RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5774
(201 letters)
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 61.9 bits (151), Expect = 2e-13
Identities = 28/52 (53%), Positives = 38/52 (73%)
Query: 23 NTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLE 74
N RER R++ ++ AF ELR L+PT P +KKLSK EILR++I YI+ L L+
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 61.3 bits (150), Expect = 3e-13
Identities = 28/52 (53%), Positives = 37/52 (71%), Gaps = 1/52 (1%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLL 69
R+ N RER R+ ++ AF ELR L+P PP+KKLSK EILR++I YI+ L
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLP-TPPNKKLSKAEILRLAIEYIKHL 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 = 59.1 bits (144), Expect = 2e-12
Identities = 29/57 (50%), Positives = 40/57 (70%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLE 74
R+ N RER R++ ++ AF ELR L+PT PP KKLSK EILR ++ YI+ L +L+
Sbjct: 4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|240427 PTZ00470, PTZ00470, glycoside hydrolase family 47 protein;
Provisional.
Length = 522
Score = 33.5 bits (77), Expect = 0.052
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 78 QNENNYNNNNTTDINANNNIITNNRDFVVNANKRGDSKTSIKETNPFERKPNGNYFNSK 136
N + N NN + N N N + A+K + K+ NPF + Y N K
Sbjct: 11 HNNADDNYNNNNNNNNQINSNNPNNNGNNQASK--LPRGKKKQENPFNKIDEVYYQNEK 67
>gnl|CDD|239118 cd02652, nuc_hydro_2, NH_2: A subgroup of nucleoside hydrolases.
This group contains eukaryotic and bacterial proteins
similar to nucleoside hydrolases. Nucleoside hydrolases
cleave the N-glycosidic bond in nucleosides generating
ribose and the respective base. These enzymes vary in
their substrate specificity. .
Length = 293
Score = 29.4 bits (66), Expect = 1.2
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 2/59 (3%)
Query: 35 GAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLEWQKQNENNYNNNNTTDINA 93
G L L+ L+ E++R ++ + ++ G N + N TD A
Sbjct: 117 GPLTNLAALLDADAD--PLTGPELVRQKVKRLVVMGGAFYDPDGNVQHREYNFVTDPKA 173
>gnl|CDD|191590 pfam06708, DUF1195, Protein of unknown function (DUF1195). This
family consists of several plant specific hypothetical
proteins of around 160 residues in length. The function
of this family is unknown.
Length = 156
Score = 27.5 bits (61), Expect = 2.9
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 16 LVRK---IFTNTRE----RWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRL 68
LVR ++T + R+ Q+ A+ EL VP + +S EI +MS+R I L
Sbjct: 92 LVRHMWDVYTRSGRVRLPRFWQEAFEAAYEELASDVPQ-VREAAVS--EIAKMSVRSIEL 148
>gnl|CDD|143597 cd07573, CPA, N-carbamoylputrescine amidohydrolase (CPA) (class 11
nitrilases). CPA (EC 3.5.1.53, also known as
N-carbamoylputrescine amidase and carbamoylputrescine
hydrolase) converts N-carbamoylputrescine to putrescine,
a step in polyamine biosynthesis in plants and bacteria.
This subgroup includes Arabidopsis thaliana CPA, also
known as nitrilase-like 1 (NLP1), and Pseudomonas
aeruginosa AguB. This subgroup belongs to a larger
nitrilase superfamily comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13),
this subgroup corresponds to class 11. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer; P.
aeruginosa AugB is a homohexamer, Arabidopsis thaliana
NLP1 is a homooctomer.
Length = 284
Score = 27.1 bits (61), Expect = 6.2
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 124 FERKPNGNYFNS-----KDVSDTQVKRKT 147
FE++ NG Y+NS D S V RK
Sbjct: 87 FEKRGNGLYYNSAVVIDADGSLLGVYRKM 115
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 27.3 bits (60), Expect = 7.7
Identities = 19/110 (17%), Positives = 45/110 (40%), Gaps = 5/110 (4%)
Query: 73 LEWQKQNENNYNNNNTTDINANNNIITNNRDFVVNANKRGDSKTSIKETNP-----FERK 127
+ NN ++N+ D +++N + +NR N + +T+ K TN + +
Sbjct: 311 DPKNIIHRNNGSSNSNNDDTSSSNHLGSNRISNRNPSSPYKKQTTTKHTNNTKNNKYNKT 370
Query: 128 PNGNYFNSKDVSDTQVKRKTNMTRQYNKISTTTITRTEIIQTFNKDELEE 177
FN + ++++M + ++E I+ F +E+ +
Sbjct: 371 KTTQKFNHPLRHHATINKRSSMLPMSEQKGRGASEKSEYIKEFTMEEVAK 420
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
0.312 0.128 0.361
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: 9,960,460
Number of extensions: 899423
Number of successful extensions: 801
Number of sequences better than 10.0: 1
Number of HSP's gapped: 778
Number of HSP's successfully gapped: 62
Length of query: 201
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 109
Effective length of database: 6,857,034
Effective search space: 747416706
Effective search space used: 747416706
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: 56 (25.3 bits)