RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12166
(94 letters)
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of
the virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA
plus-strand. lambda1 is an Orthoreovirus core protein,
VP3 is the homologous core protein in Aquareoviruses.
Length = 1166
Score = 39.8 bits (93), Expect = 5e-05
Identities = 18/37 (48%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 49 VKSAHQGHPSV-TCNVCGRTFSSIANLAEHKRSRHGI 84
K A +PS CNVC FSS+ LAEH+R+ H I
Sbjct: 63 SKKATPINPSSYVCNVCMAEFSSMDQLAEHQRTTHSI 99
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 31.0 bits (71), Expect = 0.008
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 60 TCNVCGRTFSSIANLAEHKRSRH 82
TC VCG+TFSS+ L HK+S
Sbjct: 3 TCGVCGKTFSSLQALGGHKKSHC 25
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 31.8 bits (72), Expect = 0.019
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 18 AEPLFRFDRTK---PHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANL 74
+ L++ +K P+ C LC ++ + L H++ S C VCG+ F + +
Sbjct: 59 SSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEH---SKVCPVCGKEFRNTDST 115
Query: 75 AEHKRSRHGI 84
+H +H I
Sbjct: 116 LDHVCKKHNI 125
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139)
is part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
ABC transporters are a large family of proteins
involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules.
Length = 222
Score = 27.8 bits (63), Expect = 0.69
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 36 GKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHGITGFV 88
GKT TL K + G + G S+ GR I L H+R+R GI G+V
Sbjct: 38 GKT-TLLKTIMGLLP-PRSG--SIR--FDGR---DITGLPPHERARAGI-GYV 80
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 25.5 bits (57), Expect = 0.86
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 60 TCNVCGRTFSSIANLAEHKRSR 81
C +C TF+S + L H R +
Sbjct: 2 YCELCNVTFTSESQLKSHLRGK 23
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 25.6 bits (57), Expect = 1.0
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 61 CNVCGRTFSSIANLAEHKRSR 81
C C + F S L H +S+
Sbjct: 4 CVACDKYFKSENALENHLKSK 24
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys.
The C2H2 zinc finger is composed of two short beta
strands followed by an alpha helix. The amino terminal
part of the helix binds the major groove in DNA binding
zinc fingers. The accepted consensus binding sequence
for Sp1 is usually defined by the asymmetric
hexanucleotide core GGGCGG but this sequence does not
include, among others, the GAG (=CTC) repeat that
constitutes a high-affinity site for Sp1 binding to the
wt1 promoter.
Length = 22
Score = 25.4 bits (56), Expect = 1.0
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 60 TCNVCGRTFSSIANLAEHKRS 80
C CG++FS +NL H R+
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 1.4
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 60 TCNVCGRTFSSIANLAEHKRS 80
C CG+ F S + L EH R+
Sbjct: 2 RCPECGKVFKSKSALREHMRT 22
>gnl|CDD|179013 PRK00415, rps27e, 30S ribosomal protein S27e; Reviewed.
Length = 59
Score = 25.6 bits (57), Expect = 1.4
Identities = 8/15 (53%), Positives = 9/15 (60%), Gaps = 2/15 (13%)
Query: 55 GHPS--VTCNVCGRT 67
H S V C VCG+T
Sbjct: 25 SHASTVVRCLVCGKT 39
>gnl|CDD|131081 TIGR02026, BchE, magnesium-protoporphyrin IX monomethyl ester
anaerobic oxidative cyclase. This model respresents the
cobalamin-dependent oxidative cyclase responsible for
forming the distinctive E-ring of the chlorin ring
system under anaerobic conditions. This step is
essential in the biosynthesis of both
bacteriochlorophyll and chlorophyll under anaerobic
conditions (a separate enzyme, AcsF, acts under aerobic
conditions). This model identifies two clades of
sequences, one from photosynthetic, non-cyanobacterial
bacteria and another including Synechocystis and several
non-photosynthetic bacteria. The function of the
Synechocystis gene is supported by gene clustering with
other photosynthetic genes, so the purpose of the gene
in the non-photosynthetic bacteria is uncertain. Note
that homologs of this gene are not found in plants which
rely solely on the aerobic cyclase.
Length = 497
Score = 27.2 bits (60), Expect = 1.5
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 5 WKKTAYEIGLGIPAEPLFRFDRTKPHSCDLCGK 37
WKK Y LG+ + F R P +C+ C +
Sbjct: 182 WKKYIYY-PLGVRV-AVPNFARGCPFTCNFCSQ 212
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 24.9 bits (54), Expect = 1.6
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 61 CNVCGRTFSSIANLAEHKRSRH 82
C +CG++FSS L H R H
Sbjct: 3 CPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|129544 TIGR00452, TIGR00452, tRNA (mo5U34)-methyltransferase. This model
describes a set of proteins with homology in its central
region to a large number of methyltransferases active on
a variety of substrates. The similarity includes a motif
resembling ILDVGCG[SG]G. Known examples to date are
restricted to the proteobacteria [Unknown function,
Enzymes of unknown specificity].
Length = 314
Score = 26.8 bits (59), Expect = 1.8
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 5 WKKTAYEI-GLGIPAE--PLFRFDRTKPHSCDLCGKT 38
W+K +E+ G+ I +E ++DR PH L G+T
Sbjct: 88 WRKGPFELSGIKIDSEWRSDIKWDRVLPHLSPLKGRT 124
>gnl|CDD|227928 COG5641, GAT1, GATA Zn-finger-containing transcription factor
[Transcription].
Length = 498
Score = 26.8 bits (59), Expect = 2.0
Identities = 15/62 (24%), Positives = 20/62 (32%), Gaps = 9/62 (14%)
Query: 24 FDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRHG 83
+ +PH C C T + LW S + CN CG H R
Sbjct: 153 DNSNQPHVCSNC---KTTSTPLWRRASSESSLPGNNLCNACGLYLKL------HGSPRAP 203
Query: 84 IT 85
I+
Sbjct: 204 IS 205
>gnl|CDD|224962 COG2051, RPS27A, Ribosomal protein S27E [Translation, ribosomal
structure and biogenesis].
Length = 67
Score = 25.4 bits (56), Expect = 2.3
Identities = 19/54 (35%), Positives = 21/54 (38%), Gaps = 17/54 (31%)
Query: 16 IPAEPLFRFDRTKPHSCDLCGKTYTLAKHLWGHVKSAHQGHPS--VTCNVCGRT 67
IP EP RF R K C CG + H S VTC +CG T
Sbjct: 9 IPKEPRSRFLRVK---CPDCGNEQVVF------------SHASTVVTCLICGTT 47
>gnl|CDD|235996 PRK07340, PRK07340, ornithine cyclodeaminase; Validated.
Length = 304
Score = 26.1 bits (58), Expect = 3.4
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 46 WGHVKSAHQGHPSVTCNVCGRTFSSIANLAEHKRSRH 82
H+++ G P V GRT +S A H R+
Sbjct: 138 RAHLEAFAAGLPVRRVWVRGRTAASAAAFCAHARALG 174
>gnl|CDD|215409 PLN02765, PLN02765, pyruvate kinase.
Length = 526
Score = 25.8 bits (57), Expect = 4.3
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 12 IGLGIPAEPLFRFDRTKPHSCDLCGK 37
+G+ +P E +F F + + C++ GK
Sbjct: 282 LGIDLPPEKVFLFQKAALYKCNMAGK 307
>gnl|CDD|150725 pfam10083, DUF2321, Uncharacterized protein conserved in bacteria
(DUF2321). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 158
Score = 25.3 bits (55), Expect = 4.6
Identities = 7/22 (31%), Positives = 8/22 (36%)
Query: 22 FRFDRTKPHSCDLCGKTYTLAK 43
D P C CGK + K
Sbjct: 61 LGSDYDAPSYCHNCGKPFPWTK 82
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 25.4 bits (55), Expect = 5.2
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 57 PSVTCNVCGRTFSSIANLAEHKRSR 81
P V C CGR FS H +
Sbjct: 237 PKVYCVKCGREFSRSKVFEYHLEGK 261
>gnl|CDD|149213 pfam08003, Methyltransf_9, Protein of unknown function (DUF1698).
This family contains many hypothetical proteins. It also
includes two putative methyltransferase proteins.
Length = 315
Score = 25.4 bits (56), Expect = 5.6
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 5 WKKTAYEI-GLGIPAE--PLFRFDRTKPHSCDLCGKT 38
W+K + + G+ I E +++DR PH L G+T
Sbjct: 82 WRKGPFHLHGVHIDTEWRSDWKWDRVLPHLSPLKGRT 118
>gnl|CDD|227360 COG5027, SAS2, Histone acetyltransferase (MYST family) [Chromatin
structure and dynamics].
Length = 395
Score = 25.1 bits (55), Expect = 6.1
Identities = 9/26 (34%), Positives = 10/26 (38%)
Query: 32 CDLCGKTYTLAKHLWGHVKSAHQGHP 57
C+ C K Y L H K HP
Sbjct: 161 CEFCLKYYGSQTSLVRHRKKCSLQHP 186
>gnl|CDD|204665 pfam11494, Ta0938, Ta0938. Ta0938 is a protein of unknown
function however the structure has been determined. The
protein has a novel fold and a putative Zn-binding
motif. The structure has two different parts, one
region contains a beta sheet flanked by two alpha
helices and the other contains a bundle of loops which
contain all cysteines in the protein.
Length = 106
Score = 24.4 bits (53), Expect = 8.0
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 8/64 (12%)
Query: 27 TKPHSCDLCGKTYTLAKHLWGHVKSAHQGHP-SVTCNVCGRTFSSIANLAEHKRSRHGIT 85
TK C LCG T WG G C++C F ++ N + + H +
Sbjct: 12 TKEKGCALCGAT-------WGDYYEDIDGEKLFFCCDICALEFVNMLNEVKKRTGWHKVD 64
Query: 86 GFVV 89
++
Sbjct: 65 ELII 68
>gnl|CDD|237898 PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional.
Length = 322
Score = 24.4 bits (54), Expect = 9.5
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 5 WKKTAYEI-GLGIPAE--PLFRFDRTKPHSCDLCGKT 38
W+K + + G+ I E +++DR PH L G+T
Sbjct: 89 WRKGPFSLFGIHIDTEWRSDWKWDRVLPHLSPLKGRT 125
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 24.1 bits (53), Expect = 9.7
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 60 TCNVCGRTFSSIANLAEHKRSRHG 83
C C T ++ EH HG
Sbjct: 1 DCLFCNHTSDTVEENLEHMFKSHG 24
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
0.323 0.136 0.459
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,522,007
Number of extensions: 330805
Number of successful extensions: 392
Number of sequences better than 10.0: 1
Number of HSP's gapped: 388
Number of HSP's successfully gapped: 39
Length of query: 94
Length of database: 10,937,602
Length adjustment: 61
Effective length of query: 33
Effective length of database: 8,232,008
Effective search space: 271656264
Effective search space used: 271656264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.3 bits)