RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2768
(96 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 = 58.3 bits (142), Expect = 4e-13
Identities = 27/58 (46%), Positives = 41/58 (70%), Gaps = 1/58 (1%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN-EEETNVHIVGSFFSVQE 81
T ++VPSS VGRIIGKGG ++E++ TG+ IK+P+S + EE V I G+ +V++
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEK 58
>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 = 57.2 bits (139), Expect = 8e-13
Identities = 21/60 (35%), Positives = 38/60 (63%), Gaps = 3/60 (5%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLK 84
T +++P +VGRIIGKGG N++E++ TG I++P ++ + V I G+ V++ +
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP---DDRDDTVTISGTPEQVEKAKE 57
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 53.8 bits (130), Expect = 2e-11
Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQE 81
TIE+++P+ +VG IIGKGG +++++ TG I +P +EE V I G +V++
Sbjct: 4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERV-VEITGPPENVEK 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 = 50.6 bits (122), Expect = 5e-10
Identities = 26/62 (41%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETN--VHIVGSFFSVQET 82
T+ L+VPSSQ G IIGKGG ++E++ TG+ I++ S T V I G +VQ+
Sbjct: 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60
Query: 83 LK 84
L
Sbjct: 61 LL 62
>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 = 44.4 bits (106), Expect = 1e-07
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS 75
T E+ +P IIGK G N+R++ TG I+ P+ + + I G
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-GSKSDTITITGP 50
>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 = 41.4 bits (98), Expect = 8e-07
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 34 QVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVG 74
VG IIGKGG+ ++E++ TG+ I++P E V I G
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42
>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 = 40.3 bits (95), Expect = 4e-06
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
R+ I +VV Q G +IGK GQN+R LQ+ +++
Sbjct: 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKR 62
>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 = 36.8 bits (86), Expect = 8e-05
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
+VVP Q+G IGKGGQNVR + G I +
Sbjct: 26 RARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 36.0 bits (84), Expect = 2e-04
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 4 YLIFEKMREEGLFAGADEVRLT---IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP 60
+ ++++ G E+ T + +V+ +SQ G +IGKGG N+++L + +I+L
Sbjct: 4 EFLAVELKKAG--ISDIEIERTPNRVIVVIRTSQPGIVIGKGGSNIKKLGKELRKLIELE 61
Query: 61 NS 62
Sbjct: 62 GK 63
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 36.4 bits (85), Expect = 7e-04
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVR 47
DE + ++VVP Q+ IGK GQNVR
Sbjct: 298 DEDEHSADVVVPDDQLSLAIGKNGQNVR 325
>gnl|CDD|233654 TIGR01953, NusA, transcription termination factor NusA. This model
describes NusA, or N utilization substance protein A, a
bacterial transcription termination factor. It binds to
RNA polymerase alpha subunit and promotes termination at
certain RNA hairpin structures. It is named for the
interaction in E. coli of phage lambda antitermination
protein N with the N-utilization substance, consisting
of NusA, NusB, NusE (ribosomal protein S10), and nusG.
This model represents a region of NusA shared in all
bacterial forms, and including an S1 (pfam00575) and a
KH (pfam00013) RNA binding domains. Proteobacterial
forms have an additional C-terminal region, not included
in this model, with two repeats of 50-residue domain
rich in acidic amino acids [Transcription, Transcription
factors].
Length = 341
Score = 34.5 bits (80), Expect = 0.003
Identities = 19/38 (50%), Positives = 24/38 (63%)
Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMI 57
DE + + E+VVP Q+ IGKGGQNVR + TG I
Sbjct: 297 DEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNI 334
>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional.
Length = 449
Score = 34.4 bits (79), Expect = 0.004
Identities = 22/52 (42%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 17 AGADEVRLT------IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62
A DEVRL ++VP Q+ IGK GQNVR R TG I + +S
Sbjct: 322 ARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373
>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like
protein; Validated.
Length = 140
Score = 33.3 bits (77), Expect = 0.005
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 15/61 (24%)
Query: 6 IFEKMREEGLFAGA-------DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK 58
+FE + GA D+ R+ VV +G IGKGG+NV+ L+ G I+
Sbjct: 15 LFESI------TGATVKDCIIDDDRII--FVVKEGDMGLAIGKGGENVKRLEEKLGKDIE 66
Query: 59 L 59
L
Sbjct: 67 L 67
>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 33.7 bits (78), Expect = 0.006
Identities = 16/34 (47%), Positives = 19/34 (55%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK 58
+VVP Q+ IGKGGQNVR + TG I
Sbjct: 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEID 176
Score = 26.4 bits (59), Expect = 2.0
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 28 LVVPSSQVGRIIGKGGQNVRELQR 51
VV VG IGK G V+ +
Sbjct: 80 NVVKIDPVGACIGKRGSRVKAVSE 103
>gnl|CDD|224750 COG1837, COG1837, Predicted RNA-binding protein (contains KH
domain) [General function prediction only].
Length = 76
Score = 31.8 bits (73), Expect = 0.009
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVREL 49
E +TIEL V +G++IGK G+ ++ +
Sbjct: 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAI 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 = 30.3 bits (69), Expect = 0.040
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 7 FEKMREEGLFAGADEVR--LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
EK E + G + +R L ++ + + + G +IG+GG+N+REL + L N
Sbjct: 19 LEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGLEN 75
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 31.3 bits (72), Expect = 0.045
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 18 GADEVRL----TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIV 73
G EV + + VP + ++IGKGG+ ++++++ G I + +EE
Sbjct: 471 GPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDV-RPLDEEPGEEAEE 529
Query: 74 GSFFSVQETLK 84
G +V+ET K
Sbjct: 530 GEEVTVEETKK 540
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 31.0 bits (71), Expect = 0.058
Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHI 72
+ + +P ++G +IGK G+ +E++ TG + + E V I
Sbjct: 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKL----EIDSETGEVII 47
>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 = 30.9 bits (71), Expect = 0.064
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 28 LVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS 75
+ + ++ +IG GG+ +RE+ TG+ I + E++ V I S
Sbjct: 555 IKINPDKIRDVIGPGGKVIREITEETGAKIDI-----EDDGTVKIAAS 597
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 30.6 bits (70), Expect = 0.072
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 36 GRIIGKGGQNVRELQR 51
G +IG+GG+N+REL
Sbjct: 52 GMVIGRGGKNIRELTE 67
>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 = 28.7 bits (65), Expect = 0.10
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMI 57
+P ++ +IG GG+ ++++ TG I
Sbjct: 8 IPPDKIRDVIGPGGKTIKKIIEETGVKI 35
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 30.4 bits (69), Expect = 0.11
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 21 EVRLT----IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEET 68
EV + + VP + ++IGKGG+ ++E+++ G I + EEE
Sbjct: 479 EVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEEG 530
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 30.3 bits (69), Expect = 0.11
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 36 GRIIGKGGQNVRELQRSTG 54
GRIIG+ G+N+R L+ TG
Sbjct: 217 GRIIGREGRNIRALETLTG 235
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 30.0 bits (69), Expect = 0.12
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMI 57
+P ++ +IG GG+ +RE+ TG+ I
Sbjct: 560 IPPDKIRDVIGPGGKTIREITEETGAKI 587
>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
structure and biogenesis].
Length = 233
Score = 29.9 bits (68), Expect = 0.12
Identities = 11/59 (18%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 5 LIFEKMREEGLFAGADEVR--LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
+ +++ G +G + R + + +++ G +IGK G N+ +L++ + N
Sbjct: 31 FLEKELSNAG-ISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKEN 88
>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 = 28.7 bits (65), Expect = 0.24
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 35 VGRIIGKGGQNVRELQRSTGSMI 57
VG I+G G +++L++ TG+ I
Sbjct: 17 VGLILGPRGNTLKQLEKETGAKI 39
>gnl|CDD|239097 cd02414, jag_KH, jag_K homology RNA-binding domain. The KH domain
is found in proteins homologous to the Bacillus
subtilis protein Jag, which is associated with SpoIIIJ
and is necessary for the third stage of sporulation.
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 = 77
Score = 27.9 bits (63), Expect = 0.26
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 2 AQYL--IFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQ 50
++L + E M E +E T+E+ + +G +IGK G+ + LQ
Sbjct: 1 KEFLEEVLELMGIEADVD-VEEEGDTVEVNISGDDIGLLIGKRGKTLDALQ 50
>gnl|CDD|227495 COG5166, COG5166, Uncharacterized conserved protein [Function
unknown].
Length = 657
Score = 29.2 bits (65), Expect = 0.28
Identities = 11/45 (24%), Positives = 16/45 (35%)
Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN 64
E I ++ S IIG GG ++E I N +
Sbjct: 445 TEFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK 489
>gnl|CDD|221909 pfam13083, KH_4, KH domain.
Length = 71
Score = 27.4 bits (62), Expect = 0.38
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQ 50
IEL V +G++IGK G+ + LQ
Sbjct: 29 VIELNVAGEDLGKLIGKRGRTLDALQ 54
>gnl|CDD|237061 PRK12327, nusA, transcription elongation factor NusA; Provisional.
Length = 362
Score = 28.7 bits (65), Expect = 0.38
Identities = 14/26 (53%), Positives = 15/26 (57%)
Query: 29 VVPSSQVGRIIGKGGQNVRELQRSTG 54
VVP Q+ IGK GQN R R TG
Sbjct: 308 VVPDYQLSLAIGKEGQNARLAARLTG 333
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 28.6 bits (65), Expect = 0.41
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 8/45 (17%)
Query: 19 ADEVRLTIELVVPSSQVGRIIGKGGQNV----RELQRSTGSMIKL 59
A VR+TI +++ G +IGK G + +EL++ TG +++
Sbjct: 61 AKRVRVTIH----TARPGIVIGKKGAEIEKLRKELEKLTGKPVQI 101
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 28.6 bits (65), Expect = 0.47
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 36 GRIIGKGGQNVRELQRSTG 54
GRIIG+ G+N+R L+ TG
Sbjct: 223 GRIIGREGRNIRALETLTG 241
>gnl|CDD|224760 COG1847, Jag, Predicted RNA-binding protein [General function
prediction only].
Length = 208
Score = 28.4 bits (64), Expect = 0.50
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 3 QYL--IFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQ 50
YL + E M E E + + + GR+IGK G+ + LQ
Sbjct: 69 DYLEELLELMDFEVTITV-SEEGRRVVVSIEGEDAGRLIGKHGKTLDALQ 117
>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 = 27.9 bits (63), Expect = 0.60
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTGSMI 57
+ +P ++G +IGKGG+ +E++ TG +
Sbjct: 1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKL 31
>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 = 0.77
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
D R+ VV ++G IGKGG+NV+ L+ G I+L
Sbjct: 31 DRNRVV--FVVKEGEMGAAIGKGGENVKRLEELIGKSIEL 68
>gnl|CDD|181707 PRK09221, PRK09221, beta alanine--pyruvate transaminase;
Provisional.
Length = 445
Score = 27.9 bits (63), Expect = 0.77
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 4 YLIFEKMREEGLF--AGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQ 50
Y F K E+GL D + L+ L++ +Q+ ++ G +R +
Sbjct: 397 YEAFMKCFEKGLLVRYTGDTIALSPPLIIEKAQIDELVDALGDALRAVA 445
>gnl|CDD|180402 PRK06106, PRK06106, nicotinate-nucleotide pyrophosphorylase;
Provisional.
Length = 281
Score = 27.7 bits (62), Expect = 0.95
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 11 REEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQ 44
R+ G+ AG D RL LV P ++ R + G
Sbjct: 48 RQPGVIAGLDLARLAFRLVDPEIEMRRHLPDGAA 81
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 27.3 bits (61), Expect = 1.0
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 34 QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQE 81
GRIIG+ G+ R ++ TG I + V I+G F V+
Sbjct: 112 IKGRIIGREGKTRRAIEELTGVYISV------YGKTVAIIGGFEQVEI 153
>gnl|CDD|178867 PRK00106, PRK00106, hypothetical protein; Provisional.
Length = 535
Score = 27.5 bits (61), Expect = 1.0
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 36 GRIIGKGGQNVRELQRSTG 54
GRIIG+ G+N+R L+ TG
Sbjct: 238 GRIIGREGRNIRTLESLTG 256
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 27.5 bits (62), Expect = 1.1
Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFSVQETLKGCPN 88
+ ++ +IG GG+ ++ + TG I + E++ V I S S ++ +
Sbjct: 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDI-----EDDGTVKIAASDGESAKKAKERIEA 612
Query: 89 IVDQPSID 96
I + +
Sbjct: 613 ITREVEVG 620
>gnl|CDD|239093 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation
specificity factor (CPSF) contains an N-terminal K
homology RNA-binding domain (KH). The archeal CPSFs are
predicted to be metal-dependent RNases belonging to the
beta-CASP family, a subgroup enzymes within the
metallo-beta-lactamase fold. 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
domains are known to bind single-stranded RNA or DNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 145
Score = 26.9 bits (60), Expect = 1.2
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTG 54
E+++ + + G +IGKGG +RE+ R TG
Sbjct: 79 EVIIEAEKPGLVIGKGGSTLREITRETG 106
>gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal
type. This model describes ribosomal protein S3 of the
eukaryotic cytosol and of the archaea. TIGRFAMs model
TIGR01009 describes the bacterial/organellar type,
although the organellar types have a different
architecture with long insertions and may score poorly
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 195
Score = 27.0 bits (60), Expect = 1.5
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 7 FEKMREEGLFAGADEVR--LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
+K E ++G D L ++++ + + G +IG+GG+ +REL L N
Sbjct: 19 LKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGLEN 75
>gnl|CDD|224696 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
metallo-beta-lactamase domain and an RNA-binding KH
domain [General function prediction only].
Length = 637
Score = 26.9 bits (60), Expect = 1.8
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTG 54
E+++ + + G +IGKGG +RE+ TG
Sbjct: 102 EVIIEAKKPGLVIGKGGSTLREITAETG 129
>gnl|CDD|240613 cd12795, FILIA_N_like, FILIA-N KH-like domain. This group
contains the N-terminal atypical KH domain of FILIA and
related domains. FILIA is expressed in oocytes and
embryo, and contains an atypical KH domain at the
N-terminus with an N-terminal extension that interacts
with RNA. RNA-binding may mediate RNA transcript
regulation in oogenesis and embryogenesis. FILIA-N
differs from typical KH domains by forming a stable
dimer in solution and crystal structure.
Length = 114
Score = 26.1 bits (58), Expect = 2.3
Identities = 6/55 (10%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLK 84
V + + +I G G + ++ + +++++ + + + G + +K
Sbjct: 35 VEAWLLEKIFGPDGALIPGIEWESQTLLQVEAWDSSGLAEITVFG-RPRARRRVK 88
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 26.4 bits (59), Expect = 2.5
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTG 54
E+++ + + G +IGKGG +RE+ + TG
Sbjct: 96 EVIIEAEKPGLVIGKGGSTLREITKETG 123
>gnl|CDD|179216 PRK01064, PRK01064, hypothetical protein; Provisional.
Length = 78
Score = 25.7 bits (56), Expect = 2.5
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQ 50
+ EL V +G+IIGK G+ ++ ++
Sbjct: 30 IIYELTVAKPDIGKIIGKEGRTIKAIR 56
>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 = 25.9 bits (58), Expect = 2.6
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
AD V +TI +++ G IIGK G + +L++ ++
Sbjct: 60 ADRVEVTIH----TARPGIIIGKKGAGIEKLRKELQKLLGN 96
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 26.0 bits (58), Expect = 3.0
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 8 EKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRE 48
E+ E G ++ TI V SQ G IIGK G +++
Sbjct: 217 EEFEERE--KGLLKIHATI-YVERESQKGIIIGKNGAMIKK 254
>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2. PPP4R2 (protein phosphatase 4 core
regulatory subunit R2) is the regulatory subunit of the
histone H2A phosphatase complex. It has been shown to
confer resistance to the anticancer drug cisplatin in
yeast, and may confer resistance in higher eukaryotes.
Length = 285
Score = 25.9 bits (57), Expect = 3.2
Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 12/72 (16%)
Query: 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNV--------HI 72
V T E + P SQ+ + + E ++ I LP + N E I
Sbjct: 30 HVAKTGETMPPWSQLKDLFRHKLNTIPEDFFASAPEIDLPVNPNVETIPFEEMKERILKI 89
Query: 73 VGSF----FSVQ 80
V +F F++Q
Sbjct: 90 VTNFNGIPFTIQ 101
>gnl|CDD|215752 pfam00151, Lipase, Lipase.
Length = 329
Score = 26.2 bits (58), Expect = 3.2
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 44 QNVRELQRSTGSMI-KLPNSFNEEETNVHIVGS 75
NVR + ++ +L N NVH++G
Sbjct: 123 LNVRVVGAEVAKLLVELEEELNVSPENVHLIGH 155
>gnl|CDD|223235 COG0157, NadC, Nicotinate-nucleotide pyrophosphorylase [Coenzyme
metabolism].
Length = 280
Score = 25.6 bits (57), Expect = 4.1
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 11 REEGLFAGADEVRLTIELVVPSSQV 35
+E G+ AG D EL+ PS ++
Sbjct: 42 KEAGVVAGLDVAEEVFELLGPSIEI 66
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 25.8 bits (58), Expect = 4.1
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 8 EKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRE 48
EK E GL + TI V SQ G IIGKGG +++
Sbjct: 216 EKFEERGL----VRIEATI-YVERDSQKGIIIGKGGAMLKK 251
>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 = 4.4
Identities = 9/43 (20%), Positives = 20/43 (46%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEE 67
I + + +++ G +IGK G + +L++ + N E
Sbjct: 63 KIRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTGKEVQINIAE 105
>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 = 25.5 bits (56), Expect = 5.1
Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHI 72
I + +P ++G +IG G+ + ++Q TG+ I + E++ V+I
Sbjct: 580 ITVKIPVDKIGEVIGPKGKMINQIQDETGAEISI-----EDDGTVYI 621
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 25.4 bits (56), Expect = 5.7
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 36 GRIIGKGGQNVRELQRSTG 54
GRIIG+ G+N+R + TG
Sbjct: 211 GRIIGREGRNIRAFEGLTG 229
>gnl|CDD|237435 PRK13579, gcvT, glycine cleavage system aminomethyltransferase T;
Provisional.
Length = 370
Score = 25.3 bits (56), Expect = 6.3
Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 13/66 (19%)
Query: 11 REEGLFAGADEVRLTIELVVPSSQVG-RIIGKGGQNVRELQRSTGSMIKLPNSFNEEETN 69
RE G F GA + + +VG + G+ VRE G+ + F++ T
Sbjct: 265 REAGGFPGAKAILAALAKGASRRRVGLKPEGR--APVRE-----GAPL-----FDDAGTE 312
Query: 70 VHIVGS 75
+ V S
Sbjct: 313 IGTVTS 318
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 24.9 bits (55), Expect = 7.9
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 15/44 (34%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIV 73
+ +V R+IGK GSMI + +EET I+
Sbjct: 151 IKPVKVPRVIGKK-----------GSMINML----KEETGCDII 179
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 24.8 bits (54), Expect = 8.5
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 17 AGADEVRLTIELVVPSSQVGRIIGKGGQNVREL 49
A A E T VV S V + IG+G + VRE+
Sbjct: 175 AVAHETNATFIRVVGSELVRKYIGEGARLVREI 207
>gnl|CDD|180559 PRK06418, PRK06418, transcription elongation factor NusA-like
protein; Validated.
Length = 166
Score = 24.6 bits (54), Expect = 8.5
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 39 IGKGGQNVRELQRSTGSMIK 58
IGKGG+ + L R G ++
Sbjct: 75 IGKGGKIAKALSRKLGKKVR 94
>gnl|CDD|172741 PRK14253, PRK14253, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 249
Score = 24.8 bits (54), Expect = 8.9
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 15 LFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSM 56
LF G ++ +I L +P+ QV +IG G L R M
Sbjct: 11 LFYGENQALKSINLPIPARQVTALIGPSGCGKSTLLRCLNRM 52
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 0.136 0.375
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: 4,839,536
Number of extensions: 395747
Number of successful extensions: 420
Number of sequences better than 10.0: 1
Number of HSP's gapped: 420
Number of HSP's successfully gapped: 75
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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 (24.2 bits)