RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11065
(138 letters)
>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 = 68.7 bits (169), Expect = 1e-16
Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
+V VP + VG +IGKGG IK+++ ETGA+++ +R ++G+P+ V++A
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPD-SGSGSEERIVTITGTPEAVEKA 59
Query: 106 RARIE 110
+ I
Sbjct: 60 KELIL 64
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 66.6 bits (163), Expect = 8e-16
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQV 102
I+V +P VG++IGKGG IKK++ ETG ++ +R ++G P+ V
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI---PGPGSEERVVEITGPPENV 57
Query: 103 QEARARIEELI 113
++A I E++
Sbjct: 58 EKAAELILEIL 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 = 64.5 bits (158), Expect = 4e-15
Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 5/64 (7%)
Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
++ +P VG +IGKGG IK+++ ETG +++ R+D +SG+P+QV++A
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDD-----TVTISGTPEQVEKA 55
Query: 106 RARI 109
+ I
Sbjct: 56 KELI 59
>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 = 63.6 bits (156), Expect = 9e-15
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 51 VPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI 109
VP + G +IGKGG IK+++ ETGA+++ + ++R +SG P VQ+A I
Sbjct: 6 VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64
>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 = 46.4 bits (111), Expect = 5e-08
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
+V +PK +IGK G I+K+ ETG +++F SD ++G + V++A
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRF--PDPGSKSD-TITITGPKENVEKA 57
Query: 106 RARIE 110
+ I
Sbjct: 58 KEEIL 62
>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 = 44.9 bits (107), Expect = 1e-07
Identities = 17/42 (40%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 56 VGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG 97
VG +IGKGG+ IK+++ ETGA++Q + E +R ++G
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKP-EPGSGERIVTITG 42
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 43.9 bits (105), Expect = 6e-06
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 20/75 (26%)
Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-----SPD 100
+ + +P + VIG GG I+++ ETGA++ EDD G + D
Sbjct: 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI----EDD---------GTVKIAATD 601
Query: 101 Q--VQEARARIEELI 113
+ A+ RIE +
Sbjct: 602 GEAAEAAKERIEGIT 616
>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 = 40.2 bits (95), Expect = 1e-05
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSP-DQVQE 104
+ + +P + VIG GG IKK+ ETG ++ EDD ++ S + ++
Sbjct: 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDI----EDDG---TVYIAASDKEAAEK 55
Query: 105 ARARIE 110
A+ IE
Sbjct: 56 AKKMIE 61
>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 = 42.1 bits (100), Expect = 3e-05
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGS-PDQVQ 103
E I++ + VIG GG +I+++ ETGA++ EDD ++ S + +
Sbjct: 553 ETIKI--NPDKIRDVIGPGGKVIREITEETGAKIDI----EDDG---TVKIAASDGEAAE 603
Query: 104 EARARIEELI 113
A IE +
Sbjct: 604 AAIKMIEGIT 613
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 39.9 bits (94), Expect = 2e-04
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 9/81 (11%)
Query: 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSP-DQVQ 103
+ + + + VIG GG IK + ETG ++ EDD + ++ S + +
Sbjct: 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDI----EDDGT---VKIAASDGESAK 604
Query: 104 EARARIEELIDSVMV-EQFSG 123
+A+ RIE + V V E + G
Sbjct: 605 KAKERIEAITREVEVGEVYEG 625
>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II).
KH binds single-stranded RNA or DNA. It is found in a
wide variety of proteins including ribosomal proteins
(e.g. ribosomal protein S3), transcription factors
(e.g. NusA_K), and post-transcriptional modifiers of
mRNA (e.g. hnRNP K). There are two different KH domains
that belong to different protein folds, but they share
a single KH motif. 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. In addition to
their KH core domain, KH-II proteins have an N-terminal
alpha helical extension while KH-I proteins have a
C-terminal alpha helical extension.
Length = 68
Score = 34.9 bits (81), Expect = 0.001
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR 84
I + V + G+VIGK G I+ LQ ++ +++
Sbjct: 23 DRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKRVK 64
>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 = 35.2 bits (81), Expect = 0.007
Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 9/81 (11%)
Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
+I V +P +G VIG G MI ++Q+ETGA + EDD + G + A
Sbjct: 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISI----EDDGTVYIGAADG--PSAEAA 632
Query: 106 RARIEELIDSVMV---EQFSG 123
RA I + + M E+F G
Sbjct: 633 RAMINAIANPTMPEVGERFLG 653
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 32.5 bits (75), Expect = 0.010
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 41 EVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF 80
E T + V + + G+VIGKGG IKKL E ++
Sbjct: 21 ERTPNRVIVVIRTSQPGIVIGKGGSNIKKLGKELRKLIEL 60
>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among
the 41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single
KH domain (pfam00013) which is likely to confer the
ability to bind RNA.
Length = 172
Score = 33.3 bits (77), Expect = 0.021
Identities = 14/46 (30%), Positives = 27/46 (58%), Gaps = 8/46 (17%)
Query: 51 VPKAAVGVVIGKGGDMIKKLQNETGARVQF--------VQMREDDP 88
+PK +GV+IGKGG+ K+++ TG ++ ++ ++DP
Sbjct: 4 IPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDP 49
Score = 28.3 bits (64), Expect = 1.1
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 57 GVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELID 114
G +IG+GG + ++ TG + + + G P+QVQ AR IE LI+
Sbjct: 101 GRIIGEGGKTRRIIEELTGVSISV--------YGKTVGIIGDPEQVQIAREAIEMLIE 150
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 33.3 bits (77), Expect = 0.030
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 49 VCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDR 91
V VP+ + VIGKGG IKK++ + G + V+ +++P +
Sbjct: 485 VYVPEKDIPKVIGKGGKRIKKIEKKLGIDID-VRPLDEEPGEE 526
>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 = 32.2 bits (74), Expect = 0.030
Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 15/90 (16%)
Query: 56 VGVVIGKGGDMIKKLQNETGAR--------VQFVQMREDDPSDRRCMLSG-------SPD 100
VG+++G G+ +K+L+ ETGA+ ++ + E+ + L+ +
Sbjct: 17 VGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAET 76
Query: 101 QVQEARARIEELIDSVMVEQFSGANFDKLR 130
+EA A+ E I+ ++ G N + R
Sbjct: 77 PPEEALAKAVEAIEELLKPAIEGGNDELKR 106
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 32.2 bits (74), Expect = 0.052
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARV 78
E+ V VP+ VIGK G MI L+ ETG +
Sbjct: 150 EIKPVKVPR-----VIGKKGSMINMLKEETGCDI 178
>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 31.8 bits (73), Expect = 0.057
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 55 AVGVVIGKGGDMIKKLQNETGARVQFVQMRED 86
VG IGK G +K + E G ++ V+ ED
Sbjct: 86 PVGACIGKRGSRVKAVSEELGEKIDVVEWSED 117
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 31.8 bits (73), Expect = 0.074
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 51 VPKAAVGVVIGKGGDMIKKLQNETGARVQF 80
+PK +GV+IGK G+ K+++ TG +++
Sbjct: 9 IPKDRIGVLIGKKGETKKEIEERTGVKLEI 38
Score = 27.9 bits (63), Expect = 1.3
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 57 GVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELID 114
G +IG+GG + ++ TG + + + G P+QV+ AR IE LI+
Sbjct: 107 GRIIGEGGKTRRIIEELTGVDISV--------YGKTVAIIGDPEQVEIAREAIEMLIE 156
>gnl|CDD|234256 TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1.
The Pfam domain family pfam00296 is named for
luciferase-like monooxygenases, but the family also
contains several coenzyme F420-dependent enzymes. This
protein family represents a well-resolved clade within
family pfam00296 and shows no restriction to coenzyme
F420-positive species, unlike some other clades within
pfam00296 [Unknown function, Enzymes of unknown
specificity].
Length = 323
Score = 30.9 bits (71), Expect = 0.14
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 8/35 (22%)
Query: 89 SDRRCMLSGSPDQVQEARARIEELI-----DSVMV 118
+ + GSP+ V R ++E L D +MV
Sbjct: 272 QNLSRSIVGSPETV---REQLEALAERTGADELMV 303
>gnl|CDD|233653 TIGR01952, nusA_arch, NusA family KH domain protein, archaeal.
This model represents a family of archaeal proteins
found in a single copy per genome. It contains two KH
domains (pfam00013) and is most closely related to the
central region bacterial NusA, a transcription
termination factor named for its iteraction with phage
lambda protein N in E. coli. The proteins required for
antitermination by N include NusA, NusB, nusE
(ribosomal protein S10), and nusG. This system, on the
whole, appears not to be present in the Archaea.
Length = 141
Score = 30.1 bits (68), Expect = 0.22
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 51 VPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRED 86
V + +G IGKGG+ +K+L+ G ++ ++ E+
Sbjct: 39 VKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN 74
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 30.4 bits (69), Expect = 0.26
Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 16/82 (19%)
Query: 49 VCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARAR 108
V VP+ + VIGKGG IK+++ + G ++ ++ ++
Sbjct: 490 VKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDV-------------KPLEEEEEGEKVPVE 536
Query: 109 IEELIDSVMV---EQFSGANFD 127
IEE +++ F+G
Sbjct: 537 IEEKGKHIVLYVGPDFAGKPVR 558
>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like
protein; Validated.
Length = 140
Score = 29.4 bits (67), Expect = 0.31
Identities = 12/36 (33%), Positives = 24/36 (66%)
Query: 51 VPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRED 86
V + +G+ IGKGG+ +K+L+ + G ++ V+ +D
Sbjct: 38 VKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD 73
>gnl|CDD|180559 PRK06418, PRK06418, transcription elongation factor NusA-like
protein; Validated.
Length = 166
Score = 29.6 bits (67), Expect = 0.32
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 57 GVVIGKGGDMIKKLQNETGARVQFVQMRED 86
+ IGKGG + K L + G +V+ V+ D
Sbjct: 72 RIPIGKGGKIAKALSRKLGKKVRVVEKTND 101
>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 = 27.9 bits (63), Expect = 0.38
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFV 81
+ +V VP +G+ IGKGG ++ G ++ V
Sbjct: 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDIV 61
>gnl|CDD|213754 TIGR02971, heterocyst_DevB, ABC exporter membrane fusion protein,
DevB family. Members of this protein family are found
mostly in the Cyanobacteria, but also in the
Planctomycetes. DevB from Anabaena sp. strain PCC 7120
is partially characterized as a membrane fusion protein
of the DevBCA ABC exporter, probably a glycolipid
exporter, required for heterocyst formation. Most
Cyanobacteria have one member only, but Nostoc sp. PCC
7120 has seven members.
Length = 327
Score = 29.8 bits (67), Expect = 0.46
Identities = 23/69 (33%), Positives = 30/69 (43%), Gaps = 9/69 (13%)
Query: 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ--MREDDPSDRRCMLSGSPDQV 102
EV+ V P G D IKKL G RVQ Q D +R L + Q+
Sbjct: 12 EVVAVAAPS-------SGGTDRIKKLLVAEGDRVQAGQVLAELDSRPERTAELDVARTQL 64
Query: 103 QEARARIEE 111
EA+AR+ +
Sbjct: 65 DEAKARLAQ 73
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 29.2 bits (66), Expect = 0.53
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 8/60 (13%)
Query: 55 AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELID 114
G +IG+ G + ++ TG + V + + G +QV+ AR +E LI+
Sbjct: 112 IKGRIIGREGKTRRAIEELTGVYIS-VY-------GKTVAIIGGFEQVEIAREAVEMLIN 163
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 28.9 bits (66), Expect = 0.72
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 57 GVVIGKGGDMIKK 69
G++IGKGG M+KK
Sbjct: 239 GIIIGKGGAMLKK 251
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 29.1 bits (66), Expect = 0.72
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 57 GVVIGKGGDMIKK 69
G++IGK G MIKK
Sbjct: 242 GIIIGKNGAMIKK 254
>gnl|CDD|225484 COG2932, COG2932, Predicted transcriptional regulator
[Transcription].
Length = 214
Score = 28.5 bits (64), Expect = 0.88
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 57 GVVIGKGGD-MIKKLQNETGARVQFVQMREDDPSDRRC 93
V GG+ +KKLQ E G ++ V + D D
Sbjct: 157 VYVETDGGELYVKKLQREPGGLLRLVSLNPDYYPDEIF 194
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 28.6 bits (65), Expect = 0.98
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 4/27 (14%)
Query: 57 GVVIGKGGDMIKKLQNE----TGARVQ 79
G+VIGK G I+KL+ E TG VQ
Sbjct: 74 GIVIGKKGAEIEKLRKELEKLTGKPVQ 100
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 28.3 bits (64), Expect = 0.98
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 57 GVVIGKGGDMIKKLQNE 73
G+VIG+GG I++L
Sbjct: 52 GMVIGRGGKNIRELTEI 68
>gnl|CDD|180207 PRK05696, fliL, flagellar basal body-associated protein FliL;
Reviewed.
Length = 170
Score = 28.0 bits (63), Expect = 1.2
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 112 LIDSVMVEQFSGANFDKLRS 131
LI+S ++ FS A D+L +
Sbjct: 112 LIESALLMTFSSATVDQLST 131
>gnl|CDD|193518 cd05639, M18, M18 Peptidase aminopeptidase family. Peptidase M18
aminopeptidase family is widely distributed in bacteria
and eukaryotes, but only the yeast aminopeptidase I and
mammalian aspartyl aminopeptidase have been
characterized to date. Yeast aminopeptidase I is active
only in its dodecameric form with broad substrate
specificity, acting on N-terminal leucine and most other
amino acids. In contrast, the mammalian aspartyl
aminopeptidase is highly selective for hydrolysis of
N-terminal Asp or Glu residues from peptides. These
enzymes have two catalytic zinc ions at the active site.
Length = 427
Score = 28.2 bits (63), Expect = 1.3
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 11/49 (22%)
Query: 52 PKAAVGVVIGKGGDM-----------IKKLQNETGARVQFVQMREDDPS 89
P GVVI K + ++KL N+ + Q ++ + PS
Sbjct: 329 PNLGKGVVIKKYTNQRYATDAEGVALVRKLANKNNVKWQVATLKNNSPS 377
>gnl|CDD|212032 cd10322, SLC5sbd, Solute carrier 5 family, sodium/glucose
transporters and related proteins; solute-binding
domain. This family represents the solute-binding
domain of SLC5 proteins (also called the sodium/glucose
cotransporter family or solute sodium symporter family)
that co-transport Na+ with sugars, amino acids,
inorganic ions or vitamins. Family members include: the
human glucose (SGLT1, 2, 4, 5), chiro-inositol (SGLT5),
myo-inositol (SMIT), choline (CHT), iodide (NIS),
multivitamin (SMVT), and monocarboxylate (SMCT)
cotransporters, as well as Vibrio parahaemolyticus
glucose/galactose (vSGLT), and Escherichia coli proline
(PutP) and pantothenate (PutF) cotransporters. Vibrio
parahaemolyticus Na(+)/galactose cotransporter (vSGLT)
has 13 transmembrane helices (TMs): TM-1, an inverted
topology repeat: TMs1-5 and TMs6-10, and TMs 11-12 (TMs
numbered to conform to the solute carrier 6 family
Aquifex aeolicus LeuT). One member of this family, human
SGLT3, has been characterized as a glucose sensor and
not a transporter. Members of this family are important
in human physiology and disease.
Length = 455
Score = 27.5 bits (62), Expect = 2.7
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 37 GGMWEVTW-EVIQVCV-----PKAAVGVVIGKGGDMIKKLQN 72
GG+ V W +VIQ + A + GG + L
Sbjct: 166 GGLRAVAWTDVIQGVLMLIGVILLAFFALSKVGGGGLSALAA 207
>gnl|CDD|221909 pfam13083, KH_4, KH domain.
Length = 71
Score = 25.9 bits (58), Expect = 2.8
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKLQ 71
VI++ V +G +IGK G + LQ
Sbjct: 29 VIELNVAGEDLGKLIGKRGRTLDALQ 54
>gnl|CDD|143471 cd07559, ALDH_ACDHII_AcoD-like, Ralstonia eutrophus NAD+-dependent
acetaldehyde dehydrogenase II and Staphylococcus aureus
AldA1 (SACOL0154)-like. Included in this CD is the
NAD+-dependent, acetaldehyde dehydrogenase II (AcDHII,
AcoD, EC=1.2.1.3) from Ralstonia (Alcaligenes) eutrophus
H16 involved in the catabolism of acetoin and ethanol,
and similar proteins, such as, the dimeric
dihydrolipoamide dehydrogenase of the acetoin
dehydrogenase enzyme system of Klebsiella pneumonia.
Also included are sequences similar to the
NAD+-dependent chloroacetaldehyde dehydrogenases (AldA
and AldB) of Xanthobacter autotrophicus GJ10 which are
involved in the degradation of 1,2-dichloroethane, as
well as, the uncharacterized aldehyde dehydrogenase from
Staphylococcus aureus (AldA1, locus SACOL0154) and other
similar sequences.
Length = 480
Score = 26.9 bits (60), Expect = 3.6
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETG-ARVQF 80
E+I +PK V VV G G + K L + A++ F
Sbjct: 184 ELIGDLLPKGVVNVVTGFGSEAGKPLASHPRIAKLAF 220
>gnl|CDD|192316 pfam09533, DUF2380, Predicted lipoprotein of unknown function
(DUF2380). This family consists of at least 9 paralogs
in Myxococcus xanthus, a member of the
Deltaproteobacteria. One appears truncated toward the
N-terminus; the others are predicted lipoproteins. The
function is unknown.
Length = 191
Score = 26.7 bits (59), Expect = 4.2
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 33 GDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQ 71
G GRGG W W + P A+ + G++I + +
Sbjct: 141 GGGRGGAWNQAWRDFRRRNPGASPEEIFRHAGELIFRFE 179
>gnl|CDD|225052 COG2141, COG2141, Coenzyme F420-dependent N5,N10-methylene
tetrahydromethanopterin reductase and related
flavin-dependent oxidoreductases [Energy production and
conversion].
Length = 336
Score = 26.7 bits (59), Expect = 4.5
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 82 QMREDDPSDRRCMLSGSPDQVQEARARIEELID 114
+ R L G+P++V RIEEL
Sbjct: 271 LGLVPEGLGRGTALVGTPEEV---AERIEELAA 300
>gnl|CDD|233863 TIGR02426, protocat_pcaB, 3-carboxy-cis,cis-muconate
cycloisomerase. Members of this family are
3-carboxy-cis,cis-muconate cycloisomerase, the enzyme
the catalyzes the second step in the protocatechuate
degradation to beta-ketoadipate and then to succinyl-CoA
and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate,
and vanillate all can be converted in one step to
protocatechuate. All members of the seed alignment for
this model were chosen from within protocatechuate
degradation operons of at least three genes of the
pathway, from genomes with the complete pathway through
beta-ketoadipate [Energy metabolism, Other].
Length = 338
Score = 26.6 bits (59), Expect = 4.7
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 102 VQEARARIEELIDSVMVEQFSGA 124
V AR R+ L + QF GA
Sbjct: 166 VLRARDRLAALRTRALPLQFGGA 188
>gnl|CDD|224022 COG1097, RRP4, RNA-binding protein Rrp4 and related proteins
(contain S1 domain and KH domain) [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 26.5 bits (59), Expect = 4.7
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 49 VCVPKAAVGVVIGKGGDMIKKLQNETGARV 78
V +P + V VIGK G M+ L+ +TG +
Sbjct: 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEI 179
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 26.6 bits (59), Expect = 4.8
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 57 GVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS 115
G +IG+ G I+ + TG + DD + + S +P + + AR +E+L+
Sbjct: 211 GRIIGREGRNIRAFEGLTGVDLII-----DDTPEAVVISSFNPIRREIARLTLEKLLAD 264
>gnl|CDD|220124 pfam09139, Mmp37, Mitochondrial matrix Mmp37. MMp37 is a
mitochondrial matrix protein that functions in the
translocation of proteins across the mitochondrial
inner membrane. It has been shown that MMP37 proteins
possess the NTase fold but they have only one active
site carboxylate and thus probably are not able to
carry out enzymatic reaction. These potentially
non-active members of NTase fold superfamily may bind
ATP, hydrolysis of which is necessary for the
translocation of proteins through the membrane.
Length = 324
Score = 26.5 bits (59), Expect = 4.8
Identities = 8/18 (44%), Positives = 9/18 (50%)
Query: 63 GGDMIKKLQNETGARVQF 80
G I K+Q GA V F
Sbjct: 74 GPKAISKVQENFGAGVYF 91
>gnl|CDD|239423 cd03307, Mta_CmuA_like, MtaA_CmuA_like family. MtaA/CmuA, also
MtsA, or methyltransferase 2 (MT2) MT2-A and MT2-M
isozymes, are methylcobamide:Coenzyme M
methyltransferases, which play a role in metabolic
pathways of methane formation from various substrates,
such as methylated amines and methanol. Coenzyme M,
2-mercaptoethylsulfonate or CoM, is methylated during
methanogenesis in a reaction catalyzed by three
proteins. A methyltransferase methylates the corrinoid
cofactor, which is bound to a second polypeptide, a
corrinoid protein. The methylated corrinoid protein then
serves as a substrate for MT2-A and related enzymes,
which methylate CoM.
Length = 326
Score = 26.5 bits (59), Expect = 4.9
Identities = 9/29 (31%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 92 RCMLSGSPDQVQ-EARARIEELIDSVMVE 119
+ +L+G+P+ V+ EAR +E+ +D +
Sbjct: 277 QTLLNGTPEDVKAEARKCLEDGVDILAPG 305
>gnl|CDD|181627 PRK09053, PRK09053, 3-carboxy-cis,cis-muconate cycloisomerase;
Provisional.
Length = 452
Score = 26.5 bits (59), Expect = 6.1
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 100 DQVQEARARIEELIDSVMVEQFSGA 124
D + R R+ L +V QF GA
Sbjct: 173 DALLRHRQRLAALRPRALVLQFGGA 197
>gnl|CDD|143625 cd07758, ThTPase, Thiamine Triphosphatase. ThTPase is a soluble
cytosolic enzyme which converts thiamine triphosphate
(ThTP) to thiamine diphosphate. This catalytic activity
depends on a divalent metal cofactor, for example Mg++.
ThTPase regulates the intracellular concentration of
ThTP, maintaining it at a low concentration in vivo.
ThTP acts as a messenger in cell signaling in response
to cellular stress, and in addition, can phosphorylate
proteins in certain tissues. There is another class of
membrane-associated enzymes in animal tissues which also
convert ThTP to thiamine diphosphate, however they do
not belong to this subgroup. This subgroup belongs to
the CYTH/triphosphate tunnel metalloenzyme (TTM)-like
superfamily, whose enzymes have a unique active site
located within an eight-stranded beta barrel.
Length = 196
Score = 26.2 bits (58), Expect = 6.2
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 93 CMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDK 128
+ +V A A+I+ELI ++M A
Sbjct: 152 VEEEDNEAEVPAALAKIDELISALMERY-LWAFKQG 186
>gnl|CDD|131322 TIGR02269, TIGR02269, Myxococcus xanthus paralogous lipoprotein
family TIGR02269. This family consists of at least 9
paralogs in Myxococcus xanthus, a member of the
Deltaproteobacteria. One appears truncated toward the
N-terminus; the others are predicted lipoproteins. The
function is unknown.
Length = 211
Score = 26.0 bits (57), Expect = 6.5
Identities = 11/39 (28%), Positives = 17/39 (43%)
Query: 33 GDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQ 71
G GRGG W W P A+ + G++I + +
Sbjct: 165 GAGRGGAWNQAWRDFARRYPGASPEEIWRHAGELIFRFE 203
>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional.
Length = 936
Score = 26.3 bits (58), Expect = 6.9
Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 65 DMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI-EELIDSVMVEQFSG 123
DM + L+ + + R+D ++ R ML + D+++ A I ++++ E G
Sbjct: 530 DMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIGRDIMERTAEELTIG 589
>gnl|CDD|204877 pfam12313, NPR1_like_C, NPR1/NIM1 like defence protein C terminal.
This family of proteins is found in eukaryotes. Proteins
in this family are typically between 251 and 588 amino
acids in length. The family is found in association with
pfam00023, pfam00651. There are two conserved sequence
motifs: LENRV and DLN. NPR1 (NIM1) is a defence protein
in many plant species.
Length = 203
Score = 25.8 bits (57), Expect = 7.2
Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 85 EDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLRSTVLANRS 138
+DD D + G+P++ ++ R R EL + V + FS + RS++ ++ S
Sbjct: 149 DDDLPDLAYLEKGTPEEQKQKRMRFMELKEDVQ-KAFSKDKEELNRSSLSSSSS 201
>gnl|CDD|239095 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the
prokaryotic 30S small ribosomal subunit protein S3. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. 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. 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 = 109
Score = 25.1 bits (56), Expect = 8.0
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 57 GVVIGKGGDMIKKLQNE 73
G++IGK G I+KL+ E
Sbjct: 73 GIIIGKKGAGIEKLRKE 89
>gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type. This
model describes the bacterial type of ribosomal protein
S3. Chloroplast and mitochondrial forms have large,
variable inserts between conserved N-terminal and
C-terminal domains. This model recognizes all bacterial
forms and many chloroplast forms above the trusted
cutoff score. TIGRFAMs model TIGR01008 describes S3 of
the eukaryotic cytosol and of the archaea [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 211
Score = 25.7 bits (57), Expect = 8.2
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 47 IQVCVPKAAVGVVIGKGGDMIKK----LQNETGARVQ 79
I+V + A G+VIGK G I+K LQ TG VQ
Sbjct: 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTGKEVQ 100
>gnl|CDD|223094 COG0015, PurB, Adenylosuccinate lyase [Nucleotide transport and
metabolism].
Length = 438
Score = 26.0 bits (58), Expect = 8.5
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 100 DQVQEARARIEELIDSVMVEQFSGAN 125
++ R+EE + ++V + GA
Sbjct: 163 AELLRHLERLEEAEERIIVGKIGGAV 188
>gnl|CDD|224750 COG1837, COG1837, Predicted RNA-binding protein (contains KH
domain) [General function prediction only].
Length = 76
Score = 24.4 bits (54), Expect = 9.3
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKL 70
I++ V +G VIGK G I+ +
Sbjct: 31 TIELRVAPEDMGKVIGKQGRTIQAI 55
>gnl|CDD|239094 cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of
the archaeal 30S small ribosomal subunit S3 protein. S3
is part of the head region of the 30S ribosomal
subunit and is believed to interact with mRNA as it
threads its way from the latch into the channel. 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. 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 = 85
Score = 24.5 bits (54), Expect = 9.7
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 57 GVVIGKGGDMIKKLQNE 73
G+VIG+GG I++L
Sbjct: 50 GMVIGRGGKNIRELTEI 66
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 25.6 bits (57), Expect = 9.8
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 100 DQVQEARARIEELIDSVMV 118
V R I++L+D+VMV
Sbjct: 121 GAVIRNRKEIDQLLDTVMV 139
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
0.318 0.134 0.400
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,146,090
Number of extensions: 637545
Number of successful extensions: 837
Number of sequences better than 10.0: 1
Number of HSP's gapped: 829
Number of HSP's successfully gapped: 79
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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 (21.7 bits)
S2: 54 (24.5 bits)