA 52
Query: 193 DARWGHAEGGPYDVIFFGAGT 213
DAR E G +D++ +
Sbjct: 53 DARDLPFEEGSFDLVICAGLS 73
>gnl|CDD|219265 pfam07005, DUF1537, Protein of unknown function, DUF1537. This
conserved region is found in proteins of unknown
function in a range of Proteobacteria as well as the
Gram-positive Oceanobacillus iheyensis.
Length = 224
Score = 28.8 bits (65), Expect = 4.0
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 114 VMEPPSYIARCLEQLVDHLQNGSRVL 139
+++ + I R L + L G+ VL
Sbjct: 129 LLDGEAEIERALAWALAALAAGAVVL 154
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 28.8 bits (65), Expect = 4.2
Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 17/89 (19%)
Query: 128 LVDHLQNGSRVLDIGSGQGYMATAKEWLSSVRQLLL-------PETLNNSLKNIKISRPD 180
L LQ R+LD+G+G G +A A L+ P+ L + +N + +
Sbjct: 104 LALLLQLDKRILDLGTGSGAIAIA---LAKEGPDAEVIAVDISPDALALARENAERNGLV 160
Query: 181 LLQSKTLEFILKDARWGHAEGGPYDVIFF 209
++ + G +D+I
Sbjct: 161 -------RVLVVQSDLFEPLRGKFDLIVS 182
>gnl|CDD|218754 pfam05795, Plasmodium_Vir, Plasmodium vivax Vir protein. This
family consists of several Vir proteins specific to
Plasmodium vivax. The vir genes are present at about
600-1,000 copies per haploid genome and encode proteins
that are immunovariant in natural infections, indicating
that they may have a functional role in establishing
chronic infection through antigenic variation.
Length = 348
Score = 28.7 bits (64), Expect = 4.8
Identities = 8/36 (22%), Positives = 20/36 (55%)
Query: 41 DLRSEMYDEDNENEENFFYTRSYADFLEGLKERKLL 76
D+ +++ ++++ + +Y D L+ K+RK L
Sbjct: 96 DIWNKINKKNSKKKNKCKPDFNYIDILDEWKKRKDL 131
>gnl|CDD|218885 pfam06080, DUF938, Protein of unknown function (DUF938). This
family consists of several hypothetical proteins from
both prokaryotes and eukaryotes. The function of this
family is unknown.
Length = 201
Score = 28.2 bits (63), Expect = 4.9
Identities = 26/112 (23%), Positives = 36/112 (32%), Gaps = 18/112 (16%)
Query: 106 PYAFANQVVMEPPSYIARCLEQLVDHLQNGSRVLDIGSGQG----YMATA---KEWLSSV 158
P+A A + EP I L+ + RVL+I SG G + A W S
Sbjct: 2 PFAPAAERNREP---ILSVLQSYFA--KTTERVLEIASGTGQHAVFFAPLLPNLTWQPSD 56
Query: 159 RQLLLPETLNNSLKNIKIS--RPDLLQSKTLEFILKDARWGHAEGGPYDVIF 208
L ++ + RP L L+ YD IF
Sbjct: 57 PDPNLRGSIAAWADQQGLRNLRPPL----HLDVTRPPWPVEAPAPASYDAIF 104
>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 = 27.4 bits (61), Expect = 5.1
Identities = 22/117 (18%), Positives = 33/117 (28%), Gaps = 32/117 (27%)
Query: 137 RVLDIGSGQGYMA-----------TAKEWLSSVRQLLLPETLNNSLKNIKISRPDLLQSK 185
RVLD+G G G +A T + +L N+
Sbjct: 1 RVLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAALLADNV----------- 49
Query: 186 TLEFILKDAR-WGHAEGGPYDVIFFGAGTTEVS-------KTILSQLKPNGRIVAPV 234
E + DA +DVI + + LKP G +V +
Sbjct: 50 --EVLKGDAEELPPEADESFDVIISDPPLHHLVEDLARFLEEARRLLKPGGVLVLTL 104
>gnl|CDD|129779 TIGR00696, wecG_tagA_cpsF, bacterial polymer biosynthesis proteins,
WecB/TagA/CpsF family. The WecG member of this
superfamily, believed to be
UDP-N-acetyl-D-mannosaminuronic acid transferase, plays
a role in enterobacterial common antigen (eca) synthesis
in Escherichia coli. Another family member, the Bacillus
subtilis TagA protein, is involved in the biosynthesis
of the cell wall polymer poly(glycerol phosphate). The
third family member, CpsF, CMP-N-acetylneuraminic acid
synthetase has a role in the capsular polysaccharide
biosynthesis pathway [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 177
Score = 28.2 bits (63), Expect = 5.2
Identities = 20/93 (21%), Positives = 28/93 (30%), Gaps = 24/93 (25%)
Query: 124 CLEQLVDHLQNGSRVLDIGSGQGYMATAKEWLSSVRQLLLPETLNNSLKNIKISRPDL-- 181
L+QL L L I G L PE +L I S +
Sbjct: 60 VLQQLKVKLIKEYPKLKIVGAFGP--------------LEPEERKAALAKIARSGAGIVF 105
Query: 182 --LQSKTLEFILKDARWGHAE------GGPYDV 206
L E +++ R + GG +DV
Sbjct: 106 VGLGCPKQEIWMRNHRHLKPDAVMIGVGGSFDV 138
>gnl|CDD|113013 pfam04223, CitF, Citrate lyase, alpha subunit (CitF). In
citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6
cleaves intracellular citrate into acetate and
oxaloacetate, and is organised as a functional complex
consisting of alpha, beta, and gamma subunits. The gamma
subunit serves as an acyl carrier protein (ACP), and has
a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic
group. The citrate lyase is active only if this
prosthetic group is acetylated; this acetylation is
catalyzed by an acetate:SH-citrate lyase ligase. The
alpha subunit substitutes citryl for the acetyl group to
form citryl-S-ACP. The beta subunit completes the
reaction by cleaving the citryl to yield oxaloacetate
and (regenerated) acetyl-S-ACP. This family represents
the alpha subunit EC:2.8.3.10.
Length = 466
Score = 28.6 bits (64), Expect = 5.5
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 14/55 (25%)
Query: 86 YAVRRADFI-----NVKPKFGFCDIPYAFANQVVMEPPSYIARCLEQLVDHLQNG 135
+ R D++ V K GF ++ A PS + E LV+H++NG
Sbjct: 27 HHFREGDYVVNMVMEVIAKMGFKNLTIA---------PSSLTNVHEPLVEHIKNG 72
>gnl|CDD|226495 COG4007, COG4007, Predicted dehydrogenase related to H2-forming
N5,N10-methylenetetrahydromethanopterin dehydrogenase
[General function prediction only].
Length = 340
Score = 28.6 bits (64), Expect = 5.7
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 199 AEGGPYDVIF--FGAGTTEVSKTILSQLKPNGRIVAP 233
AE G V+F FG T +++ IL + P G ++
Sbjct: 80 AEHGEIHVLFTPFGKATFGIAREILEHV-PEGAVICN 115
>gnl|CDD|237136 PRK12557, PRK12557, H(2)-dependent methylenetetrahydromethanopterin
dehydrogenase-related protein; Provisional.
Length = 342
Score = 28.5 bits (64), Expect = 5.8
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 199 AEGGPYDVIF--FGAGTTEVSKTILSQLKPNGRIVAP 233
A+ G ++F FG T E++K IL L P ++
Sbjct: 79 AKHGEIHILFTPFGKKTVEIAKNILPHL-PENAVICN 114
>gnl|CDD|217086 pfam02527, GidB, rRNA small subunit methyltransferase G. This is a
family of bacterial glucose inhibited division proteins
these are probably involved in the regulation of cell
devision. GidB has been shown to be a methyltransferase
G specific to the rRNA small subunit. Previously
identified as a glucose-inhibited division protein B
that appears to be present and in a single copy in all
complete eubacterial genomes so far sequenced. GidB
specifically methylates the N7 position of a guanosine
in 16S rRNA.
Length = 184
Score = 28.0 bits (63), Expect = 6.3
Identities = 31/113 (27%), Positives = 52/113 (46%), Gaps = 13/113 (11%)
Query: 127 QLVDHLQNG-SRVLDIGSGQGYMATAKEWLSSVRQLLLPETLN---NSLKNIKISRPDLL 182
++++L N +V D+GSG G+ ++L L E+L N L+ +K L
Sbjct: 40 VVLEYLDNIRIKVADVGSGAGFPGIPLAIAFPDKKLTLLESLLKKINFLEELKK----EL 95
Query: 183 QSKTLEFILKDA-RWGHAEGGPYDVIFFGAGTT--EVSKTILSQLKPNGRIVA 232
+ + + A + H E YDVI A + E+++ L LKP G +A
Sbjct: 96 NLENVTIVHARAEEYQHEE--QYDVITSRAVASLNELTEWALPLLKPGGYFLA 146
>gnl|CDD|240325 PTZ00237, PTZ00237, acetyl-CoA synthetase; Provisional.
Length = 647
Score = 28.6 bits (64), Expect = 6.5
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 252 SISSKILRRVSSDFLCNLEYQLHPDVFPQPLNTSAEDTYTK 292
+ + KI R++ S FL + YQL +V + ++ Y K
Sbjct: 607 TKTGKIPRQIISKFLNDSNYQLPDNVNDSEIFYKIKELYMK 647
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 28.7 bits (63), Expect = 7.1
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 10/51 (19%)
Query: 279 PQPLNTS-AEDTYTKMFP---------PPPGVRPRAVTFPLSSQERSPGNG 319
P PL TS AED+ +P PP ++ R P S Q R P +G
Sbjct: 1945 PSPLETSRAEDSEDSEYPEYSNPRLGKSPPALKSREARRPSSKQPRRPSSG 1995
>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 = 28.0 bits (63), Expect = 8.1
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 196 WGHAEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIVAPVG 235
GG +DVIF GT + +KP GRIV VG
Sbjct: 225 KAAGLGGGFDVIFDFVGTQPTFEDAQKAVKPGGRIV-VVG 263
>gnl|CDD|168320 PRK05968, PRK05968, hypothetical protein; Provisional.
Length = 389
Score = 28.1 bits (63), Expect = 8.4
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 199 AEGGPYDVIFFGAGTTEVSKTILSQLKPNGRIVA 232
EG D F +G +S T+LS ++P RIVA
Sbjct: 75 LEGAE-DARGFASGMAAISSTVLSFVEPGDRIVA 107
>gnl|CDD|223574 COG0500, SmtA, SAM-dependent methyltransferases [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 257
Score = 27.9 bits (59), Expect = 8.4
Identities = 25/116 (21%), Positives = 47/116 (40%), Gaps = 9/116 (7%)
Query: 125 LEQLVDHLQNGSRVLDIGSGQGYMATAKEWLSSVRQLLLPETLNNSLKNIKISRPDLLQS 184
+ +L+ L G VLDIG G G +A ++ + L + +R +
Sbjct: 39 VLRLLRLLPGGLGVLDIGCGTGRLALLARLGGRGAYVVGVDLSPEMLALAR-ARAEGAGL 97
Query: 185 KTLEFILKDARWGH---AEGGPYDVIFFGAGTTEVS-----KTILSQLKPNGRIVA 232
++F++ DA G + +D++ + + +L LKP GR+V
Sbjct: 98 GLVDFVVADALGGVLPFEDSASFDLVISLLVLHLLPPAKALRELLRVLKPGGRLVL 153
>gnl|CDD|233377 TIGR01367, pyrE_Therm, orotate phosphoribosyltransferase, Thermus
family. This model represents a distinct clade of
orotate phosphoribosyltransferases. Members include the
experimentally determined example from Thermus aquaticus
and additional examples from Caulobacter crescentus,
Helicobacter pylori, Mesorhizobium loti, and related
species [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 187
Score = 27.4 bits (61), Expect = 8.7
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 21 LVSRGQGWKPDPGMPIEPPPDLRSEMYDEDN 51
++ R QG KPD G+P+ +L YD
Sbjct: 141 IIDRSQGGKPDSGVPLMSLKELEFPTYDSHE 171
>gnl|CDD|233713 TIGR02081, metW, methionine biosynthesis protein MetW. This
protein is found alongside MetX, of the enzyme that
acylates homoserine as a first step toward methionine
biosynthesis, in many species. It appears to act in
methionine biosynthesis but is not fully characterized
[Amino acid biosynthesis, Aspartate family].
Length = 194
Score = 27.3 bits (61), Expect = 9.4
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 125 LEQLVDHLQNGSRVLDIGSGQG 146
LE +++ + GSRVLD+G G G
Sbjct: 4 LESILNLIPPGSRVLDLGCGDG 25
>gnl|CDD|225258 COG2384, COG2384, Predicted SAM-dependent methyltransferase
[General function prediction only].
Length = 226
Score = 27.6 bits (62), Expect = 9.5
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 125 LEQLVDHLQNGSRVLDIGSGQGYMATA 151
L + + ++ G+R+ DIGS Y+
Sbjct: 7 LTTVANLVKQGARIADIGSDHAYLPIY 33
>gnl|CDD|237872 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 27.2 bits (61), Expect = 9.8
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 125 LEQLVDHLQNGSRVLDIGSGQGYMA 149
E VD + G RVL++G+G G +A
Sbjct: 16 AENAVD--KKGDRVLEVGTGSGIVA 38
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.138 0.418
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,112,495
Number of extensions: 1862739
Number of successful extensions: 1879
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1863
Number of HSP's successfully gapped: 67
Length of query: 364
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 266
Effective length of database: 6,590,910
Effective search space: 1753182060
Effective search space used: 1753182060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (27.0 bits)