RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10921
(269 letters)
>gnl|CDD|215399 PLN02748, PLN02748, tRNA dimethylallyltransferase.
Length = 468
Score = 69.5 bits (170), Expect = 2e-13
Identities = 51/223 (22%), Positives = 100/223 (44%), Gaps = 18/223 (8%)
Query: 16 VLDKRLEGRVHTMIQNGLIEELLQFHRQYNEDRIGKQLEPDYTKGIFQSIGFKEFHNYLM 75
VLD+ + RV MI GL++E+ + DYT+G+ Q+IG +EF ++L
Sbjct: 239 VLDRYVNQRVDCMIDAGLLDEVYDIYDPG----------ADYTRGLRQAIGVREFEDFLR 288
Query: 76 LSDQDRQEPDYTKGIFQSIGFKEFHNYLMLSDSDRESDKGREIFNKSLDALVLANVQYAK 135
L + + T KE ++ D DK + + ++++D + L + +
Sbjct: 289 LYLSRNENGELTSSSNNDKVMKENSRKILNFPHD---DKLKILLDEAIDQVKLNTRRLVR 345
Query: 136 KQNQWVR--NRLLKCPDRMVPPVYSLNCTDLTTWAQSVTAPALHIVQSYLDNRAPTGIEP 193
+Q + + N + + ++ C +W V PA+ IV+ +L + +G +
Sbjct: 346 RQKRRLHRLNTVFGWNIHYIDATEAILCKSEESWNAKVVKPAVEIVRRFLSDDTSSGPDA 405
Query: 194 LAQEYVDPSYYNAGTFNCDVC-NRLFIGQHQYEQHMNSVKHRR 235
+ + V + + C+ C N++ G H++EQH HR+
Sbjct: 406 SSGKSVSRELWT--QYVCEACGNKVLRGAHEWEQHKQGRGHRK 446
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 48.8 bits (117), Expect = 9e-07
Identities = 35/133 (26%), Positives = 51/133 (38%), Gaps = 49/133 (36%)
Query: 13 NSEVLDKRLEGRVHTMIQNGLIEELLQFHRQYNEDRIGKQLEPDYTKGIFQSIGFKEFHN 72
+ EVL +R+ RV M++ GLIEE+ K L Y +G
Sbjct: 199 DREVLYERINRRVDAMLEQGLIEEV-------------KAL---YARG------------ 230
Query: 73 YLMLSDQDRQEPDYTKGIFQSIGFKEFHNYLMLSDSDRESDKGREIFNKSLDALVLANVQ 132
D Q+IG+KE YL G ++++ + A Q
Sbjct: 231 ---------LHLDLP--AMQAIGYKEILAYLD----------GGISLEEAIERIKTATRQ 269
Query: 133 YAKKQNQWVRNRL 145
YAK+Q W RN+L
Sbjct: 270 YAKRQLTWFRNQL 282
>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 = 41.8 bits (99), Expect = 6e-06
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 209 FNCDVCNRLFIGQHQYEQHMNSVKHR 234
F C C++ F ++ E H+ S KH+
Sbjct: 2 FYCVACDKYFKSENALENHLKSKKHK 27
>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 = 37.9 bits (89), Expect = 1e-04
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 209 FNCDVCNRLFIGQHQYEQHMNSVKH 233
F C++CN F + Q + H+ KH
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKKH 25
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Reviewed.
Length = 307
Score = 41.7 bits (99), Expect = 2e-04
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 16/63 (25%)
Query: 15 EVLDKRLEGRVHTMIQNGLIEE---LLQFHRQYNEDRIGKQLEPDYTKGIFQSIGFKEFH 71
E L +R+ RV M++ GL+EE LL + PD ++IG+KE
Sbjct: 200 EELYERINQRVDQMLEQGLLEEVRALLA-----------RGYLPDLP--AMRAIGYKELL 246
Query: 72 NYL 74
YL
Sbjct: 247 AYL 249
>gnl|CDD|216659 pfam01715, IPPT, IPP transferase. This is a family of IPP
transferases EC:2.5.1.8 also known as tRNA
delta(2)-isopentenylpyrophosphate transferase. These
enzymes modify both cytoplasmic and mitochondrial tRNAs
at A(37) to give isopentenyl A(37).
Length = 253
Score = 40.8 bits (96), Expect = 3e-04
Identities = 31/130 (23%), Positives = 49/130 (37%), Gaps = 51/130 (39%)
Query: 15 EVLDKRLEGRVHTMIQNGLIEELLQFHRQY-NEDRIGKQLEPDYTKGIFQSIGFKEFHNY 73
EVL +R+ RV M+++GL+EE+ + Q NED ++IG+KEF Y
Sbjct: 164 EVLHERIARRVDDMLESGLVEEVKALYAQGLNEDL-----------PAIRAIGYKEFLLY 212
Query: 74 LMLSDQDRQEPDYTKGIFQSIGFKEFHNYLMLSDSDRESDKGREIFNKSLDALVLANVQY 133
L G ++++ ++ A QY
Sbjct: 213 L---------------------------------------DGECTLEEAIERIIKATRQY 233
Query: 134 AKKQNQWVRN 143
AK+Q W R
Sbjct: 234 AKRQMTWFRK 243
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine tRNA
modification enzyme. Catalyzes the first step in the
modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 40.1 bits (94), Expect = 6e-04
Identities = 30/129 (23%), Positives = 46/129 (35%), Gaps = 49/129 (37%)
Query: 15 EVLDKRLEGRVHTMIQNGLIEELLQFHRQYNEDRIGKQLEPDYTKGIFQSIGFKEFHNYL 74
E L +R+E RVH M+++GL+ E+ K L Y +
Sbjct: 196 EPLHQRIEQRVHDMLESGLLAEV-------------KAL---YAQY-------------- 225
Query: 75 MLSDQDRQEPDYTKGIFQSIGFKEFHNYLMLSDSDRESDKGREIFNKSLDALVLANVQYA 134
Q+IG+KEF YL +G +++ + QYA
Sbjct: 226 ---------DLCDLPSIQAIGYKEFLLYL----------EGTVSLEDAIERIKCNTRQYA 266
Query: 135 KKQNQWVRN 143
K+Q W R
Sbjct: 267 KRQLTWFRK 275
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type zinc
fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 32.2 bits (74), Expect = 0.016
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 211 CDVCNRLFIGQHQYEQHMNSVKHRRMKVKM 240
C +CN F + E H+ KH++ VK
Sbjct: 6 CKLCNVTFTDEISVEAHLKGKKHKK-NVKK 34
>gnl|CDD|177823 PLN02165, PLN02165, adenylate isopentenyltransferase.
Length = 334
Score = 33.6 bits (77), Expect = 0.090
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 16 VLDKRLEGRVHTMIQNGLIEELLQFHRQYNEDRIGKQLEPDYTKGIFQSIGFKEFHNYL 74
VL + L RV M+ +G+ EEL +F+ GI ++IG EF Y
Sbjct: 187 VLFEYLSKRVDEMMDSGMFEELAEFYDPVK--------SGSEPLGIRKAIGVPEFDRYF 237
>gnl|CDD|236929 PRK11553, PRK11553, alkanesulfonate transporter substrate-binding
subunit; Provisional.
Length = 314
Score = 32.1 bits (73), Expect = 0.29
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 164 LTTWAQSVTAPALHIVQSYLDNRAPTGIEPLAQEYV 199
+ A+++ PA ++ SYLD+R PT I+PL+ E
Sbjct: 248 IALLAKTMGLPA-AVIASYLDHRPPTTIKPLSAEVA 282
>gnl|CDD|227571 COG5246, PRP11, Splicing factor 3a, subunit 2 [RNA processing and
modification].
Length = 222
Score = 30.0 bits (67), Expect = 1.0
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 11/63 (17%)
Query: 200 DPSYY--NAGTFNCDVCNRLFIGQHQYEQHMNSVKHR---------RMKVKMERQLQHIL 248
DP + G + C +C + + Y +H KH+ + + E Q H
Sbjct: 43 DPYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEEKSSLGRENQTTHDF 102
Query: 249 RNQ 251
R Q
Sbjct: 103 RQQ 105
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 29.9 bits (68), Expect = 1.2
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 137 QNQWVRNRLLKCPDRMVPPVY 157
Q W R+RL P + VPP+Y
Sbjct: 196 QFDWARSRLPVEP-QPVPPIY 215
>gnl|CDD|190413 pfam02762, Cbl_N3, CBL proto-oncogene N-terminus, SH2-like domain.
Cbl is an adaptor protein that binds EGF receptors (or
other tyrosine kinases) and SH3 domains, functioning as
a negative regulator of many signaling pathways. The
N-terminal domain is evolutionarily conserved, and is
known to bind to phosphorylated tyrosine residues. The
so called N-terminal domain is actually 3 structural
domains, of which this is the C-terminal SH2 domain.
Length = 86
Score = 28.3 bits (63), Expect = 1.3
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 141 VRNRLLKCPDRMVPPVYSLNCTDLTTWAQSVTAPALHIVQSYLDNRAPTGIEPLAQEYVD 200
V+ RL K + ++ L+CT L WA I+Q+ N+ L Q ++
Sbjct: 14 VKARLQKLIKKPGSYIFRLSCTRLGQWAIGYVTADGKILQTIPQNK------SLIQALLE 67
>gnl|CDD|197545 smart00154, ZnF_AN1, AN1-like Zinc finger. Zinc finger at the
C-terminus of An1, a ubiquitin-like protein in Xenopus
laevis.
Length = 39
Score = 27.0 bits (60), Expect = 1.5
Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 208 TFNCDVCNRLFIGQHQY-EQH 227
F C C LF G+H+ E H
Sbjct: 12 GFKCRHCGNLFCGEHRLPEDH 32
>gnl|CDD|198176 cd09920, SH2_Cbl-b_TKB, Src homology 2 (SH2) domain found in the
Cbl-b TKB domain. SH2 found in the Cbl-b TKB domain.
The Cbl (for Casitas B-lineage lymphoma) family of E3
ubiquitin ligases contains three members Cbl, Cbl-b and
Cbl-c. The founding member Cbl was discovered first as
the oncogenic protein v-Cbl, a Gag-fusion transforming
protein of Cas NS-1 retrovirus, which causes pre- and
pro-B lymphomas in mice. The N-terminus of the Cbl
proteins is composed of a tyrosine kinase-binding (TKB)
domain, also called phosphotyrosine binding (PTB)
domain, a short linker region and the RING-type zinc
finger. In addition, Cbl and Cbl-b contain a leucine
zipper motif and a proline-rich domain in the
C-terminus. The TKB domain consists of a four-helix
bundle (4H), a calcium-binding EF hand and a divergent
SH2 domain. Cbl-b plays a role in early hematopoietic
development and is a negative regulator of T-cell
receptor, B-cell receptor and high affinity
immunoglobulin epsilon receptor signal transduction
pathways. It also negatively regulates insulin-like
growth factor 1 signaling during muscle atrophy caused
by unloading and is involved in EGFR ubiquitination and
internalization. Diseases associated with defects in
Cbl-b include: multiple sclerosis, autoimmune diseases,
including type 1 diabetes, and a craniofacial phenotype.
In general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 97
Score = 28.2 bits (63), Expect = 1.8
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 141 VRNRLLKCPDRMVPPVYSLNCTDLTTWAQSVTAPALHIVQS 181
V+ RL K D+ V+ L+CT L WA I+Q+
Sbjct: 22 VKARLQKFRDKPGSYVFRLSCTRLGQWAIGYVTADGKILQT 62
>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 = 26.4 bits (58), Expect = 1.8
Identities = 5/24 (20%), Positives = 11/24 (45%)
Query: 209 FNCDVCNRLFIGQHQYEQHMNSVK 232
F C +C + F + ++H+
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|173191 PRK14729, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Provisional.
Length = 300
Score = 28.7 bits (64), Expect = 2.9
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 17/70 (24%)
Query: 15 EVLDKRLEGRVHTMIQNGLIEELLQ-FHRQYNEDRIGKQLEPDYTKGIFQSIGFKEF--- 70
E + R+ RV+ MI GL+ E+ + YNE F+ IG++EF
Sbjct: 198 EEMKSRIISRVNNMIDCGLLSEIKSLLGKGYNE-----------NTPAFKGIGYREFLLW 246
Query: 71 --HNYLMLSD 78
ML+D
Sbjct: 247 KSRPCYMLND 256
>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 = 27.6 bits (62), Expect = 3.0
Identities = 7/28 (25%), Positives = 10/28 (35%)
Query: 209 FNCDVCNRLFIGQHQYEQHMNSVKHRRM 236
C C + F QHM H ++
Sbjct: 51 NECLYCGKQFKSLEALRQHMRDKGHCKI 78
>gnl|CDD|201791 pfam01428, zf-AN1, AN1-like Zinc finger. Zinc finger at the
C-terminus of An1, a ubiquitin-like protein in Xenopus
laevis. The following pattern describes the zinc finger.
C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can
be any amino acid, and numbers in brackets indicate the
number of residues.
Length = 43
Score = 25.9 bits (57), Expect = 3.8
Identities = 7/21 (33%), Positives = 8/21 (38%), Gaps = 1/21 (4%)
Query: 209 FNCDVCNRLFIGQH-QYEQHM 228
F C C F +H E H
Sbjct: 14 FKCRFCGGTFCLKHRLPEDHN 34
>gnl|CDD|132444 TIGR03403, nifS_epsilon, cysteine desulfurase, NifS family, epsilon
proteobacteria type. Members of this family are the
NifS-like cysteine desulfurase of the epsilon division
of the Proteobacteria, similar to the NifS protein of
nitrogen-fixing bacteria. Like NifS, and unlike IscS,
this protein is found as part of a system of just two
proteins, a cysteine desulfurase and a scaffold, for
iron-sulfur cluster biosynthesis. This protein is called
NifS by Olsen, et al. (PMID:11123951), so we use this
designation.
Length = 382
Score = 28.7 bits (64), Expect = 4.0
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 182 YLDNRAPTGIEPLAQEYVDP 201
YLDN A T ++P +E +DP
Sbjct: 2 YLDNNATTMLDPKVKELMDP 21
>gnl|CDD|236544 PRK09506, mrcB, bifunctional glycosyl transferase/transpeptidase;
Reviewed.
Length = 830
Score = 28.2 bits (63), Expect = 4.9
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 175 ALHIVQSYLDNRAPTGIEPLAQE-YVDPSYYNAGTFNCD 212
A+ I Q YL+N+ PT + E VD G F C
Sbjct: 735 AMTIYQRYLENQTPTPLNLTPPEDIVDMGVDYDGNFVCG 773
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 5.3
Identities = 5/20 (25%), Positives = 10/20 (50%)
Query: 209 FNCDVCNRLFIGQHQYEQHM 228
+ C C ++F + +HM
Sbjct: 1 YRCPECGKVFKSKSALREHM 20
>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The second LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 25.0 bits (55), Expect = 7.9
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 209 FNCDVCNRLFIGQHQYEQHMNSV 231
F C VC +F Y +H +
Sbjct: 25 FTCSVCPTVFGPNDSYYEHEGKI 47
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 0.135 0.403
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,600,953
Number of extensions: 1272312
Number of successful extensions: 1066
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1054
Number of HSP's successfully gapped: 39
Length of query: 269
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 174
Effective length of database: 6,723,972
Effective search space: 1169971128
Effective search space used: 1169971128
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: 58 (26.1 bits)