RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7546
(150 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 = 65.2 bits (160), Expect = 4e-15
Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV---PDCPGPERILTIFAELENGLKV 78
LRLL+PS AGS+IGKGGS I +R + A + V ER++TI + K
Sbjct: 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60
Query: 79 IEEVL 83
+ +L
Sbjct: 61 LLLIL 65
Score = 49.8 bits (120), Expect = 3e-09
Identities = 17/26 (65%), Positives = 22/26 (84%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
+RL+V SQAG IIGKGG+ IKE+R+
Sbjct: 2 LRLLVPSSQAGSIIGKGGSTIKEIRE 27
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 55.8 bits (135), Expect = 2e-11
Identities = 21/65 (32%), Positives = 34/65 (52%)
Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKV 78
+ V + +LIP+ G +IGKGGS I ++ + + +P ER++ I EN K
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKA 60
Query: 79 IEEVL 83
E +L
Sbjct: 61 AELIL 65
Score = 35.3 bits (82), Expect = 0.001
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
I +++ + G IIGKGG+ IK++ +
Sbjct: 5 IEVLIPADKVGLIIGKGGSTIKKIEEETGV 34
>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 = 54.5 bits (132), Expect = 4e-11
Identities = 25/64 (39%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTIFAELENGLKVI 79
R+L+PS + G +IGKGGS I +R + A + +PD ERI+TI E K
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60
Query: 80 EEVL 83
E +L
Sbjct: 61 ELIL 64
Score = 39.5 bits (93), Expect = 3e-05
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
R++V S G IIGKGG+ IKE+R+ A
Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGA 31
>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 = 49.5 bits (119), Expect = 4e-09
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEE 81
R+LIP G +IGKGGSNI +R + + +PD + +TI E K E
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD--DRDDTVTISGTPEQVEKAKEL 58
Query: 82 V 82
+
Sbjct: 59 I 59
Score = 37.2 bits (87), Expect = 2e-04
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
R+++ + G IIGKGG+ IKE+R+
Sbjct: 2 ERILIPPDKVGRIIGKGGSNIKEIREETGV 31
>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 = 42.1 bits (100), Expect = 3e-06
Identities = 19/62 (30%), Positives = 29/62 (46%)
Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEE 81
+ IP ++ +IGK GSNI ++ + + PD +TI EN K EE
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEE 60
Query: 82 VL 83
+L
Sbjct: 61 IL 62
Score = 27.1 bits (61), Expect = 0.88
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 133 IIGKGGTKIKELRDTFDA 150
IIGK G+ I+++ +
Sbjct: 14 IIGKKGSNIRKIMEETGV 31
>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 = 37.5 bits (88), Expect = 8e-05
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 32 AGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTI 68
G++IGKGG I +R + A + +P ERI+TI
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTI 40
Score = 30.6 bits (70), Expect = 0.031
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 129 QAGCIIGKGGTKIKELRDTFDA 150
G IIGKGG IKE+R+ A
Sbjct: 1 LVGAIIGKGGETIKEIREETGA 22
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 32.9 bits (76), Expect = 0.011
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
+ +++ SQ G +IGKGG+ IK+L
Sbjct: 27 VIVVIRTSQPGIVIGKGGSNIKKLG 51
Score = 26.7 bits (60), Expect = 2.0
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 33 GSVIGKGGSNIARLRNDFKASVTVPDCP 60
G VIGKGGSNI +L + + + +
Sbjct: 37 GIVIGKGGSNIKKLGKELRKLIELEGKK 64
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 34.4 bits (80), Expect = 0.013
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 11 FKRFRGGPNDVELR------LLIPSRVAGSVIGKGGSNIARLRNDFKASVTV 56
KR+ GP +VE+ + +P + VIGKGG I ++ + V
Sbjct: 465 IKRYLPGPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDV 516
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 31.3 bits (72), Expect = 0.13
Identities = 10/25 (40%), Positives = 19/25 (76%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
+R+ +H ++ G +IGK G +I++LR
Sbjct: 64 VRVTIHTARPGIVIGKKGAEIEKLR 88
Score = 28.2 bits (64), Expect = 1.3
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 33 GSVIGKGGSNIARLRND 49
G VIGK G+ I +LR +
Sbjct: 74 GIVIGKKGAEIEKLRKE 90
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 31.6 bits (72), Expect = 0.15
Identities = 19/75 (25%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 11 FKRFRGGPNDVELR------LLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
KR+ G +VE+ + +P + VIGKGG I + + V E
Sbjct: 470 IKRYLPGDVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE 529
Query: 65 ILTIFAELENGLKVI 79
+ E+E K I
Sbjct: 530 GEKVPVEIEEKGKHI 544
>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
structure and biogenesis].
Length = 233
Score = 30.3 bits (69), Expect = 0.26
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTF 148
R+ +H ++ G +IGK G+ I++LR
Sbjct: 53 TRVTIHAARPGLVIGKKGSNIEKLRKEL 80
Score = 27.6 bits (62), Expect = 2.0
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 33 GSVIGKGGSNIARLRNDFK 51
G VIGK GSNI +LR + +
Sbjct: 63 GLVIGKKGSNIEKLRKELE 81
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 30.2 bits (69), Expect = 0.34
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 116 KDDYDIRLIVHQ-------SQAGCIIGKGGTKIKE 143
++ L +H SQ G IIGK G IK+
Sbjct: 220 EEREKGLLKIHATIYVERESQKGIIIGKNGAMIKK 254
>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 = 29.4 bits (67), Expect = 0.36
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
+ + +H ++ G IIGK G I++LR
Sbjct: 63 VEVTIHTARPGIIIGKKGAGIEKLR 87
Score = 26.3 bits (59), Expect = 3.8
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 33 GSVIGKGGSNIARLRND 49
G +IGK G+ I +LR +
Sbjct: 73 GIIIGKKGAGIEKLRKE 89
>gnl|CDD|227247 COG4910, PduE, Propanediol dehydratase, small subunit [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 170
Score = 29.6 bits (66), Expect = 0.41
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 44 ARLRNDFKAS---VTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKY 93
L +F+ + VPD +RIL I+ L EE+L D + Y
Sbjct: 96 PTLALNFERAAELTEVPD----DRILEIYNALRPYRSSKEELLAIADTLEDTY 144
>gnl|CDD|165467 PHA03200, PHA03200, uracil DNA glycosylase; Provisional.
Length = 255
Score = 29.7 bits (67), Expect = 0.43
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 55 TVPDCPGPERILTIFAELE 73
TV P + +F ELE
Sbjct: 107 TVRGRSAPPSLKNVFRELE 125
>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 = 29.2 bits (66), Expect = 0.66
Identities = 11/27 (40%), Positives = 20/27 (74%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147
IR+ +H ++ G +IGK G++I++LR
Sbjct: 64 IRVTIHTARPGIVIGKKGSEIEKLRKD 90
Score = 26.5 bits (59), Expect = 5.8
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 33 GSVIGKGGSNIARLRNDF------KASVTVPDCPGPERILTIFAE 71
G VIGK GS I +LR D + + + + PE + A+
Sbjct: 74 GIVIGKKGSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVAD 118
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 29.1 bits (66), Expect = 1.0
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 90 RQKYGKGRGGEDGGDGYNGGGV 111
R+K+ K GG DGG+G GG V
Sbjct: 26 REKF-KPLGGPDGGNGGRGGSV 46
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 28.5 bits (65), Expect = 1.3
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 128 SQAGCIIGKGGTKIKE 143
SQ G IIGKGG +K+
Sbjct: 236 SQKGIIIGKGGAMLKK 251
>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 = 26.8 bits (60), Expect = 1.4
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFK 51
P+ +E+ +++ G VIGK G NI L+ +
Sbjct: 22 PDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQ 55
>gnl|CDD|224750 COG1837, COG1837, Predicted RNA-binding protein (contains KH
domain) [General function prediction only].
Length = 76
Score = 26.8 bits (60), Expect = 1.6
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
I L V G +IGK G I+ +R
Sbjct: 32 IELRVAPEDMGKVIGKQGRTIQAIR 56
>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 = 27.4 bits (61), Expect = 1.9
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149
D + +V + + G IGKGG +K L +
Sbjct: 31 DRNRVVFVVKEGEMGAAIGKGGENVKRLEELIG 63
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 27.9 bits (63), Expect = 2.1
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 90 RQKYGKGRGGEDGGDGYNGGGV 111
R+K+ +GG DGGDG GG V
Sbjct: 25 REKF-VPKGGPDGGDGGRGGSV 45
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 27.8 bits (63), Expect = 2.1
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 90 RQKYGKGRGGEDGGDGYNGGGV 111
R+KY +GG DGGDG GG V
Sbjct: 23 REKY-VPKGGPDGGDGGRGGSV 43
>gnl|CDD|224719 COG1806, COG1806, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 273
Score = 27.6 bits (62), Expect = 2.3
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 56 VPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGD 104
VP+ P P+ + L GL + E L IR++ K G +
Sbjct: 177 VPEDPEPDELPAALKPLLFGLTISPE---RLSAIREERLKSLGLRENSR 222
>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 = 26.0 bits (58), Expect = 2.5
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 24 RLLIPSRVAGSVIGKGGSNIARLRN 48
R+++P G IGKGG N+
Sbjct: 28 RVVVPDDQLGLAIGKGGQNVRLASK 52
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 27.1 bits (61), Expect = 3.1
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 122 RLIVHQSQAGCIIGKGGTKIKELRDTFD 149
R+ ++ + G +IG+GG I+EL + +
Sbjct: 43 RITIYAERPGMVIGRGGKNIRELTEILE 70
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 27.6 bits (61), Expect = 3.3
Identities = 15/59 (25%), Positives = 20/59 (33%), Gaps = 5/59 (8%)
Query: 60 PGPERILTIFAELENGL-----KVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGG 113
P P R+ E ++ + E Q+ G GR G GG G GG
Sbjct: 394 PRPPRVPVEGEEADDEAGDSVGTIFREAREQRAAEEQRRGGGRSGPGGGSRSGSVGGGG 452
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 27.4 bits (61), Expect = 3.5
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 37 GKGGSNIARLRNDF---KASVTVPDCPGPERILTIFAELENGLKVIE 80
G G + + L D+ K + VP+ P+RI I+A ++ G+ V E
Sbjct: 424 GWGCAKVKELDWDWEQLKYKLRVPN---PDRIHAIYAAMKKGMTVDE 467
>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like
protein; Validated.
Length = 140
Score = 26.7 bits (60), Expect = 3.7
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 32 AGSVIGKGGSNIARLRNDFKASVTV 56
G IGKGG N+ RL + +
Sbjct: 43 MGLAIGKGGENVKRLEEKLGKDIEL 67
Score = 25.6 bits (57), Expect = 8.3
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149
DD I +V + G IGKGG +K L +
Sbjct: 30 DDDRIIFVVKEGDMGLAIGKGGENVKRLEEKLG 62
>gnl|CDD|187753 cd09281, UPF0066, Escherichia coli YaeB and related proteins.
Uncharacterized protein family UPF0066. This domain
includes Escherichia coli YeaB, Archeoglobus fulgidus
AF0241, and Agrobacterium tumefaciens VirR. Proteins
with this domain are probable
S-adenosylmethionine-dependent methyltransferases but
they have not been functionally characterized and the
substrate is unknown.
Length = 124
Score = 26.3 bits (59), Expect = 4.0
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 43 IARLRNDFKASVTVP---DCPGPERILTIFAELENGLKVIEE 81
I +R+ FK P G E + I E GLK +EE
Sbjct: 2 IGVVRSPFKERFGAPQQGLVGGVESEIEIDPEYAEGLKGLEE 43
>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 = 26.1 bits (58), Expect = 4.0
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 33 GSVIGKGGSNIARLRNDFK 51
G VIG+GG NI L +
Sbjct: 50 GMVIGRGGKNIRELTEILE 68
Score = 24.9 bits (55), Expect = 8.4
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 122 RLIVHQSQAGCIIGKGGTKIKELRDTF 148
++ ++ + G +IG+GG I+EL +
Sbjct: 41 QITIYAERPGMVIGRGGKNIRELTEIL 67
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 27.1 bits (61), Expect = 4.3
Identities = 13/22 (59%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 90 RQKYGKGRGGEDGGDGYNGGGV 111
R+KY +GG DGGDG +GG V
Sbjct: 25 REKYIP-KGGPDGGDGGDGGDV 45
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 26.6 bits (59), Expect = 6.4
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 116 KDDYDIRLIV---HQSQAGCIIGKGGTKIKEL 144
K I ++ +SQ IIGK G+ IK +
Sbjct: 216 KGLLKIHALISVERESQKKIIIGKNGSMIKAI 247
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 26.2 bits (59), Expect = 7.2
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 90 RQKYGKGRGGEDGGDGYNGGGV 111
R+KY +GG DGGDG GG V
Sbjct: 24 REKY-VPKGGPDGGDGGKGGSV 44
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 26.2 bits (59), Expect = 7.2
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 90 RQKYGKGRGGEDGGDGYNGGGV 111
R+K+ GG DGGDG GG V
Sbjct: 24 REKF-IPFGGPDGGDGGRGGSV 44
>gnl|CDD|217139 pfam02607, B12-binding_2, B12 binding domain. This B12 binding
domain is found in methionine synthase EC:2.1.1.13, and
other shorter proteins that bind to B12. This domain is
always found to the N-terminus of pfam02310. The
structure of this domain is known, it is a 4 helix
bundle. Many of the conserved residues in this domain
are involved in B12 binding, such as those in the MXXVG
motif.
Length = 79
Score = 24.9 bits (55), Expect = 8.1
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 76 LKVIEEVL-PALDEIRQKYGKGR 97
+IE+VL PALDE+ + + G
Sbjct: 35 EDIIEDVLAPALDEVGELWEAGE 57
>gnl|CDD|233801 TIGR02251, HIF-SF_euk, Dullard-like phosphatase domain. This model
represents the putative phosphatase domain of a family
of eukaryotic proteins including "Dullard" , and the NLI
interacting factor (NIF)-like phosphatases. This domain
is a member of the haloacid dehalogenase (HAD)
superfamily by virtue of a conserved set of three
catalytic motifs and a conserved fold as predicted by
PSIPRED. The third motif in this family is distinctive
(hhhhDNxPxxa) and aparrently lacking the last aspartate.
This domain is classified as a "Class III" HAD, since
there is no large "cap" domain found between motifs 1
and 2 or motifs 2 and 3. This domain is related to
domains found in FCP1-like phosphatases (TIGR02250), and
together both are detected by the pfam03031.
Length = 162
Score = 25.7 bits (57), Expect = 9.5
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 4 FIQQLSNF---KRFRGGPNDVELRLLIP 28
+ Q N K + G PND EL LIP
Sbjct: 125 YSLQPDNAIPIKSWFGDPNDTELLNLIP 152
>gnl|CDD|110047 pfam01018, GTP1_OBG, GTP1/OBG. The N-terminal domain of B.
subtilis GTPase obgE has the OBG fold, which is formed
by three glycine-rich regions inserted into a small
8-stranded beta-sandwich these regions form six
left-handed collagen-like helices packed and H-bonded
together.
Length = 156
Score = 25.4 bits (56), Expect = 9.9
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 90 RQKYGKGRGGEDGGDGYNGGGV 111
R+KY +GG DGG+G GG V
Sbjct: 23 REKY-VPKGGPDGGNGGRGGDV 43
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 0.145 0.425
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: 8,276,418
Number of extensions: 800442
Number of successful extensions: 1009
Number of sequences better than 10.0: 1
Number of HSP's gapped: 995
Number of HSP's successfully gapped: 94
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.6 bits)