RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11929
(433 letters)
>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like Hen4,
a protein that plays a role in AGAMOUS (AG) pre-mRNA
processing and important step in plant development. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 65
Score = 86.0 bits (214), Expect = 5e-21
Identities = 29/65 (44%), Positives = 47/65 (72%)
Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
L+L++P++ GS+IGKGG IK+IR+ +GA ++V+ +LP STER+VT+ G P + +A
Sbjct: 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60
Query: 185 IYQIC 189
+ I
Sbjct: 61 LLLIL 65
Score = 59.4 bits (145), Expect = 1e-11
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG---ACPDRIVTVSGSVDN 72
T+R L SS + +IG GG ++ +R+E+GAKI ++ +R+VT+SG
Sbjct: 1 TLRLLVPSS----QAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSA 56
Score = 35.9 bits (84), Expect = 0.002
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 299 AGCVIGKAGSRLLEIRQISGAQINI 323
AG +IGK GS + EIR+ +GA+I +
Sbjct: 11 AGSIIGKGGSTIKEIREETGAKIRV 35
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 64.5 bits (158), Expect = 2e-13
Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
++++P++ G +IGKGG IK+IR+ +GA +++ S ERIVT+ G P+ + +A
Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-SGSEERIVTITGTPEAVEKAK 60
Query: 186 YQIC 189
I
Sbjct: 61 ELIL 64
Score = 51.0 bits (123), Expect = 1e-08
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDN 72
V + + +IG GG ++ +R+E+GAKI I D +RIVT++G+ +
Sbjct: 6 VPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEA 55
Score = 45.2 bits (108), Expect = 1e-06
Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHT-GTESHKKMFHIQGCQEAVSLAQ 347
+++ + G +IGK GS + EIR+ +GA+I I G+ S +++ I G EAV A+
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60
Query: 348 YLI 350
LI
Sbjct: 61 ELI 63
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 56.9 bits (138), Expect = 1e-10
Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTIS 182
P+ ++++IPA G +IGKGG IK I + +G + + P S ER+V + G P+ +
Sbjct: 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI---PGPGSEERVVEITGPPENVE 58
Query: 183 QAIYQI 188
+A I
Sbjct: 59 KAAELI 64
Score = 49.6 bits (119), Expect = 4e-08
Identities = 13/48 (27%), Positives = 29/48 (60%)
Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
+ +++ +IG GG ++++ +E+G KI I +R+V ++G +N
Sbjct: 9 IPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPEN 56
Score = 46.1 bits (110), Expect = 7e-07
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSL 345
D V E+++ D G +IGK GS + +I + +G +I+I + I G E V
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERV-VEITGPPENVEK 59
Query: 346 AQYLINMCI 354
A LI +
Sbjct: 60 AAELILEIL 68
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 56.4 bits (137), Expect = 1e-10
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
+++IP G +IGKGG IK+IR+ +G +++ D + VT+ G P+ + +A
Sbjct: 2 ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD-----RDDTVTISGTPEQVEKAK 56
Query: 186 YQI 188
I
Sbjct: 57 ELI 59
Score = 47.6 bits (114), Expect = 2e-07
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQY 348
I++ D G +IGK GS + EIR+ +G +I I + I G E V A+
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP---DDRDDTVTISGTPEQVEKAKE 57
Query: 349 LI 350
LI
Sbjct: 58 LI 59
Score = 47.6 bits (114), Expect = 2e-07
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
+ +++ +IG GG ++ +R+E+G KI I D D VT+SG+ +
Sbjct: 5 LIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD--RDDTVTISGTPEQ 51
>gnl|CDD|221895 pfam13014, KH_3, KH domain. KH motifs bind RNA in vitro. This
RNA-binding domain is required for the efficient
anchoring of ASH1-mRNA to the distal tip of the daughter
cell. ASH1 is a specific repressor of transcription that
localizes asymmetrically to the daughter cell nucleus.
RNA localisation is a widespread mechanism for achieving
localised protein synthesis.
Length = 42
Score = 49.9 bits (120), Expect = 2e-08
Identities = 21/43 (48%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG 176
G++IGKGG IK+IR+ +GA +Q+ P S ERIVT+ G
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQI-PKPEPGSGERIVTITG 42
Score = 44.5 bits (106), Expect = 1e-06
Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 2/41 (4%)
Query: 30 ISCLIGPGGCIVRRLRKESGAKISI--TDGACPDRIVTVSG 68
+ +IG GG ++ +R+E+GAKI I + +RIVT++G
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42
Score = 36.4 bits (85), Expect = 0.001
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 299 AGCVIGKAGSRLLEIRQISGAQINIH-TGTESHKKMFHIQG 338
G +IGK G + EIR+ +GA+I I S +++ I G
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42
>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 62
Score = 40.2 bits (95), Expect = 6e-05
Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
++ IP +IGK G I+ I + +G ++ P S +T+ G + + +A
Sbjct: 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPD---PGSKSDTITITGPKENVEKAK 58
Query: 186 YQIC 189
+I
Sbjct: 59 EEIL 62
Score = 38.6 bits (91), Expect = 3e-04
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 33 LIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
+IG G +R++ +E+G KI D +T++G +N
Sbjct: 14 IIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKEN 53
Score = 25.9 bits (58), Expect = 8.4
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 302 VIGKAGSRLLEIRQISGAQINI 323
+IGK GS + +I + +G +I
Sbjct: 14 IIGKKGSNIRKIMEETGVKIRF 35
>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K
homology RNA-binding domain (KH). PNPase is a
polyribonucleotide nucleotidyl transferase that
degrades mRNA in prokaryotes and plant chloroplasts.
The C-terminal region of PNPase contains domains
homologous to those in other RNA binding proteins: a KH
domain and an S1 domain. KH domains bind
single-stranded RNA and are found in a wide variety of
proteins including ribosomal proteins, transcription
factors and post-transcriptional modifiers of mRNA.
Length = 61
Score = 36.7 bits (86), Expect = 0.001
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
+ ++I +IGPGG ++++ +E+G KI I D D V ++ S
Sbjct: 8 IPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----DGTVYIAAS 48
Score = 27.5 bits (62), Expect = 2.5
Identities = 12/40 (30%), Positives = 18/40 (45%)
Query: 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD 162
P + IP +IG GG IK I + +G + + D
Sbjct: 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD 40
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
RNA-binding domain (KH). Splicing factor 1 (SF1)
specifically recognizes the intron branch point
sequence (BPS) UACUAAC in the pre-mRNA transcripts
during spliceosome assembly. We show that the KH-QUA2
region of SF1 defines an enlarged KH (hnRNP K) fold
which is necessary and sufficient for BPS binding. KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 120
Score = 37.6 bits (88), Expect = 0.002
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 28 NEISCLIGPGGCIVRRLRKESGAKISI 54
N + ++GP G +++L KE+GAKISI
Sbjct: 15 NFVGLILGPRGNTLKQLEKETGAKISI 41
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 39.9 bits (94), Expect = 0.003
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNS 73
++ ++I +IGPGG ++ + +E+G KI I D D V ++ S S
Sbjct: 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDIED----DGTVKIAASDGES 602
Score = 28.7 bits (65), Expect = 7.4
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASD 162
I +IG GG IK I + +G + + D
Sbjct: 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD 590
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 39.4 bits (93), Expect = 0.003
Identities = 18/45 (40%), Positives = 29/45 (64%), Gaps = 4/45 (8%)
Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
+N ++I +IGPGG ++R + +E+GAKI I D D V ++ S
Sbjct: 557 INPDKIRDVIGPGGKVIREITEETGAKIDIED----DGTVKIAAS 597
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 38.5 bits (91), Expect = 0.007
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 10/56 (17%)
Query: 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
+ T++ + ++I +IGPGG +R + +E+GAKI I D D V ++ +
Sbjct: 555 IETIK------IPPDKIRDVIGPGGKTIREITEETGAKIDIED----DGTVKIAAT 600
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 31.7 bits (72), Expect = 0.78
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVET 80
+ V++I +IGP G ++ +++ E+GA+ISI D D V + + S+ ++
Sbjct: 584 IPVDKIGEVIGPKGKMINQIQDETGAEISIED----DGTVYIGAADGPSAEAARAM 635
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 27.7 bits (63), Expect = 0.80
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 1 MDGNGDGKIDEDTLITM 17
D +GDGKID + +
Sbjct: 9 FDKDGDGKIDFEEFKDL 25
>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA
is an essential multifunctional transcription
elongation factor that is universally conserved among
prokaryotes and archaea. NusA anti-termination function
plays an important role in the expression of ribosomal
rrn operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices.
Length = 61
Score = 28.3 bits (64), Expect = 1.3
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISIT 55
V +++ IG GG VR K G KI I
Sbjct: 31 VPDDQLGLAIGKGGQNVRLASKLLGEKIDIV 61
>gnl|CDD|238225 cd00383, trans_reg_C, Effector domain of response regulator.
Bacteria and certain eukaryotes like protozoa and
higher plants use two-component signal transduction
systems to detect and respond to changes in the
environment. The system consists of a sensor histidine
kinase and a response regulator. The former
autophosphorylates in a histidine residue on detecting
an external stimulus. The phosphate is then transferred
to an invariant aspartate residue in a highly conserved
receiver domain of the response regulator.
Phosphorylation activates a variable effector domain of
the response regulator, which triggers the cellular
response. The C-terminal effector domain contains DNA
and RNA polymerase binding sites. Several dimers or
monomers bind head to tail to small tandem repeats
upstream of the genes. The RNA polymerase binding sites
interact with the alpha or sigma subunite of RNA
polymerase.
Length = 95
Score = 28.6 bits (65), Expect = 2.1
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 41 VRRLRKESGAKISITDGACPDRIVTVSG 68
+ RLRK K+ D + P I TV G
Sbjct: 68 ISRLRK----KLE-DDPSNPRLIKTVRG 90
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
processing and modification].
Length = 269
Score = 29.9 bits (67), Expect = 2.3
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 27 VNEISCLIGPGGCIVRRLRKESGAKISI 54
N + LIGP G +++L + S AKI+I
Sbjct: 162 SNFVGLLIGPRGSTLKQLERISRAKIAI 189
>gnl|CDD|235357 PRK05177, minC, septum formation inhibitor; Reviewed.
Length = 239
Score = 29.1 bits (66), Expect = 3.6
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 249 GLAVLGIEGIGSTSLTPAALAALSGSR 275
G+ +LGIEG + L P AL G R
Sbjct: 77 GIRILGIEGARPSLLGPGMPPALVGGR 103
>gnl|CDD|148510 pfam06935, DUF1284, Protein of unknown function (DUF1284). This
family consists of several hypothetical bacterial and
archaeal proteins of around 130 residues in length. The
function of this family is unknown, although it is
thought that they may be iron-sulphur binding proteins.
Length = 103
Score = 27.7 bits (62), Expect = 4.2
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 6/30 (20%)
Query: 40 IVRRLRKESGAKISITDG------ACPDRI 63
IV RLR E G I + DG CP++
Sbjct: 13 IVERLRAEPGEDIELVDGPDDICAPCPNKR 42
>gnl|CDD|163690 cd08059, MPN_prok_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding);
prokaryotic. This family contains bacterial and
archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB,
MPN+)-like domains. These catalytically active domains
contain the signature JAB1/MPN/Mov34 metalloenzyme
(JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
ion coordination and provides the active site for
isopeptidase activity for the release of ubiquitin from
ubiquitinated proteins (thus having deubiquitinating
(DUB) activity) that are tagged for degradation. The
JAMM proteins likely hydrolyze ubiquitin conjugates in a
manner similar to thermolysin, in which the
zinc-polarized aqua ligand serves as the nucleophile,
compared with the classical DUBs that do so with a
cysteine residue in the active site.
Length = 101
Score = 27.5 bits (61), Expect = 4.3
Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 4/53 (7%)
Query: 131 PATHCGSLIGKGGCKIKDIRDLSGANVQVAS----DMLPMSTERIVTVHGNPD 179
P CG L G + ++ L + V++ L + + + VH +P
Sbjct: 15 PDEFCGFLSGSKDNVMDELIFLPFVSGSVSAVIDLAALEIGMKVVGLVHSHPS 67
>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 28.4 bits (64), Expect = 5.2
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISI 54
V ++ + IG G V+ + +E G KI +
Sbjct: 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDV 111
>gnl|CDD|221809 pfam12852, Cupin_6, Cupin. This is a family of bacterial and
eukaryotic proteins that belong to the Cupin
superfamily. Some of the proteins in this family are
annotated as being members of the AraC family of
transcription factors, in which case this domain
corresponds to the ligand binding domain.
Length = 185
Score = 28.4 bits (64), Expect = 5.6
Identities = 19/71 (26%), Positives = 25/71 (35%), Gaps = 5/71 (7%)
Query: 194 ECTLQVVKGAVIPYEPKTMNAGP-VILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAV 252
C L++ G EP + AG V+L G A+ L + P V V
Sbjct: 45 SCWLRLPGGG----EPVRLEAGDLVLLPRGDAHVLADDPGTPPVPVDALPVRDAAGEGEV 100
Query: 253 LGIEGIGSTSL 263
L G T L
Sbjct: 101 LHGGGGARTVL 111
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 26.3 bits (59), Expect = 7.1
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 122 QPLQLKLVIPATHCGSLIGKGGCKIKDIR 150
P ++ +VI + G +IGKGG IK +
Sbjct: 23 TPNRVIVVIRTSQPGIVIGKGGSNIKKLG 51
>gnl|CDD|215233 PLN02424, PLN02424, ketopantoate hydroxymethyltransferase.
Length = 332
Score = 28.2 bits (63), Expect = 9.1
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 7/54 (12%)
Query: 248 AGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGC 301
AG+AV+G G LTP A++ L G R + ++ VET + L + AGC
Sbjct: 150 AGIAVMGHVG-----LTPQAISVLGGFRPQGRTAESAVKVVETALALQE--AGC 196
>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
Length = 534
Score = 28.2 bits (63), Expect = 9.6
Identities = 21/106 (19%), Positives = 39/106 (36%), Gaps = 20/106 (18%)
Query: 58 ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVD------NVCTA------------- 98
+RI + G ++ S ++VE+ PG + W N C
Sbjct: 340 VFNNRIYVIGGIYNSISLNTVESWKPGESKWREEPPLIFPRYNPCVVNVNNLIYVIGGIS 399
Query: 99 -YNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGG 143
+ + +++E + +N N+ SP P+ H G + GG
Sbjct: 400 KNDELLKTVECFSLNTNKWSKGSPLPISHYGGCAIYHDGKIYVIGG 445
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 28.3 bits (64), Expect = 9.8
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 128 LVIPATHCGSLIGKGGCKIKDIRDLSGANVQV 159
+ +P +IGKGG +IK I G ++ V
Sbjct: 485 VYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDV 516
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 0.133 0.385
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,320,070
Number of extensions: 2032390
Number of successful extensions: 1808
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1798
Number of HSP's successfully gapped: 48
Length of query: 433
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 333
Effective length of database: 6,502,202
Effective search space: 2165233266
Effective search space used: 2165233266
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: 60 (26.9 bits)