RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781101|ref|YP_003065514.1|
UDP-N-acetylmuramoylalanyl-D-glutamyl-2,
6-diaminopimelate/D-alanyl-D-alanyl ligase [Candidatus Liberibacter
asiaticus str. psy62]
(472 letters)
>gnl|CDD|31113 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 451
Score = 376 bits (968), Expect = e-105
Identities = 175/464 (37%), Positives = 244/464 (52%), Gaps = 14/464 (3%)
Query: 4 LWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQK 63
L T +L + G +G P +G+SIDSR + P + F A+KG +DGHDFI A+
Sbjct: 2 LLTLDELADILGGALVGADPVVV-SGVSIDSRKVKPGDLFVALKGERFDGHDFIEQALAA 60
Query: 64 GAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTK 123
GA V+V ++ ++ + V V D L AL KLA A R + A +IAITGS GKTTTK
Sbjct: 61 GAAAVLVARPVLPP--AIPLVVLLVLDTLEALGKLAKAYRQKFNAKVIAITGSNGKTTTK 118
Query: 124 EMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVR 183
EML LS+ K +A G++NN IG+PLTL R+P D ++ + E+GM+H GEI L+ + R
Sbjct: 119 EMLAAILSTKGKVHATPGNFNNEIGLPLTLLRLPADTEYAVLEMGMNHPGEIAELSEIAR 178
Query: 184 PHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALG 243
P IAVIT I AHL F E IA AKAEI GL G LN D+ + AK +G
Sbjct: 179 PDIAVITNIGEAHLEGFGSREGIAEAKAEILAGLRPEGIAILNADNPLLKNWAAK---IG 235
Query: 244 IKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIV 303
+ SFG + DF+ E S + ++G E G H N L +
Sbjct: 236 NAKVLSFGLNNGGDFRATNIHLDEEGSSFTLDIEGGEAEFELPLPGRHNVTNALAAAALA 295
Query: 304 SILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQI 363
L D++ L P +GR + L TLID+SYNANP SM+AA+ +L+ +
Sbjct: 296 LELGLDLEEIAAGLKELKPVKGRLEVI---LLANGKTLIDDSYNANPDSMRAALDLLAAL 352
Query: 364 SPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIH 423
+ IAVLGDM E+GE S+ H ++ E I V+L G A+ +AL
Sbjct: 353 PG---RKGIAVLGDMLELGEESEELHEEVGEYAVEAGIDLVFLVGELSKAIAEALGN--K 407
Query: 424 VHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLEE 467
Y + L +++ L GDVV+VK S ++++ LL +
Sbjct: 408 GIYFADKEELITSLKALLRKGDVVLVKGSRGMKLEKVVDALLGK 451
>gnl|CDD|31112 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 112 bits (282), Expect = 2e-25
Identities = 93/370 (25%), Positives = 138/370 (37%), Gaps = 33/370 (8%)
Query: 27 VNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVF 86
G+++DSR + + F A G DGHDFI A+ GA VVV D+ + +PV
Sbjct: 10 PTGLTLDSRKVKEGDLFVAKPGTKVDGHDFIAGAIAPGAVAVVVEKDIKLAEA--GVPVI 67
Query: 87 GVDDVLGAL--NKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIG--- 141
V G L LA K +I +TG+ GKTTT +L L + K A IG
Sbjct: 68 VVTGTNGKLTTLALAFYGLPSGKLKVIGVTGTNGKTTTTSLLAQILKKLGKKTALIGTEG 127
Query: 142 -SYNNHIGVP-----------LTLARMPVD--VDFGIFELGMSHLGEIRFLTHLVRPHIA 187
+ I P L R +D + + E SH G ++ V +
Sbjct: 128 DELSPGILEPTGLTTPEALDLQNLLRDLLDRGAEIAVME-VSSH-GLVQGRVEGVTFDVG 185
Query: 188 VITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTI 247
V T ++ HL +E +AKA +FE L +G +N DD K +
Sbjct: 186 VFTNLSRDHLDYHGTMEYYGAAKAVLFESLPHSGEAVINPDDGHGLDYKERLKNALGD-Y 244
Query: 248 YSFGKSKNADFQLRKWKQCSEQSWM-EVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSIL 306
++G + + S + G E G N L + L
Sbjct: 245 ITYGCDFKRPDLDYRGIEESSSGSDFVFEPSGGIGEYELPLPGLFNVYNALAAVAAALAL 304
Query: 307 TADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPH 366
D++ + L P GR + G ++D Y NP ++ A+ + H
Sbjct: 305 GVDLEDILAGLETLKPVPGRMELVNIG---GKLVIVD--YAHNPDGLEKALRAV---RLH 356
Query: 367 GEGRRIAVLG 376
GR I V G
Sbjct: 357 AAGRLIVVFG 366
>gnl|CDD|31116 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope
biogenesis, outer membrane].
Length = 459
Score = 109 bits (274), Expect = 2e-24
Identities = 93/426 (21%), Positives = 161/426 (37%), Gaps = 56/426 (13%)
Query: 45 AIKGPHYDGHDFILHAVQKGAGLVVVNTDM------VASIGSLSIPVFGVDDVLGALNKL 98
A+ + GHD A +VVV+ + + + IPV ++L L
Sbjct: 50 ALGIEIFIGHD---AENILDADVVVVSNAIKEDNPEIVAALERGIPVISRAEMLAEL--- 103
Query: 99 AVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKK--TYACIGSYNNHIGVPLTLARM 156
+R + T IA+ G+ GKTTT ML L + T+ IG + G T AR+
Sbjct: 104 -----MRFR-TSIAVAGTHGKTTTTSMLAWVLEAAGLDPTFL-IGGILKNFG---TNARL 153
Query: 157 PVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEG 216
D+ + E S H P +A++T I HL + +E I A
Sbjct: 154 G-SGDYFVAEADESD----SSFLHY-NPRVAIVTNIEFDHLDYYGDLEAIKQAFHHFVRN 207
Query: 217 LEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQL 276
+ G + DD L+ + ++G AD++ +Q + +V
Sbjct: 208 VPFYGRAVVCGDD---PNLRELLSRGCWSPVVTYGFDDEADWRAENIRQDGSGTTFDVLF 264
Query: 277 QGKSMEVVHHGI-GYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALN 335
+G+ + V + G H N L + + L D + +AL+ F +G +R+
Sbjct: 265 RGEELGEVKLPLPGRHNVLNALAAIAVARELGIDPEAIAEALASF---QGVKRRFELKGE 321
Query: 336 QGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGD------MCEMGELSQSF- 388
T+ID+ Y +P +KA ++ Q P G R +AV + + +++
Sbjct: 322 VNGVTVIDD-YAHHPTEIKATLAAARQKVPGG-KRIVAVFQPHRYSRTRDLLDDFAKALS 379
Query: 389 HIDLAEVLSLY-----NISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVD 443
D +L +Y I L + + + HV + D L +
Sbjct: 380 DADEVILLDVYAAGEEPIEGDV----SSEDLAEKIRQPGHVDVPDLDD-LVELLAKVAQP 434
Query: 444 GDVVVV 449
GDV++
Sbjct: 435 GDVILF 440
>gnl|CDD|31114 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 96.9 bits (241), Expect = 1e-20
Identities = 89/357 (24%), Positives = 134/357 (37%), Gaps = 38/357 (10%)
Query: 101 AARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVP-LTLARMPVD 159
RL +A I+AITG+ GKTTT ++ L + G+ IG P L L
Sbjct: 103 FYRLSGEAPIVAITGTNGKTTTTSLIAHLLKAAGLDALLGGN----IGTPALELLEQAEP 158
Query: 160 VDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEK 219
D + EL L T +RP IAVI I+ HL +E A+AK I EG +
Sbjct: 159 ADVYVLELSSFQL----ETTSSLRPEIAVILNISEDHLDRHGSMENYAAAKLRILEG--Q 212
Query: 220 TGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGK 279
T +N DD LK + + F + E L
Sbjct: 213 TEVAVINADD---AYLKTLADEATKARVIWFSFGEPLADGDY-IYDGKLVFKGEKLLPAD 268
Query: 280 SMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFF 339
+++ G H +N L L + L + ++ALS F R + F
Sbjct: 269 ELKLP----GAHNLENALAALALARALGVPPEAILEALSSFTGLPHRLEFVGEKDGVLF- 323
Query: 340 TLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLY 399
I++S N + AA+S +G I + G + + S LAE+L+
Sbjct: 324 --INDSKATNVDATLAALSGF-------DGPVILIAGGDDKGADFS-----PLAEILAKV 369
Query: 400 NISHVWLSGFHVLALKDAL-PRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSC 455
I + L G + AL + ET++ + GDVV++ S +C
Sbjct: 370 -IKKLVLIGEDAEKIAAALKEAGPSLVICETLEEAVQLARELAQPGDVVLL--SPAC 423
>gnl|CDD|144716 pfam01225, Mur_ligase, Mur ligase family, catalytic domain. This
family contains a number of related ligase enzymes
which have EC numbers 6.3.2.*. This family includes:
MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure
and MurF catalyse consecutive steps in the synthesis of
peptidoglycan. Peptidoglycan consists of a sheet of two
sugar derivatives, with one of these N-acetylmuramic
acid attaching to a small pentapeptide. The
pentapeptide is is made of L-alanine, D-glutamic acid,
Meso-diaminopimelic acid and D-alanyl alanine. The
peptide moiety is synthesized by successively adding
these amino acids to UDP-N-acetylmuramic acid. MurC
transfers the L-alanine, MurD transfers the
D-glutamate, MurE transfers the diaminopimelic acid,
and MurF transfers the D-alanyl alanine. This family
also includes Folylpolyglutamate synthase that
transfers glutamate to folylpolyglutamate.
Length = 76
Score = 58.3 bits (142), Expect = 4e-09
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 27 VNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVF 86
++ I IDSR ++P F A+KG DG DF A+ GA VV + + + +P
Sbjct: 2 IHFIGIDSRGMSPGALFLALKGYRVDGSDFAESAIALGAVAVVSSA--IPRDPNPEVPGI 59
Query: 87 GVDDVLGALNKLA 99
V D AL +LA
Sbjct: 60 PVIDRREALAELA 72
>gnl|CDD|145824 pfam02875, Mur_ligase_C, Mur ligase family, glutamate ligase
domain. This family contains a number of related ligase
enzymes which have EC numbers 6.3.2.*. This family
includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC,
MurD, Mure and MurF catalyse consecutive steps in the
synthesis of peptidoglycan. Peptidoglycan consists of a
sheet of two sugar derivatives, with one of these
N-acetylmuramic acid attaching to a small pentapeptide.
The pentapeptide is is made of L-alanine, D-glutamic
acid, Meso-diaminopimelic acid and D-alanyl alanine. The
peptide moiety is synthesized by successively adding
these amino acids to UDP-N-acetylmuramic acid. MurC
transfers the L-alanine, MurD transfers the D-glutamate,
MurE transfers the diaminopimelic acid, and MurF
transfers the D-alanyl alanine. This family also
includes Folylpolyglutamate synthase that transfers
glutamate to folylpolyglutamate.
Length = 87
Score = 47.3 bits (113), Expect = 1e-05
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 334 LNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLA 393
N G + D Y NP +++AA+ L ++ +GR I V G G+ FH L
Sbjct: 10 ENNGVLVIDD--YAHNPDALEAALQALKEL---FDGRLILVFGA---GGDRDAEFHALLG 61
Query: 394 EVLSLYNISHV 404
+ + +
Sbjct: 62 ALAAALADVVI 72
>gnl|CDD|30633 COG0285, FolC, Folylpolyglutamate synthase [Coenzyme metabolism].
Length = 427
Score = 40.3 bits (94), Expect = 0.001
Identities = 49/226 (21%), Positives = 90/226 (39%), Gaps = 32/226 (14%)
Query: 158 VDVDFGIFELGMSHLGEIRF-LTHLVRPHIAVITTIAPAHLSNFSG--IEEIASAKAEIF 214
VD I E+G+ R T+++ P ++VIT+I H + F G +E IA KA I
Sbjct: 136 AKVDVAILEVGLG----GRLDATNVIEPDVSVITSIGLDH-TAFLGDTLESIAREKAGII 190
Query: 215 EGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEV 274
+ + ++ ++ ++ LG DFQ+ +
Sbjct: 191 KAGKPAVIGEQQPPEA-LNVIAERAEELGAPLFVL-----GPDFQVLEEGN-----GFSF 239
Query: 275 QLQGKSMEVVHHGIGYHM-AQNMLMTLGIVSILTADV--DTAIKAL-SVFHPKEGRGKRY 330
Q G +++ +G H +N + + + L ++ + K L +V P GR +R
Sbjct: 240 QGGGGLLDLPLPLLGGHHQIENAALAIAALEALGKEISEEAIRKGLANVDWP--GRLER- 296
Query: 331 RCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLG 376
L++ L+D ++ NP + +A L + R V G
Sbjct: 297 ---LSENPLILLDGAH--NPHAARALAETLKTLFND-RPRLTLVFG 336
>gnl|CDD|145608 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein
and predicted ATPase that is induced by phosphate
starvation.
Length = 205
Score = 30.9 bits (71), Expect = 0.76
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 339 FTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGD 377
F ++DE+ N P MK L++I G ++ V GD
Sbjct: 122 FIILDEAQNTTPEQMK---MFLTRI---GFNSKMVVTGD 154
>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl
alcohol dehydrogenase is similar to liver alcohol
dehydrogenase, but has some amino acid substitutions
near the active site, which may determine the enzyme's
specificity of oxidizing aromatic substrates. Also
known as aryl-alcohol dehydrogenases, they catalyze the
conversion of an aromatic alcohol + NAD+ to an aromatic
aldehyde + NADH + H+. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 365
Score = 30.2 bits (69), Expect = 1.5
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 61 VQKGAGLVVVNTDMVASIGSLSIPVFGVDDV-LGALNKLAVAARLRSKATIIAI 113
+Q GAG V+N + GS SI VFG V L A+ +AA++ TIIA+
Sbjct: 171 IQTGAG-AVLNV-LKPRPGS-SIAVFGAGAVGLAAV----MAAKIAGCTTIIAV 217
>gnl|CDD|37195 KOG1984, KOG1984, KOG1984, Vesicle coat complex COPII, subunit SFB3
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 1007
Score = 29.6 bits (66), Expect = 2.2
Identities = 27/139 (19%), Positives = 48/139 (34%), Gaps = 43/139 (30%)
Query: 338 FFTLIDESYNANPASMKAAI-----SVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDL 392
F +ID SYNA A SVL + R+ + +
Sbjct: 420 FVFMIDVSYNAISNGAVKAACEAIKSVLEDLPREEPNIRVGI---------------VTF 464
Query: 393 AEVLSLYNISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSS 452
+ + +N+S +L + D +D +F+ +DG + V +
Sbjct: 465 DKTVHFFNLSSNLAQP-QMLIVSD-------------VDDVFV----PFLDG--LFVNPN 504
Query: 453 NSCGFYRLINLLLEEFPAI 471
S ++I LLL+ P +
Sbjct: 505 ES---RKVIELLLDSIPTM 520
>gnl|CDD|145357 pfam02153, PDH, Prephenate dehydrogenase. Members of this family
are prephenate dehydrogenases EC:1.3.1.12 involved in
tyrosine biosynthesis.
Length = 258
Score = 28.9 bits (65), Expect = 3.3
Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 13/72 (18%)
Query: 178 LTHLVRPHIAVITTIAPAHL---SNFSGIEEIASAKAEIFEG-------LEKTGTIFLNY 227
+ ++ P H + SG +A+A +FE EKT T L
Sbjct: 85 IVKDAEQLLSDGVGFIPGHPMAGTEKSGP---DAARANLFENAPVILTPTEKTDTEALAL 141
Query: 228 DDSFFELLKAKS 239
E + AK
Sbjct: 142 VRELLEGIGAKV 153
>gnl|CDD|147730 pfam05735, TSP_C, Thrombospondin C-terminal region. This region is
found at the C-terminus of thrombospondin and related
proteins.
Length = 201
Score = 28.5 bits (64), Expect = 4.2
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 17/63 (26%)
Query: 214 FEGLEKTGTIFLN--YDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSW 271
FEG++ GT F+N DD + +G + FG N+ F + WK+ +EQ++
Sbjct: 32 FEGVDFEGTFFINTTTDDDY----------VG----FVFGYQSNSKFYVVMWKK-AEQTY 76
Query: 272 MEV 274
+
Sbjct: 77 WQA 79
>gnl|CDD|73403 cd04741, DHOD_1A_like, Dihydroorotate dehydrogenase (DHOD) class 1A
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 = 294
Score = 28.3 bits (63), Expect = 4.7
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 76 ASIGSLSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSV 117
SI SL +P G+D L + ++ +K I++TGS
Sbjct: 61 GSINSLGLPNLGLDYYLEYIRTISDGLPGSAKPFFISVTGSA 102
>gnl|CDD|176148 cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators that are
involved in the catabolism of dinitrotoluene,
naphthalene and gamma-hexachlorohexane; contains the
type 2 periplasmic binding fold. This CD includes
LysR-like bacterial transcriptional regulators, DntR,
NahR, and LinR, which are involved in the degradation of
aromatic compounds. The transcription of the genes
encoding enzymes involved in such degradation is
regulated and expression of these enzymes is enhanced by
inducers, which are either an intermediate in the
metabolic pathway or compounds to be degraded. DntR
from Burkholderia species controls genes encoding
enzymes for oxidative degradation of the nitro-aromatic
compound 2,4-dinitrotoluene. The active form of DntR is
homotetrameric, consisting of a dimer of dimers. NahR is
a salicylate-dependent transcription activator of the
nah and sal operons for naphthalene degradation.
Salicylic acid is an intermediate of the oxidative
degradation of the aromatic ring in soil bacteria. LinR
positively regulates expression of the genes (linD and
linE) encoding enzymes for gamma-hexachlorocyclohexane
(a haloorganic insecticide) degradation. Expression of
linD and linE are induced by their substrates,
2,5-dichlorohydroquinone (2,5-DCHQ) and
chlorohydroquinone (CHQ). The structural topology of
this substrate-binding domain is most similar to that of
the type 2 periplasmic binding proteins (PBP2), which
are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 201
Score = 27.9 bits (63), Expect = 6.6
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 10/59 (16%)
Query: 165 FELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTI 223
F + MS +GE+ FL L +A + +AP + IE + E+ E LE +G I
Sbjct: 2 FRIAMSDIGEMYFLPRL----LAALREVAP-GVR----IETVRLPVDELEEALE-SGEI 50
>gnl|CDD|100086 cd03084, phosphohexomutase, The alpha-D-phosphohexomutase
superfamily includes several related enzymes that
catalyze a reversible intramolecular phosphoryl transfer
on their sugar substrates. Members of this family
include the phosphoglucomutases (PGM1 and PGM2),
phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). These
enzymes play important and diverse roles in carbohydrate
metabolism in organisms from bacteria to humans. Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model..
Length = 355
Score = 27.7 bits (62), Expect = 8.1
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 276 LQGKSMEVVH---HGIGYHMAQNMLMTLGI-VSILTADVDTAIKALSVFHPKEGRGK 328
L K +VV +G+G +A +L LG V L + D +P G
Sbjct: 108 LSNKKFKVVVDSVNGVGGPIAPQLLEKLGAEVIPLNCEPD---GNFGNINPDPGSET 161
>gnl|CDD|30198 cd02025, PanK, Pantothenate kinase (PanK) catalyzes the
phosphorylation of pantothenic acid to form
4'-phosphopantothenic, which is the first of five steps
in coenzyme A (CoA) biosynthetic pathway. The reaction
carried out by this enzyme is a key regulatory point in
CoA biosynthesis..
Length = 220
Score = 27.5 bits (61), Expect = 9.1
Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 110 IIAITGSV--GKTTTKEMLTIALS 131
II I GSV GK+TT +L LS
Sbjct: 1 IIGIAGSVAVGKSTTARVLQALLS 24
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.137 0.401
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,636,328
Number of extensions: 303538
Number of successful extensions: 757
Number of sequences better than 10.0: 1
Number of HSP's gapped: 740
Number of HSP's successfully gapped: 26
Length of query: 472
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 375
Effective length of database: 4,167,664
Effective search space: 1562874000
Effective search space used: 1562874000
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: 59 (26.6 bits)