RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2610
(133 letters)
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 90.5 bits (225), Expect = 3e-22
Identities = 34/96 (35%), Positives = 52/96 (54%), Gaps = 3/96 (3%)
Query: 36 EDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFARLYSAKLGIREDILRKTLWGDYYLNA 95
D D+ P++G V F S GW FT+ FAR+Y+ K G+ E + + LWGD + +A
Sbjct: 187 NDELMGDVQVYPEKGTVAFGSGLQGWAFTLTTFARIYAKKFGVEESKMMERLWGDNFFDA 246
Query: 96 KAKRILK---GAQEKAKAPLFVEFVLKNVVTLYETV 128
K K+ +K AQ K F +F+L + L++ V
Sbjct: 247 KTKKWIKDETNAQGKKLKRAFCQFILDPICQLFDAV 282
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 65.9 bits (161), Expect = 1e-13
Identities = 26/99 (26%), Positives = 49/99 (49%), Gaps = 1/99 (1%)
Query: 36 EDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFARLYSAKLGIREDILRKTLWGDYYLNA 95
ED D+ P++G V F++ GW FT+ +FA++Y++K G+ E + + LWG+ + +
Sbjct: 193 EDPLLGDVQVYPEKGTVAFSAGLHGWAFTLTNFAKMYASKFGVDESKMMERLWGENFFDP 252
Query: 96 KAKRILKGAQEKAKAPL-FVEFVLKNVVTLYETVAVRKK 133
K+ FV+F + + + T +K
Sbjct: 253 ATKKWTTKNTGSPTCKRGFVQFCYEPIKQIINTCMNDQK 291
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 63.4 bits (155), Expect = 3e-13
Identities = 20/38 (52%), Positives = 24/38 (63%)
Query: 36 EDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFARLYS 73
E+ FSP +GNV F SA DGWGFTI FA +Y+
Sbjct: 169 EEFKQEKWKFSPQKGNVAFGSALDGWGFTIIKFADIYA 206
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 44.2 bits (105), Expect = 3e-06
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 40 DSDLYFSPDRGNVVFASAFDGWGFTIDDFARLYS 73
SP+ GNV+FAS+ G+ FT++ FA+ Y
Sbjct: 168 TEGFLVSPELGNVLFASSKFGFCFTLESFAKKYG 201
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 38.3 bits (90), Expect = 5e-04
Identities = 25/78 (32%), Positives = 33/78 (42%), Gaps = 19/78 (24%)
Query: 46 SPDRGNVVFASAFDGWGFTIDDFARLYSAKLGIR-EDILRKTLWGDYYLNAKAKRILKGA 104
+ G V F SA W ++ K GI+ +DI+ DYY K K + +
Sbjct: 193 DVEDGTVAFGSALYNWAISVP-----MMQKTGIKFKDII------DYYEKGKQKELAE-- 239
Query: 105 QEKAKAPLFVEFVLKNVV 122
KAPL E VL VV
Sbjct: 240 ----KAPLH-EVVLDMVV 252
>gnl|CDD|219174 pfam06780, Erp_C, Erp protein C-terminus. This family represents
the C-terminus of bacterial Erp proteins that seem to
be specific to Borrelia burgdorferi (a causative agent
of Lyme disease). Borrelia Erp proteins are
particularly heterogeneous, which might enable them to
interact with a wide variety of host components.
Length = 141
Score = 27.8 bits (62), Expect = 1.3
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 20 TSSPSDTVYTDWGTGLEDADDSDL 43
T S+++Y+ WG LE+ +DS L
Sbjct: 42 TDGNSNSIYSTWGGDLEEEEDSGL 65
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 28.2 bits (63), Expect = 1.3
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 68 FARLYSAKLGIREDILRKTLWGD--YYLNAKAKRILKGAQEKAK 109
F R Y + L +RE ILR+ L G YYL + I K A+ A+
Sbjct: 789 FVREYDS-LVVREAILREILRGGQVYYLYNDVENIQKAAERLAE 831
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 28.0 bits (63), Expect = 1.8
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 11/78 (14%)
Query: 12 VLRPGPQSTSSPSDTVYTDWGTGLEDADDSDLYFSPDRGNVVFASAFDGWGFTIDDFARL 71
V+RP P P + + E+A +D+YF G V+ + G L
Sbjct: 57 VIRPDPSVLLPPEEAIEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPG----------L 106
Query: 72 YSAKLG-IREDILRKTLW 88
K G +I ++T W
Sbjct: 107 VIGKGGSTLREITKETGW 124
>gnl|CDD|234216 TIGR03454, partition_RepB, plasmid partitioning protein RepB.
Members of this family are the RepB protein involved in
replicon partitioning. RepB is found, in general, as
part of a repABC operon in plasmids and small
chromosomes, separate from the main chromosome, in
various bacteria. This model describes a rather narrow
clade of proteins; it should be noted that additional
homologs scoring below the trusted cutoff have very
similar functions, although they may be named
differently [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 325
Score = 27.3 bits (61), Expect = 2.4
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 106 EKAKAPLFVEFVLKNVVTLYE 126
+K +AP F +F+L+ + LYE
Sbjct: 301 KKKEAPEFADFILERLDDLYE 321
>gnl|CDD|235564 PRK05691, PRK05691, peptide synthase; Validated.
Length = 4334
Score = 27.1 bits (60), Expect = 3.5
Identities = 9/18 (50%), Positives = 13/18 (72%), Gaps = 2/18 (11%)
Query: 59 DGW--GFTIDDFARLYSA 74
DGW +D+F+RLY+A
Sbjct: 813 DGWSLNILLDEFSRLYAA 830
>gnl|CDD|222040 pfam13311, DUF4080, Protein of unknown function (DUF4080). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 187
Score = 26.8 bits (60), Expect = 3.6
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 68 FARLYSAKLGIREDILRKTLWGDYYLNAKAK 98
KL ++LR+ L DY L KAK
Sbjct: 90 LLEFAEEKLPEDLELLRELLKFDYLLREKAK 120
>gnl|CDD|224696 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
metallo-beta-lactamase domain and an RNA-binding KH
domain [General function prediction only].
Length = 637
Score = 26.5 bits (59), Expect = 5.3
Identities = 12/43 (27%), Positives = 20/43 (46%)
Query: 11 LVLRPGPQSTSSPSDTVYTDWGTGLEDADDSDLYFSPDRGNVV 53
+++RP P P + E+A +D+YF D G V+
Sbjct: 62 IIIRPDPSVLKPPEEARKIILEIVPEEAGITDIYFDDDTGEVI 104
>gnl|CDD|239093 cd02410, archeal_CPSF_KH, The archaeal cleavage and
polyadenylation specificity factor (CPSF) contains an
N-terminal K homology RNA-binding domain (KH). The
archeal CPSFs are predicted to be metal-dependent
RNases belonging to the beta-CASP family, a subgroup
enzymes within the metallo-beta-lactamase fold. The KH
motif is a beta-alpha-alpha-beta-beta unit that folds
into an alpha-beta structure with a three stranded
beta-sheet interupted by two contiguous helices. In
general, KH domains are known to bind single-stranded
RNA or DNA and are found in a wide variety of proteins
including ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 145
Score = 25.7 bits (57), Expect = 6.5
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 11 LVLRPGPQSTSSPSDTVYTDWGTGLEDADDSDLYFSPDRGNVV 53
+V+RP P P + + E+A +D+YF D G V+
Sbjct: 39 IVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTGEVI 81
>gnl|CDD|237065 PRK12334, PRK12334, nucleoside triphosphate pyrophosphohydrolase;
Reviewed.
Length = 277
Score = 26.2 bits (58), Expect = 6.8
Identities = 12/32 (37%), Positives = 13/32 (40%), Gaps = 4/32 (12%)
Query: 52 VVF----ASAFDGWGFTIDDFARLYSAKLGIR 79
V+F A F IDD A AKL R
Sbjct: 123 VLFHARIAEEAPEDPFDIDDVAATLVAKLVRR 154
>gnl|CDD|217109 pfam02567, PhzC-PhzF, Phenazine biosynthesis-like protein.
PhzC/PhzF is involved in dimerisation of two
2,3-dihydro-3-oxo-anthranilic acid molecules to create
PCA by P. fluorescens. This family also contains an
uncharacterized protein Rv2715 from Mycobacterium
tuberculosis, though there is no significant sequence
similarity to pfam00303 members. This family appears to
be distantly related to pfam01678, including containing
a weak internal duplication. However members of this
family do not contain the conserved cysteines that are
hypothesised to be active site residues (Bateman A pers
obs).
Length = 280
Score = 25.8 bits (57), Expect = 7.7
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 47 PDRGNVVFASAFDGWGFTIDDFARLYSAKLGIRED 81
PD G +V +A G D AR+++ LGI ED
Sbjct: 182 PDDGVIVGPAASAGSPR--DYHARMFAPALGIVED 214
>gnl|CDD|184664 PRK14412, PRK14412, membrane protein; Provisional.
Length = 198
Score = 25.6 bits (56), Expect = 8.2
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 94 NAKAKRILKGAQEKAKAPLFVEFVLKNVVTL 124
NA A +L+ KA AP+F VLK V+ +
Sbjct: 38 NAGATNVLRVLGYKAAAPVFALDVLKGVIAV 68
>gnl|CDD|178579 PLN03002, PLN03002, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 332
Score = 25.8 bits (56), Expect = 8.8
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 81 DILRKTLWGDYYLNAKAKRILKGAQEKAKAPLFVE 115
D+L + W + + + R+L QE+ P FVE
Sbjct: 251 DMLER--WSNGFFKSTLHRVLGNGQERYSIPFFVE 283
>gnl|CDD|221334 pfam11949, DUF3466, Protein of unknown function (DUF3466). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 564 to 612 amino acids in
length.
Length = 589
Score = 25.9 bits (57), Expect = 9.0
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 18 QSTSSPSDTVYTDWGTGLEDADDSDLY 44
Q ++ + T+W GLE A D +++
Sbjct: 283 QLDATGNTVTETEWPLGLEPASDDEVF 309
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
0.318 0.136 0.412
Gapped
Lambda K H
0.267 0.0851 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,957,470
Number of extensions: 633123
Number of successful extensions: 542
Number of sequences better than 10.0: 1
Number of HSP's gapped: 541
Number of HSP's successfully gapped: 33
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.0 bits)