RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14770
(77 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 53.6 bits (130), Expect = 1e-11
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 15 KRAHHNALERKRRDHIKDSFSSLRDSVPSLQGEKVEVPGSHVDTLDQ 61
+R HN ER+RRD I D+F LR+ +P+ +K+ S + L
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPTPPNKKL----SKAEILRL 43
>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 = 46.8 bits (112), Expect = 5e-09
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 12 SAEKRAHHNALERKRRDHIKDSFSSLRDSVPSLQGEK 48
+R HN ER+RR+ I D+F LR +P+L K
Sbjct: 1 RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSK 37
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 36.8 bits (86), Expect = 4e-05
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 20 NALERKRRDHIKDSFSSLRDSVPSLQGEK 48
NA ER+RR I ++F LR +P+L K
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNK 29
>gnl|CDD|219205 pfam06862, DUF1253, Protein of unknown function (DUF1253). This
family represents the C-terminal portion (approximately
500 residues) of several hypothetical eukaryotic
proteins of unknown function.
Length = 436
Score = 29.1 bits (66), Expect = 0.17
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 10/54 (18%)
Query: 25 KRRDHIKDSFSSLRDSVPSLQGEKVEVPGSHVDTLDQGFWYKGTR-KVGFLLSF 77
K RD + + S L + E ++ + DQGF TR KV LL
Sbjct: 1 KTRDRVLKNNSKLAKN-AEASKENIDDD----EFRDQGF----TRPKVLILLPT 45
>gnl|CDD|216295 pfam01093, Clusterin, Clusterin.
Length = 434
Score = 26.6 bits (59), Expect = 1.2
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 28 DHIKDSFSSLRDSVPSLQGEKVEVPGSHVDTLDQGF 63
D ++DSFS L D V L + +V DQ F
Sbjct: 146 DDLEDSFSQLTDDVDELFNDSFKVFKQMQQFFDQAF 181
>gnl|CDD|187802 cd09671, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein of this family often fused to HTH domain; Some
proteins could have an additional fusion with
RecB-family nuclease domain; Core domain appears to have
a Rossmann-like fold; loosely associated with CRISPR/Cas
systems; also known as DxTHG family.
Length = 346
Score = 26.3 bits (58), Expect = 1.7
Identities = 7/46 (15%), Positives = 15/46 (32%)
Query: 21 ALERKRRDHIKDSFSSLRDSVPSLQGEKVEVPGSHVDTLDQGFWYK 66
++K + +K+ V K+++ G D Y
Sbjct: 62 EDKKKLEEELKEFSIEPAAFVVGGSYNKIKLEGIASDIYYLYLLYN 107
>gnl|CDD|223352 COG0275, COG0275, Predicted S-adenosylmethionine-dependent
methyltransferase involved in cell envelope biogenesis
[Cell envelope biogenesis, outer membrane].
Length = 314
Score = 25.6 bits (57), Expect = 2.6
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 10 IESAEKRAHHNALERKRRDHIKDSFSSLRDSVPSLQGEKVE-------VPGSHVDTLDQG 62
I A++R R + +F++L +++ L KV+ V +D ++G
Sbjct: 61 IAIAKERLKEF---DGRVTLVHGNFANLAEALKELGIGKVDGILLDLGVSSPQLDDAERG 117
Query: 63 FWYK 66
F ++
Sbjct: 118 FSFR 121
>gnl|CDD|222785 PHA00368, PHA00368, internal virion protein D.
Length = 1315
Score = 25.9 bits (57), Expect = 2.6
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 10 IESAEKRAHHNALERKRRDHIKDSFSSLRDSV--PSLQG 46
IE E +A+ ERK D +K+ F R+ + P++ G
Sbjct: 605 IERPELQANLTKAERKVMDILKEHFDLKREMMENPAIFG 643
>gnl|CDD|237248 PRK12890, PRK12890, allantoate amidohydrolase; Reviewed.
Length = 414
Score = 25.2 bits (56), Expect = 3.4
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 26 RRDHIKDSFSSLRDSVPSLQGEKVEVPGSHVDTLDQGFWYKG 67
RRD + F L P + GSH+DT+ G Y G
Sbjct: 56 RRDAAGNLFGRLPGRDP---DLPPLMTGSHLDTVPNGGRYDG 94
>gnl|CDD|185075 PRK15120, PRK15120, lipopolysaccharide ABC transporter permease
LptF; Provisional.
Length = 366
Score = 25.0 bits (55), Expect = 3.9
Identities = 9/24 (37%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 46 GEKVEVP-GSHVDTLDQGFWYKGT 68
G ++ GS V TL++G ++GT
Sbjct: 193 GHLTQLRDGSQVVTLNKGTRFEGT 216
>gnl|CDD|193472 pfam12999, PRKCSH-like, Glucosidase II beta subunit-like. The
sequences found in this family are similar to a region
found in the beta-subunit of glucosidase II, which is
also known as protein kinase C substrate 80K-H (PRKCSH).
The enzyme catalyzes the sequential removal of two
alpha-1,3-linked glucose residues in the second step of
N-linked oligosaccharide processing. The beta subunit is
required for the solubility and stability of the
heterodimeric enzyme, and is involved in retaining the
enzyme within the endoplasmic reticulum.
Length = 176
Score = 24.4 bits (53), Expect = 7.5
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 4 DERDYDIESAEKRAHHNALE-RKRRDHIKDSFSSLRDSVPSLQGEK 48
E + +++ K L +K+RD +K L DS+P+ Q
Sbjct: 131 TEHNNSVKNGLKIKEGLLLAAQKKRDELKKRLKELEDSLPAKQQRL 176
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 24.1 bits (53), Expect = 9.2
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 1 MSDDERDYDIESAEKRAHHNALER 24
+ D+ R D+E+ E H + R
Sbjct: 129 LRDETRRRDVETEEDIEEHQEMNR 152
>gnl|CDD|235026 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
Length = 188
Score = 23.8 bits (52), Expect = 9.9
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 5 ERDYDIESAEKRAHHNALERKRRDHIKDSFSSLRDSVPSLQGEKVE 50
R+ ++ SA+ A L R++ ++D + + D + SL G+K E
Sbjct: 58 LREQELSSAKLEAKRERLN-ARKEVLEDVRNQVEDEIASLDGDKRE 102
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
0.316 0.134 0.390
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: 3,913,319
Number of extensions: 295313
Number of successful extensions: 279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 18
Length of query: 77
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 31
Effective length of database: 8,897,318
Effective search space: 275816858
Effective search space used: 275816858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)