RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9643
(412 letters)
>gnl|CDD|236183 PRK08202, PRK08202, purine nucleoside phosphorylase; Provisional.
Length = 272
Score = 359 bits (923), Expect = e-124
Identities = 134/274 (48%), Positives = 176/274 (64%), Gaps = 8/274 (2%)
Query: 128 YELIQSIAKFLLDSISI-RPKIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHK 186
E I+ A F+ + +P+IG+I GSGL +AD I + + PY IP FPVSTV GH
Sbjct: 3 LEKIEEAAAFIREKTGAFKPEIGLILGSGLGALADEIENAVVIPYADIPGFPVSTVEGHA 62
Query: 187 GQLVFGLINGIPIMCMQGRFHYYEGYPLWKCAMPIRVMKLVGVTHLLATNAAGGLNPDYE 246
G+LV G + G P++ MQGRFHYYEGY + P+RVMK +GV L+ TNAAGGLNPD+
Sbjct: 63 GELVLGRLGGKPVLAMQGRFHYYEGYSMEAVTFPVRVMKALGVETLIVTNAAGGLNPDFG 122
Query: 247 VGDIMIIKDHINLMGFAGNNPLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSS 306
GD+M+I DHINL G NPL+G N+D FGPRFP M+ AY+ +LRA +A++L +
Sbjct: 123 PGDLMLISDHINLT---GRNPLIGPNDDEFGPRFPDMSDAYDPELRALAKKVAKELGIP- 178
Query: 307 IVKEGVYSVIGGPNFETVAELNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKC 366
++EGVY + GP++ET AE+ MLR G DAVGMSTV EVI A HCG+ V S ITN
Sbjct: 179 -LQEGVYVGVSGPSYETPAEIRMLRTLGADAVGMSTVPEVIVARHCGLKVLGISCITNLA 237
Query: 367 VTDYDDHAEANHEEVIQAGKLRGPMIKSMVTRIV 400
D +HEEV++ + P +V I+
Sbjct: 238 AGISD--EPLSHEEVLEVAERAAPKFGRLVKAIL 269
>gnl|CDD|233537 TIGR01700, PNPH, purine nucleoside phosphorylase I, inosine and
guanosine-specific. This model represents a family of
bacterial and metazoan purine phosphorylases acting
primarily on inosine and guanosine and not acting on
adenosine. PNP-I refers to the nomenclature from
Bacillus stearothermophilus where PHP-II refers to the
nucleotidase acting on adenosine as the primary
substrate.The bacterial enzymes (PUNA) are typified by
the Bacilus PupG protein which is involved in the
metabolism of nucleosides as a carbon source.Several
metazoan enzymes (PNPH) are well characterized including
the human and bovine enzymes which have been
crystallized [Purines, pyrimidines, nucleosides, and
nucleotides, Salvage of nucleosides and nucleotides].
Length = 249
Score = 332 bits (852), Expect = e-113
Identities = 133/255 (52%), Positives = 176/255 (69%), Gaps = 6/255 (2%)
Query: 147 KIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCMQGRF 206
I II GSGL +A+ + D I Y IP+FP STV GH G LVFG++ G P++ MQGRF
Sbjct: 1 DIAIILGSGLGPLAEKVEDATIIDYSEIPHFPQSTVVGHAGNLVFGILGGKPVVAMQGRF 60
Query: 207 HYYEGYPLWKCAMPIRVMKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHINLMGFAGNN 266
H YEGY + K P+RVMKL+GV L+ TNAAGG+NP+++VGD+M+I+DHINL GF N
Sbjct: 61 HMYEGYDMAKVTFPVRVMKLLGVETLVVTNAAGGINPEFKVGDLMLIRDHINLPGF---N 117
Query: 267 PLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEGVYSVIGGPNFETVAE 326
PL G NE+RFG RFP M+ AY++ LR IA+ LN+ ++EGVY ++GGP++ET AE
Sbjct: 118 PLRGPNEERFGVRFPDMSDAYDRDLRQKAHSIAKQLNIP--LQEGVYVMLGGPSYETPAE 175
Query: 327 LNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDYDDHAEANHEEVIQAGK 386
+ +LR G DAVGMSTV EVI A HCG+ V FSLITNK D + HEEV++A K
Sbjct: 176 VRLLRTLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKAAGILDYEL-SVHEEVMEAAK 234
Query: 387 LRGPMIKSMVTRIVS 401
++ V+ +++
Sbjct: 235 QAAEKLEKFVSLLIA 249
>gnl|CDD|130758 TIGR01697, PNPH-PUNA-XAPA, inosine/guanosine/xanthosine
phosphorylase family. This model is a subset of the
subfamily represented by pfam00896 (phosphorylase family
2). This model excludes the methylthioadenosine
phosphorylases (MTAP, TIGR01684) which are believed
toplay a specific role in the recycling of methionine
from methylthioadenosine. In this subfamily is found
three clades of purine phosphorylases based on a
neighbor-joining tree using the MTAP family as an
outgroup. The highest-branching clade (TIGR01698)
consists of a group of sequences from both gram positive
and gram negative bacteria which have been annotated as
purine nucleotide phosphorylases but have not been
further characterized as to substrate specificity. Of
the two remaining clades, one is xanthosine
phosphorylase (XAPA, TIGR01699), is limited to certain
gamma proteobacteria and constitutes a special purine
phosphorylase found in a specialized operon for
xanthosine catabolism. The enzyme also acts on the same
purines (inosine and guanosine) as the other
characterized members of this subfamily, but is only
induced when xanthosine must be degraded. The remaining
and largest clade consists of purine nucleotide
phosphorylases (PNPH, TIGR01700) from metazoa and
bacteria which act primarily on guanosine and inosine
(and do not act on adenosine). Sequences from
Clostridium (GP:15025051) and Thermotoga (OMNI:TM1596)
fall between these last two clades and are
uncharacterized with respect to substrate range and
operon.
Length = 248
Score = 330 bits (848), Expect = e-113
Identities = 136/254 (53%), Positives = 173/254 (68%), Gaps = 7/254 (2%)
Query: 147 KIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCMQGRF 206
+ II GSGL +AD + D I PY+ IP FPVSTV GH G+LVFG + G P++CMQGRF
Sbjct: 1 DVAIILGSGLGALADQVEDAVIIPYEKIPGFPVSTVVGHAGELVFGRLGGKPVVCMQGRF 60
Query: 207 HYYEGYPLWKCAMPIRVMKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHINLMGFAGNN 266
HYYEGY + P+RVMKL+GV L+ TNAAGGLNPD++ GD+MIIKDHINL G N
Sbjct: 61 HYYEGYDMATVTFPVRVMKLLGVEILVVTNAAGGLNPDFKPGDLMIIKDHINLPGL---N 117
Query: 267 PLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEGVYSVIGGPNFETVAE 326
PL+G N+DRFG RFP ++ AY+++LR D+A++L + EGVY ++ GP++ET AE
Sbjct: 118 PLVGPNDDRFGTRFPDLSNAYDRELRKLAQDVAKELGFP--LTEGVYVMVSGPSYETPAE 175
Query: 327 LNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDYDDHAEANHEEVIQAGK 386
+ MLRI G DAVGMSTV EVI A HCG+ V A SLITN D +HEEV+ A
Sbjct: 176 IRMLRILGADAVGMSTVPEVIVARHCGIKVLAVSLITNMAAGITD--VPLSHEEVLAAAA 233
Query: 387 LRGPMIKSMVTRIV 400
S++ I+
Sbjct: 234 AAAERFISLLEDII 247
>gnl|CDD|223084 COG0005, Pnp, Purine nucleoside phosphorylase [Nucleotide transport
and metabolism].
Length = 262
Score = 236 bits (603), Expect = 8e-76
Identities = 100/270 (37%), Positives = 142/270 (52%), Gaps = 14/270 (5%)
Query: 135 AKFLLDSISIRPKIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLI 194
A F+ + P IGII GSGL +AD + R PY I F V +VPGH G+LV +
Sbjct: 6 ADFIKERTDEMPMIGIIGGSGLYDLADLLEVR--EPYSDITPFGVPSVPGHAGELV--TL 61
Query: 195 NG-IPIMCMQGRFHYYEGYPLWKCAMPIRVMKLVGVTHLLATNAAGGLNPDYEVGDIMII 253
G + + GR H Y + + A IR +K +GV ++ TNA G L +Y+ GD+++
Sbjct: 62 GGKVAFLARHGRGHSYPPHSVNYRA-NIRALKALGVERVILTNAVGSLREEYKPGDLVVP 120
Query: 254 KDHINLMGFAGNNPLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEGVY 313
DHI+ NP G N+ G RF M+ Y+ +LR A + A++L + ++EGVY
Sbjct: 121 DDHIDFTK--RQNPFYGGND---GVRFVDMSDPYDPELREALAEAAKELRLGHPLQEGVY 175
Query: 314 SVIGGPNFETVAELNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDYDDH 373
+ GP FET AE+ M R G D VGMSTV EVI A G+ V A SL+TN
Sbjct: 176 VCVEGPRFETPAEIRMFRSLGADVVGMSTVPEVILARELGLCVAALSLVTNYAA---GIG 232
Query: 374 AEANHEEVIQAGKLRGPMIKSMVTRIVSYI 403
HEEV++ K I ++ ++ +
Sbjct: 233 QPLTHEEVLEVAKENAEKIAKLLAAAIAKL 262
>gnl|CDD|130760 TIGR01699, XAPA, xanthosine phosphorylase. This model represents a
small clade of purine nucleotide phosphorylases found in
certain gamma proteobacteria. The gene is part of an
operon for the degradation of xanthosine and is induced
by xanthosine. The enzyme is also capable of acting on
inosine and guanosine (but not adenosine) in a manner
similar to those other phosphorylases to which it is
closely related (TIGR01698, TIGR01700).
Length = 248
Score = 199 bits (507), Expect = 9e-62
Identities = 98/218 (44%), Positives = 134/218 (61%), Gaps = 5/218 (2%)
Query: 147 KIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCMQGRF 206
++ I GSGL +AD I + Y+ +P FPVSTV GH G+LV G + G+P++CM+GR
Sbjct: 1 RVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRG 60
Query: 207 HYYEGYPLWKCAMPIRVMKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHINLMGFAGNN 266
H+YEG + IR KL+G L TNAAG L P+ G ++ +KDHIN M
Sbjct: 61 HFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTM---PGT 117
Query: 267 PLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEGVYSVIGGPNFETVAE 326
P++G+N+DRFG RF + AY+ + RA +A++ + EGV+ GPNFET AE
Sbjct: 118 PMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFP--LTEGVFVSYPGPNFETAAE 175
Query: 327 LNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITN 364
+ M++I G D VGMS V EVI+A HC + V A S ITN
Sbjct: 176 IRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITN 213
>gnl|CDD|130759 TIGR01698, PUNP, purine nucleotide phosphorylase. This clade of
purine nucleotide phosphorylases has not been
experimentally characterized but is assigned based on
strong sequence homology. Closely related clades act on
inosine and guanosine (PNPH, TIGR01700), and xanthosine,
inosine and guanosine (XAPA, TIGR01699) neither of these
will act on adenosine. A more distantly related clade
(MTAP, TIGR01694) acts on methylthioadenosine.
Length = 237
Score = 196 bits (501), Expect = 6e-61
Identities = 92/256 (35%), Positives = 129/256 (50%), Gaps = 22/256 (8%)
Query: 148 IGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCMQGRFH 207
+ I+ GSG +++ + PY IP FP TV GH G+L+ I P++ + GR H
Sbjct: 2 MAIVLGSGWGGAVEALGEPVELPYAEIPGFPAPTVSGHAGELIRVRIGDGPVLVLGGRTH 61
Query: 208 YYEGYPLWKCAMPIRVMKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHINLMGFAGNNP 267
YEG P+R + G L+ TNAAGGL D+ G ++I DHINL +P
Sbjct: 62 AYEGGDARAVVHPVRTARATGAETLILTNAAGGLRQDWGPGTPVLISDHINL---TARSP 118
Query: 268 LLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEGVYSVIGGPNFETVAEL 327
L+ GPRF + AY+ +LR A ++ + EGVY+ GP++ET AE+
Sbjct: 119 LI-------GPRFVDLTDAYSPRLREL----AERVDPP--LAEGVYAWFPGPHYETPAEI 165
Query: 328 NMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKC--VTDYDDHAEANHEEVIQAG 385
M I G D VGMSTV E I A CG+ V SL+TN +T H EV AG
Sbjct: 166 RMAGILGADLVGMSTVPETIAARFCGLEVLGVSLVTNLAAGITGTPLS----HAEVKAAG 221
Query: 386 KLRGPMIKSMVTRIVS 401
G + +++ I+
Sbjct: 222 AAAGTRLAALLADIIK 237
>gnl|CDD|216264 pfam01048, PNP_UDP_1, Phosphorylase superfamily. Members of this
family include: purine nucleoside phosphorylase (PNP)
Uridine phosphorylase (UdRPase) 5'-methylthioadenosine
phosphorylase (MTA phosphorylase).
Length = 232
Score = 154 bits (391), Expect = 1e-44
Identities = 87/258 (33%), Positives = 125/258 (48%), Gaps = 29/258 (11%)
Query: 147 KIGIICGSG--LSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCMQG 204
KIGII GSG ++ +A+ + + PY P S G+ G + G P++ +
Sbjct: 1 KIGIIGGSGEEVALLAELLEE--------TPYGPPS----RGGKFYTGTLKGKPVVLARH 48
Query: 205 RFHYYEGYPLWKCAMPIRVMKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHINLMGFAG 264
G P IR++K +GV ++ T AGGLNPD + GD++I D IN F G
Sbjct: 49 G----IGPPNAAIRAEIRLLKELGVKTIIRTGTAGGLNPDLKPGDLVIPTDAIN---FDG 101
Query: 265 NNPLLGVNEDRFGPRFPPMNKA-YNKQLRAATLDIARDLNMSSIVKEGVYSVIGGPNFET 323
+PL G N+ GPRFP M A Y+ +LRA + A L + V GVY+ G FET
Sbjct: 102 TSPLTGPND---GPRFPDMAPAPYDPELRALLEEAAARLGIP--VHRGVYATTDGFYFET 156
Query: 324 VAELNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDYDDHAEANHEEVIQ 383
AE+ +LR G DAV M T E I A G+ A +I++ D E HEEV +
Sbjct: 157 PAEIRLLRRLGADAVEMETAAEAIVARELGIPFLAIRVISDYAAGGADG--EVTHEEVEE 214
Query: 384 AGKLRGPMIKSMVTRIVS 401
+ ++ ++
Sbjct: 215 VLEEAAERAAKLLLALLE 232
>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 = 79.9 bits (198), Expect = 2e-17
Identities = 26/47 (55%), Positives = 35/47 (74%)
Query: 9 ADAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALEGKEPEIGI 55
D E+ ELVEME+RELL++ G+ GD+ P V+GSAL ALEG +P +
Sbjct: 132 DDEELLELVEMEVRELLSKYGFDGDDTPIVRGSALKALEGDDPNKWV 178
Score = 67.2 bits (165), Expect = 4e-13
Identities = 26/40 (65%), Positives = 30/40 (75%), Gaps = 1/40 (2%)
Query: 93 PHCNIGTIGHVDHGKTTLTAAITKGLME-GMLGSYTYELI 131
PH N+GTIGHVDHGKTTLTAAITK L + G + Y+ I
Sbjct: 1 PHVNVGTIGHVDHGKTTLTAAITKVLAKKGGAKAKKYDEI 40
>gnl|CDD|233535 TIGR01694, MTAP, 5'-deoxy-5'-methylthioadenosine phosphorylase.
This model represents the methylthioadenosine
phosphorylase found in metazoa, cyanobacteria and a
limited number of archaea such as Sulfolobus, Aeropyrum,
Pyrobaculum, Pyrococcus, and Thermoplasma. This enzyme
is responsible for the first step in the methionine
salvage pathway after the transfer of the amino acid
moiety from S-adenosylmethionine. The enzyme from human
is well-characterized including a crystal structure. A
misleading characterization is found for a Sulfolobus
solfataricus enzyme which is called a MTAP. In fact, as
uncovered by the genome sequence of S. solfataricus,
there are at least two nucleotide phosphorylases and the
one found in the MTAP clade is not the one annotated as
such. The sequence in this clade has not been isolated
but is likely to be the authentic SsMTAP as it displays
all of the conserved active site residues found in the
human enzyme. This explains the finding that the
characterized enzyme has greater efficiency towards the
purines inosine, guanosine and adenosine over MTA. In
fact, this mis-naming of this enzyme has been carried
forward to several publications including a crystal
stucture. In between the trusted and noise cutoffs are:
1) several archaeal sequences which appear to contain
several residues characteristic of phosphorylases which
act on guanosine or inosine (according to the crystal
structure of MTAP and alignments). In any case, these
residues are not conserved. 2) sequences from
Mycobacterium tuberculosis and Streptomyces coelicolor
which have better, although not perfect retention of the
active site residues, but considering the general
observation that bacteria utilize the MTA/SAH
nucleotidase enzyme and a kinase to do this reaction,
these have been excluded pending stronger evidence of
their function, and 3) a sequence from Drosophila which
appears to be a recent divergence (long branch in
neighbor-joining trees) and lacks some of the conserved
active site residues [Central intermediary metabolism,
Other, Purines, pyrimidines, nucleosides, and
nucleotides, Salvage of nucleosides and nucleotides].
Length = 241
Score = 80.1 bits (198), Expect = 3e-17
Identities = 68/256 (26%), Positives = 100/256 (39%), Gaps = 51/256 (19%)
Query: 147 KIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCMQ--G 204
IG+I GSGL + D DT PY S +V G + G+ + + G
Sbjct: 1 MIGVIGGSGLYDLEGL-KDVEEVNVDT-PYGNPS------APIVVGRVAGVDVAFLPRHG 52
Query: 205 RFHYYEGYPLWKCAMPIRV--------MKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDH 256
R H P V +K +GV ++++ NA G L +Y GD+++
Sbjct: 53 RGHDI---------PPHEVNYRANIWALKSLGVKYVISVNAVGSLREEYPPGDLVVPDQF 103
Query: 257 INLMGFAGNNPLLGVNEDR-----FGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEG 311
I+ P + + FG Y + LR ++ R L ++ G
Sbjct: 104 ID---RTSGRPSTFFDGGKVVHVDFGD-------PYCEDLRQRLIESLRRLG-LTVHDGG 152
Query: 312 VYSVIGGPNFETVAELNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDYD 371
Y GP F T AE M + G D VGM+ V E + A + +L VTDYD
Sbjct: 153 TYVCTEGPRFSTRAESRMFKSWGADIVGMTGVPEAVLARELELCYATLAL-----VTDYD 207
Query: 372 DHAEANH---EEVIQA 384
A+H EEV +
Sbjct: 208 CWISADHVTAEEVEEV 223
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 80.2 bits (199), Expect = 1e-16
Identities = 28/48 (58%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 85 KQVYSRDKPHCNIGTIGHVDHGKTTLTAAITKGLMEGMLGSYT-YELI 131
K+ + R KPH N+GTIGHVDHGKTTLTAAITK L + Y+ I
Sbjct: 3 KEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQI 50
Score = 72.9 bits (180), Expect = 4e-14
Identities = 24/45 (53%), Positives = 33/45 (73%)
Query: 10 DAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALEGKEPEIG 54
D E+ ELVEME+RELL++ + GD+ P ++GSAL ALEG + E
Sbjct: 143 DEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEW 187
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 80.3 bits (199), Expect = 2e-16
Identities = 29/48 (60%), Positives = 34/48 (70%), Gaps = 1/48 (2%)
Query: 85 KQVYSRDKPHCNIGTIGHVDHGKTTLTAAITKGLMEGMLGSYT-YELI 131
K+ + R KPH N+GTIGHVDHGKTTLTAAITK L + G Y+ I
Sbjct: 3 KEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQI 50
Score = 72.2 bits (178), Expect = 8e-14
Identities = 24/45 (53%), Positives = 33/45 (73%)
Query: 10 DAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALEGKEPEIG 54
D E+ ELVEME+RELL++ + GD+ P ++GSAL ALEG + E
Sbjct: 143 DEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEW 187
>gnl|CDD|169548 PRK08666, PRK08666, 5'-methylthioadenosine phosphorylase;
Validated.
Length = 261
Score = 78.2 bits (193), Expect = 2e-16
Identities = 55/186 (29%), Positives = 82/186 (44%), Gaps = 12/186 (6%)
Query: 221 IRVMKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHINLMGFAGNNPLLGVNEDRFGPRF 280
I +K +GV +LAT+A G LNP+ + GD +I+ + F N + G
Sbjct: 68 IWALKELGVERILATSAVGSLNPNMKPGDFVILDQ---FLDFTKNRHYTFYDGGESGVVH 124
Query: 281 PPMNKAYNKQLRAATLDIARDLNMSSIVKEGVYSVIGGPNFETVAELNMLRICGVDAVGM 340
Y +LR A + AR+L ++ G Y GP FET AE+ M RI G D VGM
Sbjct: 125 VDFTDPYCPELRKALITAARELGLTYHPG-GTYVCTEGPRFETAAEIRMFRILGGDLVGM 183
Query: 341 STVHEVITAHHCGMTVTAFSLITNKCVTDYDDHAEAN---HEEVIQAGKLRGPMIKSMVT 397
+ V E + A M +++TN Y H EV++ IK ++
Sbjct: 184 TQVPEAVLARELEMCYATVAIVTN-----YAAGISPTKLTHSEVVELMAQNSENIKKLIM 238
Query: 398 RIVSYI 403
+ + I
Sbjct: 239 KAIELI 244
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 80.0 bits (198), Expect = 2e-16
Identities = 29/45 (64%), Positives = 31/45 (68%)
Query: 83 AEKQVYSRDKPHCNIGTIGHVDHGKTTLTAAITKGLMEGMLGSYT 127
K+ + R KPH NIGTIGHVDHGKTTLTAAITK L E L
Sbjct: 1 MAKEKFDRSKPHVNIGTIGHVDHGKTTLTAAITKVLAERGLNQAK 45
Score = 71.9 bits (177), Expect = 1e-13
Identities = 25/47 (53%), Positives = 33/47 (70%)
Query: 10 DAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALEGKEPEIGII 56
D E+ ELVEME+RELL+E + GD++P ++GSAL ALEG I
Sbjct: 143 DEELLELVEMEVRELLSEYDFPGDDIPVIRGSALKALEGDPKWEDAI 189
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 71.8 bits (176), Expect = 1e-13
Identities = 28/55 (50%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 78 SRRGYAEKQVYSRDKPHCNIGTIGHVDHGKTTLTAAITKGLME-GMLGSYTYELI 131
+ ++R KPH N+GTIGHVDHGKTTLTAAITK L E G + ++ I
Sbjct: 45 PSPWWRSMATFTRTKPHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEI 99
Score = 66.4 bits (162), Expect = 7e-12
Identities = 26/45 (57%), Positives = 34/45 (75%)
Query: 10 DAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALEGKEPEIG 54
D E+ ELVEME+RELL+ + GDE+P ++GSAL AL+G EIG
Sbjct: 192 DEELLELVEMELRELLSFYKFPGDEIPIIRGSALSALQGTNDEIG 236
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 70.8 bits (174), Expect = 2e-13
Identities = 27/48 (56%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 85 KQVYSRDKPHCNIGTIGHVDHGKTTLTAAITKGLMEGMLGSYT-YELI 131
K+ + R KPH N+GTIGHVDHGKTTLTAAIT L + Y+ I
Sbjct: 3 KEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQI 50
Score = 68.1 bits (167), Expect = 1e-12
Identities = 26/47 (55%), Positives = 33/47 (70%)
Query: 10 DAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALEGKEPEIGII 56
D E+ ELVEME+RELL+E G+ GD+ P ++GSAL ALEG I
Sbjct: 143 DEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALEGDAKWEAKI 189
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 70.0 bits (172), Expect = 4e-13
Identities = 29/50 (58%), Positives = 35/50 (70%), Gaps = 1/50 (2%)
Query: 85 KQVYSRDKPHCNIGTIGHVDHGKTTLTAAITKGL-MEGMLGSYTYELIQS 133
++ + R KPH NIGTIGHVDHGKTTLTAAIT L +G + Y+ I S
Sbjct: 3 REKFERKKPHVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDS 52
Score = 57.3 bits (139), Expect = 6e-09
Identities = 24/47 (51%), Positives = 34/47 (72%), Gaps = 2/47 (4%)
Query: 10 DAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALEG--KEPEIG 54
D E+ ELVE+E+RELL++ + GD++P V GSAL ALE + P+I
Sbjct: 143 DEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALEALTENPKIK 189
>gnl|CDD|236390 PRK09136, PRK09136, 5'-methylthioadenosine phosphorylase;
Validated.
Length = 245
Score = 64.6 bits (158), Expect = 7e-12
Identities = 63/232 (27%), Positives = 91/232 (39%), Gaps = 41/232 (17%)
Query: 148 IGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCMQGRFH 207
+ II G+GL+ +A + T PY S G L FG + G ++ F
Sbjct: 2 LAIIGGTGLTQLA-GLDIVQRQVVRT-PYGAPS------GPLTFGTLAGREVV-----FL 48
Query: 208 YYEGYPLWKCAMP---------IRVMKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHIN 258
G+ +P I +K G T +LA N GG++ D G +++ I+
Sbjct: 49 ARHGHGH---TIPPHKVNYRANIWALKQAGATRVLAVNTVGGIHADMGPGTLVVPDQIID 105
Query: 259 LMG------FAGNNPLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEGV 312
F G V F P Y+ LR L AR +S +V GV
Sbjct: 106 YTWGRKSTFFEG--DGEEVTHIDFT--HP-----YSPMLRQRLLAAARAAGVS-LVDGGV 155
Query: 313 YSVIGGPNFETVAELNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITN 364
Y+ GP ET AE+ L G D VGM+ + E A G+ +L+ N
Sbjct: 156 YAATQGPRLETAAEIARLERDGCDLVGMTGMPEAALARELGLPYACLALVAN 207
>gnl|CDD|181584 PRK08931, PRK08931, 5'-methylthioadenosine phosphorylase;
Provisional.
Length = 289
Score = 65.0 bits (159), Expect = 9e-12
Identities = 64/278 (23%), Positives = 109/278 (39%), Gaps = 44/278 (15%)
Query: 144 IRPKIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCM- 202
+ +GII GSG+ I D + D ++ P+ S L+FG + G+P++ +
Sbjct: 2 TKAVLGIIGGSGVYDI-DGLEDARWERVES-PWGEPSD------ALLFGRLGGVPMVFLP 53
Query: 203 -QGRFHYYEGYPLWKCAMPIR----VMKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHI 257
GR G+ L + R +K GVT +++ +A G + G +I+ I
Sbjct: 54 RHGR-----GHRLSPSDINYRANIDALKRAGVTDIVSLSACGSFREELPPGTFVIVDQFI 108
Query: 258 NLM-----GFAGNNPLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEGV 312
+ F G + V M +L AR ++ + + G
Sbjct: 109 DRTFAREKSFFGTGCVAHV----------SMAHPVCPRLGDRLAAAARAEGIT-VHRGGT 157
Query: 313 YSVIGGPNFETVAELNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDYD- 371
Y + GP F T+AE + R G D +GM+ + E A + ++ VTDYD
Sbjct: 158 YLCMEGPQFSTLAESKLYRSWGCDVIGMTNMPEAKLAREAEICYATVAM-----VTDYDC 212
Query: 372 ---DHAEANHEEVIQAGKLRGPMIKSMVTRIVSYIGEH 406
DH + VI +++V R+ +G
Sbjct: 213 WHPDHDAVTVDAVIAVLLANADKARALVARLAPDLGAE 250
>gnl|CDD|236290 PRK08564, PRK08564, 5'-methylthioadenosine phosphorylase II;
Reviewed.
Length = 267
Score = 64.7 bits (158), Expect = 9e-12
Identities = 77/277 (27%), Positives = 111/277 (40%), Gaps = 47/277 (16%)
Query: 145 RPKIGIICGSGLSTIADSITDRHIFPYDT-----IPYFPVSTVPGHKGQLVFGLINGIPI 199
+ IGII GSGL D IF PY S ++ G I G+ +
Sbjct: 7 KASIGIIGGSGL-------YDPGIFENSKEVKVYTPYGEPS------DNIIIGEIEGVEV 53
Query: 200 MCM--QGRFHYYEGYPLWKCAMPIRV----MKLVGVTHLLATNAAGGLNPDYEVGDIMII 253
+ GR H P K + R +K +GV ++A +A G L DY+ GD +I
Sbjct: 54 AFLPRHGRGHRI---PPHK--INYRANIWALKELGVEWVIAVSAVGSLREDYKPGDFVIP 108
Query: 254 KDHINLMGFAGNNPLLGVNEDRFGPRFP--PMNKAYNKQLRAATLDIARDLNMSSIVKEG 311
I+ + GP M + +LR ++ A++L + ++G
Sbjct: 109 DQFID---MTKKREYTFYD----GPVVAHVSMADPFCPELRKIIIETAKELGI-RTHEKG 160
Query: 312 VYSVIGGPNFETVAELNMLR-ICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDY 370
Y I GP F T AE M R + D +GM+ V EV A GM ++ I VTDY
Sbjct: 161 TYICIEGPRFSTRAESRMWREVFKADIIGMTLVPEVNLACELGM---CYATIA--MVTDY 215
Query: 371 DDHAE--ANHEEVIQAGKLRGPMIKSMVTRIVSYIGE 405
D AE EEV + K ++ + I E
Sbjct: 216 DVWAEKPVTAEEVTRVMAENTEKAKKLLYEAIPRIPE 252
>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 = 65.2 bits (159), Expect = 1e-11
Identities = 26/36 (72%), Positives = 29/36 (80%)
Query: 85 KQVYSRDKPHCNIGTIGHVDHGKTTLTAAITKGLME 120
K+ + R KPH NIGTIGHVDHGKTTLTAAIT L +
Sbjct: 3 KEKFERTKPHVNIGTIGHVDHGKTTLTAAITTVLAK 38
Score = 59.0 bits (143), Expect = 1e-09
Identities = 24/39 (61%), Positives = 31/39 (79%)
Query: 10 DAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALEG 48
D E+ ELVEME+RELL+E + GD+ P ++GSAL ALEG
Sbjct: 143 DEELLELVEMEVRELLSEYDFPGDDTPIIRGSALKALEG 181
>gnl|CDD|180977 PRK07432, PRK07432, 5'-methylthioadenosine phosphorylase;
Provisional.
Length = 290
Score = 60.2 bits (146), Expect = 3e-10
Identities = 67/253 (26%), Positives = 103/253 (40%), Gaps = 45/253 (17%)
Query: 147 KIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPI--MCMQG 204
KIGII GSGL + +++ D +T P+ S L+ G ++G + + G
Sbjct: 5 KIGIIGGSGLYKM-EALKDVEEVQLET-PFGSPSDA------LIVGTLDGTRVAFLARHG 56
Query: 205 RFHYYEGYPLWKCAMPIRV----MKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHIN-- 258
R H L +P R MK +GV +L++ +A G L + + D+++ I+
Sbjct: 57 RNHT-----LLPTELPFRANIYAMKQLGVEYLISASAVGSLKEEAKPLDMVVPDQFIDRT 111
Query: 259 ---LMGFAGNNPLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIV--KEGVY 313
+ F G + + FG P L D LN+ + + G Y
Sbjct: 112 KNRISTFFGEGIVAHIG---FGDPICP-------ALAGVLADAIASLNLPDVTLHRGGTY 161
Query: 314 SVIGGPNFETVAELNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDYD-- 371
+ GP F T AE N+ R G +GM+ + E A + +L VTDYD
Sbjct: 162 VCMEGPAFSTKAESNLYRSWGATVIGMTNLPEAKLAREAEIAYATLAL-----VTDYDCW 216
Query: 372 --DHAEANHEEVI 382
DH E VI
Sbjct: 217 HPDHDSVTVEMVI 229
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 60.8 bits (147), Expect = 5e-10
Identities = 25/36 (69%), Positives = 28/36 (77%)
Query: 83 AEKQVYSRDKPHCNIGTIGHVDHGKTTLTAAITKGL 118
A + + R KPH NIGTIGHVDHGKTTLTAA+T L
Sbjct: 70 AARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMAL 105
Score = 49.2 bits (117), Expect = 2e-06
Identities = 21/38 (55%), Positives = 29/38 (76%)
Query: 10 DAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCALE 47
D E+ ELVE+E+RELL+ + GD++P + GSAL ALE
Sbjct: 212 DEELLELVELEVRELLSSYEFPGDDIPIISGSALLALE 249
>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 = 55.2 bits (134), Expect = 4e-09
Identities = 18/27 (66%), Positives = 19/27 (70%)
Query: 92 KPHCNIGTIGHVDHGKTTLTAAITKGL 118
K H NIG IGHVDHGKTTLT A+
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVT 27
Score = 42.5 bits (101), Expect = 1e-04
Identities = 21/42 (50%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 6 ID-AADAEMAELVEMEMRELLTEMGWKGDEVPFVKGSALCAL 46
ID DAE+ E+VE RELL + G+ G+ VP V GSAL
Sbjct: 128 IDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGE 169
>gnl|CDD|236107 PRK07823, PRK07823, 5'-methylthioadenosine phosphorylase;
Validated.
Length = 264
Score = 52.0 bits (125), Expect = 1e-07
Identities = 60/254 (23%), Positives = 89/254 (35%), Gaps = 53/254 (20%)
Query: 145 RPKIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGIPIMCM-- 202
+G+I GSG + S DT PY P S + G + G + +
Sbjct: 5 GAMLGVIGGSGFYSFFGSDAREVNV--DT-PYGPPS------APITIGEVGGRRVAFLPR 55
Query: 203 QGRFHYYEGYPLWKCAMPIRV----MKLVGVTHLLATNAAGGLNPDYEVGDIMIIKDHIN 258
GR H + + +P R ++ +GV + A A G L P+ G +++ ++
Sbjct: 56 HGRDHEFSPH-----TVPYRANMWALRALGVRRVFAPCAVGSLRPELGPGTVVVPDQLVD 110
Query: 259 LMG------FAGNNPLLGVNEDRFGPRFPPMNKAYNKQLRAATLDIARDLNMSSIVKEGV 312
F GV+ P Y LRAA L + +V G
Sbjct: 111 RTSGRAQTYFDSG----GVHVSFADP--------YCPTLRAAALGLPG------VVDGGT 152
Query: 313 YSVIGGPNFETVAELNMLRICGVDAVGMSTVHEVITAHHCGMTVTAFSLITNKCVTDYDD 372
V+ GP F T AE G V M+ E + A + A +L VTD D
Sbjct: 153 MVVVQGPRFSTRAESRWFAAQGWSLVNMTGYPEAVLARELELCYAAIAL-----VTDLDA 207
Query: 373 HAEA----NHEEVI 382
EA +V
Sbjct: 208 GVEAGEGVKAVDVF 221
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 49.5 bits (119), Expect = 2e-06
Identities = 16/23 (69%), Positives = 18/23 (78%)
Query: 93 PHCNIGTIGHVDHGKTTLTAAIT 115
P NIG +GHVDHGKTTL A+T
Sbjct: 8 PEVNIGMVGHVDHGKTTLVQALT 30
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 49.3 bits (118), Expect = 2e-06
Identities = 16/28 (57%), Positives = 20/28 (71%)
Query: 88 YSRDKPHCNIGTIGHVDHGKTTLTAAIT 115
+P NIG +GHVDHGKTTLT A++
Sbjct: 4 PKHIQPEVNIGMVGHVDHGKTTLTKALS 31
>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 = 46.9 bits (112), Expect = 4e-06
Identities = 15/20 (75%), Positives = 17/20 (85%)
Query: 96 NIGTIGHVDHGKTTLTAAIT 115
NIGTIGHV HGKTTL A++
Sbjct: 2 NIGTIGHVAHGKTTLVKALS 21
>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 = 46.6 bits (111), Expect = 1e-05
Identities = 17/23 (73%), Positives = 19/23 (82%)
Query: 93 PHCNIGTIGHVDHGKTTLTAAIT 115
P NIG +GHVDHGKTTLT A+T
Sbjct: 3 PEVNIGMVGHVDHGKTTLTKALT 25
>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 = 43.8 bits (104), Expect = 4e-05
Identities = 14/20 (70%), Positives = 17/20 (85%)
Query: 96 NIGTIGHVDHGKTTLTAAIT 115
N+G IGHVDHGKTTLT ++
Sbjct: 1 NVGVIGHVDHGKTTLTGSLL 20
Score = 30.0 bits (68), Expect = 1.4
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 6 IDAADAEMAELVEMEMRELLTEMGW---KGDEVPFVKGSAL 43
ID E + V E++ELL +G+ KG +VP + SAL
Sbjct: 124 IDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISAL 164
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 43.8 bits (104), Expect = 1e-04
Identities = 14/23 (60%), Positives = 19/23 (82%)
Query: 89 SRDKPHCNIGTIGHVDHGKTTLT 111
+++KPH N+ IGHVDHGK+TL
Sbjct: 1 AKEKPHLNLAVIGHVDHGKSTLV 23
>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 = 40.3 bits (95), Expect = 5e-04
Identities = 14/19 (73%), Positives = 16/19 (84%)
Query: 97 IGTIGHVDHGKTTLTAAIT 115
IGT GH+DHGKTTL A+T
Sbjct: 2 IGTAGHIDHGKTTLIKALT 20
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 41.7 bits (98), Expect = 6e-04
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 65 EINKLNVFVPLINSRRGYAEKQVYSRDK----PHCNIGTIGHVDHGKTTLTAAITKG 117
E+ V + GY + + R H +G GHVDHGK+TL + G
Sbjct: 84 EVGASIYIVRVHEGTDGYVAEVLVRRKTEEAPEHVLVGVAGHVDHGKSTLVGVLVTG 140
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 41.6 bits (98), Expect = 6e-04
Identities = 15/19 (78%), Positives = 15/19 (78%)
Query: 97 IGTIGHVDHGKTTLTAAIT 115
I T GHVDHGKTTL AIT
Sbjct: 3 IATAGHVDHGKTTLLQAIT 21
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 41.5 bits (98), Expect = 6e-04
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 12/54 (22%)
Query: 62 DKFEINKLNVFVPLINSRRGYAEKQVYSRDKPHCNIGTIGHVDHGKTTLTAAIT 115
K +++KL P + SR+ NIGTIGHV HGK+T+ A++
Sbjct: 14 SKLDLDKLTPLTPEVISRQAT------------INIGTIGHVAHGKSTVVKALS 55
>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 = 39.1 bits (92), Expect = 0.002
Identities = 12/16 (75%), Positives = 13/16 (81%)
Query: 96 NIGTIGHVDHGKTTLT 111
NI I HVDHGKTTL+
Sbjct: 2 NICIIAHVDHGKTTLS 17
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 39.9 bits (94), Expect = 0.002
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 96 NIGTIGHVDHGKTTLTAAI 114
NIG + H+D GKTTLT I
Sbjct: 12 NIGIVAHIDAGKTTLTERI 30
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 39.8 bits (94), Expect = 0.002
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 96 NIGTIGHVDHGKTTLT 111
NIG I H+DHGKTTL+
Sbjct: 22 NIGIIAHIDHGKTTLS 37
>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 = 38.1 bits (89), Expect = 0.003
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 96 NIGTIGHVDHGKTTLTAAIT 115
N+G +GHVD GKT+L A++
Sbjct: 2 NVGLLGHVDSGKTSLAKALS 21
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 38.8 bits (91), Expect = 0.004
Identities = 32/120 (26%), Positives = 47/120 (39%), Gaps = 30/120 (25%)
Query: 91 DKPHCNIGTIGHVDHGKTTL-------TAAITKGLMEGM------LGSYTYELIQSIAKF 137
+KPH N+ IGHVD GK+TL I K ME + LG +++ +
Sbjct: 4 EKPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKF-----AW 58
Query: 138 LLDSISIRPKIGIICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGHKGQLVFGLINGI 197
+LD + G+ S TD+ F + PGH+ V +I G
Sbjct: 59 VLDKTKEERERGVTIDVAHSKF---ETDK--------YNFTIIDAPGHR-DFVKNMITGA 106
>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 = 38.7 bits (90), Expect = 0.005
Identities = 14/20 (70%), Positives = 15/20 (75%)
Query: 96 NIGTIGHVDHGKTTLTAAIT 115
I T GHVDHGKTTL A+T
Sbjct: 2 IIATAGHVDHGKTTLLKALT 21
>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 = 38.3 bits (89), Expect = 0.006
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 7/41 (17%)
Query: 89 SRDKPHCNIGTIGHVDHGKTTLT-------AAITKGLMEGM 122
+++K H N+ IGHVDHGK+T AI + +E
Sbjct: 2 AKEKEHINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKF 42
>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 = 36.4 bits (85), Expect = 0.012
Identities = 14/22 (63%), Positives = 15/22 (68%)
Query: 95 CNIGTIGHVDHGKTTLTAAITK 116
NI I HVDHGKTTL A+ K
Sbjct: 3 RNIAIIAHVDHGKTTLVDALLK 24
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 37.0 bits (86), Expect = 0.015
Identities = 14/20 (70%), Positives = 16/20 (80%)
Query: 96 NIGTIGHVDHGKTTLTAAIT 115
IGT GH+DHGKTTL A+T
Sbjct: 2 IIGTAGHIDHGKTTLLKALT 21
>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 = 36.5 bits (85), Expect = 0.022
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 9/56 (16%)
Query: 96 NIGTIGHVDHGKTTLTAAITKGLMEGML-GSYTYELIQSIAKFLLDSISIRPKIGI 150
NI I HVDHGKTT L++ +L S T+ +++A+ ++DS + + GI
Sbjct: 3 NIAIIAHVDHGKTT--------LVDALLKQSGTFRANEAVAERVMDSNDLERERGI 50
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 36.1 bits (84), Expect = 0.032
Identities = 12/15 (80%), Positives = 12/15 (80%)
Query: 96 NIGTIGHVDHGKTTL 110
NI I HVDHGKTTL
Sbjct: 7 NIAIIAHVDHGKTTL 21
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 36.0 bits (84), Expect = 0.038
Identities = 13/17 (76%), Positives = 14/17 (82%), Gaps = 1/17 (5%)
Query: 99 TI-GHVDHGKTTLTAAI 114
TI GHVDHGKT+L AI
Sbjct: 253 TIMGHVDHGKTSLLDAI 269
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 35.9 bits (83), Expect = 0.041
Identities = 14/23 (60%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 91 DKPHC--NIGTIGHVDHGKTTLT 111
DK H N+ I HVDHGK+TLT
Sbjct: 14 DKKHNIRNMSVIAHVDHGKSTLT 36
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 35.3 bits (82), Expect = 0.057
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 96 NIGTIGHVDHGKTTLTAAI 114
NIG + H+D GKTTLT I
Sbjct: 10 NIGILAHIDAGKTTLTERI 28
>gnl|CDD|238923 cd01948, EAL, EAL domain. This domain is found in diverse bacterial
signaling proteins. It is called EAL after its conserved
residues and is also known as domain of unknown function
2 (DUF2). The EAL domain has been shown to stimulate
degradation of a second messenger, cyclic di-GMP, and is
a good candidate for a diguanylate phosphodiesterase
function. Together with the GGDEF domain, EAL might be
involved in regulating cell surface adhesiveness in
bacteria.
Length = 240
Score = 34.4 bits (80), Expect = 0.063
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 294 ATLDIARDLNMSSIVKEGVYSVIGGPNFETVAELNMLRICGVDAV 338
A + +A L + + EGV ET +L +LR G D V
Sbjct: 193 AIIALAHSLGLKVVA-EGV---------ETEEQLELLRELGCDYV 227
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 35.4 bits (82), Expect = 0.065
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 91 DKPHC--NIGTIGHVDHGKTTLT 111
D P N+ I HVDHGK+TLT
Sbjct: 14 DNPDQIRNMSVIAHVDHGKSTLT 36
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 35.2 bits (82), Expect = 0.065
Identities = 24/54 (44%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 101 GHVDHGKTTLTAAITKG-LMEGMLGSYTYELIQSIA--KFLLDSISIRPKIGII 151
GHVDHGKTTL I K + G G T Q I + LD I I P I I
Sbjct: 12 GHVDHGKTTLLDKIRKTNVAAGEAGGIT----QHIGAYQVPLDVIKI-PGITFI 60
>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 = 34.0 bits (79), Expect = 0.068
Identities = 12/16 (75%), Positives = 12/16 (75%)
Query: 101 GHVDHGKTTLTAAITK 116
GHVDHGKTTL I K
Sbjct: 7 GHVDHGKTTLLDKIRK 22
>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 = 34.5 bits (80), Expect = 0.072
Identities = 28/95 (29%), Positives = 40/95 (42%), Gaps = 26/95 (27%)
Query: 96 NIGTIGHVDHGKTTLTAAITKGLMEGMLGSYTYELIQSIAKF-----LLDSISIRPKIGI 150
NIG + HVD GKTTLT E +L YT I+ + DS+ + + GI
Sbjct: 1 NIGILAHVDAGKTTLT--------ESLL--YTSGAIRELGSVDKGTTRTDSMELERQRGI 50
Query: 151 ICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGH 185
TI ++ F ++ + T PGH
Sbjct: 51 -------TIFSAVA---SFQWEDTKVNIIDT-PGH 74
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 34.7 bits (80), Expect = 0.092
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 90 RDKPHCNIGTIGHVDHGKTTLT 111
++K H N+ IGHVD GK+T T
Sbjct: 3 KEKTHINLVVIGHVDSGKSTTT 24
>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 = 33.6 bits (78), Expect = 0.11
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 96 NIGTIGHVDHGKTTLT 111
N+ IGHVD GK+TLT
Sbjct: 1 NLVVIGHVDAGKSTLT 16
>gnl|CDD|130293 TIGR01226, phe_am_lyase, phenylalanine ammonia-lyase. Members of
this family are found, so far, in plants and fungi. From
phenylalanine, this enzyme yields cinnaminic acid, a
precursor of many important plant compounds. This
protein shows extensive homology to histidine
ammonia-lyase, the first enzyme of a histidine
degradation pathway.
Length = 680
Score = 34.4 bits (79), Expect = 0.12
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 94 HCNIGTIGHVDHGKTTLTAAITKGLM----EGMLGSYT---YELIQSIAKFLLDSIS-IR 145
N G +G +L T+ M +L Y+ +E++++I K L +++
Sbjct: 111 FLNAGILGTGSDNHNSLPEEATRAAMLVRINTLLQGYSGIRFEILEAITKLLNANVTPCL 170
Query: 146 PKIGIICGSG----LSTIADSITDR 166
P G I SG LS IA IT R
Sbjct: 171 PLRGTITASGDLVPLSYIAGLITGR 195
>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 = 34.0 bits (79), Expect = 0.12
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 96 NIGTIGHVDHGKTTLT 111
NIG I H+D GKTT T
Sbjct: 1 NIGIIAHIDAGKTTTT 16
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 33.7 bits (77), Expect = 0.21
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 100 IGHVDHGKTTLTAAITK 116
+GHVDHGKTTL I K
Sbjct: 250 LGHVDHGKTTLLDKIRK 266
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 33.2 bits (77), Expect = 0.25
Identities = 10/10 (100%), Positives = 10/10 (100%)
Query: 101 GHVDHGKTTL 110
GHVDHGKTTL
Sbjct: 13 GHVDHGKTTL 22
>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 = 32.9 bits (75), Expect = 0.36
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 96 NIGTIGHVDHGKTTLTAAITKGLMEGML 123
NIG + H+DHGKTTL+ + G GM+
Sbjct: 21 NIGIVAHIDHGKTTLSDNLLAG--AGMI 46
>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 = 32.5 bits (74), Expect = 0.50
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 100 IGHVDHGKTTLTAAITK--------GLMEGMLGS--YTYELIQSIAKFLLDSISIRPKI 148
+GHVDHGKTTL I G + +G+ ++I+ I LL IR KI
Sbjct: 10 LGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDVIEGICGDLLKKFKIRLKI 68
>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 = 31.3 bits (72), Expect = 0.57
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 7/33 (21%)
Query: 96 NIGTIGHVDHGKTTL-------TAAITKGLMEG 121
N I H+DHGK+TL T +++ M+
Sbjct: 2 NFSIIAHIDHGKSTLADRLLELTGTVSEREMKE 34
>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 = 30.4 bits (69), Expect = 0.92
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 96 NIGTIGHVDHGKTTLTAAITK 116
I +G + GK+TL +
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLG 23
>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 = 30.9 bits (70), Expect = 1.2
Identities = 13/19 (68%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 99 TI-GHVDHGKTTLTAAITK 116
TI GHVDHGKT+L +I K
Sbjct: 91 TIMGHVDHGKTSLLDSIRK 109
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 30.8 bits (69), Expect = 1.5
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 90 RDKPHCNIGTIGHVDHGKTTLTA 112
++K H NI IGHVD GK+T T
Sbjct: 3 KEKVHINIVVIGHVDSGKSTTTG 25
>gnl|CDD|237731 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 30.3 bits (69), Expect = 1.6
Identities = 14/24 (58%), Positives = 14/24 (58%)
Query: 97 IGTIGHVDHGKTTLTAAITKGLME 120
IG IG D GKTTL I K L E
Sbjct: 4 IGVIGFKDSGKTTLIEKILKNLKE 27
>gnl|CDD|225110 COG2200, Rtn, c-di-GMP phosphodiesterase class I (EAL domain)
[Signal transduction mechanisms].
Length = 256
Score = 30.3 bits (69), Expect = 1.7
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 294 ATLDIARDLNMSSIVKEGVYSVIGGPNFETVAELNMLRICGVDAV 338
A + +A L ++ + EGV ET +L++LR G D +
Sbjct: 197 AIVALAHKLGLTVVA-EGV---------ETEEQLDLLRELGCDYL 231
>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 = 29.8 bits (68), Expect = 1.8
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 99 TIGHVDHGKTTLTAAI---TKGLMEGML 123
T G VD GK+TL + +K + E L
Sbjct: 4 TCGSVDDGKSTLIGRLLYDSKSIFEDQL 31
>gnl|CDD|136007 PRK06698, PRK06698, bifunctional
5'-methylthioadenosine/S-adenosylhomocysteine
nucleosidase/phosphatase; Validated.
Length = 459
Score = 30.4 bits (68), Expect = 2.1
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 229 VTHLLATNAAGGLNPDYEVGDIMI 252
V ++ T AGGL+PD +VGDI+I
Sbjct: 69 VDAIINTGVAGGLHPDVKVGDIVI 92
>gnl|CDD|184794 PRK14697, PRK14697, bifunctional
5'-methylthioadenosine/S-adenosylhomocysteine
nucleosidase/phosphatase; Provisional.
Length = 233
Score = 30.0 bits (67), Expect = 2.1
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 229 VTHLLATNAAGGLNPDYEVGDIMI 252
V ++ T AGGL+PD +VGDI+I
Sbjct: 69 VDAIINTGVAGGLHPDVKVGDIVI 92
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 29.1 bits (66), Expect = 2.3
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 106 GKTTLTAAITKGL-MEGMLGSYTYELIQS 133
GKTTL I KGL ++G + S T+ L++
Sbjct: 37 GKTTLVRGIAKGLGVDGNVKSPTFTLVEE 65
>gnl|CDD|180148 PRK05584, PRK05584, 5'-methylthioadenosine/S-adenosylhomocysteine
nucleosidase; Validated.
Length = 230
Score = 29.7 bits (68), Expect = 2.5
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 228 GVTHLLATNAAGGLNPDYEVGDIMI 252
V ++ T AGGL P +VGD+++
Sbjct: 67 KVDAVINTGVAGGLAPGLKVGDVVV 91
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 29.7 bits (68), Expect = 3.3
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 96 NIGTIGHVDHGKTTLT 111
NIG + H+D GKTT T
Sbjct: 12 NIGIMAHIDAGKTTTT 27
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 29.4 bits (67), Expect = 3.7
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 96 NIGTIGHVDHGKTTLTAAI 114
NIG + H+D GKTT T I
Sbjct: 10 NIGIMAHIDAGKTTTTERI 28
>gnl|CDD|215995 pfam00563, EAL, EAL domain. This domain is found in diverse
bacterial signaling proteins. It is called EAL after its
conserved residues. The EAL domain is a good candidate
for a diguanylate phosphodiesterase function. The domain
contains many conserved acidic residues that could
participate in metal binding and might form the
phosphodiesterase active site.
Length = 231
Score = 28.9 bits (65), Expect = 3.7
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 10/51 (19%)
Query: 288 NKQLRAATLDIARDLNMSSIVKEGVYSVIGGPNFETVAELNMLRICGVDAV 338
++ L A + +AR L + + EGV ET +L +L+ G+D V
Sbjct: 183 SRALLRALIALARSLGIKVVA-EGV---------ETEEQLELLKELGIDYV 223
>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 = 29.6 bits (67), Expect = 3.8
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 96 NIGTIGHVDHGKTTL 110
N I H+DHGK+TL
Sbjct: 5 NFSIIAHIDHGKSTL 19
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 29.3 bits (65), Expect = 3.9
Identities = 12/15 (80%), Positives = 12/15 (80%)
Query: 96 NIGTIGHVDHGKTTL 110
NI I HVDHGKTTL
Sbjct: 7 NIAIIAHVDHGKTTL 21
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 29.2 bits (67), Expect = 4.3
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 96 NIGTIGHVDHGKTTL 110
N I H+DHGK+TL
Sbjct: 9 NFSIIAHIDHGKSTL 23
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 29.1 bits (66), Expect = 4.5
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 96 NIGTIGHVDHGKTTL 110
N I H+DHGK+TL
Sbjct: 11 NFSIIAHIDHGKSTL 25
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 29.3 bits (67), Expect = 4.6
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 100 IGHVDHGKTTLTAAI 114
+GH GKTTLT AI
Sbjct: 1 VGHSGAGKTTLTEAI 15
>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 = 29.0 bits (65), Expect = 5.6
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 96 NIGTIGHVDHGKTTLTAAI 114
NIG H+D GKTT T I
Sbjct: 12 NIGISAHIDAGKTTTTERI 30
>gnl|CDD|234827 PRK00733, hppA, membrane-bound proton-translocating
pyrophosphatase; Validated.
Length = 666
Score = 29.0 bits (66), Expect = 5.8
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 111 TAAITKGLMEG--------MLGSYTYELIQSIAKFLLDSISI-RPK--IGIICG 153
T A+TKG G + +Y EL + + S+ + P +G++ G
Sbjct: 440 TKAVTKGFAIGSAALAALALFAAYIDELAGLLGGGGILSLDLSNPYVLVGLLIG 493
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 28.8 bits (65), Expect = 6.3
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 99 TIGHVDHGKTTLTAAI---TKGLMEGMLGS 125
T G VD GK+TL + TK + E L S
Sbjct: 11 TCGSVDDGKSTLIGRLLYDTKAIYEDQLAS 40
>gnl|CDD|176196 cd08234, threonine_DH_like, L-threonine dehydrogenase. L-threonine
dehydrogenase (TDH) catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine,
via NAD(H)-dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and have 2 tightly
bound zinc atoms per subunit. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Length = 334
Score = 28.6 bits (65), Expect = 6.5
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 12/35 (34%)
Query: 151 ICGSGLSTIADSITDRHIFPYDTIPYFPVSTVPGH 185
ICG TD HI+ + P+ VPGH
Sbjct: 36 ICG----------TDLHIYEGEFGAAPPL--VPGH 58
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 28.5 bits (65), Expect = 6.6
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 7 DAADAEMAELVEMEMRELLTEM 28
+ +D EM E+ + E++EL +
Sbjct: 70 EESDPEMREMAKEELKELEERL 91
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
0.321 0.139 0.418
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,184,617
Number of extensions: 2075566
Number of successful extensions: 1926
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1890
Number of HSP's successfully gapped: 112
Length of query: 412
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 313
Effective length of database: 6,546,556
Effective search space: 2049072028
Effective search space used: 2049072028
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.0 bits)