RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11278
(238 letters)
>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 = 62.1 bits (152), Expect = 3e-13
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++++ H IIG+ G I+K+MEETG + FPD KS+ ++I G +E+
Sbjct: 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKENVEK 56
Query: 61 AR 62
A+
Sbjct: 57 AK 58
Score = 46.7 bits (112), Expect = 1e-07
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSV 208
+EI + H + G N++ IM +TG +I FP+ K ++T++G ++V
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGS------KSDTITITGPKENV 54
Query: 209 YLARQML 215
A++ +
Sbjct: 55 EKAKEEI 61
>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 = 54.9 bits (133), Expect = 2e-10
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++ V + IIG+GG TIK++ EETG + PDS + + V+I G+ +E+
Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG---SGSEERIVTITGTPEAVEK 58
Query: 61 ARYRV 65
A+ +
Sbjct: 59 AKELI 63
Score = 37.9 bits (89), Expect = 3e-04
Identities = 13/64 (20%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
+ + + G +K I +TGA+I P++ ++ VT++G ++V A
Sbjct: 4 VLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSG----SEERIVTITGTPEAVEKA 59
Query: 212 RQML 215
++++
Sbjct: 60 KELI 63
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 51.5 bits (124), Expect = 3e-09
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+++ + IIG+GG TIKK+ EETG + P + V I G +E+
Sbjct: 5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-----SEERVVEITGPPENVEK 59
Query: 61 ARYRVREL 68
A + E+
Sbjct: 60 AAELILEI 67
Score = 39.6 bits (93), Expect = 7e-05
Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 6/70 (8%)
Query: 146 TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNI 205
V + + I ++ G +K I +TG +I P V ++G
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERV------VEITGPP 54
Query: 206 DSVYLARQML 215
++V A +++
Sbjct: 55 ENVEKAAELI 64
>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 = 48.7 bits (117), Expect = 3e-08
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++ + IIG+GG IK++ EETG + PD ++ + V+I+G+ +E+
Sbjct: 2 ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD-------DRDDTVTISGTPEQVEK 54
Query: 61 ARYRV 65
A+ +
Sbjct: 55 AKELI 59
Score = 40.6 bits (96), Expect = 2e-05
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSV 208
+ I P + G N+K I +TG +I P+ D VT+SG + V
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDDT--------VTISGTPEQV 52
Query: 209 YLARQML 215
A++++
Sbjct: 53 EKAKELI 59
>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 = 44.5 bits (106), Expect = 7e-07
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG 53
IIG+GG TIK++ EETG + P V+I G
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPE---PGSGERIVTITG 42
Score = 28.7 bits (65), Expect = 0.32
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 158 HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG 203
+ G +K I +TGA+I P+ + VT++G
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQIPKPEPG----SGERIVTITG 42
>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 = 34.0 bits (79), Expect = 0.007
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 11 SHIIGRGGLTIKKVMEETGCHV 32
IIG+GG TIK++ EETG +
Sbjct: 12 GSIIGKGGSTIKEIREETGAKI 33
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 34.9 bits (81), Expect = 0.032
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 10/58 (17%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELT 69
+IG GG TIK + EETG ++ E V IA S ++A+ R+ +T
Sbjct: 566 VIGPGGKTIKAITEETGV---------KIDIEDDGTVKIAASDGESAKKAKERIEAIT 614
>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 = 34.4 bits (80), Expect = 0.041
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 10/58 (17%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELT 69
+IG GG I+++ EETG ++ E V IA S E A + +T
Sbjct: 565 VIGPGGKVIREITEETGA---------KIDIEDDGTVKIAASDGEAAEAAIKMIEGIT 613
>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 = 31.4 bits (72), Expect = 0.043
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 10/54 (18%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRV 65
+IG GG TIKK++EETG ++ E V IA S E+A+ +
Sbjct: 16 VIGPGGKTIKKIIEETGV---------KIDIEDDGTVYIAASDKEAAEKAKKMI 60
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 33.9 bits (79), Expect = 0.072
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 10/58 (17%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELT 69
+IG GG TI+++ EETG ++ E V IA + E A+ R+ +T
Sbjct: 568 VIGPGGKTIREITEETGA---------KIDIEDDGTVKIAATDGEAAEAAKERIEGIT 616
>gnl|CDD|239425 cd03309, CmuC_like, CmuC_like. Proteins similar to the putative
corrinoid methyltransferase CmuC. Its function has been
inferred from sequence similarity to the
methyltransferases CmuA and MtaA. Mutants of
Methylobacterium sp. disrupted in cmuC and purU appear
deficient in some step of chloromethane metabolism.
Length = 321
Score = 32.4 bits (74), Expect = 0.15
Identities = 22/118 (18%), Positives = 37/118 (31%), Gaps = 41/118 (34%)
Query: 103 MFRN--RPKLQPTLVMVKGCEKDVERVKEATTKLIE-HMCGSLANQTSVIMMMEISPQHH 159
FR P++Q + + ++ T+ LI H CG+ A+
Sbjct: 191 TFREFILPRMQ----------RIFDFLRSNTSALIVHHSCGAAASLV------------- 227
Query: 160 PIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKK---SSVTVSGNIDSVYLARQM 214
P+ MA+ G L++ V ++G ID V L
Sbjct: 228 -----PS-------MAEMGVDSWNVVMTANNTAELRRLLGDKVVLAGAIDDVALDTAT 273
>gnl|CDD|184986 PRK15026, PRK15026, aminoacyl-histidine dipeptidase; Provisional.
Length = 485
Score = 29.7 bits (66), Expect = 1.4
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 77 YPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQ 111
YP G P+ANSP + +++E Y Q +F P +Q
Sbjct: 396 YP--GWQPDANSPVMHLVRETY--QRLFNKTPNIQ 426
>gnl|CDD|216052 pfam00668, Condensation, Condensation domain. This domain is found
in many multi-domain enzymes which synthesise peptide
antibiotics. This domain catalyzes a condensation
reaction to form peptide bonds in non- ribosomal peptide
biosynthesis. It is usually found to the carboxy side of
a phosphopantetheine binding domain (pfam00550). It has
been shown that mutations in the HHXXXDG motif abolish
activity suggesting this is part of the active site.
Length = 300
Score = 29.2 bits (66), Expect = 1.7
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 12/43 (27%)
Query: 95 QEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEH 137
AYNVQ + R L D ER+++A LIE
Sbjct: 24 TSAYNVQFVLRLEGGL------------DPERLEKALNALIER 54
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 29.5 bits (66), Expect = 1.7
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 9/58 (15%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT 69
IIG GG +K ++EETG +++ + V I L LE+++ + LT
Sbjct: 699 IIGSGGKKVKSIIEETGVE--------AIDTQDDGTVKITAKDLSSLEKSKAIISSLT 748
>gnl|CDD|234516 TIGR04236, seadorna_VP2, seadornavirus VP2 protein. This protein
family occurs in the seadornavirus virus group, with the
designation VP2 in Banna virus, Kadipiro virus, and Liao
ning virus.
Length = 953
Score = 28.3 bits (63), Expect = 4.2
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 94 IQEAYNVQVMFRNRPKLQPTLVM 116
I +A N Q + +RP+L P+
Sbjct: 269 IVKALNAQRAYYDRPELTPSENR 291
>gnl|CDD|220594 pfam10136, SpecificRecomb, Site-specific recombinase. Members of
this family of bacterial proteins are found in various
putative site-specific recombinase transmembrane
proteins.
Length = 647
Score = 27.9 bits (63), Expect = 4.7
Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 8/57 (14%)
Query: 79 LMGSTPNANSPFVQIIQEAYNVQVMFRNR--------PKLQPTLVMVKGCEKDVERV 127
+ +SPFV + +E + +R L V++ C V+RV
Sbjct: 176 RLPELAEEDSPFVALQREVEALLAAYRAADRTGDALDEDLAHLRVLLDQCRDAVDRV 232
>gnl|CDD|234139 TIGR03182, PDH_E1_alph_y, pyruvate dehydrogenase E1 component,
alpha subunit. Members of this protein family are the
alpha subunit of the E1 component of pyruvate
dehydrogenase (PDH). This model represents one branch
of a larger family that E1-alpha proteins from
2-oxoisovalerate dehydrogenase, acetoin dehydrogenase,
another PDH clade, etc [Energy metabolism, Pyruvate
dehydrogenase].
Length = 315
Score = 27.5 bits (62), Expect = 6.6
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 6/30 (20%)
Query: 6 SYTDHSHIIGRGGLTIKKVMEE-----TGC 30
SY DH H + R G+ K+VM E TGC
Sbjct: 60 SYRDHGHALAR-GVPPKEVMAELTGRETGC 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 = 26.4 bits (59), Expect = 8.2
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 13 IIGRGGLTIKKVMEETGC 30
I+G G T+K++ +ETG
Sbjct: 20 ILGPRGNTLKQLEKETGA 37
>gnl|CDD|225614 COG3072, CyaA, Adenylate cyclase [Nucleotide transport and
metabolism].
Length = 853
Score = 27.4 bits (61), Expect = 8.3
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 44 EKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPF 90
+ NQ+ + +L + A RV L PL+ +PL+ + N P
Sbjct: 13 DALNQLRVERALAAMGPAFQRVLSLLPLLLHINHPLLPGYLDGNVPA 59
>gnl|CDD|216124 pfam00795, CN_hydrolase, Carbon-nitrogen hydrolase. This family
contains hydrolases that break carbon-nitrogen bonds.
The family includes: Nitrilase EC:3.5.5.1, Aliphatic
amidase EC:3.5.1.4, Biotidinase EC:3.5.1.12,
Beta-ureidopropionase EC:3.5.1.6. Nitrilase-related
proteins generally have a conserved E-K-C catalytic
triad, and are multimeric alpha-beta-beta-alpha sandwich
proteins.
Length = 172
Score = 26.5 bits (59), Expect = 9.8
Identities = 12/68 (17%), Positives = 22/68 (32%), Gaps = 9/68 (13%)
Query: 165 PNAINLKTIMAQTGAQ-IVFPEANDPIIPVLKKSSVTVSGNIDSVYLAR--------QML 215
+ L A+ GA +V PE P + ++ I L +
Sbjct: 19 QKLLELIEEAARQGADLVVLPELFIPGYAHGATEYLELAEAIPGETLQFLSALARKNGIT 78
Query: 216 VVSSVRPR 223
VV+ + +
Sbjct: 79 VVAGIPEK 86
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
0.320 0.134 0.382
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: 11,794,912
Number of extensions: 1075689
Number of successful extensions: 942
Number of sequences better than 10.0: 1
Number of HSP's gapped: 934
Number of HSP's successfully gapped: 32
Length of query: 238
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 144
Effective length of database: 6,768,326
Effective search space: 974638944
Effective search space used: 974638944
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 (21.8 bits)
S2: 57 (25.7 bits)