RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11118
(137 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 65.6 bits (161), Expect = 1e-15
Identities = 26/53 (49%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALT 90
RR NERER R +NDAF+ LRE++P ++LSK E L LA YI L
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPTPPN-KKLSKAEILRLAIEYIKHLQ 52
>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 = 64.9 bits (159), Expect = 3e-15
Identities = 23/59 (38%), Positives = 34/59 (57%)
Query: 35 KNMRRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVI 93
+ RR N RER R +NDAF LR ++P + ++LSK E L A +YI +L ++
Sbjct: 1 RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 63.8 bits (156), Expect = 7e-15
Identities = 22/50 (44%), Positives = 30/50 (60%)
Query: 43 NERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNV 92
N RER R +N+AF LR ++P + K ++LSK E L LA YI +L
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEE 50
>gnl|CDD|219478 pfam07586, HXXSHH, Protein of unknown function (DUF1552). A family
of proteins identified in Rhodopirellula baltica.
Length = 298
Score = 31.9 bits (73), Expect = 0.080
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 15/72 (20%)
Query: 10 GGGAGGGRGGSSSGRRRKPVLNAREKNMRRLE----SNERERMRMHSLNDAFQSLREVIP 65
G G+ + RRR+ +L+A ++ + L +R ++ + S+RE+
Sbjct: 141 GSGSASLEQRKARLRRRRSILDAVLEDAKSLRRKLGKEDRAKLDEY-----LTSVREI-- 193
Query: 66 HVKKERRLSKIE 77
E+RL K E
Sbjct: 194 ----EKRLEKAE 201
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 28.8 bits (64), Expect = 0.89
Identities = 13/47 (27%), Positives = 17/47 (36%)
Query: 10 GGGAGGGRGGSSSGRRRKPVLNAREKNMRRLESNERERMRMHSLNDA 56
G G G GGS P + R ++ R+H NDA
Sbjct: 296 GHGNMGMAGGSGMNPPNPPAFMGMNNMVHRGRQKKQRFQRIHPYNDA 342
>gnl|CDD|221290 pfam11885, DUF3405, Protein of unknown function (DUF3405). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 636 to 810
amino acids in length.
Length = 483
Score = 28.5 bits (64), Expect = 1.1
Identities = 10/26 (38%), Positives = 11/26 (42%)
Query: 15 GGRGGSSSGRRRKPVLNAREKNMRRL 40
GG G+S G R RE N R
Sbjct: 409 GGPNGASGGARPSVFGWDREHNFRGT 434
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 28.2 bits (63), Expect = 1.2
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 10 GGGAGGGRGGSSSGRRRKPV 29
GG GGGRGG G K +
Sbjct: 39 RGGGGGGRGGGGGGGPGKVI 58
>gnl|CDD|178307 PLN02705, PLN02705, beta-amylase.
Length = 681
Score = 27.6 bits (61), Expect = 2.3
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 1 VSDDTCSISGGGAGGGRGGSSSGRRRKPVLNAREKNMRRLESNERER 47
++ ++ G G GG G+ ++ REK R + ER R
Sbjct: 53 IAPTENDVNNGNISSGGGGGGGGKGKR----EREKEKERTKLRERHR 95
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 27.3 bits (61), Expect = 3.2
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 33 REKNMRRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTN 91
R+ N+R NER R ++ LN +Q L+E + + E + +Y+ +T+
Sbjct: 266 RDINVRGFVYNERTRDQL--LNSLYQILKERKLALDDA---NSKEKKRFSPHYVFLITD 319
>gnl|CDD|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed.
Length = 284
Score = 26.7 bits (60), Expect = 3.7
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTL 81
LE + E R L DA + L E + + R L + TL
Sbjct: 209 DVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD-DKSTL 251
>gnl|CDD|218851 pfam06007, PhnJ, Phosphonate metabolism protein PhnJ. This family
consists of several bacterial phosphonate metabolism
(PhnJ) sequences. The exact role that PhnJ plays in
phosphonate utilisation is unknown.
Length = 279
Score = 26.9 bits (60), Expect = 3.8
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 37 MRRLESNERERMRMHSLND 55
+R +E +E E +MH+ D
Sbjct: 129 LRFVEPSEAETRKMHAEAD 147
>gnl|CDD|153326 cd07642, BAR_ASAP2, The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP
with SH3 domain, ANK repeat and PH domain containing
protein 2. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. ASAP2 (ArfGAP with SH3
domain, ANK repeat and PH domain containing protein 2)
is also known as DDEF2 (Development and Differentiation
Enhancing Factor 2), AMAP2, centaurin beta-3, or PAG3.
ASAP2 mediates the functions of Arf GTPases vial dual
mechanisms: it exhibits GTPase activating protein (GAP)
activity towards class I (Arf1) and II (Arf5) Arfs; and
binds class III Arfs (GTP-Arf6) stably without GAP
activity. It binds paxillin and is implicated in Fcgamma
receptor-mediated phagocytosis in macrophages and in
cell migration. ASAP2 contains an N-terminal BAR domain,
followed by a Pleckstrin homology (PH) domain, an Arf
GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3
domain. BAR domains form dimers that bind to membranes,
induce membrane bending and curvature, and may also be
involved in protein-protein interactions. The BAR domain
of the related protein ASAP1 mediates membrane bending,
is essential for function, and autoinhibits GAP activity
by interacting with the PH and/or Arf GAP domains.
Length = 215
Score = 26.1 bits (57), Expect = 6.3
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 23 GRRRKPVLNA---REKNMRRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIE 77
G +KP A E + ++E ++E +MH + S E+ ++KERR +++
Sbjct: 107 GDLKKPFDKAWKDYETKVTKIEKEKKEHAKMHGMIRTEISGAEIAEEMEKERRFFQLQ 164
>gnl|CDD|182582 PRK10602, PRK10602, murein peptide amidase A; Provisional.
Length = 237
Score = 25.8 bits (57), Expect = 7.4
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 102 PYVAPDSSTGLITSGTQGD 120
P A +GLI +GT GD
Sbjct: 33 PAPAASRESGLILAGTHGD 51
>gnl|CDD|235363 PRK05198, PRK05198, 2-dehydro-3-deoxyphosphooctonate aldolase;
Provisional.
Length = 264
Score = 25.8 bits (58), Expect = 7.9
Identities = 13/20 (65%), Positives = 15/20 (75%), Gaps = 2/20 (10%)
Query: 15 GGRGGSSSGRRRK-PVLNAR 33
GG+GGSS G+R PVL AR
Sbjct: 198 GGQGGSSGGQREFVPVL-AR 216
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 25.8 bits (57), Expect = 9.4
Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 11 GGAGGGRGGSSSGRRRKPVLNAREKNMRRLESNERERMRMHSLNDAFQSLREVIPHVKKE 70
GG+ R + R K + + +LE E E SL + +SL +++ ++++
Sbjct: 654 GGSRNKRSSLAQKRELKELEEELAELEAQLEKLEEEL---KSLKNELRSLEDLLEELRRQ 710
Query: 71 RRLSKIETLTLAKNYIMALT 90
+ + L K + AL
Sbjct: 711 LEELERQ-LEELKRELAALE 729
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
0.314 0.130 0.365
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: 6,878,305
Number of extensions: 600497
Number of successful extensions: 744
Number of sequences better than 10.0: 1
Number of HSP's gapped: 728
Number of HSP's successfully gapped: 49
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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 (22.0 bits)
S2: 54 (24.5 bits)