RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8853
(242 letters)
>gnl|CDD|234640 PRK00110, PRK00110, hypothetical protein; Validated.
Length = 245
Score = 281 bits (723), Expect = 1e-96
Identities = 114/243 (46%), Positives = 158/243 (65%), Gaps = 5/243 (2%)
Query: 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAI-NFGNNPDTNIKLRLAIEKALDAN 59
MAGHSKWANIK +K DAKRGKI T+++RE+ VA G +P+ N +LRLAI+KA AN
Sbjct: 1 MAGHSKWANIKHRKGAQDAKRGKIFTKLIREITVAAKLGGGDPEGNPRLRLAIDKAKAAN 60
Query: 60 IPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFN 119
+PK+NI RAI+K + NY E+RYEGY G AIIV+ +T+NR RT + +R+ F+
Sbjct: 61 MPKDNIERAIKKGTGE--LDGANYEEIRYEGYGPGGVAIIVEALTDNRNRTAAEVRHAFS 118
Query: 120 KNGGNLSKEGSVLFMFKHCGQLLFLPNTKKNTLLDLALEKGAEDFLIDKDNKITIITSPS 179
KNGGNL + GSV +MF G ++ P ++ L++ ALE GAED D D +IT+P
Sbjct: 119 KNGGNLGETGSVSYMFDRKGVIVIEPLD-EDELMEAALEAGAEDVETD-DESFEVITAPE 176
Query: 180 KFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNAL 239
F ++++LE G +AES+ + M P + + A KL KL++ L+ L DV+ VY NA
Sbjct: 177 DFEAVRDALEAAGLEAESAEVTMIPQNTVELDEETAEKLLKLIDALEDLDDVQNVYHNAE 236
Query: 240 IFD 242
I D
Sbjct: 237 ISD 239
>gnl|CDD|223295 COG0217, COG0217, Uncharacterized conserved protein [Function
unknown].
Length = 241
Score = 253 bits (649), Expect = 2e-85
Identities = 112/244 (45%), Positives = 160/244 (65%), Gaps = 5/244 (2%)
Query: 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINFGN-NPDTNIKLRLAIEKALDAN 59
MAGHSKWANIK +K DAKR KI T++++E+ VA G +P++N +LR AIEKA AN
Sbjct: 1 MAGHSKWANIKHRKAAQDAKRSKIFTKLIKEITVAAKQGGPDPESNPRLRTAIEKAKAAN 60
Query: 60 IPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFN 119
+PK+NI RAI+K + + NY E+RYEGY G AIIV+ +T+NR RT SN+R+ FN
Sbjct: 61 MPKDNIERAIKKASGG--KDGANYEEIRYEGYGPGGVAIIVEALTDNRNRTASNVRSAFN 118
Query: 120 KNGGNLSKEGSVLFMFKHCGQLLFLPNTK-KNTLLDLALEKGAEDFLIDKDNKITIITSP 178
KNGGNL + GSV +MF G ++ N ++ LL+ A+E GAED + + + I + T P
Sbjct: 119 KNGGNLGEPGSVSYMFDRKGVIVVEKNEIDEDELLEAAIEAGAED-VEEDEGSIEVYTEP 177
Query: 179 SKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNA 238
F ++K +LE G++ ES+ + M P + D +A KL+KL++ L+ DV+ VY NA
Sbjct: 178 EDFNKVKEALEAAGYEIESAELTMIPQNTVELDDEDAEKLEKLIDALEDDDDVQNVYHNA 237
Query: 239 LIFD 242
I +
Sbjct: 238 EISE 241
>gnl|CDD|216656 pfam01709, Transcrip_reg, Transcriptional regulator. This is a
family of transcriptional regulators. In mammals, it
activates the transcription of mitochondrially-encoded
COX1. In bacteria, it negatively regulates the
quorum-sensing response regulator by binding to its
promoter region.
Length = 234
Score = 252 bits (646), Expect = 5e-85
Identities = 111/236 (47%), Positives = 156/236 (66%), Gaps = 5/236 (2%)
Query: 5 SKWANIKRKKLIVDAKRGKICTRIMRELRVAI-NFGNNPDTNIKLRLAIEKALDANIPKN 63
SKWANIK +K DAKRGKI T++ +E+ VA G +P+ N +LRLAIEKA AN+PK+
Sbjct: 1 SKWANIKHRKAAQDAKRGKIFTKLGKEITVAAKMGGPDPEGNPRLRLAIEKAKAANMPKD 60
Query: 64 NIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGG 123
NI RAI+K + + NY E+RYEGY G AIIV+C+T+NR RT +++R+ F+KNGG
Sbjct: 61 NIERAIKKGSG--GLDGENYEEIRYEGYGPGGVAIIVECLTDNRNRTAADVRHAFSKNGG 118
Query: 124 NLSKEGSVLFMFKHCGQLLF-LPNTKKNTLLDLALEKGAEDFLIDKDNKITIITSPSKFI 182
NL + GSV +MF G ++F ++ LL+ ALE GAED ++D I +IT P+ F
Sbjct: 119 NLGETGSVSYMFDRKGVIVFEKEGVDEDELLEAALEAGAEDV-EEEDGSIEVITDPTDFE 177
Query: 183 EIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNA 238
+K +LE G + ES+ I M P + + +A KL+KL++ L+ L DV+ VY NA
Sbjct: 178 AVKKALEEAGLEIESAEITMIPQNTVELDEEDAEKLEKLIDALEDLDDVQNVYHNA 233
>gnl|CDD|233240 TIGR01033, TIGR01033, DNA-binding regulatory protein, YebC/PmpR
family. This model describes a minimally characterized
protein family, restricted to bacteria excepting for
some eukaryotic sequences that have possible transit
peptides. YebC from E. coli is crystallized, and PA0964
from Pseudomonas aeruginosa has been shown to be a
sequence-specific DNA-binding regulatory protein
[Regulatory functions, DNA interactions].
Length = 238
Score = 222 bits (569), Expect = 2e-73
Identities = 108/240 (45%), Positives = 156/240 (65%), Gaps = 5/240 (2%)
Query: 1 MAGHSKWANIKRKKLIVDAKRGKICTRIMRELRVAINFG-NNPDTNIKLRLAIEKALDAN 59
MAGHSKWANIK +K DAKRGKI T++++E+ VA G +P++N +LR AIEKA AN
Sbjct: 1 MAGHSKWANIKHRKAAQDAKRGKIFTKLIKEIIVAAKLGGGDPESNPRLRTAIEKAKAAN 60
Query: 60 IPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFN 119
+PK+NI RAI+K + + NY E+ YEGY+ G AIIV+C+T+N+ RT S +R+ FN
Sbjct: 61 MPKDNIERAIKKGAG--ELDGSNYEEITYEGYAPGGVAIIVECLTDNKNRTASEVRSAFN 118
Query: 120 KNGGNLSKEGSVLFMFKHCGQLLFLPNTKK-NTLLDLALEKGAEDFLIDKDNKITIITSP 178
KNGG+L + GSV ++F G + N L++ A+E GAED + D++ + T+P
Sbjct: 119 KNGGSLGEPGSVSYLFSRKGVIEVPKNEVDEEDLMEAAIEAGAED-IDVDDDEFEVYTAP 177
Query: 179 SKFIEIKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNA 238
+ ++K +LE GF ES+ I M P T + D +A KL KL++ L+ DV++VY N
Sbjct: 178 EELEKVKEALEAKGFPIESAEITMIPLTTVDLDDEQAEKLLKLIDALEDDDDVQEVYHNF 237
>gnl|CDD|237084 PRK12378, PRK12378, hypothetical protein; Provisional.
Length = 235
Score = 199 bits (508), Expect = 4e-64
Identities = 89/235 (37%), Positives = 133/235 (56%), Gaps = 6/235 (2%)
Query: 6 KWANIKRKKLIVDAKRGKICTRIMRELRVAI-NFGNNPDTNIKLRLAIEKALDANIPKNN 64
W NIK KK D + KI ++ +E+ VA G +P++N LR IE+A AN+PK+
Sbjct: 4 AWENIKAKKAKKDGAKSKIFAKLGKEIYVAAKQGGPDPESNPALRFVIERAKKANVPKDV 63
Query: 65 IFRAIQKNNSNIKNENINYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGN 124
I RAI+K +Y EVRYEG+ NG +IV+C+T+N RTV+N+R+ FNKNGGN
Sbjct: 64 IERAIKKAKGG---GGEDYEEVRYEGFGPNGVMVIVECLTDNVNRTVANVRSAFNKNGGN 120
Query: 125 LSKEGSVLFMFKHCGQLLFLPNTKKNTLLDL-ALEKGAEDFLIDKDNKITIITSPSKFIE 183
L GSV FMF H G +F + + L L + ED + +++ IT+ T P+ F +
Sbjct: 121 LGTSGSVAFMFDHKGVFVFEGDDEDELLEALIDADVDVED-VEEEEGTITVYTDPTDFHK 179
Query: 184 IKNSLEMTGFKAESSGIVMRPYTNIVFKDGEAIKLQKLLNELKKLHDVKKVYTNA 238
+K +LE G + + + M P + + + +KLL+ L+ DV+ VY N
Sbjct: 180 VKKALEAAGIEFLVAELEMIPQNPVELSGEDLEQFEKLLDALEDDDDVQNVYHNV 234
>gnl|CDD|201133 pfam00289, CPSase_L_chain, Carbamoyl-phosphate synthase L chain,
N-terminal domain. Carbamoyl-phosphate synthase
catalyzes the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. This important enzyme initiates both the
urea cycle and the biosynthesis of arginine and/or
pyrimidines. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain. The small chain promotes the hydrolysis of
glutamine to ammonia, which is used by the large chain
to synthesise carbamoyl phosphate. See pfam00988. The
small chain has a GATase domain in the carboxyl
terminus. See pfam00117.
Length = 108
Score = 33.6 bits (78), Expect = 0.018
Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 9/39 (23%)
Query: 13 KKLIVDAKRGKICTRIMRELR------VAINFGNNPDTN 45
KK++V A RG+I RI+R LR VA+N +NPDT
Sbjct: 2 KKVLV-ANRGEIAVRIIRALRELGIETVAVN--SNPDTV 37
>gnl|CDD|173854 cd08489, PBP2_NikA, The substrate-binding component of an ABC-type
nickel import system contains the type 2 periplasmic
binding fold. This family represents the periplasmic
substrate-binding domain of nickel transport system,
which functions in the import of nickel and in the
control of chemotactic response away from nickel. The
ATP-binding cassette (ABC) type nickel transport system
is comprised of five subunits NikABCDE: the two
pore-forming integral inner membrane proteins NikB and
NikC; the two inner membrane-associated proteins with
ATPase activity NikD and NikE; and the periplasmic
nickel binding NikA, the initial nickel receptor. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA. The DppA binds dipeptides and some
tripeptides and is involved in chemotaxis toward
dipeptides, whereas the OppA binds peptides of a wide
range of lengths (2-35 amino acid residues) and plays a
role in recycling of cell wall peptides, which precludes
any involvement in chemotaxis. Most of other periplasmic
binding proteins are comprised of only two globular
subdomains corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains 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
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 488
Score = 33.0 bits (76), Expect = 0.12
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 26 TRIMRELRVAINFGNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIE 85
TR + A+N + P +++K+R AI A+D I ++K + N+ Y +
Sbjct: 242 TRFL-----ALNTASEPLSDLKVREAINYAIDKEAISKGILYGLEKPADTLFAPNVPYAD 296
Query: 86 VRYEGYSVN 94
+ + YS +
Sbjct: 297 IDLKPYSYD 305
>gnl|CDD|236049 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1220
Score = 31.9 bits (73), Expect = 0.37
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 7/55 (12%)
Query: 23 KICTR----IMRELRVAINFGN---NPDTNIKLRLAIEKALDANIPKNNIFRAIQ 70
KI ++ IM+ G+ +P N L+ I+ A A +P+N I R IQ
Sbjct: 312 KIVSKHLKAIMKACVNCEGDGDDCFDPAKNPALKREIKAAKKALVPENYIKRVIQ 366
>gnl|CDD|233815 TIGR02294, nickel_nikA, nickel ABC transporter, nickel/metallophore
periplasmic binding protein. Members of this family are
periplasmic nickel-binding proteins of nickel ABC
transporters. Most appear to be lipoproteins. This
protein was previously (circa 2003) thought to mediate
binding to nickel through water molecules, but is now
thought to involve a chelating organic molecule, perhaps
butane-1,2,4-tricarboxylate, acting as a metallophore
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 500
Score = 30.2 bits (68), Expect = 1.0
Identities = 13/61 (21%), Positives = 29/61 (47%)
Query: 34 VAINFGNNPDTNIKLRLAIEKALDANIPKNNIFRAIQKNNSNIKNENINYIEVRYEGYSV 93
+ +N G N +++ +R AI A++ NI +K + +N+ Y ++ + Y
Sbjct: 253 LLLNTGKNATSDLAVRQAINHAVNKQSIAKNILYGTEKPADTLFAKNVPYADIDLKPYKY 312
Query: 94 N 94
+
Sbjct: 313 D 313
>gnl|CDD|216203 pfam00932, LTD, Lamin Tail Domain. The lamin-tail domain (LTD),
which has an immunoglobulin (Ig) fold, is found in
Nuclear Lamins, Chlo1887 from Chloroflexus, and several
bacterial proteins where it occurs with membrane
associated hydrolases of the
metallo-beta-lactamase,synaptojanin, and
calcineurin-like phosphoesterase superfamilies.
Length = 108
Score = 28.2 bits (63), Expect = 1.5
Identities = 9/46 (19%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 177 SPSKFIEIKN----SLEMTGFKAESSGIVMRPYTNIVFKDGEAIKL 218
S +++IE+ N +++++G+ + SG +V + G + +
Sbjct: 19 SNNEWIELYNTSAAAVDLSGWTLKDSGNTYTFPPGVVLEPGATVTV 64
>gnl|CDD|219554 pfam07752, DUF1608, Protein of unknown function (DUF1608). This
region is found in a number of proteins of unknown
function expressed by both archaeal and bacterial
species. It is repeated near the N-terminus of some of
these proteins, and is approximately 250 residues long.
Length = 258
Score = 28.5 bits (64), Expect = 3.2
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 15/68 (22%)
Query: 159 KGAED--------FLIDKDNKITIITSPSKFIEIKNSLEMTGFKAESSGIVMRPYTNIVF 210
+GAED FLI KD+ I + +F E++ + +GI ++ +I
Sbjct: 188 QGAEDSAVFIEGIFLISKDD-YLEIETGDEFGEMEIV------EISENGIKLKNEDSITL 240
Query: 211 KDGEAIKL 218
+ I
Sbjct: 241 WRDDDIDF 248
>gnl|CDD|131421 TIGR02368, dimeth_PyL, dimethylamine:corrinoid methyltransferase.
This family consists of dimethylamine methyltransferases
from the genus Methanosarcina. It is found in three
nearly identical copies in each of M. acetivorans, M.
barkeri, and M. Mazei. It is one of a suite of three
non-homologous enzymes with a critical UAG-encoded
pyrrolysine residue in these species (along with
trimethylamine methyltransferase and monomethylamine
methyltransferase). It demethylates dimethylamine,
leaving monomethylamine, and methylates the prosthetic
group of the small corrinoid protein MtbC. The methyl
group is then transferred by methylcorrinoid:coenzyme M
methyltransferase to coenzyme M. Note that the
pyrrolysine residue is variously translated as K or X,
or as a stop codon that truncates the sequence.
Length = 466
Score = 27.3 bits (60), Expect = 7.5
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 13 KKLIVDAKRGKICTRIMRELRVAINFG---NNPDT--NIKLRLAIEKALDANIPKNNIFR 67
KKL VD +MRELR ++ G + P I ++ IEK L I +FR
Sbjct: 405 KKLNVDI-MDLADEHVMRELREELDIGVITSVPGAAKGIAAKMNIEKLLGIKINSCELFR 463
Query: 68 A 68
Sbjct: 464 K 464
>gnl|CDD|184552 PRK14175, PRK14175, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 286
Score = 26.8 bits (59), Expect = 9.5
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 8 ANIKRKKLIVDA--KRGKICTRIMRELRVAINFGNNPDTNIKLRLAIE 53
+ +K +IV A K G + +++E V I+ GN PD N KL+ ++
Sbjct: 197 SYLKDADVIVSAVGKPGLVTKDVVKEGAVIIDVGNTPDENGKLKGDVD 244
>gnl|CDD|240537 cd13132, MATE_eukaryotic, Eukaryotic members of the multidrug and
toxic compound extrusion (MATE) family. The integral
membrane proteins from the MATE family are involved in
exporting metabolites across the cell membrane and are
responsible for multidrug resistance (MDR) in many
bacteria and animals. MATE has also been identified as a
large multigene family in plants, where the proteins are
linked to disease resistance. A number of family members
are involved in the synthesis of peptidoglycan
components in bacteria. This subfamily, which is
restricted to eukaryotes, contains vertebrate solute
transporters responsible for secretion of cationic drugs
across the brush border membranes, yeast proteins
located in the vacuole membrane, and plant proteins
involved in disease resistance and iron homeostatis
under osmotic stress.
Length = 436
Score = 27.2 bits (61), Expect = 9.9
Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 2/64 (3%)
Query: 81 INYIEVRYEGYSVNGAAIIVDCITNNRMRTVSNIRNIFNKNGGNLSKEGSVLFMFKHCGQ 140
+NY+ V G GAA+ I+ + V + IF G + G F+ G
Sbjct: 168 LNYLLVFVLGLGFIGAALAT-SISYWLI-VVLLLLYIFFSKGHKATWGGFSREAFRGWGP 225
Query: 141 LLFL 144
L L
Sbjct: 226 FLKL 229
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
0.319 0.136 0.382
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,342,413
Number of extensions: 1192167
Number of successful extensions: 1379
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1357
Number of HSP's successfully gapped: 41
Length of query: 242
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 148
Effective length of database: 6,768,326
Effective search space: 1001712248
Effective search space used: 1001712248
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 (21.7 bits)
S2: 58 (26.2 bits)