RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12229
(444 letters)
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 139 bits (353), Expect = 2e-38
Identities = 63/197 (31%), Positives = 90/197 (45%), Gaps = 41/197 (20%)
Query: 187 FSGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQYKIQ 246
E P++LSGR++ WW F I+++SYTANLAAFLTV R+ +PI+SL+DL+KQ KI
Sbjct: 54 QGHRELPRSLSGRILVGVWWFFALILLSSYTANLAAFLTVERMQSPIQSLEDLAKQNKIG 113
Query: 247 YAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQ 306
Y L G + +F+ + Y +MW+
Sbjct: 114 YGTLRGGSTFEFFKESKNPT----------------------------------YRRMWE 139
Query: 307 AMKEAK---LPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTN-CDLQMVGDEFSR 362
M K S EE VQRVR + +L ++ + Y V + C L VG+ F
Sbjct: 140 YMISFKGEVNVESYEEGVQRVRKGNG---LYAFLMESAYLEYEVARDPCKLTTVGEVFGT 196
Query: 363 KPYAIAVQQDRDARELF 379
K Y IA + R+
Sbjct: 197 KGYGIAFPKGSPLRDKL 213
>gnl|CDD|204533 pfam10613, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called
the S1 domain, is the luminal domain just upstream of
the first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan,
pfam00060.
Length = 65
Score = 90.4 bits (225), Expect = 1e-22
Identities = 31/65 (47%), Positives = 48/65 (73%), Gaps = 2/65 (3%)
Query: 16 PFVMREESEG--GGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMI 73
P+VM +E+ G +++GYCIDL++E+ K++GF YEI++ PD +G+ D+ G+WNGMI
Sbjct: 1 PYVMLKENGENLTGNERFEGYCIDLLDELAKILGFNYEIYLVPDGKYGSEDKTGEWNGMI 60
Query: 74 KELIE 78
ELI
Sbjct: 61 GELIR 65
>gnl|CDD|214911 smart00918, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called
the S1 domain, is the luminal domain just upstream of
the first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan.
Length = 62
Score = 89.6 bits (223), Expect = 2e-22
Identities = 31/62 (50%), Positives = 44/62 (70%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
P+VM +ES GG +++GYCIDL++E+ K +GF YEI + PD +G NG WNGM+ E
Sbjct: 1 PYVMLKESPDGGNDRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGARLPNGSWNGMVGE 60
Query: 76 LI 77
L+
Sbjct: 61 LV 62
>gnl|CDD|197504 smart00079, PBPe, Eukaryotic homologues of bacterial periplasmic
substrate binding proteins. Prokaryotic homologues are
represented by a separate alignment: PBPb.
Length = 133
Score = 84.3 bits (209), Expect = 1e-19
Identities = 42/142 (29%), Positives = 64/142 (45%), Gaps = 40/142 (28%)
Query: 232 PIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLA 291
PI S++DL+KQ KI+Y +GS+ + +F+R + E
Sbjct: 1 PITSVEDLAKQTKIEYGTQDGSSTLAFFKRSGNPE------------------------- 35
Query: 292 VWDYPVSDKYTKMWQAMKEAK-LPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTN 350
Y++MW MK + S E VQRVR S + ++ ++ + Y + N
Sbjct: 36 ---------YSRMWPYMKSPEVFVKSYAEGVQRVRVSN-----YAFIMESPYLDYELSRN 81
Query: 351 CDLQMVGDEFSRKPYAIAVQQD 372
CDL VG+EF RK Y IA +
Sbjct: 82 CDLMTVGEEFGRKGYGIAFPKG 103
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 66.9 bits (164), Expect = 1e-12
Identities = 27/101 (26%), Positives = 47/101 (46%), Gaps = 18/101 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF +E+ K G+ +DL + I K +G + E W+G+I
Sbjct: 11 PFSYVDENG-----KLVGFDVDLAKAIAKRLGVKVEF------------VPVSWDGLIPA 53
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L + DI + +++ ER+ VDF+ PYY G ++++K
Sbjct: 54 LKSGKVDIIIAGMTITPERKKQVDFSDPYYY-SGQVLVVRK 93
>gnl|CDD|238078 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins (PBPs)
to transport a wide variety of substrates, such as,
amino acids, peptides, sugars, vitamins and inorganic
ions. PBPs have two cell-membrane translocation
functions: bind substrate, and interact with the
membrane bound complex. A diverse group of periplasmic
transport receptors for lysine/arginine/ornithine (LAO),
glutamine, histidine, sulfate, phosphate, molybdate, and
methanol are included in the PBPb CD.
Length = 218
Score = 60.8 bits (148), Expect = 1e-10
Identities = 29/103 (28%), Positives = 47/103 (45%), Gaps = 18/103 (17%)
Query: 14 QEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMI 73
PF R+ + + G+ +DL + I K +G + + FV W+G+I
Sbjct: 9 YPPFSFRDANG-----ELTGFDVDLAKAIAKELGVKVK-FV-----------EVDWDGLI 51
Query: 74 KELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L + D+ +++ ER VDF+ PYY G IL+KK
Sbjct: 52 TALKSGKVDLIAAGMTITPERAKQVDFSDPYY-KSGQVILVKK 93
>gnl|CDD|107378 cd06383, PBP1_iGluR_AMPA_Like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of uncharacterized AMPA-like receptors.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of uncharacterized AMPA-like
receptors. While this N-terminal domain belongs to the
periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. AMPA receptors consist of
four types of subunits (GluR1, GluR2, GluR3, and GluR4)
which combine to form a tetramer and play an important
roles in mediating the rapid excitatory synaptic
current.
Length = 368
Score = 60.2 bits (146), Expect = 6e-10
Identities = 25/67 (37%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 138 ILAAYCNLDGEQMKYLIQVNPPGDILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLS 197
A+Y + YLIQ+ PP D + E IR I+ NIT+A IL+DD F K S
Sbjct: 95 FSASYGQEGDLEQPYLIQLMPPADDIVEAIRDIVSYYNITNAAILYDDDF--VMDHKYKS 152
Query: 198 GRLVAAT 204
T
Sbjct: 153 LLQNWPT 159
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 53.5 bits (129), Expect = 3e-08
Identities = 26/108 (24%), Positives = 45/108 (41%), Gaps = 18/108 (16%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF +E + G+ +DL + I K +G + E ++ ++
Sbjct: 12 PFSFADEDG-----ELTGFDVDLAKAIAKELGLKVEFVEV------------SFDSLLTA 54
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
L + D+ +++ ER VDF+ PYY G IL++K SL
Sbjct: 55 LKSGKIDVVAAGMTITPERAKQVDFSDPYYR-SGQVILVRKDSPIKSL 101
>gnl|CDD|223904 COG0834, HisJ, ABC-type amino acid transport/signal transduction
systems, periplasmic component/domain [Amino acid
transport and metabolism / Signal transduction
mechanisms].
Length = 275
Score = 53.1 bits (127), Expect = 8e-08
Identities = 29/103 (28%), Positives = 48/103 (46%), Gaps = 15/103 (14%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF + G K G+ +DL + I K +G + ++ P W+G+I
Sbjct: 47 PFEFLDAKGG----KLVGFDVDLAKAIAKRLGGDKKVEFVPVA----------WDGLIPA 92
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPK 118
L + DI + +++ ER+ VDF+ PYY G +L+KK
Sbjct: 93 LKAGKVDIIIAGMTITPERKKKVDFSDPYYY-SGQVLLVKKDS 134
>gnl|CDD|236540 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 49.7 bits (119), Expect = 8e-07
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 12/79 (15%)
Query: 28 GVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGS 87
G KY G+ IDL I K + +Y + P MD ++G+I L K D+AL
Sbjct: 43 GDKYVGFDIDLWAAIAKELKLDYTL--KP------MD----FSGIIPALQTKNVDLALAG 90
Query: 88 LSVMAERENVVDFTVPYYD 106
+++ ER+ +DF+ YY
Sbjct: 91 ITITDERKKAIDFSDGYYK 109
>gnl|CDD|238458 cd00916, Npc2_like, Niemann-Pick type C2 (Npc2) is a lysosomal
protein in which a mutation in the gene causes a rare
form of Niemann-Pick type C disease, an autosomal
recessive lipid storage disorder characterized by
accumulation of low-density lipoprotein-derived
cholesterol in lysosomes. Although Npc2 is known to bind
cholesterol, the function of this protein is unknown.
These proteins belong to the ML domain family. .
Length = 123
Score = 47.3 bits (113), Expect = 9e-07
Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 8/67 (11%)
Query: 372 DRDARELFCNVHANILSIPFPFIGVDGTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFK 431
+ D+ L VHA +L +P PF C ++ SCPL Y +
Sbjct: 41 NFDSTSLKTEVHAILLGVPVPFPLP-NPDACKNL-------GTSCPLSAGEDVTYTLSLP 92
Query: 432 ILDRYPK 438
+L YP
Sbjct: 93 VLAPYPG 99
>gnl|CDD|216934 pfam02221, E1_DerP2_DerF2, ML domain. ML domain - MD-2-related
lipid recognition domain. This family consists of
proteins from plants, animals and fungi, including dust
mite allergen Der P 2. It has been implicate in lipid
recognition, particularly in the recognition of pathogen
related products. A mutation in Npc2 causes a rare form
of Niemann-Pick type C2 disease.
Length = 132
Score = 42.4 bits (100), Expect = 6e-05
Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 8/69 (11%)
Query: 372 DRDARELFCNVHANILSIPFPFIGVDG--TSVCSSIFDTDGKTKVSCPLKKDHVYRYINT 429
++D +L V A +L + PFI + G C G +SCPLKK Y +
Sbjct: 44 NQDITKLTAVVVATLLGVKIPFITLPGETEDAC------KGLVGLSCPLKKGETVTYTLS 97
Query: 430 FKILDRYPK 438
I YP
Sbjct: 98 VPIPKEYPP 106
>gnl|CDD|214796 smart00737, ML, Domain involved in innate immunity and lipid
metabolism. ML (MD-2-related lipid-recognition) is a
novel domain identified in MD-1, MD-2, GM2A, Npc2 and
multiple proteins of unknown function in plants, animals
and fungi. These single-domain proteins were predicted
to form a beta-rich fold containing multiple strands,
and to mediate diverse biological functions through
interacting with specific lipids.
Length = 119
Score = 39.7 bits (93), Expect = 4e-04
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 8/67 (11%)
Query: 372 DRDARELFCNVHANILSIPFPFIGVDGTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFK 431
+ D +L VH I I P G +C T CP++K Y N+
Sbjct: 37 NEDISKLKVVVHVKIGGIEVPIPGET-YDLCKL-------TGSKCPIEKGETVNYTNSLT 88
Query: 432 ILDRYPK 438
+ +P
Sbjct: 89 VPGIFPP 95
>gnl|CDD|233269 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein. [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 250
Score = 40.8 bits (96), Expect = 8e-04
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 13/85 (15%)
Query: 22 ESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRA 81
ES+ G K G+ +DL + + K + + + FV + ++G+I L K+
Sbjct: 38 ESKDANG-KLVGFDVDLAKALCKRMKAKCK-FVEQN-----------FDGLIPSLKAKKV 84
Query: 82 DIALGSLSVMAERENVVDFTVPYYD 106
D + ++S+ +R+ +DF+ PYY
Sbjct: 85 DAIMATMSITPKRQKQIDFSDPYYA 109
>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
Length = 266
Score = 38.5 bits (90), Expect = 0.004
Identities = 29/87 (33%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 44 KLVGFEYEIFVAPDNSFGNMDE--NGQWNGMIKELIEKRADIALGSLSVMAERENVVDFT 101
KL GFE E A G +W+GM+ L KR D+ + +++ ER+ DF+
Sbjct: 62 KLTGFEVEFAEALAKHLGVKASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFS 121
Query: 102 VPYYDLVGITILMKKP-----KTPTSL 123
P Y + GI L+KK KT L
Sbjct: 122 TP-YTVSGIQALVKKGNEGTIKTAADL 147
>gnl|CDD|211985 TIGR04262, orph_peri_GRRM, extracellular substrate-binding orphan
protein, GRRM family. This subfamily belongs to
bacterial extracellular solute-binding protein family 3
(pfam00497). In that family, most members are ABC
transporter periplasmic substrate-binding proteins.
However, members of the present subfamily are orphans in
the sense of being adjacent to neither ABC transporter
ATP-binding proteins or permease subunits. Instead, most
members are encoded next to the two signature proteins
of the proposed Glycine-Rich Repeat Modification (GRRM)
system, a radical SAM/SPASM protein GrrM (TIGR04261) and
the Gly-rich repeat protein itself GrrA (TIGR04260).
Length = 257
Score = 36.6 bits (85), Expect = 0.016
Identities = 29/100 (29%), Positives = 44/100 (44%), Gaps = 17/100 (17%)
Query: 30 KYKGYCIDLIEEIR----KLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIAL 85
Y G D++E IR +G I NS + +L +ADIA
Sbjct: 21 GYDGLSFDVLELIRDQLQAELGKPITIQFVVVNSV---------QEGLPKLRSGKADIAC 71
Query: 86 GSLSVMAERENVVDFTVPYYDLVGITILMKKPK--TPTSL 123
G ++ ER+ VD+++P + + GI +L K TP SL
Sbjct: 72 G-VAFTWERQMFVDYSLP-FAVSGIRLLAPKGNDGTPESL 109
>gnl|CDD|184969 PRK15007, PRK15007, putative ABC transporter arginine-biding
protein; Provisional.
Length = 243
Score = 35.0 bits (80), Expect = 0.047
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 66 NGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYD 106
N ++ +I L +R + + + + ERE V FT PYYD
Sbjct: 66 NQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYD 106
>gnl|CDD|153103 cd01044, Ferritin_CCC1_N, Ferritin-CCC1, N-terminal ferritin-like
diiron-binding domain. Ferritin-like N-terminal domain
present in an uncharacterized family of proteins found
in bacteria and archaea. These proteins also have a
C-terminal CCC1-like transmembrane domain and are
thought to be involved in iron and/or manganese
transport. This domain has the conserved residues of a
diiron center found in other ferritin-like proteins.
Length = 125
Score = 30.7 bits (70), Expect = 0.56
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 259 FQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDY 295
++A+ E R E WK L R KL ++ Y
Sbjct: 33 LLKLAEDERRHAEFWKKF-LGKRGVPPPRPKLKIFFY 68
>gnl|CDD|107346 cd06351, PBP1_iGluR_N_LIVBP_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). While this
N-terminal domain belongs to the periplasmic-binding
fold type I superfamily, the glutamate-binding domain of
the iGluR is structurally homologous to the
periplasmic-binding fold type II. The LIVBP-like domain
of iGluRs is thought to play a role in the initial
assembly of iGluR subunits, but it is not well
understood how this domain is arranged and functions in
intact iGluR. Glutamate mediates the majority of
excitatory synaptic transmission in the central nervous
system via two broad classes of ionotropic receptors
characterized by their response to glutamate agonists:
N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA
receptors have intrinsically slow kinetics, are highly
permeable to Ca2+, and are blocked by extracellular Mg2+
in a voltage-dependent manner. On the other hand,
non-NMDA receptors have faster kinetics, are weakly
permeable to Ca2+, and are not blocked by extracellular
Mg2+. While non-NMDA receptors typically mediate
excitatory synaptic responses at resting membrane
potentials, NMDA receptors contribute to several forms
of synaptic plasticity and are suggested to play an
important role in the development of synaptic pathways.
Length = 328
Score = 31.7 bits (72), Expect = 0.74
Identities = 9/41 (21%), Positives = 19/41 (46%)
Query: 145 LDGEQMKYLIQVNPPGDILPEVIRAIILMQNITDAGILFDD 185
D E+ +Q+ P + L + + ++ N T I++D
Sbjct: 101 SDKEESSTTLQLYPSLEDLADALLDLLEYYNWTKFAIIYDS 141
>gnl|CDD|145227 pfam01939, DUF91, Protein of unknown function DUF91. The function
of this prokaryotic protein is unknown.
Length = 228
Score = 30.5 bits (69), Expect = 1.2
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 36 IDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADI 83
LIEE K V EY+I + G DE+G +I EL ++AD+
Sbjct: 117 PQLIEEGFKPVRREYQIAHGIVDILG-KDEDGNI--VILELKRRKADL 161
>gnl|CDD|234937 PRK01294, PRK01294, lipase chaperone; Provisional.
Length = 336
Score = 30.4 bits (69), Expect = 1.8
Identities = 26/123 (21%), Positives = 44/123 (35%), Gaps = 19/123 (15%)
Query: 218 ANLAAFLTVSRLDTPIES-LDDLSKQYKIQY--------APLNGSAAMTYFQR----MAD 264
A + + ++L P +S DL +YK Y G + Q+
Sbjct: 109 ALVEREIA-AQLPEPADSQALDLWLRYK-AYLSALAQLEDDGPGKLDLQALQQLLDARLA 166
Query: 265 IEGRFYEIWKDMSL---NDSLSDVERAKLAVWDYP-VSDKYTKMWQAMKEAKLPNSLEEA 320
+ RF+ W+ + + +L + P +SD A EA+LP L A
Sbjct: 167 LRARFFSDWEIQAFFGEENQYQRYALERLRIAQDPSLSDAQKAARLAALEAQLPEDLRAA 226
Query: 321 VQR 323
+Q
Sbjct: 227 LQE 229
>gnl|CDD|130009 TIGR00934, 2a38euk, potassium uptake protein, Trk family. The
proteins of the Trk family are derived from
Gram-negative and Gram-positive bacteria, yeast and
wheat. The proteins of E. coli K12 TrkH and TrkG as well
as several yeast proteins have been functionally
characterized.The E. coli TrkH and TrkG proteins are
complexed to two peripheral membrane proteins, TrkA, an
NAD-binding protein, and TrkE, an ATP-binding protein.
This complex forms the potassium uptake system. This
family is specific for the eukaryotic Trk system
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 800
Score = 30.7 bits (69), Expect = 2.0
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 201 VAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQYKI 245
ATWWLF F ++ +L F+ LD +D LSK K+
Sbjct: 581 SGATWWLF-FTLVGLNAIDLILFII---LDWGSSVVDGLSKGIKV 621
>gnl|CDD|176111 cd08419, PBP2_CbbR_RubisCO_like, The C-terminal substrate binding
of LysR-type transcriptional regulator (CbbR) of RubisCO
operon, which is involved in the carbon dioxide
fixation, contains the type 2 periplasmic binding fold.
CbbR, a LysR-type transcriptional regulator, is required
to activate expression of RubisCO, one of two unique
enzymes in the Calvin-Benson-Bassham (CBB) cycle
pathway. All plants, cyanobacteria, and many autotrophic
bacteria use the CBB cycle to fix carbon dioxide. Thus,
this cycle plays an essential role in assimilating CO2
into organic carbon on earth. The key CBB cycle enzyme
is ribulose 1,5-bisphosphate carboxylase/oxygenase
(RubisCO), which catalyzes the actual CO2 fixation
reaction. The CO2 concentration affects the expression
of RubisCO genes. It has also shown that NADPH enhances
the DNA-binding ability of the CbbR. RubisCO is composed
of eight large (CbbL) and eight small subunits (CbbS).
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 = 197
Score = 29.4 bits (67), Expect = 2.4
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 6 NISDSRLKQEPFVMREESEG 25
I RL +EPF++RE G
Sbjct: 88 RIPLERLAREPFLLREPGSG 107
>gnl|CDD|183381 PRK11917, PRK11917, bifunctional adhesin/ABC transporter
aspartate/glutamate-binding protein; Reviewed.
Length = 259
Score = 29.5 bits (66), Expect = 3.3
Identities = 11/36 (30%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 82 DIALGSLSVMAERENVVDFTVPYY-DLVGITILMKK 116
D + + ++ ER+ + +F+ PYY D +G+ +L +K
Sbjct: 103 DAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEK 138
>gnl|CDD|183530 PRK12444, PRK12444, threonyl-tRNA synthetase; Reviewed.
Length = 639
Score = 29.7 bits (67), Expect = 4.1
Identities = 10/29 (34%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 36 IDLIEEIRKLVGFEYEIFVA--PDNSFGN 62
+ I+ + K GFEYE+ ++ P++S G+
Sbjct: 404 MAQIDYVYKTFGFEYEVELSTRPEDSMGD 432
>gnl|CDD|240198 cd05693, S1_Rrp5_repeat_hs1_sc1, S1_Rrp5_repeat_hs1_sc1: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 1 (hs1) and S.
cerevisiae S1 repeat 1 (sc1). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 100
Score = 27.6 bits (62), Expect = 5.1
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 207 LFGFIIIAS----YTANLAAFLTVSRLDTPIESLDDLSKQYKI 245
L G++ I + YT L S + E L DL + +
Sbjct: 27 LTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSV 69
>gnl|CDD|221296 pfam11894, DUF3414, Protein of unknown function (DUF3414). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 764 to 2011 amino acids in
length. This protein has a conserved LLG sequence motif.
Length = 1612
Score = 29.2 bits (66), Expect = 5.4
Identities = 8/44 (18%), Positives = 21/44 (47%)
Query: 4 ITNISDSRLKQEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVG 47
++ + + KQ+ + G G +++ + D +EE +L+
Sbjct: 172 LSLLKEQIDKQKILGQLNTNRGLGFIEHIKFVRDFLEEEHELLA 215
>gnl|CDD|185490 PTZ00163, PTZ00163, hypothetical protein; Provisional.
Length = 230
Score = 28.5 bits (63), Expect = 5.4
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 235 SLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSD 284
SL+D K+Y P +G ++F+++ I E+ D+ +N+S++D
Sbjct: 124 SLEDRIKEYYTLTDPSDGEENNSFFKKLKLIMNILDEVHSDLLINNSVTD 173
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 29.0 bits (65), Expect = 6.7
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 292 VWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRVRD---SKSSSEGFGYLGDATDI 343
+W YP+ + ++ E P ++E ++ V D EG GY + DI
Sbjct: 1432 MWYYPL-----EFYEKTLEMPSPKEVKEFIETVEDRLGKPEQYEGIGYTHETDDI 1481
>gnl|CDD|234016 TIGR02791, VirB5, P-type DNA transfer protein VirB5. The VirB5
protein is involved in the type IV DNA secretion systems
typified by the Agrobacterium Ti plasmid vir system
where it interacts with several other proteins essential
for proper pilus formation. VirB5 is homologous to the
IncN (N-type) conjugation system protein TraC as well as
the P-type protein TrbJ and the F-type protein TraE.
Length = 220
Score = 28.3 bits (63), Expect = 7.2
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 214 ASYTANLA-AFLTVSRLDTPIESLDDLSKQYKIQYAPLNGSAAM 256
AS LA A ++ L T E L + +QYK QY L G+ M
Sbjct: 30 ASIANALAQAIEQMAALKTQYEQLSEQIEQYKQQYGSLTGNRGM 73
>gnl|CDD|219297 pfam07103, DUF1365, Protein of unknown function (DUF1365). This
family consists of several bacterial and plant proteins
of around 250 residues in length. The function of this
family is unknown.
Length = 244
Score = 27.9 bits (63), Expect = 8.7
Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 149 QMKYLIQVNPPGDILPEVIRAIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAATWWLF 208
+Y + +PPG+ R + + N G +FD + +G P L+ + +
Sbjct: 159 DGRYRFRFSPPGE------RLRVHIDNHRGGGPVFDATLAGRRRP--LTRAALLRALLRY 210
Query: 209 GF 210
Sbjct: 211 PL 212
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 0.137 0.410
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,178,446
Number of extensions: 2305199
Number of successful extensions: 1967
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1954
Number of HSP's successfully gapped: 43
Length of query: 444
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 344
Effective length of database: 6,502,202
Effective search space: 2236757488
Effective search space used: 2236757488
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: 61 (27.2 bits)