RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018852
(349 letters)
>gnl|CDD|215136 PLN02245, PLN02245, ATP phosphoribosyl transferase.
Length = 403
Score = 586 bits (1512), Expect = 0.0
Identities = 247/338 (73%), Positives = 269/338 (79%), Gaps = 6/338 (1%)
Query: 12 PYFRQCPSLSPSGLSFFCPLSSFHISVASGPTTATNKPAAAVTCCVSSSQQFESHVSVVN 71
S PS P SS + + T CVS Q S +
Sbjct: 4 LSQSPSLSSLPSSSPLLSPPSSRASRLIAPRRRCL----RLATACVSQVQSSVVAGSTDS 59
Query: 72 GNIDNRISERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWF 131
+ + +S R +IRLGLPSKGRMA DTLDLLKDCQLSVK+VNPRQYVA+IPQL NLEVWF
Sbjct: 60 AS--SVVSSRTQIRLGLPSKGRMAEDTLDLLKDCQLSVKKVNPRQYVAEIPQLPNLEVWF 117
Query: 132 QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE 191
QRPKDIVRKLLSGDLDLGIVG D + E+GQGNEDL+IVHDAL +GDC LS+AIPKYGIFE
Sbjct: 118 QRPKDIVRKLLSGDLDLGIVGYDMLREYGQGNEDLVIVHDALGFGDCHLSIAIPKYGIFE 177
Query: 192 NINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIA 251
NINSL+ELAQMPQWT E+PLRV TGFTYLGPKFMKDNG KHV FSTADGALEAAPAMGIA
Sbjct: 178 NINSLKELAQMPQWTEERPLRVVTGFTYLGPKFMKDNGFKHVTFSTADGALEAAPAMGIA 237
Query: 252 DAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAH 311
DAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASR++L+ RKG L+ HEILERLEAH
Sbjct: 238 DAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRRALLERKGALEVVHEILERLEAH 297
Query: 312 LRASGQFTVTANMRGNSAEEVAERILSQTSFSGLQGPT 349
LRA GQFTVTANMRG+SAEEVAER+LSQ S SGLQGPT
Sbjct: 298 LRAEGQFTVTANMRGSSAEEVAERVLSQPSLSGLQGPT 335
>gnl|CDD|110621 pfam01634, HisG, ATP phosphoribosyltransferase.
Length = 161
Score = 177 bits (450), Expect = 4e-55
Identities = 68/181 (37%), Positives = 101/181 (55%), Gaps = 20/181 (11%)
Query: 132 QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE 191
RP DI + G +DLGI G D V E + + LD+G C+L +A+P+ G +
Sbjct: 1 LRPADIPVFVEDGVVDLGITGEDLVREEELAD---VEELLDLDFGSCKLVVAVPESGPYR 57
Query: 192 NINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIA 251
+ L R+AT + L K+ + NG DG++EAAPA+GIA
Sbjct: 58 SPEDLAG-----------GKRIATKYPNLARKYFRKNG-IDAEIIKLDGSVEAAPALGIA 105
Query: 252 DAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAH 311
DAI+DLVS+G TLR N LKEIE +++S AVL+A++ SL ++ V+D E++ RL+
Sbjct: 106 DAIVDLVSTGETLRANGLKEIE--TIMDSSAVLIANKNSLEEKEQVID---ELVTRLQGV 160
Query: 312 L 312
+
Sbjct: 161 I 161
>gnl|CDD|234781 PRK00489, hisG, ATP phosphoribosyltransferase; Reviewed.
Length = 287
Score = 179 bits (457), Expect = 3e-54
Identities = 87/267 (32%), Positives = 138/267 (51%), Gaps = 31/267 (11%)
Query: 84 IRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLS 143
+R+ +P+KGR++ L+LL + L +++ + R +A +EV F RP DI +
Sbjct: 5 LRIAVPNKGRLSEPALELLAEAGLKIRR-DSRSLIATDEDN-PIEVLFLRPDDIPGYVAD 62
Query: 144 GDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMP 203
G +DLGI G D + E + + L +G CRL LA+P+ + + +LA
Sbjct: 63 GVVDLGITGEDLLEE----SGADVEELLDLGFGKCRLVLAVPED---SDWQGVEDLAGK- 114
Query: 204 QWTAEKPLRVATGFTYLGPKFMKDNGLK-HVVFSTADGALEAAPAMGIADAILDLVSSGT 262
R+AT + L +++ + G+ VV GA+E AP +G+ADAI+D+VS+GT
Sbjct: 115 --------RIATSYPNLTRRYLAEKGIDAEVVEL--SGAVEVAPRLGLADAIVDVVSTGT 164
Query: 263 TLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLRASGQFTVTA 322
TLR N LK +E V+L S+AVL+A + L K + ++L RL+ LRA +
Sbjct: 165 TLRANGLKIVE--VILRSEAVLIARKGWLDPEK--QEKIDQLLTRLQGVLRARESKYLMM 220
Query: 323 NMRGNSAEEVAERILSQTSFSGLQGPT 349
N + V +L GL+ PT
Sbjct: 221 NAPKEKLDAVIA-LL-----PGLESPT 241
>gnl|CDD|223118 COG0040, HisG, ATP phosphoribosyltransferase [Amino acid transport
and metabolism].
Length = 290
Score = 172 bits (438), Expect = 1e-51
Identities = 79/267 (29%), Positives = 141/267 (52%), Gaps = 26/267 (9%)
Query: 84 IRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLS 143
+R+ LP KGR++ L+LL + + ++ R+ +A+ +E+ R +DI +
Sbjct: 3 LRIALPKKGRLSEPALELLAKAGIKISALDSRKLIAETE-NPPIELLLVRAQDIPTYVED 61
Query: 144 GDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMP 203
G DLGI G D + E G + + + D L +G CRL +A+P+ + + L+
Sbjct: 62 GVADLGITGEDVLRESGLDDASVEELLD-LGFGGCRLVVAVPEESDYTSPEDLKG----- 115
Query: 204 QWTAEKPLRVATGFTYLGPKFMKDNGLK-HVVFSTADGALEAAPAMGIADAILDLVSSGT 262
LR+AT + L K+ + G+ ++ G++E APA+G+ADAI+D+VS+GT
Sbjct: 116 ------RLRIATKYPNLARKYFAEKGIDVEIIKL--SGSVELAPALGLADAIVDIVSTGT 167
Query: 263 TLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLRASGQFTVTA 322
TL+ N LKEIE V+ +S A L+ + K+ ++ K + +++ RL+ + A G +
Sbjct: 168 TLKANGLKEIE--VIYDSSARLIVNAKASLKDKQ--ELIDQLVTRLKGVIEARGSKYI-- 221
Query: 323 NMRGNSAEEVAERILSQTSFSGLQGPT 349
N+ E + + + G++GPT
Sbjct: 222 --MLNAPRERLDEVTALL--PGMEGPT 244
>gnl|CDD|232809 TIGR00070, hisG, ATP phosphoribosyltransferase. Members of this
family from B. subtilis, Aquifex aeolicus, and
Synechocystis PCC6803 (and related taxa) lack the
C-terminal third of the sequence. The sole homolog from
Archaeoglobus fulgidus lacks the N-terminal 50 residues
(as reported) and is otherwise atypical of the rest of
the family. This model excludes the C-terminal extension
[Amino acid biosynthesis, Histidine family].
Length = 182
Score = 164 bits (417), Expect = 8e-50
Identities = 77/204 (37%), Positives = 118/204 (57%), Gaps = 23/204 (11%)
Query: 84 IRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLS 143
+R+ LP KGR+ DTL LL+ L V + + R+ +A+ P +E RP+DI +
Sbjct: 1 LRIALP-KGRLLEDTLKLLEKAGLKVSREDSRKLIARDPDE-GIEFLLLRPQDIPTYVEH 58
Query: 144 GDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMP 203
G DLGI G D + E G D+ + D L +G CRL LA+P+ +I+S+ +L
Sbjct: 59 GAADLGITGYDVLLESGA---DVYELLD-LGFGKCRLVLAVPQE---SDISSVEDLKGK- 110
Query: 204 QWTAEKPLRVATGFTYLGPKFMKDNGLK-HVVFSTADGALEAAPAMGIADAILDLVSSGT 262
R+AT + L ++ + G+ ++ +G++E AP +G+ADAI+D+VS+GT
Sbjct: 111 --------RIATKYPNLARRYFEKKGIDVEIIKL--NGSVELAPLLGLADAIVDIVSTGT 160
Query: 263 TLRENNLKEIEGGVVLESQAVLVA 286
TLREN L+ IE V+LES A L+A
Sbjct: 161 TLRENGLRIIE--VILESSARLIA 182
>gnl|CDD|237438 PRK13583, hisG, ATP phosphoribosyltransferase catalytic subunit;
Provisional.
Length = 228
Score = 124 bits (314), Expect = 5e-34
Identities = 69/210 (32%), Positives = 115/210 (54%), Gaps = 2/210 (0%)
Query: 84 IRLGLPSKGRMAADTLDLLKDCQLSVKQV-NPRQYVAQIPQLSNLEVWFQRPKDIVRKLL 142
I LGLPSKGR+ T + L++ + + R+Y ++ ++E+ F +I R+L
Sbjct: 3 ITLGLPSKGRLKEKTFAWFEKAGLTLVRTGSDREYRGRVEGEDDVELLFLSASEIPRELG 62
Query: 143 SGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGI-FENINSLRELAQ 201
+G +DLG+ G D V E + + + L +G L +A+P+ I + + L ++A
Sbjct: 63 AGRVDLGVTGEDLVREKLADWDKRVEIVARLGFGHADLVVAVPEIWIDVDTMADLDDVAA 122
Query: 202 MPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIADAILDLVSSG 261
+ + LR+AT + L +F+ G++ + GA E APA G A+ I+D+ S+G
Sbjct: 123 DFRARHGRRLRIATKYWRLTQQFLSQKGVQDYRIVESLGATEGAPANGSAEIIVDITSTG 182
Query: 262 TTLRENNLKEIEGGVVLESQAVLVASRKSL 291
TLR N+LK + GV+L SQA LV +RK+
Sbjct: 183 ETLRANHLKILSDGVILRSQACLVRARKAD 212
>gnl|CDD|234971 PRK01686, hisG, ATP phosphoribosyltransferase catalytic subunit;
Reviewed.
Length = 215
Score = 115 bits (291), Expect = 8e-31
Identities = 68/243 (27%), Positives = 116/243 (47%), Gaps = 35/243 (14%)
Query: 81 RDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNP--RQYVAQIPQLSNLEVWFQRPKDIV 138
D + + LP KGR+ +TL LL + + R+ + P+ ++ R D+
Sbjct: 1 MDMLTIALP-KGRILEETLPLLAKAGIDPSEDPDKSRKLIFPTPE-PDVRFLLVRATDVP 58
Query: 139 RKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRE 198
+ G DLGIVG D + E G+ DL D L G CR+S+A+P +
Sbjct: 59 TYVEHGAADLGIVGKDVLLEHGK---DLYEPLD-LGIGKCRMSVAVPP-----GFDYAPA 109
Query: 199 LAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTAD-----GALEAAPAMGIADA 253
+ Q P+ LRVAT + + ++ + G + G++E AP +G+ADA
Sbjct: 110 VKQGPR------LRVATKYPNIARRYFAEKGE------QVEIIKLYGSVELAPLVGLADA 157
Query: 254 ILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLR 313
I+D+V +G TLR N L E+E +++ A L+ +R SL ++ + ++E+L +
Sbjct: 158 IVDIVETGNTLRANGLVEVE--EIMDISARLIVNRASLKLKREEIR---PLIEKLREAVE 212
Query: 314 ASG 316
+
Sbjct: 213 SRA 215
>gnl|CDD|172153 PRK13584, hisG, ATP phosphoribosyltransferase catalytic subunit;
Provisional.
Length = 204
Score = 46.4 bits (110), Expect = 5e-06
Identities = 45/219 (20%), Positives = 96/219 (43%), Gaps = 29/219 (13%)
Query: 90 SKGRMAADTLDLLK--DCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLD 147
+KGR+ ++ L + + + R+ + + N+E + D+ + G D
Sbjct: 7 AKGRLMDSLINYLDVIEYTTLSETLKNRERQLLL-SVDNIECILVKGSDVPIYVEQGMAD 65
Query: 148 LGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTA 207
+GIVG D + E +L+ + +G C ++A P+ T
Sbjct: 66 IGIVGSDILDERQYNVNNLL----NMPFGACHFAVA-----------------AKPETTN 104
Query: 208 EKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIADAILDLVSSGTTLREN 267
+ ++AT + + + K G+ V +G++E A + + D I+D+V +GTTL+ N
Sbjct: 105 YR--KIATSYVHTAETYFKSKGID-VELIKLNGSVELACVVDMVDGIVDIVQTGTTLKAN 161
Query: 268 NLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILE 306
L E + + + A L+ ++ + ++ +++ LE
Sbjct: 162 GLVEKQ--HISDINARLITNKAAYFKKSQLIEQFIRSLE 198
>gnl|CDD|220401 pfam09786, CytochromB561_N, Cytochrome B561, N terminal. Members
of this family are found in the N terminal region of
cytochrome B561, as well as in various other putative
uncharacterized proteins.
Length = 559
Score = 32.4 bits (74), Expect = 0.34
Identities = 20/93 (21%), Positives = 30/93 (32%), Gaps = 8/93 (8%)
Query: 1 MSVSSASLFLQPYFRQCPSLSPSGLSFFCPLSSFHISVASGPTTATNKPAAAVTCCVSSS 60
M+ S + F PS S S F P S+ S P+ P+++ S
Sbjct: 129 MNTSEPLVPGHSSFSDSPSRSASPSRKFSPSSTIQQSPQLTPSNKPASPSSS-----YQS 183
Query: 61 QQFESHVSVVN---GNIDNRISERDEIRLGLPS 90
+ S + VN + R S G
Sbjct: 184 PSYSSSLGPVNSSGNRSNLRSSPWALRSSGDKK 216
>gnl|CDD|99883 cd05808, CBM20_alpha_amylase, Alpha-amylase, C-terminal CBM20
(carbohydrate-binding module, family 20) domain. This
domain is found in several bacterial and fungal
alpha-amylases including the maltopentaose-forming
amylases (G5-amylases). Most alpha-amylases have, in
addition to the C-terminal CBM20 domain, an N-terminal
catalytic domain belonging to glycosyl hydrolase family
13, which hydrolyzes internal alpha-1,4-glucosidic bonds
in starch and related saccharides, yielding maltotriose
and maltose. Two types of soluble substrates are used by
alpha-amylases including long substrates (e.g. amylose)
and short substrates (e.g. maltodextrins or
maltooligosaccharides). The CBM20 domain is found in a
large number of starch degrading enzymes including
alpha-amylase, beta-amylase, glucoamylase, and CGTase
(cyclodextrin glucanotransferase). CBM20 is also present
in proteins that have a regulatory role in starch
metabolism in plants (e.g. alpha-amylase) or glycogen
metabolism in mammals (e.g. laforin). CBM20 folds as an
antiparallel beta-barrel structure with two starch
binding sites. These two sites are thought to differ
functionally with site 1 acting as the initial starch
recognition site and site 2 involved in the specific
recognition of appropriate regions of starch.
Length = 95
Score = 28.1 bits (63), Expect = 2.0
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 3/47 (6%)
Query: 203 PQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMG 249
P W+ L T Y K++K +G V + + PA G
Sbjct: 43 PVWSGTVDLPAGTAIEY---KYIKKDGSGTVTWESGPNRTATTPASG 86
>gnl|CDD|176102 cd05466, PBP2_LTTR_substrate, The substrate binding domain of
LysR-type transcriptional regulators (LTTRs), a member
of the type 2 periplasmic binding fold protein
superfamily. This model and hierarchy represent the the
substrate-binding domain of the LysR-type
transcriptional regulators that form the largest family
of prokaryotic transcription factor. Homologs of some of
LTTRs with similar domain organizations are also found
in the archaea and eukaryotic organisms. The LTTRs are
composed of two functional domains joined by a linker
helix involved in oligomerization: an N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, oxidative stress
responses, nodule formation of nitrogen-fixing bacteria,
synthesis of virulence factors, toxin production,
attachment and secretion, to name a few. 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. Besides transport proteins, the PBP2
superfamily includes the substrate-binding domains from
ionotropic glutamate receptors, LysR-like
transcriptional regulators, and unorthodox sensor
proteins involved in signal transduction.
Length = 197
Score = 29.1 bits (66), Expect = 2.2
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 115 RQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGL 153
+ + P + L + +++ LL G+LDL IV L
Sbjct: 20 AAFRQRYPGV-ELSLVEGGSSELLEALLEGELDLAIVAL 57
>gnl|CDD|221318 pfam11925, DUF3443, Protein of unknown function (DUF3443). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 400 to 434 amino acids in
length. This protein has two conserved sequence motifs:
NPV and DNNG.
Length = 369
Score = 29.6 bits (67), Expect = 2.3
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 36 ISVASGPTTATNKPAAAVTCCVSSSQQ 62
I+V SG + N P +VT C + Q
Sbjct: 12 ITVDSGVSGVINIPTVSVTICAPGTSQ 38
>gnl|CDD|222015 pfam13264, DUF4055, Domain of unknown function (DUF4055). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria and viruses, and is
approximately 140 amino acids in length.
Length = 138
Score = 28.8 bits (65), Expect = 2.4
Identities = 8/44 (18%), Positives = 17/44 (38%)
Query: 298 LDATHEILERLEAHLRASGQFTVTANMRGNSAEEVAERILSQTS 341
+ A E ++ E + G + +A + R ++TS
Sbjct: 70 IAAGKEAMDDKENQMAQLGARLLEKTTGNKTATQARLRQAAETS 113
>gnl|CDD|176112 cd08420, PBP2_CysL_like, C-terminal substrate binding domain of
LysR-type transcriptional regulator CysL, which
activates the transcription of the cysJI operon encoding
sulfite reductase, contains the type 2 periplasmic
binding fold. CysL, also known as YwfK, is a regular of
sulfur metabolism in Bacillus subtilis. Sulfur is
required for the synthesis of proteins and essential
cofactors in all living organism. Sulfur can be
assimilated either from inorganic sources (sulfate and
thiosulfate), or from organic sources (sulfate esters,
sulfamates, and sulfonates). CysL activates the
transcription of the cysJI operon encoding sulfite
reductase, which reduces sulfite to sulfide. Both cysL
mutant and cysJI mutant are unable to grow using sulfate
or sulfite as the sulfur source. Like other LysR-type
regulators, CysL also negatively regulates its own
transcription. In Escherichia coli, three LysR-type
activators are involved in the regulation of sulfur
metabolism: CysB, Cbl and MetR. The 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 = 28.6 bits (65), Expect = 3.4
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 135 KDIVRKLLSGDLDLGIVG 152
++I ++L G++DLG+V
Sbjct: 39 EEIAERVLDGEIDLGLVE 56
>gnl|CDD|227698 COG5411, COG5411, Phosphatidylinositol 5-phosphate phosphatase
[Signal transduction mechanisms].
Length = 460
Score = 29.0 bits (65), Expect = 3.8
Identities = 22/98 (22%), Positives = 34/98 (34%), Gaps = 23/98 (23%)
Query: 18 PSLSPSGLSFFC----PLSSFHISVASGPT----TATNKPAAAVT--------CCVSSSQ 61
P L L F +S T +++NK A A+ C V+S
Sbjct: 115 PQLGGILLRVFSLATNLPVVKPVSGTVKKTGFGGSSSNKGAVAIRFNYERTSFCFVNS-- 172
Query: 62 QFESHVSVVNGNIDNRISERDEIRLGLP-SKGRMAADT 98
H++ NI+ RI + I + S+G D
Sbjct: 173 ----HLAAGVNNIEERIFDYRSIASNICFSRGLRIYDH 206
>gnl|CDD|177701 PLN00072, PLN00072, 3-isopropylmalate isomerase/dehydratase small
subunit; Provisional.
Length = 246
Score = 28.7 bits (64), Expect = 4.4
Identities = 15/61 (24%), Positives = 23/61 (37%)
Query: 15 RQCPSLSPSGLSFFCPLSSFHISVASGPTTATNKPAAAVTCCVSSSQQFESHVSVVNGNI 74
+ S +P F SS ++ T+ P + + +SS F VV NI
Sbjct: 21 KSSSSATPRPFLRFSSTSSIFPFKPLTTSSGTSSPTISDSAESTSSTTFHGLCFVVGDNI 80
Query: 75 D 75
D
Sbjct: 81 D 81
>gnl|CDD|176103 cd08411, PBP2_OxyR, The C-terminal substrate-binding domain of the
LysR-type transcriptional regulator OxyR, a member of
the type 2 periplasmic binding fold protein superfamily.
OxyR senses hydrogen peroxide and is activated through
the formation of an intramolecular disulfide bond. The
OxyR activation induces the transcription of genes
necessary for the bacterial defense against oxidative
stress. The OxyR of LysR-type transcriptional regulator
family is composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The C-terminal domain also
contains the redox-active cysteines that mediate the
redox-dependent conformational switch. Thus, the
interaction between the OxyR-tetramer and DNA is notably
different between the oxidized and reduced forms. 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 = 200
Score = 28.3 bits (64), Expect = 4.8
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 122 PQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGL 153
P+L L + + + ++ KL SG+LD ++ L
Sbjct: 28 PKL-RLYLREDQTERLLEKLRSGELDAALLAL 58
>gnl|CDD|182659 PRK10700, PRK10700, 23S rRNA pseudouridylate synthase B;
Provisional.
Length = 289
Score = 28.2 bits (63), Expect = 6.5
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 175 YGDCRLSLAIPKYGIFE----NINSLRELAQMPQWTAEK 209
YGD L +P+ G E N LREL ++P T+ K
Sbjct: 215 YGDIPLPKGLPRGGWTELDLAQTNYLRELVELPPETSSK 253
>gnl|CDD|232846 TIGR00153, TIGR00153, TIGR00153 family protein. An apparent
homolog with a suggested function is Pit accessory
protein from Sinorhizobium meliloti, which may be
involved in phosphate (Pi) transport [Hypothetical
proteins, Conserved].
Length = 216
Score = 27.8 bits (62), Expect = 6.8
Identities = 24/89 (26%), Positives = 32/89 (35%), Gaps = 20/89 (22%)
Query: 270 KEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLE--AHLRASGQFTVTANMRG- 326
+EI LE A L R+ L+ +LD EIL+ LE A L +F +R
Sbjct: 64 REIRLN--LEKGAFLPNDRRDLLELAELLD---EILDSLEHAAMLYELRKFEFPEELRDE 118
Query: 327 ------------NSAEEVAERILSQTSFS 343
V E I +T S
Sbjct: 119 FLLVLKITVDMIQHLHRVVEVIELETDLS 147
>gnl|CDD|224263 COG1344, FlgL, Flagellin and related hook-associated proteins [Cell
motility and secretion].
Length = 360
Score = 28.2 bits (63), Expect = 7.1
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 296 GVLDATHEILERLEAHLRASGQFTVTANMRGNSAEEVAE------RILSQTSFSG 344
G L +IL+R++ + T++ R +E+ + I + TSF+G
Sbjct: 78 GALSEISKILQRIKELAVQAANGTLSDADRAAIQKEIEQLLDELDNIANTTSFNG 132
>gnl|CDD|173848 cd01159, NcnH, Naphthocyclinone hydroxylase. Naphthocyclinone is
an aromatic polyketide and an antibiotic, which is
active against Gram-positive bacteria. Polyketides are
secondary metabolites, which have important biological
functions such as antitumor, immunosupressive or
antibiotic activities. NcnH is a hydroxylase involved in
the biosynthesis of naphthocyclinone and possibly other
polyketides.
Length = 370
Score = 28.1 bits (63), Expect = 7.2
Identities = 27/114 (23%), Positives = 38/114 (33%), Gaps = 18/114 (15%)
Query: 244 AAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHE 303
AA ++G A+ L R + A ++ L LDA
Sbjct: 226 AAVSLGAAEGALAEFLELAGKR------VRQYGAAVKMAEAPITQLRLAEAAAELDAARA 279
Query: 304 ILER----LEAHLRASGQFTV--TANMRGNSAE------EVAERILSQTSFSGL 345
LER L AH A G V A +R ++A E +R+ S L
Sbjct: 280 FLERATRDLWAHALAGGPIDVEERARIRRDAAYAAKLSAEAVDRLFHAAGGSAL 333
>gnl|CDD|182121 PRK09863, PRK09863, putative frv operon regulatory protein;
Provisional.
Length = 584
Score = 27.9 bits (62), Expect = 8.7
Identities = 19/102 (18%), Positives = 36/102 (35%), Gaps = 20/102 (19%)
Query: 114 PRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLII---VH 170
+ +A I QL I +K+L+ + + + + + LII +
Sbjct: 358 DQNSIATINQLI-----------IEQKVLNIRVIIVRSLSELEAIREEIEPLLIINNSHY 406
Query: 171 DALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212
L AI Y F+N+ + + Q+ A +R
Sbjct: 407 LVD------LQDAINFYITFKNVITAAGIEQLKHLLATAYIR 442
>gnl|CDD|237172 PRK12683, PRK12683, transcriptional regulator CysB-like protein;
Reviewed.
Length = 309
Score = 27.7 bits (62), Expect = 8.8
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 115 RQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIV--GLDTVSE 158
RQ+ P++ +L + P++I LL+G+ D+GI LD +
Sbjct: 113 RQFKEVFPKV-HLALRQGSPQEIAEMLLNGEADIGIATEALDREPD 157
>gnl|CDD|235969 PRK07213, PRK07213, chlorohydrolase; Provisional.
Length = 375
Score = 27.7 bits (62), Expect = 9.0
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 9/51 (17%)
Query: 228 NGLKHVVFSTA-DGALEAAPAMGIADAILDLVSSGTT----LRENNLKEIE 273
NGLKH ++ D L G+ + + D+ ++G RE +K I
Sbjct: 81 NGLKHKFLNSCSDKELVE----GMKEGLYDMYNNGIKAFCDFREGGIKGIN 127
>gnl|CDD|187595 cd05334, DHPR_SDR_c_like, dihydropteridine reductase (DHPR),
classical (c) SDRs. Dihydropteridine reductase is an
NAD-binding protein related to the SDRs. It converts
dihydrobiopterin into tetrahydrobiopterin, a cofactor
necessary in catecholamines synthesis. Dihydropteridine
reductase has the YXXXK of these tyrosine-dependent
oxidoreductases, but lacks the typical upstream Asn and
Ser catalytic residues. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 221
Score = 27.7 bits (62), Expect = 9.1
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 220 LGPKFMKDNGLKHVVFSTADGALEAAPAMG 249
L K + GL +V + A ALE P M
Sbjct: 110 LATKHLLSGGL--LVLTGAKAALEPTPGMI 137
>gnl|CDD|214333 CHL00013, rpoA, RNA polymerase alpha subunit.
Length = 327
Score = 27.6 bits (62), Expect = 9.4
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 103 KDCQL--SVKQVNPRQYVAQIPQLSNLEVWFQ 132
+D L SV+ V+P Q++A I + +LE+ +
Sbjct: 111 QDIILPPSVEIVDPTQHIATITEPIDLEIELK 142
>gnl|CDD|237080 PRK12370, PRK12370, invasion protein regulator; Provisional.
Length = 553
Score = 27.9 bits (62), Expect = 9.5
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 14 FRQCPSLSPSGLSFFCPLSSFHISVA 39
QC ++SP+ ++ +C L+ ++S+A
Sbjct: 284 LTQCVNMSPNSIAPYCALAECYLSMA 309
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 27.9 bits (63), Expect = 9.8
Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 198 ELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA 244
E+ ++ +T ++ L +A +L PK +K++GLK + D A++
Sbjct: 488 EVIRLSGYTEDEKLEIAKR--HLIPKQLKEHGLKKGELTITDEAIKD 532
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
0.317 0.133 0.378
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,516,356
Number of extensions: 1710394
Number of successful extensions: 1646
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1624
Number of HSP's successfully gapped: 38
Length of query: 349
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 251
Effective length of database: 6,590,910
Effective search space: 1654318410
Effective search space used: 1654318410
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.6 bits)