RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021609
(310 letters)
>gnl|CDD|179769 PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS; Provisional.
Length = 293
Score = 561 bits (1449), Expect = 0.0
Identities = 207/284 (72%), Positives = 247/284 (86%), Gaps = 1/284 (0%)
Query: 26 VKVGLAQMLRGGVIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIK 85
VK G A+ML+GGVIMDVV EQA++AEEAGA AVMALERVPADIR+ GGVARM+DP++I+
Sbjct: 8 VKRGFAEMLKGGVIMDVVNAEQAKIAEEAGAVAVMALERVPADIRAAGGVARMADPKMIE 67
Query: 86 EIKQSVTIPVMAKARIGHFVEAQILEAIGIDYVDESEVLTPADEENHINKHNFRIPFVCG 145
EI +V+IPVMAKARIGHFVEAQILEA+G+DY+DESEVLTPADEE HI+K +F +PFVCG
Sbjct: 68 EIMDAVSIPVMAKARIGHFVEAQILEALGVDYIDESEVLTPADEEYHIDKWDFTVPFVCG 127
Query: 146 CRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVMGDIRVLRNMDDDEVFTFAKK 205
RNLGEALRRI EGAAMIRTKGEAGTGN++EAVRH+R + G+IR L +M +DE++T AK+
Sbjct: 128 ARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHMRQINGEIRRLTSMSEDELYTAAKE 187
Query: 206 IAAPYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRA 265
+ APY+LV + +LGRLPVV+FAAGG+ATPADAA+MMQLG DGVFVGSG+FKSGDP KRA
Sbjct: 188 LQAPYELVKEVAELGRLPVVNFAAGGIATPADAALMMQLGADGVFVGSGIFKSGDPEKRA 247
Query: 266 QAIVRAVTHYSDPEVLAEVSCGLGEAMVGLNLSDHKV-ERFASR 308
+AIV A THY DPEVLAEVS GLGEAMVG+++ + ER R
Sbjct: 248 RAIVEATTHYDDPEVLAEVSKGLGEAMVGIDIDELPPEERLQER 291
>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 = 531 bits (1371), Expect = 0.0
Identities = 207/283 (73%), Positives = 247/283 (87%), Gaps = 1/283 (0%)
Query: 28 VGLAQMLRGGVIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEI 87
G AQML+GGVIMDV EQAR+AEEAGA AVMALERVPADIR+ GGVARM+DP++IKEI
Sbjct: 1 RGFAQMLKGGVIMDVTNAEQARIAEEAGAVAVMALERVPADIRAAGGVARMADPKMIKEI 60
Query: 88 KQSVTIPVMAKARIGHFVEAQILEAIGIDYVDESEVLTPADEENHINKHNFRIPFVCGCR 147
+V+IPVMAK RIGHFVEAQILEA+G+D +DESEVLTPADEE+HI+KH F++PFVCG R
Sbjct: 61 MDAVSIPVMAKVRIGHFVEAQILEALGVDMIDESEVLTPADEEHHIDKHKFKVPFVCGAR 120
Query: 148 NLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVMGDIRVLRNMDDDEVFTFAKKIA 207
NLGEALRRI EGAAMIRTKGEAGTGN++EAVRH+R+V G+IR L++M ++E++ AK+I
Sbjct: 121 NLGEALRRISEGAAMIRTKGEAGTGNVVEAVRHMRAVNGEIRKLQSMSEEELYAVAKEIQ 180
Query: 208 APYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQA 267
APY+LV +T +LGRLPVV+FAAGGVATPADAA+MMQLG DGVFVGSG+FKS +P KRA+A
Sbjct: 181 APYELVKETAKLGRLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSENPEKRARA 240
Query: 268 IVRAVTHYSDPEVLAEVSCGLGEAMVGLNL-SDHKVERFASRS 309
IV AVTHY DPE+LAEVS GLGEAMVG+++ S + ER R
Sbjct: 241 IVEAVTHYDDPEILAEVSEGLGEAMVGIDIASLKEEERMQERG 283
>gnl|CDD|223292 COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme
metabolism].
Length = 296
Score = 510 bits (1316), Expect = 0.0
Identities = 207/293 (70%), Positives = 245/293 (83%), Gaps = 1/293 (0%)
Query: 17 TETKKSPFSVKVGLAQMLRGGVIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVA 76
E + VK G AQML+GGVIMDVV EQAR+AEEAGA AVMALERVPADIR+ GGVA
Sbjct: 2 EELRTGTERVKRGFAQMLKGGVIMDVVNAEQARIAEEAGAVAVMALERVPADIRAAGGVA 61
Query: 77 RMSDPQLIKEIKQSVTIPVMAKARIGHFVEAQILEAIGIDYVDESEVLTPADEENHINKH 136
RM+DP++I+EI +V+IPVMAK RIGHFVEAQILEA+G+D +DESEVLTPADEE HINK
Sbjct: 62 RMADPKMIEEIMDAVSIPVMAKVRIGHFVEAQILEALGVDMIDESEVLTPADEEFHINKW 121
Query: 137 NFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVMGDIRVLRNMDD 196
F +PFVCG RNLGEALRRI EGAAMIRTKGEAGTGN++EAVRH+R + G+IR L++M +
Sbjct: 122 KFTVPFVCGARNLGEALRRISEGAAMIRTKGEAGTGNVVEAVRHMRKINGEIRRLQSMTE 181
Query: 197 DEVFTFAKKIAAPYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVF 256
DE++ AK++ APY+LV + +LGRLPVV+FAAGGVATPADAA+MMQLG DGVFVGSG+F
Sbjct: 182 DELYVVAKELQAPYELVKEVAKLGRLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIF 241
Query: 257 KSGDPVKRAQAIVRAVTHYSDPEVLAEVSCGLGEAMVGLNLSDHKV-ERFASR 308
KS +P KRA+AIV A THY DPEVLAEVS GLGEAM G+++S+ ER R
Sbjct: 242 KSSNPEKRAKAIVEATTHYDDPEVLAEVSEGLGEAMKGIDISELPEEERLQER 294
>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 = 447 bits (1151), Expect = e-160
Identities = 193/274 (70%), Positives = 234/274 (85%), Gaps = 1/274 (0%)
Query: 26 VKVGLAQMLRGGVIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIK 85
+K GLAQML+GGVIMDVV PEQA++AEEAGA AVMALERVPADIR+ GGVARMSDP++IK
Sbjct: 1 LKKGLAQMLKGGVIMDVVNPEQAKIAEEAGAVAVMALERVPADIRASGGVARMSDPKMIK 60
Query: 86 EIKQSVTIPVMAKARIGHFVEAQILEAIGIDYVDESEVLTPADEENHINKHNFRIPFVCG 145
EI +V+IPVMAK RIGHFVEAQILEA+G+DY+DESEVLTPAD HI+K F++PFVCG
Sbjct: 61 EIMDAVSIPVMAKVRIGHFVEAQILEALGVDYIDESEVLTPADWTFHIDKKKFKVPFVCG 120
Query: 146 CRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVMGDIRVLRNMDDDEVF-TFAK 204
R+LGEALRRI EGAAMIRTKGEAGTGNI+EAVRH+R + +IR ++NM ++E AK
Sbjct: 121 ARDLGEALRRINEGAAMIRTKGEAGTGNIVEAVRHMRKINEEIRQIQNMLEEEDLAAVAK 180
Query: 205 KIAAPYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKR 264
++ P +L+++ +LG+LPVV+FAAGGVATPADAA+MMQLG DGVFVGSG+FKS +P K
Sbjct: 181 ELRVPVELLLEVLKLGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSSNPEKL 240
Query: 265 AQAIVRAVTHYSDPEVLAEVSCGLGEAMVGLNLS 298
A+AIV A THY +PE LAEVS LGEAM G+++S
Sbjct: 241 AKAIVEATTHYDNPEKLAEVSKDLGEAMKGISIS 274
>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 = 363 bits (933), Expect = e-128
Identities = 148/197 (75%), Positives = 175/197 (88%)
Query: 33 MLRGGVIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVT 92
ML+GGVIMDVV EQAR+AEEAGA AVMALERVPADIR+ GGVARMSDP++IKEI +V+
Sbjct: 1 MLKGGVIMDVVNAEQARIAEEAGAVAVMALERVPADIRAAGGVARMSDPKMIKEIMNAVS 60
Query: 93 IPVMAKARIGHFVEAQILEAIGIDYVDESEVLTPADEENHINKHNFRIPFVCGCRNLGEA 152
IPVMAK RIGHFVEAQILEAIG+DY+DESEVLTPADE HI+K F +PFVCG RNLGEA
Sbjct: 61 IPVMAKVRIGHFVEAQILEAIGVDYIDESEVLTPADEFFHIDKKKFTVPFVCGARNLGEA 120
Query: 153 LRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVMGDIRVLRNMDDDEVFTFAKKIAAPYDL 212
LRRI EGAAMIRTKGEAGTGN++EAVRH+R + G+IR L++M +DE++T AK++AAPY+L
Sbjct: 121 LRRIWEGAAMIRTKGEAGTGNVVEAVRHMRLMNGEIRRLQSMSEDELYTVAKELAAPYEL 180
Query: 213 VMQTKQLGRLPVVHFAA 229
V Q +LG+LPVV+FAA
Sbjct: 181 VKQVAELGKLPVVNFAA 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 = 52.6 bits (126), Expect = 3e-08
Identities = 48/220 (21%), Positives = 72/220 (32%), Gaps = 47/220 (21%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAKARIGHFV 105
E A+ A EAGA A++ R A D +++KE+ +P+ + I
Sbjct: 16 ELAKAAAEAGADAIIVGTRSSDPEE-----AETDDKEVLKEVAAETDLPLGVQLAINDAA 70
Query: 106 EAQ-----ILEAIGIDYVDESEVLTPADEENHINKHNFR-----IPFVCGCRNLGEALRR 155
A A G D V+ + E+ R + V GE
Sbjct: 71 AAVDIAAAAARAAGADGVEIHGAVGYLAREDLELIRELREAVPDVKVVVKLSPTGELAAA 130
Query: 156 --IREGAAMIRTKGEAGTGNIIEAVRHVRSVMGDIRVLRNMDDDEVFTFAKKIAAPYDLV 213
G + G G +AV + +
Sbjct: 131 AAEEAGVDEVGLGNGGGGGGGRDAVPIADLL----------------------------L 162
Query: 214 MQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGS 253
+ K+ ++PV A GG+ P DAA + LG DGV VGS
Sbjct: 163 ILAKRGSKVPV--IAGGGINDPEDAAEALALGADGVIVGS 200
>gnl|CDD|224933 COG2022, ThiG, Uncharacterized enzyme of thiazole biosynthesis
[Nucleotide transport and metabolism].
Length = 262
Score = 50.3 bits (121), Expect = 3e-07
Identities = 21/53 (39%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 221 RLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAVT 273
+PV+ A G+ TP+DAA M+LG D V + + + ++ DPV A+A AV
Sbjct: 182 DVPVIVDA--GIGTPSDAAQAMELGADAVLLNTAIARAKDPVAMARAFALAVE 232
>gnl|CDD|147701 pfam05690, ThiG, Thiazole biosynthesis protein ThiG. This family
consists of several bacterial thiazole biosynthesis
protein G sequences. ThiG, together with ThiF and ThiH,
is proposed to be involved in the synthesis of
4-methyl-5-(b-hydroxyethyl)thiazole (THZ) which is an
intermediate in the thiazole production pathway.
Length = 246
Score = 49.5 bits (119), Expect = 5e-07
Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 221 RLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAV 272
+PV+ A G+ TP+DAA M+LG D V + + + ++ DPV A+A AV
Sbjct: 174 DVPVIVDA--GIGTPSDAAQAMELGADAVLLNTAIARAKDPVAMARAFKLAV 223
>gnl|CDD|234687 PRK00208, thiG, thiazole synthase; Reviewed.
Length = 250
Score = 48.9 bits (118), Expect = 9e-07
Identities = 19/42 (45%), Positives = 27/42 (64%)
Query: 231 GVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAV 272
G+ TP+DAA M+LG D V + + + +GDPV A+A AV
Sbjct: 183 GIGTPSDAAQAMELGADAVLLNTAIAVAGDPVAMARAFKLAV 224
>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 = 48.6 bits (117), Expect = 1e-06
Identities = 19/42 (45%), Positives = 27/42 (64%)
Query: 231 GVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAV 272
G+ TP+DAA M+LG D V + + + K+ DPV A+A AV
Sbjct: 183 GIGTPSDAAQAMELGADAVLLNTAIAKAKDPVAMARAFKLAV 224
>gnl|CDD|236998 PRK11840, PRK11840, bifunctional sulfur carrier protein/thiazole
synthase protein; Provisional.
Length = 326
Score = 47.0 bits (112), Expect = 4e-06
Identities = 22/52 (42%), Positives = 35/52 (67%), Gaps = 2/52 (3%)
Query: 221 RLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAV 272
+PV+ A GV T +DAA+ M+LGCDGV + + + ++ +PV A+A+ AV
Sbjct: 249 TVPVLVDA--GVGTASDAAVAMELGCDGVLMNTAIAEAKNPVLMARAMKLAV 298
Score = 35.9 bits (83), Expect = 0.018
Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 45 PEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAKARIGHF 104
P A+ E+AGA AVM L A I S G + +P I+ I + T+PV+ A +G
Sbjct: 208 PIAAKRLEDAGAVAVMPL---GAPIGSGLG---IQNPYTIRLIVEGATVPVLVDAGVGTA 261
Query: 105 VEAQILEAIGIDYV 118
+A + +G D V
Sbjct: 262 SDAAVAMELGCDGV 275
>gnl|CDD|214380 CHL00162, thiG, thiamin biosynthesis protein G; Validated.
Length = 267
Score = 42.4 bits (100), Expect = 1e-04
Identities = 18/52 (34%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 221 RLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAV 272
++PV+ A G+ TP++A+ M+LG GV + + V ++ +P + A+A+ AV
Sbjct: 189 KIPVIIDA--GIGTPSEASQAMELGASGVLLNTAVAQAKNPEQMAKAMKLAV 238
>gnl|CDD|238317 cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP
synthase)/TenI. TMP synthase catalyzes an important step
in the thiamine biosynthesis pathway, the substitution
of the pyrophosphate of 2-methyl-4-amino-5-
hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-
(beta-hydroxyethyl) thiazole phosphate to yield thiamine
phosphate. TenI is a enzymatically inactive regulatory
protein involved in the regulation of several
extracellular enzymes. This superfamily also contains
other enzymatically inactive proteins with unknown
functions.
Length = 196
Score = 40.6 bits (96), Expect = 3e-04
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 211 DLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVR 270
+L+ + +L +PVV A GG+ TP +AA ++ G DGV V S + + DP A+ ++
Sbjct: 140 ELLREIAELVEIPVV--AIGGI-TPENAAEVLAAGADGVAVISAITGADDPAAAARELLA 196
>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 = 40.5 bits (96), Expect = 5e-04
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 206 IAAPYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGS 253
+ LV + + +PV+ AAGG+A A + LG DGV +G+
Sbjct: 141 DIGTFALVPEVRDAVDIPVI--AAGGIADGRGIAAALALGADGVQMGT 186
Score = 35.9 bits (84), Expect = 0.015
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 17/67 (25%)
Query: 38 VIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVA-------RMSDPQLIKEIKQS 90
VI V + E+AR AE AGA A++A QG A + L+ E++ +
Sbjct: 105 VIPTVTSVEEARKAEAAGADALVA----------QGAEAGGHRGTFDIGTFALVPEVRDA 154
Query: 91 VTIPVMA 97
V IPV+A
Sbjct: 155 VDIPVIA 161
>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 = 40.4 bits (95), Expect = 6e-04
Identities = 55/244 (22%), Positives = 80/244 (32%), Gaps = 92/244 (37%)
Query: 43 VTPEQARVAEEAGACAVMALERVPAD--IRSQGGVARMSDPQLIKEIKQ----SVTIPVM 96
E A++ EE GA + P + G A + DP LI +I + +V IPV
Sbjct: 76 TMAEAAKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVT 135
Query: 97 AKARIGHFVEAQILEAIGIDYVDESEVLTPADEENHINKHNFRIPFVCGCRNLGEALRRI 156
K RI G D + HIN
Sbjct: 136 VKIRI------------GWD-------------DAHIN-----------AVEAARIAED- 158
Query: 157 REGAAMI----RTKGEAGTGNIIEAVRHVRSVMGDIRVLRNMDDDEVFTFAKKIAAPYDL 212
GA + RT+ + +G A +D+
Sbjct: 159 -AGAQAVTLHGRTRAQGYSGE----------------------------------ANWDI 183
Query: 213 VMQTKQLGRLPVVHFAAGGVATPADA-AMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRA 271
+ + KQ R+PV G + +P DA AM+ GCDGV +G G G+P + R
Sbjct: 184 IARVKQAVRIPV--IGNGDIFSPEDAKAMLETTGCDGVMIGRGAL--GNPW-----LFRQ 234
Query: 272 VTHY 275
+ Y
Sbjct: 235 IEQY 238
>gnl|CDD|234590 PRK00043, thiE, thiamine-phosphate pyrophosphorylase; Reviewed.
Length = 212
Score = 39.0 bits (92), Expect = 0.001
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 217 KQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAVTHY 275
+G +P+V A GG+ TP +A +++ G DGV V S + + DP A+A++ A
Sbjct: 156 AAVGDIPIV--AIGGI-TPENAPEVLEAGADGVAVVSAITGAEDPEAAARALLAAFRAA 211
>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 = 39.0 bits (92), Expect = 0.001
Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 28/91 (30%)
Query: 48 ARVAEEAGACAVMALERVPADI----------RSQGGVARMSDPQLIKEI----KQSVTI 93
A++ EE GA + D+ + G A + DP+L+ EI +++V I
Sbjct: 73 AKIVEELGADGI--------DLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPI 124
Query: 94 PVMAKARIG-----HFVE-AQILEAIGIDYV 118
PV K R+G +E A+ LE G +
Sbjct: 125 PVTVKIRLGWDDEEETLELAKALEDAGASAL 155
>gnl|CDD|181086 PRK07695, PRK07695, transcriptional regulator TenI; Provisional.
Length = 201
Score = 38.8 bits (91), Expect = 0.001
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 211 DLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVR 270
+ + + +PV+ A GG+ TP + ++ G G+ V SG+F S +P +A+
Sbjct: 139 EELSDIARALSIPVI--AIGGI-TPENTRDVLAAGVSGIAVMSGIFSSANPYSKAKRYAE 195
Query: 271 AV 272
++
Sbjct: 196 SI 197
Score = 29.2 bits (66), Expect = 2.1
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 42 VVTPEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMA 97
V + E+A AE+ GA V+ P D + +G AR + + +I ++++IPV+A
Sbjct: 102 VHSLEEAIQAEKNGADYVVYGHVFPTDCK-KGVPAR--GLEELSDIARALSIPVIA 154
>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 = 37.9 bits (89), Expect = 0.003
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 210 YDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGS 253
++L+ + ++ +PV+ A G + +P AA ++LG D V VGS
Sbjct: 166 FELLKELRKALGIPVI--AEGRINSPEQAAKALELGADAVVVGS 207
Score = 30.6 bits (70), Expect = 0.76
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 19/69 (27%)
Query: 41 DVVTPEQARVAEEAGACAVMALERVPADIRSQ------GGVARMSDP--QLIKEIKQSVT 92
D+ T E+A A + G DI A+ DP +L+KE+++++
Sbjct: 129 DISTLEEALNAAKLGF-----------DIIGTTLSGYTEETAKTEDPDFELLKELRKALG 177
Query: 93 IPVMAKARI 101
IPV+A+ RI
Sbjct: 178 IPVIAEGRI 186
>gnl|CDD|236051 PRK07565, PRK07565, dihydroorotate dehydrogenase 2; Reviewed.
Length = 334
Score = 37.9 bits (89), Expect = 0.005
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 14/78 (17%)
Query: 48 ARVAEEAGACAVMALE----RVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAK----- 98
AR E+AGA ALE +P D G +++ +K +V+IPV K
Sbjct: 120 ARQIEQAGA---DALELNIYYLPTDPDISGAEVEQRYLDILRAVKSAVSIPVAVKLSPYF 176
Query: 99 ARIGHFVEAQILEAIGID 116
+ + + + L+A G D
Sbjct: 177 SNLANMAKR--LDAAGAD 192
>gnl|CDD|223429 COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme
metabolism].
Length = 211
Score = 37.2 bits (87), Expect = 0.005
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 204 KKIAAPY--DLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDP 261
K A P + + + ++L +PVV A GG+ + +++ G DGV V S + + DP
Sbjct: 139 KPDAPPLGLEGLREIRELVNIPVV--AIGGI-NLENVPEVLEAGADGVAVVSAITSAADP 195
Query: 262 VKRAQAIVRAV 272
A+A+ A+
Sbjct: 196 AAAAKALRNAL 206
>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 = 36.7 bits (86), Expect = 0.007
Identities = 10/41 (24%), Positives = 21/41 (51%)
Query: 228 AAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAI 268
+ G++TP D + + G D V +G + ++ DP + +
Sbjct: 177 SESGISTPEDVKRLAEAGADAVLIGESLMRAPDPGAALREL 217
Score = 29.0 bits (66), Expect = 2.6
Identities = 28/108 (25%), Positives = 47/108 (43%), Gaps = 28/108 (25%)
Query: 16 ITETKK-SPFSVKVGLAQMLRGGVIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGG 74
I E K+ SP +G + D E A+ E+AGA A+ L + + G
Sbjct: 14 IAEVKRASPS----------KGLIREDFDPVEIAKAYEKAGAAAISVL----TEPKYFQG 59
Query: 75 VARMSDPQLIKEIKQSVTIPVMAKARIGHFV--EAQILEA--IGIDYV 118
+ ++ ++++V++PV+ K F+ QI EA G D V
Sbjct: 60 -----SLEDLRAVREAVSLPVLRK----DFIIDPYQIYEARAAGADAV 98
>gnl|CDD|234907 PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase;
Provisional.
Length = 221
Score = 36.7 bits (86), Expect = 0.007
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 204 KKIAAP-YDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGS 253
KK P + L+ + + PV+ A G + TP A ++LG V VG
Sbjct: 155 KKPEEPDFALLKELLKAVGCPVI--AEGRINTPEQAKKALELGAHAVVVGG 203
Score = 27.8 bits (63), Expect = 5.8
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 20/75 (26%)
Query: 36 GGVIM-DVVTPEQARVAEEAGACAVMALERVPADIRSQ------GGVARMSDP--QLIKE 86
G ++M D T E+ A++ G D + +P L+KE
Sbjct: 119 GQLLMADCSTLEEGLAAQKLGF-----------DFIGTTLSGYTEETKKPEEPDFALLKE 167
Query: 87 IKQSVTIPVMAKARI 101
+ ++V PV+A+ RI
Sbjct: 168 LLKAVGCPVIAEGRI 182
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 36.9 bits (86), Expect = 0.010
Identities = 66/298 (22%), Positives = 108/298 (36%), Gaps = 86/298 (28%)
Query: 24 FSVKVGLAQMLRGGVIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVARMSD-PQ 82
+V LA M V R+A E GA ++ E V A G + +
Sbjct: 9 LRNRVILAPM------AGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLLDE 62
Query: 83 LIKEIKQSVTI-----PVMAKARIGHFVEAQILEAIGIDYVDESEVLTPADEENHINKHN 137
L +E +V + ++A+A A+I E +G D +D +N
Sbjct: 63 LEEERPVAVQLGGSDPELLAEA-------AKIAEELGADIID-------------LN--- 99
Query: 138 FRIPFVCGCRNLGEALR--RIREGAAMIRTKGEAGTGNIIEAVRHVRSVMGD------IR 189
CGC + + + GAA+++ I++A+ +GD IR
Sbjct: 100 ------CGCP----SPKVVKGGAGAALLKNPELLA--EIVKAMV---EAVGDIPVTVKIR 144
Query: 190 VLRNMDDDEVFTFAKKIA---------------------APYDLVMQTKQ-LGRLPVVHF 227
+ + DD A+ + A +D + + K+ + +PV
Sbjct: 145 LGWDDDDILALEIARILEDAGADALTVHGRTRAQGYLGPADWDYIKELKEAVPSIPV--I 202
Query: 228 AAGGVATPADA-AMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAVTHYSDPEVLAEV 284
A G + + DA M+ G DGV +G G G+P + I T P LAEV
Sbjct: 203 ANGDIKSLEDAKEMLEYTGADGVMIGRGAL--GNPW-LFRQIDYLETGELLPPTLAEV 257
Score = 35.8 bits (83), Expect = 0.021
Identities = 34/102 (33%), Positives = 52/102 (50%), Gaps = 14/102 (13%)
Query: 18 ETKKSPFSVKVGLAQMLRGGVIM-DVVTPEQARVAEEAGACAVMALERVPADIRSQGGVA 76
P +VK+ R G D++ E AR+ E+AGA A+ V R+QG +
Sbjct: 133 AVGDIPVTVKI------RLGWDDDDILALEIARILEDAGADALT----VHGRTRAQGYLG 182
Query: 77 RMSDPQLIKEIKQSV-TIPVMAKARIGHFVEAQ-ILEAIGID 116
+D IKE+K++V +IPV+A I +A+ +LE G D
Sbjct: 183 P-ADWDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGAD 223
>gnl|CDD|223227 COG0149, TpiA, Triosephosphate isomerase [Carbohydrate transport
and metabolism].
Length = 251
Score = 36.1 bits (84), Expect = 0.015
Identities = 12/43 (27%), Positives = 18/43 (41%)
Query: 230 GGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAV 272
G V A + Q DG VG K+ D + +A+ +A
Sbjct: 209 GSVKPGNAAELAAQPDIDGALVGGASLKADDFLAILEALAKAK 251
>gnl|CDD|240075 cd04724, Tryptophan_synthase_alpha, Ttryptophan synthase (TRPS)
alpha subunit (TSA). TPRS is a bifunctional tetrameric
enzyme (2 alpha and 2 beta subunits) that catalyzes the
last two steps of L-tryptophan biosynthesis. Alpha and
beta subunit catalyze two distinct reactions which are
both strongly stimulated by the formation of the
complex. The alpha subunit catalyzes the cleavage of
indole 3-glycerol phosphate (IGP) to indole and
d-glyceraldehyde 3-phosphate (G3P). Indole is then
channeled to the active site of the beta subunit, a
PLP-dependent enzyme that catalyzes a replacement
reaction to convert L-serine into L-tryptophan.
Length = 242
Score = 35.5 bits (83), Expect = 0.023
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 18/75 (24%)
Query: 211 DLVMQTKQLGRLPVVHFAAG-GVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIV 269
+L+ + ++ LP+ A G G++TP AA + + DGV VGS A+V
Sbjct: 177 ELIKRIRKYTDLPI---AVGFGISTPEQAAEVAKY-ADGVIVGS-------------ALV 219
Query: 270 RAVTHYSDPEVLAEV 284
+ + + E L +
Sbjct: 220 KIIEEGGEEEALEAL 234
>gnl|CDD|237285 PRK13111, trpA, tryptophan synthase subunit alpha; Provisional.
Length = 258
Score = 35.1 bits (82), Expect = 0.034
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 20/75 (26%)
Query: 211 DLVMQTKQLGRLPVVHFAAG-GVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIV 269
+LV + K LPV A G G++TP AA + DGV VGS A+V
Sbjct: 190 ELVARLKAHTDLPV---AVGFGISTPEQAAAIAA-VADGVIVGS-------------ALV 232
Query: 270 RAVTHYSDPEVLAEV 284
+ + +PE L +
Sbjct: 233 KIIE--ENPEALEAL 245
>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 = 35.0 bits (81), Expect = 0.036
Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 44 TPEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAKARIGH 103
E AR E+AGA A+ R A +D IK++KQ+V+IPV+A I
Sbjct: 140 AVEIARRVEDAGAQALTVHGRTRAQNYEG-----PADWDAIKQVKQAVSIPVIANGDITD 194
Query: 104 FVEAQ-ILEAIGIDYV 118
+AQ L G D V
Sbjct: 195 AEDAQRCLSYTGADGV 210
Score = 31.5 bits (72), Expect = 0.43
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 206 IAAPYDLVMQTKQLGRLPVVHFAAGGVATPADA-AMMMQLGCDGVFVGSG 254
A +D + Q KQ + + A G + DA + G DGV +G G
Sbjct: 168 GPADWDAIKQVKQ--AVSIPVIANGDITDAEDAQRCLSYTGADGVMIGRG 215
Score = 30.7 bits (70), Expect = 0.98
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 13/86 (15%)
Query: 46 EQARVAEEAGACAVMALERVPAD--IRSQGGVARMSDPQLI----KEIKQSVTIPVMAKA 99
E A++ + GA + PA R G A + DP L+ K + ++V IPV K
Sbjct: 70 EAAKLVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIVKAVVKAVDIPVTVKI 129
Query: 100 RIG-------HFVEAQILEAIGIDYV 118
RIG A+ +E G +
Sbjct: 130 RIGWDESHENAVEIARRVEDAGAQAL 155
>gnl|CDD|215798 pfam00218, IGPS, Indole-3-glycerol phosphate synthase.
Length = 254
Score = 34.6 bits (80), Expect = 0.050
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 36 GGVIMDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPV 95
G + D E ARV E AGA A+ L QG + ++E++++V++PV
Sbjct: 62 GLIREDFDPAEIARVYEAAGASAISVLTEPK---YFQG------SLEYLREVREAVSLPV 112
Query: 96 MAKARIGHFVEAQILEA 112
+ K I E QI EA
Sbjct: 113 LRKDFI--IDEYQIYEA 127
Score = 27.2 bits (61), Expect = 9.8
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 224 VVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDP 261
V+ A G++TP D + + G + VG + ++ D
Sbjct: 210 VLLVAESGISTPEDVEKLAKHGANAFLVGESLMRAPDV 247
>gnl|CDD|240090 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like
proteins. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
This subgroup has the conserved FMN binding site, but
lacks some catalytic residues and may therefore be
inactive.
Length = 325
Score = 34.5 bits (80), Expect = 0.050
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 48 ARVAEEAGACAV-MALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAK-----ARI 101
AR EEAGA A+ + + +P D G +++ +K +VTIPV K + +
Sbjct: 118 ARQIEEAGADALELNIYALPTDPDISGAEVEQRYLDILRAVKSAVTIPVAVKLSPFFSAL 177
Query: 102 GHFVEAQILEAIGID 116
H + L+A G D
Sbjct: 178 AHMAKQ--LDAAGAD 190
Score = 27.6 bits (62), Expect = 9.1
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 4/57 (7%)
Query: 220 GRLPVVHFAA-GGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAVTHY 275
GR+ AA GGV D + G D V S + + G ++ + +
Sbjct: 234 GRVKA-SLAASGGVHDAEDVVKYLLAGADVVMTTSALLRHG--PDYIGTLLAGLEAW 287
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 33.3 bits (77), Expect = 0.10
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 222 LPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRA 271
+PV+ A+GGV T D + + G GV VGS ++K ++ A V+
Sbjct: 194 IPVI--ASGGVTTLDDLRALKEAGAAGVVVGSALYKGKFTLEEAIEAVKG 241
>gnl|CDD|201134 pfam00290, Trp_syntA, Tryptophan synthase alpha chain.
Length = 258
Score = 33.4 bits (77), Expect = 0.10
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 210 YDLVMQTKQLGRLPV-VHFAAGGVATPADAAMMMQLGCDGVFVGS 253
+LV + K+ +PV V F G++TP + G DGV VGS
Sbjct: 186 DELVERLKKYTNVPVAVGF---GISTPEHVKKIA-AGADGVIVGS 226
>gnl|CDD|218318 pfam04898, Glu_syn_central, Glutamate synthase central domain. The
central domain of glutamate synthase connects the amino
terminal amidotransferase domain with the FMN-binding
domain and has an alpha / beta overall topology. This
domain appears to be a rudimentary form of the
FMN-binding TIM barrel according to SCOP.
Length = 288
Score = 33.3 bits (77), Expect = 0.14
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 18/75 (24%)
Query: 55 GACAV---MALERVPADIRSQGGVARMSDPQLIKEIKQSVT---IPVMAKARI------- 101
GA A+ +A E + D+ +G + +S + +K ++++ + +M+K I
Sbjct: 218 GASAINPYLAYETI-RDLHRRGLLKELSLEEAVKNYRKAIEKGLLKIMSKMGISTLQSYR 276
Query: 102 GHFVEAQILEAIGID 116
G AQI EA+G+
Sbjct: 277 G----AQIFEAVGLS 287
>gnl|CDD|234723 PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase;
Reviewed.
Length = 264
Score = 33.1 bits (77), Expect = 0.15
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 15/50 (30%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPV 95
E A+ EEAGA A++ LE VPA+ L KEI ++++IP
Sbjct: 165 EDAKALEEAGAFALV-LECVPAE--------------LAKEITEALSIPT 199
>gnl|CDD|223212 COG0134, TrpC, Indole-3-glycerol phosphate synthase [Amino acid
transport and metabolism].
Length = 254
Score = 32.6 bits (75), Expect = 0.18
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 230 GGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIV 269
G++TP D + + G D VG + ++ DP + + ++
Sbjct: 214 SGISTPEDVRRLAKAGADAFLVGEALMRADDPEEALRELL 253
Score = 31.4 bits (72), Expect = 0.50
Identities = 31/107 (28%), Positives = 42/107 (39%), Gaps = 26/107 (24%)
Query: 16 ITETKK-SPFSVKVGLAQMLRGGVI-MDVVTPEQARVAEEAGACAVMALERVPADIRSQG 73
I E KK SP G+I D E A+ EE GA A+ L QG
Sbjct: 49 IAEVKKASP-----------SKGLIREDFDPVEIAKAYEEGGAAAISVLTDPK---YFQG 94
Query: 74 GVARMSDPQLIKEIKQSVTIPVMAKARIGHFVEAQILEA--IGIDYV 118
+ ++ ++ +V +PV+ K I QI EA G D V
Sbjct: 95 ------SFEDLRAVRAAVDLPVLRKDFI--IDPYQIYEARAAGADAV 133
>gnl|CDD|181670 PRK09140, PRK09140, 2-dehydro-3-deoxy-6-phosphogalactonate
aldolase; Reviewed.
Length = 206
Score = 32.5 bits (75), Expect = 0.19
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 224 VVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPV----KRAQAIVRA 271
V FA GGV TP + A + G G +GS +++ G +RA+A V A
Sbjct: 152 VPVFAVGGV-TPENLAPYLAAGAAGFGLGSALYRPGQSAEEVAERARAFVAA 202
>gnl|CDD|238223 cd00381, IMPDH, IMPDH: The catalytic domain of the inosine
monophosphate dehydrogenase. IMPDH catalyzes the
NAD-dependent oxidation of inosine 5'-monophosphate
(IMP) to xanthosine 5' monophosphate (XMP). It is a
rate-limiting step in the de novo synthesis of the
guanine nucleotides. There is often a CBS domain
inserted in the middle of this domain, which is proposed
to play a regulatory role. IMPDH is a key enzyme in the
regulation of cell proliferation and differentiation. It
has been identified as an attractive target for
developing chemotherapeutic agents.
Length = 325
Score = 32.5 bits (75), Expect = 0.23
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 217 KQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSG 254
K+ + V+ AG V T A ++ G DGV VG G
Sbjct: 131 KKYPNVDVI---AGNVVTAEAARDLIDAGADGVKVGIG 165
>gnl|CDD|235973 PRK07226, PRK07226, fructose-bisphosphate aldolase; Provisional.
Length = 267
Score = 32.5 bits (75), Expect = 0.24
Identities = 22/64 (34%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 222 LPVVHFAAGGVATPADAAMM------MQLGCDGVFVGSGVFKSGDPVKRAQAIVRAVTHY 275
+PVV AGG T D + M+ G GV VG VF+ DP +AI V
Sbjct: 197 VPVV--IAGGPKTDTDREFLEMVRDAMEAGAAGVAVGRNVFQHEDPEAITRAISAVVHEG 254
Query: 276 SDPE 279
+ E
Sbjct: 255 ASVE 258
>gnl|CDD|223361 COG0284, PyrF, Orotidine-5'-phosphate decarboxylase [Nucleotide
transport and metabolism].
Length = 240
Score = 32.3 bits (74), Expect = 0.27
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 221 RLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRA 271
G V TP +A ++ G D + VG + ++GDPV A+AI R
Sbjct: 186 GAGSQGGDQGRVMTPGEA---VRAGADYIVVGRPITQAGDPVAAARAIARE 233
>gnl|CDD|240076 cd04725, OMP_decarboxylase_like, Orotidine 5'-phosphate
decarboxylase (ODCase) is a dimeric enzyme that
decarboxylates orotidine 5'-monophosphate (OMP) to form
uridine 5'-phosphate (UMP), an essential step in the
pyrimidine biosynthetic pathway. In mammals, UMP
synthase contains two domains: the orotate
phosphoribosyltransferase (OPRTase) domain that
catalyzes the transfer of phosphoribosyl
5'-pyrophosphate (PRPP) to orotate to form OMP, and the
orotidine-5'-phosphate decarboxylase (ODCase) domain
that decarboxylates OMP to form UMP.
Length = 216
Score = 31.8 bits (73), Expect = 0.28
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 232 VATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAI 268
TP DA ++ G D + VG + ++ DPV A+AI
Sbjct: 183 GGTPEDA---IRAGADYIVVGRPITQAADPVAAAEAI 216
>gnl|CDD|239202 cd02808, GltS_FMN, Glutamate synthase (GltS) FMN-binding domain.
GltS is a complex iron-sulfur flavoprotein that
catalyzes the reductive synthesis of L-glutamate from
2-oxoglutarate and L-glutamine via intramolecular
channelling of ammonia, a reaction in the plant, yeast
and bacterial pathway for ammonia assimilation. It is a
multifunctional enzyme that functions through three
distinct active centers, carrying out L-glutamine
hydrolysis, conversion of 2-oxoglutarate into
L-glutamate, and electron uptake from an electron donor.
Length = 392
Score = 32.5 bits (75), Expect = 0.29
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 228 AAGGVATPADAAMMMQLGCDGVFVGSG 254
A+GG+ T AD A + LG D V +G+
Sbjct: 290 ASGGLRTGADVAKALALGADAVGIGTA 316
>gnl|CDD|224981 COG2070, COG2070, Dioxygenases related to 2-nitropropane
dioxygenase [General function prediction only].
Length = 336
Score = 32.3 bits (74), Expect = 0.30
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 222 LPVVHFAAGGVATPADAAMMMQLGCDGVFVGS 253
+PV+ AAGG+A A + LG DGV +G+
Sbjct: 185 IPVI--AAGGIADGRGIAAALALGADGVQMGT 214
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 32.2 bits (74), Expect = 0.30
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 220 GRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSG 259
G +P++ GG+ T DA + G V VG+ + G
Sbjct: 240 GDIPII--GVGGIETGEDALEFILAGASAVQVGTALIYKG 277
>gnl|CDD|240466 cd12886, SPRY_like, SPRY domain-like in bacteria. This family
contains SPRY-like domains that are found only in
bacterial and are mostly uncharacterized. SPRY domains,
first identified in the SP1A kinase of Dictyostelium and
rabbit Ryanodine receptor (hence the name), are
homologous to B30.2. SPRY domains have been identified
in at least 11 eukaryotic protein families, covering a
wide range of functions, including regulation of
cytokine signaling (SOCS), RNA metabolism (DDX1 and
hnRNP), immunity to retroviruses (TRIM5alpha),
intracellular calcium release (ryanodine receptors or
RyR) and regulatory and developmental processes (HERC1
and Ash2L).
Length = 128
Score = 30.9 bits (70), Expect = 0.38
Identities = 19/54 (35%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 227 FAAG---GVATPADAAMMMQLGCDGVFVGSGVFKSGD-PVKRAQAIVRAVTHYS 276
F AG GVA DA + +GV+ GSG G P + AVT S
Sbjct: 65 FTAGDVIGVALDLDAGKI-WFYKNGVWQGSGSPAPGTNPAFAGTQVYPAVTGGS 117
>gnl|CDD|238244 cd00429, RPE, Ribulose-5-phosphate 3-epimerase (RPE). This enzyme
catalyses the interconversion of D-ribulose 5-phosphate
(Ru5P) into D-xylulose 5-phosphate, as part of the
Calvin cycle (reductive pentose phosphate pathway) in
chloroplasts and in the oxidative pentose phosphate
pathway. In the Calvin cycle Ru5P is phosphorylated by
phosphoribulose kinase to ribulose-1,5-bisphosphate,
which in turn is used by RubisCO
(ribulose-1,5-bisphosphate carboxylase/oxygenase) to
incorporate CO2 as the central step in carbohydrate
synthesis.
Length = 211
Score = 30.9 bits (71), Expect = 0.55
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 230 GGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAI 268
GG+ ++ + G D + GS +F S D + + +
Sbjct: 173 GGI-NLETIPLLAEAGADVLVAGSALFGSDDYAEAIKEL 210
>gnl|CDD|225555 COG3010, NanE, Putative N-acetylmannosamine-6-phosphate epimerase
[Carbohydrate transport and metabolism].
Length = 229
Score = 31.1 bits (71), Expect = 0.57
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 210 YDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGV 255
+ LV Q G V+ A G TP A +++G D V VGS +
Sbjct: 170 FQLVKQLSDAGC-RVI--AEGRYNTPEQAKKAIEIGADAVVVGSAI 212
>gnl|CDD|225110 COG2200, Rtn, c-di-GMP phosphodiesterase class I (EAL domain)
[Signal transduction mechanisms].
Length = 256
Score = 31.1 bits (71), Expect = 0.57
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 212 LVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGV 249
+V +LG L VV A GV T ++ +LGCD +
Sbjct: 198 IVALAHKLG-LTVV---AEGVETEEQLDLLRELGCDYL 231
>gnl|CDD|224329 COG1411, COG1411, Uncharacterized protein related to proFAR
isomerase (HisA) [General function prediction only].
Length = 229
Score = 30.9 bits (70), Expect = 0.58
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 209 PYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQA 267
Y+L+ + +L PV+ GGV D +++ +G GV V + + + P++ QA
Sbjct: 169 DYELLTKVLELSEHPVL--LGGGVGGMEDLELLLGMGVSGVLVATALHEGVVPLEVEQA 225
>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 = 31.2 bits (71), Expect = 0.62
Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 220 GRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPV 262
+P++ GG+ + D M+ G V V + + G V
Sbjct: 242 LDIPII--GVGGIDSGEDVLEMLMAGASAVQVATALMWDGPDV 282
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 31.3 bits (72), Expect = 0.63
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 16/52 (30%)
Query: 78 MSDPQL----IKEIKQSVTIPVMAKARIGHFVEAQILEAIGIDYVDESEVLT 125
M++P+L +K +K +V+IPV K R IGID D E L
Sbjct: 115 MAEPELVADCVKAMKDAVSIPVTVKHR------------IGIDDQDSYEFLC 154
>gnl|CDD|239201 cd02803, OYE_like_FMN_family, Old yellow enzyme (OYE)-like FMN
binding domain. OYE was the first flavin-dependent
enzyme identified, however its true physiological role
remains elusive to this day. Each monomer of OYE
contains FMN as a non-covalently bound cofactor, uses
NADPH as a reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 327
Score = 31.0 bits (71), Expect = 0.66
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 8/77 (10%)
Query: 48 ARVAEEAGACAV-----MALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAKARIG 102
A+ EEAG A+ P + L ++IK++V IPV+A I
Sbjct: 234 AKALEEAGVDALHVSGGSYESPPPIIPPPYVPEGYFLE--LAEKIKKAVKIPVIAVGGIR 291
Query: 103 HFVEA-QILEAIGIDYV 118
A +IL D V
Sbjct: 292 DPEVAEEILAEGKADLV 308
>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 = 30.9 bits (71), Expect = 0.69
Identities = 10/50 (20%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 229 AGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRA------QAIVRAV 272
GG+ + DA +++ G D V + S ++ + ++ Q +V ++
Sbjct: 77 GGGIRSLEDARRLLRAGADKVSINSAAVENPELIREIAKRFGSQCVVVSI 126
Score = 28.2 bits (64), Expect = 4.8
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 83 LIKEIKQSVTIPVMAKARIG---HFVEAQILEAIGID 116
LI+ + +V IPV+A G HFVEA E G D
Sbjct: 184 LIRAVSSAVNIPVIASGGAGKPEHFVEA--FEEGGAD 218
>gnl|CDD|235912 PRK07028, PRK07028, bifunctional hexulose-6-phosphate
synthase/ribonuclease regulator; Validated.
Length = 430
Score = 31.1 bits (71), Expect = 0.70
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 209 PYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAI 268
P +L+ + + +P+ AGG+ AA + G D V VG + KS D + A+ I
Sbjct: 150 PLELLKEVSEEVSIPIA--VAGGL-DAETAAKAVAAGADIVIVGGNIIKSADVTEAARKI 206
Query: 269 VRAVTH 274
A+
Sbjct: 207 REAIDS 212
>gnl|CDD|240077 cd04726, KGPDC_HPS, 3-Keto-L-gulonate 6-phosphate decarboxylase
(KGPDC) and D-arabino-3-hexulose-6-phosphate synthase
(HPS). KGPDC catalyzes the formation of L-xylulose
5-phosphate and carbon dioxide from 3-keto-L-gulonate
6-phosphate as part of the anaerobic pathway for
L-ascorbate utilization in some eubacteria. HPS
catalyzes the formation of
D-arabino-3-hexulose-6-phosphate from D-ribulose
5-phosphate and formaldehyde in microorganisms that can
use formaldehyde as a carbon source. Both catalyze
reactions that involve the Mg2+-assisted formation and
stabilization of 1,2-enediolate reaction intermediates.
Length = 202
Score = 30.6 bits (70), Expect = 0.73
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 203 AKKIAAPYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPV 262
A P D + + K+L + V AGG+ TP + G D V VG + + DP
Sbjct: 140 AAGGWWPEDDLKKVKKLLGVKVA--VAGGI-TPDTLPEFKKAGADIVIVGRAITGAADPA 196
Query: 263 KRAQAI 268
+ A+
Sbjct: 197 EAAREF 202
>gnl|CDD|234710 PRK00278, trpC, indole-3-glycerol-phosphate synthase; Reviewed.
Length = 260
Score = 30.9 bits (71), Expect = 0.75
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 231 GVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRA 271
G+ TP D + + G D V VG + ++ DP + ++ A
Sbjct: 219 GIFTPEDLKRLAKAGADAVLVGESLMRADDPGAALRELLGA 259
Score = 27.4 bits (62), Expect = 9.9
Identities = 29/101 (28%), Positives = 40/101 (39%), Gaps = 28/101 (27%)
Query: 16 ITETKK-SPFSVKVGLAQMLRGGVI-MDVVTPEQARVAEEAGACAVMALERVPADIRSQG 73
I E KK SP S GVI D E A+ E GA + L D R
Sbjct: 53 IAEVKKASP-S----------KGVIREDFDPVEIAKAYEAGGAACLSVL----TDERFFQ 97
Query: 74 GVARMSDPQLIKEIKQSVTIPVMAKARIGHFV--EAQILEA 112
G + ++ + +V++PV+ K F+ QI EA
Sbjct: 98 G-----SLEYLRAARAAVSLPVLRK----DFIIDPYQIYEA 129
>gnl|CDD|217120 pfam02581, TMP-TENI, Thiamine monophosphate synthase/TENI.
Thiamine monophosphate synthase (TMP) (EC:2.5.1.3)
catalyzes the substitution of the pyrophosphate of
2-methyl-4-amino-5- hydroxymethylpyrimidine
pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole
phosphate to yield thiamine phosphate. This Pfam family
also includes the regulatory protein TENI.
Length = 180
Score = 30.2 bits (69), Expect = 0.87
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 201 TFAKKIAAPY--DLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGV 255
T K A P + + + +PVV A GG+ TP + +++ G DGV V S +
Sbjct: 127 TPTKPDAPPLGLEGLRAIAEAVNIPVV--AIGGI-TPENVPEVLEAGADGVAVVSAI 180
>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 = 30.6 bits (70), Expect = 0.88
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 220 GRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGV 255
GRLP++ A G + TP DA ++ G D V +G G+
Sbjct: 283 GRLPLI--AVGSINTPDDALEALETGADLVAIGRGL 316
>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 = 30.6 bits (70), Expect = 0.90
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 216 TKQL-GRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGS 253
TK+L + V A+GGV++ D + +LG GV VG
Sbjct: 181 TKELVKAVNVPVIASGGVSSIDDLIALKKLGVYGVIVGK 219
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 30.5 bits (69), Expect = 0.91
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAKARIGHFV 105
E A ++AGA ++ R D G A + Q I EI+Q +TIPV+A I +
Sbjct: 152 EIADAVQQAGATELVVHGRTKED----GYRAEHINWQAIGEIRQRLTIPVIANGEIWDWQ 207
Query: 106 EAQ-ILEAIGIDYV 118
AQ + G D V
Sbjct: 208 SAQQCMAITGCDAV 221
>gnl|CDD|119342 cd06557, KPHMT-like, Ketopantoate hydroxymethyltransferase (KPHMT)
is the first enzyme in the pantothenate biosynthesis
pathway. Ketopantoate hydroxymethyltransferase (KPHMT)
catalyzes the first committed step in the biosynthesis
of pantothenate (vitamin B5), which is a precursor to
coenzyme A and is required for penicillin biosynthesis.
Length = 254
Score = 30.5 bits (70), Expect = 0.92
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 15/50 (30%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPV 95
E A EEAGA A++ LE VPA+ L KEI ++++IP
Sbjct: 162 EDALALEEAGAFALV-LECVPAE--------------LAKEITEALSIPT 196
>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 = 30.3 bits (69), Expect = 0.93
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 40 MDVVTPEQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAKA 99
D V E AR AE+ GA ++ L + D +G D +LIK + +V+IPV+A
Sbjct: 153 RDPV--EWAREAEQLGAGEIL-LNSIDRDGTMKG-----YDLELIKTVSDAVSIPVIALG 204
Query: 100 RIGHF 104
G
Sbjct: 205 GAGSL 209
>gnl|CDD|215995 pfam00563, EAL, EAL domain. This domain is found in diverse
bacterial signaling proteins. It is called EAL after its
conserved residues. The EAL domain is a good candidate
for a diguanylate phosphodiesterase function. The domain
contains many conserved acidic residues that could
participate in metal binding and might form the
phosphodiesterase active site.
Length = 231
Score = 30.4 bits (69), Expect = 0.95
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 10/63 (15%)
Query: 187 DIRVLRNMDDDEVFTFAKKIAAPYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGC 246
D ++++ D E + + A + LG V A GV T ++ +LG
Sbjct: 171 DRSFIKDLSDPESRALLRALIA------LARSLGIKVV----AEGVETEEQLELLKELGI 220
Query: 247 DGV 249
D V
Sbjct: 221 DYV 223
>gnl|CDD|161792 TIGR00262, trpA, tryptophan synthase, alpha subunit. Tryptophan
synthase catalyzes the last step in the biosynthesis of
tryptophan. The alpha chain is responsible for the aldol
cleavage of indoleglycerol phosphate to indole and
glyceraldehyde 3-phosphate. In bacteria and plants each
domain is found on a separate subunit (alpha and beta
chains), while in fungi the two domains are fused
together on a single multifunctional protein. The
signature pattern for trpA contains three conserved
acidic residues
[LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-
[AGLI]-[DE]-G and this is located between residues 43-58
of the model. The Sulfolobus solfataricus trpA is known
to be quite divergent from other known trpA sequences
[Amino acid biosynthesis, Aromatic amino acid family].
Length = 256
Score = 30.4 bits (69), Expect = 1.0
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 201 TFAKKIAAP--YDLVMQTKQLGRLPV-VHFAAGGVATPADAAMMMQLGCDGVFVGSGVFK 257
T A+ AA +LV + K PV V F G++ P + G DGV VGS + K
Sbjct: 176 TGARNRAASALNELVKRLKAYSAKPVLVGF---GISKPEQVKQAIDAGADGVIVGSAIVK 232
>gnl|CDD|235274 PRK04302, PRK04302, triosephosphate isomerase; Provisional.
Length = 223
Score = 30.2 bits (69), Expect = 1.0
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 227 FAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAVT 273
G++T D ++LG DGV + SGV K+ DP + +V +
Sbjct: 177 LCGAGISTGEDVKAALELGADGVLLASGVVKAKDPEAALRDLVSPLA 223
>gnl|CDD|188634 cd00945, Aldolase_Class_I, Class I aldolases. Class I aldolases.
The class I aldolases use an active-site lysine which
stabilizes a reaction intermediates via Schiff base
formation, and have TIM beta/alpha barrel fold. The
members of this family include
2-keto-3-deoxy-6-phosphogluconate (KDPG) and
2-keto-4-hydroxyglutarate (KHG) aldolases,
transaldolase, dihydrodipicolinate synthase sub-family,
Type I 3-dehydroquinate dehydratase, DeoC and DhnA
proteins, and metal-independent
fructose-1,6-bisphosphate aldolase. Although
structurally similar, the class II aldolases use a
different mechanism and are believed to have an
independent evolutionary origin.
Length = 201
Score = 30.0 bits (68), Expect = 1.1
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 220 GRLPVVHFAAGGVATPADAAMMMQLGCDGVFVG 252
GR+ V AAGG+ T DA ++ G DG+
Sbjct: 171 GRVGVK--AAGGIKTLEDALAAIEAGADGIGTS 201
>gnl|CDD|233555 TIGR01740, pyrF, orotidine 5'-phosphate decarboxylase, subfamily 1.
This model represents orotidine 5'-monophosphate
decarboxylase, the PyrF protein of pyrimidine nucleotide
biosynthesis. In many eukaryotes, the region hit by this
model is part of a multifunctional protein [Purines,
pyrimidines, nucleosides, and nucleotides, Pyrimidine
ribonucleotide biosynthesis].
Length = 214
Score = 30.0 bits (68), Expect = 1.1
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 238 AAMMMQLGCDGVFVGSGVFKSGDPVKRAQAI 268
+ G D + VG G++ + DPV+ A+ I
Sbjct: 183 LEDAKEAGADVIIVGRGIYAAEDPVEAAKRI 213
>gnl|CDD|238923 cd01948, EAL, EAL domain. This domain is found in diverse bacterial
signaling proteins. It is called EAL after its conserved
residues and is also known as domain of unknown function
2 (DUF2). The EAL domain has been shown to stimulate
degradation of a second messenger, cyclic di-GMP, and is
a good candidate for a diguanylate phosphodiesterase
function. Together with the GGDEF domain, EAL might be
involved in regulating cell surface adhesiveness in
bacteria.
Length = 240
Score = 29.8 bits (68), Expect = 1.4
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 217 KQLGRLPVVHFAAGGVATPADAAMMMQLGCDGV 249
LG L VV A GV T ++ +LGCD V
Sbjct: 199 HSLG-LKVV---AEGVETEEQLELLRELGCDYV 227
>gnl|CDD|234812 PRK00694, PRK00694, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate
synthase; Validated.
Length = 606
Score = 30.2 bits (68), Expect = 1.4
Identities = 43/162 (26%), Positives = 73/162 (45%), Gaps = 38/162 (23%)
Query: 84 IKE--IKQSVTIPVMAKARIGHFVEAQILEAIGIDYVDESEVLTPADEENHINKHNF--- 138
IKE I+Q ++IP++A I F +A + A D+VD+ + + N+++K N
Sbjct: 78 IKERLIQQGISIPLVAD--IHFFPQAAMHVA---DFVDKVRI----NPGNYVDKRNMFTG 128
Query: 139 -------------RI-----PFVCGCRNLGEALR-RIREGAAMIRTKGEAGTGNIIEAVR 179
R+ P V C+ LG+A+R + G+ R G+ IE +
Sbjct: 129 KIYTDEQYAHSLLRLEEKFSPLVEKCKRLGKAMRIGVNHGSLSERVMQR--YGDTIEGM- 185
Query: 180 HVRSVMGDIRVLRNMDDDEVFTFAKKIAAPYDLVMQTKQLGR 221
V S + I V +D +V F+ K + P +V +QL +
Sbjct: 186 -VYSALEYIEVCEKLDYRDV-VFSMKSSNPKVMVAAYRQLAK 225
>gnl|CDD|233094 TIGR00693, thiE, thiamine-phosphate pyrophosphorylase. This model
represents the thiamine-phosphate pyrophosphorylase,
ThiE, of a number of bacteria, and N-terminal domains of
bifunctional thiamine proteins of Saccharomyces
cerevisiae and Schizosaccharomyces pombe, in which the
C-terminal domain corresponds to the bacterial
hydroxyethylthiazole kinase (EC 2.7.1.50), ThiM. This
model includes ThiE from Bacillus subtilis but excludes
its paralog, the regulatory protein TenI , and neighbors
of TenI [Biosynthesis of cofactors, prosthetic groups,
and carriers, Thiamine].
Length = 196
Score = 29.5 bits (67), Expect = 1.5
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 217 KQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAI 268
+P+V A GG+ T +AA ++ G DGV V S + ++ DP A+ +
Sbjct: 148 ATSIDIPIV--AIGGI-TLENAAEVLAAGADGVAVVSAIMQAADPKAAAKQL 196
>gnl|CDD|177986 PLN02353, PLN02353, probable UDP-glucose 6-dehydrogenase.
Length = 473
Score = 30.0 bits (68), Expect = 1.5
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 9/38 (23%)
Query: 255 VFKSGDPVKRAQAIVRAVTH---------YSDPEVLAE 283
V KS PVK A+AI + +TH S+PE LAE
Sbjct: 124 VEKSTVPVKTAEAIEKILTHNSKGINFQILSNPEFLAE 161
>gnl|CDD|214921 smart00934, OMPdecase, Orotidine 5'-phosphate decarboxylase / HUMPS
family. Orotidine 5'-phosphate decarboxylase
(OMPdecase) catalyzes the last step in the de novo
biosynthesis of pyrimidines, the decarboxylation of OMP
into UMP. In higher eukaryotes OMPdecase is part, with
orotate phosphoribosyltransferase, of a bifunctional
enzyme, while the prokaryotic and fungal OMPdecases are
monofunctional protein.
Length = 212
Score = 29.4 bits (67), Expect = 2.0
Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 230 GGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAI 268
G VATPA A G D + VG + ++ DPV+ A+AI
Sbjct: 177 GRVATPAVAI---GAGADIIVVGRPITQAADPVEAAEAI 212
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 29.1 bits (66), Expect = 2.5
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 9/65 (13%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMA---KARIG 102
E A+ E GA ++ L + D G + D +L+K + ++ IP++A +
Sbjct: 156 ELAKEYEALGAGEIL-LNSIDRD-----GTMKGYDLELLKSFRNALKIPLIALGGAGSLD 209
Query: 103 HFVEA 107
VEA
Sbjct: 210 DIVEA 214
>gnl|CDD|234923 PRK01222, PRK01222, N-(5'-phosphoribosyl)anthranilate isomerase;
Provisional.
Length = 210
Score = 29.0 bits (66), Expect = 2.8
Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 25/90 (27%)
Query: 44 TPEQARVAEEAGACAV--MALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAKARI 101
TPE A A E GA A+ + + P R P+ E+ ++ V +
Sbjct: 12 TPEDAEAAAELGADAIGFVFYPKSP----------RYVSPEQAAELAAALPPFV---KVV 58
Query: 102 GHFVEA------QILEAIGIDYV----DES 121
G FV A +I+E + +D + DE+
Sbjct: 59 GVFVNASDEEIDEIVETVPLDLLQLHGDET 88
>gnl|CDD|233564 TIGR01768, GGGP-family, geranylgeranylglyceryl phosphate synthase
family protein. This model represents a family of
sequences including geranylgeranylglyceryl phosphate
synthase which catalyzes the first committed step in the
synthesis of ether-linked membrane lipids in archaea.
The clade of bacterial sequences may have the same
function or a closely related function. This model
supercedes TIGR00265, which has been retired.
Length = 223
Score = 29.0 bits (65), Expect = 2.9
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 227 FAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGD 260
F GG+ + A M + G D + G+ + + D
Sbjct: 183 FVGGGIRSVEKAREMAEAGADTIVTGNVIEEDVD 216
>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 = 28.8 bits (65), Expect = 2.9
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 228 AAGGVATPADAAMMMQLGCDGVFVGSGV 255
AAGGV + D ++ +LG G V S +
Sbjct: 194 AAGGVRSVEDLELLKKLGASGALVASAL 221
>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 = 28.6 bits (65), Expect = 3.2
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 221 RLPVVHFAAGGVATPADAAMMMQLGCDGVFVGS 253
+PV+ A+GGV++ D + +LG GV VG
Sbjct: 190 GIPVI--ASGGVSSLDDIKALKELGVAGVIVGK 220
>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
This family represents a region of the glutamate
synthase protein. This region is expressed as a separate
subunit in the glutamate synthase alpha subunit from
archaebacteria, or part of a large multidomain enzyme in
other organisms. The aligned region of these proteins
contains a putative FMN binding site and Fe-S cluster.
Length = 367
Score = 29.2 bits (66), Expect = 3.2
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 224 VVHFAAGGVATPADAAMMMQLGCDGVFVGSG 254
V A GG+ T AD A LG D V++G+
Sbjct: 274 VSLIADGGLRTGADVAKAAALGADAVYIGTA 304
>gnl|CDD|234695 PRK00230, PRK00230, orotidine 5'-phosphate decarboxylase; Reviewed.
Length = 230
Score = 28.6 bits (65), Expect = 3.5
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 232 VATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVR 270
V TPA A + G D + VG + ++ DP +AI+
Sbjct: 190 VMTPAQA---IAAGSDYIVVGRPITQAADPAAAYEAILA 225
>gnl|CDD|240093 cd04742, NPD_FabD, 2-Nitropropane dioxygenase (NPD)-like domain,
associated with the (acyl-carrier-protein)
S-malonyltransferase FabD. NPD is part of the
nitroalkaneoxidizing enzyme family, that catalyzes
oxidative denitrification of nitroalkanes to their
corresponding carbonyl compounds and nitrites. NDPs are
members 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 = 418
Score = 29.1 bits (66), Expect = 3.5
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 228 AAGGVATPADAAMMMQLGCDGVFVGS 253
AAGG+ TP AA LG D + GS
Sbjct: 224 AAGGIGTPEAAAAAFALGADFIVTGS 249
>gnl|CDD|129513 TIGR00419, tim, triosephosphate isomerase. Triosephosphate
isomerase (tim/TPIA) is the glycolytic enzyme that
catalyzes the reversible interconversion of
glyceraldehyde 3-phosphate and dihydroxyacetone
phosphate. The active site of the enzyme is located
between residues 240-258 of the model
([AV]-Y-E-P-[LIVM]-W-[SA]-I-G-T-[GK]) with E being the
active site residue. There is a slight deviation from
this sequence within the archeal members of this family
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 205
Score = 28.6 bits (64), Expect = 3.6
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 230 GGVATPADAAMMMQLGCDGVFVGSGVFKS 258
G++T DA + QLG +GV + SG K+
Sbjct: 176 AGISTGEDAELAAQLGAEGVLLASGSLKA 204
>gnl|CDD|236318 PRK08639, PRK08639, threonine dehydratase; Validated.
Length = 420
Score = 29.0 bits (66), Expect = 3.6
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 13/51 (25%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQ-------GG---VARMSDPQLIKE 86
++ VAE AGA ++ ALE +I+ + GG + RM + IKE
Sbjct: 280 KEGIVAEPAGALSIAALELYKDEIKGKTVVCVISGGNNDIERMPE---IKE 327
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 28.7 bits (65), Expect = 3.7
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 229 AGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRA------QAIVRAV 272
GG+ + DA +++ G D V + S K + + A Q IV A+
Sbjct: 80 GGGIRSVEDARKLLRAGADKVSINSAAVKDPELITEAADRFGSQCIVVAI 129
>gnl|CDD|235465 PRK05437, PRK05437, isopentenyl pyrophosphate isomerase;
Provisional.
Length = 352
Score = 29.0 bits (66), Expect = 3.7
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 84 IKEIKQSVTIPVMAKARIGH---FVEAQILEAIGIDYVD 119
I EI ++ +PV+ K +G A+ L G+ +D
Sbjct: 178 IAEIVSALPVPVIVKE-VGFGISKETAKRLADAGVKAID 215
>gnl|CDD|217097 pfam02548, Pantoate_transf, Ketopantoate hydroxymethyltransferase.
Ketopantoate hydroxymethyltransferase (EC:2.1.2.11) is
the first enzyme in the pantothenate biosynthesis
pathway.
Length = 261
Score = 28.6 bits (65), Expect = 4.0
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 15/50 (30%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPV 95
E A+ EEAGA A++ LE VPA+ L KEI + ++IP
Sbjct: 166 EDAKALEEAGAFALV-LECVPAE--------------LAKEITEKLSIPT 200
>gnl|CDD|223490 COG0413, PanB, Ketopantoate hydroxymethyltransferase [Coenzyme
metabolism].
Length = 268
Score = 28.7 bits (65), Expect = 4.0
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 15/50 (30%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPV 95
E A+ EEAGA A++ LE VPA+ L KEI + ++IP
Sbjct: 165 EDAKALEEAGAFALV-LECVPAE--------------LAKEITEKLSIPT 199
>gnl|CDD|166620 PLN02979, PLN02979, glycolate oxidase.
Length = 366
Score = 28.5 bits (63), Expect = 4.3
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 206 IAAPYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGV 255
I+A ++V T+ GR+PV F GGV D + LG G+F+G V
Sbjct: 265 ISALEEVVKATQ--GRIPV--FLDGGVRRGTDVFKALALGASGIFIGRPV 310
>gnl|CDD|215273 PLN02495, PLN02495, oxidoreductase, acting on the CH-CH group of
donors.
Length = 385
Score = 28.7 bits (64), Expect = 4.5
Identities = 16/33 (48%), Positives = 19/33 (57%)
Query: 230 GGVATPADAAMMMQLGCDGVFVGSGVFKSGDPV 262
GGV T DAA + LG D V V +GV G P+
Sbjct: 277 GGVETGGDAAEFILLGADTVQVCTGVMMHGYPL 309
>gnl|CDD|239203 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous
FMN-dependent alpha-hydroxyacid oxidizing enzymes. This
family occurs in both prokaryotes and eukaryotes.
Members of this family include flavocytochrome b2
(FCB2), glycolate oxidase (GOX), lactate monooxygenase
(LMO), mandelate dehydrogenase (MDH), and long chain
hydroxyacid oxidase (LCHAO). In green plants, glycolate
oxidase is one of the key enzymes in photorespiration
where it oxidizes glycolate to glyoxylate. LMO catalyzes
the oxidation of L-lactate to acetate and carbon
dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate.
It is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate.
Length = 299
Score = 28.2 bits (64), Expect = 5.5
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 231 GVATPADAAMMMQLGCDGVFV 251
G+ TP DA + G DG+ V
Sbjct: 179 GILTPEDALRAVDAGADGIVV 199
>gnl|CDD|181306 PRK08227, PRK08227, autoinducer 2 aldolase; Validated.
Length = 264
Score = 28.1 bits (63), Expect = 5.5
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 223 PVVHFAAGGVATPADAAMMM-----QLGCDGVFVGSGVFKSGDPVKRAQAIVRAVTH 274
PV AGG P A+ M G GV +G +F+S PV +A V AV H
Sbjct: 192 PVPIVIAGGKKLPERDALEMCYQAIDEGASGVDMGRNIFQSEHPVAMIKA-VHAVVH 247
>gnl|CDD|178226 PLN02617, PLN02617, imidazole glycerol phosphate synthase hisHF.
Length = 538
Score = 28.1 bits (63), Expect = 6.1
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQGGVARMSDPQLIKEIKQSVTIPVMAKARIG--- 102
E A+ EE GA ++ L + D + +G D +L+K + +VTIPV+A + G
Sbjct: 442 ELAKAVEELGAGEIL-LNCIDCDGQGKG-----FDIELVKLVSDAVTIPVIASSGAGTPE 495
Query: 103 HFVE 106
HF +
Sbjct: 496 HFSD 499
>gnl|CDD|166134 PLN02493, PLN02493, probable peroxisomal (S)-2-hydroxy-acid
oxidase.
Length = 367
Score = 28.2 bits (62), Expect = 6.6
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 206 IAAPYDLVMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGV 255
I+A ++V T+ GR+PV F GGV D + LG G+F+G V
Sbjct: 266 ISALEEVVKATQ--GRIPV--FLDGGVRRGTDVFKALALGASGIFIGRPV 311
>gnl|CDD|232930 TIGR00342, TIGR00342, tRNA sulfurtransferase ThiI. Members of this
protein family are "ThiI", a sulfurtransferase involved
in 4-thiouridine modification of tRNA. This protein
often is bifunctional, with genetically separable
activities, where the C-terminal rhodanese-like domain
(residues 385 to 482 in E. coli ThiI), a domain not
included in this model, is sufficient to synthesize the
thiazole moiety of thiamine (see TIGR04271). Note that
ThiI, because of its role in tRNA modification, may
occur in species (such as Mycoplasma genitalium) that
lack de novo thiamine biosynthesis [Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine,
Protein synthesis, tRNA and rRNA base modification].
Length = 371
Score = 28.1 bits (63), Expect = 6.6
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 16/71 (22%)
Query: 187 DIRVLRNMDDDEVFTFAKKIAAPYDLVMQTKQLGRLP------VVHFAAGGVATPADAAM 240
DI V + +DE ++ G LP V+ +GG+ +P A M
Sbjct: 142 DITVHIEIREDEFLIITERYEGI----------GGLPVGTQGKVLALLSGGIDSPVAAFM 191
Query: 241 MMQLGCDGVFV 251
MM+ GC V V
Sbjct: 192 MMKRGCRVVAV 202
>gnl|CDD|233350 TIGR01302, IMP_dehydrog, inosine-5'-monophosphate dehydrogenase.
This model describes IMP dehydrogenase, an enzyme of GMP
biosynthesis. This form contains two CBS domains. This
model describes a rather tightly conserved cluster of
IMP dehydrogenase sequences, many of which are
characterized. The model excludes two related families
of proteins proposed also to be IMP dehydrogenases, but
without characterized members. These are related
families are the subject of separate models [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 450
Score = 28.1 bits (63), Expect = 7.1
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 223 PVVHFAAGGVATPADAAMMMQLGCDGVFVGSG 254
P + AG VAT A ++ G DG+ VG G
Sbjct: 264 PDLDIIAGNVATAEQAKALIDAGADGLRVGIG 295
>gnl|CDD|216281 pfam01070, FMN_dh, FMN-dependent dehydrogenase.
Length = 302
Score = 27.8 bits (63), Expect = 7.5
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 231 GVATPADAAMMMQLGCDGVFV 251
G+ +P DA ++ G DG+ V
Sbjct: 177 GILSPEDAKRAVEAGVDGIVV 197
>gnl|CDD|178201 PLN02591, PLN02591, tryptophan synthase.
Length = 250
Score = 27.7 bits (62), Expect = 7.6
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 212 LVMQTKQLGRLPV-VHFAAGGVATPADAAMMMQLGCDGVFVGSGVFK 257
L+ + K++ PV V F G++ P A + G DGV VGS + K
Sbjct: 180 LLQELKEVTDKPVAVGF---GISKPEHAKQIAGWGADGVIVGSAMVK 223
>gnl|CDD|223347 COG0269, SgbH, 3-hexulose-6-phosphate synthase and related proteins
[Carbohydrate transport and metabolism].
Length = 217
Score = 27.6 bits (62), Expect = 7.9
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 229 AGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAVTHY 275
AGG+ TP D + +G D V VG + + DP + A+ +
Sbjct: 170 AGGI-TPEDIPLFKGIGADIVIVGRAITGAKDPAEAARKFKEEIDKI 215
>gnl|CDD|205939 pfam13766, ECH_C, 2-enoyl-CoA Hydratase C-terminal region. This
is the C-terminal region of enoyl-CoA hydratase.
Length = 117
Score = 26.7 bits (60), Expect = 8.3
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 20 KKSPFSVKVGLAQMLRG 36
SP S+KV L Q+ RG
Sbjct: 41 SGSPLSLKVTLEQLRRG 57
>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 = 27.5 bits (62), Expect = 8.7
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 14/78 (17%)
Query: 30 LAQMLRGG---VIMDVVTPEQARVAEEAGACAV------MALERVPADIRSQGGVARMSD 80
L +L G V+ AR+AE AG A+ +A D GG+ + +
Sbjct: 1 LRALLESGGPLVLPGAWDALSARLAERAGFKAIYTSGAGVAASLGLPD----GGLLTLDE 56
Query: 81 -PQLIKEIKQSVTIPVMA 97
++ I ++V +PV+A
Sbjct: 57 VLAAVRRIARAVDLPVIA 74
>gnl|CDD|236782 PRK10871, nlpD, lipoprotein NlpD; Provisional.
Length = 319
Score = 27.5 bits (61), Expect = 8.8
Identities = 16/35 (45%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 206 IAAPYDL-VMQTKQLGRLPVVHFAAGGVATPADAA 239
I APY L V QT Q+G G T ADAA
Sbjct: 91 IQAPYSLNVGQTLQVGNASGTPITGGNAITQADAA 125
>gnl|CDD|180317 PRK05942, PRK05942, aspartate aminotransferase; Provisional.
Length = 394
Score = 27.8 bits (62), Expect = 9.4
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 9/56 (16%)
Query: 109 ILEAIGIDYVDESEVLTPADEENHINKHNFRIPFVCGCRNLGEALRRIREGAAMIR 164
+L+ G+ V+TP + + RI + C LGEAL R+++ A IR
Sbjct: 346 VLQKTGV-------VVTPGNAFGEGGEGYVRISLIADCDRLGEALDRLKQ--AGIR 392
>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 = 27.2 bits (61), Expect = 9.6
Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 5/58 (8%)
Query: 46 EQARVAEEAGACAVMALERVPADIRSQG-GVARMSDPQLIKEI----KQSVTIPVMAK 98
E A++ EEAGA A+ P + +G G A DP+L++EI +++V IPV+AK
Sbjct: 117 ELAKLVEEAGADALELNFSCPHGMPERGMGAAVGQDPELVEEICRWVREAVKIPVIAK 174
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 27.4 bits (62), Expect = 10.0
Identities = 17/87 (19%), Positives = 28/87 (32%), Gaps = 21/87 (24%)
Query: 213 VMQTKQLGRLPVVHFAAGGVATPADAAMMMQLGCDGVFVGSGVFKSGDPVKRAQAIVRAV 272
V Q Q +P+ GG+++ DA + G V VG+ F
Sbjct: 226 VYQVYQAVDIPI--IGMGGISSAEDAIEFIMAGASAVQVGTANFY--------------- 268
Query: 273 THYSDPEVLAEVSCGLGEAMVGLNLSD 299
DP ++ GL + +
Sbjct: 269 ----DPYAFPKIIEGLEAYLDKYGIKS 291
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 0.135 0.384
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,508,624
Number of extensions: 1690365
Number of successful extensions: 2291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2260
Number of HSP's successfully gapped: 222
Length of query: 310
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 213
Effective length of database: 6,635,264
Effective search space: 1413311232
Effective search space used: 1413311232
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: 59 (26.4 bits)