RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026945
(230 letters)
>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 = 154 bits (393), Expect = 5e-47
Identities = 50/129 (38%), Positives = 77/129 (59%), Gaps = 3/129 (2%)
Query: 1 MDNLPLVKSLVEKLALNLNVPVSCKIRVFPNLQD-TIKYAKMLEDAGCSLLAVHGRTRDE 59
+ + LV +V + + +PV+ KIR+ + ++ T++ AK LEDAG S L VHGRTR++
Sbjct: 105 LKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEETLELAKALEDAGASALTVHGRTREQ 164
Query: 60 KDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
ADW+ I +K A+ IPV+ANG++ +ED +CLE+TG +GV+ L NP L
Sbjct: 165 --RYSGPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWL 222
Query: 120 FAGFRTAEW 128
F +
Sbjct: 223 FREIKELLE 231
>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 = 128 bits (323), Expect = 7e-36
Identities = 71/213 (33%), Positives = 101/213 (47%), Gaps = 26/213 (12%)
Query: 6 LVKSLVEKLALNLNVPVSCKIRVFP--NLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGK 63
LV +V+ + +++PV+ KIR+ + ++ ++ A+ +EDAG L VHGRTR
Sbjct: 109 LVAQIVKAVVKAVDIPVTVKIRIGWDESHENAVEIARRVEDAGAQALTVHGRTR--AQNY 166
Query: 64 KFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGF 123
+ ADW+AIK VK A+ IPV+ANG++ ED Q+CL TG +GV+ L NP LFA
Sbjct: 167 EGPADWDAIKQVKQAVSIPVIANGDITDAEDAQRCLSYTGADGVMIGRGALGNPWLFAEQ 226
Query: 124 RTAEWIVGSEEISKDGNLDQADLLVEYL-KLCEKYP---------VPWRMIRSHVHKLLG 173
T + G D L E + E R R H+ L
Sbjct: 227 HTVKT----------GEFDPRPPLAEEAEIVLEHLSYLEEFYGEDKGLRHARKHLAWYL- 275
Query: 174 EWFRIQPGVREDLNAQNRLTFEFLYNLVDRLRE 206
+ F +R +LN T E L NL LR
Sbjct: 276 KGFPGAAELRRELNDVFDPT-EALINLDAALRA 307
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 128 bits (323), Expect = 1e-35
Identities = 67/199 (33%), Positives = 103/199 (51%), Gaps = 16/199 (8%)
Query: 1 MDNLPLVKSLVEKL-ALNLNVPVSCKIRVFPNLQD--TIKYAKMLEDAGCSLLAVHGRTR 57
+ N L+ +V+ + ++PV+ KIR+ + D ++ A++LEDAG L VHGRTR
Sbjct: 117 LKNPELLAEIVKAMVEAVGDIPVTVKIRLGWDDDDILALEIARILEDAGADALTVHGRTR 176
Query: 58 DEKDGKKFRADWNAIKAVKNALR-IPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLEN 116
G ADW+ IK +K A+ IPV+ANG+++ +ED ++ LE TG +GV+ L N
Sbjct: 177 --AQGYLGPADWDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMIGRGALGN 234
Query: 117 PALFAGFRTAEWIVGSEEISKDGNLDQADLLVEYLKLCEKYP--VPWRMIRSHVHKLLGE 174
P LF E + E+ + D+L E+L+L +Y R +R H+ L
Sbjct: 235 PWLFRQIDYLE----TGELLPPTLAEVLDILREHLELLLEYYGKKGLRRLRKHLGYYLKG 290
Query: 175 WFRIQPGVREDLNAQNRLT 193
PG RE A N+
Sbjct: 291 L----PGARELRRALNKAE 305
>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 = 100 bits (251), Expect = 3e-25
Identities = 61/208 (29%), Positives = 106/208 (50%), Gaps = 20/208 (9%)
Query: 6 LVKSLVEKLALNLNVPVSCKIRVF--PNLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGK 63
L+ +V+ + +++PV+ KIR+ + ++ A++ EDAG + +HGRTR + G
Sbjct: 118 LIGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDAGAQAVTLHGRTRAQ--GY 175
Query: 64 KFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGF 123
A+W+ I VK A+RIPV+ NG++ ED + LE TGC+GV+ L NP LF
Sbjct: 176 SGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFR-- 233
Query: 124 RTAEWIVGSEEISKDGNLDQADLLVEYLKLCEKY---PVPWRMIRSHV-HKLLGEWFRIQ 179
+ +++ + ++ D ++ +L+L Y R+ R H+ L G
Sbjct: 234 QIEQYLTTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHIAWYLKGF----- 288
Query: 180 PGV---REDLNAQNRLTFEFLYNLVDRL 204
PG R+ LN + +F+ + L+D
Sbjct: 289 PGNAALRQTLNHAS--SFQEVKQLLDDF 314
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 69.5 bits (170), Expect = 5e-14
Identities = 35/107 (32%), Positives = 61/107 (57%), Gaps = 4/107 (3%)
Query: 15 ALNLNVPVSCKIRV-FPNLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDG-KKFRADWNAI 72
A+ ++PV+ K+R+ + + + + A ++ AG + L VHGRT++ DG + +W AI
Sbjct: 129 AVPAHLPVTVKVRLGWDSGERKFEIADAVQQAGATELVVHGRTKE--DGYRAEHINWQAI 186
Query: 73 KAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
++ L IPV+ANG + + Q+C+ TGC+ V+ L P L
Sbjct: 187 GEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIPNL 233
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 64.2 bits (156), Expect = 4e-12
Identities = 38/118 (32%), Positives = 70/118 (59%), Gaps = 6/118 (5%)
Query: 6 LVKSLVEKLALNLNVPVSCKIRV--FPNLQDTIKYAKMLEDAGCSLLAVHGRTRD-EKDG 62
LVKS++ ++ ++VPV+ KIR P ++ ++ A++ ED G L +HGRTR +G
Sbjct: 120 LVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG 179
Query: 63 KKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALF 120
+ A++++I+AVK + IPV+ANG++ + L+ TG + ++ + P +F
Sbjct: 180 E---AEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIF 234
>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 = 60.7 bits (148), Expect = 6e-11
Identities = 30/113 (26%), Positives = 51/113 (45%), Gaps = 12/113 (10%)
Query: 19 NVPVSCKI---RVFPN---LQDTIKYAKMLEDAGCSLLAVHGRTRDEK----DGKKFRAD 68
+ PV ++ P L++ I+ AK LE+AG L V G + +
Sbjct: 208 DFPVGVRLSADDFVPGGLTLEEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVPEG 267
Query: 69 WNA--IKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
+ + +K A++IPV+A G +R E ++ L E + V +LL +P L
Sbjct: 268 YFLELAEKIKKAVKIPVIAVGGIRDPEVAEEILAEGKADLVALGRALLADPDL 320
>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 = 44.0 bits (105), Expect = 2e-05
Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 34 DTIKYAKMLEDAGCS---LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVR 90
D +++AK LE+ G L + +DG D + + A+ IPV+A+G V
Sbjct: 149 DAVEWAKKLEELGAGEILLTDID------RDGTLSGPDLELTRELAEAVNIPVIASGGVG 202
Query: 91 HMEDVQKCLEETGCEGVLSAESLLEN 116
+ED+++ L G +GV++ +L E
Sbjct: 203 SLEDLKE-LFSEGVDGVIAGSALHEG 227
Score = 30.1 bits (69), Expect = 0.68
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 21/109 (19%)
Query: 34 DTIKYAKMLEDAGCSLL-------AVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
D ++ AK E+ G L A GR + I+ + + IPV
Sbjct: 30 DPVELAKRYEEEGADELHFVDLDAAKEGRPVNLD----------LIEEIAEEVFIPVQVG 79
Query: 87 GNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGFRTAEWIVGSEEI 135
G +R +ED ++ L G + V+ + ++NP L + A GS+ I
Sbjct: 80 GGIRSLEDAERLLSA-GADKVIIGTAAVKNPEL---IKEAAEKFGSQCI 124
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 42.5 bits (101), Expect = 7e-05
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
D +++AK +E+ AG LL T ++DG K D +AV+ A+ IPV+A+G
Sbjct: 156 DAVEWAKEVEELGAGEILL-----TSMDRDGTKAGYDLELTRAVREAVNIPVIASGGAGK 210
Query: 92 MEDVQKCLEETGCEGVLSA 110
E + E + L+A
Sbjct: 211 PEHFVEAFTEGKADAALAA 229
>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 = 42.1 bits (100), Expect = 8e-05
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 36 IKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDV 95
+ AK E+ G + T +DG ++ K + A IPV+A+G V ++D+
Sbjct: 149 EELAKRFEELGVKAIIY---TDISRDGTLSGPNFELYKELAAATGIPVIASGGVSSLDDI 205
Query: 96 QKCLEETGCEGVLSAESLLEN 116
+ L+E G GV+ ++L E
Sbjct: 206 KA-LKELGVAGVIVGKALYEG 225
Score = 29.8 bits (68), Expect = 1.0
Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 20/105 (19%)
Query: 69 WNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGFRTAEW 128
I+ + A+ IPV G +R +ED+++ L + G V+ + ++NP L E
Sbjct: 62 LELIEEIVKAVGIPVQVGGGIRSLEDIERLL-DLGVSRVIIGTAAVKNPELV-----KEL 115
Query: 129 I--VGSEEI-----SKDGN------LDQADL-LVEYLKLCEKYPV 159
+ G E I +KDG L+ +++ L E K E+ V
Sbjct: 116 LKEYGGERIVVGLDAKDGKVATKGWLETSEVSLEELAKRFEELGV 160
>gnl|CDD|223184 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide
ribonucleotide (ProFAR) isomerase [Amino acid transport
and metabolism].
Length = 241
Score = 41.8 bits (99), Expect = 1e-04
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 39 AKMLEDAGCSLLAVHGRTRD-EKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQK 97
AK LE+ G + + D +DG + + +K + A+ IPV+A+G V ++D++
Sbjct: 153 AKRLEEVGLAHILYT----DISRDGTLSGPNVDLVKELAEAVDIPVIASGGVSSLDDIKA 208
Query: 98 CLEETGCEGVLSAESLLEN 116
E +G EGV+ +L E
Sbjct: 209 LKELSGVEGVIVGRALYEG 227
>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 = 40.5 bits (96), Expect = 3e-04
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 34 DTIKYAKMLEDAGCS--LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
D +++AK +E+ G LL T ++DG K D I+AV +A+ IPV+A+G
Sbjct: 150 DAVEWAKEVEELGAGEILL-----TSMDRDGTKKGYDLELIRAVSSAVNIPVIASGGAGK 204
Query: 92 MEDVQKCLEETGCEGVLSA 110
E + EE G + L+A
Sbjct: 205 PEHFVEAFEEGGADAALAA 223
>gnl|CDD|239242 cd02932, OYE_YqiM_FMN, Old yellow enzyme (OYE) YqjM-like FMN
binding domain. YqjM is involved in the oxidative stress
response of Bacillus subtilis. Like the other OYE
members, each monomer of YqjM contains FMN as a
non-covalently bound cofactor and uses NADPH as a
reducing agent. The YqjM enzyme exists as a
homotetramer that is assembled as a dimer of
catalytically dependent dimers, while other OYE members
exist only as monomers or dimers. Moreover, the protein
displays a shared active site architecture where an
arginine finger at the COOH terminus of one monomer
extends into the active site of the adjacent monomer and
is directly involved in substrate recognition. Another
remarkable difference in the binding of the ligand in
YqjM is represented by the contribution of the
NH2-terminal tyrosine instead of a COOH-terminal
tyrosine in OYE and its homologs.
Length = 336
Score = 38.6 bits (91), Expect = 0.002
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 8/91 (8%)
Query: 32 LQDTIKYAKMLEDAGCSLLAV-----HGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
L+D+++ AK L++ G L+ V + G ++ + A + ++ IPV+A
Sbjct: 240 LEDSVELAKALKELGVDLIDVSSGGNSPAQKIPV-GPGYQVPF-A-ERIRQEAGIPVIAV 296
Query: 87 GNVRHMEDVQKCLEETGCEGVLSAESLLENP 117
G + E + LE + V LL NP
Sbjct: 297 GLITDPEQAEAILESGRADLVALGRELLRNP 327
>gnl|CDD|184072 PRK13475, PRK13475, ribulose bisphosphate carboxylase; Provisional.
Length = 443
Score = 37.8 bits (88), Expect = 0.003
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 12/66 (18%)
Query: 35 TIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVK-------NALRIP----V 83
T+ Y KM E + + RD G + +W +K NALR+P
Sbjct: 324 TMGYGKM-EGEADDRVIAYMIERDSAQGPFYHQEWYGMKPTTPIISGGMNALRLPGFFDN 382
Query: 84 LANGNV 89
L +GNV
Sbjct: 383 LGHGNV 388
>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 = 37.1 bits (86), Expect = 0.005
Identities = 32/143 (22%), Positives = 54/143 (37%), Gaps = 35/143 (24%)
Query: 1 MDNLPLVKSLVEKLALNLNVPVSCKIRVFPNLQDT----IKYAKMLEDAGCSLLAVHGRT 56
M N LV V+ + +N+PV+ K R+ + D+ + +++ GC VH R
Sbjct: 105 MGNADLVADCVKAMQEAVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHARK 164
Query: 57 RDEKDGKKFRADWNAIKAVKNALRIPVL------------------ANGNVRHMEDVQKC 98
W + + K IP L NG +++ E +++
Sbjct: 165 A-----------WLSGLSPKENREIPPLRYERVYQLKKDFPHLTIEINGGIKNSEQIKQH 213
Query: 99 LEETGCEGVLSAESLLENPALFA 121
L +GV+ ENP L A
Sbjct: 214 LSHV--DGVMVGREAYENPYLLA 234
>gnl|CDD|233108 TIGR00735, hisF, imidazoleglycerol phosphate synthase, cyclase
subunit. [Amino acid biosynthesis, Histidine family].
Length = 254
Score = 36.2 bits (84), Expect = 0.007
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
D +++AK +E AG LL T +KDG K D KAV A++IPV+A+G
Sbjct: 156 DAVEWAKEVEKLGAGEILL-----TSMDKDGTKSGYDLELTKAVSEAVKIPVIASGGAGK 210
Query: 92 MEDVQKCLEETGCEGVLSA 110
E + + + L+A
Sbjct: 211 PEHFYEAFTKGKADAALAA 229
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 35.3 bits (82), Expect = 0.014
Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 6/85 (7%)
Query: 33 QDTIKYAKMLEDAG-CSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
++ AK E+ G S+L T + +G + +K + +++ IPV+A+G V
Sbjct: 149 YTPVEAAKRFEELGAGSILF----TNVDVEGLLEGVNTEPVKELVDSVDIPVIASGGVTT 204
Query: 92 MEDVQKCLEETGCEGVLSAESLLEN 116
++D++ L+E G GV+ +L +
Sbjct: 205 LDDLRA-LKEAGAAGVVVGSALYKG 228
>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 = 35.3 bits (82), Expect = 0.016
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 39 AKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKC 98
AK LE+ G L T +DG ++ K + A+ +PV+A+G V ++D+
Sbjct: 151 AKRLEELG---LEGIIYTDISRDGTLSGPNFELTKELVKAVNVPVIASGGVSSIDDLIA- 206
Query: 99 LEETGCEGVLSAESLLEN 116
L++ G GV+ ++L E
Sbjct: 207 LKKLGVYGVIVGKALYEG 224
>gnl|CDD|173976 cd08211, RuBisCO_large_II, Ribulose bisphosphate carboxylase large
chain, Form II. Ribulose bisphosphate carboxylase
(Rubisco) plays an important role in the Calvin
reductive pentose phosphate pathway. It catalyzes the
primary CO2 fixation step. Rubisco is activated by
carbamylation of an active site lysine, stabilized by a
divalent cation, which then catalyzes the proton
abstraction from the substrate ribulose 1,5 bisphosphate
(RuBP) and leads to the formation of two molecules of
3-phosphoglycerate. Members of the Rubisco family can be
divided into 4 subgroups, Form I-IV , which differ in
their taxonomic distribution and subunit composition.
Form II is mainly found in bacteria, and forms large
subunit oligomers (dimers, tetramers, etc.) that do not
include small subunits.
Length = 439
Score = 35.6 bits (82), Expect = 0.019
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 12/67 (17%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVK-------NALRIP---- 82
T+ + KM ++ ++A + RDE G F W +K NALR+P
Sbjct: 322 GTMGFGKMEGESSDKVIA-YMIERDEAQGPLFNQKWYGMKPTTPIISGGMNALRLPGFFE 380
Query: 83 VLANGNV 89
L NGNV
Sbjct: 381 NLGNGNV 387
>gnl|CDD|224814 COG1902, NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme
family [Energy production and conversion].
Length = 363
Score = 35.3 bits (82), Expect = 0.020
Identities = 22/103 (21%), Positives = 37/103 (35%), Gaps = 4/103 (3%)
Query: 21 PVSCKIRVFPNLQDTIKYAKMLEDAG-CSLLAV---HGRTRDEKDGKKFRADWNAIKAVK 76
P +++ ++ AK LE+AG + V +K
Sbjct: 225 PDDFFDGGGLTIEEAVELAKALEEAGLVDYIHVSEGGYERGGTITVSGPGYQVEFAARIK 284
Query: 77 NALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
A+RIPV+A G + E ++ L + V L +P L
Sbjct: 285 KAVRIPVIAVGGINDPEQAEEILASGRADLVAMGRPFLADPDL 327
>gnl|CDD|240074 cd04723, HisA_HisF, Phosphoribosylformimino-5-aminoimidazole
carboxamide ribonucleotide (ProFAR) isomerase (HisA) and
the cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). The 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. The 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 = 233
Score = 34.9 bits (81), Expect = 0.021
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 60 KDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLE 115
+ G D ++ + IPV+A G VR +ED++ L++ G G L A +L +
Sbjct: 169 RVGSGQGPDLELLERLAARADIPVIAAGGVRSVEDLEL-LKKLGASGALVASALHD 223
>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 = 34.6 bits (80), Expect = 0.022
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 93
D +++A+ E G + + ++DG D IK V +A+ IPV+A G ++
Sbjct: 154 DPVEWAREAEQLGAGEILL---NSIDRDGTMKGYDLELIKTVSDAVSIPVIALGGAGSLD 210
Query: 94 DVQKCLEETGCEGVLSAESLL 114
D+ + E G V +A SL
Sbjct: 211 DLVEVALEAGASAV-AAASLF 230
>gnl|CDD|215729 pfam00117, GATase, Glutamine amidotransferase class-I.
Length = 186
Score = 34.2 bits (79), Expect = 0.028
Identities = 14/30 (46%), Positives = 16/30 (53%)
Query: 196 FLYNLVDRLRELGVRIPLYKKDADDAEILA 225
F YNL LRELGV + + D EIL
Sbjct: 9 FTYNLARALRELGVEVEVVPNDTPAEEILE 38
>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 = 33.8 bits (78), Expect = 0.039
Identities = 21/101 (20%), Positives = 42/101 (41%), Gaps = 12/101 (11%)
Query: 1 MDNLPLVKSLVEKLALNLNVPVSCKIRVFPNLQ-DTIKYAKMLEDAGCSLLAVHGRTRDE 59
+ + + ++ L VPVS KIR + D + A+++E AG +H D
Sbjct: 122 LKDPERLSEFIKALK-ETGVPVSVKIRA--GVDVDDEELARLIEKAGA--DIIHVDAMDP 176
Query: 60 KDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLE 100
+ AD I+ + + ++ N +V +E ++
Sbjct: 177 GNH----ADLKKIRDIST--ELFIIGNNSVTTIESAKEMFS 211
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 33.8 bits (78), Expect = 0.054
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 34 DTIKYAKMLEDAG-CSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHM 92
D ++ AK E G +L ++DG D +K+ +NAL+IP++A G +
Sbjct: 153 DPLELAKEYEALGAGEILL----NSIDRDGTMKGYDLELLKSFRNALKIPLIALGGAGSL 208
Query: 93 EDVQKCLEETGCEGVLSAESLL 114
+D+ + + G + +A SL
Sbjct: 209 DDIVEAILNLGADAA-AAGSLF 229
>gnl|CDD|234996 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 253
Score = 33.5 bits (78), Expect = 0.059
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 13/82 (15%)
Query: 34 DTIKYAKMLEDAGCS--LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANG---N 88
D +++AK +E+ G LL T ++DG K D +AV +A+ +PV+A+G N
Sbjct: 154 DAVEWAKEVEELGAGEILL-----TSMDRDGTKNGYDLELTRAVSDAVNVPVIASGGAGN 208
Query: 89 VRHMEDVQKCLEETGCEGVLSA 110
+ H + E G + L+A
Sbjct: 209 LEHFVEA---FTEGGADAALAA 227
>gnl|CDD|179108 PRK00748, PRK00748,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Validated.
Length = 233
Score = 33.5 bits (78), Expect = 0.060
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 69 WNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLEN 116
A + + A+ IPV+A+G V ++D++ EGV+ +L E
Sbjct: 179 VEATRELAAAVPIPVIASGGVSSLDDIKALKGLGAVEGVIVGRALYEG 226
Score = 30.8 bits (71), Expect = 0.39
Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 18/90 (20%)
Query: 39 AKMLEDAGCSLL-------AVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
AK ED G L A G+ + + I+A+ A+ IPV G +R
Sbjct: 36 AKAWEDQGAKWLHLVDLDGAKAGKPVNLE----------LIEAIVKAVDIPVQVGGGIRS 85
Query: 92 MEDVQKCLEETGCEGVLSAESLLENPALFA 121
+E V+ L + G V+ + ++NP L
Sbjct: 86 LETVEALL-DAGVSRVIIGTAAVKNPELVK 114
>gnl|CDD|235552 PRK05670, PRK05670, anthranilate synthase component II;
Provisional.
Length = 189
Score = 33.2 bits (77), Expect = 0.062
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 196 FLYNLVDRLRELGVRIPLYKKDADDAEILA 225
F YNLV L ELG + +Y+ D E +
Sbjct: 11 FTYNLVQYLGELGAEVVVYRNDEITLEEIE 40
>gnl|CDD|178226 PLN02617, PLN02617, imidazole glycerol phosphate synthase hisHF.
Length = 538
Score = 33.1 bits (76), Expect = 0.11
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 62 GKKFRADWNAIKAVKNALRIPVLAN---GNVRHMEDVQKCLEETGCEGVLSA 110
GK F D +K V +A+ IPV+A+ G H DV +T L+A
Sbjct: 466 GKGF--DIELVKLVSDAVTIPVIASSGAGTPEHFSDV---FSKTNASAALAA 512
>gnl|CDD|172156 PRK13587, PRK13587,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 234
Score = 32.5 bits (74), Expect = 0.12
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 12/81 (14%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRD-----------EKDGKKFRADWNAIKAVKNALRIP 82
+ IK ED +L + + D KDGK ++ + A IP
Sbjct: 135 EDIKVNGWEEDTELNLFSFVRQLSDIPLGGIIYTDIAKDGKMSGPNFELTGQLVKATTIP 194
Query: 83 VLANGNVRHMEDVQKCLEETG 103
V+A+G +RH +D+Q+ L
Sbjct: 195 VIASGGIRHQQDIQR-LASLN 214
>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 = 32.5 bits (75), Expect = 0.13
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 34 DTIKYAKMLEDAGCSLL--AVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
T++ A G ++ + G T + + D+ +K ++ AL IPV+A G +
Sbjct: 131 STLEEALNAAKLGFDIIGTTLSGYTEETAKTED--PDFELLKELRKALGIPVIAEGRINS 188
Query: 92 MEDVQKCLE 100
E K LE
Sbjct: 189 PEQAAKALE 197
>gnl|CDD|132172 TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. Members of
this protein family are 3-hexulose-6-phosphate synthase
(HPS), or the HPS domain of a fusion protein. This
enzyme is part of the ribulose monophosphate (RuMP)
pathway, which in one direction removes the toxic
metabolite formaldehyde by assimilation into
fructose-6-phosphate. In the other direction, in species
lacking a complete pentose phosphate pathway, the RuMP
pathway yields ribulose-5-phosphate, necessary for
nucleotide biosynthesis, at the cost of also yielding
formaldehyde. These latter species tend usually have a
formaldehyde-activating enzyme to attach formaldehyde to
the C1 carrier tetrahydromethanopterin. In these
species, the enzyme is viewed as a lyase rather than a
synthase and is called D-arabino 3-hexulose 6-phosphate
formaldehyde lyase. Note that there is some overlap in
specificity with the Escherichia coli enzyme
3-keto-L-gulonate 6-phosphate decarboxylase.
Length = 206
Score = 32.0 bits (73), Expect = 0.17
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 31 NLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVR 90
N++D +K AK L++ G + VH ++ G+ D I + R+ V N+
Sbjct: 111 NVKDKVKRAKELKELGADYIGVHTGLDEQAKGQNPFEDLQTILKLVKEARVAVAGGINLD 170
Query: 91 HMEDVQK 97
+ DV K
Sbjct: 171 TIPDVIK 177
>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 = 32.0 bits (73), Expect = 0.19
Identities = 32/113 (28%), Positives = 47/113 (41%), Gaps = 24/113 (21%)
Query: 3 NLPLVKSLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLL----AVHGRTRD 58
+ L +V+ + +VPV K+ PN+ D + AK E+AG L + G D
Sbjct: 141 DPELSADVVKAVKDKTDVPVFAKLS--PNVTDITEIAKAAEEAGADGLTLINTLRGMKID 198
Query: 59 EKDGKKFRADWN------AIKAVKNALR----------IPVLANGNVRHMEDV 95
K GK A+ AIK + ALR IP++ G + ED
Sbjct: 199 IKTGKPILANKTGGLSGPAIKPI--ALRMVYDVYKMVDIPIIGVGGITSFEDA 249
>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 = 32.2 bits (74), Expect = 0.22
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 48 SLLAVHGRTRDEKDGKKFRADWNAIKAVKNAL--RIPVLANGNVRHMEDVQKCLEETGCE 105
SL ++R +D + ++ VK + R+P++A G++ +D + L ETG +
Sbjct: 255 SLWDFDRKSRRGRDDNQTI-----MELVKERIAGRLPLIAVGSINTPDDALEAL-ETGAD 308
Query: 106 GVLSAESLLENP 117
V LL +P
Sbjct: 309 LVAIGRGLLVDP 320
>gnl|CDD|224329 COG1411, COG1411, Uncharacterized protein related to proFAR
isomerase (HisA) [General function prediction only].
Length = 229
Score = 31.7 bits (72), Expect = 0.23
Identities = 25/82 (30%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 93
+T+K D G +L + G K D+ + V PVL G V ME
Sbjct: 141 ETVKDLNYRRDPGLIVLDIGAV------GTKSGPDYELLTKVLELSEHPVLLGGGVGGME 194
Query: 94 DVQKCLEETGCEGVLSAESLLE 115
D++ L G GVL A +L E
Sbjct: 195 DLELLL-GMGVSGVLVATALHE 215
>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 = 31.3 bits (71), Expect = 0.26
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 39 AKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRHMEDV 95
A++ E+AG +++A+ D G R +D IK + NA+ IPV+A + H +
Sbjct: 16 ARIAEEAGAVAVMALERVPADIRAAGGVARMSDPKMIKEIMNAVSIPVMAKVRIGHFVEA 75
Query: 96 QKCLEETGCEGVLSAESL 113
Q LE G + + +E L
Sbjct: 76 Q-ILEAIGVDYIDESEVL 92
>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 = 31.3 bits (71), Expect = 0.32
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 39 AKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRHMEDV 95
AK+ E+AG +++A+ D G R +D IK + +A+ IPV+A + H +
Sbjct: 23 AKIAEEAGAVAVMALERVPADIRASGGVARMSDPKMIKEIMDAVSIPVMAKVRIGHFVEA 82
Query: 96 QKCLEETGCEGVLSAESL 113
Q LE G + + +E L
Sbjct: 83 Q-ILEALGVDYIDESEVL 99
>gnl|CDD|236998 PRK11840, PRK11840, bifunctional sulfur carrier protein/thiazole
synthase protein; Provisional.
Length = 326
Score = 31.3 bits (71), Expect = 0.35
Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 39 AKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKC 98
AK LEDAG +AV G + + I+ + +PVL + V D
Sbjct: 211 AKRLEDAGA--VAVMPLGAPIGSGLGIQ-NPYTIRLIVEGATVPVLVDAGVGTASDAAVA 267
Query: 99 LEETGCEGVLSAESLLE--NPALFA 121
+ E GC+GVL ++ E NP L A
Sbjct: 268 M-ELGCDGVLMNTAIAEAKNPVLMA 291
>gnl|CDD|235465 PRK05437, PRK05437, isopentenyl pyrophosphate isomerase;
Provisional.
Length = 352
Score = 31.3 bits (72), Expect = 0.39
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 19/79 (24%)
Query: 39 AKMLEDAGCSLLAVHG------------RTRDEKDGKKFRADW-----NAIKAVKNAL-R 80
AK L DAG + V G R RD++ F ADW ++ ++ L
Sbjct: 203 AKRLADAGVKAIDVAGAGGTSWAAIENYRARDDRLASYF-ADWGIPTAQSLLEARSLLPD 261
Query: 81 IPVLANGNVRHMEDVQKCL 99
+P++A+G +R+ D+ K L
Sbjct: 262 LPIIASGGIRNGLDIAKAL 280
>gnl|CDD|223586 COG0512, PabA, Anthranilate/para-aminobenzoate synthases component
II [Amino acid transport and metabolism / Coenzyme
metabolism].
Length = 191
Score = 29.8 bits (68), Expect = 0.86
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 196 FLYNLVDRLRELGVRIPLYKKDADDAEILADD 227
F YNLV LRELG + + + D E++
Sbjct: 13 FTYNLVQYLRELGAEVTVVRNDDISLELIEAL 44
>gnl|CDD|234907 PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase;
Provisional.
Length = 221
Score = 29.3 bits (67), Expect = 1.1
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 34 DTIKYAKMLEDAGCSLLA--VHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
T++ + G + + G T + K K D+ +K + A+ PV+A G +
Sbjct: 127 STLEEGLAAQKLGFDFIGTTLSGYTEETK--KPEEPDFALLKELLKAVGCPVIAEGRINT 184
Query: 92 MEDVQKCLEETGCEGV 107
E +K L E G V
Sbjct: 185 PEQAKKAL-ELGAHAV 199
>gnl|CDD|239240 cd02930, DCR_FMN, 2,4-dienoyl-CoA reductase (DCR) FMN-binding
domain. DCR in E. coli is an iron-sulfur flavoenzyme
which contains FMN, FAD, and a 4Fe-4S cluster. It is
also a monomer, unlike that of its eukaryotic
counterparts which form homotetramers and lack the
flavin and iron-sulfur cofactors. Metabolism of
unsaturated fatty acids requires auxiliary enzymes in
addition to those used in b-oxidation. After a given
number of cycles through the b-oxidation pathway, those
unsaturated fatty acyl-CoAs with double bonds at
even-numbered carbon positions contain 2-trans, 4-cis
double bonds that can not be modified by enoyl-CoA
hydratase. DCR utilizes NADPH to remove the C4-C5 double
bond. DCR can catalyze the reduction of both natural
fatty acids with cis double bonds, as well as substrates
containing trans double bonds. The reaction is initiated
by hybrid transfer from NADPH to FAD, which in turn
transfers electrons, one at a time, to FMN via the
4Fe-4S cluster. The fully reduced FMN provides a hydrid
ion to the C5 atom of substrate, and Tyr and His are
proposed to form a catalytic dyad that protonates the C4
atom of the substrate and completes the reaction.
Length = 353
Score = 29.9 bits (68), Expect = 1.2
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 66 RADWN-AIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFA 121
R + A +K A+ IPV+A+ + E ++ L + + V A L +P A
Sbjct: 261 RGAFAWATAKLKRAVDIPVIASNRINTPEVAERLLADGDADMVSMARPFLADPDFVA 317
>gnl|CDD|240079 cd04728, ThiG, Thiazole synthase (ThiG) is the tetrameric enzyme
that is involved in the formation of the thiazole moiety
of thiamin pyrophosphate, an essential ubiquitous
cofactor that plays an important role in carbohydrate
and amino acid metabolism. ThiG catalyzes the formation
of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP)
and dehydroglycine, with the help of the sulfur carrier
protein ThiS that carries the sulfur needed for thiazole
assembly on its carboxy terminus (ThiS-COSH).
Length = 248
Score = 29.0 bits (66), Expect = 1.6
Identities = 27/106 (25%), Positives = 46/106 (43%), Gaps = 15/106 (14%)
Query: 28 VFPNLQDTIKYAKMLEDAGCS----LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPV 83
V P D AK LEDAGC+ L + G G+ +N ++ + +PV
Sbjct: 126 VLPYCTDDPVLAKRLEDAGCAAVMPLGSPIG------SGQGLLNPYN-LRIIIERADVPV 178
Query: 84 LANGNVRHMEDVQKCLEETGCEGVL--SAESLLENPALFA-GFRTA 126
+ + + D + + E G + VL +A + ++P A F+ A
Sbjct: 179 IVDAGIGTPSDAAQAM-ELGADAVLLNTAIAKAKDPVAMARAFKLA 223
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 29.4 bits (67), Expect = 1.7
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 12/63 (19%)
Query: 2 DNLPLVKSLVEKLALNLNVPVSCKIRVFPNL-QDTIKYAKMLEDAGCSLLAVHG----RT 56
+ LP ++ L L + P SC VF N ++ + A L G S LA+HG R
Sbjct: 228 ERLPALQRL-----LLHHQPESCV--VFCNTKKECQEVADALNAQGFSALALHGDLEQRD 280
Query: 57 RDE 59
RD+
Sbjct: 281 RDQ 283
>gnl|CDD|119340 cd00377, ICL_PEPM, Members of the ICL/PEPM enzyme family catalyze
either P-C or C-C bond formation/cleavage. Known members
are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate
hydrolase (PPH), carboxyPEP mutase (CPEP mutase),
oxaloacetate hydrolase (OAH), isocitrate lyase (ICL),
and 2-methylisocitrate lyase (MICL). Isocitrate lyase
(ICL) catalyzes the conversion of isocitrate to
succinate and glyoxylate, the first committed step in
the glyoxylate pathway. This carbon-conserving pathway
is present in most prokaryotes, lower eukaryotes and
plants, but has not been observed in vertebrates. PEP
mutase (PEPM) turns phosphoenolpyruvate (PEP) into
phosphonopyruvate (P-pyr), an important intermediate in
the formation of organophosphonates, which function as
antibiotics or play a role in pathogenesis or signaling.
P-pyr can be hydrolyzed by phosphonopyruvate hydrolase
(PPH) to from pyruvate and phosphate. Oxaloacetate
acetylhydrolase (OAH) catalyzes the hydrolytic cleavage
of oxaloacetate to form acetate and oxalate, an
important pathway to produce oxalate in filamentous
fungi. 2-methylisocitrate lyase (MICL) cleaves
2-methylisocitrate to pyruvate and succinate, part of
the methylcitrate cycle for the alpha-oxidation of
propionate.
Length = 243
Score = 29.0 bits (66), Expect = 1.8
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 11/55 (20%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
L + I+ AK +AG + V G D I+A A +P+ N
Sbjct: 159 LDEAIERAKAYAEAGADGIFVEGLK-----------DPEEIRAFAEAPDVPLNVN 202
>gnl|CDD|225877 COG3340, PepE, Peptidase E [Amino acid transport and metabolism].
Length = 224
Score = 28.9 bits (65), Expect = 1.9
Identities = 22/129 (17%), Positives = 43/129 (33%), Gaps = 21/129 (16%)
Query: 37 KYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQ 96
K L G + +H + AI+ I + GN ++
Sbjct: 53 KVRNALAKLGLEVSELH----------LSKPPLAAIENKLMKADIIYVGGGNTFNL---L 99
Query: 97 KCLEETGCEGVLSAESLLENPALFAGFRTAEWIVGSEEISKDGNLD---QADLLVEY--L 151
+ L+ETG + ++ ++ + G+ +A + I +D A L ++ L
Sbjct: 100 QELKETGLDDIIRER--VKAGTPYIGW-SAGANIAGPTIETTSYMDMPIVAPQLGDFDGL 156
Query: 152 KLCEKYPVP 160
L P
Sbjct: 157 NLVPFQVNP 165
>gnl|CDD|176855 cd07813, COQ10p_like, Coenzyme Q-binding protein COQ10p and similar
proteins. Coenzyme Q-binding protein COQ10p and similar
proteins. COQ10p is a hydrophobic protein located in the
inner membrane of mitochondria that binds coenzyme Q
(CoQ), also called ubiquinone, which is an essential
electron carrier of the respiratory chain. Deletion of
the gene encoding COQ10p (COQ10 or YOL008W) in
Saccharomyces cerevisiae results in respiratory defect
because of the inability to oxidize NADH and succinate.
COQ10p may function in the delivery of CoQ (Q6 in
budding yeast) to its proper location for electron
transport. The human homolog, called Q-binding protein
COQ10 homolog A (COQ10A), is able to fully complement
for the absence of COQ10p in fission yeast. Human COQ10A
also has a splice variant COQ10B. COQ10p belongs to the
SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket and they bind diverse ligands.
Length = 138
Score = 28.2 bits (64), Expect = 2.2
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 22/91 (24%)
Query: 128 WIVGSEEISKDGNLDQADLLVEYLKLCEKY-----PVPWRMIRSH-----VHKLLGEWFR 177
W S + +D + +A+L V + + E + VP I + L GEW R
Sbjct: 30 WCTASRVLERDEDELEAELTVGFGGIRESFTSRVTLVPPESIEAELVDGPFKHLEGEW-R 88
Query: 178 IQPGVRE----DLNAQNRLTFEF---LYNLV 201
+P + + L FEF L +
Sbjct: 89 FKPLGENACKVEFD----LEFEFKSRLLEAL 115
>gnl|CDD|153214 cd01743, GATase1_Anthranilate_Synthase, Type 1 glutamine
amidotransferase (GATase1) domain found in Anthranilate
synthase. Type 1 glutamine amidotransferase (GATase1)
domain found in Anthranilate synthase (ASase). This
group contains proteins similar to para-aminobenzoate
(PABA) synthase and ASase. These enzymes catalyze
similar reactions and produce similar products, PABA and
ortho-aminobenzoate (anthranilate). Each enzyme is
composed of non-identical subunits: a glutamine
amidotransferase subunit (component II) and a subunit
that produces an aminobenzoate products (component I).
ASase catalyses the synthesis of anthranilate from
chorismate and glutamine and is a tetrameric protein
comprising two copies each of components I and II.
Component II of ASase belongs to the family of triad
GTases which hydrolyze glutamine and transfer nascent
ammonia between the active sites. In some bacteria, such
as Escherichia coli, component II can be much larger
than in other organisms, due to the presence of
phosphoribosyl-anthranilate transferase (PRTase)
activity. PRTase catalyses the second step in tryptophan
biosynthesis and results in the addition of
5-phosphoribosyl-1-pyrophosphate to anthranilate to
create N-5'-phosphoribosyl-anthranilate. In E.coli, the
first step in the conversion of chorismate to PABA
involves two proteins: PabA and PabB which co-operate to
transfer the amide nitrogen of glutamine to chorismate
forming 4-amino-4 deoxychorismate (ADC). PabA acts as a
glutamine amidotransferase, supplying an amino group to
PabB, which carries out the amination reaction. A third
protein PabC then mediates elimination of pyruvate and
aromatization to give PABA. Several organisms have
bipartite proteins containing fused domains homologous
to PabA and PabB commonly called PABA synthases. These
hybrid PABA synthases may produce ADC and not PABA.
Length = 184
Score = 27.9 bits (63), Expect = 3.0
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 196 FLYNLVDRLRELGVRIPLYKKDADDAEILA 225
F YNLV LRELG + + + D E L
Sbjct: 10 FTYNLVQYLRELGAEVVVVRNDEITLEELE 39
>gnl|CDD|224815 COG1903, CbiD, Cobalamin biosynthesis protein CbiD [Coenzyme
metabolism].
Length = 367
Score = 28.5 bits (64), Expect = 3.1
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 157 YPVPWRMIRSHVHKLLGE 174
PVP RMI V ++LGE
Sbjct: 122 NPVPRRMIEEAVREVLGE 139
>gnl|CDD|239435 cd03319, L-Ala-DL-Glu_epimerase, L-Ala-D/L-Glu epimerase catalyzes
the epimerization of L-Ala-D/L-Glu and other dipeptides.
The genomic context and the substrate specificity of
characterized members of this family from E.coli and
B.subtilis indicates a possible role in the metabolism
of the murein peptide of peptidoglycan, of which
L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a
member of the enolase-superfamily, which is
characterized by the presence of an enolate anion
intermediate which is generated by abstraction of the
alpha-proton of the carboxylate substrate by an active
site residue and is stabilized by coordination to the
essential Mg2+ ion.
Length = 316
Score = 28.3 bits (64), Expect = 3.3
Identities = 12/90 (13%), Positives = 34/90 (37%), Gaps = 18/90 (20%)
Query: 24 CKIRVFPN----LQDTIKYAKMLEDAGCSLL--AVHGRTRDEKDGKKFRADWNAIKAVKN 77
++RV N ++ ++ + L + G L+ V D + + +++
Sbjct: 178 ARLRVDANQGWTPEEAVELLRELAELGVELIEQPVP------------AGDDDGLAYLRD 225
Query: 78 ALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+P++A+ + D + +G+
Sbjct: 226 KSPLPIMADESCFSAADAARLAGGGAYDGI 255
>gnl|CDD|233750 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase,
type 2. Isopentenyl-diphosphate delta-isomerase (IPP
isomerase) interconverts isopentenyl diphosphate and
dimethylallyl diphosphate. This model represents the
type 2 enzyme. FMN, NADPH, and Mg2+ are required by this
form, which lacks homology to the type 1 enzyme
(TIGR02150). IPP is precursor to many compounds,
including enzyme cofactors, sterols, and isoprenoids
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 333
Score = 28.4 bits (64), Expect = 3.4
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 19/79 (24%)
Query: 39 AKMLEDAGCSLLAVHG------------RTRDEKDGKKFRADWN-----AIKAVKN-ALR 80
AK+L DAG S + V G R + F DW ++ V++ A
Sbjct: 196 AKLLADAGVSAIDVAGAGGTSWAQVENYRAKGSNLASFF-NDWGIPTAASLLEVRSDAPD 254
Query: 81 IPVLANGNVRHMEDVQKCL 99
P++A+G +R DV K +
Sbjct: 255 APIIASGGLRTGLDVAKAI 273
>gnl|CDD|225311 COG2513, PrpB, PEP phosphonomutase and related enzymes
[Carbohydrate transport and metabolism].
Length = 289
Score = 28.0 bits (63), Expect = 3.6
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 11/56 (19%)
Query: 31 NLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
L D I+ A+ +AG + T D I+A A+ +P+ AN
Sbjct: 164 GLDDAIERAQAYVEAGADAIFPEALT-----------DLEEIRAFAEAVPVPLPAN 208
>gnl|CDD|181086 PRK07695, PRK07695, transcriptional regulator TenI; Provisional.
Length = 201
Score = 28.1 bits (63), Expect = 3.7
Identities = 26/97 (26%), Positives = 38/97 (39%), Gaps = 11/97 (11%)
Query: 29 FPNLQ-----DTIKYAKMLEDAGC-SLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIP 82
FP L +++ A E G ++ H D K G R + + AL IP
Sbjct: 93 FPYLHVGYSVHSLEEAIQAEKNGADYVVYGHVFPTDCKKGVPARG-LEELSDIARALSIP 151
Query: 83 VLANGNVRHMEDVQKCLEETGCEG--VLSAESLLENP 117
V+A G + E+ + L G G V+S NP
Sbjct: 152 VIAIGGI-TPENTRDVL-AAGVSGIAVMSGIFSSANP 186
>gnl|CDD|239204 cd02810, DHOD_DHPD_FMN, Dihydroorotate dehydrogenase (DHOD) and
Dihydropyrimidine dehydrogenase (DHPD) 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.
DHPD catalyzes the first step in pyrimidine degradation:
the NADPH-dependent reduction of uracil and thymine to
the corresponding 5,6-dihydropyrimidines. DHPD contains
two FAD, two FMN and eight [4Fe-4S] clusters, arranged
in two electron transfer chains that pass its
homodimeric interface twice. Two of the Fe-S clusters
show a hitherto unobserved coordination involving a
glutamine residue.
Length = 289
Score = 27.7 bits (62), Expect = 4.5
Identities = 21/92 (22%), Positives = 45/92 (48%), Gaps = 8/92 (8%)
Query: 31 NLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRAD----WNAIKAVKNALRIPVLA- 85
+ +D ++ A+ +E AG L ++ + G++ D N +KAVK A+ IP+L
Sbjct: 109 SKEDYVELARKIERAGAKALELNLSCPNVGGGRQLGQDPEAVANLLKAVKAAVDIPLLVK 168
Query: 86 ---NGNVRHMEDVQKCLEETGCEGVLSAESLL 114
++ + ++ K E G +G+ + ++
Sbjct: 169 LSPYFDLEDIVELAKAAERAGADGLTAINTIS 200
>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 = 27.6 bits (62), Expect = 5.1
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 39 AKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRHMEDV 95
A++ E+AG +++A+ D G R AD IK + +A+ IPV+A + H +
Sbjct: 21 ARIAEEAGAVAVMALERVPADIRAAGGVARMADPKMIKEIMDAVSIPVMAKVRIGHFVEA 80
Query: 96 QKCLEETG 103
Q LE G
Sbjct: 81 Q-ILEALG 87
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 27.4 bits (62), Expect = 5.8
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 6 LVKSLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLE------DAGCSLLAVHGR 55
LV V+ + +++PV+ K R+ + QD+ Y + + +AGC VH R
Sbjct: 120 LVADCVKAMKDAVSIPVTVKHRIGIDDQDS--YEFLCDFVDTVAEAGCDTFIVHAR 173
>gnl|CDD|221990 pfam13225, DUF4033, Domain of unknown function (DUF4033). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria and eukaryotes, and
is approximately 80 amino acids in length.
Length = 85
Score = 26.1 bits (58), Expect = 6.4
Identities = 8/15 (53%), Positives = 12/15 (80%), Gaps = 2/15 (13%)
Query: 95 VQKC--LEETGCEGV 107
++KC LEE+GC G+
Sbjct: 25 IKKCRYLEESGCAGM 39
>gnl|CDD|222337 pfam13714, PEP_mutase, Phosphoenolpyruvate phosphomutase. This
domain includes the enzyme Phosphoenolpyruvate
phosphomutase (EC:5.4.2.9). The PEP mutase from
Streptomyces viridochromogenes has been characterized as
catalyzing the formation of a carbon-phosphorus bond by
converting phosphoenolpyruvate (PEP) to
phosphonopyruvate (P-Pyr). This enzyme has a TIM barrel
fold.
Length = 238
Score = 27.1 bits (61), Expect = 6.4
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 11/52 (21%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPV 83
L++ I+ A+ +AG + V G + I A+ A+ +P+
Sbjct: 154 LEEAIERARAYAEAGADGIFVPGLKDPD-----------EIAALAAAVPLPL 194
>gnl|CDD|236430 PRK09249, PRK09249, coproporphyrinogen III oxidase; Provisional.
Length = 453
Score = 27.4 bits (62), Expect = 6.6
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 13/34 (38%)
Query: 177 RIQPGVREDLNAQNRLTFEFLYNLVDRLRELGVR 210
RIQP FEF + LV+ RELG
Sbjct: 182 RIQP-------------FEFTFALVEAARELGFT 202
>gnl|CDD|197263 cd09166, PLDc_PPK1_C1_unchar, Catalytic C-terminal domain, first
repeat, of uncharacterized prokaryotic polyphosphate
kinases. Catalytic C-terminal domain, first repeat (C1
domain), of a group of uncharacterized prokaryotic
polyphosphate kinases (Poly P kinase 1 or PPK1, EC
2.7.4.1). Inorganic polyphosphate (Poly P) plays an
important role in bacterial stress responses and
stationary-phase survival. PPK1 is the key enzyme
responsible for the synthesis of Poly P in bacteria. It
can catalyze the reversible conversion of the
terminal-phosphate of ATP to Poly P. Therefore, PPK1 is
essential for bacterial motility, quorum sensing,
biofilm formation, and the production of virulence
factors and may serve as an attractive antimicrobial
drug target. Dimerization is crucial for the enzymatic
activity of PPK1. Each PPK1 monomer includes four
structural domains, the N-terminal (N) domain, the head
(H) domain, and two closely related C-terminal (C1 and
C2) domains. The N domain provides the upper binding
interface for the adenine ring of the ATP. The H domain
is involved in dimerization, while both the C1 and C2
domains contain residues crucial for catalytic
activity. The intersection of the N, C1, and C2 domains
forms a structural tunnel in which the PPK catalytic
reactions are carried out. In spite of the lack of
sequence homology, the C1 and C2 domains of PPK1 are
structurally similar to the two repetitive catalytic
domains of phospholipase D (PLD). Moreover, some
residues in the HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) of the PLD
superfamily are spatially conserved in the active site
of PPK1. It is possible that the bacterial PPK1 family
and the PLD family have a common ancestor and diverged
early in evolution.
Length = 162
Score = 27.0 bits (60), Expect = 6.6
Identities = 14/45 (31%), Positives = 29/45 (64%)
Query: 6 LVKSLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLL 50
LV+ L+E +V V ++R + ++ I++A+ LE+AGC+++
Sbjct: 52 LVEYLIEAAENGKDVTVLMELRARFDEENNIEWAERLEEAGCTVI 96
>gnl|CDD|223576 COG0502, BioB, Biotin synthase and related enzymes [Coenzyme
metabolism].
Length = 335
Score = 27.2 bits (61), Expect = 6.6
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 31 NLQDTIKYAKMLEDAG----CSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
+++ ++ AK + AG C A G +D ++ AIKAVK L + V A+
Sbjct: 85 EVEEILEAAKKAKAAGATRFCMGAAGRGP---GRDMEEVVE---AIKAVKEELGLEVCAS 138
>gnl|CDD|240081 cd04730, NPD_like, 2-Nitropropane dioxygenase (NPD), one of the
nitroalkane oxidizing enzyme families, catalyzes
oxidative denitrification of nitroalkanes to their
corresponding carbonyl compounds and nitrites. NDP is a
member of the NAD(P)H-dependent flavin oxidoreductase
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.
Length = 236
Score = 27.1 bits (61), Expect = 6.7
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 15/80 (18%)
Query: 35 TIKYAKMLEDAGCSLLAV-------HGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANG 87
+++ A+ E AG L H T D + + V++A+ IPV+A G
Sbjct: 111 SVEEARKAEAAGADALVAQGAEAGGHRGTFD-------IGTFALVPEVRDAVDIPVIAAG 163
Query: 88 NVRHMEDVQKCLEETGCEGV 107
+ + L G +GV
Sbjct: 164 GIADGRGIAAALAL-GADGV 182
>gnl|CDD|180709 PRK06815, PRK06815, hypothetical protein; Provisional.
Length = 317
Score = 27.3 bits (61), Expect = 6.9
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 201 VDRLRELGVRIPLYKKDADDAEILADDLA 229
+D +R LG + LY DA +AE+ A A
Sbjct: 107 LDAIRALGAEVRLYGGDALNAELAARRAA 135
>gnl|CDD|237285 PRK13111, trpA, tryptophan synthase subunit alpha; Provisional.
Length = 258
Score = 27.0 bits (61), Expect = 7.5
Identities = 6/22 (27%), Positives = 14/22 (63%)
Query: 29 FPNLQDTIKYAKMLEDAGCSLL 50
P+L+ +++ K L +AG ++
Sbjct: 22 DPDLETSLEIIKALVEAGADII 43
>gnl|CDD|216765 pfam01888, CbiD, CbiD. CbiD is essential for cobalamin
biosynthesis in both S. typhimurium and B. megaterium,
no functional role has been ascribed to the protein. The
CbiD protein has a putative S-AdoMet binding site. It is
possible that CbiD might have the same role as CobF in
undertaking the C-1 methylation and deacylation
reactions required during the ring contraction process.
Length = 261
Score = 27.0 bits (60), Expect = 8.0
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 157 YPVPWRMIRSHVHKLLGE 174
PVP RMIR ++ K L E
Sbjct: 117 NPVPRRMIRENLQKALRE 134
>gnl|CDD|238203 cd00331, IGPS, Indole-3-glycerol phosphate synthase (IGPS); an
enzyme in the tryptophan biosynthetic pathway,
catalyzing the ring closure reaction of
1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate
(CdRP) to indole-3-glycerol phosphate (IGP),
accompanied by the release of carbon dioxide and water.
IGPS is active as a separate monomer in most organisms,
but is also found fused to other enzymes as part of a
bifunctional or multifunctional enzyme involved in
tryptophan biosynthesis.
Length = 217
Score = 26.7 bits (60), Expect = 8.8
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVL 84
D ++ AK E AG + ++V T + K F+ ++AV+ A+ +PVL
Sbjct: 32 DPVEIAKAYEKAGAAAISVL--T----EPKYFQGSLEDLRAVREAVSLPVL 76
>gnl|CDD|130848 TIGR01788, Glu-decarb-GAD, glutamate decarboxylase. This model
represents the pyridoxal phosphate-dependent glutamate
(alpha) decarboxylase found in bacteria (low and hi-GC
gram positive, proteobacteria and cyanobacteria),
plants, fungi and at least one archaon (Methanosarcina).
The product of the enzyme is gamma-aminobutyrate (GABA).
Length = 431
Score = 27.0 bits (60), Expect = 9.2
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 197 LYNLVDRLRELGVRIPLYK--KDADDAEIL 224
LY+L RLRE G +P Y K+A+D ++
Sbjct: 374 LYDLSHRLRERGWIVPAYTLPKNAEDIVVM 403
>gnl|CDD|234615 PRK00075, cbiD, cobalt-precorrin-6A synthase; Reviewed.
Length = 361
Score = 26.7 bits (60), Expect = 10.0
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 157 YPVPWRMIRSHVHKLLGE 174
PVP RMI +V ++L E
Sbjct: 121 NPVPRRMIEENVREVLPE 138
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.138 0.411
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,997,214
Number of extensions: 1145842
Number of successful extensions: 1600
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1575
Number of HSP's successfully gapped: 102
Length of query: 230
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 136
Effective length of database: 6,768,326
Effective search space: 920492336
Effective search space used: 920492336
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: 57 (25.6 bits)