RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 023442
(282 letters)
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 236 bits (606), Expect = 5e-77
Identities = 89/218 (40%), Positives = 126/218 (57%), Gaps = 16/218 (7%)
Query: 4 CGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDF 63
GCPS +V +G FG LM +P+ V + + + ++PV+VK RIG+DD DSY LCDF
Sbjct: 98 VGCPSDRVQ-NGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIGIDDQDSYEFLCDF 156
Query: 64 IYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGIN 123
+ V+ + FI+H+RKA L G+SP ENR IPPL Y+ Y L RDFP LT +NGGI
Sbjct: 157 VDTVAE-AGCDTFIVHARKAWLKGLSPKENREIPPLDYDRVYRLKRDFPHLTIEINGGIK 215
Query: 124 TVDEVNAALRK--GAHHVMVGRAAYQNPWYTLGHVDTAIYGAPSSGLTRRQVVEKYQIYG 181
T++E L+ G VM+GRAAY NP+ L VD ++G P+ L+R +V+E Y
Sbjct: 216 TLEEAKEHLQHVDG---VMIGRAAYHNPYL-LAEVDRELFGEPAPPLSRSEVLEAMLPYI 271
Query: 182 DAIL--GTYGNNRPHVRDVMKPLLHFFHSEPGNGLFKR 217
+ L G + + + +L F PG ++R
Sbjct: 272 ERHLAQGGR------LNHITRHMLGLFQGLPGARAWRR 303
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. This model
represents one branch of COG0042 (Predicted TIM-barrel
enzymes, possibly dehydrogenases, nifR3 family). It
represents a distinct subset by a set of shared unique
motifs, a conserved pattern of insertions/deletions
relative to other nifR3 homologs, and by subclustering
based on cross-genome bidirectional best hits. Members
are found in species as diverse as the proteobacteria, a
spirochete, a cyanobacterium, and Deinococcus
radiodurans. NifR3 itself, a protein of unknown function
associated with nitrogen regulation in Rhodobacter
capsulatus, is not a member of this branch. Members of
this family show a distant relationship to alpha/beta
(TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase [Protein synthesis,
tRNA and rRNA base modification].
Length = 318
Score = 184 bits (468), Expect = 1e-56
Identities = 90/238 (37%), Positives = 130/238 (54%), Gaps = 8/238 (3%)
Query: 5 GCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDFI 64
GCPS +V +G FG LM + V + + + N+PV+VK RIG+D DSY LCDF+
Sbjct: 89 GCPSDRVQ-NGNFGACLMGNADLVADCVKAMQEAVNIPVTVKHRIGIDPLDSYEFLCDFV 147
Query: 65 YKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINT 124
VS ++FI+H+RKA L+G+SP ENR IPPL+YE Y L +DFP LT +NGGI
Sbjct: 148 EIVSGKG-CQNFIVHARKAWLSGLSPKENREIPPLRYERVYQLKKDFPHLTIEINGGIKN 206
Query: 125 VDEVNAALRKGAHHVMVGRAAYQNPWYTLGHVDTAIYGAPSSGLTRRQVVEKYQIYGDAI 184
+++ L VMVGR AY+NP Y L +VD I+ LTR+++VE+ Y
Sbjct: 207 SEQIKQHLSH-VDGVMVGREAYENP-YLLANVDREIFNETDEILTRKEIVEQMLPY---- 260
Query: 185 LGTYGNNRPHVRDVMKPLLHFFHSEPGNGLFKRKADAAFQTCKTVKSFLEETIVAIPD 242
+ Y + + + + LL F +PG ++R LE + +P+
Sbjct: 261 IEEYLSQGLSLNHITRHLLGLFQGKPGAKQWRRYLSENAPKAGAGIEVLETALETVPE 318
>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present.
Length = 231
Score = 133 bits (337), Expect = 5e-38
Identities = 41/148 (27%), Positives = 67/148 (45%), Gaps = 15/148 (10%)
Query: 4 CGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDF 63
GCPSPKV G G +L+ DP+ V E + + +PV+VK R+G DD + + +
Sbjct: 88 MGCPSPKVT-KGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEE---ETLEL 143
Query: 64 IYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGIN 123
+ + +H R E R P ++Y +++ + NG I
Sbjct: 144 AKALED-AGASALTVHGRT--------REQRYSGPADWDYIAE-IKEAVSIPVIANGDIF 193
Query: 124 TVDEVNAALRK-GAHHVMVGRAAYQNPW 150
++++ L + G VM+GR A NPW
Sbjct: 194 SLEDALRCLEQTGVDGVMIGRGALGNPW 221
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 132 bits (335), Expect = 7e-37
Identities = 61/234 (26%), Positives = 102/234 (43%), Gaps = 19/234 (8%)
Query: 4 CGCPSPKVAGHGCFGVSLMLDPKFVGEAMS-VIAANTNVPVSVKCRIGVDDHDSYNQLCD 62
CGCPSPKV G G +L+ +P+ + E + ++ A ++PV+VK R+G DD D L
Sbjct: 100 CGCPSPKVVKGG-AGAALLKNPELLAEIVKAMVEAVGDIPVTVKIRLGWDDDDI---LAL 155
Query: 63 FIYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGI 122
I ++ + +H R + PA+ ++Y L P + NG I
Sbjct: 156 EIARILEDAGADALTVHGRTRAQGYLGPAD--------WDYIKELKEAVPSIPVIANGDI 207
Query: 123 NTVDEVNAALRK-GAHHVMVGRAAYQNPWYTLGHVDTAIYGAPSSGLTRRQVVEKYQIYG 181
++++ L GA VM+GR A NPW L + T +V++ + +
Sbjct: 208 KSLEDAKEMLEYTGADGVMIGRGALGNPW--LFRQIDYLETGELLPPTLAEVLDILREHL 265
Query: 182 DAILGTYGNNRPHVRDVMKPLLHFFHSEPGNGLFKRKADAAFQTCKTVKSFLEE 235
+ +L YG +R + K L ++ PG +R + V+ LE
Sbjct: 266 ELLLEYYGKK--GLRRLRKHLGYYLKGLPGARELRRAL-NKAEDGAEVRRALEA 316
>gnl|CDD|216365 pfam01207, Dus, Dihydrouridine synthase (Dus). Members of this
family catalyze the reduction of the 5,6-double bond of
a uridine residue on tRNA. Dihydrouridine modification
of tRNA is widely observed in prokaryotes and
eukaryotes, and also in some archae. Most
dihydrouridines are found in the D loop of t-RNAs. The
role of dihydrouridine in tRNA is currently unknown, but
may increase conformational flexibility of the tRNA. It
is likely that different family members have different
substrate specificities, which may overlap. Dus 1 from
Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
as a single subunit, requiring NADPH or NADH, and is
stimulated by the presence of FAD. Some family members
may be targeted to the mitochondria and even have a role
in mitochondria.
Length = 309
Score = 113 bits (286), Expect = 9e-30
Identities = 52/223 (23%), Positives = 86/223 (38%), Gaps = 16/223 (7%)
Query: 4 CGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDF 63
GCP+ KV G G +L+ DP V + + + ++PV+VK RIG D +S+ +
Sbjct: 87 MGCPAKKVTRGG-AGAALLRDPDLVAQIVKAVVKAVDIPVTVKIRIGWD--ESHENAVEI 143
Query: 64 IYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGIN 123
+V +H R + A+N P ++ + + + NG I
Sbjct: 144 ARRVEDAGAQ-ALTVHGR-------TRAQNYEG-PADWDAIKQVKQAVS-IPVIANGDIT 193
Query: 124 TVDEVNAALRK-GAHHVMVGRAAYQNPWYTLGHVDTAIYGAPSSGLTRRQVVEKYQIYGD 182
++ L GA VM+GR A NPW T G + E +
Sbjct: 194 DAEDAQRCLSYTGADGVMIGRGALGNPWL-FAEQHTVKTGEFDPRPPLAEEAEIVLEHLS 252
Query: 183 AILGTYGNNRPHVRDVMKPLLHFFHSEPGNGLFKRKADAAFQT 225
+ YG ++ +R K L + PG +R+ + F
Sbjct: 253 YLEEFYGEDK-GLRHARKHLAWYLKGFPGAAELRRELNDVFDP 294
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 70.9 bits (174), Expect = 4e-14
Identities = 56/241 (23%), Positives = 98/241 (40%), Gaps = 20/241 (8%)
Query: 4 CGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDF 63
GCP PK+ G G +L+ DP +G+ + + ++PV+VK RIG DD N
Sbjct: 96 MGCPVPKITKKGA-GSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWDD-AHIN--AVE 151
Query: 64 IYKVSSLSPTRHFIIHSRKA--LLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGG 121
+++ + + +H R +G A I +K +R P + NG
Sbjct: 152 AARIAEDAGAQAVTLHGRTRAQGYSG--EANWDIIARVK-----QAVR-IPVIG---NGD 200
Query: 122 INTVDEVNAAL-RKGAHHVMVGRAAYQNPWYTLGHVDTAIYGAPSSGLTRRQVVEKYQIY 180
I + ++ A L G VM+GR A NPW G T + ++ +
Sbjct: 201 IFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYLTTGKYKPPPTFAEKLDAILRH 260
Query: 181 GDAILGTYGNNRPHVRDVMKPLLHFFHSEPGNGLFKRKADAAFQTCKTVKSFLEETIVAI 240
+ YG ++ +R K + + PGN ++ + A + + VK L++ +
Sbjct: 261 LQLLADYYGESK-GLRIARKHIAWYLKGFPGNAALRQTLNHA-SSFQEVKQLLDDFFETV 318
Query: 241 P 241
Sbjct: 319 G 319
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 43.4 bits (102), Expect = 6e-05
Identities = 41/149 (27%), Positives = 65/149 (43%), Gaps = 18/149 (12%)
Query: 5 GCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDFI 64
GCP+ KV G +L+ P V ++ + +VPV++K R G ++ C I
Sbjct: 99 GCPAKKV-NRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTGWAPE---HRNCVEI 154
Query: 65 YKVSSLSPTRHFIIH--SRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGI 122
+++ + IH +R L NG AE +I +K + ++ NG I
Sbjct: 155 AQLAEDCGIQALTIHGRTRACLFNG--EAEYDSIRAVKQKVSIPVIA---------NGDI 203
Query: 123 NTVDEVNAALR-KGAHHVMVGRAAYQNPW 150
+ A L GA +M+GRAA PW
Sbjct: 204 TDPLKARAVLDYTGADALMIGRAAQGRPW 232
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 40.2 bits (94), Expect = 6e-04
Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 5/63 (7%)
Query: 3 SCGCPSPKVAGHGCFGVSLMLDPKFV---GEAMSVIAANTNVPVSVKCRIGVDDHDSYNQ 59
+CGCPS V G G G +L+ DP+ + +AM A ++PV+VK R+G D + +
Sbjct: 95 NCGCPSKTVNGSGG-GATLLKDPELIYQGAKAMRE-AVPAHLPVTVKVRLGWDSGERKFE 152
Query: 60 LCD 62
+ D
Sbjct: 153 IAD 155
>gnl|CDD|240082 cd04731, HisF, The cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). Imidazole glycerol phosphate synthase
(IGPS) catalyzes the fifth step of histidine
biosynthesis, the formation of the imidazole ring. IGPS
converts
N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-
carboxamide ribonucleotide (PRFAR) to imidazole glycerol
phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide)
ribonucleotide (AICAR). This conversion involves two
tightly coupled reactions in distinct active sites of
IGPS. The two catalytic domains can be fused, like in
fungi and plants, or peformed by a heterodimer
(HisH-glutaminase and HisF-cyclase), like in bacteria.
Length = 243
Score = 37.1 bits (87), Expect = 0.005
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 116 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
T+ GGI ++++ LR GA V + AA +NP
Sbjct: 74 LTVGGGIRSLEDARRLLRAGADKVSINSAAVENP 107
>gnl|CDD|234996 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 253
Score = 37.0 bits (87), Expect = 0.007
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 116 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
T+ GGI +V++ LR GA V + AA NP
Sbjct: 77 LTVGGGIRSVEDARRLLRAGADKVSINSAAVANP 110
>gnl|CDD|216225 pfam00977, His_biosynth, Histidine biosynthesis protein. Proteins
involved in steps 4 and 6 of the histidine biosynthesis
pathway are contained in this family. Histidine is
formed by several complex and distinct biochemical
reactions catalyzed by eight enzymes. The enzymes in
this Pfam entry are called His6 and His7 in eukaryotes
and HisA and HisF in prokaryotes. The structure of HisA
is known to be a TIM barrel fold. In some archaeal HisA
proteins the TIM barrel is composed of two tandem
repeats of a half barrel . This family belong to the
common phosphate binding site TIM barrel family.
Length = 230
Score = 36.3 bits (85), Expect = 0.010
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 113 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
+ + GGI ++++ L GA V++G AA +NP
Sbjct: 73 FIPVQVGGGIRSLEDAERLLSAGADKVIIGTAAVKNP 109
>gnl|CDD|223292 COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme
metabolism].
Length = 296
Score = 35.0 bits (81), Expect = 0.030
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 18 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 50
GV+ M DPK + E M ++ +PV K RIG
Sbjct: 59 GVARMADPKMIEEIMDAVS----IPVMAKVRIG 87
>gnl|CDD|179769 PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS;
Provisional.
Length = 293
Score = 34.7 bits (81), Expect = 0.034
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 18 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 50
GV+ M DPK + E M ++ +PV K RIG
Sbjct: 56 GVARMADPKMIEEIMDAVS----IPVMAKARIG 84
>gnl|CDD|233108 TIGR00735, hisF, imidazoleglycerol phosphate synthase, cyclase
subunit. [Amino acid biosynthesis, Histidine family].
Length = 254
Score = 34.6 bits (80), Expect = 0.037
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 113 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
+ T+ GGI ++++V+ LR GA V + AA +NP
Sbjct: 74 FIPLTVGGGIKSIEDVDKLLRAGADKVSINTAAVKNP 110
>gnl|CDD|132611 TIGR03572, WbuZ, glycosyl amidation-associated protein WbuZ. This
clade of sequences is highly similar to the HisF
protein, but generally represents the second HisF
homolog in the genome where the other is an authentic
HisF observed in the context of a complete histidine
biosynthesis operon. The similarity between these WbuZ
sequences and true HisFs is such that often the closest
match by BLAST of a WbuZ is a HisF. Only by making a
multiple sequence alignment is the homology relationship
among the WbuZ sequences made apparent. WbuZ genes are
invariably observed in the presence of a homolog of the
HisH protein (designated WbuY) and a proposed N-acetyl
sugar amidotransferase designated in WbuX in E. coli ,
IfnA in P. aeriginosa and PseA in C. jejuni. Similarly,
this trio of genes is invariably found in the context of
saccharide biosynthesis loci. It has been shown that the
WbuYZ homologs are not essential components of the
activity expressed by WbuX, leading to the proposal that
these to proteins provide ammonium ions to the
amidotransferase when these are in low concentration.
WbuY (like HisH) is proposed to act as a glutaminase to
release ammonium. In histidine biosynthesis this is also
dispensible in the presence of exogenous ammonium ion.
HisH and HisF form a complex such that the ammonium ion
is passed directly to HisF where it is used in an
amidation reaction causing a subsequent cleavage and
cyclization. In the case of WbuYZ, the ammonium ion
would be passed from WbuY to WbuZ. WbuZ, being
non-essential and so similar to HisF that a sugar
substrate is unlikely, would function instead as a
amoonium channel to the WbuX protein which does the
enzymatic work.
Length = 232
Score = 34.2 bits (79), Expect = 0.044
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 116 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
T+ GGI ++++ L GA V + AA +NP
Sbjct: 77 LTVGGGIRSLEDAKKLLSLGADKVSINTAALENP 110
>gnl|CDD|129443 TIGR00343, TIGR00343, pyridoxal 5'-phosphate synthase, synthase
subunit Pdx1. This protein had been believed to be a
singlet oxygen resistance protein. Subsequent work
showed that it is a protein of pyridoxine (vitamin B6)
biosynthesis, and that pyridoxine quenches the highly
toxic singlet form of oxygen produced by light in the
presence of certain chemicals [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Pyridoxine].
Length = 287
Score = 34.0 bits (78), Expect = 0.073
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 18 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 50
GV+ M DPK + E M ++ +PV K RIG
Sbjct: 49 GVARMSDPKMIKEIMDAVS----IPVMAKVRIG 77
>gnl|CDD|240078 cd04727, pdxS, PdxS is a subunit of the pyridoxal 5'-phosphate
(PLP) synthase, an important enzyme in deoxyxylulose
5-phosphate (DXP)-independent pathway for de novo
biosynthesis of PLP, present in some eubacteria, in
archaea, fungi, plants, plasmodia, and some metazoa.
Together with PdxT, PdxS forms the PLP synthase, a
heteromeric glutamine amidotransferase (GATase),
whereby PdxT produces ammonia from glutamine and PdxS
combines ammonia with five- and three-carbon
phosphosugars to form PLP. PLP is the biologically
active form of vitamin B6, an essential cofactor in
many biochemical processes. PdxS subunits form two
hexameric rings.
Length = 283
Score = 33.8 bits (78), Expect = 0.086
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 18 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 50
GV+ M DPK + E M ++ +PV K RIG
Sbjct: 47 GVARMADPKMIKEIMDAVS----IPVMAKVRIG 75
>gnl|CDD|201920 pfam01680, SOR_SNZ, SOR/SNZ family. Members of this family are
enzymes involved in a new pathway of
pyridoxine/pyridoxal 5-phosphate biosynthesis. This
family was formerly known as UPF0019.
Length = 197
Score = 32.8 bits (75), Expect = 0.10
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 18 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 50
GV+ M DPK + E M+ ++ +PV K RIG
Sbjct: 42 GVARMSDPKMIKEIMNAVS----IPVMAKVRIG 70
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 33.3 bits (77), Expect = 0.11
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 116 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
T+ GGI +V++ LR GA V + AA ++P
Sbjct: 77 LTVGGGIRSVEDARKLLRAGADKVSINSAAVKDP 110
>gnl|CDD|232779 TIGR00007, TIGR00007, phosphoribosylformimino-5-aminoimidazole
carboxamide ribotide isomerase. This protein family
consists of HisA,
phosphoribosylformimino-5-aminoimidazole carboxamide
ribotide isomerase, the enzyme catalyzing the fourth
step in histidine biosynthesis. It is closely related to
the enzyme HisF for the sixth step. Examples of this
enzyme in Actinobacteria have been found to be
bifunctional, also possessing phosphoribosylanthranilate
isomerase activity ; the trusted cutoff here has now
been raised to 275.0 to exclude the bifunctional group,
now represented by model TIGR01919. HisA from
Lactococcus lactis was reported to be inactive
(MEDLINE:93322317) [Amino acid biosynthesis, Histidine
family].
Length = 230
Score = 32.6 bits (75), Expect = 0.15
Identities = 11/41 (26%), Positives = 25/41 (60%)
Query: 108 LRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 148
L ++ +GG++++D++ A + G + V+VG+A Y+
Sbjct: 184 LVKAVNVPVIASGGVSSIDDLIALKKLGVYGVIVGKALYEG 224
Score = 31.4 bits (72), Expect = 0.41
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 120 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
GGI ++++V L G V++G AA +NP
Sbjct: 79 GGIRSLEDVEKLLDLGVDRVIIGTAAVENP 108
>gnl|CDD|130109 TIGR01037, pyrD_sub1_fam, dihydroorotate dehydrogenase (subfamily
1) family protein. This family includes subfamily 1
dihydroorotate dehydrogenases while excluding the
closely related subfamily 2 (TIGR01036). This family
also includes a number of uncharacterized proteins and a
domain of dihydropyrimidine dehydrogenase. The
uncharacterized proteins might all be dihydroorotate
dehydrogenase.
Length = 300
Score = 32.8 bits (75), Expect = 0.18
Identities = 33/149 (22%), Positives = 55/149 (36%), Gaps = 11/149 (7%)
Query: 6 CPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLC---- 61
CP K G +++ DP+ + + + T+VPV K V D +
Sbjct: 128 CPHVKGGG-----IAIGQDPELSADVVKAVKDKTDVPVFAKLSPNVTDITEIAKAAEEAG 182
Query: 62 -DFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNG 120
D + +++L + I + L N I P+ Y + + D+ G
Sbjct: 183 ADGLTLINTLRGMKIDIKTGKPILANKTGGLSGPAIKPIALRMVYDVYKMV-DIPIIGVG 241
Query: 121 GINTVDEVNAALRKGAHHVMVGRAAYQNP 149
GI + ++ L GA V VG A Y
Sbjct: 242 GITSFEDALEFLMAGASAVQVGTAVYYRG 270
>gnl|CDD|237589 PRK14024, PRK14024, phosphoribosyl isomerase A; Provisional.
Length = 241
Score = 32.2 bits (74), Expect = 0.23
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 113 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP-W 150
D+ L+GGI + + AAL G V +G AA +NP W
Sbjct: 75 DVKVELSGGIRDDESLEAALATGCARVNIGTAALENPEW 113
>gnl|CDD|223184 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide
ribonucleotide (ProFAR) isomerase [Amino acid transport
and metabolism].
Length = 241
Score = 31.8 bits (73), Expect = 0.27
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 120 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
GGI ++++V A L G V++G AA +NP
Sbjct: 82 GGIRSLEDVEALLDAGVARVIIGTAAVKNP 111
>gnl|CDD|239237 cd02911, arch_FMN, Archeal FMN-binding domain. This family of
archaeal proteins are part of the NAD(P)H-dependent
flavin oxidoreductase (oxidored) FMN-binding family that
reduce a range of alternative electron acceptors. Most
use FAD/FMN as a cofactor and NAD(P)H as electron donor.
Some contain 4Fe-4S cluster to transfer electron from
FAD to FMN. The specific function of this group is
unknown.
Length = 233
Score = 31.5 bits (72), Expect = 0.38
Identities = 35/142 (24%), Positives = 53/142 (37%), Gaps = 23/142 (16%)
Query: 4 CGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDF 63
C P++ G G +L+ DP+ + E + + T VPVSVK R GVD +L
Sbjct: 105 AHCRQPEMVEAGA-GEALLKDPERLSEFIKALKE-TGVPVSVKIRAGVD--VDDEELARL 160
Query: 64 IYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGIN 123
I K + IIH + P + + +L N +
Sbjct: 161 IEKAGAD------IIHV-------------DAMDPGNHADLKKIRDISTELFIIGNNSVT 201
Query: 124 TVDEVNAALRKGAHHVMVGRAA 145
T++ GA V V RA+
Sbjct: 202 TIESAKEMFSYGADMVSVARAS 223
>gnl|CDD|239201 cd02803, OYE_like_FMN_family, Old yellow enzyme (OYE)-like FMN
binding domain. OYE was the first flavin-dependent
enzyme identified, however its true physiological role
remains elusive to this day. Each monomer of OYE
contains FMN as a non-covalently bound cofactor, uses
NADPH as a reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 327
Score = 31.4 bits (72), Expect = 0.51
Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 6/69 (8%)
Query: 87 GISPAENRTIPPLKYEYYY-----ALLRDFPDLTFTLNGGINTVDEVNAALRKG-AHHVM 140
G + IPP Y ++ + GGI + L +G A V
Sbjct: 250 GSYESPPPIIPPPYVPEGYFLELAEKIKKAVKIPVIAVGGIRDPEVAEEILAEGKADLVA 309
Query: 141 VGRAAYQNP 149
+GRA +P
Sbjct: 310 LGRALLADP 318
>gnl|CDD|176126 cd08435, PBP2_GbpR, The C-terminal substrate binding domain of
galactose-binding protein regulator contains the type 2
periplasmic binding fold. Galactose-binding protein
regulator (GbpR), a member of the LysR family of
bacterial transcriptional regulators, regulates the
expression of chromosomal virulence gene chvE. The
chvE gene is involved in the uptake of specific sugars,
in chemotaxis to these sugars, and in the VirA-VirG
two-component signal transduction system. In the
presence of an inducing sugar such as L-arabinose,
D-fucose, or D-galactose, GbpR activates chvE
expression, while in the absence of an inducing sugar,
GbpR represses expression. 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 = 201
Score = 30.7 bits (70), Expect = 0.63
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 106 ALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAA 145
LL P LT + G T DE+ LR G + +GR A
Sbjct: 21 RLLARHPRLTVRVVEG--TSDELLEGLRAGELDLAIGRLA 58
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 292
Score = 30.7 bits (70), Expect = 0.82
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 116 FTLNGGINTVDEVNAALRKGAHHVM 140
+TL G+ +V+ ++ A++ GA+H M
Sbjct: 203 YTLYEGVGSVEAIDTAMKLGANHPM 227
>gnl|CDD|217235 pfam02800, Gp_dh_C, Glyceraldehyde 3-phosphate dehydrogenase,
C-terminal domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
C-terminal domain is a mixed alpha/antiparallel beta
fold.
Length = 157
Score = 29.8 bits (68), Expect = 0.89
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 113 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 146
DLT L + TV+EVNAAL++ A + G Y
Sbjct: 87 DLTVELEKPV-TVEEVNAALKEAAEGALKGILGY 119
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 29.9 bits (68), Expect = 1.2
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 118 LNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
L GGI + ++ + L G V++G AA +NP
Sbjct: 81 LGGGIRSAEDAASLLDLGVDRVILGTAAVENP 112
>gnl|CDD|239206 cd02812, PcrB_like, PcrB_like proteins. One member of this family,
a protein from Archaeoglobus fulgidus, has been
characterized as a (S)-3-O-geranylgeranylglyceryl
phosphate synthase (AfGGGPS). AfGGGPS catalyzes the
formation of an ether linkage between
sn-glycerol-1-phosphate (G1P) and geranylgeranyl
diphosphate (GGPP), the committed step in archaeal lipid
biosynthesis. Therefore, it has been proposed that
PcrB-like proteins are either prenyltransferases or are
involved in lipoteichoic acid biosynthesis although the
exact function is still unknown.
Length = 219
Score = 29.9 bits (68), Expect = 1.2
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 120 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
GGI + ++ GA ++VG ++P
Sbjct: 182 GGIRSGEQAKEMAEAGADTIVVGNIVEEDP 211
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 30.1 bits (69), Expect = 1.3
Identities = 17/52 (32%), Positives = 20/52 (38%), Gaps = 9/52 (17%)
Query: 3 SCGCPSPKVAGHG-CFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDD 53
SC P V G FG DP+ E + + VPV VK V D
Sbjct: 127 SC----PNVKHGGMAFGT----DPELAYEVVKAVKEVVKVPVIVKLTPNVTD 170
>gnl|CDD|130974 TIGR01919, hisA-trpF,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide
isomerase/N-(5'phosphoribosyl)anthranilate isomerase.
This model represents a bifunctional protein posessing
both hisA
(1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase) and trpF
(N-(5'phosphoribosyl)anthranilate isomerase) activities.
Thus, it is involved in both the histidine and
tryptophan biosynthetic pathways. Enzymes with this
property have been described only in the Actinobacteria
(High-GC gram-positive). The enzyme is closely related
to the monofunctional HisA proteins (TIGR00007) and in
Actinobacteria, the classical monofunctional TrpF is
generally absent.
Length = 243
Score = 29.2 bits (65), Expect = 1.9
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 118 LNGGINTVDEVNAALRKGAHHVMVGRAAYQNPWYT 152
L+GG + AAL G V G AA +NPW+
Sbjct: 79 LSGGRRDDSSLRAALTGGRARVNGGTAALENPWWA 113
>gnl|CDD|240080 cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE)
converts N-acetylmannosamine-6-phosphate to
N-acetylglucosamine-6-phosphate. This reaction is part
of the pathway that allows the usage of sialic acid as a
carbohydrate source. Sialic acids are a family of
related sugars that are found as a component of
glycoproteins, gangliosides, and other
sialoglycoconjugates.
Length = 219
Score = 29.1 bits (66), Expect = 2.1
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 85 LNGISPAENRTIPPLKYEYYYALLRDF---PDLTFTLNGGINTVDEVNAALRKGAHHVMV 141
L+G + +T P + LL++ + G IN+ ++ AL GA V+V
Sbjct: 151 LSGYTEETAKTEDPD-----FELLKELRKALGIPVIAEGRINSPEQAAKALELGADAVVV 205
Query: 142 GRA 144
G A
Sbjct: 206 GSA 208
>gnl|CDD|234907 PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase;
Provisional.
Length = 221
Score = 28.6 bits (65), Expect = 2.8
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 120 GGINTVDEVNAALRKGAHHVMVGRA 144
G INT ++ AL GAH V+VG A
Sbjct: 180 GRINTPEQAKKALELGAHAVVVGGA 204
>gnl|CDD|167709 PRK04128, PRK04128,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 228
Score = 28.6 bits (64), Expect = 2.9
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 113 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 148
D F GG+++ ++V G V++G+A Y+
Sbjct: 182 DEEFIYAGGVSSAEDVKKLAEIGFSGVIIGKALYEG 217
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 29.1 bits (66), Expect = 2.9
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 113 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 146
DLT L + TV+E+NAAL+ + + G Y
Sbjct: 243 DLTVELEKEV-TVEEINAALKAASEIGLKGILGY 275
>gnl|CDD|222800 PHA00458, PHA00458, single-stranded DNA-binding protein.
Length = 233
Score = 28.6 bits (64), Expect = 3.4
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 183 AILGTYGNNRPHVRDVMKPL------LHFFHSEPGNGLFKRKADAAFQTCKTVKSFLEET 236
A L Y N P V+ KPL + FF + G FK K A+++ KT ++ +
Sbjct: 69 AALEEYEANPPKVQRGKKPLKPYEGDMPFFDNGDGTVTFKFKCYASYKDKKTGEN--KPI 126
Query: 237 IVAIPDS 243
++ + DS
Sbjct: 127 VLRVVDS 133
>gnl|CDD|240086 cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 4. Each monomer of OYE contains
FMN as a non-covalently bound cofactor, uses NADPH as a
reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Other members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 353
Score = 28.7 bits (65), Expect = 3.5
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 120 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
G INT D+ AL GA V +GR +P
Sbjct: 291 GSINTPDDALEALETGADLVAIGRGLLVDP 320
>gnl|CDD|234119 TIGR03140, AhpF, alkyl hydroperoxide reductase subunit F. This
enzyme is the partner of the peroxiredoxin (alkyl
hydroperoxide reductase) AhpC which contains the
peroxide-reactive cysteine. AhpF contains the reductant
(NAD(P)H) binding domain (pfam00070) and presumably
acts to resolve the disulfide which forms after
oxidation of the active site cysteine in AphC. This
proteins contains two paired conserved cysteine motifs,
CxxCP and CxHCDGP [Cellular processes, Detoxification,
Cellular processes, Adaptations to atypical
conditions].
Length = 515
Score = 28.9 bits (65), Expect = 3.8
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 22 MLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFII 78
MLD + + S +A+ N V + H+ +L + + +++SLS
Sbjct: 1 MLDQSLLAQLKSYLASLEN---PVTLVLSAGSHEKSKELLELLDEIASLSDKISLTQ 54
>gnl|CDD|188481 TIGR03966, actino_HemFlav, heme/flavin dehydrogenase, mycofactocin
system. Members of this protein family possess an
N-terminal heme-binding domain and C-terminal
flavodehydrogenase domain, and share homology to yeast
flavocytochrome b2, to E. coli L-lactate dehydrogenase
[cytochrome], to (S)-mandelate dehydrogenase, etc. This
enzyme appears only in the context of the mycofactocin
system. Interestingly, it is absent from the four
species detected so far with mycofactocin but without an
F420 biosynthesis system.
Length = 385
Score = 28.6 bits (64), Expect = 4.2
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 118 LNGGINTVDEVNAALRKGAHHVMVGRA 144
L+GGI +V AL GA VM+GRA
Sbjct: 307 LDGGIRRGSDVVKALALGARAVMIGRA 333
>gnl|CDD|235237 PRK04169, PRK04169, geranylgeranylglyceryl phosphate synthase-like
protein; Reviewed.
Length = 232
Score = 28.2 bits (64), Expect = 4.2
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 120 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
GGI + ++ + GA ++VG ++P
Sbjct: 191 GGIRSPEQARELMAAGADTIVVGNIIEEDP 220
>gnl|CDD|237105 PRK12457, PRK12457, 2-dehydro-3-deoxyphosphooctonate aldolase;
Provisional.
Length = 281
Score = 28.2 bits (63), Expect = 4.3
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 113 DLTFTLNGGINTVDEVNAALRKGAHHVMVGR 143
DL F L GGIN ++ ++ L +V V R
Sbjct: 14 DLPFVLFGGINVLESLDFTLDVCGEYVEVTR 44
>gnl|CDD|240090 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like
proteins. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
This subgroup has the conserved FMN binding site, but
lacks some catalytic residues and may therefore be
inactive.
Length = 325
Score = 28.3 bits (64), Expect = 4.9
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 89 SPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 148
SPAE R PL++ A+L + +GG++ ++V L GA VM A ++
Sbjct: 218 SPAEIRL--PLRW---IAILSGRVKASLAASGGVHDAEDVVKYLLAGADVVMTTSALLRH 272
>gnl|CDD|240091 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
Length = 296
Score = 28.3 bits (64), Expect = 5.1
Identities = 43/158 (27%), Positives = 67/158 (42%), Gaps = 25/158 (15%)
Query: 3 SCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLC- 61
SC P V G G++ DP+ V E + + T+VPV VK V D +
Sbjct: 124 SC----PNVKG---GGMAFGTDPEAVAEIVKAVKKATDVPVIVKLTPNVTDIVEIARAAE 176
Query: 62 ----DFIYKVSSLSPTRHFI-IHSRKALLN----GIS-PAENRTIPPLKYEYYYALLRDF 111
D + +++L I I +RK +L G+S PA I P+ Y + +
Sbjct: 177 EAGADGLTLINTLKGMA--IDIETRKPILGNVTGGLSGPA----IKPIALRMVYQVYKAV 230
Query: 112 PDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
++ GGI + ++ L GA V VG A + +P
Sbjct: 231 -EIPIIGVGGIASGEDALEFLMAGASAVQVGTANFVDP 267
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 28.0 bits (63), Expect = 5.2
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 105 YALLRDFPDLTF---TLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
Y L+ + F GGI T+++ G V + AA ++P
Sbjct: 63 YELIENLASECFMPLCYGGGIKTLEQAKKIFSLGVEKVSINTAALEDP 110
>gnl|CDD|240083 cd04732, HisA, HisA. Phosphoribosylformimino-5-aminoimidazole
carboxamide ribonucleotide (ProFAR) isomerase catalyzes
the fourth step in histidine biosynthesis, an
isomerisation of the aminoaldose moiety of ProFAR to the
aminoketose of PRFAR
(N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-
phospho-ribosyl)-4-imidazolecarboxamide). In bacteria
and archaea, ProFAR isomerase is encoded by the HisA
gene.
Length = 234
Score = 27.8 bits (63), Expect = 5.6
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 120 GGINTVDEVNAALRKGAHHVMVGRAAYQN 148
GG++++D++ A G V+VG+A Y+
Sbjct: 197 GGVSSLDDIKALKELGVAGVIVGKALYEG 225
Score = 27.1 bits (61), Expect = 9.8
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 120 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 149
GGI +++++ L G V++G AA +NP
Sbjct: 80 GGIRSLEDIERLLDLGVSRVIIGTAAVKNP 109
>gnl|CDD|233453 TIGR01534, GAPDH-I, glyceraldehyde-3-phosphate dehydrogenase, type
I. This model represents glyceraldehyde-3-phosphate
dehydrogenase (GAPDH), the enzyme responsible for the
interconversion of 1,3-diphosphoglycerate and
glyceraldehyde-3-phosphate, a central step in glycolysis
and gluconeogenesis. Forms exist which utilize NAD (EC
1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In
some species, NAD- and NADP- utilizing forms exist,
generally being responsible for reactions in the
anabolic and catabolic directions respectively. Two PFAM
models cover the two functional domains of this protein;
pfam00044 represents the N-terminal NAD(P)-binding
domain and pfam02800 represents the C-terminal catalytic
domain. An additional form of gap gene is found in gamma
proteobacteria and is responsible for the conversion of
erythrose-4-phosphate (E4P) to 4-phospho-erythronate in
the biosynthesis of pyridoxine. This pathway of
pyridoxine biosynthesis appears to be limited, however,
to a relatively small number of bacterial species
although it is prevalent among the gamma-proteobacteria.
This enzyme is described by TIGR001532. These sequences
generally score between trusted and noise to this GAPDH
model due to the close evolutionary relationship. There
exists the possiblity that some forms of GAPDH may be
bifunctional and act on E4P in species which make
pyridoxine and via hydroxythreonine and lack a separate
E4PDH enzyme (for instance, the GAPDH from Bacillus
stearothermophilus has been shown to posess a limited
E4PD activity as well as a robust GAPDH activity). There
are a great number of sequences in the databases which
score between trusted and noise to this model, nearly
all of them due to fragmentary sequences. It seems that
study of this gene has been carried out in many species
utilizing PCR probes which exclude the extreme ends of
the consenses used to define this model. The noise level
is set relative not to E4PD, but the next closest
outliers, the class II GAPDH's (found in archaea,
TIGR01546) and aspartate semialdehyde dehydrogenase
(ASADH, TIGR01296) both of which have highest-scoring
hits around -225 to the prior model [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 326
Score = 28.0 bits (63), Expect = 6.3
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 113 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 146
DL L + TV+EVNAAL++ A + G Y
Sbjct: 242 DLVVNLEKDV-TVEEVNAALKEAAEGELKGVLGY 274
>gnl|CDD|237236 PRK12858, PRK12858, tagatose 1,6-diphosphate aldolase; Reviewed.
Length = 340
Score = 27.7 bits (62), Expect = 6.5
Identities = 7/46 (15%), Positives = 11/46 (23%), Gaps = 11/46 (23%)
Query: 121 GINTVDEVNAALRKGAHHVMVGRAAYQNPWYTLGHVDTAIYGAPSS 166
G+ + +N L + A PW I
Sbjct: 303 GVANITRLNEVLERTAT-----------PWKDKYGGKDGIEVNDLP 337
>gnl|CDD|189016 cd09609, M3B_PepF_4, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 586
Score = 27.9 bits (63), Expect = 6.6
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 217 RKADAAFQTCKTVKSFLEETIVAIPDSVLDSPIEEAPRGR 256
K D+ SF E ++A+ + +L+ IEE P
Sbjct: 89 AKFDSLAAKINAKLSFFESELLALDEKILEEVIEELPEYA 128
>gnl|CDD|225555 COG3010, NanE, Putative N-acetylmannosamine-6-phosphate epimerase
[Carbohydrate transport and metabolism].
Length = 229
Score = 27.6 bits (62), Expect = 6.8
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 105 YALLRDFPDLTFTL--NGGINTVDEVNAALRKGAHHVMVGRA 144
+ L++ D + G NT ++ A+ GA V+VG A
Sbjct: 170 FQLVKQLSDAGCRVIAEGRYNTPEQAKKAIEIGADAVVVGSA 211
>gnl|CDD|233304 TIGR01180, aman2_put, alpha-1,2-mannosidase, putative. The
identification of members of this family as putative
alpha-1,2-mannosidases is based on an unpublished
characterization of the aman2 gene in Bacillus sp. M-90
by Maruyama,Y., Nakajima,M. and Nakajima,T. (Genbank
accession BAA76709, pid g4587313). Most members of this
family appear to have signal sequences. Members from the
dental pathogen Porphyromonas gingivalis have been
described as immunoreactive with periodontitis patient
serum [Cell envelope, Biosynthesis and degradation of
surface polysaccharides and lipopolysaccharides].
Length = 750
Score = 27.9 bits (62), Expect = 7.5
Identities = 33/143 (23%), Positives = 50/143 (34%), Gaps = 15/143 (10%)
Query: 21 LMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHS 80
L+L G +S++ +T V R G N C F + +P ++ +
Sbjct: 173 LLLLASTGGSEISIVDPHTVVGTISGYRGGF----PANFACYFR--LFFDTPMSDVLLET 226
Query: 81 RKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKG----A 136
G S R ++ Y +RD + + V E NAA G A
Sbjct: 227 TT----GSSDEGTRAWAAQRFGYQLVTVRDLAGTDLASSFASSEVSEANAAENLGQEFQA 282
Query: 137 HHVMVGRAAYQNPW-YTLGHVDT 158
+ GR A+ W LG V T
Sbjct: 283 RIFLAGREAWNKVWGRALGEVGT 305
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.138 0.426
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,895,407
Number of extensions: 1448501
Number of successful extensions: 1338
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1307
Number of HSP's successfully gapped: 65
Length of query: 282
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 186
Effective length of database: 6,679,618
Effective search space: 1242408948
Effective search space used: 1242408948
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: 58 (26.1 bits)