RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 023070
(287 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 = 233 bits (597), Expect = 6e-77
Identities = 75/183 (40%), Positives = 109/183 (59%), Gaps = 4/183 (2%)
Query: 5 PPEDRPLFVQFCANDPEILLNAARRVEP-YCDYVDINLGCPQRIARRGNYGAFLMDNLPL 63
PE+RPL VQ +DPE L AA+ VE D +D+N+GCP +G GA L+ + L
Sbjct: 51 NPEERPLIVQLGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPEL 110
Query: 64 VKSLVEKLALNLNVPVSCKIRVFPNLQD-TIKYAKMLEDAGCSLLAVHGRTRDEKDGKKF 122
V +V + + +PV+ KIR+ + ++ T++ AK LEDAG S L VHGRTR++
Sbjct: 111 VAEIVRAVREAVPIPVTVKIRLGWDDEEETLELAKALEDAGASALTVHGRTREQ--RYSG 168
Query: 123 RADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGFRT 182
ADW+ I +K A+ IPV+ANG++ +ED +CLE+TG +GV+ L NP LF +
Sbjct: 169 PADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKE 228
Query: 183 AEW 185
Sbjct: 229 LLE 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 = 185 bits (473), Expect = 2e-57
Identities = 94/272 (34%), Positives = 132/272 (48%), Gaps = 27/272 (9%)
Query: 5 PPEDRPLFVQFCANDPEILLNAARRVEP-YCDYVDINLGCPQRIARRGNYGAFLMDNLPL 63
E PL VQ +DP +L AA+ V D +DIN+GCP + RG GA L+ + L
Sbjct: 50 LEEPTPLAVQLGGSDPALLAEAAKLVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDL 109
Query: 64 VKSLVEKLALNLNVPVSCKIRVFP--NLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKK 121
V +V+ + +++PV+ KIR+ + ++ ++ A+ +EDAG L VHGRTR +
Sbjct: 110 VAQIVKAVVKAVDIPVTVKIRIGWDESHENAVEIARRVEDAGAQALTVHGRTR--AQNYE 167
Query: 122 FRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGFR 181
ADW+AIK VK A+ IPV+ANG++ ED Q+CL TG +GV+ L NP LFA
Sbjct: 168 GPADWDAIKQVKQAVSIPVIANGDITDAEDAQRCLSYTGADGVMIGRGALGNPWLFAEQH 227
Query: 182 TAEWIVGSEEISKDGNLDQADLLVEYL-KLCEKYP---------VPWRMIRSHVHKLLGE 231
T + G D L E + E R R H+ L +
Sbjct: 228 TVKT----------GEFDPRPPLAEEAEIVLEHLSYLEEFYGEDKGLRHARKHLAWYL-K 276
Query: 232 WFRIQPGVREDLNAQNRLTFEFLYNLVDRLRE 263
F +R +LN T E L NL LR
Sbjct: 277 GFPGAAELRRELNDVFDPT-EALINLDAALRA 307
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 180 bits (458), Expect = 6e-55
Identities = 88/254 (34%), Positives = 132/254 (51%), Gaps = 19/254 (7%)
Query: 5 PPEDRPLFVQFCANDPEILLNAARRVEPYCDY--VDINLGCPQRIARRGNYGAFLMDNLP 62
E+RP+ VQ +DPE+L AA+ E +D+N GCP +G GA L+ N
Sbjct: 63 LEEERPVAVQLGGSDPELLAEAAKIAE-ELGADIIDLNCGCPSPKVVKGGAGAALLKNPE 121
Query: 63 LVKSLVEKL-ALNLNVPVSCKIRVFPNLQD--TIKYAKMLEDAGCSLLAVHGRTRDEKDG 119
L+ +V+ + ++PV+ KIR+ + D ++ A++LEDAG L VHGRTR G
Sbjct: 122 LLAEIVKAMVEAVGDIPVTVKIRLGWDDDDILALEIARILEDAGADALTVHGRTR--AQG 179
Query: 120 KKFRADWNAIKAVKNALR-IPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFA 178
ADW+ IK +K A+ IPV+ANG+++ +ED ++ LE TG +GV+ L NP LF
Sbjct: 180 YLGPADWDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMIGRGALGNPWLFR 239
Query: 179 GFRTAEWIVGSEEISKDGNLDQADLLVEYLKLCEKYP--VPWRMIRSHVHKLLGEWFRIQ 236
E + E+ + D+L E+L+L +Y R +R H+ L
Sbjct: 240 QIDYLE----TGELLPPTLAEVLDILREHLELLLEYYGKKGLRRLRKHLGYYLKGL---- 291
Query: 237 PGVREDLNAQNRLT 250
PG RE A N+
Sbjct: 292 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 = 132 bits (333), Expect = 2e-36
Identities = 80/267 (29%), Positives = 140/267 (52%), Gaps = 23/267 (8%)
Query: 6 PEDRPLFVQFCANDPEILLNAARRVEPY-CDYVDINLGCP-QRIARRGNYGAFLMDNLPL 63
++ P+ VQ +DP+ + AA+ E D +DIN+GCP +I ++G G+ L+ + L
Sbjct: 60 EDETPISVQLFGSDPDTMAEAAKINEELGADIIDINMGCPVPKITKKGA-GSALLRDPDL 118
Query: 64 VKSLVEKLALNLNVPVSCKIRVF--PNLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKK 121
+ +V+ + +++PV+ KIR+ + ++ A++ EDAG + +HGRTR + G
Sbjct: 119 IGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDAGAQAVTLHGRTRAQ--GYS 176
Query: 122 FRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGFR 181
A+W+ I VK A+RIPV+ NG++ ED + LE TGC+GV+ L NP LF +
Sbjct: 177 GEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFR--Q 234
Query: 182 TAEWIVGSEEISKDGNLDQADLLVEYLKLCEKY---PVPWRMIRSHV-HKLLGEWFRIQP 237
+++ + ++ D ++ +L+L Y R+ R H+ L G P
Sbjct: 235 IEQYLTTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHIAWYLKGF-----P 289
Query: 238 GV---REDLNAQNRLTFEFLYNLVDRL 261
G R+ LN + +F+ + L+D
Sbjct: 290 GNAALRQTLNHAS--SFQEVKQLLDDF 314
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 91.2 bits (226), Expect = 3e-21
Identities = 56/169 (33%), Positives = 97/169 (57%), Gaps = 7/169 (4%)
Query: 13 VQFCANDPEILLNAAR-RVEPYCDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKL 71
VQ +DP+ + +AAR VE +DIN+GCP + R G+ L+ LVKS++ ++
Sbjct: 69 VQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEV 128
Query: 72 ALNLNVPVSCKIRV--FPNLQDTIKYAKMLEDAGCSLLAVHGRTRD-EKDGKKFRADWNA 128
++VPV+ KIR P ++ ++ A++ ED G L +HGRTR +G+ A++++
Sbjct: 129 VNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNGE---AEYDS 185
Query: 129 IKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALF 177
I+AVK + IPV+ANG++ + L+ TG + ++ + P +F
Sbjct: 186 IRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIF 234
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 89.9 bits (223), Expect = 8e-21
Identities = 57/178 (32%), Positives = 93/178 (52%), Gaps = 11/178 (6%)
Query: 6 PEDRPLFVQFCANDPEILL-NAARRVEPYCDYVDINLGCPQRIARRGNYGAFLMDNLPLV 64
P + +Q P+ L NAAR VE VD+N GCP + GA L+ + L+
Sbjct: 60 PSGTLVRIQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELI 119
Query: 65 ----KSLVEKLALNLNVPVSCKIRV-FPNLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDG 119
K++ E A+ ++PV+ K+R+ + + + + A ++ AG + L VHGRT++ DG
Sbjct: 120 YQGAKAMRE--AVPAHLPVTVKVRLGWDSGERKFEIADAVQQAGATELVVHGRTKE--DG 175
Query: 120 -KKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 176
+ +W AI ++ L IPV+ANG + + Q+C+ TGC+ V+ L P L
Sbjct: 176 YRAEHINWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIPNL 233
>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 = 73.7 bits (181), Expect = 4e-15
Identities = 51/199 (25%), Positives = 84/199 (42%), Gaps = 36/199 (18%)
Query: 3 NLPPEDRPLFVQFCANDPEILLNAARRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNL 61
PE+ P+ +Q +DP L A+ E D +++N+GCP + GN+GA LM N
Sbjct: 49 KFSPEESPVALQLGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGACLMGNA 108
Query: 62 PLVKSLVEKLALNLNVPVSCKIRVFPNLQDT----IKYAKMLEDAGCSLLAVHGRTRDEK 117
LV V+ + +N+PV+ K R+ + D+ + +++ GC VH R
Sbjct: 109 DLVADCVKAMQEAVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHARKA--- 165
Query: 118 DGKKFRADWNAIKAVKNALRIPVL------------------ANGNVRHMEDVQKCLEET 159
W + + K IP L NG +++ E +++ L
Sbjct: 166 --------WLSGLSPKENREIPPLRYERVYQLKKDFPHLTIEINGGIKNSEQIKQHLSHV 217
Query: 160 GCEGVLSAESLLENPALFA 178
+GV+ ENP L A
Sbjct: 218 --DGVMVGREAYENPYLLA 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 = 60.3 bits (147), Expect = 1e-10
Identities = 30/113 (26%), Positives = 51/113 (45%), Gaps = 12/113 (10%)
Query: 76 NVPVSCKI---RVFPN---LQDTIKYAKMLEDAGCSLLAVHGRTRDEK----DGKKFRAD 125
+ PV ++ P L++ I+ AK LE+AG L V G + +
Sbjct: 208 DFPVGVRLSADDFVPGGLTLEEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVPEG 267
Query: 126 WNA--IKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 176
+ + +K A++IPV+A G +R E ++ L E + V +LL +P L
Sbjct: 268 YFLELAEKIKKAVKIPVIAVGGIRDPEVAEEILAEGKADLVALGRALLADPDL 320
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 60.1 bits (147), Expect = 2e-10
Identities = 36/114 (31%), Positives = 60/114 (52%), Gaps = 9/114 (7%)
Query: 6 PEDRPLFVQFCANDPEILLNAARRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLV 64
PE+ P+ +Q +DP L AA+ E + D +++N+GCP + G +GA LM LV
Sbjct: 62 PEEHPVALQLGGSDPADLAEAAKLAEDWGYDEINLNVGCPSDRVQNGRFGACLMAEPELV 121
Query: 65 KSLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLE------DAGCSLLAVHGR 112
V+ + +++PV+ K R+ + QD+ Y + + +AGC VH R
Sbjct: 122 ADCVKAMKDAVSIPVTVKHRIGIDDQDS--YEFLCDFVDTVAEAGCDTFIVHAR 173
>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 = 49.6 bits (119), Expect = 4e-07
Identities = 34/142 (23%), Positives = 59/142 (41%), Gaps = 12/142 (8%)
Query: 17 ANDPEILLNAARRVEPYCDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLN 76
++ E LLNAA V ++IN C Q G L+ + + ++ L
Sbjct: 81 SSSLEPLLNAAALVAKNAAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKALK-ETG 139
Query: 77 VPVSCKIRVFPNLQ-DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNA 135
VPVS KIR + D + A+++E AG +H D + AD I+ +
Sbjct: 140 VPVSVKIRA--GVDVDDEELARLIEKAGA--DIIHVDAMDPGNH----ADLKKIRDIST- 190
Query: 136 LRIPVLANGNVRHMEDVQKCLE 157
+ ++ N +V +E ++
Sbjct: 191 -ELFIIGNNSVTTIESAKEMFS 211
>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 = 47.0 bits (112), Expect = 4e-06
Identities = 45/168 (26%), Positives = 66/168 (39%), Gaps = 31/168 (18%)
Query: 8 DRPLFVQFCANDPEILLNAARRVE---PYCDYVDINLGCPQRIARRGNYGAFLMDNLPLV 64
PL + E A ++E PY D ++NL CP G + + L
Sbjct: 90 PTPLIASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCPHVKG----GGIAIGQDPELS 145
Query: 65 KSLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLL----AVHGRTRDEKDGK 120
+V+ + +VPV K+ PN+ D + AK E+AG L + G D K GK
Sbjct: 146 ADVVKAVKDKTDVPVFAKLS--PNVTDITEIAKAAEEAGADGLTLINTLRGMKIDIKTGK 203
Query: 121 KFRADWN------AIKAVKNALR----------IPVLANGNVRHMEDV 152
A+ AIK + ALR IP++ G + ED
Sbjct: 204 PILANKTGGLSGPAIKPI--ALRMVYDVYKMVDIPIIGVGGITSFEDA 249
>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 = 44.4 bits (106), Expect = 2e-05
Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 91 DTIKYAKMLEDAGCS---LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVR 147
D +++AK LE+ G L + +DG D + + A+ IPV+A+G V
Sbjct: 149 DAVEWAKKLEELGAGEILLTDID------RDGTLSGPDLELTRELAEAVNIPVIASGGVG 202
Query: 148 HMEDVQKCLEETGCEGVLSAESLLEN 173
+ED+++ L G +GV++ +L E
Sbjct: 203 SLEDLKE-LFSEGVDGVIAGSALHEG 227
Score = 30.9 bits (71), Expect = 0.63
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 21/109 (19%)
Query: 91 DTIKYAKMLEDAGCSLL-------AVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 143
D ++ AK E+ G L A GR + I+ + + IPV
Sbjct: 30 DPVELAKRYEEEGADELHFVDLDAAKEGRPVNLD----------LIEEIAEEVFIPVQVG 79
Query: 144 GNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGFRTAEWIVGSEEI 192
G +R +ED ++ L G + V+ + ++NP L + A GS+ I
Sbjct: 80 GGIRSLEDAERLLSA-GADKVIIGTAAVKNPEL---IKEAAEKFGSQCI 124
>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 = 42.9 bits (102), Expect = 8e-05
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 93 IKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDV 152
+ AK E+ G + T +DG ++ K + A IPV+A+G V ++D+
Sbjct: 149 EELAKRFEELGVKAIIY---TDISRDGTLSGPNFELYKELAAATGIPVIASGGVSSLDDI 205
Query: 153 QKCLEETGCEGVLSAESLLEN 173
+ L+E G GV+ ++L E
Sbjct: 206 KA-LKELGVAGVIVGKALYEG 225
Score = 30.5 bits (70), Expect = 0.82
Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 20/105 (19%)
Query: 126 WNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGFRTAEW 185
I+ + A+ IPV G +R +ED+++ L + G V+ + ++NP L E
Sbjct: 62 LELIEEIVKAVGIPVQVGGGIRSLEDIERLL-DLGVSRVIIGTAAVKNPELV-----KEL 115
Query: 186 I--VGSEEI-----SKDGN------LDQADL-LVEYLKLCEKYPV 216
+ G E I +KDG L+ +++ L E K E+ V
Sbjct: 116 LKEYGGERIVVGLDAKDGKVATKGWLETSEVSLEELAKRFEELGV 160
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 42.5 bits (101), Expect = 8e-05
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 91 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 148
D +++AK +E+ AG LL T ++DG K D +AV+ A+ IPV+A+G
Sbjct: 156 DAVEWAKEVEELGAGEILL-----TSMDRDGTKAGYDLELTRAVREAVNIPVIASGGAGK 210
Query: 149 MEDVQKCLEETGCEGVLSA 167
E + E + L+A
Sbjct: 211 PEHFVEAFTEGKADAALAA 229
>gnl|CDD|223184 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide
ribonucleotide (ProFAR) isomerase [Amino acid transport
and metabolism].
Length = 241
Score = 42.6 bits (101), Expect = 9e-05
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 96 AKMLEDAGCSLLAVHGRTRD-EKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQK 154
AK LE+ G + + D +DG + + +K + A+ IPV+A+G V ++D++
Sbjct: 153 AKRLEEVGLAHILYT----DISRDGTLSGPNVDLVKELAEAVDIPVIASGGVSSLDDIKA 208
Query: 155 CLEETGCEGVLSAESLLEN 173
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 = 4e-04
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 91 DTIKYAKMLEDAGCS--LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 148
D +++AK +E+ G LL T ++DG K D I+AV +A+ IPV+A+G
Sbjct: 150 DAVEWAKEVEELGAGEILL-----TSMDRDGTKKGYDLELIRAVSSAVNIPVIASGGAGK 204
Query: 149 MEDVQKCLEETGCEGVLSA 167
E + EE G + L+A
Sbjct: 205 PEHFVEAFEEGGADAALAA 223
>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 = 39.8 bits (94), Expect = 8e-04
Identities = 42/194 (21%), Positives = 69/194 (35%), Gaps = 51/194 (26%)
Query: 8 DRPLFVQFCANDPEILLNAARRVEPYC-DYVDINLGCPQRIARRGNYGAFLMDNLPLVKS 66
P+ + E + A ++ D +++N+ CP G + V
Sbjct: 89 GTPVIASIAGSTVEEFVEVAEKLADAGADAIELNISCPNV----KGGGMAFGTDPEAVAE 144
Query: 67 LVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRAD- 125
+V+ + +VPV K+ PN+ D ++ A+ E+AG AD
Sbjct: 145 IVKAVKKATDVPVIVKLT--PNVTDIVEIARAAEEAG--------------------ADG 182
Query: 126 WNAIKAVKNALRI------PVLANGN------------VRHMEDVQKCLEET--GCEGVL 165
I +K + I P+L N +R + V K +E G G+
Sbjct: 183 LTLINTLK-GMAIDIETRKPILGNVTGGLSGPAIKPIALRMVYQVYKAVEIPIIGVGGIA 241
Query: 166 SAESLLENPALFAG 179
S E LE L AG
Sbjct: 242 SGEDALE--FLMAG 253
>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: 89 LQDTIKYAKMLEDAGCSLLAV-----HGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 143
L+D+++ AK L++ G L+ V + G ++ + A + ++ IPV+A
Sbjct: 240 LEDSVELAKALKELGVDLIDVSSGGNSPAQKIPV-GPGYQVPF-A-ERIRQEAGIPVIAV 296
Query: 144 GNVRHMEDVQKCLEETGCEGVLSAESLLENP 174
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 = 0.005
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 12/66 (18%)
Query: 92 TIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVK-------NALRIP----V 140
T+ Y KM E + + RD G + +W +K NALR+P
Sbjct: 324 TMGYGKM-EGEADDRVIAYMIERDSAQGPFYHQEWYGMKPTTPIISGGMNALRLPGFFDN 382
Query: 141 LANGNV 146
L +GNV
Sbjct: 383 LGHGNV 388
>gnl|CDD|233108 TIGR00735, hisF, imidazoleglycerol phosphate synthase, cyclase
subunit. [Amino acid biosynthesis, Histidine family].
Length = 254
Score = 36.6 bits (85), Expect = 0.008
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 91 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 148
D +++AK +E AG LL T +KDG K D KAV A++IPV+A+G
Sbjct: 156 DAVEWAKEVEKLGAGEILL-----TSMDKDGTKSGYDLELTKAVSEAVKIPVIASGGAGK 210
Query: 149 MEDVQKCLEETGCEGVLSA 167
E + + + L+A
Sbjct: 211 PEHFYEAFTKGKADAALAA 229
>gnl|CDD|216348 pfam01180, DHO_dh, Dihydroorotate dehydrogenase.
Length = 290
Score = 36.5 bits (85), Expect = 0.010
Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 11/100 (11%)
Query: 6 PEDRPLFVQFCANDPEILLNAARRVEPYCDYVDINLGCPQRIARRGN--YGAFLMDNLPL 63
P + + + E + AR++ P+ DY+++N+ CP N L + L
Sbjct: 91 PRPLGIILSKAGSTVEDYVEVARKIGPFADYLELNVSCP-------NTPGLRALQTDPEL 143
Query: 64 VKSLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAG 103
L++ + VPV K+ P+L D + AG
Sbjct: 144 AAILLKVVKEVSKVPVLVKLA--PDLTDIVIIDIADVAAG 181
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 36.0 bits (84), Expect = 0.012
Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 6/85 (7%)
Query: 90 QDTIKYAKMLEDAG-CSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 148
++ AK E+ G S+L T + +G + +K + +++ IPV+A+G V
Sbjct: 149 YTPVEAAKRFEELGAGSILF----TNVDVEGLLEGVNTEPVKELVDSVDIPVIASGGVTT 204
Query: 149 MEDVQKCLEETGCEGVLSAESLLEN 173
++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 = 35.6 bits (83), Expect = 0.014
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 96 AKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKC 155
AK LE+ G L T +DG ++ K + A+ +PV+A+G V ++D+
Sbjct: 151 AKRLEELG---LEGIIYTDISRDGTLSGPNFELTKELVKAVNVPVIASGGVSSIDDLIA- 206
Query: 156 LEETGCEGVLSAESLLEN 173
L++ G GV+ ++L E
Sbjct: 207 LKKLGVYGVIVGKALYEG 224
>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 = 35.8 bits (83), Expect = 0.017
Identities = 22/97 (22%), Positives = 45/97 (46%), Gaps = 6/97 (6%)
Query: 8 DRPLFVQFCANDPEILLNAARRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKS 66
+PL + E + AR++E +++NL CP R + V +
Sbjct: 98 GQPLIASVGGSSKEDYVELARKIERAGAKALELNLSCPNVGGGRQLG-----QDPEAVAN 152
Query: 67 LVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAG 103
L++ + +++P+ K+ + +L+D ++ AK E AG
Sbjct: 153 LLKAVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAG 189
Score = 27.7 bits (62), Expect = 6.6
Identities = 21/92 (22%), Positives = 45/92 (48%), Gaps = 8/92 (8%)
Query: 88 NLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRAD----WNAIKAVKNALRIPVLA- 142
+ +D ++ A+ +E AG L ++ + G++ D N +KAVK A+ IP+L
Sbjct: 109 SKEDYVELARKIERAGAKALELNLSCPNVGGGRQLGQDPEAVANLLKAVKAAVDIPLLVK 168
Query: 143 ---NGNVRHMEDVQKCLEETGCEGVLSAESLL 171
++ + ++ K E G +G+ + ++
Sbjct: 169 LSPYFDLEDIVELAKAAERAGADGLTAINTIS 200
>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 = 35.3 bits (82), Expect = 0.023
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 117 KDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLE 172
+ 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 = 34.9 bits (81), Expect = 0.027
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 91 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 150
D +++A+ E G + + ++DG D IK V +A+ IPV+A G ++
Sbjct: 154 DPVEWAREAEQLGAGEILL---NSIDRDGTMKGYDLELIKTVSDAVSIPVIALGGAGSLD 210
Query: 151 DVQKCLEETGCEGVLSAESLL 171
D+ + E G V +A SL
Sbjct: 211 DLVEVALEAGASAV-AAASLF 230
>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 = 35.2 bits (81), Expect = 0.031
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 12/67 (17%)
Query: 91 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVK-------NALRIP---- 139
T+ + KM ++ ++A + RDE G F W +K NALR+P
Sbjct: 322 GTMGFGKMEGESSDKVIA-YMIERDEAQGPLFNQKWYGMKPTTPIISGGMNALRLPGFFE 380
Query: 140 VLANGNV 146
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 = 34.9 bits (81), Expect = 0.035
Identities = 22/103 (21%), Positives = 37/103 (35%), Gaps = 4/103 (3%)
Query: 78 PVSCKIRVFPNLQDTIKYAKMLEDAG-CSLLAV---HGRTRDEKDGKKFRADWNAIKAVK 133
P +++ ++ AK LE+AG + V +K
Sbjct: 225 PDDFFDGGGLTIEEAVELAKALEEAGLVDYIHVSEGGYERGGTITVSGPGYQVEFAARIK 284
Query: 134 NALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 176
A+RIPV+A G + E ++ L + V L +P L
Sbjct: 285 KAVRIPVIAVGGINDPEQAEEILASGRADLVAMGRPFLADPDL 327
>gnl|CDD|129819 TIGR00736, nifR3_rel_arch, TIM-barrel protein, putative. Members
of this family show a distant relationship by PSI-BLAST
to alpha/beta (TIM) barrel enzymes such as
dihydroorotate dehydrogenase and glycolate oxidase. At
least two closely related but well-separable families
among the bacteria, the nifR3/yhdG family and the yjbN
family, share a more distant relationship to this family
of shorter, exclusively archaeal proteins [Unknown
function, General].
Length = 231
Score = 34.5 bits (79), Expect = 0.042
Identities = 25/98 (25%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 13 VQFCANDPEILLNAARRVEPYCDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLA 72
V+F + + + + D ++IN C Q G L+ N L+K + K+
Sbjct: 74 VRFVDLEEA--YDVLLTIAEHADIIEINAHCRQPEITEIGIGQELLKNKELLKEFLTKMK 131
Query: 73 LNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAVH 110
LN P+ KIR D + A L D G +H
Sbjct: 132 -ELNKPIFVKIRGNCIPLDELIDALNLVDDGF--DGIH 166
>gnl|CDD|215729 pfam00117, GATase, Glutamine amidotransferase class-I.
Length = 186
Score = 34.2 bits (79), Expect = 0.042
Identities = 14/30 (46%), Positives = 16/30 (53%)
Query: 253 FLYNLVDRLRELGVRIPLYKKDADDAEILA 282
F YNL LRELGV + + D EIL
Sbjct: 9 FTYNLARALRELGVEVEVVPNDTPAEEILE 38
>gnl|CDD|234996 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 253
Score = 33.9 bits (79), Expect = 0.068
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 13/82 (15%)
Query: 91 DTIKYAKMLEDAGCS--LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANG---N 145
D +++AK +E+ G LL T ++DG K D +AV +A+ +PV+A+G N
Sbjct: 154 DAVEWAKEVEELGAGEILL-----TSMDRDGTKNGYDLELTRAVSDAVNVPVIASGGAGN 208
Query: 146 VRHMEDVQKCLEETGCEGVLSA 167
+ H + E G + L+A
Sbjct: 209 LEHFVEA---FTEGGADAALAA 227
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 33.8 bits (78), Expect = 0.068
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 91 DTIKYAKMLEDAG-CSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHM 149
D ++ AK E G +L ++DG D +K+ +NAL+IP++A G +
Sbjct: 153 DPLELAKEYEALGAGEILL----NSIDRDGTMKGYDLELLKSFRNALKIPLIALGGAGSL 208
Query: 150 EDVQKCLEETGCEGVLSAESLL 171
+D+ + + G + +A SL
Sbjct: 209 DDIVEAILNLGADAA-AAGSLF 229
>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 = 0.073
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 126 WNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLEN 173
A + + A+ IPV+A+G V ++D++ EGV+ +L E
Sbjct: 179 VEATRELAAAVPIPVIASGGVSSLDDIKALKGLGAVEGVIVGRALYEG 226
Score = 31.2 bits (72), Expect = 0.41
Identities = 36/175 (20%), Positives = 57/175 (32%), Gaps = 69/175 (39%)
Query: 96 AKMLEDAGCSLL-------AVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 148
AK ED G L A G+ + + I+A+ A+ IPV G +R
Sbjct: 36 AKAWEDQGAKWLHLVDLDGAKAGKPVNLE----------LIEAIVKAVDIPVQVGGGIRS 85
Query: 149 MEDVQKCLEETGCEGVLSAESLLENPALFA------------------GF-RTAEWIVGS 189
+E V+ L + G V+ + ++NP L G T W+ S
Sbjct: 86 LETVEALL-DAGVSRVIIGTAAVKNPELVKEACKKFPGKIVVGLDARDGKVATDGWLETS 144
Query: 190 E---------------------EISKDG-----NLDQADLLVEYLKLCEKYPVPW 218
+IS+DG N++ +L P+P
Sbjct: 145 GVTAEDLAKRFEDAGVKAIIYTDISRDGTLSGPNVEA------TRELAAAVPIPV 193
>gnl|CDD|235552 PRK05670, PRK05670, anthranilate synthase component II;
Provisional.
Length = 189
Score = 33.2 bits (77), Expect = 0.090
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 253 FLYNLVDRLRELGVRIPLYKKDADDAEILA 282
F YNLV L ELG + +Y+ D E +
Sbjct: 11 FTYNLVQYLGELGAEVVVYRNDEITLEEIE 40
>gnl|CDD|172156 PRK13587, PRK13587,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 234
Score = 32.9 bits (75), Expect = 0.12
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 12/81 (14%)
Query: 91 DTIKYAKMLEDAGCSLLAVHGRTRD-----------EKDGKKFRADWNAIKAVKNALRIP 139
+ IK ED +L + + D KDGK ++ + A IP
Sbjct: 135 EDIKVNGWEEDTELNLFSFVRQLSDIPLGGIIYTDIAKDGKMSGPNFELTGQLVKATTIP 194
Query: 140 VLANGNVRHMEDVQKCLEETG 160
V+A+G +RH +D+Q+ L
Sbjct: 195 VIASGGIRHQQDIQR-LASLN 214
>gnl|CDD|178226 PLN02617, PLN02617, imidazole glycerol phosphate synthase hisHF.
Length = 538
Score = 33.1 bits (76), Expect = 0.15
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 119 GKKFRADWNAIKAVKNALRIPVLAN---GNVRHMEDVQKCLEETGCEGVLSA 167
GK F D +K V +A+ IPV+A+ G H DV +T L+A
Sbjct: 466 GKGF--DIELVKLVSDAVTIPVIASSGAGTPEHFSDV---FSKTNASAALAA 512
>gnl|CDD|233243 TIGR01036, pyrD_sub2, dihydroorotate dehydrogenase, subfamily 2.
This model describes enzyme protein dihydroorotate
dehydrogenase exclusively for subfamily 2. It includes
members from bacteria, yeast, plants etc. The
subfamilies 1 and 2 share extensive homology,
particularly toward the C-terminus. This subfamily has a
longer N-terminal region [Purines, pyrimidines,
nucleosides, and nucleotides, Pyrimidine ribonucleotide
biosynthesis].
Length = 336
Score = 32.8 bits (75), Expect = 0.16
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 27 ARRVEPYCDYVDINLGCPQRIARRG-NYGAFLMDNLPLVKSLVEKLALNLNVPVSCKIRV 85
R++ PY Y+ +N+ P R YG L D L +K+ L + +VP++ KI
Sbjct: 160 LRKIYPYAGYIVVNISSPNTPGLRDLQYGEALDDLLTAIKNEQNDLQAHHHVPIAVKIA- 218
Query: 86 FPNLQD 91
P+L +
Sbjct: 219 -PDLSE 223
>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 = 32.3 bits (74), Expect = 0.17
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 88 NLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVR 147
N++D +K AK L++ G + VH ++ G+ D I + R+ V N+
Sbjct: 111 NVKDKVKRAKELKELGADYIGVHTGLDEQAKGQNPFEDLQTILKLVKEARVAVAGGINLD 170
Query: 148 HMEDVQK 154
+ DV K
Sbjct: 171 TIPDVIK 177
>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 = 0.18
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 91 DTIKYAKMLEDAGCSLL--AVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 148
T++ A G ++ + G T + + D+ +K ++ AL IPV+A G +
Sbjct: 131 STLEEALNAAKLGFDIIGTTLSGYTEETAKTED--PDFELLKELRKALGIPVIAEGRINS 188
Query: 149 MEDVQKCLE 157
E K LE
Sbjct: 189 PEQAAKALE 197
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 32.2 bits (73), Expect = 0.21
Identities = 37/166 (22%), Positives = 53/166 (31%), Gaps = 33/166 (19%)
Query: 8 DRPLFVQFCANDP-EILLNAARRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVK 65
D PL VQ ND + AA D V+I+ ++L L++
Sbjct: 57 DLPLGVQLAINDAAAAVDIAAAAARAAGADGVEIHGAVGYLAR----------EDLELIR 106
Query: 66 SLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDG------ 119
L E +V V K+ L A V G
Sbjct: 107 ELREA---VPDVKVVVKLSPTG----------ELAAAAAEEAGVDEVGLGNGGGGGGGRD 153
Query: 120 KKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVL 165
AD I A K ++PV+A G + ED + G +GV+
Sbjct: 154 AVPIADLLLILA-KRGSKVPVIAGGGINDPEDAAE-ALALGADGVI 197
>gnl|CDD|224329 COG1411, COG1411, Uncharacterized protein related to proFAR
isomerase (HisA) [General function prediction only].
Length = 229
Score = 32.1 bits (73), Expect = 0.23
Identities = 25/82 (30%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 91 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 150
+T+K D G +L + G K D+ + V PVL G V ME
Sbjct: 141 ETVKDLNYRRDPGLIVLDIGAV------GTKSGPDYELLTKVLELSEHPVLLGGGVGGME 194
Query: 151 DVQKCLEETGCEGVLSAESLLE 172
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 = 31.6 bits (72), Expect = 0.30
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 96 AKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRHMEDV 152
A++ E+AG +++A+ D G R +D IK + NA+ IPV+A + H +
Sbjct: 16 ARIAEEAGAVAVMALERVPADIRAAGGVARMSDPKMIKEIMNAVSIPVMAKVRIGHFVEA 75
Query: 153 QKCLEETGCEGVLSAESL 170
Q LE G + + +E L
Sbjct: 76 Q-ILEAIGVDYIDESEVL 92
>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 = 0.30
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 105 SLLAVHGRTRDEKDGKKFRADWNAIKAVKNAL--RIPVLANGNVRHMEDVQKCLEETGCE 162
SL ++R +D + ++ VK + R+P++A G++ +D + L ETG +
Sbjct: 255 SLWDFDRKSRRGRDDNQTI-----MELVKERIAGRLPLIAVGSINTPDDALEAL-ETGAD 308
Query: 163 GVLSAESLLENP 174
V LL +P
Sbjct: 309 LVAIGRGLLVDP 320
>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 = 31.7 bits (72), Expect = 0.34
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 96 AKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRHMEDV 152
AK+ E+AG +++A+ D G R +D IK + +A+ IPV+A + H +
Sbjct: 23 AKIAEEAGAVAVMALERVPADIRASGGVARMSDPKMIKEIMDAVSIPVMAKVRIGHFVEA 82
Query: 153 QKCLEETGCEGVLSAESL 170
Q LE G + + +E L
Sbjct: 83 Q-ILEALGVDYIDESEVL 99
>gnl|CDD|235465 PRK05437, PRK05437, isopentenyl pyrophosphate isomerase;
Provisional.
Length = 352
Score = 31.7 bits (73), Expect = 0.42
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 19/79 (24%)
Query: 96 AKMLEDAGCSLLAVHG------------RTRDEKDGKKFRADW-----NAIKAVKNAL-R 137
AK L DAG + V G R RD++ F ADW ++ ++ L
Sbjct: 203 AKRLADAGVKAIDVAGAGGTSWAAIENYRARDDRLASYF-ADWGIPTAQSLLEARSLLPD 261
Query: 138 IPVLANGNVRHMEDVQKCL 156
+P++A+G +R+ D+ K L
Sbjct: 262 LPIIASGGIRNGLDIAKAL 280
>gnl|CDD|239244 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
FMN-binding domain. 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 the dimer interface twice. Two
of the Fe-S clusters show a hitherto unobserved
coordination involving a glutamine residue.
Length = 299
Score = 31.5 bits (72), Expect = 0.43
Identities = 25/100 (25%), Positives = 45/100 (45%), Gaps = 5/100 (5%)
Query: 8 DRPLFVQ-FCANDPEILLNAARRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVK 65
D+ L C + E A+ VE D +++N CP + RG GA + + LV+
Sbjct: 99 DKILIASIMCEYNKEDWTELAKLVEEAGADALELNFSCPHGMPERG-MGAAVGQDPELVE 157
Query: 66 SLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCS 105
+ + + +PV K+ PN+ D + A+ ++ G
Sbjct: 158 EICRWVREAVKIPVIAKLT--PNITDIREIARAAKEGGAD 195
>gnl|CDD|236998 PRK11840, PRK11840, bifunctional sulfur carrier protein/thiazole
synthase protein; Provisional.
Length = 326
Score = 31.3 bits (71), Expect = 0.47
Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 96 AKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKC 155
AK LEDAG +AV G + + I+ + +PVL + V D
Sbjct: 211 AKRLEDAGA--VAVMPLGAPIGSGLGIQ-NPYTIRLIVEGATVPVLVDAGVGTASDAAVA 267
Query: 156 LEETGCEGVLSAESLLE--NPALFA 178
+ E GC+GVL ++ E NP L A
Sbjct: 268 M-ELGCDGVLMNTAIAEAKNPVLMA 291
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 30.6 bits (70), Expect = 0.92
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 27 ARRVEPY--CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLNVPVSCKIR 84
AR +E D +++N+ CP G L + L++ L+E + VPV K+
Sbjct: 115 ARLLEEAGDADAIELNISCPNTPG-----GRALGQDPELLEKLLEAVKAATKVPVFVKLA 169
Query: 85 VFPNLQDTIKYAKMLEDAG 103
PN+ D + AK E+AG
Sbjct: 170 --PNITDIDEIAKAAEEAG 186
>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 = 1.3
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 253 FLYNLVDRLRELGVRIPLYKKDADDAEILADD 284
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 = 1.6
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 91 DTIKYAKMLEDAGCSLLA--VHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 148
T++ + G + + G T + K K D+ +K + A+ PV+A G +
Sbjct: 127 STLEEGLAAQKLGFDFIGTTLSGYTEETK--KPEEPDFALLKELLKAVGCPVIAEGRINT 184
Query: 149 MEDVQKCLEETGCEGV 164
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 = 29.6 bits (67), Expect = 2.0
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 123 RADWN-AIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFA 178
R + A +K A+ IPV+A+ + E ++ L + + V A L +P A
Sbjct: 261 RGAFAWATAKLKRAVDIPVIASNRINTPEVAERLLADGDADMVSMARPFLADPDFVA 317
>gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 669
Score = 29.8 bits (67), Expect = 2.2
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 8/58 (13%)
Query: 25 NAARRVEPYCDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLAL-NLNVPVSC 81
NA+ + Y D + +N+G +I+RRG D +P V+ ++EKL++ +P +C
Sbjct: 351 NASLHNQDYIDSIGLNVGDVVKISRRG-------DVIPAVELVIEKLSVGFFKIPDNC 401
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 29.4 bits (67), Expect = 2.2
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 12/63 (19%)
Query: 59 DNLPLVKSLVEKLALNLNVPVSCKIRVFPNL-QDTIKYAKMLEDAGCSLLAVHG----RT 113
+ LP ++ L L + P SC VF N ++ + A L G S LA+HG R
Sbjct: 228 ERLPALQRL-----LLHHQPESCV--VFCNTKKECQEVADALNAQGFSALALHGDLEQRD 280
Query: 114 RDE 116
RD+
Sbjct: 281 RDQ 283
>gnl|CDD|225877 COG3340, PepE, Peptidase E [Amino acid transport and metabolism].
Length = 224
Score = 28.9 bits (65), Expect = 2.3
Identities = 22/129 (17%), Positives = 43/129 (33%), Gaps = 21/129 (16%)
Query: 94 KYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQ 153
K L G + +H + AI+ I + GN ++
Sbjct: 53 KVRNALAKLGLEVSELH----------LSKPPLAAIENKLMKADIIYVGGGNTFNL---L 99
Query: 154 KCLEETGCEGVLSAESLLENPALFAGFRTAEWIVGSEEISKDGNLD---QADLLVEY--L 208
+ L+ETG + ++ ++ + G+ +A + I +D A L ++ L
Sbjct: 100 QELKETGLDDIIRER--VKAGTPYIGW-SAGANIAGPTIETTSYMDMPIVAPQLGDFDGL 156
Query: 209 KLCEKYPVP 217
L P
Sbjct: 157 NLVPFQVNP 165
>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 = 2.3
Identities = 27/106 (25%), Positives = 46/106 (43%), Gaps = 15/106 (14%)
Query: 85 VFPNLQDTIKYAKMLEDAGCS----LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPV 140
V P D AK LEDAGC+ L + G G+ +N ++ + +PV
Sbjct: 126 VLPYCTDDPVLAKRLEDAGCAAVMPLGSPIG------SGQGLLNPYN-LRIIIERADVPV 178
Query: 141 LANGNVRHMEDVQKCLEETGCEGVL--SAESLLENPALFA-GFRTA 183
+ + + D + + E G + VL +A + ++P A F+ A
Sbjct: 179 IVDAGIGTPSDAAQAM-ELGADAVLLNTAIAKAKDPVAMARAFKLA 223
>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 = 2.4
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 11/55 (20%)
Query: 89 LQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 143
L + I+ AK +AG + V G D I+A A +P+ N
Sbjct: 159 LDEAIERAKAYAEAGADGIFVEGLK-----------DPEEIRAFAEAPDVPLNVN 202
>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 = 2.8
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 22/91 (24%)
Query: 185 WIVGSEEISKDGNLDQADLLVEYLKLCEKY-----PVPWRMIRSH-----VHKLLGEWFR 234
W S + +D + +A+L V + + E + VP I + L GEW R
Sbjct: 30 WCTASRVLERDEDELEAELTVGFGGIRESFTSRVTLVPPESIEAELVDGPFKHLEGEW-R 88
Query: 235 IQPGVRE----DLNAQNRLTFEF---LYNLV 258
+P + + L FEF L +
Sbjct: 89 FKPLGENACKVEFD----LEFEFKSRLLEAL 115
>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 = 28.8 bits (65), Expect = 3.3
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 19/79 (24%)
Query: 96 AKMLEDAGCSLLAVHG------------RTRDEKDGKKFRADWN-----AIKAVKN-ALR 137
AK+L DAG S + V G R + F DW ++ V++ A
Sbjct: 196 AKLLADAGVSAIDVAGAGGTSWAQVENYRAKGSNLASFF-NDWGIPTAASLLEVRSDAPD 254
Query: 138 IPVLANGNVRHMEDVQKCL 156
P++A+G +R DV K +
Sbjct: 255 APIIASGGLRTGLDVAKAI 273
>gnl|CDD|181086 PRK07695, PRK07695, transcriptional regulator TenI; Provisional.
Length = 201
Score = 28.4 bits (64), Expect = 3.4
Identities = 26/97 (26%), Positives = 38/97 (39%), Gaps = 11/97 (11%)
Query: 86 FPNLQ-----DTIKYAKMLEDAGC-SLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIP 139
FP L +++ A E G ++ H D K G R + + AL IP
Sbjct: 93 FPYLHVGYSVHSLEEAIQAEKNGADYVVYGHVFPTDCKKGVPARG-LEELSDIARALSIP 151
Query: 140 VLANGNVRHMEDVQKCLEETGCEG--VLSAESLLENP 174
V+A G + E+ + L G G V+S NP
Sbjct: 152 VIAIGGI-TPENTRDVL-AAGVSGIAVMSGIFSSANP 186
>gnl|CDD|224815 COG1903, CbiD, Cobalamin biosynthesis protein CbiD [Coenzyme
metabolism].
Length = 367
Score = 28.8 bits (65), Expect = 3.8
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 214 YPVPWRMIRSHVHKLLGE 231
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 = 28.7 bits (65), Expect = 3.8
Identities = 12/90 (13%), Positives = 34/90 (37%), Gaps = 18/90 (20%)
Query: 81 CKIRVFPN----LQDTIKYAKMLEDAGCSLL--AVHGRTRDEKDGKKFRADWNAIKAVKN 134
++RV N ++ ++ + L + G L+ V D + + +++
Sbjct: 178 ARLRVDANQGWTPEEAVELLRELAELGVELIEQPVP------------AGDDDGLAYLRD 225
Query: 135 ALRIPVLANGNVRHMEDVQKCLEETGCEGV 164
+P++A+ + D + +G+
Sbjct: 226 KSPLPIMADESCFSAADAARLAGGGAYDGI 255
>gnl|CDD|240089 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2.
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, their cellular
location and their natural electron acceptor used to
reoxidize the flavin group. Members of class 1 are
cytosolic enzymes and multimers, while class 2 enzymes
are membrane associated, monomeric and use respiratory
quinones as their physiological electron acceptors.
Length = 327
Score = 28.6 bits (65), Expect = 3.8
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 7/51 (13%)
Query: 1 MKNLPPEDRPLFVQFCAN----DPEIL---LNAARRVEPYCDYVDINLGCP 44
+K P PL V N + + + R++ PY DY+ +N+ P
Sbjct: 121 LKKRRPRGGPLGVNIGKNKDTPLEDAVEDYVIGVRKLGPYADYLVVNVSSP 171
>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 = 27.7 bits (62), Expect = 4.3
Identities = 21/96 (21%), Positives = 46/96 (47%), Gaps = 25/96 (26%)
Query: 12 FVQFCANDPEILLNAARRVEPYCDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKL 71
++ A DPE++ + ++ Y R+A++ LV+ L+E
Sbjct: 26 LLKEAAEDPEVI---SIKITLY------------RLAKQSR----------LVEYLIEAA 60
Query: 72 ALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLL 107
+V V ++R + ++ I++A+ LE+AGC+++
Sbjct: 61 ENGKDVTVLMELRARFDEENNIEWAERLEEAGCTVI 96
>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 = 4.4
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 253 FLYNLVDRLRELGVRIPLYKKDADDAEILA 282
F YNLV LRELG + + + D E L
Sbjct: 10 FTYNLVQYLRELGAEVVVVRNDEITLEELE 39
>gnl|CDD|225311 COG2513, PrpB, PEP phosphonomutase and related enzymes
[Carbohydrate transport and metabolism].
Length = 289
Score = 28.0 bits (63), Expect = 5.0
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 11/56 (19%)
Query: 88 NLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 143
L D I+ A+ +AG + T D I+A A+ +P+ AN
Sbjct: 164 GLDDAIERAQAYVEAGADAIFPEALT-----------DLEEIRAFAEAVPVPLPAN 208
>gnl|CDD|223049 PHA03334, PHA03334, putative DNA polymerase catalytic subunit;
Provisional.
Length = 1545
Score = 28.7 bits (64), Expect = 5.3
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 16 CANDPEILLNAARRVEPYCD--YV-----DINLGCPQRIARRGNYGAFLMDNLPLVKSLV 68
CA++ E+LL R+ + YV D+ + I R NY AF PL K+L+
Sbjct: 328 CADELEMLLAFLNRLRKSVNVLYVYNAEFDVQV-----IQSRLNYYAFKQRPHPLTKALM 382
Query: 69 EK 70
E
Sbjct: 383 EA 384
>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 = 28.0 bits (63), Expect = 5.9
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 96 AKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRHMEDV 152
A++ E+AG +++A+ D G R AD IK + +A+ IPV+A + H +
Sbjct: 21 ARIAEEAGAVAVMALERVPADIRAAGGVARMADPKMIKEIMDAVSIPVMAKVRIGHFVEA 80
Query: 153 QKCLEETG 160
Q LE G
Sbjct: 81 Q-ILEALG 87
>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 = 27.4 bits (62), Expect = 8.3
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 15/80 (18%)
Query: 92 TIKYAKMLEDAGCSLLAV-------HGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANG 144
+++ A+ E AG L H T D + + V++A+ IPV+A G
Sbjct: 111 SVEEARKAEAAGADALVAQGAEAGGHRGTFD-------IGTFALVPEVRDAVDIPVIAAG 163
Query: 145 NVRHMEDVQKCLEETGCEGV 164
+ + L G +GV
Sbjct: 164 GIADGRGIAAALAL-GADGV 182
>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 = 8.5
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 11/52 (21%)
Query: 89 LQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPV 140
L++ I+ A+ +AG + V G + I A+ A+ +P+
Sbjct: 154 LEEAIERARAYAEAGADGIFVPGLKDPD-----------EIAALAAAVPLPL 194
>gnl|CDD|223576 COG0502, BioB, Biotin synthase and related enzymes [Coenzyme
metabolism].
Length = 335
Score = 27.6 bits (62), Expect = 8.7
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 88 NLQDTIKYAKMLEDAG----CSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 143
+++ ++ AK + AG C A G +D ++ AIKAVK L + V A+
Sbjct: 85 EVEEILEAAKKAKAAGATRFCMGAAGRGP---GRDMEEVVE---AIKAVKEELGLEVCAS 138
>gnl|CDD|180709 PRK06815, PRK06815, hypothetical protein; Provisional.
Length = 317
Score = 27.3 bits (61), Expect = 8.9
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 258 VDRLRELGVRIPLYKKDADDAEILADDLA 286
+D +R LG + LY DA +AE+ A A
Sbjct: 107 LDAIRALGAEVRLYGGDALNAELAARRAA 135
>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 = 27.4 bits (61), Expect = 9.4
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 214 YPVPWRMIRSHVHKLLGE 231
PVP RMIR ++ K L E
Sbjct: 117 NPVPRRMIRENLQKALRE 134
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 27.6 bits (62), Expect = 9.4
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 27 ARRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLNVPVSCKIRV 85
A VE D +++N GCP ++ RG G+ + LV+ + +PV K+
Sbjct: 119 APLVEETGADGIELNFGCPHGMSERG-MGSAVGQVPELVEMYTRWVKRGSRLPVIVKLT- 176
Query: 86 FPNLQDTIKYAKMLEDAGC 104
PN+ D + A+ + G
Sbjct: 177 -PNITDIREPARAAKRGGA 194
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 0.140 0.424
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: 15,236,003
Number of extensions: 1482107
Number of successful extensions: 1892
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1855
Number of HSP's successfully gapped: 102
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
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 (21.9 bits)
S2: 58 (26.0 bits)