RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781111|ref|YP_003065524.1| geranyltranstransferase
protein [Candidatus Liberibacter asiaticus str. psy62]
(237 letters)
>gnl|CDD|144078 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 177 bits (451), Expect = 2e-45
Identities = 80/198 (40%), Positives = 117/198 (59%), Gaps = 7/198 (3%)
Query: 39 LLSAIRYALL-GGKKIRSFLVTECASLFNVNHLTALRVGAAIECIHCYSLIHDDLPSMDN 97
LL+A+ Y LL GGK+IR LV A V T L + AIE IH SL+HDDL MDN
Sbjct: 1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL--MDN 58
Query: 98 GYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQ 157
+RRGKPT H ++ E AI+AG+ LL+ AF++++ ++ + L+ L + +G Q
Sbjct: 59 SDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLAL-LGHVRPEPKYILISELANAVGAQ 117
Query: 158 GMLGGQMLDIQDEFIDETQV--FMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGE 215
G + GQ++D++ E D T I KT AL + + GAI+A A + +++ L FG
Sbjct: 118 GEV-GQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFGR 176
Query: 216 NLGIIFQLADDLLDCEED 233
+LG+ FQ+ DD+LD D
Sbjct: 177 DLGLAFQIQDDILDLTGD 194
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases,
head-to-tail. These trans-Isoprenyl Diphosphate
Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4)
condensation reactions. This CD includes all-trans
(E)-isoprenyl diphosphate synthases which synthesize
various chain length (C10, C15, C20, C25, C30, C35, C40,
C45, and C50) linear isoprenyl diphosphates from
precursors, isopentenyl diphosphate (IPP) and
dimethylallyl diphosphate (DMAPP). They catalyze the
successive 1'-4 condensation of the 5-carbon IPP to
allylic substrates geranyl-, farnesyl-, or
geranylgeranyl-diphosphate. Isoprenoid chain elongation
reactions proceed via electrophilic alkylations in which
a new carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions (DDXX(XX)D)
located on opposite walls. These residues mediate
binding of prenyl phosphates via bridging Mg2+ ions,
inducing proposed conformational changes that close the
active site to solvent, protecting and stabilizing
reactive carbocation intermediates. Farnesyl diphosphate
synthases produce the precursors of steroids,
cholesterol, sesquiterpenes, farnsylated proteins, heme,
and vitamin K12; and geranylgeranyl diphosphate and
longer chain synthases produce the precursors of
carotenoids, retinoids, diterpenes, geranylgeranylated
chlorophylls, ubiquinone, and archaeal ether linked
lipids. Isoprenyl diphosphate synthases are widely
distributed among archaea, bacteria, and eukareya.
Length = 259
Score = 173 bits (440), Expect = 5e-44
Identities = 80/205 (39%), Positives = 117/205 (57%), Gaps = 13/205 (6%)
Query: 34 QHNDRLLSAIRYALL-GGKKIRSFLVTECASLFNVNHL-TALRVGAAIECIHCYSLIHDD 91
+ L A+RY LL GGK++R LV A L ALR+ AAIE +H SL+HDD
Sbjct: 1 SEVELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDD 60
Query: 92 LPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLT 151
+ MDN +RRGKPTVH + TAI+AG+ LL AFE+++ +L + + + +
Sbjct: 61 V--MDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLA----RLGNPYYPRALELFS 114
Query: 152 HNIGLQGMLGGQMLDIQDEF---IDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKE 208
+ ++ GQ+LD+ E+ + E + I ++KT AL A GA++A A + E E
Sbjct: 115 E--AILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAE 172
Query: 209 RLRCFGENLGIIFQLADDLLDCEED 233
L+ FG NLG+ FQ+ DD+LD D
Sbjct: 173 ALKRFGRNLGLAFQIQDDILDLFGD 197
>gnl|CDD|30491 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 171 bits (435), Expect = 1e-43
Identities = 90/236 (38%), Positives = 129/236 (54%), Gaps = 23/236 (9%)
Query: 5 LPSKLQENSKRIDTILDDLLLQTASHMQTQHNDRLLSAIRYALL-GGKKIRSFLVTECAS 63
L + L + RI+ +L +LL + LL A+RY LL GGK++R LV A
Sbjct: 3 LLALLLKRLARIEELLSELL-------SGSDPELLLEAMRYLLLAGGKRLRPLLVLLAAE 55
Query: 64 LFNVNHLT----ALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIA 119
++ T AL + AAIE IH SLIHDDL MD+ +RRGKPTVH ++ E TAI+A
Sbjct: 56 ALGIDLETGGNDALDLAAAIELIHTASLIHDDL--MDDDDLRRGKPTVHAKFGEATAILA 113
Query: 120 GNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDEF--IDETQV 177
G+ LL AFE++S ++ + I++ + G+ GGQ LD+ E + +
Sbjct: 114 GDALLAAAFELLSKLGSEALEAIKAL-------AEAINGLCGGQALDLAFENKPVTLEEY 166
Query: 178 FMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEED 233
+ ++KT AL A GAI+A A + E L +G NLG+ FQ+ DD+LD D
Sbjct: 167 LRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGD 222
>gnl|CDD|35995 KOG0776, KOG0776, KOG0776, Geranylgeranyl pyrophosphate
synthase/Polyprenyl synthetase [Coenzyme transport and
metabolism].
Length = 384
Score = 128 bits (322), Expect = 2e-30
Identities = 62/191 (32%), Positives = 103/191 (53%), Gaps = 4/191 (2%)
Query: 41 SAIRYALL-GGKKIRSFLV-TECASLFNVNHLTALRVGAAIECIHCYSLIHDDLPSMDNG 98
A+RY LL GGK++R L C + + + + + +E IH SLIHDD+P MD+
Sbjct: 97 EAMRYLLLAGGKRVRPLLCLAACELVGSGDESSQRSLAEIVEMIHTASLIHDDVPCMDDA 156
Query: 99 YIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQG 158
+RRGKPT H + A++AG+ LL A E ++S + + + + + L QG
Sbjct: 157 DLRRGKPTNHKVFGNKMAVLAGDALLALASEHLASLENPVVVELMASAIADLVRGEFTQG 216
Query: 159 MLGGQMLDIQDEFIDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLG 218
++ G+ LD+ D ++ + +KT +L+ +C + AI+ S+ E +G LG
Sbjct: 217 LVAGEGLDLDDVGLEYLE--FKTLLKTASLLAKSCVAAAILGGGSEEVIEAAFEYGRCLG 274
Query: 219 IIFQLADDLLD 229
+ FQ+ DD+LD
Sbjct: 275 LAFQVVDDILD 285
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases.
Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of
class 1 isoprenoid biosynthesis enzymes which either
synthesis geranyl/farnesyl diphosphates (GPP/FPP) or
longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids,
diterpenes, ubiquinone, and archaeal ether linked
lipids; and are widely distributed among archaea,
bacteria, and eukareya. The enzymes in this family share
the same 'isoprenoid synthase fold' and include the
head-to-tail (HT) IPPS which catalyze the successive
1'-4 condensation of the 5-carbon IPP to the growing
isoprene chain to form linear, all-trans, C10-, C15-,
C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid
diphosphates. The head-to-head (HH) IPPS catalyze the
successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Isoprenoid chain
elongation reactions proceed via electrophilic
alkylations in which a new carbon-carbon single bond is
generated through interaction between a highly reactive
electron-deficient allylic carbocation and an
electron-rich carbon-carbon double bond. The catalytic
site consists of a large central cavity formed by mostly
antiparallel alpha helices with two aspartate-rich
regions located on opposite walls. These residues
mediate binding of prenyl phosphates via bridging Mg2+
ions, inducing proposed conformational changes that
close the active site to solvent, stabilizing reactive
carbocation intermediates. Mechanistically and
structurally distinct, cis-IPPS are not included in this
CD.
Length = 236
Score = 125 bits (315), Expect = 1e-29
Identities = 60/185 (32%), Positives = 93/185 (50%), Gaps = 15/185 (8%)
Query: 53 IRSFLVTECASLFNVNHLTALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVH-IQY 111
R LV A + ALR+ AA+E +H SL+HDD+ +D+ +RRGKPT H ++
Sbjct: 1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDI--VDDSDLRRGKPTAHLRRF 58
Query: 112 DEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDEF 171
AI+AG+ LL AF++++ + ++ L+ +L GQ LD++ E
Sbjct: 59 GNALAILAGDYLLARAFQLLARLGYPRALELFAE---------ALRELLEGQALDLEFER 109
Query: 172 ---IDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLL 228
+ + KT L+ C GA ++ A + E L+ +G LG+ FQL DDLL
Sbjct: 110 DTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLL 169
Query: 229 DCEED 233
D D
Sbjct: 170 DVFGD 174
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 97.6 bits (243), Expect = 2e-21
Identities = 58/229 (25%), Positives = 107/229 (46%), Gaps = 18/229 (7%)
Query: 9 LQENSKRIDTILDDLLL--QTASHMQTQHNDRLLSAIRYAL-LGGKKIRSFLVTECASLF 65
+ NS + I ++LL+ + + L +A ++ GGK+IR +V A
Sbjct: 1 MATNSNLLTPIEEELLILEDNLKKLIGSGHPILYAAAKHLFSAGGKRIRPAIVLLVAKAT 60
Query: 66 NVNHLTAL---RVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNG 122
N R+ E IH SL+HDD+ +D IRRG PTVH + A++AG+
Sbjct: 61 GGNMEIKTSQQRLAEITEIIHTASLVHDDV--IDECSIRRGIPTVHKIFGTKIAVLAGDF 118
Query: 123 LLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDEFIDETQVFMIQK 182
L + +++ + S+++ QG++ D ++ I+K
Sbjct: 119 LFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLV---QFDTTLSILN-----YIEK 170
Query: 183 M--KTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLD 229
KT +L+ +C++ A+++ A + + +G++LG+ FQ+ DD+LD
Sbjct: 171 SFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLD 219
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes,
Class 1. Superfamily of trans-isoprenyl diphosphate
synthases (IPPS) and class I terpene cyclases which
either synthesis geranyl/farnesyl diphosphates (GPP/FPP)
or longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids, and
diterpenes; and are widely distributed among archaea,
bacteria, and eukaryota.The enzymes in this superfamily
share the same 'isoprenoid synthase fold' and include
several subgroups. The head-to-tail (HT) IPPS catalyze
the successive 1'-4 condensation of the 5-carbon IPP to
the growing isoprene chain to form linear, all-trans,
C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or
C50-isoprenoid diphosphates. Cyclic monoterpenes,
diterpenes, and sesquiterpenes, are formed from their
respective linear isoprenoid diphosphates by class I
terpene cyclases. The head-to-head (HH) IPPS catalyze
the successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Cyclization of
these 30- and 40-carbon linear forms are catalyzed by
class II cyclases. Both the isoprenoid chain elongation
reactions and the class I terpene cyclization reactions
proceed via electrophilic alkylations in which a new
carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions located on
opposite walls. These residues mediate binding of prenyl
phosphates via bridging Mg2+ ions, inducing proposed
conformational changes that close the active site to
solvent, stabilizing reactive carbocation intermediates.
Generally, the enzymes in this family exhibit an
all-trans reaction pathway, an exception, is the
cis-trans terpene cyclase, trichodiene synthase.
Mechanistically and structurally distinct, class II
terpene cyclases and cis-IPPS are not included in this
CD.
Length = 243
Score = 95.3 bits (237), Expect = 1e-20
Identities = 56/168 (33%), Positives = 80/168 (47%), Gaps = 17/168 (10%)
Query: 72 ALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQ---YDEVTAIIAGNGLLTYAF 128
A R+ AA+E +H SL+HDD+ +D+ RRG PT H+ AI+AG+ LL AF
Sbjct: 12 ASRLRAAVEKLHAASLVHDDI--VDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAF 69
Query: 129 EIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDEF---IDETQVFMIQKMKT 185
E ++ S L + L +L GQ+LD++ + + KT
Sbjct: 70 EELA--------REGSPEALEILAEA-LLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKT 120
Query: 186 GALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEED 233
L+ C GA ++ E LR G LG+ FQL +DLLD E D
Sbjct: 121 AGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYEGD 168
>gnl|CDD|35930 KOG0711, KOG0711, KOG0711, Polyprenyl synthetase [Coenzyme
transport and metabolism].
Length = 347
Score = 55.0 bits (132), Expect = 2e-08
Identities = 58/238 (24%), Positives = 97/238 (40%), Gaps = 26/238 (10%)
Query: 9 LQENSKRIDTILDDLLLQTASHMQTQHNDRLLSAIRYALLGGKKIRSFLVTEC-ASLFNV 67
LQ + + +DL+ S T+ L + Y ++GGK R V + +L
Sbjct: 13 LQVFPVLVRVLTEDLMAHGESGDATE---WLKEVLDYNVIGGKLNRGLSVVDSFKALVEP 69
Query: 68 NHLT------ALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEV--TAIIA 119
L AL +G +E + + L+ DD+ MDN RRG+P + Q V AI
Sbjct: 70 RKLDEEELQLALILGWCVELLQAFFLVADDI--MDNSKTRRGQPCWY-QKPGVGLDAIND 126
Query: 120 GNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQD-----EFIDE 174
L ++++ + + ++ L H + Q LG + + +F E
Sbjct: 127 AFLLEAAIYKLLKKHFRNIYCYVD---LVELFHEVTFQTELGDLLTTPEGNKDLSKFSLE 183
Query: 175 TQVFMIQKMKTGALMCFACESGAIMAHASQNEKE--RLRCFGENLGIIFQLADDLLDC 230
VF+++ KT + + A++ N KE + LG FQ+ DD LDC
Sbjct: 184 KYVFIVEY-KTAYYSFYLPVALALLLAGIANLKEHACEKKVLLLLGEYFQVQDDYLDC 240
>gnl|CDD|35996 KOG0777, KOG0777, KOG0777, Geranylgeranyl pyrophosphate
synthase/Polyprenyl synthetase [Coenzyme transport and
metabolism].
Length = 322
Score = 52.8 bits (126), Expect = 9e-08
Identities = 61/214 (28%), Positives = 88/214 (41%), Gaps = 22/214 (10%)
Query: 22 DLLLQTASHMQTQHNDRLLSAIRYAL-LGGKKIRSFLVTECASLFNVNHLTALRVGAAIE 80
D L+ Q+Q+ LL Y L GK+ R L+ N+ + +E
Sbjct: 6 DELINNDPVTQSQNESILLKPYNYILQKPGKQFRLNLIVAFNHWLNLPKDKLAIISQIVE 65
Query: 81 CIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKD 140
+H SL+ DD+ DN +RRG+P H Y + I N + A E +S
Sbjct: 66 MLHNSSLLIDDIE--DNSPLRRGQPVAHSIYGVPSTINTANYMYFLALEKVSQLDHPNAI 123
Query: 141 NIRSQLMLSLTHNIGLQGMLGGQMLDI--QDEFIDETQVFMIQKM---KTGALMCFACES 195
I ++ +L L GQ LDI +D T+ M + M KTG L A
Sbjct: 124 KIFTEQLLELHR---------GQGLDIYWRDFLTCPTEE-MYKNMVMNKTGGLFRLALRL 173
Query: 196 GAIMAHASQNEKERLRCFGENLGIIFQLADDLLD 229
+ +H KE L LG+IFQ+ DD L+
Sbjct: 174 MQLFSH----HKEDLVPLINLLGLIFQIRDDYLN 203
>gnl|CDD|173976 cd08211, RuBisCO_large_II, Ribulose bisphosphate carboxylase large
chain, Form II. Ribulose bisphosphate carboxylase
(Rubisco) plays an important role in the Calvin
reductive pentose phosphate pathway. It catalyzes the
primary CO2 fixation step. Rubisco is activated by
carbamylation of an active site lysine, stabilized by a
divalent cation, which then catalyzes the proton
abstraction from the substrate ribulose 1,5 bisphosphate
(RuBP) and leads to the formation of two molecules of
3-phosphoglycerate. Members of the Rubisco family can be
divided into 4 subgroups, Form I-IV , which differ in
their taxonomic distribution and subunit composition.
Form II is mainly found in bacteria, and forms large
subunit oligomers (dimers, tetramers, etc.) that do not
include small subunits.
Length = 439
Score = 27.9 bits (62), Expect = 2.9
Identities = 10/42 (23%), Positives = 18/42 (42%)
Query: 126 YAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDI 167
Y E+ T + + S L L + +N G+ + +M D
Sbjct: 84 YPVELFDRNLTDGRAMVASFLTLIIGNNQGMGDVEYLKMHDF 125
>gnl|CDD|173960 cd08550, GlyDH-like, Glycerol_dehydrogenase-like. Families of
proteins related to glycerol dehydrogenases. Glycerol
dehydrogenases (GlyDH) is a key enzyme in the glycerol
dissimilation pathway. In anaerobic conditions, many
microorganisms utilize glycerol as a source of carbon
through coupled oxidative and reductive pathways. One of
the pathways involves the oxidation of glycerol to
dihydroxyacetone with the reduction of NAD+ to NADH
catalyzed by glycerol dehydrogenases. Dihydroxyacetone
is then phosphorylated by dihydroxyacetone kinase and
enters the glycolytic pathway for further degradation.
The activity of GlyDH is zinc-dependent. The zinc ion
plays a role in stabilizing an alkoxide intermediate at
the active site. Some subfamilies have not been
characterized till now.
Length = 349
Score = 27.5 bits (61), Expect = 3.1
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 203 SQNEKERLRCFGENLGIIFQLAD-DLLDCEEDLPK 236
+ E E L F LG+ LAD L +ED+ K
Sbjct: 284 PREEIEELVEFYRQLGLPVTLADLGLEFSDEDIKK 318
>gnl|CDD|112354 pfam03531, SSrecog, Structure-specific recognition protein (SSRP1).
SSRP1 has been implicated in transcriptional initiation
and elongation and in DNA replication and repair.
Length = 216
Score = 27.4 bits (61), Expect = 3.6
Identities = 10/44 (22%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 76 GAAIECIHCYSLIHDD--LPSMDNGYIRRGKPTVHIQYDEVTAI 117
AA++C S ++ L ++ G+ KP + I+++E++++
Sbjct: 130 TAAVKC----SYKANEGLLYPLEKGFFFLPKPPLLIRFEEISSV 169
>gnl|CDD|107293 cd06298, PBP1_CcpA_like, Ligand-binding domain of the catabolite
control protein A (CcpA), which functions as the major
transcriptional regulator of carbon catabolite
repression/regulation. Ligand-binding domain of the
catabolite control protein A (CcpA), which functions as
the major transcriptional regulator of carbon catabolite
repression/regulation (CCR), a process in which enzymes
necessary for the metabolism of alternative sugars are
inhibited in the presence of glucose. In gram-positive
bacteria, CCR is controlled by HPr, a
phosphoenolpyruvate:sugar phsophotrasnferase system
(PTS) and a transcriptional regulator CcpA. Moreover,
CcpA can regulate sporulation and antibiotic resistance
as well as play a role in virulence development of
certain pathogens such as the group A streptococcus. The
ligand binding domain of CcpA is a member of the
LacI-GalR family of bacterial transcription regulators.
Length = 268
Score = 26.8 bits (60), Expect = 4.7
Identities = 28/111 (25%), Positives = 41/111 (36%), Gaps = 33/111 (29%)
Query: 96 DNGYIRRGKPTVHIQYD---------EVTAIIAGN-----GLLTYA----------FEII 131
D I G T Y+ + TA + G+L A FEII
Sbjct: 151 DESLIFEGDYTYESGYELAEELLEDGKPTAAFVTDDELAIGILNAAQDAGLKVPEDFEII 210
Query: 132 SSPKTQLKDNIRSQLMLSLTH---NIGLQGMLGGQMLD--IQDEFIDETQV 177
T+L +R QL S+T +IG M ++L + E ++ QV
Sbjct: 211 GFNNTKLASMVRPQLT-SVTQPLYDIGAVAM---RLLTKLMNKEEVENKQV 257
>gnl|CDD|35746 KOG0526, KOG0526, KOG0526, Nucleosome-binding factor SPN, POB3
subunit [Transcription, Replication, recombination and
repair, Chromatin structure and dynamics].
Length = 615
Score = 26.1 bits (57), Expect = 8.1
Identities = 5/23 (21%), Positives = 18/23 (78%)
Query: 95 MDNGYIRRGKPTVHIQYDEVTAI 117
++ G++ KP ++I+++E++++
Sbjct: 357 LEKGFLFLPKPPLYIRFEEISSV 379
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 0.138 0.399
Gapped
Lambda K H
0.267 0.0665 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,748,723
Number of extensions: 138947
Number of successful extensions: 287
Number of sequences better than 10.0: 1
Number of HSP's gapped: 267
Number of HSP's successfully gapped: 16
Length of query: 237
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 146
Effective length of database: 4,297,318
Effective search space: 627408428
Effective search space used: 627408428
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: 56 (25.5 bits)