RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043481
(351 letters)
>gnl|CDD|233147 TIGR00840, b_cpa1, sodium/hydrogen exchanger 3. The Monovalent
Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36)The
CPA1 family is a large family of proteins derived from
Gram-positive and Gram-negative bacteria, blue green
bacteria, yeast, plants and animals.Transporters from
eukaryotes have been functionally characterized, and all
of these catalyze Na+:H+ exchange. Their primary
physiological functions may be in(1) cytoplasmic pH
regulation, extruding the H+ generated during
metabolism, and (2) salt tolerance (in plants), due to
Na+ uptake into vacuoles.This model is specific for the
eukaryotic members members of this family [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 559
Score = 166 bits (423), Expect = 5e-47
Identities = 93/308 (30%), Positives = 156/308 (50%), Gaps = 13/308 (4%)
Query: 22 TSTIIALSVFFTLLCACIIIGHLIEE-NRWANESITALLLGLCAGGVVLLASKDRSSHLL 80
+ ++ L I HL + R ES+ ++ GL GG++ +
Sbjct: 5 VQSPYEFILWILLASLAKIGFHLTHKVIRAVPESVLLIVYGLLVGGIIKASPHIDP---P 61
Query: 81 VFNEDLFFLYLLPPIIFNAGFQVKKKQFFKNFTTMLLFGICGTVISFYLISVGAFSIFKK 140
+ FFLYLLPPI+ +AG+ + ++ FF+N ++L+F + GT+I+ ++I + + I
Sbjct: 62 TLDSSYFFLYLLPPIVLDAGYFMPQRNFFENLGSILIFAVVGTLINAFVIGLSLYGICLI 121
Query: 141 MGMTSLRIQ--DFLAIGAILSATDSVCTLQVLSQ-DETPFLYSIVFGEGVVNDATSIVLF 197
G S+ I D L G+++SA D V L V + LY I+FGE ++NDA ++VL+
Sbjct: 122 GGFGSIDIGLLDNLLFGSLISAVDPVAVLAVFEEYHVNEKLYIIIFGESLLNDAVTVVLY 181
Query: 198 NAIQSFDFNNIDGTVALNLLGTFLYLY---FTSTALGIVLGLLSAYIIKTLYFLRHSTDR 254
N F + +++ + +G+V G L A+I + F H
Sbjct: 182 NTFIKFHKTADEPVTIVDVFEGCASFFVVTCGGLLVGVVFGFLVAFITR---FTHHIRQI 238
Query: 255 EGAPMMLMAYLSCILAELLNLSGILTIFFCGIIMSHYTWHNVTESSRITTKHAFATISFI 314
E + L++YLS + AE L+LSGIL + FCGI M Y N++ S+ T K+ +S +
Sbjct: 239 EPLFVFLISYLSYLFAETLHLSGILALIFCGITMKKYVEANMSRRSQTTIKYFMKMLSSL 298
Query: 315 AETFIFLY 322
+ET IF++
Sbjct: 299 SETLIFIF 306
>gnl|CDD|223104 COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic
ion transport and metabolism].
Length = 429
Score = 98.5 bits (246), Expect = 6e-23
Identities = 64/275 (23%), Positives = 120/275 (43%), Gaps = 15/275 (5%)
Query: 53 ESITALLLGLCAGGVVLLASKDRSSHLLVFNEDLFFLYLLPPIIFNAGFQVKKKQFFKNF 112
E LLLGL G L S L + +LF + L ++F G ++ ++ + +
Sbjct: 32 EIPLLLLLGLLGGPPGLNLI----SPDLELDPELFLVLFLAILLFAGGLELDLRELRRVW 87
Query: 113 TTMLLFGICGTVISFYLISVGAFSIFKKMGMTSLRIQDFLAIGAILSATDSVCTLQVLSQ 172
++L+ + +I+ I + A + + + +GAILS TD V + +
Sbjct: 88 RSILVLALPLVLITALGIGLLAHWLLPGIPLA-----AAFLLGAILSPTDPVAVSPIFKR 142
Query: 173 DETPF-LYSIVFGEGVVNDATSIVLFNAIQSFDFNNIDGTVALNLLGTFLYLYFTSTALG 231
P + +I+ GE ++ND IVLF + ++ L FL LG
Sbjct: 143 VRVPKRIRTILEGESLLNDGVGIVLFKVALAALLGTGAFSLG-WALLLFLIEALGGILLG 201
Query: 232 IVLGLLSAYIIKTLYFLRHSTDR--EGAPMMLMAYLSCILAELLNLSGILTIFFCGIIMS 289
++LG L +++ L R T E +L+A+ + +LAE L +SGIL + G+++
Sbjct: 202 LLLGYLLGRLLRRLDR-RGWTSPLLETLLTLLLAFAAYLLAEALGVSGILAVVVAGLVLG 260
Query: 290 HYT-WHNVTESSRITTKHAFATISFIAETFIFLYV 323
+ S+R+ + + F+ +F+ +
Sbjct: 261 EAVRINLSPASARLRLSSFWEVLDFLLNGLLFVLL 295
>gnl|CDD|216235 pfam00999, Na_H_Exchanger, Sodium/hydrogen exchanger family. Na/H
antiporters are key transporters in maintaining the pH
of actively metabolising cells. The molecular mechanisms
of antiport are unclear. These antiporters contain 10-12
transmembrane regions (M) at the amino-terminus and a
large cytoplasmic region at the carboxyl terminus. The
transmembrane regions M3-M12 share identity with other
members of the family. The M6 and M7 regions are highly
conserved. Thus, this is thought to be the region that
is involved in the transport of sodium and hydrogen
ions. The cytoplasmic region has little similarity
throughout the family.
Length = 370
Score = 86.9 bits (216), Expect = 4e-19
Identities = 64/241 (26%), Positives = 109/241 (45%), Gaps = 17/241 (7%)
Query: 85 DLFFLYLLPPIIFNAGFQVKKKQFFKNFTTMLLFGICGTVISFYLISVGAFSIFKKMGMT 144
++ LP ++F AG ++ ++ KN ++LL + G +I F L + A + +
Sbjct: 48 EVLAELGLPLLLFLAGLELDLRELRKNGKSILLLALLGVLIPFLLGLLLALLGGLGIPLL 107
Query: 145 SLRIQDFLAIGAILSATDSVCTLQVL--SQDETPFLYSIVFGEGVVNDATSIVLFNAIQS 202
+ L GA LSAT V L +L L +++ GE V+NDA ++VL + +
Sbjct: 108 -----EALLFGAALSATSPVVVLAILKERGRLNTRLGTLILGESVLNDAVAVVLLAVLLA 162
Query: 203 FDFNNIDGTVALNLLGTFLYLYFTSTALGIVLGLLSAYIIKTLYFLRHSTDREGAPMMLM 262
+ LL FL + LG+V G L I + F + E ++ +
Sbjct: 163 L-AGVGGLSDLGLLLLIFLVVALGGLLLGLVFGWLLRLITR---FTSGDRELEVLLVLAL 218
Query: 263 AYLSCILAELLNLSGILTIFFCGIIMSHYTWHNVTESSRITTKHAFATISFIAETFIFLY 322
A L+ +LAELL LSGIL F G+++S+Y ++ ++ K + F+
Sbjct: 219 ALLAALLAELLGLSGILGAFLAGLVLSNY-----AFANELSEK-LEPFGYGLFLPLFFVS 272
Query: 323 V 323
V
Sbjct: 273 V 273
>gnl|CDD|129911 TIGR00831, a_cpa1, Na+/H+ antiporter, bacterial form. The
Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC
2.A.36) The CPA1 family is a large family of proteins
derived from Gram-positive and Gram-negative bacteria,
blue green bacteria, yeast, plants and animals.
Transporters from eukaryotes have been functionally
characterized, and all of these catalyze Na+:H+
exchange. Their primary physiological functions may be
in (1) cytoplasmic pH regulation, extruding the H+
generated during metabolism, and (2) salt tolerance (in
plants), due to Na+ uptake into vacuoles. This model is
specific for the bacterial members of this family
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 525
Score = 80.7 bits (199), Expect = 9e-17
Identities = 61/250 (24%), Positives = 107/250 (42%), Gaps = 24/250 (9%)
Query: 82 FNEDLFFLYLLPPIIFNAGFQVKKKQFFKNFTTMLLFGICGTVISFYLISVGAFSIFKKM 141
+ ++ LPP++F A ++ +NF + L V++ ++ FS+ +
Sbjct: 46 LDREIVLFLFLPPLLFEAAMNTDLRELRENFRPIALIAFLLVVVTTVVVG---FSLNWIL 102
Query: 142 GMTSLRIQDFLAIGAILSATDSVCTLQVLSQDETPFLYSIVF-GEGVVNDATSIVLFNAI 200
G+ L +GA+LS TD+V L P SI+ GE ++ND ++V+F AI
Sbjct: 103 GIPLALA---LILGAVLSPTDAVAVLGTFKSIRAPKKLSILLEGESLLNDGAALVVF-AI 158
Query: 201 QSFDFNNIDGTVALNLLGTFLYLYFTSTALGIVLGLLSAYIIKTLYFLRHSTDR---EGA 257
LN F + A G+ +G L+ + LR D E A
Sbjct: 159 AVAVALGKGVFDPLNAALDFAVVCVGGIAAGLAVGYLAYRL------LRAKIDDPLVEIA 212
Query: 258 PMMLMAYLSCILAELLNLSGILTIFFCGIIMSHYTWHNVTESSRITTK---HAF-ATISF 313
+L + +LAE + SG++ + G+I+++Y S TT+ F + I F
Sbjct: 213 LTILAPFAGFLLAERFHFSGVIAVVAAGLILTNY---GRDFSMSPTTRLIALDFWSVIVF 269
Query: 314 IAETFIFLYV 323
+ IF+ +
Sbjct: 270 LVNGIIFILI 279
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 41.6 bits (98), Expect = 4e-04
Identities = 51/233 (21%), Positives = 89/233 (38%), Gaps = 26/233 (11%)
Query: 95 IIFNAGFQVKKKQFFKNFTTMLLFGICGTVISFYLISVGAFSIFKKMGMTSLRIQDFLAI 154
I+F+ GF + F L G +I+ L V A + + L I
Sbjct: 71 ILFDGGFGTQLSSFRVAAGPALSLATLGVLITSGLTGVAAAYLLNLDWLEGL------LI 124
Query: 155 GAILSATDSVCTLQVLS----QDETPFLYSIVFGEGVVNDATSIVLFNAIQSFDFNNIDG 210
GAI+ +TD+ +L + I E ND ++ L + +
Sbjct: 125 GAIVGSTDAAAVFSLLGGKNLNERVASTLEI---ESGSNDPMAVFL-----TITLIELIA 176
Query: 211 TVALNLLGTFLYLYFTSTALGIVLGLLSAYIIKTLYFLRHSTDREGAPMMLMAY--LSCI 268
NL FL + LG++LGL ++ L R + D P++ +A L
Sbjct: 177 GGETNLSWGFLLGFLQQFGLGLLLGLGGGKLLLQL-INRINLDSGLYPILALAGGLLIFS 235
Query: 269 LAELLNLSGILTIFFCGIIMSHYTWHNVTESSRITTKHAFATISFIAETFIFL 321
L + SGIL ++ G+++ N +R F ++++A+ +FL
Sbjct: 236 LTGAIGGSGILAVYLAGLLLG-----NRPIRARHGILRFFDGLAWLAQILMFL 283
>gnl|CDD|233195 TIGR00932, 2a37, transporter, monovalent cation:proton antiporter-2
(CPA2) family. [Transport and binding proteins, Cations
and iron carrying compounds].
Length = 273
Score = 35.3 bits (82), Expect = 0.035
Identities = 42/199 (21%), Positives = 78/199 (39%), Gaps = 19/199 (9%)
Query: 97 FNAGFQVKKKQFFKNFTTMLLFGICGTVISFYLISVGAFSIFKKMGMTSLRIQDFLAIGA 156
F G ++ ++ +K G+ ++ L+ + + ++ IG
Sbjct: 56 FLIGLELDLERLWKLRKAAFGVGVLQVLVPGVLLGLLLGHLLGLALGAAV------VIGI 109
Query: 157 ILSATDSVCTLQVL---SQDETPFLYSIVFGEGVVNDATSIVLFNAIQSFDFNNIDGTVA 213
IL+ + + +QVL +TPF V G + D + L + + VA
Sbjct: 110 ILALSSTAVVVQVLKERGLLKTPF-GQTVLGILLFQDIAVVPLLALLPLLATSASTEHVA 168
Query: 214 LNLLGTFLYLYFTSTALGIVLGLLSAYIIKTLYFLRHSTD-REGAPMM--LMAYLSCILA 270
L LL ++L F +L LL ++++ + L E L+ + S A
Sbjct: 169 LALLLLKVFLAFL------LLVLLGRWLLRPVLRLTAELRPSELFTAGSLLLMFGSAYFA 222
Query: 271 ELLNLSGILTIFFCGIIMS 289
+LL LS L F G+++S
Sbjct: 223 DLLGLSMALGAFLAGVVLS 241
>gnl|CDD|223551 COG0475, KefB, Kef-type K+ transport systems, membrane components
[Inorganic ion transport and metabolism].
Length = 397
Score = 33.0 bits (76), Expect = 0.25
Identities = 57/272 (20%), Positives = 102/272 (37%), Gaps = 32/272 (11%)
Query: 28 LSVFFTLLCACIIIGHLIEENRWANESITALLLGLCAGGVVLLASKDRSSHLLVFNEDLF 87
L LL +I+G L + R + LL G L SS ++ +L
Sbjct: 8 LLQLLILLLVAVILGPLFK--RLGLPPVLGYLLAGIILGPWGLLLIIESSEIIELLAELG 65
Query: 88 FLYLLPPIIFNAGFQVKKKQFFKNF----TTMLLFGICGTVISFYLISVGAFSIFKKMGM 143
++LL F G + ++ K + G+ + L+ +G
Sbjct: 66 VVFLL----FLIGLEFDLERLKKVGRSVGLGVAQVGLTAPFLLGLLLLLGILG------- 114
Query: 144 TSLRIQDFLAIGAILSATDSVCTLQVLS---QDETPFLYSIVFGEGVVNDATSIVLFNAI 200
L + L +GA L+ + + L++L +T ++ G V +D +I+L +
Sbjct: 115 --LSLIAALFLGAALALSSTAIVLKILMELGLLKTREG-QLILGALVFDDIAAILLLAIV 171
Query: 201 QSFDFNNIDGTVALNLLGTFLYLYFTSTALGIVLGLLSAYIIKTL-YFLRHSTDREGAPM 259
+ +G L L A +L LL Y++ L + + E +
Sbjct: 172 PAL------AGGGSGSVGFILGLLLAILAFLALLLLLGRYLLPPLFRRVAKTESSELFIL 225
Query: 260 MLMAY--LSCILAELLNLSGILTIFFCGIIMS 289
++ + LAELL LS IL F G+++S
Sbjct: 226 FVLLLVLGAAYLAELLGLSMILGAFLAGLLLS 257
>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 = 29.9 bits (68), Expect = 1.3
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 137 IFKKMGMT---SLRIQDFLAIGAILSATDSVCTL 167
++ G+ +LR+ FLA+ I++ TD V T+
Sbjct: 115 ALREAGIRRRIALRVPHFLALPLIVAQTDLVATV 148
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
processing and modification].
Length = 1175
Score = 29.9 bits (67), Expect = 2.2
Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 1/83 (1%)
Query: 242 IKTLYFLRHSTDREGAPMMLMAYLSCILAELLNLSGILTIFFCGIIMSHYTWHNVTESSR 301
L F+R D + L +LA+L LS + + II ++ + +S+
Sbjct: 676 PGVLAFIRDPGDPNIKILH-DVLLYPMLAQLFRLSWSVIHYAMFIIRGEGSFPFMLKSAG 734
Query: 302 ITTKHAFATISFIAETFIFLYVF 324
H + T L
Sbjct: 735 ELCPHGIVNVYINFNTVYPLLGS 757
>gnl|CDD|217621 pfam03573, OprD, outer membrane porin, OprD family. This family
includes outer membrane proteins related to OprD. OprD
has been described as a serine type peptidase. However
the proposed catalytic residues are not conserved
suggesting that many of these proteins are not
peptidases.
Length = 391
Score = 29.5 bits (67), Expect = 2.9
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 8/34 (23%)
Query: 174 ETPFLYSIVFGEGVVNDATSIVLFNAIQSFDFNN 207
+T F Y VN SI L N++Q DFN
Sbjct: 270 DTGFDY--------VNGTDSIYLANSVQYSDFNG 295
>gnl|CDD|220299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 29.1 bits (66), Expect = 3.7
Identities = 28/101 (27%), Positives = 38/101 (37%), Gaps = 3/101 (2%)
Query: 30 VFFTLLCACIIIGHLIEENRWANESITALLLGLCAGGVVLLASKDRSSHLLVFNEDLFFL 89
F LL A + HL + + I+ LLL L V LL S L N L L
Sbjct: 346 SFLILLLAAEALLHLKQLKKL-KILISILLLVLLFILVFLLNLSKHYSFLTQTNLLLTLL 404
Query: 90 YLLPPIIFNAGFQVKKKQFFKNFTTMLLFGICGTVISFYLI 130
+LL ++ F KKQ K +LL + +
Sbjct: 405 FLLLYLLLLLLFL--KKQIRKKLVIILLLLVVVLELGLNAY 443
>gnl|CDD|187648 cd08944, SDR_c12, classical (c) SDR, subgroup 12. These are
classical SDRs, with the canonical active site tetrad
and glycine-rich NAD-binding motif. 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 catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). 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) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 246
Score = 28.6 bits (64), Expect = 4.3
Identities = 16/35 (45%), Positives = 22/35 (62%)
Query: 187 VVNDATSIVLFNAIQSFDFNNIDGTVALNLLGTFL 221
+VN+A ++ L AI D D T+A+NL GTFL
Sbjct: 81 LVNNAGAMHLTPAIIDTDLAVWDQTMAINLRGTFL 115
>gnl|CDD|171522 PRK12468, flhB, flagellar biosynthesis protein FlhB; Reviewed.
Length = 386
Score = 28.8 bits (64), Expect = 4.9
Identities = 30/109 (27%), Positives = 44/109 (40%), Gaps = 9/109 (8%)
Query: 214 LNLLGTFLYLYFTSTALGIVLG--LLSAYIIKTLYFLRHSTDREGAPMMLMAYLSCILAE 271
L +L F L + A+ ++LG L S IK + L+ + G M + S LAE
Sbjct: 91 LAMLPIFAGLVIVALAVPMLLGGVLFSGESIK--FDLKRMSPVAGLKRM---FSSQALAE 145
Query: 272 LLNLSGILTIFFCGIIMSHYTWHNVTESSRITTKHAFATISFIAETFIF 320
LL IL G + + WHN + R+ A + IF
Sbjct: 146 LLK--AILKATLVGWVTGLFLWHNWPDMMRLIAAPPVAALGDALHLIIF 192
>gnl|CDD|206215 pfam14045, YIEGIA, YIEGIA protein. This family includes the B.
subtilis YphB protein, which is functionally
uncharacterized. Its expression is regulated by the
sporulation transcription factor sigma-F, however it is
not essential for sporulation or germination. This is
not a homologue of E. coli YphB, which belongs to
pfam01263. This family of proteins is found in bacteria.
Proteins in this family are typically between 276 and
300 amino acids in length and contain a conserved YIEGIA
motif.
Length = 286
Score = 28.3 bits (64), Expect = 5.1
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 216 LLGTFLYLYFTSTALGIVLGLLSAYIIKTL 245
LL + Y+ F S +GI+ GL+ I+K L
Sbjct: 118 LLTSLAYILFQSIIIGIIAGLILFLILKRL 147
>gnl|CDD|176109 cd08417, PBP2_Nitroaromatics_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators that
involved in the catabolism of nitroaromatic/naphthalene
compounds and that of related regulators; contains the
type 2 periplasmic binding fold. This CD includes the
C-terminal substrate binding domain of LysR-type
transcriptional regulators involved in the catabolism of
dinitrotoluene and similar compounds, such as DntR,
NahR, and LinR. 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. Also included are
related LysR-type regulators clustered together in
phylogenetic trees, including NodD, ToxR, LeuO, SyrM,
TdcA, and PnbR. This substrate-binding domain shows
significant homology to 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 = 27.9 bits (63), Expect = 5.7
Identities = 9/34 (26%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 137 IFKKMGMT---SLRIQDFLAIGAILSATDSVCTL 167
++G++ +L + FLA A+++ TD + T+
Sbjct: 115 ALAELGLSRRVALTVPHFLAAPALVAGTDLIATV 148
>gnl|CDD|171821 PRK12937, PRK12937, short chain dehydrogenase; Provisional.
Length = 245
Score = 28.2 bits (63), Expect = 5.9
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 187 VVNDATSIVLFNAIQSFDFNNIDGTVALNLLGTFLYL 223
+VN+A ++ I FD + D T+A NL G F+ L
Sbjct: 87 LVNNA-GVMPLGTIADFDLEDFDRTIATNLRGAFVVL 122
>gnl|CDD|235410 PRK05326, PRK05326, potassium/proton antiporter; Reviewed.
Length = 562
Score = 27.9 bits (63), Expect = 9.9
Identities = 20/103 (19%), Positives = 40/103 (38%), Gaps = 9/103 (8%)
Query: 189 NDATSIVLFNAIQSFDFNNIDGTVALNLLGTFLYLYFTSTALGIVLGLLSAYIIKTLYFL 248
ND ++ L + + ++ L FL + +G++ G L ++ +
Sbjct: 161 NDPMAVFLTITLIELITGG-ETGLSWGFLLLFLQQFGLGALIGLLGGWLLVQLLNRIAL- 218
Query: 249 RHSTDREG--APMML-MAYLSCILAELLNLSGILTIFFCGIIM 288
EG ++L A L L L SG L ++ G+++
Sbjct: 219 ----PAEGLYPILVLAGALLIFALTAALGGSGFLAVYLAGLVL 257
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
0.330 0.141 0.413
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,747,576
Number of extensions: 1775018
Number of successful extensions: 3011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2939
Number of HSP's successfully gapped: 196
Length of query: 351
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 253
Effective length of database: 6,590,910
Effective search space: 1667500230
Effective search space used: 1667500230
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 59 (26.5 bits)