RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2609
(161 letters)
>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 = 233 bits (597), Expect = 3e-79
Identities = 79/138 (57%), Positives = 107/138 (77%), Gaps = 2/138 (1%)
Query: 8 YMDSRKDEQERGITMKSSSISLY--YKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLC 65
Y+D+R+DEQERGIT+KSS+ISLY Y++ K +YLINLIDSPGHVDFSSEV+ A+RL
Sbjct: 37 YLDTREDEQERGITIKSSAISLYFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLT 96
Query: 66 DGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQLL 125
DG ++VVD VEG+C QT+ L+QA E+++P+LV+NKIDRLILE+KLSP + Y L +++
Sbjct: 97 DGALVVVDAVEGVCVQTETVLRQALEERVKPVLVINKIDRLILELKLSPEEAYQRLLRIV 156
Query: 126 EQVNAVMGELFASQVMDE 143
E VNA++ + E
Sbjct: 157 EDVNAIIETYAPEEFKQE 174
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 182 bits (465), Expect = 2e-54
Identities = 70/129 (54%), Positives = 100/129 (77%), Gaps = 3/129 (2%)
Query: 8 YMDSRKDEQERGITMKSSSISLYYK---DNKDTPEEYLINLIDSPGHVDFSSEVSTAVRL 64
+ D+R DEQERGIT+KS+ ISLYY+ ++ D + +LINLIDSPGHVDFSSEV+ A+R+
Sbjct: 56 FTDTRADEQERGITIKSTGISLYYEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRV 115
Query: 65 CDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQL 124
DG ++VVDCVEG+C QT+ L+QA E+I+P+L +NK+DR ILE++L P +IY + +
Sbjct: 116 TDGALVVVDCVEGVCVQTETVLRQALQERIRPVLFINKVDRAILELQLDPEEIYQNFVKT 175
Query: 125 LEQVNAVMG 133
+E VN ++
Sbjct: 176 IENVNVIIA 184
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 168 bits (427), Expect = 4e-49
Identities = 68/134 (50%), Positives = 94/134 (70%), Gaps = 9/134 (6%)
Query: 8 YMDSRKDEQERGITMKSSSISLYYK----DNKDTP-----EEYLINLIDSPGHVDFSSEV 58
D+R DE ERGIT+KS+ ISLYY+ KD EYLINLIDSPGHVDFSSEV
Sbjct: 56 MTDTRADEAERGITIKSTGISLYYEMTDESLKDFKGERDGNEYLINLIDSPGHVDFSSEV 115
Query: 59 STAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIY 118
+ A+R+ DG ++VVDC+EG+C QT+ L+QA E+I+P+L +NK+DR LE+++ + Y
Sbjct: 116 TAALRITDGALVVVDCIEGVCVQTETVLRQALGERIRPVLTVNKMDRCFLELQVDGEEAY 175
Query: 119 VHLSQLLEQVNAVM 132
S+++E N +M
Sbjct: 176 QTFSRVIENANVIM 189
>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 = 153 bits (389), Expect = 9e-48
Identities = 64/122 (52%), Positives = 90/122 (73%), Gaps = 2/122 (1%)
Query: 8 YMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDG 67
Y D+RKDEQERGI++KS+ ISL +D+K YLIN+ID+PGHV+F EV+ A+RLCDG
Sbjct: 40 YTDTRKDEQERGISIKSNPISLVLEDSKGK--SYLINIIDTPGHVNFMDEVAAALRLCDG 97
Query: 68 TIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQLLEQ 127
++VVD VEG+ + T+ ++ A E + +LV+NKIDRLILE+KL P D Y L +++
Sbjct: 98 VVLVVDVVEGLTSVTERLIRHAIQEGLPMVLVINKIDRLILELKLPPTDAYYKLRHTIDE 157
Query: 128 VN 129
+N
Sbjct: 158 IN 159
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 147 bits (373), Expect = 9e-42
Identities = 57/125 (45%), Positives = 90/125 (72%), Gaps = 7/125 (5%)
Query: 8 YMDSRKDEQERGITMKSSSISLY--YKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLC 65
+D ++EQ RGIT+K++++S+ Y+ +EYLINLID+PGHVDF +V+ A+R
Sbjct: 57 ALDFDEEEQARGITIKAANVSMVHEYEG-----KEYLINLIDTPGHVDFGGDVTRAMRAV 111
Query: 66 DGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQLL 125
DG I+VVD VEG+ QT+ L+QA E+++P+L +NK+DRLI E+KL+P ++ L +++
Sbjct: 112 DGAIVVVDAVEGVMPQTETVLRQALRERVKPVLFINKVDRLIKELKLTPQEMQQRLLKII 171
Query: 126 EQVNA 130
+ VN
Sbjct: 172 KDVNK 176
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 147 bits (372), Expect = 1e-41
Identities = 50/127 (39%), Positives = 75/127 (59%), Gaps = 6/127 (4%)
Query: 7 SYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCD 66
+ MD + EQERGIT+ S++ +L++K +Y INLID+PGHVDF+ EV ++R+ D
Sbjct: 48 ATMDWMEQEQERGITITSAATTLFWKG------DYRINLIDTPGHVDFTIEVERSLRVLD 101
Query: 67 GTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQLLE 126
G ++VVD VEG+ QT+ +QA + IL +NK+DRL + L + L
Sbjct: 102 GAVVVVDAVEGVEPQTETVWRQADKYGVPRILFVNKMDRLGADFYLVVEQLKERLGANPV 161
Query: 127 QVNAVMG 133
V +G
Sbjct: 162 PVQLPIG 168
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 131 bits (331), Expect = 2e-39
Identities = 42/100 (42%), Positives = 60/100 (60%), Gaps = 7/100 (7%)
Query: 8 YMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDG 67
+D K+E+ERGIT+K +++S K LIN+ID+PGHVDF+ E+ DG
Sbjct: 40 VLDKLKEERERGITIKIAAVSFETKK-------RLINIIDTPGHVDFTKEMIRGASQADG 92
Query: 68 TIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLI 107
I+VVD VEG+ QT+ L A + I+ +NKIDR+
Sbjct: 93 AILVVDAVEGVMPQTREHLLLAKTLGVPIIVFINKIDRVD 132
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 121 bits (305), Expect = 1e-32
Identities = 59/142 (41%), Positives = 95/142 (66%), Gaps = 7/142 (4%)
Query: 8 YMDSRKDEQERGITMKSSSISLY--YKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLC 65
Y+D + EQERGIT+ ++++S+ Y+ N EYLINLID+PGHVDF +V+ A+R
Sbjct: 56 YLDFDEQEQERGITINAANVSMVHEYEGN-----EYLINLIDTPGHVDFGGDVTRAMRAV 110
Query: 66 DGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQLL 125
DG I+VV VEG+ QT+ L+QA E ++P+L +NK+DRLI E+KL+P ++ +++
Sbjct: 111 DGAIVVVCAVEGVMPQTETVLRQALKENVKPVLFINKVDRLINELKLTPQELQERFIKII 170
Query: 126 EQVNAVMGELFASQVMDETAVK 147
+VN ++ + + D+ V+
Sbjct: 171 TEVNKLIKAMAPEEFRDKWKVR 192
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 109 bits (274), Expect = 7e-31
Identities = 38/102 (37%), Positives = 57/102 (55%), Gaps = 7/102 (6%)
Query: 8 YMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDG 67
++D+ K+E+ERGIT+K+ + + IN ID+PGH DFS E + DG
Sbjct: 36 FLDTLKEERERGITIKTGVVEFEWPK-------RRINFIDTPGHEDFSKETVRGLAQADG 88
Query: 68 TIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILE 109
++VVD EG+ QT+ L A + I+ +NKIDR+ E
Sbjct: 89 ALLVVDANEGVEPQTREHLNIALAGGLPIIVAVNKIDRVGEE 130
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 108 bits (271), Expect = 2e-30
Identities = 47/101 (46%), Positives = 66/101 (65%), Gaps = 2/101 (1%)
Query: 4 MVSSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVR 63
M +DS E+ERGIT+K+ ++ L+YK EEYL+NLID+PGHVDFS EVS ++
Sbjct: 32 MKEQVLDSMDLERERGITIKAQAVRLFYKA--KDGEEYLLNLIDTPGHVDFSYEVSRSLA 89
Query: 64 LCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKID 104
C+G ++VVD +G+ AQT A ++ I V+NKID
Sbjct: 90 ACEGALLVVDATQGVEAQTLANFYLALENNLEIIPVINKID 130
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The properties
thus far described for BipA are related to its role in
the process of pathogenesis by enteropathogenic E. coli.
It appears to be involved in the regulation of several
processes important for infection, including
rearrangements of the cytoskeleton of the host,
bacterial resistance to host defense peptides,
flagellum-mediated cell motility, and expression of K5
capsular genes. It has been proposed that BipA may
utilize a novel mechanism to regulate the expression of
target genes. In addition, BipA from enteropathogenic E.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 100 bits (252), Expect = 2e-27
Identities = 42/97 (43%), Positives = 61/97 (62%), Gaps = 7/97 (7%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MDS E+ERGIT+ + + ++ YKD IN+ID+PGH DF EV + + DG
Sbjct: 40 MDSNDLERERGITILAKNTAITYKD-------TKINIIDTPGHADFGGEVERVLSMVDGV 92
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
+++VD EG QT+ LK+A ++PI+V+NKIDR
Sbjct: 93 LLLVDASEGPMPQTRFVLKKALEAGLKPIVVINKIDR 129
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 103 bits (259), Expect = 2e-26
Identities = 46/101 (45%), Positives = 66/101 (65%), Gaps = 2/101 (1%)
Query: 4 MVSSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVR 63
M + +DS E+ERGIT+K+ ++ L YK E Y++NLID+PGHVDFS EVS ++
Sbjct: 41 MRAQVLDSMDIERERGITIKAQAVRLNYKAKDG--ETYVLNLIDTPGHVDFSYEVSRSLA 98
Query: 64 LCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKID 104
C+G ++VVD +G+ AQT + A ++ I VLNKID
Sbjct: 99 ACEGALLVVDASQGVEAQTLANVYLALENNLEIIPVLNKID 139
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 102 bits (255), Expect = 7e-26
Identities = 45/101 (44%), Positives = 65/101 (64%), Gaps = 2/101 (1%)
Query: 4 MVSSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVR 63
M +DS E+ERGIT+K+ ++ L YK E Y++NLID+PGHVDFS EVS ++
Sbjct: 35 MREQVLDSMDLERERGITIKAQAVRLNYKAKDG--ETYVLNLIDTPGHVDFSYEVSRSLA 92
Query: 64 LCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKID 104
C+G +++VD +GI AQT + A ++ I V+NKID
Sbjct: 93 ACEGALLLVDAAQGIEAQTLANVYLALENDLEIIPVINKID 133
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 100 bits (251), Expect = 3e-25
Identities = 49/104 (47%), Positives = 68/104 (65%), Gaps = 8/104 (7%)
Query: 4 MVSSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVR 63
M + +DS E+ERGIT+K+ ++ L YK E Y++NLID+PGHVDFS EVS ++
Sbjct: 39 MKAQVLDSMDLERERGITIKAQAVRLNYKAKDG--ETYILNLIDTPGHVDFSYEVSRSLA 96
Query: 64 LCDGTIIVVDCVEGICAQTQVALKQAWLE---KIQPILVLNKID 104
C+G ++VVD +G+ AQT + A LE +I P VLNKID
Sbjct: 97 ACEGALLVVDASQGVEAQTLANVYLA-LENDLEIIP--VLNKID 137
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 95.4 bits (238), Expect = 2e-23
Identities = 38/97 (39%), Positives = 60/97 (61%), Gaps = 7/97 (7%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
D EQERGIT++S++ S + + + INLID+PGH+DF+ EV ++R+ DG
Sbjct: 48 TDWMPQEQERGITIESAATSCDWDN-------HRINLIDTPGHIDFTGEVERSLRVLDGA 100
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
++V D V G+ QT+ +QA I ++ +NK+DR
Sbjct: 101 VVVFDAVTGVQPQTETVWRQADRYGIPRLIFINKMDR 137
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 95.4 bits (238), Expect = 2e-23
Identities = 40/97 (41%), Positives = 60/97 (61%), Gaps = 7/97 (7%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MDS E+ERGIT+ + + ++ Y K IN++D+PGH DF EV + + DG
Sbjct: 39 MDSNDLERERGITILAKNTAIRYNGTK-------INIVDTPGHADFGGEVERVLGMVDGV 91
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
+++VD EG QT+ LK+A ++PI+V+NKIDR
Sbjct: 92 LLLVDASEGPMPQTRFVLKKALELGLKPIVVINKIDR 128
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with it.
The ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation of
EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains both
eukaryotic and bacterial members.
Length = 270
Score = 92.6 bits (231), Expect = 2e-23
Identities = 39/98 (39%), Positives = 62/98 (63%), Gaps = 7/98 (7%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MD + E+ERGIT++S++ + ++KD + IN+ID+PGHVDF+ EV ++R+ DG
Sbjct: 39 MDWMEQERERGITIQSAATTCFWKD-------HRINIIDTPGHVDFTIEVERSLRVLDGA 91
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRL 106
+ V D V G+ QT+ +QA + I +NK+DR
Sbjct: 92 VAVFDAVAGVQPQTETVWRQADRYGVPRIAFVNKMDRT 129
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 92.7 bits (231), Expect = 1e-22
Identities = 39/97 (40%), Positives = 59/97 (60%), Gaps = 7/97 (7%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MDS E+ERGIT+ + + ++ Y IN++D+PGH DF EV + + DG
Sbjct: 43 MDSNDLEKERGITILAKNTAVNYNG-------TRINIVDTPGHADFGGEVERVLSMVDGV 95
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
+++VD EG QT+ LK+A ++PI+V+NKIDR
Sbjct: 96 LLLVDASEGPMPQTRFVLKKALALGLKPIVVINKIDR 132
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 87.9 bits (219), Expect = 6e-21
Identities = 40/100 (40%), Positives = 64/100 (64%), Gaps = 7/100 (7%)
Query: 6 SSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLC 65
++ MD +E+ERGI++ S++ + +K +K INLID+PGHVDF+ EV A+R+
Sbjct: 32 TTTMDFMPEERERGISITSAATTCEWKGHK-------INLIDTPGHVDFTGEVERALRVL 84
Query: 66 DGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
DG ++VV V G+ QT+ +QA + I+ +NK+DR
Sbjct: 85 DGAVVVVCAVGGVEPQTETVWRQAEKYGVPRIIFVNKMDR 124
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 85.0 bits (211), Expect = 7e-21
Identities = 39/104 (37%), Positives = 65/104 (62%), Gaps = 13/104 (12%)
Query: 6 SSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLC 65
++ DS + E++RGIT+ S+ S ++D K +N+ID+PGH+DF +EV ++ +
Sbjct: 36 TTRTDSMELERQRGITIFSAVASFQWEDTK-------VNIIDTPGHMDFIAEVERSLSVL 88
Query: 66 DGTIIVVDCVEGICAQTQV---ALKQAWLEKIQPILVLNKIDRL 106
DG I+V+ VEG+ AQT++ L++ I I+ +NKIDR
Sbjct: 89 DGAILVISAVEGVQAQTRILFRLLRKL---NIPTIIFVNKIDRA 129
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 84.9 bits (210), Expect = 7e-20
Identities = 36/99 (36%), Positives = 64/99 (64%), Gaps = 7/99 (7%)
Query: 7 SYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCD 66
+ MD + E+ERGIT+ S++ ++++K + IN+ID+PGHVDF+ EV ++R+ D
Sbjct: 48 ATMDWMEQEKERGITITSAATTVFWKG-------HRINIIDTPGHVDFTVEVERSLRVLD 100
Query: 67 GTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
G + V+D V G+ Q++ +QA ++ I +NK+D+
Sbjct: 101 GAVAVLDAVGGVQPQSETVWRQANRYEVPRIAFVNKMDK 139
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 78.7 bits (195), Expect = 1e-17
Identities = 38/97 (39%), Positives = 62/97 (63%), Gaps = 7/97 (7%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MD + EQERGIT+ S++ + ++K ++ IN+ID+PGHVDF+ EV ++R+ DG
Sbjct: 48 MDWMEQEQERGITITSAATTCFWKGHR-------INIIDTPGHVDFTIEVERSLRVLDGA 100
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
+ V D V G+ Q++ +QA + I+ +NK+DR
Sbjct: 101 VAVFDAVSGVEPQSETVWRQADKYGVPRIVFVNKMDR 137
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 77.8 bits (191), Expect = 2e-17
Identities = 37/97 (38%), Positives = 60/97 (61%), Gaps = 7/97 (7%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MDS E+ERGIT+ + + ++ + D Y IN++D+PGH DF EV + + D
Sbjct: 43 MDSNDLEKERGITILAKNTAIKWND-------YRINIVDTPGHADFGGEVERVMSMVDSV 95
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
++VVD +G QT+ K+A+ ++PI+V+NK+DR
Sbjct: 96 LLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVINKVDR 132
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 74.2 bits (183), Expect = 1e-16
Identities = 30/100 (30%), Positives = 55/100 (55%), Gaps = 7/100 (7%)
Query: 6 SSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLC 65
++ D +E++R +++++S L + +K INLID+PG+ DF E +A+R
Sbjct: 36 NTVSDYDPEEKKRKMSIETSVAPLEWNGHK-------INLIDTPGYADFVGETLSALRAV 88
Query: 66 DGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
D +IVV+ G+ T+ + K+ I+ +NK+DR
Sbjct: 89 DAALIVVEAQSGVEVGTEKVWEFLDDAKLPRIIFINKMDR 128
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 74.4 bits (184), Expect = 3e-16
Identities = 40/98 (40%), Positives = 63/98 (64%), Gaps = 7/98 (7%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MD + EQERGIT+ S++ + ++KD++ IN+ID+PGHVDF+ EV ++R+ DG
Sbjct: 50 MDWMEQEQERGITITSAATTCFWKDHR-------INIIDTPGHVDFTIEVERSLRVLDGA 102
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRL 106
+ V D V G+ Q++ +QA K+ I +NK+DR
Sbjct: 103 VAVFDAVGGVEPQSETVWRQADKYKVPRIAFVNKMDRT 140
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. Peptide
chain release factor 3 (RF3) is a protein involved in
the termination step of translation in bacteria.
Termination occurs when class I release factors (RF1 or
RF2) recognize the stop codon at the A-site of the
ribosome and activate the release of the nascent
polypeptide. The class II release factor RF3 then
initiates the release of the class I RF from the
ribosome. RF3 binds to the RF/ribosome complex in the
inactive (GDP-bound) state. GDP/GTP exchange occurs,
followed by the release of the class I RF. Subsequent
hydrolysis of GTP to GDP triggers the release of RF3
from the ribosome. RF3 also enhances the efficiency of
class I RFs at less preferred stop codons and at stop
codons in weak contexts.
Length = 268
Score = 67.6 bits (166), Expect = 3e-14
Identities = 36/106 (33%), Positives = 57/106 (53%), Gaps = 17/106 (16%)
Query: 15 EQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSE---VSTAVRLCDGTIIV 71
E++RGI++ SS + YK +INL+D+PGH DFS + TAV D ++V
Sbjct: 52 EKQRGISVTSSVMQFEYKG-------CVINLLDTPGHEDFSEDTYRTLTAV---DSAVMV 101
Query: 72 VDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDI 117
+D +G+ QT+ + L I I +NK+DR + PL++
Sbjct: 102 IDAAKGVEPQTRKLFEVCRLRGIPIITFINKLDREGRD----PLEL 143
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 63.8 bits (156), Expect = 1e-12
Identities = 40/117 (34%), Positives = 61/117 (52%), Gaps = 22/117 (18%)
Query: 5 VSSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSE---VSTA 61
S +M+ E++RGI++ SS + Y D L+NL+D+PGH DFS + TA
Sbjct: 55 KSDWMEI---EKQRGISVTSSVMQFDYAD-------CLVNLLDTPGHEDFSEDTYRTLTA 104
Query: 62 VRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPIL-VLNKIDRLILEMKLSPLDI 117
V D ++V+D +GI QT + L I PI +NK+DR + PL++
Sbjct: 105 V---DSAVMVIDAAKGIEPQTLKLFEVCRLRDI-PIFTFINKLDREGRD----PLEL 153
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 61.7 bits (151), Expect = 8e-12
Identities = 42/123 (34%), Positives = 66/123 (53%), Gaps = 26/123 (21%)
Query: 15 EQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSE---VSTAVRLCDGTIIV 71
E++RGI++ SS + Y+D LINL+D+PGH DFS + TAV D ++V
Sbjct: 60 EKQRGISVTSSVMQFPYRD-------CLINLLDTPGHEDFSEDTYRTLTAV---DSALMV 109
Query: 72 VDCVEGICAQTQVALKQAWLEKIQPILV-LNKIDRLILEMKLSPLDIYVHLSQLLEQVNA 130
+D +G+ QT+ ++ L PI +NK+DR E PL+ LL+++
Sbjct: 110 IDAAKGVEPQTRKLMEVCRLRDT-PIFTFINKLDRDGRE----PLE-------LLDEIEE 157
Query: 131 VMG 133
V+G
Sbjct: 158 VLG 160
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 57.0 bits (138), Expect = 3e-10
Identities = 33/99 (33%), Positives = 48/99 (48%), Gaps = 12/99 (12%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTI 69
D +E++RGIT + YY+ +D ++ ID PGH DF S + + D +
Sbjct: 26 DRLPEEKKRGIT---IDLGFYYRKLED----GVMGFIDVPGHPDFISNLLAGLGGIDYAL 78
Query: 70 IVVDCVEGICAQTQ---VALKQAWLEKIQPILVLNKIDR 105
+VV EG+ AQT + L L I+VL K DR
Sbjct: 79 LVVAADEGLMAQTGEHLLILDL--LGIKNGIIVLTKADR 115
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 56.1 bits (135), Expect = 6e-10
Identities = 31/111 (27%), Positives = 58/111 (52%), Gaps = 11/111 (9%)
Query: 15 EQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVDC 74
E++RGI++ +S + Y+D L+NL+D+PGH DFS + + D ++V+D
Sbjct: 61 EKQRGISITTSVMQFPYRDC-------LVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDA 113
Query: 75 VEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQLL 125
+G+ +T+ ++ L +NK+DR I + PL++ + L
Sbjct: 114 AKGVETRTRKLMEVTRLRDTPIFTFMNKLDRDIRD----PLELLDEVENEL 160
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 51.8 bits (125), Expect = 7e-09
Identities = 36/146 (24%), Positives = 60/146 (41%), Gaps = 20/146 (13%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTI 69
D +E++RGIT I L + D P+ + ID PGH F + D +
Sbjct: 25 DRLPEEKKRGIT-----IDLGFA-YLDLPDGKRLGFIDVPGHEKFVKNMLAGAGGIDAVL 78
Query: 70 IVVDCVEGICAQTQVALKQAWLEKI-QPILVLNKIDRLILEMKLSPLDIYVHLSQLLEQV 128
+VV EGI QT+ L+ L I + ++VL K D + + L + E++
Sbjct: 79 LVVAADEGIMPQTREHLEILELLGIKKGLVVLTKADLVDEDR----------LELVEEEI 128
Query: 129 NAVMGELFASQVMDETAVKTTAQDNE 154
++ F + D ++ E
Sbjct: 129 LELLAGTF---LADAPIFPVSSVTGE 151
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 51.4 bits (123), Expect = 3e-08
Identities = 29/97 (29%), Positives = 41/97 (42%), Gaps = 8/97 (8%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTI 69
D +E++RG+T+ +Y + ID PGH F S D +
Sbjct: 26 DRLPEEKKRGMTIDLGFAYF-------PLPDYRLGFIDVPGHEKFISNAIAGGGGIDAAL 78
Query: 70 IVVDCVEGICAQTQVALKQAWLEKIQP-ILVLNKIDR 105
+VVD EG+ QT L L I I+V+ K DR
Sbjct: 79 LVVDADEGVMTQTGEHLAVLDLLGIPHTIVVITKADR 115
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 49.8 bits (120), Expect = 3e-08
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 9/91 (9%)
Query: 18 RGIT--MKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVDCV 75
GIT + + + + K I ID+PGH F++ + + D I+VV
Sbjct: 31 GGITQHIGAYQVPIDVKIPG-------ITFIDTPGHEAFTNMRARGASVTDIAILVVAAD 83
Query: 76 EGICAQTQVALKQAWLEKIQPILVLNKIDRL 106
+G+ QT A+ A + I+ +NKID+
Sbjct: 84 DGVMPQTIEAINHAKAANVPIIVAINKIDKP 114
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 50.7 bits (122), Expect = 4e-08
Identities = 33/102 (32%), Positives = 52/102 (50%), Gaps = 16/102 (15%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MD K+E+ERG+T I L +K K ++Y ++D PGH DF + T D
Sbjct: 59 MDRLKEERERGVT-----IDLAHK--KFETDKYYFTIVDCPGHRDFVKNMITGASQADAA 111
Query: 69 IIVV--DCVEGICAQTQVALKQAWLEKI----QPILVLNKID 104
++VV D G+ QT+ + +L + Q I+ +NK+D
Sbjct: 112 VLVVAADDAGGVMPQTR---EHVFLARTLGINQLIVAINKMD 150
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 50.0 bits (120), Expect = 8e-08
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 6 SSYMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLC 65
+ +D K+E+ERG+T+ + +T + Y +ID+PGH DF + T
Sbjct: 57 AWVLDKTKEERERGVTIDVAHSKF------ETDK-YNFTIIDAPGHRDFVKNMITGASQA 109
Query: 66 DGTIIVVDCVEG 77
D ++VVD +G
Sbjct: 110 DVAVLVVDARDG 121
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 48.5 bits (116), Expect = 1e-07
Identities = 32/102 (31%), Positives = 43/102 (42%), Gaps = 7/102 (6%)
Query: 10 DSRKDEQERGITM-------KSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAV 62
D QERGIT+ + + E Y I L+D PGH +
Sbjct: 30 DKNPQSQERGITLDLGFSSFEVDKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGA 89
Query: 63 RLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKID 104
++ D ++VVD +GI QT L L I+VLNKID
Sbjct: 90 QIIDLMLLVVDAKKGIQTQTAECLVIGELLCKPLIVVLNKID 131
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 48.3 bits (115), Expect = 3e-07
Identities = 29/102 (28%), Positives = 50/102 (49%), Gaps = 11/102 (10%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
MD K+E+ERG+T I + + K ++Y + ++D PGH DF + T D
Sbjct: 60 MDRLKEERERGVT-----IDVAHW--KFETDKYEVTIVDCPGHRDFIKNMITGASQADAA 112
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKI----QPILVLNKIDRL 106
++VV +G + A+L + Q I+ +NK+D +
Sbjct: 113 VLVVAVGDGEFEVQPQTREHAFLARTLGINQLIVAINKMDSV 154
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 46.4 bits (111), Expect = 8e-07
Identities = 27/97 (27%), Positives = 50/97 (51%), Gaps = 8/97 (8%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
+D + E+E+GIT+ + Y+ K +++I D+PGH ++ + T D
Sbjct: 53 VDGLQAEREQGITIDVAYR--YFSTPK---RKFII--ADTPGHEQYTRNMVTGASTADLA 105
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKI-QPILVLNKID 104
I++VD +G+ QT+ A L I ++ +NK+D
Sbjct: 106 ILLVDARKGVLEQTRRHSYIASLLGIRHVVVAVNKMD 142
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 44.8 bits (106), Expect = 5e-06
Identities = 29/92 (31%), Positives = 42/92 (45%), Gaps = 13/92 (14%)
Query: 19 GITMKSSSISLY-----YKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVD 73
GIT K I Y YKD I +D+PGH FSS S + D I+++
Sbjct: 276 GITQK---IGAYEVEFEYKDENQK-----IVFLDTPGHEAFSSMRSRGANVTDIAILIIA 327
Query: 74 CVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
+G+ QT A+ + I+ +NKID+
Sbjct: 328 ADDGVKPQTIEAINYIQAANVPIIVAINKIDK 359
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 44.0 bits (105), Expect = 7e-06
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 8 YMDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDG 67
+D K+E+ERG+T+ + L + E+Y +ID+PGH DF + T D
Sbjct: 51 VLDKLKEERERGVTI---DVGLAKFET----EKYRFTIIDAPGHRDFVKNMITGASQADV 103
Query: 68 TIIVVDCVEG 77
++VV +G
Sbjct: 104 AVLVVSARKG 113
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 44.0 bits (104), Expect = 9e-06
Identities = 24/61 (39%), Positives = 33/61 (54%)
Query: 46 IDSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
ID+PGH F++ L D I++VD EG QTQ AL + K ++ NKIDR
Sbjct: 74 IDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYKTPFVVAANKIDR 133
Query: 106 L 106
+
Sbjct: 134 I 134
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 44.1 bits (105), Expect = 1e-05
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 46 IDSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILV-LNKID 104
ID+PGH F++ + + D I+VV +G+ QT A+ A + PI+V +NKID
Sbjct: 60 IDTPGHEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGV-PIVVAINKID 118
Query: 105 R 105
+
Sbjct: 119 K 119
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 43.2 bits (102), Expect = 2e-05
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 9/70 (12%)
Query: 9 MDSRKDEQERGITMKSSSISLY-YKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDG 67
+D K E+ERGIT+ I+L+ ++ K Y +ID+PGH DF + T D
Sbjct: 60 LDKLKAERERGITI---DIALWKFETPK-----YYFTIIDAPGHRDFIKNMITGTSQADV 111
Query: 68 TIIVVDCVEG 77
I+VV G
Sbjct: 112 AILVVASTAG 121
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 43.2 bits (102), Expect = 2e-05
Identities = 28/99 (28%), Positives = 49/99 (49%), Gaps = 12/99 (12%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
+D+ +E+ RGIT+ ++ + Y +N+ +D PGH D+ + T DG
Sbjct: 50 IDNAPEEKARGITINTAHVE-YETENRHYAH------VDCPGHADYVKNMITGAAQMDGA 102
Query: 69 IIVVDCVEGICAQTQVAL---KQAWLEKIQPILVLNKID 104
I+VV +G QT+ + +Q + I ++ LNK D
Sbjct: 103 ILVVSATDGPMPQTREHILLARQVGVPYI--VVFLNKCD 139
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 41.9 bits (99), Expect = 4e-05
Identities = 29/122 (23%), Positives = 51/122 (41%), Gaps = 28/122 (22%)
Query: 8 YMDSRKDEQERGITMK--SSSISLYYKDNKDTPEEYL------------------INLID 47
+ K+E +R IT+K ++ +Y N P Y ++ +D
Sbjct: 24 WTVRHKEELKRNITIKLGYANAKIYKCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVD 83
Query: 48 SPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQ-----VALKQAWLEKIQPILVLNK 102
PGH + + + + DG ++++ E C Q Q AL+ L+ I I++ NK
Sbjct: 84 CPGHEILMATMLSGAAVMDGALLLIAANEP-CPQPQTSEHLAALEIMGLKHI--IILQNK 140
Query: 103 ID 104
ID
Sbjct: 141 ID 142
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 42.4 bits (100), Expect = 4e-05
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 19 GITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGI 78
GIT + + +D K +I +D+PGH F+S + ++ D ++VV +G+
Sbjct: 119 GITQHIGAYHVENEDGK------MITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGV 172
Query: 79 CAQTQVALKQAWLEKIQPILVLNKIDR 105
QT A+ A + I+ +NKID+
Sbjct: 173 MPQTIEAISHAKAANVPIIVAINKIDK 199
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 42.3 bits (100), Expect = 4e-05
Identities = 30/119 (25%), Positives = 54/119 (45%), Gaps = 27/119 (22%)
Query: 10 DSRKDEQERGITMK--SSSISLYYKDNKDTPEEYL-----------------INLIDSPG 50
D+ +E +RGI+++ + +Y D PE Y ++ +D+PG
Sbjct: 30 DTHSEELKRGISIRLGYADAEIYKCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPG 89
Query: 51 HVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQ-----VALKQAWLEKIQPILVLNKID 104
H + + + L DG ++V+ E C Q Q +AL+ ++ I ++V NKID
Sbjct: 90 HETLMATMLSGAALMDGALLVIAANEP-CPQPQTREHLMALEIIGIKNI--VIVQNKID 145
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 41.2 bits (97), Expect = 5e-05
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 8/81 (9%)
Query: 38 PEEYLINLIDSPGHVDFSS-------EVSTAVRLCDGTIIVVDCVEGICAQTQVALKQAW 90
+ Y NL+D+ G D+ + V +++R+ D I+V+D E + QT+ + A
Sbjct: 48 GKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHA- 106
Query: 91 LEKIQPILVLNKIDRLILEMK 111
+ ILV NKID ++K
Sbjct: 107 ESGVPIILVGNKIDLRDAKLK 127
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 41.9 bits (99), Expect = 5e-05
Identities = 30/105 (28%), Positives = 48/105 (45%), Gaps = 22/105 (20%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINL-----IDSPGHVDFSSEVSTAVRL 64
DS +E+ RGIT+ ++ + EY +D PGH D+ + T
Sbjct: 51 DSAPEEKARGITINTAHV------------EYETENRHYAHVDCPGHADYVKNMITGAAQ 98
Query: 65 CDGTIIVVDCVEGICAQTQVAL---KQAWLEKIQPILVLNKIDRL 106
DG I+VV +G QT+ + KQ + I ++ LNK D++
Sbjct: 99 MDGAILVVSAADGPMPQTKEHILLAKQVGVPNI--VVFLNKEDQV 141
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 41.6 bits (98), Expect = 6e-05
Identities = 28/97 (28%), Positives = 50/97 (51%), Gaps = 8/97 (8%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
+D + E+E+GIT I + Y+ T + I + D+PGH ++ ++T D
Sbjct: 55 VDGLQAEREQGIT-----IDVAYR-YFSTDKRKFI-VADTPGHEQYTRNMATGASTADLA 107
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKI-QPILVLNKID 104
+++VD +G+ QT+ A L I +L +NK+D
Sbjct: 108 VLLVDARKGVLEQTRRHSYIASLLGIRHVVLAVNKMD 144
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 40.4 bits (95), Expect = 1e-04
Identities = 27/98 (27%), Positives = 49/98 (50%), Gaps = 12/98 (12%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTI 69
D+ +E+ RGIT+ ++ + +T + + +D PGH D+ + T DG I
Sbjct: 51 DNAPEEKARGITINTAHVEY------ETANRHYAH-VDCPGHADYVKNMITGAAQMDGAI 103
Query: 70 IVVDCVEGICAQTQVAL---KQAWLEKIQPILVLNKID 104
+VV +G QT+ + +Q + I ++ LNK+D
Sbjct: 104 LVVAATDGPMPQTREHILLARQVGVPYI--VVFLNKVD 139
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 40.5 bits (94), Expect = 1e-04
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
+D K E+ERGIT+ I+L+ K +Y +ID+PGH DF + T D
Sbjct: 60 LDKLKAERERGITI---DIALW----KFETTKYYCTVIDAPGHRDFIKNMITGTSQADCA 112
Query: 69 IIVVDCVEG 77
++++D G
Sbjct: 113 VLIIDSTTG 121
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 39.4 bits (92), Expect = 2e-04
Identities = 24/97 (24%), Positives = 36/97 (37%), Gaps = 12/97 (12%)
Query: 17 ERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFS-----SEVSTAVRLCDGTIIV 71
G T K + L+D+PG +F +R D ++V
Sbjct: 28 VPGTTRDPDVYVKELDKGK-----VKLVLVDTPGLDEFGGLGREELARLLLRGADLILLV 82
Query: 72 VDCVEGICAQTQ--VALKQAWLEKIQPILVLNKIDRL 106
VD + + + L++ E I ILV NKID L
Sbjct: 83 VDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLL 119
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 39.9 bits (94), Expect = 2e-04
Identities = 28/98 (28%), Positives = 50/98 (51%), Gaps = 12/98 (12%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTI 69
D+ +E+ERGIT+ ++ + Y + + +D PGH D+ + T DG I
Sbjct: 51 DAAPEEKERGITINTAHVE-YETEKRHYAH------VDCPGHADYVKNMITGAAQMDGAI 103
Query: 70 IVVDCVEGICAQTQ--VAL-KQAWLEKIQPILVLNKID 104
+VV +G QT+ + L +Q + + ++ LNK+D
Sbjct: 104 LVVAATDGPMPQTREHILLARQVGVPYL--VVFLNKVD 139
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 40.0 bits (94), Expect = 2e-04
Identities = 28/91 (30%), Positives = 49/91 (53%), Gaps = 8/91 (8%)
Query: 15 EQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVDC 74
E+E+GIT I + Y+ T + I + D+PGH ++ ++T D I++VD
Sbjct: 67 EREQGIT-----IDVAYR-YFSTEKRKFI-IADTPGHEQYTRNMATGASTADLAILLVDA 119
Query: 75 VEGICAQTQVALKQAWLEKIQPILV-LNKID 104
+G+ QT+ A L I+ ++V +NK+D
Sbjct: 120 RKGVLEQTRRHSFIASLLGIRHVVVAVNKMD 150
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 39.8 bits (94), Expect = 3e-04
Identities = 23/61 (37%), Positives = 31/61 (50%)
Query: 46 IDSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
ID+PGH F++ L D I+VVD EG QT A+ K ++ NKIDR
Sbjct: 76 IDTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAINILKRRKTPFVVAANKIDR 135
Query: 106 L 106
+
Sbjct: 136 I 136
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 39.6 bits (92), Expect = 4e-04
Identities = 36/133 (27%), Positives = 62/133 (46%), Gaps = 25/133 (18%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
+D+ +E+ RGIT+ ++++ Y +N+ +D PGH D+ + T DG
Sbjct: 119 IDAAPEERARGITINTATVE-YETENRHYAH------VDCPGHADYVKNMITGAAQMDGA 171
Query: 69 IIVVDCVEGICAQTQ---VALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQLL 125
I+VV +G QT+ + KQ + + ++ LNK D+ V +LL
Sbjct: 172 ILVVSGADGPMPQTKEHILLAKQVGVPNM--VVFLNKQDQ-------------VDDEELL 216
Query: 126 EQVNAVMGELFAS 138
E V + EL +S
Sbjct: 217 ELVELEVRELLSS 229
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 39.1 bits (92), Expect = 5e-04
Identities = 32/124 (25%), Positives = 52/124 (41%), Gaps = 37/124 (29%)
Query: 10 DSRKDEQERGITMK--SSSISLYYKDNKDTPEEYL-----------------INLIDSPG 50
D +E +RGIT++ + ++ + + PE Y ++ +D+PG
Sbjct: 35 DRHSEELKRGITIRLGYADATIRKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPG 94
Query: 51 HVDFSSEVSTAVRLC-----DGTIIVVDCVEGICAQTQ-----VALKQAWLEKIQPILVL 100
H E A L DG I+V+ E C Q Q +AL ++ I ++V
Sbjct: 95 H-----ETLMATMLSGAALMDGAILVIAANEP-CPQPQTKEHLMALDIIGIKNI--VIVQ 146
Query: 101 NKID 104
NKID
Sbjct: 147 NKID 150
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 38.7 bits (90), Expect = 5e-04
Identities = 30/117 (25%), Positives = 55/117 (47%), Gaps = 19/117 (16%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
+D +E+ RGIT+ ++ + Y + +D PGH D+ + T DG
Sbjct: 99 IDKAPEEKARGITIATAHVE-YETAKRHYAH------VDCPGHADYVKNMITGAAQMDGG 151
Query: 69 IIVVDCVEGICAQTQ---VALKQAWLEKIQPILVLNKIDRL-------ILEMKLSPL 115
I+VV +G QT+ + +Q + + ++ LNK+D + ++EM+L L
Sbjct: 152 ILVVSAPDGPMPQTKEHILLARQVGVPSL--VVFLNKVDVVDDEELLELVEMELREL 206
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 37.9 bits (89), Expect = 7e-04
Identities = 29/103 (28%), Positives = 45/103 (43%), Gaps = 22/103 (21%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINL-----IDSPGHVDFSSEVSTAVRL 64
D +E+ RGIT+ ++ + EY +D PGH D+ + T
Sbjct: 41 DKAPEEKARGITINTAHV------------EYETANRHYAHVDCPGHADYIKNMITGAAQ 88
Query: 65 CDGTIIVVDCVEGICAQTQVAL---KQAWLEKIQPILVLNKID 104
DG I+VV +G QT+ L +Q + I ++ LNK D
Sbjct: 89 MDGAILVVSATDGPMPQTREHLLLARQVGVPYI--VVFLNKAD 129
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 36.6 bits (85), Expect = 0.003
Identities = 34/120 (28%), Positives = 54/120 (45%), Gaps = 29/120 (24%)
Query: 10 DSRKDEQERGITMK--SSSISLYYKDNKDTPEEYL-----------------INLIDSPG 50
D +E +RGIT+K + +Y PE Y ++ +D+PG
Sbjct: 36 DRHSEELKRGITIKLGYADAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPG 95
Query: 51 H-VDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQ-----VALKQAWLEKIQPILVLNKID 104
H ++ +S A L DG ++V+ E C Q Q +AL+ ++ I I+V NKID
Sbjct: 96 HETLMATMLSGAA-LMDGALLVIAANEP-CPQPQTREHLMALEIIGIKNI--IIVQNKID 151
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 36.0 bits (83), Expect = 0.005
Identities = 22/61 (36%), Positives = 30/61 (49%)
Query: 46 IDSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDR 105
ID+PGH F+S L D ++VVD EG QT A+ K ++ NKID
Sbjct: 531 IDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVVAANKIDL 590
Query: 106 L 106
+
Sbjct: 591 I 591
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 34.8 bits (81), Expect = 0.014
Identities = 32/105 (30%), Positives = 46/105 (43%), Gaps = 26/105 (24%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTI 69
D+ +E+ RGIT+ +S + Y N+ Y +D PGH D+ + T DG I
Sbjct: 51 DNAPEEKARGITINTSHVE-YETANR----HY--AHVDCPGHADYVKNMITGAAQMDGAI 103
Query: 70 IVVDCVEGICAQT--------QVALKQAWLEKIQPILV--LNKID 104
+VV +G QT QV + P +V LNK D
Sbjct: 104 LVVSAADGPMPQTREHILLARQVGV---------PYIVVFLNKCD 139
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 33.4 bits (77), Expect = 0.017
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 39 EEYLINLIDSPG---------HVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQA 89
I L+D+PG V+ + A+R D ++VVD EG+ + L++
Sbjct: 44 LGRQIILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEEL 103
Query: 90 -WLEKIQPILVLNK 102
L K ILVLNK
Sbjct: 104 EKLPKKPIILVLNK 117
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 33.6 bits (78), Expect = 0.032
Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 12/98 (12%)
Query: 10 DSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTI 69
D +E+ RGIT+ ++ + Y + + Y +D PGH D+ + T DG I
Sbjct: 51 DKAPEEKARGITINTAHVE-YETEKR----HY--AHVDCPGHADYVKNMITGAAQMDGAI 103
Query: 70 IVVDCVEGICAQTQ--VAL-KQAWLEKIQPILVLNKID 104
+VV +G QT+ + L +Q + I ++ LNK D
Sbjct: 104 LVVSAADGPMPQTREHILLARQVGVPYI--VVFLNKCD 139
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 31.9 bits (73), Expect = 0.12
Identities = 33/95 (34%), Positives = 48/95 (50%), Gaps = 11/95 (11%)
Query: 14 DEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVD 73
+E++RG+T I L Y P+ ++ ID PGH F S + V D ++VV
Sbjct: 30 EEKKRGMT-----IDLGYA-YWPQPDGRVLGFIDVPGHEKFLSNMLAGVGGIDHALLVVA 83
Query: 74 CVEGICAQTQVALKQAWLEKI-QPIL--VLNKIDR 105
C +G+ AQT+ L A L+ P+L L K DR
Sbjct: 84 CDDGVMAQTREHL--AILQLTGNPMLTVALTKADR 116
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 31.2 bits (72), Expect = 0.16
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 88 QAWLEKIQPILVLNKID 104
A I+P++VLNK D
Sbjct: 28 AAEASGIEPVIVLNKAD 44
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 30.9 bits (70), Expect = 0.19
Identities = 23/94 (24%), Positives = 35/94 (37%), Gaps = 4/94 (4%)
Query: 39 EEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPIL 98
E+ ++L +PG F R G I++VD I + + P++
Sbjct: 66 EDTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVV 125
Query: 99 V-LNKIDRLILEMKLSPLDIYVHLSQLLEQVNAV 131
V +NK D L L P I L L V +
Sbjct: 126 VAINKQD---LFDALPPEKIREALKLELLSVPVI 156
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 31.4 bits (72), Expect = 0.21
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 12/68 (17%)
Query: 43 INLIDSPGHVDFSSEVSTAVR-----LCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPI 97
I +D+PGH F TA+R + D ++VV +G+ QT A+ A + PI
Sbjct: 298 ITFLDTPGHEAF-----TAMRARGAQVTDIVVLVVAADDGVMPQTIEAINHAKAAGV-PI 351
Query: 98 LV-LNKID 104
+V +NKID
Sbjct: 352 IVAINKID 359
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 31.1 bits (71), Expect = 0.28
Identities = 30/97 (30%), Positives = 51/97 (52%), Gaps = 8/97 (8%)
Query: 9 MDSRKDEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGT 68
+D E+E+GIT I + Y+ TP+ I + D+PGH ++ + T D
Sbjct: 79 VDGLAAEREQGIT-----IDVAYR-YFATPKRKFI-VADTPGHEQYTRNMVTGASTADLA 131
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILV-LNKID 104
II+VD +G+ QT+ A L I+ +++ +NK+D
Sbjct: 132 IILVDARKGVLTQTRRHSFIASLLGIRHVVLAVNKMD 168
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 30.5 bits (69), Expect = 0.39
Identities = 14/54 (25%), Positives = 24/54 (44%)
Query: 51 HVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKID 104
+S+ AV L D + VVD G+ + + ++ +L +NKID
Sbjct: 341 DSAIASQAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLAVNKID 394
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 30.1 bits (69), Expect = 0.47
Identities = 25/97 (25%), Positives = 37/97 (38%), Gaps = 18/97 (18%)
Query: 19 GITMKSSSISLYYKDNKDTPEEYLINLIDSPG---------HVDFSSEVST--AVRLCDG 67
G T S I ++Y LID+ G V+ S + T A+ D
Sbjct: 205 GTTRDSIDIPFERNG-----KKYT--LIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADV 257
Query: 68 TIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKID 104
++V+D EGI Q A ++V+NK D
Sbjct: 258 VLLVLDATEGITEQDLRIAGLALEAGKALVIVVNKWD 294
Score = 27.8 bits (63), Expect = 2.5
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 14/71 (19%)
Query: 45 LIDSPGHVD----FSSEVS----TAVRLCDGTIIVVDCVEGICAQ-TQVALKQAWLEKIQ 95
LID+ G + ++ A+ D + VVD EG+ + ++A WL K
Sbjct: 51 LIDTGGIEEDDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIA---KWLRKSG 107
Query: 96 P--ILVLNKID 104
ILV NKID
Sbjct: 108 KPVILVANKID 118
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 29.6 bits (67), Expect = 0.71
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 85 ALKQAWLEKIQPILVLNKIDRLILE 109
L A I+P++VLNKID L E
Sbjct: 102 YLVLAEAGGIEPVIVLNKIDLLDDE 126
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 29.4 bits (67), Expect = 0.82
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 85 ALKQAWLEKIQPILVLNKIDRLI-LEMKLSPLDIYVHL 121
L A I+PI+VLNKID L LE L +Y +
Sbjct: 103 FLVLAEANGIKPIIVLNKIDLLDDLEEARELLALYRAI 140
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 29.1 bits (66), Expect = 0.90
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 94 IQPILVLNKIDRL 106
I+P++VLNKID L
Sbjct: 151 IEPLIVLNKIDLL 163
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 29.1 bits (66), Expect = 0.97
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 37 TPEEYLINLIDSPG-HVD-------FSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQ 88
T + I +D+PG H + +A++ D + VVD EG + L+Q
Sbjct: 50 TTDNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQ 109
Query: 89 AWLEKIQPILVLNKIDR 105
K ILV+NKID+
Sbjct: 110 LKKTKTPVILVVNKIDK 126
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 28.7 bits (65), Expect = 1.3
Identities = 23/73 (31%), Positives = 30/73 (41%), Gaps = 13/73 (17%)
Query: 43 INLIDSPGHVDFSSE---------VSTAVRLCDGTIIVVDCVEGICAQTQVALKQAWL-E 92
LID+ G D + A+ D + VVD EGI + K L
Sbjct: 53 FILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAK--ILRR 110
Query: 93 KIQP-ILVLNKID 104
+P ILV+NKID
Sbjct: 111 SKKPVILVVNKID 123
Score = 27.5 bits (62), Expect = 3.0
Identities = 26/122 (21%), Positives = 43/122 (35%), Gaps = 19/122 (15%)
Query: 19 GITMKSSSISLYYKDNKDTPEEYLINLIDSPG----------HVDFSSEVST-AVRLCDG 67
G T S I K LID+ G +S + A+ D
Sbjct: 211 GTTRDSIDIEFERDGRK-------YVLIDTAGIRRKGKITESVEKYSVARTLKAIERADV 263
Query: 68 TIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLSQLLEQ 127
++V+D EGI Q ++V+NK D L+ E + + + L + L
Sbjct: 264 VLLVIDATEGISEQDLRIAGLIEEAGRGIVIVVNKWD-LVEEDEATMEEFKKKLRRKLPF 322
Query: 128 VN 129
++
Sbjct: 323 LD 324
>gnl|CDD|218496 pfam05204, Hom_end, Homing endonuclease. Homing endonucleases
are encoded by mobile DNA elements that are found
inserted within host genes in all domains of life.
Length = 110
Score = 27.7 bits (62), Expect = 1.7
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 39 EEYLINLIDSPGHVDFSSEVSTAVRLCDGTII 70
E +L LIDS G+VD + ++ +V+ D +++
Sbjct: 15 EAFLAGLIDSDGYVDKAKNITASVKTEDKSVM 46
>gnl|CDD|206639 cd00066, G-alpha, Alpha subunit of G proteins (guanine nucleotide
binding). The alpha subunit of G proteins contains the
guanine nucleotide binding site. The heterotrimeric
GNP-binding proteins are signal transducers that
communicate signals from many hormones,
neurotransmitters, chemokines, and autocrine and
paracrine factors. Extracellular signals are received by
receptors, which activate the G proteins, which in turn
route the signals to several distinct intracellular
signaling pathways. The alpha subunit of G proteins is a
weak GTPase. In the resting state, heterotrimeric G
proteins are associated at the cytosolic face of the
plasma membrane and the alpha subunit binds to GDP. Upon
activation by a receptor GDP is replaced with GTP, and
the G-alpha/GTP complex dissociates from the beta and
gamma subunits. This results in activation of downstream
signaling pathways, such as cAMP synthesis by adenylyl
cyclase, which is terminated when GTP is hydrolized and
the heterotrimers reconstitute.
Length = 315
Score = 28.3 bits (64), Expect = 2.1
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 90 WLEKIQPILVLNKIDRLILEMKL--SPLDIY 118
W IL LNK D + E K+ SPL Y
Sbjct: 225 WFANTSIILFLNKKD--LFEEKIKKSPLTDY 253
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 27.8 bits (63), Expect = 2.2
Identities = 29/120 (24%), Positives = 45/120 (37%), Gaps = 21/120 (17%)
Query: 19 GITMKSSSISLYYKDNKDTPEEYLINLIDSPG---------HVDFSSEVST--AVRLCDG 67
G T S + Y K Y LID+ G ++ S + T A+ D
Sbjct: 35 GTTRDSIDVPFEYDGQK-----YT--LIDTAGIRKKGKVTEGIEKYSVLRTLKAIERADV 87
Query: 68 TIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNK---IDRLILEMKLSPLDIYVHLSQL 124
++V+D EGI Q E I+V+NK +++ MK ++ L L
Sbjct: 88 VLLVLDASEGITEQDLRIAGLILEEGKALIIVVNKWDLVEKDEKTMKEFEKELRRKLPFL 147
>gnl|CDD|237615 PRK14121, PRK14121, tRNA (guanine-N(7)-)-methyltransferase;
Provisional.
Length = 390
Score = 28.0 bits (63), Expect = 2.4
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 83 QVALKQAWLEKIQPILVLNKIDRLILEMKLSPL--DIYVH 120
QV LKQ L ++ +L++N RL+LE+ S I+VH
Sbjct: 161 QV-LKQIELLNLKNLLIINYDARLLLELLPSNSVEKIFVH 199
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 27.5 bits (62), Expect = 2.5
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 69 IIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKIDRLILEMKLSPLDIYVHLS 122
++VVD EG+ + L+ K I+VLNK D L +S L+ ++
Sbjct: 87 LLVVDASEGLDEEDLEILEL--PAKKPVIVVLNKSDLLSDAEGISELNGKPIIA 138
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 27.8 bits (62), Expect = 2.6
Identities = 16/26 (61%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 94 IQPILVLNKIDRLILE-MKLSPLDIY 118
I+PI+VLNKID L E M+ LDIY
Sbjct: 68 IEPIIVLNKIDLLDDEDMEKEQLDIY 93
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 27.0 bits (60), Expect = 2.7
Identities = 24/106 (22%), Positives = 37/106 (34%), Gaps = 26/106 (24%)
Query: 23 KSSSIS-LYYKDNKDTPEEY-----------------LINLIDSPGHVDFSSEVSTAVRL 64
KSS +S L + P E L+N+ D G + E ++
Sbjct: 12 KSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREELKFEHIIFMKW 71
Query: 65 CDGTIIVVDCVEGICAQTQVALKQAWLEKIQP-------ILVLNKI 103
D ++V D + L AWL ++ ILV NK+
Sbjct: 72 ADAILLVYDLTDRESLNEVSRLI-AWLPNLRKLGGKIPVILVGNKL 116
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 27.7 bits (63), Expect = 2.8
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 14/81 (17%)
Query: 37 TPEEYLINLIDSPG-H----------VDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVA 85
T ++ I +D+PG H ++++ D + VVD E I +
Sbjct: 49 TEDDAQIIFVDTPGIHKPKRALNRAMNKA---AWSSLKDVDLVLFVVDADEKIGPGDEFI 105
Query: 86 LKQAWLEKIQPILVLNKIDRL 106
L++ K ILVLNKID +
Sbjct: 106 LEKLKKVKTPVILVLNKIDLV 126
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 27.4 bits (61), Expect = 2.8
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 30 YYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQA 89
Y K EE +N++D+ G D+++ R +G ++V + ++
Sbjct: 37 YRKKVVLDGEEVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQ 96
Query: 90 WL-----EKIQPILVLNKID 104
L + + +LV NK D
Sbjct: 97 ILRVKEDDNVPLLLVGNKCD 116
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 27.2 bits (61), Expect = 3.0
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 12/73 (16%)
Query: 43 INLIDSPGHVD-------FSSEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQ 95
+ LID+PG + E D ++VVD + K L +
Sbjct: 48 VVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEA---KLGLLRERG 104
Query: 96 -P-ILVLNKIDRL 106
P +LVLNKID +
Sbjct: 105 KPVLLVLNKIDLV 117
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 27.1 bits (61), Expect = 3.0
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 10/66 (15%)
Query: 67 GTIIVVDCVEGICAQTQVALKQAWLE--KIQPILVLNKIDRLILEMKLSPLDIYVHLSQL 124
G ++++D G L+ +LE I ++VL K D KL ++ L ++
Sbjct: 84 GVVLLIDARHGPTPIDLEMLE--FLEELGIPFLIVLTKAD------KLKKSELAKVLKKI 135
Query: 125 LEQVNA 130
E++N
Sbjct: 136 KEELNL 141
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 27.0 bits (61), Expect = 3.1
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 14/73 (19%)
Query: 43 INLIDSPGHVDFSSEVST--------AVRLCDGTIIVVDCVEGICAQ-TQVALKQAWLEK 93
LID+ G +S A+ D + VVD EG+ ++A +L K
Sbjct: 47 FILIDTGGIEPDDEGISKEIREQAEIAIEEADVILFVVDGREGLTPADEEIA---KYLRK 103
Query: 94 IQP--ILVLNKID 104
+ ILV+NKID
Sbjct: 104 SKKPVILVVNKID 116
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 27.6 bits (62), Expect = 3.3
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 90 WLEKIQPILVLNKIDRLILEMKLSPLDIYV 119
W + IL LNK D ++K PL Y
Sbjct: 232 WFKNTPIILFLNKKDLFEEKLKKGPLSDYF 261
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 27.6 bits (62), Expect = 3.6
Identities = 13/46 (28%), Positives = 18/46 (39%)
Query: 59 STAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILVLNKID 104
A+R D + VVD G A + + IL NK+D
Sbjct: 112 EVAMRTADAVLFVVDATVGATATDEAVARVLRRSGKPVILAANKVD 157
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2
of PHIP1. A. thaliana PHIP1 and its homologs represent
a novel class of plant-specific RNA-binding proteins
that may play a unique role in the polarized mRNA
transport to the vicinity of the cell plate. The family
members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 25.8 bits (57), Expect = 3.9
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 50 GHVDFSSEVSTAVRL-CDGTII 70
GHVDF+ E S L DGT++
Sbjct: 43 GHVDFADEESLDAALKLDGTVL 64
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 27.2 bits (61), Expect = 4.5
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 47 DSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQT 82
D+PGH ++ ++T CD I+++D +G+ QT
Sbjct: 113 DTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQT 148
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 26.7 bits (60), Expect = 4.6
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 17/75 (22%)
Query: 43 INLIDSPGHVDFSSEVSTAV-----RLCDGTIIVVDCVEGICAQTQVA------LKQAWL 91
+ L+D+PG ++ + E T + D I V+ T+ + +
Sbjct: 48 VVLVDTPG-LNSTIEHHTEITESFLPRADAVIFVLSA---DQPLTESEREFLKEILKWSG 103
Query: 92 EKIQPILVLNKIDRL 106
+KI VLNKID L
Sbjct: 104 KKI--FFVLNKIDLL 116
>gnl|CDD|204544 pfam10712, NAD-GH, NAD-specific glutamate dehydrogenase. The
members of this are annotated as being NAD-specific
glutamate dehydrogenase encoded in antisense gene pair
with DnaK-J. However, this could not be confirmed.
Length = 574
Score = 27.3 bits (61), Expect = 4.7
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 125 LEQVNAVMGELFASQVMDETAVKT-TAQ 151
L QV+AV+ QV+D+ V+ TA+
Sbjct: 326 LAQVDAVLLLELVGQVVDDAHVEVFTAE 353
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 26.8 bits (60), Expect = 4.7
Identities = 25/134 (18%), Positives = 50/134 (37%), Gaps = 17/134 (12%)
Query: 3 CMVSSYMDSRKDEQERGITMKSSSISLYYKDNKDTPE--EYLINLIDSPGHVDFSSEVST 60
+V Y++++ +E+ S+ + + + D+ G + +
Sbjct: 15 SLVLRYVENKFNEKHE------STTQASFFQKTVNIGGKRIDLAIWDTAGQERYHALGPI 68
Query: 61 AVRLCDGTIIVVDCVEG---ICAQTQV-ALKQAWLEKIQPILVLNKIDRLILEMKLSPLD 116
R DG I+V D + + + LKQ I ++V NKID L + +S +
Sbjct: 69 YYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKID-LERQRVVSKSE 127
Query: 117 IYVHLSQLLEQVNA 130
+ + V A
Sbjct: 128 A----EEYAKSVGA 137
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 26.3 bits (59), Expect = 6.2
Identities = 28/106 (26%), Positives = 44/106 (41%), Gaps = 14/106 (13%)
Query: 37 TPEEYLINLIDSPG-HVDFS-------SEVSTAVRLCDGTIIVVDCVEGICAQTQVALKQ 88
T ++ I +D+PG H +A++ D + VVD E I + L+
Sbjct: 47 TDDDAQIIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILEL 106
Query: 89 AWLEKIQP--ILVLNKIDRLILEMKLSPLDIYVHLSQLLEQVNAVM 132
L+K + ILVLNKID + + L L + L +L
Sbjct: 107 --LKKSKTPVILVLNKIDLVKDKEDL--LPLLEKLKELHPFAEIFP 148
>gnl|CDD|214854 smart00849, Lactamase_B, Metallo-beta-lactamase superfamily.
Apart from the beta-lactamases a number of other
proteins contain this domain. These proteins include
thiolesterases, members of the glyoxalase II family,
that catalyse the hydrolysis of S-D-lactoyl-glutathione
to form glutathione and D-lactic acid and a competence
protein that is essential for natural transformation in
Neisseria gonorrhoeae and could be a transporter
involved in DNA uptake. Except for the competence
protein these proteins bind two zinc ions per molecule
as cofactor.
Length = 177
Score = 26.4 bits (58), Expect = 6.4
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 59 STAVRLCDGTIIVVDCVEGICAQTQVALKQAWLEKIQPILV 99
S VR DG I++D G LK+ +KI I++
Sbjct: 2 SYLVR-DDGGAILIDTGPGEAEDLLAELKKLGPKKIDAIIL 41
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 26.2 bits (58), Expect = 7.7
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 14 DEQERGITMKSSSISLYYKDNKDTPEEYLINLIDSPGHVDFSSEVSTAVRLCD---GTII 70
++ +T + S + Y +K LID PGHV ++ ++ G +
Sbjct: 26 GTVKKTVTSQEPSAAYKYMLHKGFSFT----LIDFPGHVKLRQKLLETIKDSSSLRGIVF 81
Query: 71 VVD 73
VVD
Sbjct: 82 VVD 84
>gnl|CDD|173832 cd00684, Terpene_cyclase_plant_C1, Plant Terpene Cyclases, Class 1.
This CD includes a diverse group of monomeric plant
terpene cyclases (Tspa-Tspf) that convert the acyclic
isoprenoid diphosphates, geranyl diphosphate (GPP),
farnesyl diphosphate (FPP), or geranylgeranyl
diphosphate (GGPP) into cyclic monoterpenes, diterpenes,
or sesquiterpenes, respectively; a few form acyclic
species. Terpnoid cyclases are soluble enzymes localized
to the cytosol (sesquiterpene synthases) or plastids
(mono- and diterpene synthases). All monoterpene and
diterpene synthases have restrict substrate specificity,
however, some sesquiterpene synthases can accept both
FPP and GPP. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions located on
opposite walls. These residues mediate binding of prenyl
diphosphates, via bridging Mg2+ ions (K+ preferred by
gymnosperm cyclases), inducing conformational changes
such that an N-terminal region forms a cap over the
catalytic core. Loss of diphosphate from the
enzyme-bound substrate (GPP, FPP, or GGPP) results in an
allylic carbocation that electrophilically attacks a
double bond further down the terpene chain to effect the
first ring closure. Unlike monoterpene, sesquiterene,
and macrocyclic diterpenes synthases, which undergo
substrate ionization by diphosphate ester scission,
Tpsc-like diterpene synthases catalyze cyclization
reactions by an initial protonation step producing a
copalyl diphosphate intermediate. These enzymes lack the
aspartate-rich sequences mentioned above. Most diterpene
synthases have an N-terminal, internal element (approx
210 aa) whose function is unknown.
Length = 542
Score = 26.4 bits (59), Expect = 9.3
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 2 LCMVSSYMD---SRKDEQERGITMKSSSISLYYKDNKDTPEE---YLINLIDS 48
+ M+ + +DE +RG +SSI Y K+ + EE + +I+
Sbjct: 433 SSTIGRLMNDIATYEDEMKRGDV--ASSIECYMKEYGVSEEEAREEIKKMIED 483
>gnl|CDD|234215 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
Members of this family are the RepA (or ParA) protein
involved in replicon partitioning. All known examples
occur in bacterial species with two or more replicons,
on a plasmid or the smaller chromosome. Note that an
apparent exception may be seen as a pseudomolecule from
assembly of an incompletely sequenced genome. Members of
this family belong to a larger family that also includes
the enzyme cobyrinic acid a,c-diamide synthase, but
assignment of that name to members of this family would
be in error [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 387
Score = 26.1 bits (58), Expect = 9.5
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 127 QVNAVMGELFASQVMDETAVKTTAQDNE--TKQT 158
Q+ A + LF V+ +K+TA + TKQT
Sbjct: 316 QMVAFLRSLFGDHVLTNPMLKSTAISDAGLTKQT 349
>gnl|CDD|149404 pfam08332, CaMKII_AD, Calcium/calmodulin dependent protein kinase
II Association. This domain is found at the C-terminus
of the Calcium/calmodulin dependent protein kinases II
(CaMKII). These proteins also have a Ser/Thr protein
kinase domain (pfam00069) at their N-terminus. The
function of the CaMKII association domain is the
assembly of the single proteins into large (8 to 14
subunits) multimers.
Length = 128
Score = 25.5 bits (56), Expect = 9.9
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 123 QLLEQVNAVMGELFASQVMDETAVKTTAQDNETKQTSRF 161
LL A + + +Q MD+ T Q ET+ +
Sbjct: 75 HLLGDDAACIAYVRLTQYMDKNGKAHTVQSEETRVWHKR 113
>gnl|CDD|132063 TIGR03018, pepcterm_TyrKin, exopolysaccharide/PEP-CTERM locus
tyrosine autokinase. Members of this protein family are
related to a known protein-tyrosine autokinase and to
numerous homologs from exopolysaccharide biosynthesis
region proteins, many of which are designated as chain
length determinants. Most members of this family contain
a short region, immediately C-terminal to the region
modeled here, with an abundance of Tyr residues. These
C-terminal tyrosine residues are likely to be
autophosphorylation sites. Some members of this family
are fusion proteins.
Length = 207
Score = 25.7 bits (57), Expect = 9.9
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 35 KDTPEEYLINLIDSPGHVDFSSEVSTAVRLCDGTIIVVDCVEGICAQTQV 84
+ P+ +I ID+P + FS E RL ++VV+ EG Q V
Sbjct: 145 RRYPDRIII--IDTPPLLVFS-EARALARLVGQIVLVVE--EGRTTQEAV 189
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
0.317 0.131 0.363
Gapped
Lambda K H
0.267 0.0616 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,626,558
Number of extensions: 678203
Number of successful extensions: 747
Number of sequences better than 10.0: 1
Number of HSP's gapped: 673
Number of HSP's successfully gapped: 121
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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: 55 (25.2 bits)