RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4862
(81 letters)
>gnl|CDD|214935 smart00955, RNB, This domain is the catalytic domain of
ribonuclease II.
Length = 286
Score = 95.4 bits (238), Expect = 1e-25
Identities = 31/52 (59%), Positives = 38/52 (73%)
Query: 30 EVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
+GVHIADVSH++KPG+ LD EA R T+VYL D+ I M+P LS LCSL
Sbjct: 35 RLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSNGLCSLN 86
>gnl|CDD|216112 pfam00773, RNB, RNB domain. This domain is the catalytic domain
of ribonuclease II.
Length = 322
Score = 93.5 bits (233), Expect = 9e-25
Identities = 30/52 (57%), Positives = 39/52 (75%)
Query: 30 EVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
+GVHIADVSH++ PG+PLD+EA R T+VYL + I M+P LS +LCSL
Sbjct: 35 RLGVHIADVSHYVPPGSPLDKEARKRGTSVYLPEGVIPMLPEELSNDLCSLL 86
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 84.4 bits (209), Expect = 6e-21
Identities = 30/52 (57%), Positives = 39/52 (75%)
Query: 30 EVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
+GVHIADVSH+++PG+ LD+EA R T+VYL D+ I M+P LS LCSL
Sbjct: 282 RLGVHIADVSHYVQPGSALDKEARKRGTSVYLPDRVIPMLPEALSNGLCSLN 333
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 79.2 bits (196), Expect = 4e-19
Identities = 29/60 (48%), Positives = 41/60 (68%), Gaps = 2/60 (3%)
Query: 24 KSKKKG--EVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
+ K G ++GV IADVSH+++ G+ LD+EA R T+VYL D+ I M+P LS +CSL
Sbjct: 272 EKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLN 331
>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases
[Transcription, Degradation of RNA].
Length = 654
Score = 67.8 bits (166), Expect = 4e-15
Identities = 26/60 (43%), Positives = 35/60 (58%)
Query: 22 KKKSKKKGEVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
KK ++ V IADVS+++ +PLD+EA R +VYL I M+P LS LCSL
Sbjct: 220 KKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLN 279
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 58.2 bits (141), Expect = 9e-12
Identities = 28/58 (48%), Positives = 39/58 (67%), Gaps = 3/58 (5%)
Query: 26 KKKG---EVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSL 80
KK+G + V IADVS++++P TPLD EA R T+VY + + M+P +LS LCSL
Sbjct: 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSL 344
>gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional.
Length = 644
Score = 54.1 bits (131), Expect = 3e-10
Identities = 24/49 (48%), Positives = 30/49 (61%)
Query: 33 VHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
V IAD + +I G+ LD+ A RA T YL I M+P LS +LCSLR
Sbjct: 227 VAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLR 275
>gnl|CDD|227117 COG4776, Rnb, Exoribonuclease II [Transcription].
Length = 645
Score = 47.5 bits (113), Expect = 5e-08
Identities = 25/49 (51%), Positives = 32/49 (65%)
Query: 33 VHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
V IAD + +I G+ LD+EA +RA T YL I M+P LS +LCSLR
Sbjct: 227 VAIADPTAYIAEGSKLDKEAKIRAFTNYLPGFNIPMLPRELSDDLCSLR 275
>gnl|CDD|131117 TIGR02062, RNase_B, exoribonuclease II. This family consists of
exoribonuclease II, the product of the rnb gene, as
found in a number of gamma proteobacteria. In
Escherichia coli, it is one of eight different
exoribonucleases. It is involved in mRNA degradation and
tRNA precursor end processing [Transcription,
Degradation of RNA].
Length = 639
Score = 47.5 bits (113), Expect = 6e-08
Identities = 23/49 (46%), Positives = 30/49 (61%)
Query: 33 VHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
V IAD + +I G+ LD+ A +R T YL I M+P LS +LCSLR
Sbjct: 223 VAIADPTAYIAEGSKLDKAAKIRGFTNYLPGFNIPMLPRELSDDLCSLR 271
>gnl|CDD|235569 PRK05702, flhB, flagellar biosynthesis protein FlhB; Reviewed.
Length = 359
Score = 28.6 bits (65), Expect = 0.29
Identities = 12/31 (38%), Positives = 22/31 (70%), Gaps = 4/31 (12%)
Query: 1 MEEGEKEEERKGSEEPETKKRKKKSKKKGEV 31
M E + +E+ +EEP T K+ +K+++KG+V
Sbjct: 1 MAEDDDDEK---TEEP-TPKKLEKAREKGQV 27
>gnl|CDD|152111 pfam11675, DUF3271, Protein of unknown function (DUF3271). This
family of proteins with unknown function appears to be
restricted to Plasmodium.
Length = 249
Score = 27.0 bits (60), Expect = 0.97
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 15 EPETKKRKKKSKKKGEVGVHIADVS---HFIK 43
EPE +K K +K+ + V+ + ++ +FIK
Sbjct: 172 EPENEKLHKSAKEIFKALVNNSSMNIKGYFIK 203
>gnl|CDD|224295 COG1377, FlhB, Flagellar biosynthesis pathway, component FlhB
[Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 363
Score = 26.8 bits (60), Expect = 1.0
Identities = 8/31 (25%), Positives = 20/31 (64%), Gaps = 4/31 (12%)
Query: 1 MEEGEKEEERKGSEEPETKKRKKKSKKKGEV 31
++ +E+ +E+P T K+ + +++KG+V
Sbjct: 1 ADDMADDEK---TEKP-TPKKLRDAREKGQV 27
>gnl|CDD|226448 COG3938, COG3938, Proline racemase [Amino acid transport and
metabolism].
Length = 341
Score = 26.6 bits (59), Expect = 1.2
Identities = 17/48 (35%), Positives = 18/48 (37%), Gaps = 4/48 (8%)
Query: 34 HIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
I VSH G P+ A LR Y K ID P G S R
Sbjct: 219 DIRGVSHCQFAGPPVRPGADLRNAVFY-GPKAIDRSPC---GTGTSAR 262
>gnl|CDD|222697 pfam14345, GDYXXLXY, GDYXXLXY protein. This family of proteins is
functionally uncharacterized. This family of proteins is
found in bacteria, archaea and eukaryotes. Proteins in
this family are typically between 171 and 199 amino
acids in length. It contains a conserved GDYXXLXY motif.
Length = 148
Score = 26.4 bits (59), Expect = 1.3
Identities = 10/35 (28%), Positives = 11/35 (31%)
Query: 27 KKGEVGVHIADVSHFIKPGTPLDEEAALRATTVYL 61
K E GV A +P E ALR
Sbjct: 72 KLDEDGVARAVRVSLERPKPLAPGEVALRGRVRGG 106
>gnl|CDD|149438 pfam08374, Protocadherin, Protocadherin. The structure of
protocadherins is similar to that of classic cadherins
(pfam00028), but particularly on the cytoplasmic domains
they also have some unique features. They are expressed
in a variety of organisms and are found in high
concentrations in the brain where they seem to be
localised mainly at cell-cell contact sites. Their
expression seems to be developmentally regulated.
Length = 223
Score = 26.3 bits (58), Expect = 1.8
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 2 EEGEKEEERKGSEEPETKKRKKKSKKKG 29
+ G+KE E S E K++KKK KK
Sbjct: 73 QAGKKETEDWFSPNQENKQKKKKKDKKK 100
>gnl|CDD|181628 PRK09054, PRK09054, phosphogluconate dehydratase; Validated.
Length = 603
Score = 26.3 bits (59), Expect = 1.8
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 5/30 (16%)
Query: 32 GVHIADVSHFIKPGTPLDE----EAALRAT 57
G+H+ S F+ PGTPL + EAA R
Sbjct: 238 GLHLPGSS-FVNPGTPLRDALTREAARRVL 266
>gnl|CDD|184428 PRK13971, PRK13971, hydroxyproline-2-epimerase; Provisional.
Length = 333
Score = 26.1 bits (58), Expect = 1.8
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 34 HIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPG 71
I VSH + G P+ A R V+ DK ID P
Sbjct: 217 RIRGVSHVLWTGKPISPGADARN-AVFYGDKAIDRSPC 253
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 26.1 bits (57), Expect = 2.3
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 2 EEGEKEEERKGSEEPETKKRKKKSKKKGE 30
EGE ERKG +E E + K++ KGE
Sbjct: 681 SEGEIPAERKGEQEGEGEIEAKEADHKGE 709
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 26.0 bits (57), Expect = 2.4
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 1 MEEGEKEEERKGSEEPE---TKKRKKKSKKKGEVGVHIADVSHFIK 43
+E GE E+ + E E + K+ KKSKKK +G + V IK
Sbjct: 227 LEGGELIEKPQAEAENEAGKSDKKDKKSKKKKVLGKGTSAVLQLIK 272
>gnl|CDD|110998 pfam02055, Glyco_hydro_30, O-Glycosyl hydrolase family 30.
Length = 495
Score = 26.1 bits (57), Expect = 2.4
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 34 HIADVSHFIKPGT 46
IA SHFIKPG
Sbjct: 415 AIAHFSHFIKPGA 427
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 25.3 bits (56), Expect = 3.4
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 6 KEEERKGSEEPETKKRKKKSKKKG 29
E++ K E+P+ KKR + +K G
Sbjct: 400 AEKKEKEKEKPKVKKRHRDTKNIG 423
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 25.4 bits (56), Expect = 4.0
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 2 EEGEKEEERKGSEEPETKKRKKKSKKKGE 30
E+ E ++K ++ + KK KK+ K +GE
Sbjct: 60 EDKNNESKKKSEKKKKKKKEKKEPKSEGE 88
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 25.1 bits (55), Expect = 5.4
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 5 EKEEERKGSE--EPETKKRKKKSKKKGE 30
K+ E K S+ E +TKK+KKK KKK E
Sbjct: 730 GKDAEFKISDSVEEKTKKKKKKEKKKEE 757
>gnl|CDD|238301 cd00539, MCR_gamma, Methyl-coenzyme M reductase (MCR) gamma
subunit. MCR catalyzes the terminal step of methane
formation in the energy metabolism of all methanogenic
archaea, in which methyl-coenzyme M and coenzyme B are
converted to methane and the heterodisulfide of coenzyme
M and coenzyme B (CoM-S-S-CoB). MCR is a dimer of
trimers, each of which consists of one alpha, one beta,
and one gamma subunit, with two identical active sites
containing nickel porphinoid factor 430 (F430).
Length = 246
Score = 24.8 bits (54), Expect = 5.8
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 45 GTPLDEEAALRATTVYLVD 63
G PL EE + TT+Y VD
Sbjct: 200 GKPLPEEELKKRTTIYRVD 218
>gnl|CDD|110325 pfam01312, Bac_export_2, FlhB HrpN YscU SpaS Family. This family
includes the following members: FlhB, HrpN, YscU, SpaS,
HrcU SsaU and YopU. All of these proteins export
peptides using the type III secretion system. The
peptides exported are quite diverse.
Length = 343
Score = 24.5 bits (54), Expect = 6.3
Identities = 8/19 (42%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 13 SEEPETKKRKKKSKKKGEV 31
+E+P T K+ + ++KKG+V
Sbjct: 6 TEKP-TPKKLRDARKKGQV 23
>gnl|CDD|130264 TIGR01196, edd, 6-phosphogluconate dehydratase. A close homolog,
designated MocB (mannityl opine catabolism), is found in
a mannopine catabolism region of a plasmid of
Agrobacterium tumefaciens. However, it is not essential
for mannopine catabolism, branches within the cluster of
6-phosphogluconate dehydratases (with a short branch
length) in a tree rooted by the presence of other
dehydyatases. It may represent an authentic
6-phosphogluconate dehydratase, redundant with the
chromosomal copy shown to exist in plasmid-cured
strains. This model includes mocB above the trusted
cutoff, although the designation is somewhat tenuous
[Energy metabolism, Entner-Doudoroff].
Length = 601
Score = 24.8 bits (54), Expect = 6.3
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 31 VGVHIADVSHFIKPGTP----LDEEAALRAT 57
+G+H+ S F+ P TP L EAA R
Sbjct: 236 MGLHLPGAS-FVNPNTPLRDALTREAAKRLA 265
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 24.6 bits (53), Expect = 6.5
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 7 EEERKGSEEPETKKRKKKSKKK 28
EEER+ + E KR+KK ++K
Sbjct: 85 EEERRHRQRLEKDKREKKKREK 106
>gnl|CDD|175980 cd04013, C2_SynGAP_like, C2 domain present in Ras GTPase activating
protein (GAP) family. SynGAP, GAP1, RasGAP, and
neurofibromin are all members of the Ras-specific GAP
(GTPase-activating protein) family. SynGAP regulates
the MAP kinase signaling pathway and is critical for
cognition and synapse function. Mutations in this gene
causes mental retardation in humans. SynGAP contains a
PH-like domain, a C2 domain, and a Ras-GAP domain. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 146
Score = 24.6 bits (54), Expect = 6.9
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 15 EPETKKRKKKSKKKGEVGVHIADVS 39
E + KK+K KS+ G V + + DVS
Sbjct: 76 ESDKKKKKDKSQLIGTVNIPVTDVS 100
>gnl|CDD|183737 PRK12773, flhB, flagellar biosynthesis protein FlhB; Reviewed.
Length = 646
Score = 24.6 bits (53), Expect = 7.0
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 9 ERKGSEEPETKKRKKKSKKKGEV 31
E +G EP +++R+++ ++KG V
Sbjct: 296 EDEGRTEPGSERRRREEREKGNV 318
>gnl|CDD|215192 PLN02334, PLN02334, ribulose-phosphate 3-epimerase.
Length = 229
Score = 24.6 bits (54), Expect = 7.1
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 8/29 (27%)
Query: 42 IKPGTPLDEEAALRATTVYLVDK-RIDMV 69
+ PGTP++ +V+K +DMV
Sbjct: 122 LNPGTPVEA-------VEPVVEKGLVDMV 143
>gnl|CDD|202170 pfam02240, MCR_gamma, Methyl-coenzyme M reductase gamma subunit.
Methyl-coenzyme M reductase (MCR) is the enzyme
responsible for microbial formation of methane. It is a
hexamer composed of 2 alpha (pfam02249), 2 beta
(pfam02241), and 2 gamma (this family) subunits with two
identical nickel porphinoid active sites.
Length = 247
Score = 24.4 bits (53), Expect = 7.8
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 45 GTPLDEEAALRATTVYLVD 63
G PLDEE + TT+Y VD
Sbjct: 201 GEPLDEEELKKRTTIYRVD 219
>gnl|CDD|132303 TIGR03259, met_CoM_red_gam, methyl-coenzyme M reductase, gamma
subunit. Members of this protein family are the gamma
subunit of methyl coenzyme M reductase, also called
coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This
enzyme, with alpha, beta, and gamma subunits, catalyzes
the last step in methanogenesis. Several methanogens
have encode two such enzymes, designated I and II; this
model does not separate the isozymes [Energy metabolism,
Methanogenesis].
Length = 244
Score = 24.4 bits (53), Expect = 8.1
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 45 GTPLDEEAALRATTVYLVD 63
G PL EE + TT+Y VD
Sbjct: 200 GEPLSEEELKKITTIYRVD 218
>gnl|CDD|143524 cd06966, NR_DBD_CAR, DNA-binding domain of constitutive
androstane receptor (CAR) is composed of two C4-type
zinc fingers. DNA-binding domain (DBD) of constitutive
androstane receptor (CAR) is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. CAR
DBD interacts with CAR response element, a perfect
repeat of two AGTTCA motifs with a 4 bp spacer upstream
of the target gene, and modulates the rate of
transcriptional initiation. The constitutive androstane
receptor (CAR) is a ligand-regulated transcription
factor that responds to a diverse array of chemically
distinct ligands, including many endogenous compounds
and clinical drugs. It functions as a heterodimer with
RXR. The CAR/RXR heterodimer binds many common response
elements in the promoter regions of a diverse set of
target genes involved in the metabolism, transport, and
ultimately, elimination of these molecules from the
body. CAR is a closest mammalian relative of PXR and is
activated by some of the same ligands as PXR and
regulates a subset of common genes. The sequence
homology and functional similarity suggests that the
CAR gene arose from a duplication of an ancestral PXR
gene. Like other nuclear receptors, CAR has a central
well conserved DNA binding domain, a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain.
Length = 94
Score = 23.9 bits (52), Expect = 8.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 1 MEEGEKEEERKGSEEPETKKR 21
M E +K E+R+ EE KKR
Sbjct: 74 MSEEDKSEKRQKIEENRAKKR 94
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
0.308 0.130 0.355
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,148,782
Number of extensions: 335917
Number of successful extensions: 1026
Number of sequences better than 10.0: 1
Number of HSP's gapped: 955
Number of HSP's successfully gapped: 122
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 53 (24.1 bits)