RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030503
(176 letters)
>gnl|CDD|239090 cd02406, CRS2, Chloroplast RNA splicing 2 (CRS2) is a
nuclear-encoded protein required for the splicing of
group II introns in the chloroplast. CRS2 forms stable
complexes with two CRS2-associated factors, CAF1 and
CAF2, which are required for the splicing of distinct
subsets of CRS2-dependent introns. CRS2 is closely
related to bacterial peptidyl-tRNA hydrolases (PTH).
Length = 191
Score = 170 bits (433), Expect = 2e-54
Identities = 59/88 (67%), Positives = 75/88 (85%)
Query: 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAK 134
PWLI GLGNPG +Y GTRHNVGFEMVD IAEAEGI+++++ FK+ G G IG+VPV+LAK
Sbjct: 2 PWLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAK 61
Query: 135 PQTFMNASGQSVGSIVSYYKIPLKQVLV 162
PQT+MN SG+SVG + +YYK+PL+ +LV
Sbjct: 62 PQTYMNYSGESVGPLAAYYKVPLRHILV 89
>gnl|CDD|238259 cd00462, PTH, Peptidyl-tRNA hydrolase (PTH) is a monomeric protein
that cleaves the ester bond linking the nascent peptide
and tRNA when peptidyl-tRNA is released prematurely from
the ribosome. This ensures the recycling of
peptidyl-tRNAs into tRNAs produced through abortion of
translation and is essential for cell viability.This
group also contains chloroplast RNA splicing 2 (CRS2),
which is closely related nuclear-encoded protein
required for the splicing of nine group II introns in
chloroplasts.
Length = 171
Score = 145 bits (368), Expect = 6e-45
Identities = 45/86 (52%), Positives = 61/86 (70%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAKPQ 136
LIVGLGNPG +Y TRHNVGF ++DA+AE G+S K G+G IG V+L KPQ
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQ 60
Query: 137 TFMNASGQSVGSIVSYYKIPLKQVLV 162
T+MN SG++V ++ ++YKIP + +LV
Sbjct: 61 TYMNLSGEAVAALANFYKIPPEDILV 86
>gnl|CDD|235457 PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional.
Length = 189
Score = 141 bits (357), Expect = 6e-43
Identities = 42/89 (47%), Positives = 58/89 (65%), Gaps = 1/89 (1%)
Query: 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVN-FKAHFGKGFIGNVPVMLA 133
LIVGLGNPG +Y TRHN+GF +VD +A G S+ FK +G I V+L
Sbjct: 2 MKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILL 61
Query: 134 KPQTFMNASGQSVGSIVSYYKIPLKQVLV 162
KPQT+MN SG++V ++ ++YKIP + +LV
Sbjct: 62 KPQTYMNLSGKAVAALANFYKIPPEDILV 90
>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase.
Length = 183
Score = 134 bits (341), Expect = 1e-40
Identities = 45/87 (51%), Positives = 59/87 (67%), Gaps = 1/87 (1%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVS-SVNFKAHFGKGFIGNVPVMLAKP 135
LIVGLGNPG +Y TRHNVGF ++D +AE G+S+ FK KG I V+L KP
Sbjct: 1 LIVGLGNPGPKYENTRHNVGFMVIDRLAERLGVSLKKKKKFKGLIAKGRIEGEKVILLKP 60
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLV 162
QT+MN SG++V +I +YKIP + +LV
Sbjct: 61 QTYMNLSGEAVRAIARFYKIPPEDILV 87
>gnl|CDD|223271 COG0193, Pth, Peptidyl-tRNA hydrolase [Translation, ribosomal
structure and biogenesis].
Length = 190
Score = 126 bits (320), Expect = 3e-37
Identities = 43/89 (48%), Positives = 56/89 (62%), Gaps = 1/89 (1%)
Query: 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVS-SVNFKAHFGKGFIGNVPVMLA 133
LIVGLGNPGK+Y TRHNVGF +VD +A +S F KG I V+L
Sbjct: 2 MKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILL 61
Query: 134 KPQTFMNASGQSVGSIVSYYKIPLKQVLV 162
KP T+MN SG++VG++ S+YKI + +LV
Sbjct: 62 KPTTYMNLSGKAVGALASFYKIKPEDILV 90
>gnl|CDD|213531 TIGR00447, pth, peptidyl-tRNA hydrolase. The natural substrate for
this enzyme may be peptidyl-tRNAs that drop off the
ribosome during protein synthesis. Peptidyl-tRNA
hydrolase is a bacterial protein; YHR189W from
Saccharomyces cerevisiae appears to be orthologous and
likely has the same function [Protein synthesis, Other].
Length = 188
Score = 102 bits (255), Expect = 1e-27
Identities = 39/87 (44%), Positives = 59/87 (67%), Gaps = 1/87 (1%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSS-VNFKAHFGKGFIGNVPVMLAKP 135
LIVGLGNPGK+Y GTRHN GF ++D +A G+S+ + F + +G + V+L KP
Sbjct: 3 LIVGLGNPGKKYAGTRHNAGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKP 62
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLV 162
T+MN SG++V ++ S+Y+I ++LV
Sbjct: 63 LTYMNLSGEAVRALASFYRIKPAELLV 89
>gnl|CDD|233836 TIGR02363, dhaK1, dihydroxyacetone kinase, DhaK subunit. Two types
of dihydroxyacetone kinase (glycerone kinase) are
described. In yeast and a few bacteria, e.g. Citrobacter
freundii, the enzyme is a single chain that uses ATP as
phosphoryl donor and is designated EC 2.7.1.29. By
contract, E. coli and many other bacterial species have
a multisubunit form (EC 2.7.1.-) with a phosphoprotein
donor related to PTS transport proteins. This family
represents the DhaK subunit of the latter type of
dihydroxyacetone kinase, but it specifically excludes
the DhaK paralog DhaK2 (TIGR02362) found in the same
operon as DhaK and DhaK in the Firmicutes.
Length = 329
Score = 32.3 bits (74), Expect = 0.11
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 86 KQYNGTRHNVGFEMVDAIAEAEGISVSSV 114
K Y G N FEM +AE EGI V++V
Sbjct: 105 KNYTGDVMN--FEMAAELAEDEGIKVATV 131
>gnl|CDD|237724 PRK14481, PRK14481, dihydroxyacetone kinase subunit DhaK;
Provisional.
Length = 331
Score = 31.3 bits (72), Expect = 0.18
Identities = 18/38 (47%), Positives = 21/38 (55%), Gaps = 8/38 (21%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSV 114
LIV K Y+G N FEM +AE EGI V+SV
Sbjct: 101 LIV------KNYSGDVMN--FEMAAELAEMEGIEVASV 130
>gnl|CDD|217094 pfam02542, YgbB, YgbB family. The ygbB protein is a putative
enzyme of deoxy-xylulose pathway (terpenoid
biosynthesis).
Length = 156
Score = 30.9 bits (71), Expect = 0.21
Identities = 13/32 (40%), Positives = 13/32 (40%), Gaps = 2/32 (6%)
Query: 98 EMVDAIAEAEGISVSSVNFKA--HFGKGFIGN 127
M IAE GI VN KA GF G
Sbjct: 111 AMRANIAELLGIPEDRVNVKATTTEKLGFTGR 142
>gnl|CDD|100025 cd00554, MECDP_synthase, MECDP_synthase
(2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase),
encoded by the ispF gene, catalyzes the formation of
2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in
the non-mevalonate deoxyxylulose (DOXP) pathway for
isoprenoid biosynthesis. This pathway is present in
bacteria, plants and some protozoa but is distinct from
that used by mammals and Archaea. MECDP_synthase forms
a homotrimer, carrying three active sites, each of which
is formed in a cleft between pairs of subunits.
Length = 153
Score = 28.9 bits (66), Expect = 0.79
Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 98 EMVDAIAEAEGISVSSVNFKA--HFGKGFIGN 127
M +AE GI S VN KA G GF G
Sbjct: 110 AMRANLAELLGIPPSRVNIKATTTEGLGFTGR 141
>gnl|CDD|223323 COG0245, IspF, 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
[Lipid metabolism].
Length = 159
Score = 28.7 bits (65), Expect = 1.2
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 98 EMVDAIAEAEGISVSSVNFKAHFGK--GFIG 126
M IAE GI V +N KA + GF G
Sbjct: 111 AMRANIAELLGIPVDRINVKATTTEKLGFTG 141
>gnl|CDD|213893 TIGR04176, MarR_EPS, EPS-associated transcriptional regulator, MarR
family. Members of this family of MarR-family
transcriptional regulators are associated with long
genomic loci consisting of genes encoding enzymes for
the biosynthesis of exopolysaccharides. These genes
include glycosyl transferases, sugar modifying enzymes
(epimerases, isomerases, methyltransferases,
aminotransferases, etc.), and exopolysaccharide
polymerases (wzx, wzy). In Leptospira interrogans,
borgpeterenii and biflexa, this gene is observed first
in unidirectional EPS biosynthesis loci as long as 90
genes. MarR genes (pfam01407) are known to bind to DNA
regions with palindromic or pseudopalindromic sequences
as homodimers, and to bind small molecules as triggers
for conformational changes controlling on/off states.
Length = 105
Score = 27.7 bits (62), Expect = 1.6
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 10/41 (24%)
Query: 103 IAEAEGISVSSVNF--KAHFGKGFIGNVPVMLAKPQTFMNA 141
+A+ G+S+ N+ KA KG + K F N+
Sbjct: 24 LAKELGVSLGKTNYCLKALIEKGLV--------KAGNFRNS 56
>gnl|CDD|178851 PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
synthase; Reviewed.
Length = 159
Score = 27.8 bits (63), Expect = 2.0
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 97 FEMVDAIAEAEGISVSSVNFKAHFGK--GFIG 126
EM IAE GI + VN KA + GF G
Sbjct: 112 EEMRANIAEDLGIPLDDVNVKATTTEKLGFTG 143
>gnl|CDD|115821 pfam07192, SNURF, SNURF/RPN4 protein. This family consists of
several mammalian SNRPN upstream reading frame (SNURF)
proteins. SNURF or RPF4 is a RING-finger protein and a
coregulator of androgen receptor-dependent
transcription. It has been suggested that SNURF is
involved in the regulation of processes required for
late steps of spermatid maturation.
Length = 71
Score = 25.9 bits (56), Expect = 3.6
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 51 RNFSSSISNEESLVSPKPKQQQQHP 75
R ++S++N+E + + QQQQ P
Sbjct: 27 RRRTASLNNQECHLYLRRSQQQQIP 51
>gnl|CDD|217197 pfam02711, Pap_E4, E4 protein. This is is a family of
Papillomavirus proteins, E4, coded for by ORF4. A
splice variant, E1--E4, exists but neither the function
of E4 or E1--E4 is known.
Length = 95
Score = 26.5 bits (59), Expect = 4.1
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 5/46 (10%)
Query: 31 PLCCWGRRTRMSRSPSNSTIRNFSSSISNEESLVSPKPKQQQQHPW 76
P W + R R + S S S P P+ + PW
Sbjct: 28 PPPPWAPKKRCRRRLESD-----SDSSSTTSPSSPPTPQPTTECPW 68
>gnl|CDD|238952 cd01994, Alpha_ANH_like_IV, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily.Adeninosine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins is predicted to bind ATP.
This domainhas a strongly conserved motif SGGKD at the
N terminus.
Length = 194
Score = 26.8 bits (60), Expect = 5.4
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 72 QQHPWLIVGLGN--PGKQYNGTRHNVGFEMVDAIAEAEGISV 111
+ +V L N P + + H V E+++ AEA GI +
Sbjct: 20 LEEGHEVVALLNLTPEEGSSMMYHTVNHELLELQAEAMGIPL 61
>gnl|CDD|129255 TIGR00151, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
synthase. Members of this protein family are
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase,
the IspF protein of the deoxyxylulose (non-mevalonate)
pathway of IPP biosynthesis. This protein occurs as an
IspDF bifunctional fusion protein in about 20 percent of
bacterial genomes [Biosynthesis of cofactors, prosthetic
groups, and carriers, Other].
Length = 155
Score = 26.1 bits (58), Expect = 8.0
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 97 FEMVDAIAEAEGISVSSVNFKAHFGK--GFIG 126
M + IAE GI + SVN KA + GF G
Sbjct: 109 PAMRENIAELLGIPLDSVNVKATTTEKLGFTG 140
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 0.133 0.400
Gapped
Lambda K H
0.267 0.0497 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,640,719
Number of extensions: 752786
Number of successful extensions: 652
Number of sequences better than 10.0: 1
Number of HSP's gapped: 648
Number of HSP's successfully gapped: 20
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
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 (21.9 bits)
S2: 56 (25.9 bits)