RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2365
(285 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 78.3 bits (194), Expect = 5e-19
Identities = 27/52 (51%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 174 RRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYL 225
RR N++ERRR IN+AF +LRE +P P + KLSK + LRLA YI +L
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPT-PPNKKLSKAEILRLAIEYIKHL 51
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four helix
bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide sequences
such as N-box (5-CACGc/aG-3), those which have a COE
domain (Collier/Olf-1/EBF) which is involved in both in
dimerization and in DNA binding, and those which bind
pentanucleotides ACGTG or GCGTG and have a PAS domain
which allows the dimerization between PAS proteins, the
binding of small molecules (e.g., dioxin), and
interactions with non-PAS proteins.
Length = 60
Score = 75.3 bits (186), Expect = 8e-18
Identities = 26/59 (44%), Positives = 36/59 (61%)
Query: 172 VKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILE 230
RR N +ERRR + IN+AF +LR +P +P KLSK + LR A YI L ++L+
Sbjct: 2 KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 72.6 bits (179), Expect = 7e-17
Identities = 25/53 (47%), Positives = 34/53 (64%)
Query: 179 NKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILET 231
N +ERRR + IN AF +LR +P +P + KLSK + LRLA YI L + L+
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53
>gnl|CDD|236707 PRK10522, PRK10522, multidrug transporter membrane
component/ATP-binding component; Provisional.
Length = 547
Score = 31.1 bits (71), Expect = 0.71
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 205 SDTKLSKIKTLRLATSYISYLMKILETDDIISIDDFKAD 243
S+ KLSK + RLA L+ + E DI+ +D++ AD
Sbjct: 446 SNLKLSKGQKKRLA-----LLLALAEERDILLLDEWAAD 479
>gnl|CDD|200439 cd11283, ADF_GMF-beta_like, ADF-homology domain of glia maturation
factor beta and related proteins. Actin
depolymerization factor/cofilin-like domains (ADF
domains) are present in a family of essential eukaryotic
actin regulatory proteins. Most of these proteins
enhance the turnover rate of actin and interact with
actin monomers as well as actin filaments. The glia
maturation factor (GMF), however, does not bind actin
but interacts with the Arp2/3 complex (which contains
actin-related proteins, amongst others) and suppresses
Arp2/3 activity, inducing the dissociation of branched
daughter filaments from their mother filaments. This
family includes both mammalian GMF isoforms, GMF-beta
and GMF-gamma. GMF-beta regulates cellular growth,
fission, differentiation and apoptosis. GMF-gamma is
important in myeloid cell development and is an
important regulator for cell migration and polarity in
neutrophils.
Length = 122
Score = 28.4 bits (64), Expect = 2.0
Identities = 11/57 (19%), Positives = 20/57 (35%), Gaps = 12/57 (21%)
Query: 203 VPSDTKLSKIKTLRLATSYI-----------SYLMKILETDDIISIDDFKADLSNHS 248
+ + K +K R S + + E + ISI++ +L HS
Sbjct: 2 ISDEVK-EALKKFRFRKSKANAALILKIDKEKQEIVVDEELEDISIEELAEELPEHS 57
>gnl|CDD|220961 pfam11064, DUF2865, Protein of unknown function (DUF2865). This
bacterial family of proteins has no known function.
Length = 115
Score = 27.9 bits (62), Expect = 3.2
Identities = 11/56 (19%), Positives = 19/56 (33%), Gaps = 6/56 (10%)
Query: 60 TGATDCIYWSEDMQSPDSRYVTRSMSTSSDGFDEDEDQSERFCPSNDYTKYYYQDG 115
T C +++ D Y S T++ +D + CP + YY
Sbjct: 2 GARTYC------VRTCDGYYFPLSNLTAASSDPKDAQACQALCPGAETDLYYDGGS 51
>gnl|CDD|114155 pfam05414, DUF1717, Viral domain of unknown function (DUF1717).
This domain is found in viral proteins of unknown
function.
Length = 103
Score = 27.4 bits (60), Expect = 3.2
Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 1/84 (1%)
Query: 195 DLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILETDDIISIDDFKADLSNHSSHRKNK 254
DL++CI + D +S + + + ++ Y + I + D II ++D + H + KN
Sbjct: 14 DLKDCIEELNLDHGISH-ELIEVCCKFLGYEVHITKGDSIIKLNDDIEMAAIHIGYGKNG 72
Query: 255 SQYDSPSEISSNQSSQYVMDPSCQ 278
+ E S + C+
Sbjct: 73 HLFCINQERSKIPKDSQIKGNECE 96
>gnl|CDD|107323 cd06328, PBP1_SBP_like_2, Periplasmic solute-binding domain of
active transport proteins found in gram-negative and
gram-positive bacteria. Periplasmic solute-binding
domain of active transport proteins found in
gram-negative and gram-positive bacteria. Members of
this group are initial receptors in the process of
active transport across cellular membrane, but their
substrate specificities are not known in detail.
However, they closely resemble the group of AmiC and
active transport systems for short-chain amides and urea
(FmdDEF), and thus are likely to exhibit a
ligand-binding mode similar to that of the amide sensor
protein AmiC from Pseudomonas aeruginosa. Moreover, this
binding domain has high sequence identity to the family
of hydrophobic amino acid transporters (HAAT), and thus
it may also be involved in transport of amino acids.
Length = 333
Score = 28.1 bits (63), Expect = 4.8
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 11/56 (19%)
Query: 1 MSADILHAGSHY----GGSNESF-YHYNTPNNNVMSYNSGYH------PPPLYTAG 45
++ DIL + Y G S S+ YHY P N V + H PP L+TAG
Sbjct: 223 LAGDILANLTMYKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARFGSPPDLFTAG 278
>gnl|CDD|153090 cd08025, RNR_PFL_like_DUF711, Uncharacterized proteins with
similarity to Ribonucleotide reductase and Pyruvate
formate lyase. This subfamily contains Streptococcus
pneumoniae Sp0239 and similar uncharacterized proteins.
Sp0239 is structurally similar to ribonucleotide
reductase (RNR) and pyruvate formate lyase (PFL), which
are believed to have diverged from a common ancestor.
RNR and PFL possess a ten-stranded alpha-beta barrel
domain that hosts the active site, and are radical
enzymes. RNRs are found in all organisms and provide the
only mechanism by which nucleotides are converted to
deoxynucleotides. PFL is an essential enzyme in
anaerobic bacteria that catalyzes the conversion of
pyruvate and CoA to acteylCoA and formate.
Length = 400
Score = 28.4 bits (64), Expect = 5.2
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 187 QSINNAFSDLRECIPNVPSDTKLS-KIKTLRLATSYISYLMKILETDDIISI 237
+ I +A L E + V S +L I R++ + I+ L L+ +D + I
Sbjct: 43 EKITSAAKRLVETVEEVSS--ELGVPIVNKRISVTPIAILAAGLDAEDYVEI 92
>gnl|CDD|131685 TIGR02637, RhaS, rhamnose ABC transporter, rhamnose-binding
protein. This sugar-binding component of ABC
transporter complexes is found in rhamnose catabolism
operon contexts. Mutation of this gene in Rhizobium
leguminosarum abolishes rhamnose transport and prevents
growth on rhamnose as a carbon source.
Length = 302
Score = 27.9 bits (62), Expect = 6.4
Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 18/103 (17%)
Query: 53 ATLSNITTGATDCIYWSEDM--QSPDSRYVTRSMSTSSDGFDEDEDQSERFCPSNDYTKY 110
A LS +T AT+ W E M + D +Y + + G D+D +S
Sbjct: 127 AILSAAST-ATNQNAWIEIMKKELKDPKYPKVKLVATVYG-DDDAQKS------------ 172
Query: 111 YYQDGVGP-GAYPNVKHIVEPSYVNLDTATKTLRTVSKAGSIK 152
YQ+ G +YPN+K I+ P+ V + A + + G +K
Sbjct: 173 -YQEAQGLLKSYPNLKGIIAPTTVGIKAAAQAVSDAKLIGKVK 214
>gnl|CDD|236261 PRK08412, flgL, flagellar hook-associated protein FlgL; Validated.
Length = 827
Score = 28.2 bits (63), Expect = 6.5
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 7/50 (14%)
Query: 92 DEDEDQSERFCPSNDYTKYYYQDGVGP-GAYPNVKHIVEPSYVNLDTATK 140
D D+D P+ND +++Y GV P G+ K + +Y N ++ATK
Sbjct: 232 DNDKD------PTNDPKEFFYLQGVRPDGSSFKEKFSLSKAYQNKESATK 275
>gnl|CDD|205352 pfam13171, DUF4004, Protein of unknown function (DUF4004). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 210 amino acids in length.
Length = 199
Score = 27.3 bits (61), Expect = 7.7
Identities = 8/48 (16%), Positives = 18/48 (37%)
Query: 227 KILETDDIISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMD 274
KI + D +S+D+ S + + + I S + + +
Sbjct: 58 KIQKMKDDLSLDELAKMFSPNMEEVELTEEELLRKGIVSETALEVFEE 105
>gnl|CDD|223032 PHA03283, PHA03283, envelope glycoprotein E; Provisional.
Length = 542
Score = 27.6 bits (61), Expect = 7.9
Identities = 16/73 (21%), Positives = 20/73 (27%), Gaps = 18/73 (24%)
Query: 66 IYWSEDMQSPDSRYVTRSMSTSSDGFDEDEDQSERFCPSNDYTKYYYQDGVGPGAYPNVK 125
+Y S P+ R S S D FD D+ P P
Sbjct: 442 VYTSVPSNDPEVLVFERLASDSDDSFDSSSDEELEPPP------------------PPGP 483
Query: 126 HIVEPSYVNLDTA 138
YV+LD
Sbjct: 484 AGQLGPYVSLDAE 496
>gnl|CDD|239804 cd04277, ZnMc_serralysin_like, Zinc-dependent metalloprotease,
serralysin_like subfamily. Serralysins and related
proteases are important virulence factors in pathogenic
bacteria. They may be secreted into the medium via a
mechanism found in gram-negative bacteria, that does not
require n-terminal signal sequences which are cleaved
after the transmembrane translocation. A calcium-binding
domain c-terminal to the metalloprotease domain, which
contains multiple tandem repeats of a nine-residue motif
including the pattern GGxGxD, and which forms a parallel
beta roll may be involved in the translocation mechanism
and/or substrate binding. Serralysin family members may
have a broad spectrum of substrates each, including host
immunoglobulins, complement proteins, cell matrix and
cytoskeletal proteins, as well as antimicrobial
peptides.
Length = 186
Score = 27.0 bits (60), Expect = 9.0
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 7 HAGS-HYGGSNESFYHYNTPNNNVMSYNSGYHPPPLYTAGPPED 49
H G + G Y ++ VMSYNSGY G P+
Sbjct: 129 HPGDYNGGDPVPPTYALDSREYTVMSYNSGYGNGASAGGGYPQT 172
>gnl|CDD|183411 PRK12293, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 281
Score = 27.3 bits (61), Expect = 9.2
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 194 SDLRECIPNVPSDTK--LSKIKTLRLATSYISY 224
DL E I VP + K L K+K L I Y
Sbjct: 193 EDLDEVIELVPDEIKEELEKLKEL---AESIKY 222
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
0.311 0.127 0.371
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,935,176
Number of extensions: 1254613
Number of successful extensions: 805
Number of sequences better than 10.0: 1
Number of HSP's gapped: 804
Number of HSP's successfully gapped: 21
Length of query: 285
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 189
Effective length of database: 6,679,618
Effective search space: 1262447802
Effective search space used: 1262447802
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (26.0 bits)