RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1760
(793 letters)
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 904 bits (2339), Expect = 0.0
Identities = 328/565 (58%), Positives = 434/565 (76%), Gaps = 6/565 (1%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+NIAIIAHVDHGKTTL+D LL+QSGTFR+ + + R+MDSN++EKERGITI +KN ++ Y
Sbjct: 6 RNIAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTAVNY 65
Query: 271 NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 330
NGTRINI+DTPGHADFGGEVER+LSMVD VLLL+DA EGPMPQTRFV +KAL LG KPIV
Sbjct: 66 NGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLKPIV 125
Query: 331 VVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIP 390
V+NKIDR +ARP+ VVD FDLF +L AT+EQLDFP++Y SA +G A+ + + +M P
Sbjct: 126 VINKIDRPDARPDEVVDEVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADDMAP 185
Query: 391 LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDD 450
LFE IL +VP K + + PLQ+Q+ L+Y+SY+G+IGIGRI G +K Q V ++ D
Sbjct: 186 LFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKS-DG 244
Query: 451 KPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDE 510
+I ++ F GL+R+ + EA +GDIV I G+E+I IG TICDP P LP L++DE
Sbjct: 245 TTENGRITKLLGFLGLERIEIEEAEAGDIVAIAGLEDINIGDTICDPDNPEALPALSVDE 304
Query: 511 PTLTINFMVNNSPLAGREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGE 570
PTL++ F VN+SP AG+EGKF+T+RQI++RL+ E++ N+ LRV + + D+ +EVSGRGE
Sbjct: 305 PTLSMTFSVNDSPFAGKEGKFVTSRQIRDRLNKELETNVALRVEETESPDA-FEVSGRGE 363
Query: 571 LHLTILIENMRREGYELSVSRPRVIFKTLNGELYEPYENLFVDIEEINQGIIMQKLNYRG 630
LHL+ILIENMRREG+EL VSRP VI K ++G EP+E + +D+ E +QG +++KL R
Sbjct: 364 LHLSILIENMRREGFELQVSRPEVIIKEIDGVKCEPFEEVTIDVPEEHQGAVIEKLGERK 423
Query: 631 GDLKNIEINEKERVRLEYRIPSRGLIGFQNEFITLTRGTGLISHVFEEYAPFYNKSKYDL 690
G++K++ + K RVRLE+ IP+RGLIGF+ EF+T+TRGTG+++H F+ Y P K ++
Sbjct: 424 GEMKDMAPDGKGRVRLEFVIPARGLIGFRTEFLTMTRGTGIMNHSFDHYRPV----KGEI 479
Query: 691 GKRRNGVLISQYSGKAVAYSLWKLQDRGRLFINHNDLVYEGMIIGIHSRDNDLLVNPIKE 750
G R NGVLIS +GKAVAY+L+ LQDRG+LFI VYEGMIIG HSRDNDL VN +K
Sbjct: 480 GGRHNGVLISNETGKAVAYALFNLQDRGKLFIEPGTKVYEGMIIGEHSRDNDLTVNVLKG 539
Query: 751 KQLTNIRSSGSDEAIQLINIIKIIL 775
K+LTN+R+SG DEA+ L I++ L
Sbjct: 540 KKLTNMRASGKDEAVTLTPPIRMTL 564
>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 = 843 bits (2181), Expect = 0.0
Identities = 314/565 (55%), Positives = 423/565 (74%), Gaps = 6/565 (1%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+NIAIIAHVDHGKTTL+D LL+QSGTFR N+ + R+MDSN++E+ERGITI +KN +I Y
Sbjct: 2 RNIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITILAKNTAIRY 61
Query: 271 NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 330
NGT+INI+DTPGHADFGGEVER+L MVD VLLL+DA EGPMPQTRFV +KAL+LG KPIV
Sbjct: 62 NGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPIV 121
Query: 331 VVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIP 390
V+NKIDR +ARP+ VVD FDLF +L A +EQLDFP++Y S G+A+ + NM P
Sbjct: 122 VINKIDRPSARPDEVVDEVFDLFAELGADDEQLDFPIVYASGRAGWASLDLDDPSDNMAP 181
Query: 391 LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDD 450
LF+AI+++VP K + + PLQ+ + +L+Y YLG+I IGR+ G +K Q V +M D
Sbjct: 182 LFDAIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMK-RDG 240
Query: 451 KPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDE 510
+I+++ F+GL+RV ++EA +GDIV + G+E+I IG TI DP P LP + +DE
Sbjct: 241 TIENGRISKLLGFEGLERVEIDEAGAGDIVAVAGLEDINIGETIADPEVPEALPTITVDE 300
Query: 511 PTLTINFMVNNSPLAGREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGE 570
PTL++ F VN+SPLAG+EGK +T+R I++RL E++ N+ LRV + D +EVSGRGE
Sbjct: 301 PTLSMTFSVNDSPLAGKEGKKVTSRHIRDRLMRELETNVALRVEDTESADK-FEVSGRGE 359
Query: 571 LHLTILIENMRREGYELSVSRPRVIFKTLNGELYEPYENLFVDIEEINQGIIMQKLNYRG 630
LHL+ILIE MRREG+EL V RP+VI+K ++G+ EP E L +D+ E + G +++KL R
Sbjct: 360 LHLSILIETMRREGFELQVGRPQVIYKEIDGKKLEPIEELTIDVPEEHVGAVIEKLGKRK 419
Query: 631 GDLKNIEINEKERVRLEYRIPSRGLIGFQNEFITLTRGTGLISHVFEEYAPFYNKSKYDL 690
G++ ++E + R RLE++IPSRGLIGF+ EF+T TRGTG+++HVF+EY P+ K ++
Sbjct: 420 GEMVDMEPSGNGRTRLEFKIPSRGLIGFRTEFLTDTRGTGIMNHVFDEYEPW----KGEI 475
Query: 691 GKRRNGVLISQYSGKAVAYSLWKLQDRGRLFINHNDLVYEGMIIGIHSRDNDLLVNPIKE 750
RRNG L+S G A AY+LW LQ+RG +F++ VYEGMIIG HSR+NDL VNP K
Sbjct: 476 ETRRNGSLVSMEDGTATAYALWNLQERGVMFVSPGTEVYEGMIIGEHSRENDLDVNPCKA 535
Query: 751 KQLTNIRSSGSDEAIQLINIIKIIL 775
K+LTN+RSSG DEA++L K+ L
Sbjct: 536 KKLTNVRSSGKDEAVKLTPPRKLSL 560
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 637 bits (1645), Expect = 0.0
Identities = 313/565 (55%), Positives = 423/565 (74%), Gaps = 5/565 (0%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+NIAIIAHVDHGKTTL+D LL+QSGTF R+MDSN++EKERGITI +KN +I++
Sbjct: 6 RNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKW 65
Query: 271 NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 330
N RINI+DTPGHADFGGEVER++SMVD+VLL++DA +GPMPQTRFVT+KA G KPIV
Sbjct: 66 NDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIV 125
Query: 331 VVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIP 390
V+NK+DR ARP+WVVD FDLF L AT+EQLDFP++Y SAL+G A + + +M P
Sbjct: 126 VINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTP 185
Query: 391 LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDD 450
L++AI+ +VP + + P Q+QI L+Y+SY+G IGIGRI G++K Q V I++ +
Sbjct: 186 LYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDS-EG 244
Query: 451 KPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDE 510
K AK+ ++ GL+R+ + A +GDIV ITG+ E+ I T+CD LP L++DE
Sbjct: 245 KTRNAKVGKVLGHLGLERIETDLAEAGDIVAITGLGELNISDTVCDTQNVEALPALSVDE 304
Query: 511 PTLTINFMVNNSPLAGREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGE 570
PT+++ F VN SP G+EGKF+T+RQI +RL+ E+ +N+ LRV + + D+ + VSGRGE
Sbjct: 305 PTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVEETEDADA-FRVSGRGE 363
Query: 571 LHLTILIENMRREGYELSVSRPRVIFKTLNGELYEPYENLFVDIEEINQGIIMQKLNYRG 630
LHL++LIENMRREG+EL+VSRP+VIF+ ++G EPYEN+ +D+EE +QG +MQ L R
Sbjct: 364 LHLSVLIENMRREGFELAVSRPKVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGERK 423
Query: 631 GDLKNIEINEKERVRLEYRIPSRGLIGFQNEFITLTRGTGLISHVFEEYAPFYNKSKYDL 690
GDLKN+ + K RVRL+Y IPSRGLIGF++EF+T+T GTGL+ F Y + ++
Sbjct: 424 GDLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYD---DVRPGEV 480
Query: 691 GKRRNGVLISQYSGKAVAYSLWKLQDRGRLFINHNDLVYEGMIIGIHSRDNDLLVNPIKE 750
G+R+NGVLIS GKAVA++L+ LQDRG+LF+ H VYEG IIGIHSR NDL VN +
Sbjct: 481 GQRQNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRSNDLTVNCLTG 540
Query: 751 KQLTNIRSSGSDEAIQLINIIKIIL 775
K+LTN+R+SG+DEA+ L+ I++ L
Sbjct: 541 KKLTNMRASGTDEAVVLVPPIRMTL 565
>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 = 360 bits (926), Expect = e-120
Identities = 128/190 (67%), Positives = 159/190 (83%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+NIAIIAHVDHGKTTL+D LL+QSGTFR+N+ + R+MDSN++E+ERGITI +KN +I Y
Sbjct: 3 RNIAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGITILAKNTAITY 62
Query: 271 NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 330
T+INIIDTPGHADFGGEVER+LSMVD VLLL+DA EGPMPQTRFV +KAL+ G KPIV
Sbjct: 63 KDTKINIIDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALEAGLKPIV 122
Query: 331 VVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIP 390
V+NKIDR +ARPE VVD FDLF +L AT+EQLDFP++Y SA +G+A+ N ++ P
Sbjct: 123 VINKIDRPDARPEEVVDEVFDLFLELNATDEQLDFPIVYASAKNGWASLNLDDPSEDLDP 182
Query: 391 LFEAILKYVP 400
LFE I+++VP
Sbjct: 183 LFETIIEHVP 192
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 304 bits (781), Expect = 3e-97
Identities = 100/195 (51%), Positives = 136/195 (69%), Gaps = 1/195 (0%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP G+SSN+AL+K+K L NA K G+TG LDP ATG+LP+C GEATKFS YL ++DK Y
Sbjct: 17 KPQGMSSNDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEATKFSQYLLDSDKRYRV 76
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 136
LG T+T D +G++++ + + S E +E L F G I Q+P MYSALKY+G PLY
Sbjct: 77 TARLGQRTDTSDADGEVVE-ERPVTLSAEQLEAALEKFRGDIEQVPSMYSALKYQGQPLY 135
Query: 137 KYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHL 196
+YAR GI ++R+ R I IY++ +I + L L +HCSKGTYIR L +D+G+ LGCGAH+
Sbjct: 136 EYARQGIEVEREARPITIYELELIRFEGDELELEVHCSKGTYIRTLVDDLGEKLGCGAHV 195
Query: 197 KYLRRIGIDKLTLDK 211
YLRR + L++
Sbjct: 196 IYLRRTQVAPYPLER 210
>gnl|CDD|211339 cd02573, PseudoU_synth_EcTruB, Pseudouridine synthase, Escherichia
coli TruB like. This group consists of bacterial
pseudouridine synthases similar to E. coli TruB and
Mycobacterium tuberculosis TruB. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
E. coli TruB and M. tuberculosis TruB make psi55 in the
T loop of tRNAs. Psi55 is nearly universally conserved.
E. coli TruB is not inhibited by RNA containing
5-fluorouridine.
Length = 213
Score = 290 bits (746), Expect = 2e-93
Identities = 96/201 (47%), Positives = 131/201 (65%), Gaps = 2/201 (0%)
Query: 12 VIPKYKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 71
++ KP GL+S++ ++K++ LL KKVG+TGTLDP ATG+LP+ GEATK S YL +AD
Sbjct: 2 ILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDAD 61
Query: 72 KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYK 131
K Y A + LG T+T D EG+II+ + + E IE L F G+I Q+PPMYSA+K
Sbjct: 62 KTYRATVRLGEATDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVD 121
Query: 132 GIPLYKYARSGITIKRKLRYIKIYKITIIDYT--IPYLTLRIHCSKGTYIRVLSEDIGKM 189
G LY+ AR+G ++R R + IY + ++ + P +HCSKGTYIR L+ D+GK
Sbjct: 122 GKRLYELARAGEEVERPPRKVTIYSLELLSFDPENPEADFEVHCSKGTYIRSLARDLGKA 181
Query: 190 LGCGAHLKYLRRIGIDKLTLD 210
LGCGAHL LRR TL+
Sbjct: 182 LGCGAHLSALRRTRSGPFTLE 202
>gnl|CDD|234986 PRK01851, truB, tRNA pseudouridine synthase B; Provisional.
Length = 303
Score = 293 bits (753), Expect = 3e-93
Identities = 110/194 (56%), Positives = 143/194 (73%), Gaps = 1/194 (0%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP GLSSN+AL++ K LL AKK G+TGTLDP ATGLLPLCFGEATKFS L +ADK YEA
Sbjct: 23 KPLGLSSNDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEATKFSQDLLDADKTYEA 82
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 136
+ LG+ T TGD EG+++ + + +E L F G+I Q+PPMYSALK G PLY
Sbjct: 83 TLRLGVRTSTGDAEGEVLA-TRPVDCDPAALEAALARFTGEIRQVPPMYSALKKDGKPLY 141
Query: 137 KYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHL 196
+YAR+GIT++R+ R + I+ + ++ +P +T+R+ CSKGTYIR L+EDIG+ LGCGAHL
Sbjct: 142 EYARAGITVEREARDVTIHALDLLACDLPDVTIRVTCSKGTYIRTLAEDIGEALGCGAHL 201
Query: 197 KYLRRIGIDKLTLD 210
LRR G+ LTL+
Sbjct: 202 TALRRTGVGGLTLE 215
>gnl|CDD|129523 TIGR00431, TruB, tRNA pseudouridine(55) synthase. TruB, the tRNA
pseudouridine 55 synthase, converts uracil to
pseudouridine in the T loop of most tRNAs in all three
domains of life. This model is built on a seed alignment
of bacterial proteins only. Saccharomyces cerevisiae
protein YNL292w (Pus4) has been shown to be the
pseudouridine 55 synthase of both cytosolic and
mitochondrial compartments, active at no other position
on tRNA and the only enzyme active at that position in
the species. A distinct yeast protein YLR175w,
(centromere/microtubule-binding protein CBF5) is an rRNA
pseudouridine synthase, and the archaeal set is much
more similar to CBF5 than to Pus4. It is unclear whether
the archaeal proteins found by this model are tRNA
pseudouridine 55 synthases like TruB, rRNA pseudouridine
synthases like CBF5, or (as suggested by the absence of
paralogs in the Archaea) both. CBF5 likely has
additional, eukaryotic-specific functions. The trusted
cutoff is set above the scores for the archaeal homologs
of unknown function, so yeast Pus4p scores between
trusted and noise [Protein synthesis, tRNA and rRNA base
modification].
Length = 209
Score = 251 bits (642), Expect = 2e-78
Identities = 102/204 (50%), Positives = 141/204 (69%), Gaps = 1/204 (0%)
Query: 12 VIPKYKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 71
V+ KP G++S +AL K++ LLN KKVG+TGTLDPFATG+LP+ G+ATK S YL++ D
Sbjct: 4 VLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLD 63
Query: 72 KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYK 131
K Y A I LG+ T+T D +G+I++ P E +E L F G+I QIPPMYSALK
Sbjct: 64 KEYRAEIRLGVRTDTLDPDGQIVETRPVNPT-TEDVEAALPTFRGEIEQIPPMYSALKVN 122
Query: 132 GIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLG 191
G LY+YAR GI ++RK R + +Y + + Y P LTL +HCSKGTYIR L+ D+G+ LG
Sbjct: 123 GKRLYEYARQGIEVERKARPVTVYDLQFLKYEGPELTLEVHCSKGTYIRTLARDLGEKLG 182
Query: 192 CGAHLKYLRRIGIDKLTLDKNIAI 215
CGA++ +LRR + LD+++ +
Sbjct: 183 CGAYVSHLRRTAVGDFPLDQSVTL 206
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal
domain). Members of this family are involved in
modifying bases in RNA molecules. They carry out the
conversion of uracil bases to pseudouridine. This family
includes TruB, a pseudouridylate synthase that
specifically converts uracil 55 to pseudouridine in most
tRNAs. This family also includes Cbf5p that modifies
rRNA.
Length = 149
Score = 228 bits (583), Expect = 1e-70
Identities = 74/149 (49%), Positives = 104/149 (69%)
Query: 31 KYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEAIIHLGITTETGDIE 90
K +L AKKVG+TGTLDP ATG+LP+C G+ATK YL +ADK Y A I LG+ T+T D E
Sbjct: 1 KRILGAKKVGHTGTLDPLATGVLPVCVGKATKLLQYLLDADKEYRATIRLGVATDTLDAE 60
Query: 91 GKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLYKYARSGITIKRKLR 150
G+I++ + E IE++L +F G+I Q+PPMYSA+K G LY+ AR GI ++R R
Sbjct: 61 GEIVEEPPVDHITEEKIEEVLASFTGEIEQVPPMYSAVKVNGKRLYELAREGIEVERPPR 120
Query: 151 YIKIYKITIIDYTIPYLTLRIHCSKGTYI 179
+ IY + ++++ +P +T + CSKGTYI
Sbjct: 121 PVTIYSLELLEFDLPEVTFEVSCSKGTYI 149
>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 = 218 bits (557), Expect = 2e-66
Identities = 81/191 (42%), Positives = 98/191 (51%), Gaps = 12/191 (6%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYN 271
NI II HVDHGKTTL D LL +G K AR++D + E+ERGITI S E
Sbjct: 5 NIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFETK 64
Query: 272 GTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV 331
INIIDTPGH DF E+ R S D +L++DAVEG MPQTR A LG IV
Sbjct: 65 KRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGVPIIVF 124
Query: 332 VNKIDR-SNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIP 390
+NKIDR +A E VV+ + PV+ SAL G +
Sbjct: 125 INKIDRVDDAELEEVVEEISRELLEK-YGFGGETVPVVPGSALTGE----------GIDE 173
Query: 391 LFEAILKYVPV 401
L EA+ Y+P
Sbjct: 174 LLEALDLYLPS 184
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional.
Length = 290
Score = 218 bits (558), Expect = 4e-65
Identities = 89/200 (44%), Positives = 130/200 (65%)
Query: 16 YKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYE 75
KP G++S + ++KI+ + KKVG+TGTLDP A+G+LP+C G+ATK +YL E K Y
Sbjct: 8 LKPPGMTSFDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKATKIVDYLMEGKKTYR 67
Query: 76 AIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
A I LG+ T+T D EG+I+ + + E I + +++F G+I Q+PPMYSALK G L
Sbjct: 68 AEIKLGVETDTYDREGEILKEKEVSHLTEEEIREAILSFQGEIDQVPPMYSALKINGKKL 127
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAH 195
Y+ AR GI ++R+ R I IY I I++ +PY+ + CSKGTYIR L DIG+ L CGA+
Sbjct: 128 YELARQGIEVEREARKITIYDIEILEIDLPYVIFDVKCSKGTYIRSLCFDIGEKLNCGAY 187
Query: 196 LKYLRRIGIDKLTLDKNIAI 215
+ L R ++ +I +
Sbjct: 188 MWNLIRTETGPFNIENSITL 207
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 204 bits (521), Expect = 3e-60
Identities = 81/220 (36%), Positives = 117/220 (53%), Gaps = 32/220 (14%)
Query: 12 VIPKYKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 71
VI KP G +S+ + +K +L +K G+ GTLDP ATG+LP+C GEATK YL +AD
Sbjct: 17 VINLDKPPGPTSHEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLGEATKLVQYLLDAD 76
Query: 72 KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYK 131
K Y A + LG T++ E + L F G+I QIPPM+SA+K
Sbjct: 77 KEYVATVRLGDQTDS-----------------EEEVRAALEAFTGEIYQIPPMFSAVK-- 117
Query: 132 GIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLG 191
++R R I IY + +D+ +TLR+ CSKGTYIR L+ D+G+ LG
Sbjct: 118 -----------REVER--RKITIYDLLELDFDRNLVTLRVECSKGTYIRTLARDLGEALG 164
Query: 192 CGAHLKYLRRIGIDKLTLDKNIAIIAHVDHGKTTLIDHLL 231
CGAH+ LRR + + + + + + +L+ LL
Sbjct: 165 CGAHMSELRRTRVGPFSEEDAVTLELLDELDAESLLRLLL 204
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional.
Length = 244
Score = 200 bits (509), Expect = 6e-59
Identities = 96/206 (46%), Positives = 131/206 (63%), Gaps = 8/206 (3%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP GLSSN+AL++ K ++A K G+TGTLDPFATGLL C G ATK S + EADK Y+A
Sbjct: 17 KPVGLSSNHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRATKISGRMLEADKTYQA 76
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEK-----ILINFHGKISQIPPMYSALKYK 131
+ G T++GD+ G I+ P+ +E+ +L F G I QIPPMYSALK
Sbjct: 77 TLQFGEETDSGDLTGHIV---ARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMYSALKRD 133
Query: 132 GIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLG 191
G PLY+YAR+GI + R R + I I ++ ++ + + CSKGTYIR L++DIG+ LG
Sbjct: 134 GKPLYEYARAGIELDRPPRQVTIRHIELLSFSGMQAQIDVACSKGTYIRTLAQDIGRALG 193
Query: 192 CGAHLKYLRRIGIDKLTLDKNIAIIA 217
C AHL LRR + +LD+ + + A
Sbjct: 194 CHAHLAALRRTHVGPFSLDRAVTLEA 219
>gnl|CDD|179870 PRK04642, truB, tRNA pseudouridine synthase B; Provisional.
Length = 300
Score = 197 bits (503), Expect = 2e-57
Identities = 96/218 (44%), Positives = 138/218 (63%), Gaps = 8/218 (3%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP GLSSNNAL+ + LL A+K G+TG+LDP ATGLLPLCFGEATK + L + K Y+A
Sbjct: 17 KPAGLSSNNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEATKIAGLLLGSAKAYDA 76
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPN-SIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
I LG+TT+T D +G+++ + +P+ S ++ L G+I Q P+YSALK G PL
Sbjct: 77 EIVLGVTTDTDDADGQVL-RERPVPDLSAAALQAALAPLIGRIRQRAPIYSALKQGGEPL 135
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAH 195
Y AR G I+ +R ++++ I ++ Y P L LR+ C GTYIR L+ D+G++LGCGAH
Sbjct: 136 YAKARRGEVIEAPVREVEVHAIEVLGYAAPRLRLRVTCGSGTYIRSLARDLGEVLGCGAH 195
Query: 196 LKYLRRIGIDK------LTLDKNIAIIAHVDHGKTTLI 227
+ LRR+ ++ +TL+ A + T L+
Sbjct: 196 IAALRRLWVEPFRAPQMITLEALEAALEAGAEADTLLL 233
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional.
Length = 304
Score = 193 bits (493), Expect = 9e-56
Identities = 85/207 (41%), Positives = 128/207 (61%), Gaps = 9/207 (4%)
Query: 12 VIPKYKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 71
V+ +KP G++S++ + K++ +L KKVG+TGTLDP +G+LP+C G ATK + YL++
Sbjct: 4 VLLLHKPRGMTSHDCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRATKIAEYLTDEG 63
Query: 72 KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSI--EIIEKILINFHGKISQIPPMYSALK 129
K YE + LG +T T D +G++++ K + I E IE L + G I QIPPMYSA+K
Sbjct: 64 KTYEGEVTLGFSTTTEDADGEVVE-TKPVDRPITREEIEAALASLTGTIEQIPPMYSAVK 122
Query: 130 YKGIPLYKYARSGITIKRKLRYIKIYKITIIDYT------IPYLTLRIHCSKGTYIRVLS 183
G LY+YAR+GI ++R +R I I++ ++D R+ CSKGTY+R L+
Sbjct: 123 VNGKKLYEYARAGIEVERPVRQITIHEFVLLDSREDFEGETQSFRFRVTCSKGTYVRTLA 182
Query: 184 EDIGKMLGCGAHLKYLRRIGIDKLTLD 210
IG+ LG AH+ +L R TL+
Sbjct: 183 VMIGEKLGYPAHMSHLVRTASGGFTLE 209
>gnl|CDD|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M.
tuberculosis TruB, S. cerevisiae Cbf5 and human
dyskerin. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruB, M. tuberculosis TruB and S.
cerevisiae Pus4, make psi55 in the T loop of tRNAs.
Pus4 catalyses the formation of psi55 in both
cytoplasmic and mitochondrial tRNAs. Psi55 is almost
universally conserved. S. cerevisiae Cbf5 and human
dyskerin are nucleolar proteins that, with the help of
guide RNAs, make the hundreds of psueudouridnes present
in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin
is the catalytic subunit of eukaryotic box H/ACA small
nucleolar ribonucleoprotein (snoRNP) particles.
Mutations in human dyskerin cause X-linked dyskeratosis
congenitas.
Length = 210
Score = 190 bits (483), Expect = 1e-55
Identities = 77/197 (39%), Positives = 114/197 (57%), Gaps = 2/197 (1%)
Query: 16 YKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYE 75
KP G SS++ + I+ + A+KVG+ GTLDPFATG+L + G+ATK +L A K Y
Sbjct: 6 DKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYT 65
Query: 76 AIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
AI LG T+T D G++I+ + E +E+ L G I Q+PP+YSA+K +G
Sbjct: 66 AIGRLGQATDTFDATGQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQGQRA 125
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDYTIPY--LTLRIHCSKGTYIRVLSEDIGKMLGCG 193
Y+ AR G+ + + R IY++ I + P+ L + + C GTYIR L D+G LG G
Sbjct: 126 YELARRGLLVPDEARPPTIYELLCIRFNPPHFLLEVEVVCETGTYIRTLIHDLGLELGVG 185
Query: 194 AHLKYLRRIGIDKLTLD 210
AH+ LRR + ++
Sbjct: 186 AHVTELRRTRVGPFKVE 202
>gnl|CDD|179199 PRK00989, truB, tRNA pseudouridine synthase B; Provisional.
Length = 230
Score = 189 bits (481), Expect = 4e-55
Identities = 81/210 (38%), Positives = 132/210 (62%), Gaps = 3/210 (1%)
Query: 5 SISPVSVVIPKYKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEA-TKF 63
+ ++ KP G +S + ++ + L+ KK+G+ GTLDPFATG++ + G T+
Sbjct: 4 ATESKEGILLVDKPQGRTSFSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRKFTRL 63
Query: 64 SNYLSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPP 123
S+ L DK Y A+ HLG TT++ D +GKI+ +K IP ++E + F G+I Q+PP
Sbjct: 64 SDILLFEDKEYAAVAHLGTTTDSYDCDGKIVGRSKKIP-TLEEVLSAASYFQGEIQQVPP 122
Query: 124 MYSALKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLS 183
M+SA K +G LY+YAR G++I+R+ ++++ + + Y P L + CSKGTYIR ++
Sbjct: 123 MFSAKKVQGKKLYEYARQGLSIERRPSTVQVH-LQLTKYEYPLLHFVVQCSKGTYIRSIA 181
Query: 184 EDIGKMLGCGAHLKYLRRIGIDKLTLDKNI 213
++G MLGCGA+L+ LRR+ ++D+ I
Sbjct: 182 HELGNMLGCGAYLEELRRLRSGSFSIDQCI 211
>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 = 201 bits (512), Expect = 1e-54
Identities = 150/523 (28%), Positives = 244/523 (46%), Gaps = 109/523 (20%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSI-- 268
+NI I+AH+DHGKTTL D+LL +G + +D +E E+ERGITI + N S+
Sbjct: 20 RNIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGITINAANVSMVH 79
Query: 269 EYNGTR--INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGF 326
EY G IN+IDTPGH DFGG+V R + VD ++++ AVEG MPQT V R+ALK
Sbjct: 80 EYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQALKENV 139
Query: 327 KPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQL------------------DFPVI 368
KP++ +NK+DR + + F K+ +L D V
Sbjct: 140 KPVLFINKVDRLINELKLTPQELQERFIKIITEVNKLIKAMAPEEFRDKWKVRVEDGSVA 199
Query: 369 YTSALHGYA--------------------NENSKARQGNMIPLFEAILKYVPVH------ 402
+ SA + +A E+ + PL + +L V H
Sbjct: 200 FGSAYYNWAISVPSMKKTGIGFKDIYKYCKEDKQKELAKKSPLHQVVLDMVIRHLPSPIE 259
Query: 403 -----------------------KDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSL 439
+ PL L I + + G++ +GR+ SG I+
Sbjct: 260 AQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAVGRLYSGTIRPG 319
Query: 440 QDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSK 499
+V I++ + KA+I Q+ V+ G +RV V+E +G+IV + G+++ G TIC +
Sbjct: 320 MEVYIVD----RKAKARIQQVGVYMGPERVEVDEIPAGNIVAVIGLKDAVAGETICTTVE 375
Query: 500 PNGLP---MLNIDEPTLTINFMVNNS---PLAGREGKFITT-RQIKNRLDHEIKNNIGLR 552
N P + +I EP +T+ N+ P K I RQ+ K + +
Sbjct: 376 -NITPFESIKHISEPVVTVAIEAKNTKDLP------KLIEVLRQVA-------KEDPTVH 421
Query: 553 VTQNKHDDSIYEVSGRGELHLTILIENMRRE-GYELSVSRPRVIFK-TLNG-----ELYE 605
V N+ + +SG GELHL I++E +R + G ++ S P V+++ T+ G E
Sbjct: 422 VEINEETGE-HLISGMGELHLEIIVEKIREDYGLDVETSPPIVVYRETVTGTSPVVEGKS 480
Query: 606 P--YENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRL 646
P + ++ +E + + +I ++ G + ++++ +KER RL
Sbjct: 481 PNKHNRFYIVVEPLEESVIQA---FKEGKIVDMKMKKKERRRL 520
Score = 30.3 bits (68), Expect = 5.8
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 603 LYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEF 662
L EPY+ +F+++ + G +++ R G + ++ E + V + + P + GF
Sbjct: 621 LLEPYQKVFINVPQDMMGAATREIQNRRGQILEMK-QEGDMVTIIAKAPVAEMFGFAGAI 679
Query: 663 ITLTRGTGLIS 673
T G L S
Sbjct: 680 RGATSGRCLWS 690
>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 = 180 bits (459), Expect = 1e-52
Identities = 75/191 (39%), Positives = 99/191 (51%), Gaps = 12/191 (6%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYN 271
N+ +I HVDHGKTTL LL Q+G + +D+ + E+ERGITI + E+
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 272 GTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV 331
RIN IDTPGH DF E R L+ D LL++DA EG PQTR AL G IV
Sbjct: 61 KRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGGLPIIVA 120
Query: 332 VNKIDR-SNARPEWVVDATFDLFDKLCAT-EEQLDFPVIYTSALHGYANENSKARQGNMI 389
VNKIDR + V+ +L + T + D P+I SAL G E
Sbjct: 121 VNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIE---------- 170
Query: 390 PLFEAILKYVP 400
L +AI++++P
Sbjct: 171 ELLDAIVEHLP 181
>gnl|CDD|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional.
Length = 294
Score = 182 bits (463), Expect = 8e-52
Identities = 83/226 (36%), Positives = 136/226 (60%), Gaps = 10/226 (4%)
Query: 12 VIPKYKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 71
+I K G++S++A+ K++ +L KK+G+ GTLDP G+LP+ G+AT+ Y++EA
Sbjct: 5 IINLKKEAGMTSHDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKATRLIEYMTEAG 64
Query: 72 KYYEAIIHLGITTETGDIEGKIIDFNK-NIPNSIEIIEKILINFHGKISQIPPMYSALKY 130
K YE I LG +T T D G+++ P + E +++ + +F GKI+QIPPMYSA+K
Sbjct: 65 KVYEGEITLGYSTTTEDASGEVVAETPLTQPLTEEEVDQAMTSFTGKITQIPPMYSAVKV 124
Query: 131 KGIPLYKYARSGITIKRKLRYIKIY------KITIIDYTIPYLTLRIHCSKGTYIRVLSE 184
G LY+YAR+G ++R R + IY ++ + + + R+ CSKGTY+R L+
Sbjct: 125 NGKKLYEYARAGEEVERPKRQVTIYQFERTSPLSFDEDGLCRFSFRVACSKGTYVRTLAV 184
Query: 185 DIGKMLGCGAHLKYLRRIGIDKLTLDKNIA---IIAHVDHGKTTLI 227
D+G+ LG AH+ +L R LTL++ + I V+ G+ + +
Sbjct: 185 DLGEKLGYAAHMSFLTRTASAGLTLEQAVTLEEIAEKVEAGELSFL 230
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 190 bits (484), Expect = 7e-51
Identities = 135/480 (28%), Positives = 208/480 (43%), Gaps = 127/480 (26%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSI-- 268
+NI IIAH+DHGKTTL D+LL +G + +D +E E+ RGITI + N S+
Sbjct: 21 RNIGIIAHIDHGKTTLSDNLLAGAGMISEELAGEQLALDFDEEEQARGITIKAANVSMVH 80
Query: 269 EYNGTR--INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGF 326
EY G IN+IDTPGH DFGG+V R + VD ++++DAVEG MPQT V R+AL+
Sbjct: 81 EYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQALRERV 140
Query: 327 KP----------------------------IVVVNKIDRSNARPE----WVVDATFDLFD 354
KP I VNK+ + A E W VD
Sbjct: 141 KPVLFINKVDRLIKELKLTPQEMQQRLLKIIKDVNKLIKGMAPEEFKEKWKVDVE----- 195
Query: 355 KLCATEEQLDFPVIYTSALHGYANENSKA--------------RQGNM------IPLFEA 394
D V + SAL+ +A +G PL E
Sbjct: 196 ---------DGTVAFGSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKELAEKAPLHEV 246
Query: 395 IL--------------KY-VPV--HKD------------NSNNPLQLQIISLEYSSYLGK 425
+L KY +P D + N PL + + + + G+
Sbjct: 247 VLDMVVKHLPNPIEAQKYRIPKIWKGDLNSEVGKAMLNCDPNGPLVMMVTDIIVDPHAGE 306
Query: 426 IGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGI 485
+ GR+ SG ++ Q+V ++ K ++ Q+ ++ G +R V E +G+I +TG+
Sbjct: 307 VATGRVFSGTLRKGQEVYLVGAK----KKNRVQQVGIYMGPEREEVEEIPAGNIAAVTGL 362
Query: 486 EEICIGSTICDPSKPNGLP---MLNIDEPTLTINFMVNNS---PLAGREGKFITT-RQIK 538
++ G T+ + P + +I EP +T+ N P K I RQ+
Sbjct: 363 KDARAGETVVSVE--DMTPFESLKHISEPVVTVAIEAKNPKDLP------KLIEVLRQLA 414
Query: 539 NRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGELHLTILIENMRRE-GYELSVSRPRVIFK 597
K + L V N+ + + +SG GELHL ++ ++R+ G E+ S P V+++
Sbjct: 415 -------KEDPTLVVKINE-ETGEHLLSGMGELHLEVITYRIKRDYGIEVVTSEPIVVYR 466
Score = 32.1 bits (74), Expect = 1.4
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 603 LYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEF 662
L EP + + +++ + G + +++ R G + ++E E + +E P + GF E
Sbjct: 623 LLEPIQKVDINVPQDYMGAVTREIQGRRGKILDME-QEGDMAIIEAEAPVAEMFGFAGEI 681
Query: 663 ITLTRGTGLISHVFEEYAP 681
+ T G L S F + P
Sbjct: 682 RSATEGRALWSTEFAGFEP 700
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
Length = 295
Score = 179 bits (456), Expect = 1e-50
Identities = 80/190 (42%), Positives = 117/190 (61%), Gaps = 6/190 (3%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP GL+S++ + +++ LL K+VG+ GTLDP ATG+LP+ G+AT+ YL +K Y
Sbjct: 10 KPAGLTSHDCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKATRLLPYLPG-EKTYRG 68
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPN-SIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
I G+ T T D++G+I+ ++ P+ S+ IE L F GKI Q PP YSA++ G L
Sbjct: 69 TIRFGVRTSTDDLQGEILS-SQPWPHLSLAEIETALPQFRGKIEQRPPQYSAIQVDGERL 127
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDY---TIPYLTLRIHCSKGTYIRVLSEDIGKMLGC 192
Y AR G T++ R + I+++ ++D+ P L L IHC GTYIR L+ D+G +LG
Sbjct: 128 YALARRGETMELPARTVTIFRLQLLDWRPGDQPELDLEIHCGAGTYIRSLARDLGAVLGT 187
Query: 193 GAHLKYLRRI 202
G L LRR
Sbjct: 188 GGTLAALRRT 197
>gnl|CDD|235442 PRK05389, truB, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 179 bits (456), Expect = 1e-50
Identities = 75/202 (37%), Positives = 118/202 (58%), Gaps = 8/202 (3%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP G++S A+ K+K+L +A+K G+ GTLDP A+G+LP+ GEATK Y+ + K Y
Sbjct: 20 KPAGMTSTEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEATKTVPYVMDGTKRYRF 79
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 136
+ G +T D+EG++ + P + E I L F G+I Q+PP +SA+K G Y
Sbjct: 80 TVAWGEERDTDDLEGEVTATSDVRP-TDEEIRAALPAFTGEIMQVPPQFSAIKIDGERAY 138
Query: 137 KYARSGITIKRKLRYIKIYKITIIDYTIP-YLTLRIHCSKGTYIRVLSEDIGKMLGCGAH 195
AR G T++ R ++I ++T+++ + + C KGTY+R L+ D+G+ LGC H
Sbjct: 139 DLAREGETVELPARPVEIDRLTLVERPDADHAVFEVECGKGTYVRSLARDLGRALGCYGH 198
Query: 196 LKYLRRIGI------DKLTLDK 211
+ LRR + D +TL+K
Sbjct: 199 IAALRRTRVGPFTEEDAITLEK 220
>gnl|CDD|184522 PRK14123, PRK14123, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 169 bits (431), Expect = 3e-47
Identities = 93/264 (35%), Positives = 144/264 (54%), Gaps = 25/264 (9%)
Query: 12 VIPKYKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 71
++P YK GL+S++ + K++ +L KK+G+TGTLDP G+LP+C G AT+ S+Y+ +
Sbjct: 5 ILPVYKERGLTSHDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNATRVSDYVMDMG 64
Query: 72 KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEI--IEKILINFHGKISQIPPMYSALK 129
K YEA + +G +T T D G ++ I+++L F G I QIPPMYS++K
Sbjct: 65 KAYEATVSIGRSTTTEDQTGDTLETKGVHSADFNKDDIDRLLEQFKGIIEQIPPMYSSVK 124
Query: 130 YKGIPLYKYARSGITIKRKLRYIKIYKITIIDYT-----IPYLTLRIHCSKGTYIRVLSE 184
G LY+YAR+ T++R R + I I I + +R+ C KGTYIR L+
Sbjct: 125 VNGKKLYEYARNNETVERPKRKVNIKDIGRISELDFKENECHFKIRVICGKGTYIRTLAT 184
Query: 185 DIGKMLGCGAHLKYLRRIGI------DKLTLDKNIAIIAHVDHGKTTLIDHL------LR 232
DIG LG AH+ L RI D LTL++ I + H + +L + L L+
Sbjct: 185 DIGVKLGFPAHMSKLTRIESGGFVLKDSLTLEQ----IKEL-HEQDSLQNKLFPLEYGLK 239
Query: 233 QSGTFR-KNQNINARIMDSNEIEK 255
+ + K+ +I RI++ + K
Sbjct: 240 GLPSIKIKDSHIKKRILNGQKFNK 263
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional.
Length = 308
Score = 166 bits (423), Expect = 4e-46
Identities = 80/198 (40%), Positives = 118/198 (59%), Gaps = 1/198 (0%)
Query: 16 YKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYE 75
YKP G +S++ + +++ L +KVG+ GTLDPFATG+L + +AT+ YL K Y
Sbjct: 9 YKPKGPTSHDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKATRLLEYLKNEKKVYY 68
Query: 76 AIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
+ LG+ TET DI G++++ + + E I + + +F G+ Q+PP YSA KYKG L
Sbjct: 69 VKMRLGLITETFDITGEVVE-ERECNVTEEEIREAIFSFVGEYKQVPPAYSAKKYKGERL 127
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAH 195
YK AR G I + +KIY+I I P ++ R+ S GTYIR L DIG LGCGA
Sbjct: 128 YKLAREGKIINLPPKEVKIYEIWDISIEGPDVSFRVEVSPGTYIRSLCMDIGYKLGCGAT 187
Query: 196 LKYLRRIGIDKLTLDKNI 213
L R+ + K +++ +I
Sbjct: 188 AVELVRLSVGKFSIEDSI 205
>gnl|CDD|179739 PRK04099, truB, tRNA pseudouridine synthase B; Provisional.
Length = 273
Score = 160 bits (407), Expect = 3e-44
Identities = 80/231 (34%), Positives = 118/231 (51%), Gaps = 17/231 (7%)
Query: 16 YKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYE 75
KP G+SSN L ++K KK G++GTLDPFA G+L + FG+ TK +L + K Y
Sbjct: 8 NKPAGMSSNAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQYTKLFRFLKKTPKTYR 67
Query: 76 AIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
A + LG ++ + DIE I P ++IEKIL + G+IS PP +SA K G
Sbjct: 68 ATLWLGASSPSLDIE-NIESIQIIKPFDKDLIEKILKSLQGEISYTPPKFSAKKINGKRA 126
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAH 195
Y+ AR G + K ++I+ ++ Y P+LT I S+G YIR L E I K LG
Sbjct: 127 YELARKGEEFELKPITMEIFDCKLLSYNHPFLTFEITVSEGAYIRSLGELIAKKLGVNGT 186
Query: 196 LKYLRRIG--------------IDKLTLDKNIAI--IAHVDHGKTTLIDHL 230
L L R+ ++ L L +N + +++ GK ++ L
Sbjct: 187 LSSLERLSEGKFVYENEKALNPLEYLNLPQNFYLGDKNNLELGKKLFVEDL 237
>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 = 154 bits (392), Expect = 6e-43
Identities = 65/136 (47%), Positives = 84/136 (61%), Gaps = 9/136 (6%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+NI IIAHVDHGKTTL D LL +G + AR +D+ E E+ERGITI S S+ +
Sbjct: 1 RNICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGITIKSSAISLYF 60
Query: 271 ---------NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKA 321
N IN+ID+PGH DF EV L + D L+++DAVEG QT V R+A
Sbjct: 61 EYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQTETVLRQA 120
Query: 322 LKLGFKPIVVVNKIDR 337
L+ KP++V+NKIDR
Sbjct: 121 LEERVKPVLVINKIDR 136
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional.
Length = 279
Score = 149 bits (379), Expect = 2e-40
Identities = 82/203 (40%), Positives = 115/203 (56%), Gaps = 5/203 (2%)
Query: 16 YKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYE 75
YKP G+SS +K N KK+G+TGTLDP A+GLL + E TK +YL + DK Y
Sbjct: 6 YKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKTYI 65
Query: 76 AIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
A I G + T D EG+II+ ++NI + E +E+ L N G Q+PP++SA K G
Sbjct: 66 AKIKFGFISTTYDSEGQIINVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVNGKRA 125
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDYTIP--YLTLRIHCSKGTYIRVLSEDIGKMLGCG 193
Y AR G I+ K IKI KI ++++ S+GTYIR L D+GKML G
Sbjct: 126 YDLARQGKQIELKPIEIKISKIELLNFDEKLQNCVFMWVVSRGTYIRSLIHDLGKMLKTG 185
Query: 194 AHLKYLRRI---GIDKLTLDKNI 213
A++ L R +DK L++++
Sbjct: 186 AYMSDLERTKIGNLDKNFLNQSL 208
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 157 bits (398), Expect = 7e-40
Identities = 67/154 (43%), Positives = 94/154 (61%), Gaps = 6/154 (3%)
Query: 198 YLRRIGIDKLTLDKNIAIIAHVDHGKTTLIDHLLRQSGTFRK--NQNINARIMDSNEIEK 255
R + ++++ +NI I+AH+D GKTTL + +L +G K + A MD E E+
Sbjct: 1 MARLMPLERI---RNIGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQ 57
Query: 256 ERGITIFSKNCSIEYNGT-RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQT 314
ERGITI S ++ + G RIN+IDTPGH DF EVER L ++D ++++DAVEG PQT
Sbjct: 58 ERGITITSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQT 117
Query: 315 RFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDA 348
V R+A K G I+ VNK+DR A VV+
Sbjct: 118 ETVWRQADKYGVPRILFVNKMDRLGADFYLVVEQ 151
Score = 88.5 bits (220), Expect = 5e-18
Identities = 67/262 (25%), Positives = 117/262 (44%), Gaps = 47/262 (17%)
Query: 358 ATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFEAILKYVP----------------- 400
T PV+ SA K Q PL +A++ Y+P
Sbjct: 246 GTIAGKIVPVLCGSAFKN------KGVQ----PLLDAVVDYLPSPLDVPPIKGDLDDEIE 295
Query: 401 ---VHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKI 457
+ K + PL + + ++GK+ R+ SG +KS +V+ N K K ++
Sbjct: 296 KAVLRKASDEGPLSALVFKIMTDPFVGKLTFVRVYSGTLKSGSEVL--NSTKGK--KERV 351
Query: 458 NQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINF 517
++ + G +R V+E +GDIV + G+++ G T+CD +KP L + EP +++
Sbjct: 352 GRLLLMHGNEREEVDEVPAGDIVALVGLKDATTGDTLCDENKPVILESMEFPEPVISV-- 409
Query: 518 MVNNSPLAGRE-GKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGELHLTIL 576
V P + K N+L E RV ++ + +SG GELHL I+
Sbjct: 410 AVE--PKTKADQEKLSEAL---NKLAEEDP---TFRVETDE-ETGETIISGMGELHLEII 460
Query: 577 IENMRRE-GYELSVSRPRVIFK 597
++ ++RE G E+ V +P+V ++
Sbjct: 461 VDRLKREFGVEVEVGKPQVAYR 482
Score = 38.0 bits (89), Expect = 0.023
Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 1/84 (1%)
Query: 603 LYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIE-INEKERVRLEYRIPSRGLIGFQNE 661
L EP + + E G ++ LN R G + +E ++ +P + G+ +
Sbjct: 599 LLEPIMKVEITTPEEYMGDVIGDLNSRRGQILGMEQRPGGGLDVIKAEVPLAEMFGYATD 658
Query: 662 FITLTRGTGLISHVFEEYAPFYNK 685
+ T+G S F+ Y +
Sbjct: 659 LRSATQGRASFSMEFDHYEEVPSS 682
>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 = 145 bits (369), Expect = 2e-39
Identities = 70/139 (50%), Positives = 87/139 (62%), Gaps = 4/139 (2%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKN---QNINARIMDSNEIEKERGITIFSKNCSI 268
NI I+AHVD GKTTL + LL SG R+ R DS E+E++RGITIFS S
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTR-TDSMELERQRGITIFSAVASF 59
Query: 269 EYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP 328
++ T++NIIDTPGH DF EVER LS++D +L+I AVEG QTR + R KL
Sbjct: 60 QWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILFRLLRKLNIPT 119
Query: 329 IVVVNKIDRSNARPEWVVD 347
I+ VNKIDR+ A E V
Sbjct: 120 IIFVNKIDRAGADLEKVYQ 138
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 153 bits (389), Expect = 4e-39
Identities = 96/303 (31%), Positives = 156/303 (51%), Gaps = 38/303 (12%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+N +IIAH+DHGK+TL D LL +G + + + A+++DS +IE+ERGITI ++ + Y
Sbjct: 10 RNFSIIAHIDHGKSTLADRLLELTGGLSERE-MRAQVLDSMDIERERGITIKAQAVRLNY 68
Query: 271 NGTR-----INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLG 325
+N+IDTPGH DF EV R L+ + LL++DA +G QT AL+
Sbjct: 69 KAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALENN 128
Query: 326 FKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQ 385
+ I V+NKID A PE V D+ + A++ + SA K
Sbjct: 129 LEIIPVLNKIDLPAADPERVKQEIEDIIG-IDASD------AVLVSA---------KTGI 172
Query: 386 GNMIP-LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVI 444
G I + EAI++ +P K + + PL+ I Y +YLG + + RI G +K + +
Sbjct: 173 G--IEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKIRM 230
Query: 445 MNGPDDKPNKAK--INQIRVFKGLDRVLVNEALSGDI-VLITGIEEIC---IGSTICDPS 498
M+ + ++++ +F V V+E +G++ +I GI+++ +G TI S
Sbjct: 231 MS------TGKEYEVDEVGIFTP-KMVKVDELKAGEVGYIIAGIKDVRDARVGDTITLAS 283
Query: 499 KPN 501
P
Sbjct: 284 NPA 286
Score = 34.1 bits (79), Expect = 0.29
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 21/104 (20%)
Query: 569 GELHLTILIENMRRE-GYELSVSRPRVIFK--TLNGE------------------LYEPY 607
G LH+ I+ E + RE +L + P V++K +GE + EPY
Sbjct: 349 GLLHMEIIQERLEREFDLDLITTAPSVVYKVELTDGEEIEVDNPSDLPDPNKIEEIEEPY 408
Query: 608 ENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIP 651
+ + G +M+ + G ++E ++ RV L Y +P
Sbjct: 409 VKATIITPQEYLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELP 452
>gnl|CDD|235113 PRK03287, truB, tRNA pseudouridine synthase B; Provisional.
Length = 298
Score = 144 bits (366), Expect = 2e-38
Identities = 71/201 (35%), Positives = 105/201 (52%), Gaps = 10/201 (4%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP G++S++ + + + L +KVG+ GTLDP ATG+L L ATK +L+ DK Y A
Sbjct: 16 KPAGMTSHDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERATKLLGHLTLTDKSYTA 75
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPNS---IEIIEKILINFHGKISQIPPMYSALKYKGI 133
I LG T T D EG+++ + S E I + G+I Q+P SA+K G
Sbjct: 76 TIRLGQATTTDDAEGEVL---ASADASAVTDEAIAAAVAALTGEIMQVPSAVSAIKVDGK 132
Query: 134 PLYKYARSGITIKRKLRYIKIYKITIIDY--TIPYLTL--RIHCSKGTYIRVLSEDIGKM 189
Y R+G ++ R + + + ++ ++ L + CS GTYIR L+ D+G
Sbjct: 133 RAYARVRAGEEVELPARPVTVSRFEVLAVRRDGDFIDLDVEVDCSSGTYIRALARDLGAA 192
Query: 190 LGCGAHLKYLRRIGIDKLTLD 210
LG G HL LRR + TLD
Sbjct: 193 LGVGGHLTALRRTRVGPFTLD 213
>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 = 139 bits (352), Expect = 5e-38
Identities = 70/196 (35%), Positives = 103/196 (52%), Gaps = 25/196 (12%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+N +IIAH+DHGK+TL D LL +GT + + +++DS ++E+ERGITI ++ + Y
Sbjct: 1 RNFSIIAHIDHGKSTLADRLLELTGTVSEREM-KEQVLDSMDLERERGITIKAQAVRLFY 59
Query: 271 ---NGTR--INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLG 325
+G +N+IDTPGH DF EV R L+ + LL++DA +G QT AL+
Sbjct: 60 KAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQTLANFYLALENN 119
Query: 326 FKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQ 385
+ I V+NKID A P+ V D+ E I SA K
Sbjct: 120 LEIIPVINKIDLPAADPDRVKQEIEDVLG--LDASE-----AILVSA---------KTGL 163
Query: 386 GNMIP-LFEAILKYVP 400
G + L EAI++ +P
Sbjct: 164 G--VEDLLEAIVERIP 177
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 147 bits (373), Expect = 4e-37
Identities = 93/301 (30%), Positives = 154/301 (51%), Gaps = 38/301 (12%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY- 270
N +IIAH+DHGK+TL D L+ +GT + + + A+++DS ++E+ERGITI ++ + Y
Sbjct: 9 NFSIIAHIDHGKSTLADRLIELTGTLSERE-MKAQVLDSMDLERERGITIKAQAVRLNYK 67
Query: 271 --NGTR--INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGF 326
+G +N+IDTPGH DF EV R L+ + LL++DA +G QT AL+
Sbjct: 68 AKDGETYILNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALENDL 127
Query: 327 KPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQG 386
+ I V+NKID A PE V D+ + + SA K G
Sbjct: 128 EIIPVLNKIDLPAADPERVKQEIEDVIG--IDASD-----AVLVSA---------KTGIG 171
Query: 387 NMIP-LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIM 445
I + EAI++ +P K + + PL+ I Y +Y G + + R++ G +K + +M
Sbjct: 172 --IEEVLEAIVERIPPPKGDPDAPLKALIFDSWYDNYRGVVVLVRVVDGTLKKGDKIKMM 229
Query: 446 NGPDDKPNKAK--INQIRVFKGLDRVLVNEALSGDI-VLITGIEEIC---IGSTICDPSK 499
+ + ++++ VF V V+E +G++ +I GI+++ +G TI
Sbjct: 230 S------TGKEYEVDEVGVFT-PKMVPVDELSAGEVGYIIAGIKDVRDARVGDTITLAKN 282
Query: 500 P 500
P
Sbjct: 283 P 283
>gnl|CDD|184521 PRK14122, PRK14122, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 139 bits (351), Expect = 2e-36
Identities = 72/238 (30%), Positives = 113/238 (47%), Gaps = 34/238 (14%)
Query: 12 VIPKYKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 71
V KP GL+S++ + + + L ++VG+TGTLDP ATG+L LC ++TK +LS D
Sbjct: 3 VYAVDKPLGLTSHDVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDSTKLVPFLSAED 62
Query: 72 KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYK 131
K Y A + G TT T D EG I + P + +E L F G Q+PP YSA+K
Sbjct: 63 KEYLAWVSFGATTPTLDAEGPISEEAPVSPLDEKDLEAALPGFLGLTEQVPPQYSAIKVG 122
Query: 132 GIPLYKYARSGITIKRKLRYIKIYKITIIDY----------------------------- 162
G+ Y+ AR+G ++ R + +++ ++ +
Sbjct: 123 GVRAYEAARAGGALELPARPVVYHELELLAFEPSVAPIPRPIAPSAEGWTPDPRGRPVTL 182
Query: 163 -----TIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHLKYLRRIGIDKLTLDKNIAI 215
P LR+ GTY+R + D+G LG AHL L R + + L+ +++
Sbjct: 183 PEPLGEYPTALLRLVVGSGTYVRSFARDLGAALGVPAHLSGLVRTRVGRYGLEDAVSL 240
>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 = 144 bits (364), Expect = 5e-36
Identities = 94/300 (31%), Positives = 148/300 (49%), Gaps = 34/300 (11%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+N +IIAH+DHGK+TL D LL +G + + + +++DS ++E+ERGITI ++ + Y
Sbjct: 4 RNFSIIAHIDHGKSTLADRLLEYTGAISERE-MREQVLDSMDLERERGITIKAQAVRLNY 62
Query: 271 -----NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLG 325
+N+IDTPGH DF EV R L+ + LLL+DA +G QT AL+
Sbjct: 63 KAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLALEND 122
Query: 326 FKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQ 385
+ I V+NKID +A PE V ++ E I SA K
Sbjct: 123 LEIIPVINKIDLPSADPERVKKEIEEVIG--LDASE-----AILASA---------KTGI 166
Query: 386 GNMIP-LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVI 444
G I + EAI+K VP K + + PL+ I Y +Y G + + R+ G IK +
Sbjct: 167 G--IEEILEAIVKRVPPPKGDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDKIRF 224
Query: 445 MNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDI-VLITGIEEIC---IGSTICDPSKP 500
M+ + ++++ VF +E +G++ +I GI+++ +G TI P
Sbjct: 225 MSTGKEYE----VDEVGVFT-PKLTKTDELSAGEVGYIIAGIKDVSDVRVGDTITHVKNP 279
Score = 38.5 bits (90), Expect = 0.016
Identities = 33/135 (24%), Positives = 54/135 (40%), Gaps = 22/135 (16%)
Query: 569 GELHLTILIENMRRE-GYELSVSRPRVIFK--TLNGE------------------LYEPY 607
G LH+ I+ E + RE +L + P VI++ NGE + EPY
Sbjct: 343 GLLHMEIIQERLEREFNLDLITTAPSVIYRVYLTNGEVIEVDNPSDLPDPGKIEHVEEPY 402
Query: 608 ENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIP-SRGLIGFQNEFITLT 666
+ G IM + G N+E + RV L Y +P + + F ++ +++
Sbjct: 403 VKATIITPTEYLGPIMTLCQEKRGVQTNMEYLDPNRVELIYEMPLAEIVYDFFDKLKSIS 462
Query: 667 RGTGLISHVFEEYAP 681
RG + Y P
Sbjct: 463 RGYASFDYELIGYRP 477
>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 = 133 bits (338), Expect = 5e-35
Identities = 63/138 (45%), Positives = 80/138 (57%), Gaps = 2/138 (1%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNI--NARIMDSNEIEKERGITIFSKNCSIE 269
NI IIAH+D GKTT + +L +G K + MD E E+ERGITI S +
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDWMEQERERGITIQSAATTCF 60
Query: 270 YNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 329
+ RINIIDTPGH DF EVER L ++D + + DAV G PQT V R+A + G I
Sbjct: 61 WKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQTETVWRQADRYGVPRI 120
Query: 330 VVVNKIDRSNARPEWVVD 347
VNK+DR+ A VV+
Sbjct: 121 AFVNKMDRTGADFYRVVE 138
>gnl|CDD|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional.
Length = 292
Score = 132 bits (332), Expect = 4e-34
Identities = 82/198 (41%), Positives = 108/198 (54%), Gaps = 11/198 (5%)
Query: 16 YKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYE 75
YKP G+SS + +K +L K+G+ GTLD A G+LPL GEATK L +A K Y
Sbjct: 9 YKPRGISSAKLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEATKLVQLLIDAKKTYI 68
Query: 76 AIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
+ G T++GD GK+I IP S E + F G I+QIPP +SALK G+
Sbjct: 69 FTVKFGKQTDSGDYAGKVIATKDYIP-SKEEAYAVCSKFIGNITQIPPAFSALKVNGVRA 127
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDY-----TIPYLTLRIHCSKGTYIRVLSEDIGKML 190
YK AR G ++ K R I IY + +++ T Y T CSKGTYIR L+ED+ L
Sbjct: 128 YKLAREGKEVELKPRNITIYDLKCLNFDEKNATATYYT---ECSKGTYIRTLAEDLALSL 184
Query: 191 GCGAHLKYLRR--IGIDK 206
+ LRR +GI K
Sbjct: 185 QSLGFVIELRRTQVGIFK 202
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 129 bits (328), Expect = 2e-33
Identities = 65/186 (34%), Positives = 92/186 (49%), Gaps = 35/186 (18%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP G +S+ ++ +L +K G+ GTLDP TG+LP+ G+ATK L E+ K Y
Sbjct: 29 KPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYVC 88
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 136
++HL GD+ E I K+ F G+I Q PP+ SA
Sbjct: 89 VMHL-----HGDV-------------PEEDIRKVFKEFTGEIYQKPPLKSA--------- 121
Query: 137 KYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHL 196
+KR+LR IY++ I++ + R+ C GTYIR L DIG LG GAH+
Sbjct: 122 --------VKRRLRVRTIYELEILEIDGRDVLFRVRCESGTYIRKLCHDIGLALGTGAHM 173
Query: 197 KYLRRI 202
+ LRR
Sbjct: 174 QELRRT 179
>gnl|CDD|211344 cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4.
This group consists of Eukaryotic TruB proteins similar
to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4,
makes psi55 in the T loop of both cytoplasmic and
mitochondrial tRNAs. Psi55 is almost universally
conserved. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi).
Length = 312
Score = 129 bits (327), Expect = 4e-33
Identities = 69/222 (31%), Positives = 92/222 (41%), Gaps = 39/222 (17%)
Query: 12 VIPKYKPYGLSSNNALKKIKYLLNAK-----------------------------KVGYT 42
V KP G++S L +K L K+G+
Sbjct: 2 VFAINKPSGITSAQVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHG 61
Query: 43 GTLDPFATGLLPLCFGEATKFSNYLSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPN 102
GTLDP ATG+L + G TK K YEA G +T T D EGKI+ K P
Sbjct: 62 GTLDPLATGVLVVGVGAGTKQLQDYLSCSKTYEATGLFGASTTTYDREGKIL---KKKPY 118
Query: 103 SI---EIIEKILINFHGKISQIPPMYSALKYKGIPLYKYARSGI----TIKRKLRYIKIY 155
S E IE++L F G I Q+PP+YSALK G LY+YAR G I+R+ +
Sbjct: 119 SHITREDIEEVLAKFRGDIKQVPPLYSALKMDGKRLYEYAREGKPLPRPIERRQVVVSEL 178
Query: 156 KITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHLK 197
+ P T + Y R + + +GK L A +
Sbjct: 179 LVKDWIEPGPLFTRTVEEEGKQYERSVVKMLGKELKTFAEVT 220
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 136 bits (344), Expect = 4e-33
Identities = 64/154 (41%), Positives = 88/154 (57%), Gaps = 12/154 (7%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNIN--ARIMDSNEIEKERGITIFSKNCSIE 269
NI I+AH+D GKTTL + +L +G K + + D E+ERGITI S S +
Sbjct: 10 NIGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGITIESAATSCD 69
Query: 270 YNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 329
++ RIN+IDTPGH DF GEVER L ++D +++ DAV G PQT V R+A + G +
Sbjct: 70 WDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQADRYGIPRL 129
Query: 330 VVVNKIDRSNARPEWVVDATFDLFDKLCATEEQL 363
+ +NK+DR A DLF L EE+
Sbjct: 130 IFINKMDRVGA----------DLFKVLEDIEERF 153
Score = 86.5 bits (215), Expect = 2e-17
Identities = 65/254 (25%), Positives = 111/254 (43%), Gaps = 47/254 (18%)
Query: 365 FPVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKD------------------NS 406
PV++ SAL E PL +A++ Y+P + +
Sbjct: 253 VPVLFGSALKNIGIE----------PLLDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDP 302
Query: 407 NNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNK-AKINQIRVFKG 465
PL + ++Y Y GK+ R+ SG ++ + NG K K ++ R+ G
Sbjct: 303 EKPLLALVFKVQYDPYAGKLTYLRVYSGTLR--AGSQLYNGTGGKREKVGRL--FRLQ-G 357
Query: 466 LDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVNNSPL- 524
R V+ A +GDIV + G++E+ G T+ D + P L +L EP + P
Sbjct: 358 NKREEVDRAKAGDIVAVAGLKELETGDTLHDSADPVLLELLTFPEPV----VSLAVEPER 413
Query: 525 AGREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGELHLTILIENMRRE- 583
G E K + L+ + + LRV +++ +SG GELHL + +E +RRE
Sbjct: 414 RGDEQK------LAEALEKLVWEDPSLRVEEDEETGQTI-LSGMGELHLEVALERLRREF 466
Query: 584 GYELSVSRPRVIFK 597
E++ +P+V ++
Sbjct: 467 KLEVNTGKPQVAYR 480
>gnl|CDD|237834 PRK14846, truB, tRNA pseudouridine synthase B; Provisional.
Length = 345
Score = 128 bits (322), Expect = 3e-32
Identities = 80/198 (40%), Positives = 108/198 (54%), Gaps = 11/198 (5%)
Query: 16 YKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYE 75
YKP G+SS + +K +L K+G+ GTLD A G+LP GEATK + L +A K Y
Sbjct: 9 YKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYI 68
Query: 76 AIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPL 135
+ G+ T +GD GK+I IP S E + F G ++QIPP +SALK G+
Sbjct: 69 FTVKFGMQTNSGDCAGKVIATKDCIP-SQEEAYAVCSKFIGNVTQIPPAFSALKVNGVRA 127
Query: 136 YKYARSGITIKRKLRYIKIYKITIIDY-----TIPYLTLRIHCSKGTYIRVLSEDIGKML 190
YK AR G ++ K R I IY + +++ T Y T CSKGTYIR L+ED+ L
Sbjct: 128 YKLAREGKKVELKPRNITIYDLKCLNFDEKNATATYYT---ECSKGTYIRTLAEDLALSL 184
Query: 191 GCGAHLKYLRR--IGIDK 206
+ LRR +GI K
Sbjct: 185 QSLGFVIELRRTQVGIFK 202
>gnl|CDD|239681 cd03710, BipA_TypA_C, BipA_TypA_C: a C-terminal portion of BipA or
TypA having homology to the C terminal domains of the
elongation factors EF-G and EF-2. A member of the
ribosome binding GTPase superfamily, BipA is widely
distributed in bacteria and plants. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion.
Length = 79
Score = 118 bits (299), Expect = 4e-32
Identities = 38/78 (48%), Positives = 58/78 (74%)
Query: 605 EPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEFIT 664
EP E L +D+ E G +++KL R G++ ++E + R RLE++IPSRGLIGF++EF+T
Sbjct: 1 EPIEELTIDVPEEYSGAVIEKLGKRKGEMVDMEPDGNGRTRLEFKIPSRGLIGFRSEFLT 60
Query: 665 LTRGTGLISHVFEEYAPF 682
TRGTG+++HVF+ Y P+
Sbjct: 61 DTRGTGIMNHVFDGYEPY 78
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 131 bits (331), Expect = 1e-31
Identities = 57/142 (40%), Positives = 79/142 (55%), Gaps = 16/142 (11%)
Query: 216 IAHVDHGKTTLIDHLLRQSGTFRKNQNINAR--------IMDSNEIEKERGITIFSKNCS 267
+ H GKTTL + +L +G I+ MD E+ERGI+I S +
Sbjct: 1 VGHSGAGKTTLTEAILFYTGA------IHRIGEVEDGTTTMDFMPEERERGISITSAATT 54
Query: 268 IEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK 327
E+ G +IN+IDTPGH DF GEVER L ++D ++++ AV G PQT V R+A K G
Sbjct: 55 CEWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYG-V 113
Query: 328 P-IVVVNKIDRSNARPEWVVDA 348
P I+ VNK+DR+ A V+
Sbjct: 114 PRIIFVNKMDRAGADFFRVLAQ 135
Score = 88.6 bits (221), Expect = 4e-18
Identities = 65/267 (24%), Positives = 110/267 (41%), Gaps = 66/267 (24%)
Query: 358 ATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFEAILKYVP-------VHKDNSNN-- 408
AT PV SAL + L +A++ Y+P V ++
Sbjct: 230 ATLAGEIVPVFCGSALKNKG----------VQRLLDAVVDYLPSPLEVPPVDGEDGEEGA 279
Query: 409 --------PLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQI 460
PL + ++GK+ + R+ SG +K + N K K ++ ++
Sbjct: 280 ELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSGTLKK--GDTLYNSGTGK--KERVGRL 335
Query: 461 RVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVN 520
G R V+EA++GDIV + +++ G T+CD P L + EP +
Sbjct: 336 YRMHGKQREEVDEAVAGDIVAVAKLKDAATGDTLCDKGDPILLEPMEFPEPVI------- 388
Query: 521 NSPLAGREGKFITTRQIKNRLDHE-IKNNIG--------LRVTQNKHDDS---IYEVSGR 568
LA I K++ D E + +G LRV +++ ++ I +SG
Sbjct: 389 --SLA------IEP---KDKGDEEKLSEALGKLAEEDPTLRVERDE--ETGQTI--LSGM 433
Query: 569 GELHLTILIENMRRE-GYELSVSRPRV 594
GELHL + +E ++RE G E+ P+V
Sbjct: 434 GELHLDVALERLKREYGVEVETGPPQV 460
Score = 31.2 bits (72), Expect = 2.7
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 603 LYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIE-INEKERVRLEYRIPSRGLIGFQNE 661
L EP + V + E G ++ L+ R G + +E + VR E +P + G+ +
Sbjct: 580 LLEPIMKVEVSVPEEFVGDVIGDLSSRRGRILGMESRGGGDVVRAE--VPLAEMFGYATD 637
Query: 662 FITLTRGTGLISHVFEEYAP 681
+LT+G G S F Y
Sbjct: 638 LRSLTQGRGSFSMEFSHYEE 657
>gnl|CDD|211338 cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human
dyskerin like. This group consists of eukaryotic and
archeal pseudouridine synthases similar to human
dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila
melanogaster Mfl (minifly protein). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactor is required. S.
cerevisiae Cbf5 and human dyskerin are nucleolar
proteins that, with the help of guide RNAs, make the
hundreds of psueudouridnes present in rRNA and small
nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic
subunit of eukaryotic box H/ACA small nucleolar
ribonucleoprotein (snoRNP) particles. D. melanogaster
mfl hosts in its fourth intron, a box H/AC snoRNA gene.
In addition dyskerin is likely to have a structural role
in the telomerase complex. Mutations in human dyskerin
cause X-linked dyskeratosis congenitas. Mutations in
Drosophila Mfl results in miniflies that suffer
abnormalities.
Length = 182
Score = 119 bits (301), Expect = 5e-31
Identities = 64/199 (32%), Positives = 93/199 (46%), Gaps = 37/199 (18%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP G SS+ + IK +L +K G++GTLDP TG LP+C AT+ EA K Y
Sbjct: 9 KPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVC 68
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 136
++ L D+ E + ++L F G I Q PP+ SA
Sbjct: 69 VMRL-----HDDV-------------DEEKVRRVLEEFTGAIFQRPPLISA--------- 101
Query: 137 KYARSGITIKRKLRYIKIYKITIIDY--TIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGA 194
+KR+LR IY+ +++Y + R+ C GTYIR L IG +LG GA
Sbjct: 102 --------VKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGA 153
Query: 195 HLKYLRRIGIDKLTLDKNI 213
H++ LRR + + N+
Sbjct: 154 HMQELRRTRSGPFSEEDNM 172
>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 = 128 bits (324), Expect = 9e-31
Identities = 65/159 (40%), Positives = 91/159 (57%), Gaps = 5/159 (3%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNIN--ARIMDSNEIEKERGITIFSKNCSI 268
+NI I AH+D GKTT + +L +G K ++ A MD E EKERGITI S ++
Sbjct: 11 RNIGISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITITSAATTV 70
Query: 269 EYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP 328
+ G RINIIDTPGH DF EVER L ++D + ++DAV G PQ+ V R+A +
Sbjct: 71 FWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRYEVPR 130
Query: 329 IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPV 367
I VNK+D++ A VV+ + +L A + P+
Sbjct: 131 IAFVNKMDKTGANFLRVVNQ---IKQRLGANAVPIQLPI 166
Score = 57.9 bits (140), Expect = 2e-08
Identities = 54/264 (20%), Positives = 107/264 (40%), Gaps = 66/264 (25%)
Query: 365 FPVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKD---------NSNNPLQLQI- 414
FPV+ SA + N+ + L +A++ Y+P D ++ ++ +
Sbjct: 254 FPVLCGSA---FKNKGVQL-------LLDAVVDYLPSPTDVPAIKGIDPDTEKEIERKAS 303
Query: 415 ---------ISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKG 465
+ ++G++ R+ SG +KS V N +K K ++ ++
Sbjct: 304 DDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSYV--KNSRKNK--KERVGRLVKMHA 359
Query: 466 LDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVNNSPLA 525
+R + E +GDI G+++ G T+CDP L + EP +++
Sbjct: 360 NNREEIKEVRAGDICAAIGLKDTTTGDTLCDPKIDVILERMEFPEPVISLAV-------- 411
Query: 526 GREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEV-----------SGRGELHLT 574
+ K + D E +G+ + + +D + +G GELHL
Sbjct: 412 ----------EPKTKADQE---KMGIALGKLAEEDPTFRTFTDPETGQTIIAGMGELHLD 458
Query: 575 ILIENMRRE-GYELSVSRPRVIFK 597
I+++ M+RE E +V P+V ++
Sbjct: 459 IIVDRMKREFKVEANVGAPQVAYR 482
Score = 29.8 bits (67), Expect = 6.3
Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 596 FKTLNGELYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGL 655
K N L EP + V++ E G +M L+ R G ++ +E + ++ +P +
Sbjct: 591 GKKANPVLLEPIMKVEVEVPEEYMGDVMGDLSSRRGIIEGMEARGNVQK-IKAEVPLSEM 649
Query: 656 IGFQNEFITLTRGTGLISHVFEEYA 680
G+ + + T+G G S F Y
Sbjct: 650 FGYATDLRSFTQGRGTYSMEFLHYG 674
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 128 bits (324), Expect = 1e-30
Identities = 56/138 (40%), Positives = 82/138 (59%), Gaps = 10/138 (7%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+N+++IAHVDHGK+TL D L+ ++G +AR D+ E+ERGITI S S+ Y
Sbjct: 20 RNMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIKSTGISLYY 79
Query: 271 NGTR----------INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRK 320
IN+ID+PGH DF EV L + D L+++D VEG QT V R+
Sbjct: 80 EHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGVCVQTETVLRQ 139
Query: 321 ALKLGFKPIVVVNKIDRS 338
AL+ +P++ +NK+DR+
Sbjct: 140 ALQERIRPVLFINKVDRA 157
Score = 30.8 bits (70), Expect = 3.4
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 405 NSNNPLQLQIISLEYSSYLGKI-GIGRILSGRIKSLQDVVIMNGPDDKPNK 454
+ N PL + I + +S G+ GR+ SG + + Q V I GP+ P K
Sbjct: 367 DPNGPLMMYISKMVPTSDKGRFYAFGRVFSGTVATGQKVRIQ-GPNYVPGK 416
Score = 29.6 bits (67), Expect = 8.2
Identities = 11/35 (31%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 565 VSGRGELHLTILIENMRRE--GYELSVSRPRVIFK 597
V+G GELH+ I ++++ + ++ VS P V ++
Sbjct: 524 VAGCGELHVEICLKDLEDDYANIDIIVSDPVVSYR 558
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 119 bits (299), Expect = 2e-29
Identities = 64/194 (32%), Positives = 92/194 (47%), Gaps = 35/194 (18%)
Query: 17 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 76
KP G SS+ + ++ +LN +K G+ GTLDP TG+LP+C AT+ EA K Y
Sbjct: 41 KPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERATRLVKSQQEAPKEYVC 100
Query: 77 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 136
++ L D + E I ++L F G+I Q PP+ SA
Sbjct: 101 LMRL-----HRDAKE-------------EDILRVLKEFTGRIFQRPPLKSA--------- 133
Query: 137 KYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHL 196
+KR+LR IY+ +++ + R+ C GTYIR L DIG+ LG GAH+
Sbjct: 134 --------VKRQLRVRTIYESELLEKDGKDVLFRVSCEAGTYIRKLCVDIGEALGTGAHM 185
Query: 197 KYLRRIGIDKLTLD 210
+ LRR D
Sbjct: 186 QELRRTRSGCFGED 199
>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called
TypA) having homology to domain II of the elongation
factors (EFs) EF-G and EF-Tu. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion.
Length = 86
Score = 107 bits (271), Expect = 3e-28
Identities = 44/87 (50%), Positives = 58/87 (66%), Gaps = 1/87 (1%)
Query: 410 LQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRV 469
LQ+ + +L+Y Y+G+I IGRI G +K Q V ++ D K KAKI ++ F+GL RV
Sbjct: 1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQVAVVK-RDGKIEKAKITKLFGFEGLKRV 59
Query: 470 LVNEALSGDIVLITGIEEICIGSTICD 496
V EA +GDIV I GIE+I IG TICD
Sbjct: 60 EVEEAEAGDIVAIAGIEDITIGDTICD 86
>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 = 112 bits (282), Expect = 4e-28
Identities = 50/136 (36%), Positives = 79/136 (58%), Gaps = 10/136 (7%)
Query: 211 KNIAIIAHVDHGKTTLIDHLL----RQSGTFRKNQNINARIMDSNEIEKERGITIFSKNC 266
+N+ I H+ HGKT+L+D L+ +++ + + R D+ + E+ERGI+I S
Sbjct: 1 RNVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPL-RYTDTRKDEQERGISIKSNPI 59
Query: 267 SIEYNGTR-----INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKA 321
S+ ++ INIIDTPGH +F EV L + D V+L++D VEG T + R A
Sbjct: 60 SLVLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIRHA 119
Query: 322 LKLGFKPIVVVNKIDR 337
++ G ++V+NKIDR
Sbjct: 120 IQEGLPMVLVINKIDR 135
>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 = 112 bits (283), Expect = 1e-27
Identities = 49/155 (31%), Positives = 77/155 (49%), Gaps = 14/155 (9%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINAR--------IMDSNEIEKERGITIFS 263
NIA++ H GKTTL + LL +G I+ + D + EK+R ++I +
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGA------IDRLGRVEDGNTVSDYDPEEKKRKMSIET 54
Query: 264 KNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALK 323
+E+NG +IN+IDTPG+ADF GE L VD L++++A G T V
Sbjct: 55 SVAPLEWNGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQSGVEVGTEKVWEFLDD 114
Query: 324 LGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCA 358
I+ +NK+DR+ A + + A + F +
Sbjct: 115 AKLPRIIFINKMDRARADFDKTLAALREAFGRPVV 149
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 119 bits (300), Expect = 1e-27
Identities = 62/155 (40%), Positives = 87/155 (56%), Gaps = 17/155 (10%)
Query: 199 LRRIGIDKLTLDKNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERG 258
LRRI +DK +N+++IAHVDHGK+TL D L+ +G + + R+ D+ E ERG
Sbjct: 9 LRRI-MDKKHNIRNMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERG 67
Query: 259 ITIFSKNCSIEY----------------NGTRINIIDTPGHADFGGEVERILSMVDNVLL 302
ITI S S+ Y N IN+ID+PGH DF EV L + D L+
Sbjct: 68 ITIKSTGISLYYEMTDESLKDFKGERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALV 127
Query: 303 LIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKIDR 337
++D +EG QT V R+AL +P++ VNK+DR
Sbjct: 128 VVDCIEGVCVQTETVLRQALGERIRPVLTVNKMDR 162
Score = 35.9 bits (83), Expect = 0.11
Identities = 52/218 (23%), Positives = 98/218 (44%), Gaps = 37/218 (16%)
Query: 405 NSNNPLQLQIISLEYSSYLGK-IGIGRILSGRIKSLQDVVIMNGPDDKPNKAK------I 457
+ N PL L + + +S G+ GR+ SG + + V IM GP+ P + K +
Sbjct: 371 DPNGPLMLYVSKMIPASDKGRFFAFGRVFSGTVATGMKVRIM-GPNYVPGEKKDLYVKSV 429
Query: 458 NQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGS-TICDPSKPNGLPMLNIDEPTLTIN 516
+ ++ G + V + G+ V + G+++ + T+ + + + P+ +
Sbjct: 430 QRTVIWMGKKQESVEDVPCGNTVAMVGLDQFITKNATLTNEKEVDAHPIKAM-------K 482
Query: 517 FMVNNSPLAGREGKFITTRQIKNRLDHEIKNNIGLR-------VTQNKHDDS-IYEVSGR 568
F V SP+ Q KN D K GL+ + Q ++S + ++G
Sbjct: 483 FSV--SPVVRV------AVQCKNASDLP-KLVEGLKRLAKSDPMVQCTIEESGEHIIAGA 533
Query: 569 GELHLTILIENMRRE---GYELSVSRPRVIFK-TLNGE 602
GELHL I +++++ + G E+ VS P V F+ T+ +
Sbjct: 534 GELHLEICLKDLQDDFMGGAEIKVSDPVVSFRETVLEK 571
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 118 bits (297), Expect = 3e-27
Identities = 66/147 (44%), Positives = 84/147 (57%), Gaps = 8/147 (5%)
Query: 206 KLTLDKNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNIN-----ARIMDSNEIEKERGIT 260
L +NI I+AH+D GKTT + +L +G K+ I A MD E E+ERGIT
Sbjct: 4 PLEKTRNIGIMAHIDAGKTTTTERILYYTG---KSHKIGEVHDGAATMDWMEQEQERGIT 60
Query: 261 IFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRK 320
I S + + G RINIIDTPGH DF EVER L ++D + + DAV G PQ+ V R+
Sbjct: 61 ITSAATTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWRQ 120
Query: 321 ALKLGFKPIVVVNKIDRSNARPEWVVD 347
A K G IV VNK+DR A V+
Sbjct: 121 ADKYGVPRIVFVNKMDRIGADFFRSVE 147
Score = 45.6 bits (109), Expect = 8e-05
Identities = 38/139 (27%), Positives = 61/139 (43%), Gaps = 33/139 (23%)
Query: 471 VNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVNNSPLAGREGK 530
+ E +GDI G+++ G T+CD P L + EP I+ V P
Sbjct: 364 IKEVYAGDIAAAVGLKDTTTGDTLCDEKAPIILESMEFPEPV--ISLAV--EP------- 412
Query: 531 FITTRQIKNRLDHEIKNNIGL----------RVTQNKHD-DSIYEVSGRGELHLTILIEN 579
K + D + K + L RV ++ +I +SG GELHL I+++
Sbjct: 413 -------KTKADQD-KMGLALQKLAEEDPTFRVETDEETGQTI--ISGMGELHLDIIVDR 462
Query: 580 MRRE-GYELSVSRPRVIFK 597
M+RE E +V P+V ++
Sbjct: 463 MKREFKVEANVGAPQVAYR 481
>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 = 111 bits (279), Expect = 4e-27
Identities = 55/138 (39%), Positives = 79/138 (57%), Gaps = 22/138 (15%)
Query: 214 AIIAHVDHGKTTLIDHLL------RQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCS 267
AII+H D GKTTL + LL +++G + ++ D EIEK+RGI++ S
Sbjct: 6 AIISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQ 65
Query: 268 IEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK 327
EY G IN++DTPGH DF + R L+ VD+ +++IDA +G PQTR KL F+
Sbjct: 66 FEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTR-------KL-FE 117
Query: 328 -------PIV-VVNKIDR 337
PI+ +NK+DR
Sbjct: 118 VCRLRGIPIITFINKLDR 135
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 116 bits (293), Expect = 9e-27
Identities = 66/153 (43%), Positives = 85/153 (55%), Gaps = 11/153 (7%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNI-----NARIMDSNEIEKERGITIFSKNC 266
NI I+AH+D GKTT + +L +G N I A MD E E+ERGITI S
Sbjct: 12 NIGIMAHIDAGKTTTTERILFYTG---VNHKIGEVHDGAATMDWMEQEQERGITITSAAT 68
Query: 267 SIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGF 326
+ + RINIIDTPGH DF EVER L ++D + + DAV G PQ+ V R+A K
Sbjct: 69 TCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVGGVEPQSETVWRQADKYKV 128
Query: 327 KPIVVVNKIDRSNARPEWVVDATFDLFDKLCAT 359
I VNK+DR+ A VV+ + D+L A
Sbjct: 129 PRIAFVNKMDRTGADFYRVVE---QIKDRLGAN 158
Score = 42.0 bits (100), Expect = 0.001
Identities = 52/190 (27%), Positives = 81/190 (42%), Gaps = 47/190 (24%)
Query: 422 YLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVL 481
++GK+ R+ SG ++S V +N K K +I +I R + E +GDI
Sbjct: 322 FVGKLTFFRVYSGVLESGSYV--LNSTKGK--KERIGRILQMHANKREEIKEVRAGDIAA 377
Query: 482 ITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVNNSPLAGREGKFITTRQIKNRL 541
G+++ G T+CD P L + EP I+ V P K +
Sbjct: 378 AVGLKDTTTGDTLCDEKNPIILESMEFPEP--VISVAV--EP--------------KTKA 419
Query: 542 DHEIKNNIGL----------RVTQNKHDDSIYEVSGR------GELHLTILIENMRRE-G 584
D E K I L RV+ + E +G+ GELHL I+++ M+RE
Sbjct: 420 DQE-KMGIALQKLAEEDPSFRVSTD-------EETGQTIIAGMGELHLDIIVDRMKREFK 471
Query: 585 YELSVSRPRV 594
E +V +P+V
Sbjct: 472 VEANVGKPQV 481
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 112 bits (282), Expect = 2e-26
Identities = 87/321 (27%), Positives = 131/321 (40%), Gaps = 41/321 (12%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTF---------RKNQNIN------ARIMDSNEIEKE 256
N+ I HVD GK+TL+ LL G ++ + + A ++D + E+E
Sbjct: 9 NLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTKEERE 68
Query: 257 RGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEG------- 309
RG+TI + E + IID PGH DF + S D +L++DA +G
Sbjct: 69 RGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFEAGFG 128
Query: 310 PMPQTRFVTRKALKLGFKP-IVVVNKIDR---SNARPEWVVDATFDLFDKLCATEEQLDF 365
QTR A LG K IV VNK+D R E +V L K+ + D
Sbjct: 129 VGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLL-KMVGYNPK-DV 186
Query: 366 PVIYTSALHG-YANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLG 424
P I S G + S+ P L + + + PL+L I + S +G
Sbjct: 187 PFIPISGFKGDNLTKKSENMPWYKGPTLLEALDQLEPPERPLDKPLRLPIQDVYSISGIG 246
Query: 425 KIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LI 482
+ +GR+ SG IK Q V M P +++ + +++A GD V +
Sbjct: 247 TVPVGRVESGVIKPGQKVTFM------PAGVV-GEVKSIEM-HHEEISQAEPGDNVGFNV 298
Query: 483 TGIE--EICIGSTICDPSKPN 501
G+E +I G I P
Sbjct: 299 RGVEKNDIRRGDVIGHSDNPP 319
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 107 bits (268), Expect = 2e-24
Identities = 89/304 (29%), Positives = 143/304 (47%), Gaps = 35/304 (11%)
Query: 212 NIAIIAHVDHGKTTL---IDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSI 268
N+ I HVDHGKTTL I +L + G K + + +D EK RGITI + +
Sbjct: 63 NVGTIGHVDHGKTTLTAAITKVLAEEG---KAKAVAFDEIDKAPEEKARGITIATAHVEY 119
Query: 269 EYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP 328
E +D PGHAD+ + + +D +L++ A +GPMPQT+ A ++G
Sbjct: 120 ETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPS 179
Query: 329 IVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQLDF--------PVIYTSALHGYA 377
+VV +NK+D VVD +L + L E E L F P+I SAL
Sbjct: 180 LVVFLNKVD--------VVDDE-ELLE-LVEMELRELLSFYKFPGDEIPIIRGSALSALQ 229
Query: 378 NENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIK 437
N + + ++ L +A+ +Y+P + P + I + G + GR+ G IK
Sbjct: 230 GTNDEIGKNAILKLMDAVDEYIPEPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIK 289
Query: 438 SLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGI--EEICIGST 493
++V I+ P K + + +FK ++++ +GD V L+ G+ E++ G
Sbjct: 290 VGEEVEIVGLRPGGPLKTTVTGVEMFKK----ILDQGQAGDNVGLLLRGLKREDVQRGQV 345
Query: 494 ICDP 497
IC P
Sbjct: 346 ICKP 349
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 107 bits (269), Expect = 3e-24
Identities = 54/138 (39%), Positives = 80/138 (57%), Gaps = 16/138 (11%)
Query: 211 KNIAIIAHVDHGKTTLIDHLL------RQSGTFR-KNQNINARIMDSNEIEKERGITIFS 263
+ AII+H D GKTTL + LL +++GT + + +A+ D EIEK+RGI++ S
Sbjct: 13 RTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAK-SDWMEIEKQRGISVTS 71
Query: 264 KNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTR--F-VTRK 320
+Y +N++DTPGH DF + R L+ VD+ +++IDA +G PQT F V R
Sbjct: 72 SVMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCR- 130
Query: 321 ALKLGFKPIV-VVNKIDR 337
L PI +NK+DR
Sbjct: 131 ---LRDIPIFTFINKLDR 145
Score = 29.1 bits (66), Expect = 9.4
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 453 NKAKINQIRVFKGLDRVLVNEALSGDIVLI--TGIEEICIGSTICD 496
K++ F DR V EA +GDI+ + G I IG T +
Sbjct: 337 KDVKLSDALTFMAQDRETVEEAYAGDIIGLHNHGT--IQIGDTFTE 380
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 101 bits (255), Expect = 2e-22
Identities = 56/145 (38%), Positives = 79/145 (54%), Gaps = 30/145 (20%)
Query: 211 KNIAIIAHVDHGKTTLIDHLL------RQSGTF--RKNQNINARIMDSN--EIEKERGIT 260
+ AII+H D GKTTL + LL +++GT RK+ R S+ E+EK+RGI+
Sbjct: 11 RTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSG----RHATSDWMEMEKQRGIS 66
Query: 261 IFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRK 320
+ S Y IN++DTPGH DF + R L+ VD+ L++IDA +G PQTR
Sbjct: 67 VTSSVMQFPYRDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTR----- 121
Query: 321 ALKLGFK-------PIVV-VNKIDR 337
KL + PI +NK+DR
Sbjct: 122 --KL-MEVCRLRDTPIFTFINKLDR 143
>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 = 98.8 bits (246), Expect = 8e-22
Identities = 72/258 (27%), Positives = 116/258 (44%), Gaps = 31/258 (12%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINAR---------------IMDSNEIEKE 256
N+A I HVDHGK+T + HLL + G + +MD + E+E
Sbjct: 9 NVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLKEERE 68
Query: 257 RGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGP---MPQ 313
RG+TI + E + + I+D PGH DF + S D +L++ +G PQ
Sbjct: 69 RGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFEVQPQ 128
Query: 314 TRFVTRKALKLGFKPIVV-VNKIDRSN---ARPEWVVDATFDLFDKLCATEEQLDFPVIY 369
TR A LG ++V +NK+D N E + +L K+ + + F I
Sbjct: 129 TREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPF--IP 186
Query: 370 TSALHG----YANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGK 425
SA +G +EN+ +G L EA+ P K ++ PL++ I + + +G
Sbjct: 187 ISAWNGDNVIKKSENTPWYKGKT--LLEALDALEPPEKP-TDKPLRIPIQDVYSITGVGT 243
Query: 426 IGIGRILSGRIKSLQDVV 443
+ +GR+ +G +K VV
Sbjct: 244 VPVGRVETGVLKPGDKVV 261
>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 = 96.0 bits (239), Expect = 4e-21
Identities = 89/297 (29%), Positives = 141/297 (47%), Gaps = 25/297 (8%)
Query: 212 NIAIIAHVDHGKTTL---IDHLLRQSG--TFRKNQNINARIMDSNEIEKERGITIFSKNC 266
NI I HVDHGKTTL I +L + G R I D+ EK RGITI + +
Sbjct: 14 NIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQI-----DNAPEEKARGITINTAHV 68
Query: 267 SIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGF 326
E +D PGHAD+ + + +D +L++ A +GPMPQTR A ++G
Sbjct: 69 EYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLARQVGV 128
Query: 327 KPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE-EQLDFPVIYTSALHGYANENSKAR 384
IVV +NK D + E + ++ + L + D P+I SAL A E
Sbjct: 129 PYIVVFLNKCDMVD-DEELLELVEMEVRELLSEYDFPGDDTPIIRGSALK--ALEGDAEW 185
Query: 385 QGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVI 444
+ ++ L +A+ +Y+P + ++ P + I + + G + GR+ G +K ++V I
Sbjct: 186 EAKILELMDAVDEYIPTPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVKVGEEVEI 245
Query: 445 MNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGI--EEICIGSTICDP 497
+ D + K + + +F R ++E +GD V L+ GI EEI G + P
Sbjct: 246 VGLKDTR--KTTVTGVEMF----RKELDEGRAGDNVGLLLRGIKREEIERGMVLAKP 296
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 96.1 bits (240), Expect = 5e-21
Identities = 86/271 (31%), Positives = 128/271 (47%), Gaps = 54/271 (19%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINAR---------------IMDSNEIEKE 256
N+A+I HVDHGK+TL+ LL ++G ++ R +MD + E+E
Sbjct: 8 NLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEERE 67
Query: 257 RGITI---FSKNCSIEYNGTRINIIDTPGHADFGGEVERIL---SMVDNVLLLIDA--VE 308
RG+TI K + +Y T I+D PGH DF V+ ++ S D +L++ A
Sbjct: 68 RGVTIDLAHKKFETDKYYFT---IVDCPGHRDF---VKNMITGASQADAAVLVVAADDAG 121
Query: 309 GPMPQTR---FVTRKALKLGFKP-IVVVNKIDRSN---ARPEWVVDATFDLFDKLCATEE 361
G MPQTR F+ R LG IV +NK+D N R E V + L + +
Sbjct: 122 GVMPQTREHVFLAR---TLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPD 178
Query: 362 QLDFPVIYTSALHGYANENSKARQGNMIP------LFEAILKYVPVHKDNSNNPLQLQII 415
D P I SA G +N + NM P L EA L + + ++ PL++ I
Sbjct: 179 --DIPFIPVSAFEG---DNVVKKSENM-PWYNGPTLLEA-LDNLKPPEKPTDKPLRIPIQ 231
Query: 416 SLEYS-SYLGKIGIGRILSGRIKSLQDVVIM 445
+ YS S +G + +GR+ +G +K VV M
Sbjct: 232 DV-YSISGVGTVPVGRVETGVLKVGDKVVFM 261
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 93.5 bits (233), Expect = 3e-20
Identities = 84/307 (27%), Positives = 138/307 (44%), Gaps = 45/307 (14%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEI---EKERGITIFSKNCSI 268
N+ I HVDHGKTTL + + K A+ D + EK RGITI + +
Sbjct: 14 NVGTIGHVDHGKTTLTAAI---TTVLAKKGGAEAKAYDQIDNAPEEKARGITINTAHVEY 70
Query: 269 EYNGTRINIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFVTRKAL 322
E +D PGHAD+ + +M+ D +L++ A +GPMPQTR A
Sbjct: 71 ETANRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVAATDGPMPQTREHILLAR 124
Query: 323 KLGFKPIVV-VNKIDRSNARP--EWVVDATFDLFDKLCATEEQLDF-----PVIYTSALH 374
++G IVV +NK+D + E V +L + F P+I SAL
Sbjct: 125 QVGVPYIVVFLNKVDMVDDEELLELVEMEVRELL-------SEYGFPGDDTPIIRGSALK 177
Query: 375 GYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSG 434
A E + + L +A+ Y+P + + + P + + + S G + GR+ G
Sbjct: 178 --ALEGDAKWEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERG 235
Query: 435 RIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGI--EEICI 490
+K ++V I+ + + K + + +F R L++E +GD V L+ G+ E++
Sbjct: 236 ILKVGEEVEIVGIKETQ--KTTVTGVEMF----RKLLDEGQAGDNVGVLLRGVKREDVER 289
Query: 491 GSTICDP 497
G + P
Sbjct: 290 GQVLAKP 296
>gnl|CDD|201388 pfam00679, EFG_C, Elongation factor G C-terminus. This domain
includes the carboxyl terminal regions of Elongation
factor G, elongation factor 2 and some tetracycline
resistance proteins and adopt a ferredoxin-like fold.
Length = 89
Score = 85.3 bits (212), Expect = 3e-20
Identities = 26/80 (32%), Positives = 40/80 (50%)
Query: 602 ELYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNE 661
L EP + + + E G ++ LN R G++ ++E + RV +E +P L GF E
Sbjct: 1 VLLEPIMKVEITVPEEYLGDVIGDLNQRRGEILDMEPDGGGRVVIEAEVPLAELFGFSTE 60
Query: 662 FITLTRGTGLISHVFEEYAP 681
+LT+G G S F Y P
Sbjct: 61 LRSLTQGRGSFSMEFSGYEP 80
>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 = 88.7 bits (221), Expect = 8e-20
Identities = 61/211 (28%), Positives = 87/211 (41%), Gaps = 45/211 (21%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGT--------FRKN-QNIN------ARIMDSNEIEKE 256
N+ +I HVD GK+TL HLL + G + K + + A ++D + E+E
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 257 RGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEG- 309
RG+TI E R IID PGH DF + +M+ D +L++ A +G
Sbjct: 61 RGVTIDVGLAKFETEKYRFTIIDAPGHRDF------VKNMITGASQADVAVLVVSARKGE 114
Query: 310 ------PMPQTRFVTRKALKLGFKP-IVVVNKIDR-----SNARPEWVVDATFDLFDKLC 357
QTR A LG K IV VNK+D S R + + K+
Sbjct: 115 FEAGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVG 174
Query: 358 ATEEQLDFPVIYTSALHGYANENSKARQGNM 388
+ D P I S G +N + NM
Sbjct: 175 YNPK--DVPFIPISGFTG---DNLIEKSENM 200
>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 = 86.0 bits (214), Expect = 2e-19
Identities = 51/167 (30%), Positives = 70/167 (41%), Gaps = 21/167 (12%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKE-RGIT--IFSKNCSIE 269
+ ++ HVDHGKTTL+D + RK +N E GIT I + I+
Sbjct: 3 VTVMGHVDHGKTTLLDKI-------RK----------TNVAAGEAGGITQHIGAYQVPID 45
Query: 270 YNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 329
I IDTPGH F R S+ D +L++ A +G MPQT A I
Sbjct: 46 VKIPGITFIDTPGHEAFTNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVPII 105
Query: 330 VVVNKIDRSNARPEWVVDATFDLFDKLCATEEQL-DFPVIYTSALHG 375
V +NKID+ +L + EE D ++ SA G
Sbjct: 106 VAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTG 152
>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 = 91.5 bits (227), Expect = 3e-19
Identities = 53/147 (36%), Positives = 77/147 (52%), Gaps = 14/147 (9%)
Query: 211 KNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINAR------IMDSNEIEKERGITIFSK 264
+ AII+H D GKTT+ + +L G + + R D E+EK+RGI+I +
Sbjct: 12 RTFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTS 71
Query: 265 NCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRF---VTRKA 321
Y +N++DTPGH DF + R L+ VDN L++IDA +G +TR VTR
Sbjct: 72 VMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTR-- 129
Query: 322 LKLGFKPIVV-VNKIDRSNARPEWVVD 347
L PI +NK+DR P ++D
Sbjct: 130 --LRDTPIFTFMNKLDRDIRDPLELLD 154
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 86.6 bits (215), Expect = 6e-18
Identities = 92/305 (30%), Positives = 137/305 (44%), Gaps = 55/305 (18%)
Query: 212 NIAIIAHVDHGKTTL---IDHLLRQSGT--FRKNQNINARIMDSNEIEKERGITIFSKNC 266
NI I HVDHGKTTL I L G +K I DS EK RGITI + +
Sbjct: 14 NIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEI-----DSAPEEKARGITINTAHV 68
Query: 267 SIEYNGTRINIIDTPGHADFGGEVERILSM------VDNVLLLIDAVEGPMPQTRFVTRK 320
E +D PGHAD+ + +M +D +L++ A +GPMPQT+
Sbjct: 69 EYETENRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTKEHILL 122
Query: 321 ALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQLDF-----PVIYTSA 372
A ++G IVV +NK D+ V D +L E + DF P++ SA
Sbjct: 123 AKQVGVPNIVVFLNKEDQ-------VDDEELLELVELEVRELLSKYDFPGDDIPIVSGSA 175
Query: 373 LHG--YANENSKARQGN------MIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLG 424
L EN K ++G + L +A+ Y+P + +++ P + I + + G
Sbjct: 176 LLALEALTENPKIKRGENKWVDKIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRG 235
Query: 425 KIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVF-KGLDRVLVNEALSGDIV--L 481
+ GRI G +K + D V + G + + + +F K LD E L+GD V L
Sbjct: 236 TVATGRIERGTVK-VGDTVEIVGLRETKT-TTVTGLEMFQKTLD-----EGLAGDNVGIL 288
Query: 482 ITGIE 486
+ GI+
Sbjct: 289 LRGIQ 293
>gnl|CDD|238772 cd01514, Elongation_Factor_C, Elongation factor G C-terminus. This
domain includes the carboxyl terminal regions of
elongation factors (EFs) bacterial EF-G, eukaryotic and
archeal EF-2 and eukaryotic mitochondrial mtEFG1s and
mtEFG2s. This group also includes proteins similar to
the ribosomal protection proteins Tet(M) and Tet(O),
BipA, LepA and, spliceosomal proteins: human 116kD U5
small nuclear ribonucleoprotein (snRNP) protein (U5-116
kD) and yeast counterpart Snu114p. This domain adopts a
ferredoxin-like fold consisting of an alpha-beta
sandwich with anti-parallel beta-sheets, resembling the
topology of domain III found in the elongation factors
EF-G and eukaryotic EF-2, with which it forms the
C-terminal block. The two domains however are not
superimposable and domain III lacks some of the
characteristics of this domain. EF-2/EF-G in complex
with GTP, promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site, the uncharged tRNA
from the P site to the E-site and, the mRNA is shifted
one codon relative to the ribosome. Tet(M) and Tet(O)
mediate Tc resistance. Typical Tcs bind to the ribosome
and inhibit the elongation phase of protein synthesis,
by inhibiting the occupation of site A by
aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release
of tetracycline (Tc) from the ribosome in a
GTP-dependent manner. BipA is a highly conserved
protein with global regulatory properties in Escherichia
coli. Yeast Snu114p is essential for cell viability and
for splicing in vivo. Experiments suggest that GTP
binding and probably GTP hydrolysis is important for the
function of the U5-116 kD/Snu114p. The function of LepA
proteins is unknown.
Length = 79
Score = 78.3 bits (194), Expect = 8e-18
Identities = 20/77 (25%), Positives = 36/77 (46%)
Query: 605 EPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEFIT 664
EP + + + E G ++ L+ R G++ +E RV ++ +P + GF + +
Sbjct: 1 EPIMKVEITVPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPLAEMFGFATDLRS 60
Query: 665 LTRGTGLISHVFEEYAP 681
LT+G S F Y P
Sbjct: 61 LTQGRASFSMEFSHYEP 77
>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 = 80.3 bits (199), Expect = 1e-17
Identities = 52/169 (30%), Positives = 74/169 (43%), Gaps = 36/169 (21%)
Query: 218 HVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY----NGT 273
H+DHGKTTLI + + D EK+RGITI + Y +G
Sbjct: 7 HIDHGKTTLI-------------KALTGIETDRLPEEKKRGITI---DLGFAYLDLPDGK 50
Query: 274 RINIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFVTRKALKLGFK 327
R+ ID PGH F + +M+ D VLL++ A EG MPQTR LG K
Sbjct: 51 RLGFIDVPGHEKF------VKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIK 104
Query: 328 P-IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHG 375
+VV+ K D + + ++ + L T D P+ S++ G
Sbjct: 105 KGLVVLTKADL--VDEDRLELVEEEILELLAGTFLA-DAPIFPVSSVTG 150
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 84.2 bits (209), Expect = 3e-17
Identities = 94/315 (29%), Positives = 150/315 (47%), Gaps = 61/315 (19%)
Query: 212 NIAIIAHVDHGKTTL---IDHLL--RQSGTFRKNQNINARIMDSNEIEKERGITIFSKNC 266
NI I HVDHGKTTL I +L R + +I D+ EKERGITI N
Sbjct: 14 NIGTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSI-----DAAPEEKERGITI---NT 65
Query: 267 S-IEYN-GTR-INIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFV 317
+ +EY R +D PGHAD+ + +M+ D +L++ A +GPMPQTR
Sbjct: 66 AHVEYETEKRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVAATDGPMPQTREH 119
Query: 318 TRKALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQL--------DFP 366
A ++G +VV +NK+D +VD +L + L E E L D P
Sbjct: 120 ILLARQVGVPYLVVFLNKVD--------LVDDE-ELLE-LVEMEVRELLSEYDFPGDDIP 169
Query: 367 VIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKI 426
VI SAL A E + ++ L +A+ +Y+P + +++ P + + + + G +
Sbjct: 170 VIRGSALK--ALEGDPKWEDAIMELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGRGTV 227
Query: 427 GIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITG 484
GR+ G +K +V I+ + + K + + +F R L++E +GD V L+ G
Sbjct: 228 VTGRVERGTVKVGDEVEIVGIKETQ--KTVVTGVEMF----RKLLDEGQAGDNVGVLLRG 281
Query: 485 I--EEICIGSTICDP 497
+ +E+ G + P
Sbjct: 282 VDRDEVERGQVLAKP 296
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 83.5 bits (206), Expect = 1e-16
Identities = 78/291 (26%), Positives = 139/291 (47%), Gaps = 19/291 (6%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYN 271
NI I HVDHGKTTL L + + +D+ E+ RGITI + E
Sbjct: 83 NIGTIGHVDHGKTTLTAALTMALASMGGSAPKKYDEIDAAPEERARGITINTATVEYETE 142
Query: 272 GTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV 331
+D PGHAD+ + + +D +L++ +GPMPQT+ A ++G +VV
Sbjct: 143 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVV 202
Query: 332 -VNKIDRSNARPEWVVDATFDLFDKLCATE-EQLDFPVIYTSALHGYAN--ENSKARQGN 387
+NK D+ + E + ++ + L + E D P+I SAL EN ++G+
Sbjct: 203 FLNKQDQVDDE-ELLELVELEVRELLSSYEFPGDDIPIISGSALLALEALMENPNIKRGD 261
Query: 388 ------MIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQD 441
+ L +A+ Y+P+ + ++ P L + + + G + GR+ G +K + +
Sbjct: 262 NKWVDKIYELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTVK-VGE 320
Query: 442 VVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGIEEICI 490
V + G + + + + +F+ +++EAL+GD V L+ GI++ I
Sbjct: 321 TVDIVGLRETRS-TTVTGVEMFQK----ILDEALAGDNVGLLLRGIQKADI 366
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 82.7 bits (205), Expect = 1e-16
Identities = 89/321 (27%), Positives = 137/321 (42%), Gaps = 64/321 (19%)
Query: 218 HVDHGKTTLIDHLLRQSGTFRKNQ-----NINAR------------IMDSNEIEKERGIT 260
VD GK+TLI LL + ++Q + R ++D E E+E+GIT
Sbjct: 14 SVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQGIT 73
Query: 261 I------FS--KNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMP 312
I FS K I I DTPGH + + S D +LL+DA +G +
Sbjct: 74 IDVAYRYFSTEKRKFI--------IADTPGHEQYTRNMATGASTADLAILLVDARKGVLE 125
Query: 313 QTRFVTRKALKLGFKPIVV-VNKID---RSNARPEWVVDATFDLFDKLCATEEQLDFPVI 368
QTR + A LG + +VV VNK+D S E +V +L + + I
Sbjct: 126 QTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVR----FI 181
Query: 369 YTSALHGYANENSKARQGNMIPLFE-----AILKYVPVHKDNSNNPLQL--QIISLEYSS 421
SAL G +N ++ NM P ++ IL+ V + D S + Q ++
Sbjct: 182 PISALLG---DNVVSKSENM-PWYKGPTLLEILETVEIADDRSAKAFRFPVQYVNRPNLD 237
Query: 422 YLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVL 481
+ G G I SG +K +VV++ P K +++ +I F G + +A +G+ V
Sbjct: 238 FRGY--AGTIASGSVKVGDEVVVL--PSGK--TSRVKRIVTFDG----ELAQASAGEAVT 287
Query: 482 ITGIEEICI--GSTICDPSKP 500
+ +EI I G I P
Sbjct: 288 LVLADEIDISRGDLIVAADAP 308
>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 = 73.9 bits (182), Expect = 2e-15
Identities = 45/187 (24%), Positives = 68/187 (36%), Gaps = 58/187 (31%)
Query: 210 DKNIAIIAHVDHGKTTLIDHLL--------RQSGTFRKNQNINARIMDSNEIEKERGITI 261
+ I I+ + GK+TL++ LL + GT R + +E G T
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTR---------NYVTTVIEEDGKTY 51
Query: 262 FSKNCSIEYNGTRINIIDTPGHADF-------GGEVERILSMVDNVLLLIDAVEGPMPQT 314
+ N++DT G D+ VE L + D V+L++D E QT
Sbjct: 52 ------------KFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQT 99
Query: 315 RFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF------PVI 368
+ + + G I+V NKID + DA T F P+I
Sbjct: 100 KEIIH-HAESGVPIILVGNKID--------LRDAKLK-------THVAFLFAKLNGEPII 143
Query: 369 YTSALHG 375
SA G
Sbjct: 144 PLSAETG 150
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 78.3 bits (194), Expect = 3e-15
Identities = 93/315 (29%), Positives = 144/315 (45%), Gaps = 59/315 (18%)
Query: 212 NIAIIAHVDHGKTTL---IDHLLRQSG--TFRKNQNINARIMDSNEIEKERGITIFSKNC 266
N+ I HVDHGKTTL I +L + G + I D+ EK RGITI N
Sbjct: 14 NVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQI-----DNAPEEKARGITI---NT 65
Query: 267 S-IEYNGTRINI--IDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFV 317
S +EY + +D PGHAD+ + +M+ D +L++ A +GPMPQTR
Sbjct: 66 SHVEYETANRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTREH 119
Query: 318 TRKALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQL--------DFP 366
A ++G IVV +NK D V D +L + L E E L D P
Sbjct: 120 ILLARQVGVPYIVVFLNKCDM-------VDDE--ELLE-LVEMEVRELLSKYDFPGDDTP 169
Query: 367 VIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKI 426
+I SAL ++ + + ++ L +A+ Y+P + + P + I + S G +
Sbjct: 170 IIRGSALKALEGDDDEEWEAKILELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTV 229
Query: 427 GIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITG 484
GR+ G +K +V I+ G + K + + +F R L++E +GD V L+ G
Sbjct: 230 VTGRVERGIVKVGDEVEIV-GIKE-TQKTTVTGVEMF----RKLLDEGQAGDNVGVLLRG 283
Query: 485 I--EEICIGSTICDP 497
E++ G + P
Sbjct: 284 TKREDVERGQVLAKP 298
>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 = 77.2 bits (190), Expect = 1e-14
Identities = 47/129 (36%), Positives = 55/129 (42%), Gaps = 14/129 (10%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYN 271
IA HVDHGKTTL+ L I A D EK+RG+TI
Sbjct: 2 IIATAGHVDHGKTTLLKAL----------TGIAA---DRLPEEKKRGMTIDLGFAYFPLP 48
Query: 272 GTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP-IV 330
R+ ID PGH F +D LL++DA EG M QT LG IV
Sbjct: 49 DYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTIV 108
Query: 331 VVNKIDRSN 339
V+ K DR N
Sbjct: 109 VITKADRVN 117
>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 = 71.5 bits (176), Expect = 4e-14
Identities = 53/140 (37%), Positives = 71/140 (50%), Gaps = 29/140 (20%)
Query: 212 NIAIIAHVDHGKTTL---IDHLLRQSG--TFRKNQNINARIMDSNEIEKERGITIFSKNC 266
N+ I HVDHGKTTL I +L + G +K I D EK RGITI N
Sbjct: 4 NVGTIGHVDHGKTTLTAAITKVLAKKGGAKAKKYDEI-----DKAPEEKARGITI---NT 55
Query: 267 S-IEYNGTRINI--IDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFV 317
+ +EY + +D PGHAD+ I +M+ D +L++ A +GPMPQTR
Sbjct: 56 AHVEYETANRHYAHVDCPGHADY------IKNMITGAAQMDGAILVVSATDGPMPQTREH 109
Query: 318 TRKALKLGFKPIVV-VNKID 336
A ++G IVV +NK D
Sbjct: 110 LLLARQVGVPYIVVFLNKAD 129
>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 = 69.8 bits (171), Expect = 7e-14
Identities = 39/191 (20%), Positives = 75/191 (39%), Gaps = 37/191 (19%)
Query: 214 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 273
++ GK++L++ LL S+ R ++ K ++
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEV-----------SDVPGTTRDPDVYVK--ELDKGKV 47
Query: 274 RINIIDTPGHADFGG-----EVERILSMVDNVLLLIDAVEGPMPQT-RFVTRKALKLGFK 327
++ ++DTPG +FGG +L D +LL++D+ + + + + + L+
Sbjct: 48 KLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGI 107
Query: 328 PIVVV-NKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQG 386
PI++V NKID R + +L + L PV SA G
Sbjct: 108 PIILVGNKIDLLEEREVEELLRLEEL-------AKILGVPVFEVSAKTGE---------- 150
Query: 387 NMIPLFEAILK 397
+ LFE +++
Sbjct: 151 GVDELFEKLIE 161
>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 = 70.3 bits (173), Expect = 1e-13
Identities = 60/212 (28%), Positives = 86/212 (40%), Gaps = 57/212 (26%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSG----------TFRKNQNINAR------IMDSNEIEK 255
VD GK+TLI LL S K+ ++D + E+
Sbjct: 1 RFITCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAER 60
Query: 256 ERGITI------FS--KNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAV 307
E+GITI FS K I I DTPGH + + S D +LL+DA
Sbjct: 61 EQGITIDVAYRYFSTPKRKFI--------IADTPGHEQYTRNMVTGASTADLAILLVDAR 112
Query: 308 EGPMPQTR---FVTRKALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCA----T 359
+G + QTR ++ LG + +VV VNK+D +VD ++F+++ A
Sbjct: 113 KGVLEQTRRHSYIAS---LLGIRHVVVAVNKMD--------LVDYDEEVFEEIKADYLAF 161
Query: 360 EEQLDFPVIY---TSALHGYANENSKARQGNM 388
L I SAL G +N +R NM
Sbjct: 162 AASLGIEDITFIPISALEG---DNVVSRSENM 190
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 72.9 bits (180), Expect = 2e-13
Identities = 95/320 (29%), Positives = 144/320 (45%), Gaps = 69/320 (21%)
Query: 212 NIAIIAHVDHGKTTL---IDHLL--RQSGTFRKNQNINARIMDSNEIEKERGITIFSKNC 266
N+ I HVDHGKTTL I +L + + I D EK RGITI N
Sbjct: 14 NVGTIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQI-----DKAPEEKARGITI---NT 65
Query: 267 S-IEYN-GTR-INIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFV 317
+ +EY R +D PGHAD+ + +M+ D +L++ A +GPMPQTR
Sbjct: 66 AHVEYETEKRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTREH 119
Query: 318 TRKALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQL--------DFP 366
A ++G IVV +NK D V D +L + L E E L D P
Sbjct: 120 ILLARQVGVPYIVVFLNKCDM-------VDDE--ELLE-LVEMEVRELLSKYDFPGDDTP 169
Query: 367 VIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQI-----ISLEYSS 421
+I SAL ++ + + ++ L +A+ Y+P + + P + I IS
Sbjct: 170 IIRGSALKALEGDDDEEWEKKILELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGR--- 226
Query: 422 YLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV- 480
G + GR+ G IK ++V I+ D + K + + +F R L++E +GD V
Sbjct: 227 --GTVVTGRVERGIIKVGEEVEIVGIRDTQ--KTTVTGVEMF----RKLLDEGQAGDNVG 278
Query: 481 -LITGI--EEICIGSTICDP 497
L+ GI E++ G + P
Sbjct: 279 ALLRGIKREDVERGQVLAKP 298
>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 = 69.7 bits (171), Expect = 2e-12
Identities = 84/301 (27%), Positives = 136/301 (45%), Gaps = 46/301 (15%)
Query: 219 VDHGKTTLIDHLLRQSGTFRKNQ----------------NIN-ARIMDSNEIEKERGITI 261
VD GK+TLI LL + ++Q I+ A ++D + E+E+GITI
Sbjct: 9 VDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQGITI 68
Query: 262 FSKNCSIEYNGT--RINII-DTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVT 318
+ + Y T R I+ DTPGH + + S D +LL+DA +G + QTR +
Sbjct: 69 ---DVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRRHS 125
Query: 319 RKALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYA 377
A LG + +V+ VNK+D + E V + + D I SAL G
Sbjct: 126 YIASLLGIRHVVLAVNKMDLVDYDEE-VFENIKKDYLAFAEQLGFRDVTFIPLSALKG-- 182
Query: 378 NENSKARQGNMIPLFEA-----ILKYVPVHKDNSNNPLQL--QIISLEYSSYLGKIGIGR 430
+N +R +M P + IL+ V V +D + PL+ Q ++ + G G
Sbjct: 183 -DNVVSRSESM-PWYSGPTLLEILETVEVERDAQDLPLRFPVQYVNRPNLDFRGYAGT-- 238
Query: 431 ILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICI 490
I SG + +VV++ P + +++ +I F G + +A +G V +T +EI I
Sbjct: 239 IASGSVHVGDEVVVL--PSGR--SSRVARIVTFDG----DLEQARAGQAVTLTLDDEIDI 290
Query: 491 G 491
Sbjct: 291 S 291
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 69.9 bits (172), Expect = 3e-12
Identities = 50/146 (34%), Positives = 71/146 (48%), Gaps = 46/146 (31%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKE-RGIT--I--FSKNCS 267
+ I+ HVDHGKT+L+D + RK +N E GIT I +
Sbjct: 252 VTIMGHVDHGKTSLLDAI-------RK----------TNVAAGEAGGITQHIGAY----Q 290
Query: 268 IEYNGTRINIIDTPGHADF------GGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKA 321
+E NG +I +DTPGH F G +V I V+L++ A +G MPQ T +A
Sbjct: 291 VETNGGKITFLDTPGHEAFTAMRARGAQVTDI------VVLVVAADDGVMPQ----TIEA 340
Query: 322 L---KLGFKPIVV-VNKIDRSNARPE 343
+ K PI+V +NKID+ A P+
Sbjct: 341 INHAKAAGVPIIVAINKIDKPGANPD 366
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 68.5 bits (168), Expect = 4e-12
Identities = 68/237 (28%), Positives = 100/237 (42%), Gaps = 64/237 (27%)
Query: 212 NIAIIAHVDHGKTTLIDHL-----LRQSGTFRKNQNI-----NARIMDSNEIEKERGITI 261
NI ++ HVDHGKTTL L R S ++ I +A+I E + T
Sbjct: 12 NIGMVGHVDHGKTTLTKALSGVWTDRHSEELKRGITIKLGYADAKIYKCPECYRPECYTT 71
Query: 262 --FSKNCSIEYNGTR-INIIDTPGHADFGGEVERILS---MVDNVLLLIDAVEG-PMPQT 314
NC E R ++ +D PGH + +LS ++D LL+I A E P PQT
Sbjct: 72 EPKCPNCGAETELVRRVSFVDAPGHETL---MATMLSGAALMDGALLVIAANEPCPQPQT 128
Query: 315 R--FVTRKALK-LGFKPIVVV-NKID---RSNARPEWVVDATFDLFDKLCATEEQLDF-- 365
R + AL+ +G K I++V NKID R A + E+ +F
Sbjct: 129 REHLM---ALEIIGIKNIIIVQNKIDLVSRERALENY---------------EQIKEFVK 170
Query: 366 -------PVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQII 415
P+I SA H N+ L EAI KY+P + + + P ++ +
Sbjct: 171 GTVAENAPIIPISAQHKA----------NIDALIEAIEKYIPTPERDLDKPPRMYVA 217
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 69.1 bits (170), Expect = 4e-12
Identities = 46/140 (32%), Positives = 65/140 (46%), Gaps = 31/140 (22%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNG 272
+ I+ HVDHGKTTL+D +R++ N+ A ++ I + G +
Sbjct: 8 VTIMGHVDHGKTTLLDK-IRKT-------NVAAG--EAGGITQHIGAYQVPLD---VIKI 54
Query: 273 TRINIIDTPGHADF------GGEVERILSMVDNVLLLIDAVEGPMPQTR--FVTRKALKL 324
I IDTPGH F G V I +L++ A +G MPQT KA +
Sbjct: 55 PGITFIDTPGHEAFTAMRARGASVTDI------AILVVAADDGVMPQTIEAINHAKAAGV 108
Query: 325 GFKPIVV-VNKIDRSNARPE 343
PIVV +NKID+ A P+
Sbjct: 109 ---PIVVAINKIDKPEANPD 125
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 68.6 bits (167), Expect = 4e-12
Identities = 71/258 (27%), Positives = 107/258 (41%), Gaps = 37/258 (14%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKN---------QNINAR------IMDSNEIEKE 256
NI +I HVD GK+T HL+ + G K +N R ++D + E+E
Sbjct: 9 NIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLDKLKAERE 68
Query: 257 RGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMP---- 312
RGITI E +ID PGH DF + S D +L+ID+ G
Sbjct: 69 RGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEAGIS 128
Query: 313 ---QTRFVTRKALKLGFKPIV-VVNKIDR-----SNARPEWVVDATFDLFDKLCATEEQL 363
QTR A LG K ++ NK+D S AR + +V K+ +++
Sbjct: 129 KDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPDKI 188
Query: 364 DFPVIYTSALHGYANENSKARQGNMI----PLFEAILKYVPVHKDNSNNPLQLQIISLEY 419
F I G+ +N R N+ P L + K S+ PL+L + +
Sbjct: 189 PFVPI-----SGFEGDNMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYK 243
Query: 420 SSYLGKIGIGRILSGRIK 437
+G + +GR+ +G IK
Sbjct: 244 IGGIGTVPVGRVETGVIK 261
>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 = 68.6 bits (168), Expect = 6e-12
Identities = 44/135 (32%), Positives = 60/135 (44%), Gaps = 19/135 (14%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKER-GITIFSKNCSIEYN 271
+ I+ HVDHGKT+L+D I + + E GIT +E
Sbjct: 90 VTIMGHVDHGKTSLLDS-----------------IRKTKVAQGEAGGITQHIGAYHVENE 132
Query: 272 -GTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 330
G I +DTPGH F R + D V+L++ A +G MPQT A IV
Sbjct: 133 DGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIV 192
Query: 331 VVNKIDRSNARPEWV 345
+NKID+ A P+ V
Sbjct: 193 AINKIDKPEANPDRV 207
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 65.9 bits (161), Expect = 3e-11
Identities = 69/259 (26%), Positives = 107/259 (41%), Gaps = 39/259 (15%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSG-----TFRKNQNINARI----------MDSNEIEKE 256
N+ +I HVD GK+T HL+ + G T K + A + +D + E+E
Sbjct: 9 NLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERE 68
Query: 257 RGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMP---- 312
RGITI E IID PGH DF + S D +L++ + G
Sbjct: 69 RGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGIS 128
Query: 313 ---QTRFVTRKALKLGFKPIVV-VNKIDR-----SNARPEWVVDATFDLFDKLCATEEQL 363
QTR A LG K ++V +NK+D S R + + K+ E++
Sbjct: 129 KDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKV 188
Query: 364 DFPVIYTSALHGYANENSKARQGNMI-----PLFEAILKYVPVHKDNSNNPLQLQIISLE 418
F I G+ +N + NM L EA+ P K + PL+L + +
Sbjct: 189 PFIPI-----SGWQGDNMIEKSDNMPWYKGPTLLEALDTLEP-PKRPVDKPLRLPLQDVY 242
Query: 419 YSSYLGKIGIGRILSGRIK 437
+G + +GR+ +G +K
Sbjct: 243 KIGGIGTVPVGRVETGILK 261
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 66.1 bits (162), Expect = 3e-11
Identities = 88/348 (25%), Positives = 139/348 (39%), Gaps = 89/348 (25%)
Query: 219 VDHGKTTLIDHLLRQSGTFRKNQ-----NINARI------------MDSNEIEKERGITI 261
VD GK+TLI LL + ++Q N + R +D + E+E+GITI
Sbjct: 36 VDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQAEREQGITI 95
Query: 262 ------FSKNCSIEYNGTRINII-DTPGHADF------GGEVERILSMVDNVLLLIDAVE 308
FS R II DTPGH + G S D +LLIDA +
Sbjct: 96 DVAYRYFSTE-------KRKFIIADTPGHEQYTRNMATGA------STCDLAILLIDARK 142
Query: 309 GPMPQTRFVTRKALKLGFKPIVV-VNKID---RSNARPEWVVDATFDLFDKLCATEEQLD 364
G + QTR + A LG K +VV VNK+D S E + + ++L LD
Sbjct: 143 GVLDQTRRHSFIATLLGIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAEQL---PGNLD 199
Query: 365 FPVIYTSALHGYANENSKARQGNM-----IPLFEAILKYVPVHKDNSNNPLQL--QIIS- 416
+ SAL G +N ++ +M L E +L+ V + + P + Q ++
Sbjct: 200 IRFVPLSALEG---DNVVSQSESMPWYSGPTLLE-VLETVDIQRVVDAQPFRFPVQYVNR 255
Query: 417 --LEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEA 474
L++ Y G + SG +K V ++ P K ++ + +I F G D EA
Sbjct: 256 PNLDFRGYAGTLA-----SGVVKVGDRVKVL--PSGK--ESNVARIVTFDG-DL---EEA 302
Query: 475 LSGDIVLITGIEEICI--GSTICDPSKPNGLPMLNIDEPTLTINFMVN 520
+G+ + + +EI I G + + + +
Sbjct: 303 FAGEAITLVLEDEIDISRGDLLVAAD----------EALQAVQHASAD 340
>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 = 65.5 bits (160), Expect = 4e-11
Identities = 67/234 (28%), Positives = 98/234 (41%), Gaps = 54/234 (23%)
Query: 210 DKNIAIIAHVDHGKTTLIDHL-----LRQSGTFRKNQNI-----NARIMDSNEIEKERGI 259
+ NI ++ HVDHGKTTL L S ++ +I +A I E +
Sbjct: 4 EVNIGMVGHVDHGKTTLTKALTGVWTDTHSEELKRGISIRLGYADAEIYKCPECDGPECY 63
Query: 260 TIFSK--NCSIEYNGTR-INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEG-PMPQTR 315
T NC E R ++ +D PGH + +++D LL+I A E P PQTR
Sbjct: 64 TTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQPQTR 123
Query: 316 FVTRKALKL-GFKPIVVV-NKIDRSNARPEWVVDATFDLFDKLCATE--EQL-------- 363
AL++ G K IV+V NKID L K A E E++
Sbjct: 124 -EHLMALEIIGIKNIVIVQNKID---------------LVSKEKALENYEEIKEFVKGTI 167
Query: 364 --DFPVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQII 415
+ P+I SALH N+ L EAI K++P + + + P + +
Sbjct: 168 AENAPIIPVSALHN----------ANIDALLEAIEKFIPTPERDLDKPPLMYVA 211
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 64.7 bits (158), Expect = 7e-11
Identities = 52/180 (28%), Positives = 75/180 (41%), Gaps = 22/180 (12%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYN 271
I H+DHGKTTL+ + + + D EK+RGITI +
Sbjct: 2 IIGTAGHIDHGKTTLL-------------KALTGGVTDRLPEEKKRGITIDLGFYYRKLE 48
Query: 272 GTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK-PIV 330
+ ID PGH DF + L +D LL++ A EG M QT LG K I+
Sbjct: 49 DGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGII 108
Query: 331 VVNKIDRSN-ARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMI 389
V+ K DR + AR E + ++ A + + TSA G E K +++
Sbjct: 109 VLTKADRVDEARIEQKI-------KQILADLSLANAKIFKTSAKTGRGIEELKNELIDLL 161
>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 = 61.2 bits (149), Expect = 1e-10
Identities = 43/142 (30%), Positives = 64/142 (45%), Gaps = 29/142 (20%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITI---FS----- 263
N+ ++ HVD GKT+L L + T D N +ERGIT+ FS
Sbjct: 2 NVGLLGHVDSGKTSLAKALSEIAST---------AAFDKNPQSQERGITLDLGFSSFEVD 52
Query: 264 ------KNCSIEYNGTRINIIDTPGHADFGGEVERILS---MVDNVLLLIDAVEGPMPQT 314
N + + +I ++D PGHA + I+ ++D +LL++DA +G QT
Sbjct: 53 KPKHLEDNENPQIENYQITLVDCPGHASL---IRTIIGGAQIIDLMLLVVDAKKGIQTQT 109
Query: 315 RFVTRKALKLGFKPIVVVNKID 336
L IVV+NKID
Sbjct: 110 AECLVIGELLCKPLIVVLNKID 131
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 64.1 bits (156), Expect = 2e-10
Identities = 45/135 (33%), Positives = 59/135 (43%), Gaps = 20/135 (14%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGIT--IFSKNCSIEY 270
+ I+ HVDHGKTTL+D + RK Q GIT I + EY
Sbjct: 247 VTILGHVDHGKTTLLDKI-------RKTQIAQKEA---------GGITQKIGAYEVEFEY 290
Query: 271 NGTRINII--DTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP 328
I+ DTPGH F R ++ D +L+I A +G PQT
Sbjct: 291 KDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPI 350
Query: 329 IVVVNKIDRSNARPE 343
IV +NKID++NA E
Sbjct: 351 IVAINKIDKANANTE 365
>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 = 60.4 bits (147), Expect = 2e-10
Identities = 57/242 (23%), Positives = 82/242 (33%), Gaps = 101/242 (41%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITI--------FS 263
NI I HV HGKTTL+ + ++ ++ E +R ITI
Sbjct: 2 NIGTIGHVAHGKTTLV-------------KALSGVWTVRHKEELKRNITIKLGYANAKIY 48
Query: 264 K-------NCSIEYNGTR------------INIIDTPGHADFGGEVERIL--------SM 296
K ++ +D PGH IL ++
Sbjct: 49 KCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGH--------EILMATMLSGAAV 100
Query: 297 VDNVLLLIDAVEG-PMPQTR--FVTRKALK-LGFKPIVVV-NKID---RSNARPEWVVDA 348
+D LLLI A E P PQT AL+ +G K I+++ NKID A +
Sbjct: 101 MDGALLLIAANEPCPQPQTSEHLA---ALEIMGLKHIIILQNKIDLVKEEQALENY---- 153
Query: 349 TFDLFDKLCATEEQLDF---------PVIYTSALHGYANENSKARQGNMIPLFEAILKYV 399
E+ +F P+I SA Y N+ L E I+K +
Sbjct: 154 -----------EQIKEFVKGTIAENAPIIPISAQLKY----------NIDVLCEYIVKKI 192
Query: 400 PV 401
P
Sbjct: 193 PT 194
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is involved
in binding to charged tRNA. Domain II is found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This group also includes the C2
subdomain of domain IV of IF-2 that has the same fold as
domain II of (EF-Tu). Like IF-2 from certain prokaryotes
such as Thermus thermophilus, mitochondrial IF-2 lacks
domain II, which is thought to be involved in binding
of E.coli IF-2 to 30S subunits.
Length = 83
Score = 56.6 bits (137), Expect = 3e-10
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 410 LQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRV 469
L+ + + G + GR+ SG +K V + P K K+ ++ FKG
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVG--PGGGGVKGKVKSLKRFKG---- 54
Query: 470 LVNEALSGDIVLITG--IEEICIGSTICD 496
V+EA++GDIV I ++I IG T+ D
Sbjct: 55 EVDEAVAGDIVGIVLKDKDDIKIGDTLTD 83
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 61.9 bits (151), Expect = 8e-10
Identities = 78/315 (24%), Positives = 128/315 (40%), Gaps = 78/315 (24%)
Query: 183 SEDIGKMLGCGAHLKYLRRIGIDKLTLDKNIAIIAHVDHGKTTLIDHLL----------- 231
+EDI L LR VD GK+TLI LL
Sbjct: 9 AEDILAYLAQHERKSLLR------------FITCGSVDDGKSTLIGRLLYDSKMIFEDQL 56
Query: 232 -------RQSGTFRKNQNIN-ARIMDSNEIEKERGITIFSKNCSIEYNGT--RINII-DT 280
++ GT + I+ A ++D E+E+GITI + + Y T R I+ DT
Sbjct: 57 AALERDSKKVGT--QGDEIDLALLVDGLAAEREQGITI---DVAYRYFATPKRKFIVADT 111
Query: 281 PGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV-VNKIDRSN 339
PGH + + S D ++L+DA +G + QTR + A LG + +V+ VNK+D
Sbjct: 112 PGHEQYTRNMVTGASTADLAIILVDARKGVLTQTRRHSFIASLLGIRHVVLAVNKMD--- 168
Query: 340 ARPEWVVDATFDLFDKLCAT----EEQLDFPVIYT---SALHGYANENSKARQGNMIPLF 392
+VD ++FD++ A +L + SAL G +N R M P +
Sbjct: 169 -----LVDYDQEVFDEIVADYRAFAAKLGLHDVTFIPISALKG---DNVVTRSARM-PWY 219
Query: 393 E-----AILKYVPVHKDNSNNPLQL--QII---SLEYSSYLGKIGIGRIL---------S 433
E L+ V + D + + Q + +L++ + G + G + S
Sbjct: 220 EGPSLLEHLETVEIASDRNLKDFRFPVQYVNRPNLDFRGFAGTVASGVVRPGDEVVVLPS 279
Query: 434 GRIKSLQDVVIMNGP 448
G+ ++ +V +G
Sbjct: 280 GKTSRVKRIVTPDGD 294
>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 = 61.0 bits (148), Expect = 2e-09
Identities = 44/134 (32%), Positives = 65/134 (48%), Gaps = 12/134 (8%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRK-----NQNINARIMDSNEIEKERGITIFSKNCS 267
++++ HVDHGKTTL+D +R S ++ Q+I A + + IE G K
Sbjct: 7 VSVLGHVDHGKTTLLDK-IRGSAVAKREAGGITQHIGATEIPMDVIEGICG--DLLKKFK 63
Query: 268 IEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTR--KALKLG 325
I + IDTPGH F +R ++ D +L++D EG PQT+ + K
Sbjct: 64 IRLKIPGLLFIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYKTP 123
Query: 326 FKPIVVVNKIDRSN 339
F +V NKIDR
Sbjct: 124 F--VVAANKIDRIP 135
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 59.9 bits (146), Expect = 2e-09
Identities = 66/235 (28%), Positives = 96/235 (40%), Gaps = 90/235 (38%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITI--------FS 263
NI ++ HVDHGKTTL+ L +G + D + E +RGITI
Sbjct: 11 NIGMVGHVDHGKTTLVQAL---TGVW----------TDRHSEELKRGITIRLGYADATIR 57
Query: 264 K--NC----------SIEYNGT------RINIIDTPGHADFGGEV--ERILS---MVDNV 300
K +C G+ R++ +D PGH E +LS ++D
Sbjct: 58 KCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGH-----ETLMATMLSGAALMDGA 112
Query: 301 LLLIDAVEG-PMPQTR--FVTRKALK-LGFKPIVVV-NKIDRSNARPEWVVDATFDLFDK 355
+L+I A E P PQT+ + AL +G K IV+V NKID +V ++
Sbjct: 113 ILVIAANEPCPQPQTKEHLM---ALDIIGIKNIVIVQNKID--------LVSK-----ER 156
Query: 356 LCATEEQL----------DFPVIYTSALHGYANENSKARQGNMIPLFEAILKYVP 400
EQ+ + P+I SALH N+ L EAI + +P
Sbjct: 157 ALENYEQIKEFVKGTVAENAPIIPVSALHKV----------NIDALIEAIEEEIP 201
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 59.8 bits (146), Expect = 3e-09
Identities = 46/145 (31%), Positives = 67/145 (46%), Gaps = 38/145 (26%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRK-----NQNINARIMDSNEIEKERGITIFSKNCS 267
+ ++ HVDHGKTTL+D +R + K Q+I A + + IEK G
Sbjct: 9 VVVLGHVDHGKTTLLDK-IRGTAVAAKEAGGITQHIGATEVPIDVIEKIAG-------PL 60
Query: 268 IEYNGTRINI-----IDTPGHADF------GGEVERILSMVDNVLLLIDAVEGPMPQTRF 316
+ ++ I IDTPGH F GG ++ D +L++D EG PQ
Sbjct: 61 KKPLPIKLKIPGLLFIDTPGHEAFTNLRKRGG------ALADIAILVVDINEGFQPQ--- 111
Query: 317 VTRKALKL--GFK-P-IVVVNKIDR 337
T +A+ + K P +V NKIDR
Sbjct: 112 -TIEAINILKRRKTPFVVAANKIDR 135
>gnl|CDD|239671 cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: this subfamily
represents domain II of elongation factor (EF) EF-2
found eukaryotes and archaea and, the C-terminal portion
of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. During the process of peptide
synthesis and tRNA site changes, the ribosome is moved
along the mRNA a distance equal to one codon with the
addition of each amino acid. This translocation step is
catalyzed by EF-2_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Yeast Snu114p is essential for cell viability and for
splicing in vivo. U5-116 kD binds GTP. Experiments
suggest that GTP binding and probably GTP hydrolysis is
important for the function of the U5-116 kD/Snu114p.
Length = 93
Score = 53.0 bits (128), Expect = 9e-09
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 424 GKIGIGRILSGRIKSLQDVVIMN-----GPDDKPNKAKINQIRVFKGLDRVLVNEALSGD 478
G I GR+ SG I+ Q V ++ ++ +K I ++ + G R V+E +G+
Sbjct: 16 GFIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGN 75
Query: 479 IVLITGIEEICIGSTICD 496
IVLI G++++ G+T
Sbjct: 76 IVLIVGLDQLKSGTTATI 93
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 51.9 bits (125), Expect = 1e-08
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 424 GKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLIT 483
G + GR+ SG +K VVI P+ K ++ + +F G R V A +G I+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIG--PNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGI 58
Query: 484 GIEEICIGSTIC 495
G+++I G T+
Sbjct: 59 GLKDIKRGDTLT 70
Score = 27.2 bits (61), Expect = 7.5
Identities = 8/46 (17%), Positives = 17/46 (36%)
Query: 233 QSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRINII 278
+SGT +K + + + + + +F + G II
Sbjct: 9 ESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGII 54
>gnl|CDD|239755 cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the
domain II of elongation factor G (EF-G) in bacteria and,
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2)_like proteins found in
eukaryotes. During the process of peptide synthesis and
tRNA site changes, the ribosome is moved along the mRNA
a distance equal to one codon with the addition of each
amino acid. In bacteria this translocation step is
catalyzed by EF-G_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Eukaryotic cells harbor 2 protein synthesis systems: one
localized in the cytoplasm, the other in the
mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. mtEFG1 and mtEFG2 show significant
homology to bacterial EF-Gs. Mutants in yeast mtEFG1
have impaired mitochondrial protein synthesis,
respiratory defects and a tendency to lose mitochondrial
DNA. No clear phenotype has been found for mutants in
the yeast homologue of mtEFG2, MEF2.
Length = 83
Score = 51.7 bits (125), Expect = 2e-08
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 422 YLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVL 481
++GK+ R+ SG +K+ + N K K ++ ++ G + V EA +GDI
Sbjct: 13 FVGKLSFVRVYSGTLKA--GSTLYNSTKGK--KERVGRLLRMHGKKQEEVEEAGAGDIGA 68
Query: 482 ITGIEEICIGSTICD 496
+ G+++ G T+CD
Sbjct: 69 VAGLKDTATGDTLCD 83
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 56.2 bits (136), Expect = 4e-08
Identities = 40/117 (34%), Positives = 53/117 (45%), Gaps = 40/117 (34%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY-- 270
IA HVDHGKTTL+ Q+ T +NA D EK+RG+TI + Y
Sbjct: 3 IATAGHVDHGKTTLL-----QAIT-----GVNA---DRLPEEKKRGMTI-----DLGYAY 44
Query: 271 ----NGTRINIIDTPGHADF--------GGEVERILSMVDNVLLLIDAVEGPMPQTR 315
+G + ID PGH F GG +D+ LL++ +G M QTR
Sbjct: 45 WPQPDGRVLGFIDVPGHEKFLSNMLAGVGG--------IDHALLVVACDDGVMAQTR 93
>gnl|CDD|211345 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine synthase,
humanTRUB2_like. This group consists of eukaryotic
pseudouridine synthases similar to human TruB
pseudouridine synthase homolog 2 (TRUB2). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi).
Length = 226
Score = 52.0 bits (125), Expect = 2e-07
Identities = 48/201 (23%), Positives = 75/201 (37%), Gaps = 19/201 (9%)
Query: 16 YKPYGLSSNNALKKI-----KYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 70
YKP G+ + I KY K + LD F++G+L L K ++L
Sbjct: 6 YKPPGVHWKHVRDTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGNKLLSHLYSN 65
Query: 71 D--KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSAL 128
+ Y LG TE G++I+ + E IE++L Q A
Sbjct: 66 HPTRVYTIRGLLGKATENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQQ-----KAF 120
Query: 129 KYKGIPL-----YKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGT--YIRV 181
+ + + A G+ IY I ++++ P TL + C T Y+R
Sbjct: 121 ELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLEFRPPEFTLEVQCINETQEYLRK 180
Query: 182 LSEDIGKMLGCGAHLKYLRRI 202
L +IG L A +RR
Sbjct: 181 LIHEIGLELRSSAVCTQVRRT 201
>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 = 50.6 bits (122), Expect = 4e-07
Identities = 35/199 (17%), Positives = 67/199 (33%), Gaps = 38/199 (19%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYN 271
+A++ GK+TL++ LL + E+ + + Y
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGE------------------EVLPTGVTPTTAVITVLRY- 42
Query: 272 GTR--INIIDTPG-------HADFGGEVERILSMVDNVLLLIDAVEGPMPQT--RFVTRK 320
G + ++DTPG H + E L D V+ ++ A + P+ ++ F+
Sbjct: 43 GLLKGVVLVDTPGLNSTIEHHTE---ITESFLPRADAVIFVLSA-DQPLTESEREFLKEI 98
Query: 321 ALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTS---ALHGYA 377
G K V+NKID + E + + + + S AL
Sbjct: 99 LKWSGKKIFFVLNKIDLL-SEEELEEVLEYSREELGVLELGGGEPRIFPVSAKEALEARL 157
Query: 378 NENSKARQGNMIPLFEAIL 396
+ + + + E L
Sbjct: 158 QGDEELLEQSGFEELEEHL 176
>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 = 52.4 bits (127), Expect = 5e-07
Identities = 39/160 (24%), Positives = 62/160 (38%), Gaps = 35/160 (21%)
Query: 268 IEYNGTRINIIDTPGHADFGGE--------VERILSMVDNVLLLIDAVEGPMPQTRFVTR 319
E+ G +IDT G + E + D +L ++D EG P+ + +
Sbjct: 42 AEWGGREFILIDTGGIEEDDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAK 101
Query: 320 KALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFP-VIYTSALHGYAN 378
K G I+V NKID + + V A F L F I SA HG
Sbjct: 102 WLRKSGKPVILVANKID--GKKED-AVAAEF----------YSLGFGEPIPISAEHGR-- 146
Query: 379 ENSKARQGNMIPLFEAILKYVP---VHKDNSNNPLQLQII 415
+ L +AIL+ +P ++ + P+++ II
Sbjct: 147 --------GIGDLLDAILELLPEEEEEEEEEDGPIKIAII 178
Score = 47.8 bits (115), Expect = 1e-05
Identities = 54/185 (29%), Positives = 76/185 (41%), Gaps = 52/185 (28%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQ--------SGTFRKNQNINARIMDSNEIEKERGITIFSK 264
IAII + GK+TL++ LL + +GT R DS +I
Sbjct: 175 IAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTR----------DSIDIP---------- 214
Query: 265 NCSIEYNGTRINIIDTPG-----HADFGGE------VERILSMVDNVLLLIDAVEGPMPQ 313
E NG + +IDT G G E + + D VLL++DA EG Q
Sbjct: 215 ---FERNGKKYTLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQ 271
Query: 314 TRFVTRKALKLGFKPIVVVNKID--RSNARPEWVVDATFDLFDKLCATEEQLDF-PVIYT 370
+ AL+ G ++VVNK D + E +L KL LDF P+++
Sbjct: 272 DLRIAGLALEAGKALVIVVNKWDLVKDEKTREEFKK---ELRRKL----PFLDFAPIVFI 324
Query: 371 SALHG 375
SAL G
Sbjct: 325 SALTG 329
>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 = 49.7 bits (120), Expect = 7e-07
Identities = 50/179 (27%), Positives = 76/179 (42%), Gaps = 37/179 (20%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNG 272
IAII + GK++L++ LL + R++ S+ G T S + EY+G
Sbjct: 5 IAIIGRPNVGKSSLLNALLGEE-----------RVIVSDI----AGTTRDSIDVPFEYDG 49
Query: 273 TRINIIDTPG-----HADFGGE------VERILSMVDNVLLLIDAVEGPMPQTRFVTRKA 321
+ +IDT G G E + + D VLL++DA EG Q +
Sbjct: 50 QKYTLIDTAGIRKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQDLRIAGLI 109
Query: 322 LKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF----PVIYTSALHGY 376
L+ G I+VVNK D + T F+K +L F P+++ SAL G
Sbjct: 110 LEEGKALIIVVNKWDLVEKDEK-----TMKEFEKE--LRRKLPFLDYAPIVFISALTGQ 161
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 50.4 bits (122), Expect = 1e-06
Identities = 33/107 (30%), Positives = 46/107 (42%), Gaps = 19/107 (17%)
Query: 297 VDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKL 356
VD VL ++DA E P F+ K K+ I+V+NKID + E L L
Sbjct: 85 VDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKIDLVKDKEE--------LLPLL 136
Query: 357 CATEEQLDF-PVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVH 402
E +DF ++ SAL G N+ L + I KY+P
Sbjct: 137 EELSELMDFAEIVPISALKGD----------NVDELLDVIAKYLPEG 173
>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 = 47.1 bits (113), Expect = 5e-06
Identities = 45/165 (27%), Positives = 61/165 (36%), Gaps = 36/165 (21%)
Query: 222 GKTTLIDHLLRQ--SGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRINIID 279
GK+TL++ L+ Q S K Q RI RGI +I +D
Sbjct: 15 GKSTLLNALVGQKISIVSPKPQTTRNRI---------RGIYTDDD--------AQIIFVD 57
Query: 280 TPG-HADFGG-------EVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV 331
TPG H L VD VL ++DA E F+ K I+V
Sbjct: 58 TPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTPVILV 117
Query: 332 VNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF-PVIYTSALHG 375
+NKID + + L +KL +E F + SAL G
Sbjct: 118 LNKIDLVKDKEDL-----LPLLEKL---KELHPFAEIFPISALKG 154
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 46.5 bits (111), Expect = 6e-06
Identities = 34/109 (31%), Positives = 52/109 (47%), Gaps = 20/109 (18%)
Query: 290 VERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDAT 349
V RI+ D VL ++DA + + ++R + R AL+LG K I+V+NK D P V++
Sbjct: 5 VRRIIKEADVVLEVVDARDPELTRSRKLERMALELGKKLIIVLNKADLV---PREVLEKW 61
Query: 350 FDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFEAILKY 398
++F E PV+Y SA + R G I L I +
Sbjct: 62 KEVF-------ESEGLPVVYVSA---------RERLGTRI-LRRTIKEL 93
>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 = 46.3 bits (111), Expect = 7e-06
Identities = 30/117 (25%), Positives = 42/117 (35%), Gaps = 22/117 (18%)
Query: 268 IEYNGTRINIIDTPGHADFGGE--------VERILSMVDNVLLLIDAVEGPMPQTRFVTR 319
E+ G +IDT G E + D +L ++D EG P + +
Sbjct: 40 AEWGGREFILIDTGGIEPDDEGISKEIREQAEIAIEEADVILFVVDGREGLTPADEEIAK 99
Query: 320 KALKLGFKPIVVVNKIDRSNARPEWVVDATFDL-FDKLCATEEQLDFPVIYTSALHG 375
K I+VVNKID N + E + L F + I SA HG
Sbjct: 100 YLRKSKKPVILVVNKID--NIKEEEEAAEFYSLGFGE-----------PIPISAEHG 143
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 48.5 bits (117), Expect = 9e-06
Identities = 57/203 (28%), Positives = 84/203 (41%), Gaps = 55/203 (27%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNG 272
IAII + GK++LI+ LL + R++ S+ G T S + E +G
Sbjct: 176 IAIIGRPNVGKSSLINALLGEE-----------RVIVSDI----AGTTRDSIDTPFERDG 220
Query: 273 TRINIIDTPG-------HADFGGEVE--------RILSMVDNVLLLIDAVEGPMPQTRFV 317
+ +IDT G VE + + D VLL+IDA EG Q +
Sbjct: 221 QKYTLIDTAGIRRKGKVTEG----VEKYSVIRTLKAIERADVVLLVIDATEGITEQDLRI 276
Query: 318 TRKALKLGFKPIV-VVNKIDRSNARPEWVVDATFDLFDKLCATE-EQLDF-PVIYTSALH 374
AL+ G + +V VVNK D V + T + F K LD+ P+++ SAL
Sbjct: 277 AGLALEAG-RALVIVVNKWDL-------VDEKTMEEFKKELRRRLPFLDYAPIVFISALT 328
Query: 375 GYANENSKARQGNMIPLFEAILK 397
G + L EAI +
Sbjct: 329 GQ----------GVDKLLEAIDE 341
Score = 44.3 bits (106), Expect = 2e-04
Identities = 38/159 (23%), Positives = 62/159 (38%), Gaps = 34/159 (21%)
Query: 268 IEYNGTRINIIDTPG----HADFGGEV----ERILSMVDNVLLLIDAVEGPMPQTRFVTR 319
E+ G +IDT G F ++ E + D +L ++D G P + +
Sbjct: 44 AEWLGREFILIDTGGIEPDDDGFEKQIREQAELAIEEADVILFVVDGRAGLTPADEEIAK 103
Query: 320 KALKLGFKP-IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYAN 378
K KP I+VVNK+D + ++ F L E SA HG
Sbjct: 104 ILRKSN-KPVILVVNKVDGPDEE-----ADAYE-FYSLGLGE------PYPISAEHGR-- 148
Query: 379 ENSKARQGNMIPLFEAILKYVPVHK--DNSNNPLQLQII 415
+ L +AIL+ +P + D + P+++ II
Sbjct: 149 --------GIGDLLDAILEELPEEEEEDEEDEPIKIAII 179
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 48.3 bits (116), Expect = 9e-06
Identities = 35/121 (28%), Positives = 50/121 (41%), Gaps = 19/121 (15%)
Query: 277 IIDTPGHADFG--GE--VER---ILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 329
+IDT G D G GE VE+ +L D LL++DA GP + + + I
Sbjct: 59 LIDTAGLDDEGELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKIPYI 118
Query: 330 VVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMI 389
VV+NKID E E++ P I+ SAL G + K ++
Sbjct: 119 VVINKIDLGEESAELEKL------------EKKFGLPPIFVSALTGEGIDELKEAIIELL 166
Query: 390 P 390
P
Sbjct: 167 P 167
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 48.3 bits (116), Expect = 1e-05
Identities = 56/208 (26%), Positives = 83/208 (39%), Gaps = 63/208 (30%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNG 272
IAII + GK++LI+ +L + R++ S+ G T S + E +G
Sbjct: 181 IAIIGRPNVGKSSLINAILGEE-----------RVIVSDI----AGTTRDSIDIEFERDG 225
Query: 273 TRINIIDTPG---HADFGGEVE--------RILSMVDNVLLLIDAVEGPMPQTRFVTRKA 321
+ +IDT G VE + + D VLL+IDA EG Q +
Sbjct: 226 RKYVLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLI 285
Query: 322 LKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEE-----------QLDF-PVIY 369
+ G ++VVNK W DL ++ AT E LDF P+++
Sbjct: 286 EEAGRGIVIVVNK---------W------DLVEEDEATMEEFKKKLRRKLPFLDFAPIVF 330
Query: 370 TSALHGYANENSKARQGNMIPLFEAILK 397
SAL G + LFEAI +
Sbjct: 331 ISALTGQ----------GLDKLFEAIKE 348
Score = 44.1 bits (105), Expect = 2e-04
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 267 SIEYNGTRINIIDTPGHADFGGE---------VERILSMVDNVLLLIDAVEGPMPQTRFV 317
E+ G +IDT G D + + D +L ++D EG P +
Sbjct: 45 DAEWLGREFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEI 104
Query: 318 TRKALKLGFKPIVVVNKID 336
+ + I+VVNKID
Sbjct: 105 AKILRRSKKPVILVVNKID 123
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 47.2 bits (113), Expect = 2e-05
Identities = 49/174 (28%), Positives = 68/174 (39%), Gaps = 36/174 (20%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQ--SGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+AII + GK+TL++ L+ Q S K Q RI RGI I
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRI---------RGIVTTDNAQII-- 57
Query: 271 NGTRINIIDTPG----HADFG----GEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKAL 322
+DTPG G L VD +L ++DA EG P F+ +
Sbjct: 58 ------FVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLK 111
Query: 323 KLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF-PVIYTSALHG 375
K I+VVNKID+ V L + ++ L F ++ SAL G
Sbjct: 112 KTKTPVILVVNKIDK--------VKPKTVLLKLIAFLKKLLPFKEIVPISALKG 157
>gnl|CDD|239682 cd03711, Tet_C, Tet_C: C-terminus of ribosomal protection proteins
Tet(M) and Tet(O). This domain has homology to the C
terminal domains of the elongation factors EF-G and
EF-2. Tet(M) and Tet(O) catalyze the release of
tetracycline (Tc) from the ribosome in a GTP-dependent
manner thereby mediating Tc resistance. Tcs are
broad-spectrum antibiotics. Typical Tcs bind to the
ribosome and inhibit the elongation phase of protein
synthesis, by inhibiting the occupation of site A by
aminoacyl-tRNA.
Length = 78
Score = 41.5 bits (98), Expect = 6e-05
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 605 EPYENLFVDIE-EINQ---GIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQN 660
EPY E E+ Q G M L G ++ +I + V LE IP +Q+
Sbjct: 1 EPYL----RFELEVPQDALGRAMSDLAKMGATFEDPQIKG-DEVTLEGTIPVATSQDYQS 55
Query: 661 EFITLTRGTGLISHVFEEYAP 681
E + T G G++ F+ Y P
Sbjct: 56 ELPSYTHGEGVLETEFKGYRP 76
>gnl|CDD|239661 cd03690, Tet_II, Tet_II: This subfamily represents domain II of
ribosomal protection proteins Tet(M) and Tet(O). This
domain has homology to domain II of the elongation
factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the
release of tetracycline (Tc) from the ribosome in a
GTP-dependent manner thereby mediating Tc resistance.
Tcs are broad-spectrum antibiotics. Typical Tcs bind to
the ribosome and inhibit the elongation phase of protein
synthesis, by inhibiting the occupation of site A by
aminoacyl-tRNA.
Length = 85
Score = 40.7 bits (96), Expect = 2e-04
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 430 RILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEIC 489
R+ SG ++ L+D V +N + K KI ++RVF + V + +GDI ++TG++ +
Sbjct: 24 RLYSGTLR-LRDSVRVNREE----KIKITELRVFNNGEVVTADTVTAGDIAILTGLKGLR 78
Query: 490 IGSTI 494
+G +
Sbjct: 79 VGDVL 83
>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 = 42.2 bits (100), Expect = 2e-04
Identities = 45/194 (23%), Positives = 70/194 (36%), Gaps = 57/194 (29%)
Query: 222 GKTTLIDHLLRQ--------SGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 273
GK++L++ LL Q GT R + + E+ +
Sbjct: 9 GKSSLLNALLGQNVGIVSPIPGTTR---DPVRKEW---ELLPLGPVV------------- 49
Query: 274 RINIIDTPGHADFGGE----VERILSM---VDNVLLLIDAVEGPMPQTRFVTRKALKLGF 326
+IDTPG + GG VE + D VLL++D+ P+ + + +
Sbjct: 50 ---LIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEAKLGLLRERG-- 104
Query: 327 KPIVVV-NKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQ 385
KP+++V NKID E KL D PVI SAL G
Sbjct: 105 KPVLLVLNKIDLVPESEE----EELLRERKLELL---PDLPVIAVSALPG---------- 147
Query: 386 GNMIPLFEAILKYV 399
+ L + I + +
Sbjct: 148 EGIDELRKKIAELL 161
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 43.2 bits (102), Expect = 4e-04
Identities = 69/325 (21%), Positives = 117/325 (36%), Gaps = 68/325 (20%)
Query: 212 NIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITI--------FS 263
+ + HVDHGK+TL+ L+ +G +D + E ERG++ F
Sbjct: 119 LVGVAGHVDHGKSTLVGVLV--TGRLDDGDGATRSYLDVQKHEVERGLSADISLRVYGFD 176
Query: 264 ---------------KNCSIEYNGTRINIIDTPGHADFGGEVERIL--SMVDNVLLLIDA 306
K ++ ++ +DT GH + R L VD LL++ A
Sbjct: 177 DGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAA 236
Query: 307 VEGPMPQTRFVTRKALKLGFKPIVVVNKID------------------RSNARPEWVVDA 348
+G T+ AL + IVVV KID + R +V
Sbjct: 237 DDGVTKMTKEHLGIALAMELPVIVVVTKIDMVPDDRFQGVVEEISALLKRVGRIPLIVKD 296
Query: 349 TFDLFDKLCATE-EQLDFPVIYTSA--LHGYANENSKARQGNMIPLFEAILKYVPVHKDN 405
T D+ A + + P+ YTS+ G L + +P +
Sbjct: 297 TDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLD-------------LLDEFFLLLPKRRRW 343
Query: 406 SNNPLQLQIISLEYS-SYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFK 464
+ L I YS + +G + G + SG + V++ D K + + I +
Sbjct: 344 DDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPFKDGKFREVVVKSIEM-- 401
Query: 465 GLDRVLVNEALSGDIV--LITGIEE 487
V+ A +G I+ + G+E+
Sbjct: 402 --HHYRVDSAKAGSIIGIALKGVEK 424
>gnl|CDD|239757 cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514/C terminal
domain:eEF2_C_snRNP: This family includes C-terminal
portion of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. This domain is homologous to
domain II of the eukaryotic translational elongation
factor EF-2. Yeast Snu114p is essential for cell
viability and for splicing in vivo. U5-116 kD binds GTP.
Experiments suggest that GTP binding and probably GTP
hydrolysis is important for the function of the U5-116
kD/Snu114p. In complex with GTP, EF-2 promotes the
translocation step of translation. During translocation
the peptidyl-tRNA is moved from the A site to the P
site, the uncharged tRNA from the P site to the E-site
and, the mRNA is shifted one codon relative to the
ribosome.
Length = 94
Score = 38.3 bits (90), Expect = 0.001
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 429 GRILSGRIKSLQDVVIMN---GPDDKPN--KAKINQIRVFKGLDRVLVNEALSGDIVLIT 483
GRI SG IK Q V ++ DD+ + I ++ + G ++ VNEA +G+ VLI
Sbjct: 21 GRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWILGGRYKIEVNEAPAGNWVLIK 80
Query: 484 GIEEICI-GSTICD 496
GI+ + +TI
Sbjct: 81 GIDSSIVKTATITS 94
>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 = 38.0 bits (89), Expect = 0.002
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 271 NGTRINIIDTPG------HADFGGEVERILSMVDN---VLLLIDAVEGPMPQTRFVTRKA 321
G +I ++DTPG R L + +LL++DA EG + +
Sbjct: 44 LGRQIILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEEL 103
Query: 322 LKLGFKP-IVVVNK 334
KL KP I+V+NK
Sbjct: 104 EKLPKKPIILVLNK 117
>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 = 38.9 bits (92), Expect = 0.004
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 14/82 (17%)
Query: 297 VDNVLLLIDAVEGPMPQTRFVTR---KALKLGFKPIVVVNKIDRSNARPEWVVDATFDLF 353
VD VL++ +++ P R + R A G +P++V+NK D +VD +
Sbjct: 3 VDQVLIVF-SLKEPFFNLRLLDRYLVAAEASGIEPVIVLNKAD--------LVDD--EEL 51
Query: 354 DKLCATEEQLDFPVIYTSALHG 375
++L E+L +PV+ SA G
Sbjct: 52 EELLEIYEKLGYPVLAVSAKTG 73
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 38.6 bits (90), Expect = 0.005
Identities = 40/176 (22%), Positives = 61/176 (34%), Gaps = 21/176 (11%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNG 272
I +I V GKTT + L + I S + +R T+ SIE +
Sbjct: 13 IVVIGPVGAGKTTFVRALSDKPLV------ITEADASSVSGKGKRPTTVAMDFGSIELDE 66
Query: 273 -TRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV 331
T +++ TPG F E + ++L+D+ + P+VV
Sbjct: 67 DTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVV 126
Query: 332 -VNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQG 386
+NK D +A P + + E L PVI A E AR
Sbjct: 127 AINKQDLFDALP---PEKIREALKL-----ELLSVPVIEID-----ATEGEGARDQ 169
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 39.7 bits (94), Expect = 0.005
Identities = 31/117 (26%), Positives = 45/117 (38%), Gaps = 26/117 (22%)
Query: 267 SIEYNGTRINIIDTPGHADFGGEVERI--------LSMVDNVLLLIDAVEGPMPQTRFVT 318
I +G + +IDT G + EVE+I + D VLL++DA E + +
Sbjct: 257 HINLDGIPLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEIL 316
Query: 319 RKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHG 375
+ IVV+NK D + EE+ PVI SA G
Sbjct: 317 EELKDKPV--IVVLNKADLTGEIDL----------------EEENGKPVIRISAKTG 355
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 38.9 bits (91), Expect = 0.007
Identities = 48/203 (23%), Positives = 65/203 (32%), Gaps = 45/203 (22%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQ--SGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 270
+AI+ + GK+TL++ L Q S T K Q RI S IF
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRI--SGIHTTGASQIIF-------- 52
Query: 271 NGTRINIIDTPG----HADFG----GEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKAL 322
IDTPG E + VD +L ++D+ + FV K
Sbjct: 53 -------IDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQWN-GDGEFVLTKLQ 104
Query: 323 KLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF-PVIYTSALHGYANENS 381
L ++ NK+D D L DK DF ++ SAL G
Sbjct: 105 NLKRPVVLTRNKLDNKFK------DKLLPLIDKY---AILEDFKDIVPISALTGDNTSFL 155
Query: 382 KARQGNMIPLFEAILKYVPVHKD 404
A E L P
Sbjct: 156 AA-------FIEVHLPEGPFRYP 171
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are polypeptides
of 30-65kDa with three characteristic GTPase motifs
(G-1, G-3 and G-4) that are similar to those of the Ras
family. The G-4 motif is strictly conserved with a
unique septin consensus of AKAD. Most septins are
thought to have at least one coiled-coil region, which
in some cases is necessary for intermolecular
interactions that allow septins to polymerise to form
rod-shaped complexes. In turn, these are arranged into
tandem arrays to form filaments. They are
multifunctional proteins, with roles in cytokinesis,
sporulation, germ cell development, exocytosis and
apoptosis.
Length = 280
Score = 38.8 bits (91), Expect = 0.007
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 222 GKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRIN--IID 279
GKTTLI+ L I R + + ++ + I + IE +G ++N +ID
Sbjct: 16 GKTTLINTLFLTD-------LIPERGIPGPSEKIKKTVEIKATTVEIEEDGVKLNLTVID 68
Query: 280 TPGHADF 286
TPG D
Sbjct: 69 TPGFGDA 75
>gnl|CDD|239669 cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II of
the eukaryotic class II release factor (eRF3). In
eukaryotes, translation termination is mediated by two
interacting release factors, eRF1 and eRF3, which act as
class I and II factors, respectively. eRF1 functions as
an omnipotent release factor, decoding all three stop
codons and triggering the release of the nascent peptide
catalyzed by the ribsome. eRF3 is a GTPase, which
enhances the termination efficiency by stimulating the
eRF1 activity in a GTP-dependent manner. Sequence
comparison of class II release factors with elongation
factors shows that eRF3 is more similar to eEF1alpha
whereas prokaryote RF3 is more similar to EF-G, implying
that their precise function may differ. Only eukaryote
RF3s are found in this group. Saccharomyces cerevisiae
eRF3 (Sup35p) is a translation termination factor which
is divided into three regions N, M and a C-terminal
eEF1a-like region essential for translation termination.
Sup35NM is a non-pathogenic prion-like protein with
the property of aggregating into polymer-like fibrils.
This group also contains proteins similar to S.
cerevisiae Hbs1, a G protein known to be important for
efficient growth and protein synthesis under conditions
of limiting translation initiation 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 = 83
Score = 35.6 bits (83), Expect = 0.009
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 16/84 (19%)
Query: 419 YSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNK--AKINQIRVFKGLDRVLVNEALS 476
Y G + G++ SG I+ +++M P+K ++ I V D V+ A++
Sbjct: 10 YKDQGGTVVSGKVESGSIQKGDTLLVM------PSKESVEVKSIYV----DDEEVDYAVA 59
Query: 477 GDIVLIT--GIEE--ICIGSTICD 496
G+ V + GI+E I G +C
Sbjct: 60 GENVRLKLKGIDEEDISPGDVLCS 83
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 37.9 bits (89), Expect = 0.019
Identities = 32/152 (21%), Positives = 50/152 (32%), Gaps = 32/152 (21%)
Query: 267 SIEYNGTRINIIDTPGHADFGGEVERI--------LSMVDNVLLLIDAVEGPMPQTRFVT 318
I NG + ++DT G + VERI + D VL ++DA + + +
Sbjct: 259 DINLNGIPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDKEDLALI 318
Query: 319 RKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYAN 378
L IVV+NK D + +L + + +I SA G
Sbjct: 319 EL-LPKKKPIIVVLNKADLVSK-------------IELESEKLANGDAIISISAKTGEGL 364
Query: 379 ENSKARQGNMIPLFEAILKYVPVHKDNSNNPL 410
+ L EAI + N
Sbjct: 365 DA----------LREAIKQLFGKGLGNQEGLF 386
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 38.3 bits (89), Expect = 0.020
Identities = 27/71 (38%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 277 IIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV-VNKI 335
IDTPGH F +R S+ D +L++D EG PQT L+ P VV NKI
Sbjct: 530 FIDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQT-IEAINILRQYKTPFVVAANKI 588
Query: 336 DRSNARPEWVV 346
D P W +
Sbjct: 589 DLI---PGWNI 596
>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 = 36.3 bits (85), Expect = 0.023
Identities = 36/172 (20%), Positives = 62/172 (36%), Gaps = 42/172 (24%)
Query: 222 GKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRINIIDTP 281
GK++LI+ L + AR S + + I F+ G + ++D P
Sbjct: 11 GKSSLINALTNRKK--------LART--SKTPGRTQLINFFN-------VGDKFRLVDLP 53
Query: 282 GHADFGG------EVERILSMVDN----------VLLLIDAVEGPMPQTRFVTRKALKLG 325
G +G E+ +++ V+LLIDA GP P + +LG
Sbjct: 54 G---YGYAKVSKEVREKWGKLIEEYLENRENLKGVVLLIDARHGPTPIDLEMLEFLEELG 110
Query: 326 FKPIVVVNKIDRSNARP-EWVVDATFDLFDKLCATEEQLDFPVIYTSALHGY 376
++V+ K D+ V+ + + PVI S+ G
Sbjct: 111 IPFLIVLTKADKLKKSELAKVLKKIKEELNLFNI-----LPPVILFSSKKGT 157
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 36.3 bits (85), Expect = 0.030
Identities = 34/128 (26%), Positives = 57/128 (44%), Gaps = 23/128 (17%)
Query: 258 GITIFSKNCSIEYNGTRINIIDTPGHADFGG--EVERILSMV------DNVLLLIDAV-- 307
G+T+ K + +Y G I I+D PG E E++ D ++ ++DA
Sbjct: 32 GVTVEKKEGTFKYKGYEIEIVDLPGTYSLSPYSEEEKVARDYLLEEKPDVIINVVDATNL 91
Query: 308 EGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPV 367
E + ++T + L+LG +V +N +D + + D+ KL E L PV
Sbjct: 92 ERNL----YLTLQLLELGIPVVVALNMMDEAEKK-----GIKIDI-KKL---SELLGVPV 138
Query: 368 IYTSALHG 375
+ TSA G
Sbjct: 139 VPTSARKG 146
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 35.1 bits (82), Expect = 0.045
Identities = 39/139 (28%), Positives = 54/139 (38%), Gaps = 45/139 (32%)
Query: 258 GITIFSKNCSIEYNGTRINIIDTPG----HA---------DF--GGEVERILSMVD---- 298
G+T+ K + G I I+D PG DF G E + I+++VD
Sbjct: 29 GVTVEKKEGEFKLGGKEIEIVDLPGTYSLTPYSEDEKVARDFLLGEEPDLIVNVVDATNL 88
Query: 299 --NVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKL 356
N+ L + +E LG +V +N ID + R DL DKL
Sbjct: 89 ERNLYLTLQLLE---------------LGLPVVVALNMIDEAEKR-----GIKIDL-DKL 127
Query: 357 CATEEQLDFPVIYTSALHG 375
E L PV+ TSA G
Sbjct: 128 ---SELLGVPVVPTSARKG 143
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 36.6 bits (85), Expect = 0.055
Identities = 43/171 (25%), Positives = 73/171 (42%), Gaps = 25/171 (14%)
Query: 258 GITIFSKNCSIEYNGTRINIIDTPGHADFGG-----EVER---ILSMVDNVLLLIDAVEG 309
G+T+ K + + G I I+D PG EV R + D V+ ++DA
Sbjct: 26 GVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSLEEEVARDYLLNEKPDLVVNVVDASN- 84
Query: 310 PMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWV-VDATFDLFDKLCATEEQLDFPVI 368
+ + ++T + L+LG I+ +N +D A + + +D +KL EE+L PV+
Sbjct: 85 -LERNLYLTLQLLELGIPMILALNLVDE--AEKKGIRIDE-----EKL---EERLGVPVV 133
Query: 369 YTSALHGYANENSKARQGNMIPLFEAILKYVP----VHKDNSNNPLQLQII 415
TSA G E K I L E + + ++ ++II
Sbjct: 134 PTSATEGRGIERLKDAIRKAIGLKELKKRAIEIVPEAYQVVEVVEGLIEII 184
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 36.3 bits (84), Expect = 0.067
Identities = 32/135 (23%), Positives = 57/135 (42%), Gaps = 29/135 (21%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNE--IEKERGITIFSKNCSIEY 270
+AI+ + GK+TL++ RI+ E +E G+T + E+
Sbjct: 278 VAIVGRPNVGKSTLVN-----------------RILGRREAVVEDTPGVTRDRVSYDAEW 320
Query: 271 NGTRINIIDTPG--------HADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKAL 322
GT ++DT G + + + +S+ D V+ ++D G T + L
Sbjct: 321 AGTDFKLVDTGGWEADVEGIDSAIASQAQIAVSLADAVVFVVDGQVGLT-STDERIVRML 379
Query: 323 KLGFKPI-VVVNKID 336
+ KP+ + VNKID
Sbjct: 380 RRAGKPVVLAVNKID 394
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 35.6 bits (83), Expect = 0.068
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 9/67 (13%)
Query: 222 GKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRI--NIID 279
GK+T I+ L + ++ + + + I +E NG ++ +ID
Sbjct: 16 GKSTFINTLF-------GTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKLKLTVID 68
Query: 280 TPGHADF 286
TPG D
Sbjct: 69 TPGFGDN 75
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They 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. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 34.2 bits (79), Expect = 0.079
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 266 CSIEYNGTRINIIDTPG-------HADFGGEVERILSMVDNVLLLIDA 306
+ G + ++D PG ++ R+L D VL L+DA
Sbjct: 38 YVWQTGGDGLVLLDLPGVGERGRRDREYEELYRRLLPEADLVLWLLDA 85
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 35.7 bits (83), Expect = 0.11
Identities = 37/116 (31%), Positives = 51/116 (43%), Gaps = 22/116 (18%)
Query: 269 EYNGTRINIIDTPG--------HADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRK 320
E+NG R ++DT G A + E + D VL ++DA G V R
Sbjct: 82 EWNGRRFTVVDTGGWEPDAKGLQASVAEQAEVAMRTADAVLFVVDATVGATATDEAVARV 141
Query: 321 ALKLGFKPIVVV-NKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHG 375
+ G KP+++ NK+D + R E DA L+ L E PV SALHG
Sbjct: 142 LRRSG-KPVILAANKVD--DERGE--ADAA-ALW-SLGLGEP---HPV---SALHG 184
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 35.5 bits (82), Expect = 0.12
Identities = 33/133 (24%), Positives = 55/133 (41%), Gaps = 26/133 (19%)
Query: 213 IAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNG 272
+AI+ + GK++L++ LL+Q D + +G T E NG
Sbjct: 206 LAIVGSPNVGKSSLLNALLKQ---------------DRAIVSDIKGTTRDVVEGDFELNG 250
Query: 273 TRINIIDTPGHADFGGEVERI--------LSMVDNVLLLIDAVEGPMPQTR-FVTRKALK 323
I ++DT G + VER+ + D V+ ++DA + + K
Sbjct: 251 ILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDLNKSK 310
Query: 324 LGFKPIVVVNKID 336
F I+V+NKID
Sbjct: 311 KPF--ILVLNKID 321
>gnl|CDD|239756 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II
release factor (eRF3). In eukaryotes, translation
termination is mediated by two interacting release
factors, eRF1 and eRF3, which act as class I and II
factors, respectively. eRF1 functions as an omnipotent
release factor, decoding all three stop codons and
triggering the release of the nascent peptide catalyzed
by the ribsome. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. Sequence comparison of class
II release factors with elongation factors shows that
eRF3 is more similar to eEF1alpha whereas prokaryote RF3
is more similar to EF-G, implying that their precise
function may differ. Only eukaryote RF3s are found in
this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a
translation termination factor which is divided into
three regions N, M and a C-terminal eEF1a-like region
essential for translation termination. Sup35NM is a
non-pathogenic prion-like protein with the property of
aggregating into polymer-like fibrils.
Length = 82
Score = 32.1 bits (74), Expect = 0.13
Identities = 28/92 (30%), Positives = 47/92 (51%), Gaps = 14/92 (15%)
Query: 409 PLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDR 468
PL+L II +Y +G + +G++ SG IK +++M PNK ++ + ++ +
Sbjct: 1 PLRLPIID-KYKD-MGTVVLGKVESGTIKKGDKLLVM------PNKTQVEVLSIYN--ED 50
Query: 469 VLVNEALSGDIVLI--TGIEE--ICIGSTICD 496
V V A G+ V + GIEE I G +C
Sbjct: 51 VEVRYARPGENVRLRLKGIEEEDISPGFVLCS 82
>gnl|CDD|216219 pfam00965, TIMP, Tissue inhibitor of metalloproteinase. Members of
this family are common in extracellular regions of
vertebrate species.
Length = 174
Score = 33.9 bits (78), Expect = 0.16
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 13/53 (24%)
Query: 440 QDVVI---------MNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLIT 483
D VI + +DK + K+ Q ++FKG + S DI +
Sbjct: 15 ADFVIRAKVVGKKLVEQGNDKRIRYKVKQTKMFKGFSKAG----SSLDIQYVY 63
>gnl|CDD|211324 cd01291, PseudoU_synth, Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule
to pseudouridines (5-ribosyluracil, psi).
Pseudouridine synthases contains the RsuA/RluD, TruA,
TruB and TruD families. This group consists of
eukaryotic, bacterial and archeal pseudouridine
synthases. Some psi sites such as psi55,13,38 and 39
in tRNA are highly conserved, being in the same
position in eubacteria, archeabacteria and eukaryotes.
Other psi sites occur in a more restricted fashion, for
example psi2604in 23S RNA made by E.coli RluF has only
been detected in E.coli. Human dyskerin with the help
of guide RNAs makes the hundreds of psueudouridnes
present in rRNA and small nuclear RNAs (snRNAs).
Mutations in human dyskerin cause X-linked dyskeratosis
congenitas. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia
(MLASA).
Length = 87
Score = 32.2 bits (74), Expect = 0.17
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 16 YKPYGLSSNNALKKIKYLL--NAKKVGYTGTLDPFATGLLPLC 56
YKP G + A +++ LL K+VGY G D A +
Sbjct: 2 YKP-GGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS 43
>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 = 33.6 bits (78), Expect = 0.19
Identities = 31/118 (26%), Positives = 43/118 (36%), Gaps = 27/118 (22%)
Query: 267 SIEYNGTRINIIDTPGHADFGGEVERI-----LSMVDN---VLLLIDAVEGPMPQTRFVT 318
I+ G + +IDT G + E+E+I ++ VLL++DA EG
Sbjct: 45 EIDLGGIPVRLIDTAGLRETEDEIEKIGIERAREAIEEADLVLLVVDASEG---LDEEDL 101
Query: 319 RKALKLGFKP-IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHG 375
KP IVV+NK DL E P+I SA G
Sbjct: 102 EILELPAKKPVIVVLNKS---------------DLLSDAEGISELNGKPIIAISAKTG 144
>gnl|CDD|239683 cd03713, EFG_mtEFG_C, EFG_mtEFG_C: domains similar to the
C-terminal domain of the bacterial translational
elongation factor (EF) EF-G. Included in this group is
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells
harbor 2 protein synthesis systems: one localized in the
cytoplasm, the other in the mitochondria. Most factors
regulating mitochondrial protein synthesis are encoded
by nuclear genes, translated in the cytoplasm, and then
transported to the mitochondria. The eukaryotic system
of elongation factor (EF) components is more complex
than that in prokaryotes, with both cytoplasmic and
mitochondrial elongation factors and multiple isoforms
being expressed in certain species. During the process
of peptide synthesis and tRNA site changes, the ribosome
is moved along the mRNA a distance equal to one codon
with the addition of each amino acid. In bacteria this
translocation step is catalyzed by EF-G_GTP, which is
hydrolyzed to provide the required energy. Thus, this
action releases the uncharged tRNA from the P site and
transfers the newly formed peptidyl-tRNA from the A site
to the P site. Eukaryotic mtEFG1 proteins show
significant homology to bacterial EF-Gs. Mutants in
yeast mtEFG1 have impaired mitochondrial protein
synthesis, respiratory defects and a tendency to lose
mitochondrial DNA. No clear phenotype has been found for
mutants in the yeast homologue of mtEFG2, MEF2.
Length = 78
Score = 31.0 bits (71), Expect = 0.42
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 1/77 (1%)
Query: 605 EPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEFIT 664
EP + V + E G ++ L+ R G + E +V ++ +P + G+ + +
Sbjct: 1 EPIMKVEVTVPEEYMGDVIGDLSSRRGQILGTESRGGWKV-IKAEVPLAEMFGYSTDLRS 59
Query: 665 LTRGTGLISHVFEEYAP 681
LT+G G + F Y
Sbjct: 60 LTQGRGSFTMEFSHYEE 76
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 32.9 bits (76), Expect = 0.43
Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 15/83 (18%)
Query: 268 IEYNGTRINIIDTPGHA------DFGGEVERILSMVDN--VLLLIDAVEGPMPQTRFVTR 319
IE ++DTPG + G ++ LS V+ LIDAV P FV+
Sbjct: 92 IESLDADYVLVDTPGQMELFAFRESGRKLVERLSGSSKSVVVFLIDAVLAKTPSD-FVSL 150
Query: 320 KAL------KLGFKPIVVVNKID 336
L +LG I V+NK D
Sbjct: 151 LLLALSVQLRLGLPQIPVLNKAD 173
>gnl|CDD|217719 pfam03767, Acid_phosphat_B, HAD superfamily, subfamily IIIB (Acid
phosphatase). This family proteins includes acid
phosphatases and a number of vegetative storage
proteins.
Length = 213
Score = 32.7 bits (75), Expect = 0.47
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 556 NKHDDSIYEVSGRGELHLTILIENMRREGYELSVSRPRVIFKTLNG 601
+ I+ VSGR E +EN+++ G+ ++I +
Sbjct: 116 VELGVKIFFVSGRSEDLRAATVENLKKAGFH---GWEKLILRGKKD 158
>gnl|CDD|239680 cd03709, lepA_C, lepA_C: This family represents the C-terminal
region of LepA, a GTP-binding protein localized in the
cytoplasmic membrane. LepA is ubiquitous in Bacteria
and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but
is missing from Archaea. LepA exhibits significant
homology to elongation factors (EFs) Tu and G. The
function(s) of the proteins in this family are unknown.
The N-terminal domain of LepA is homologous to a domain
of similar size found in initiation factor 2 (IF2), and
in EF-Tu and EF-G (factors required for translation in
Escherichia coli). Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including S. cerevisiae GUF1)
originated within the bacterial LepA family. LepA has
never been observed in archaea, and eukaryl LepA is
organellar. LepA is therefore a true bacterial GTPase,
found only in the bacterial lineage.
Length = 80
Score = 30.2 bits (69), Expect = 0.65
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 605 EPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIP 651
EP+ + G IM+ R G K++E + RV L Y +P
Sbjct: 1 EPFVKATIITPSEYLGAIMELCQERRGVQKDMEYLDANRVMLTYELP 47
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 33.1 bits (76), Expect = 0.65
Identities = 64/262 (24%), Positives = 99/262 (37%), Gaps = 71/262 (27%)
Query: 199 LRRIGIDKLTLDK----------NIAIIAHVDHGKTTLIDHLLRQSG--TFR----KNQN 242
L ++ +DKLT NI I HV HGK+T++ L SG T R K +N
Sbjct: 13 LSKLDLDKLTPLTPEVISRQATINIGTIGHVAHGKSTVVKAL---SGVKTVRFKREKVRN 69
Query: 243 I-------NARIMDSNEIEKERGITIFS---------KNCSIEYNGTR-INIIDTPGHAD 285
I NA+I + + + C + R ++ +D PGH D
Sbjct: 70 ITIKLGYANAKIYKCPKCPRPTCYQSYGSSKPDNPPCPGCGHKMTLKRHVSFVDCPGH-D 128
Query: 286 F-------GGEVERILSMVDNVLLLIDAVEG-PMPQTRFVTRKALKLGFKPIVVV-NKID 336
G V +D LLLI A E P PQT + K I+++ NKID
Sbjct: 129 ILMATMLNGAAV------MDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIIILQNKID 182
Query: 337 ---RSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFE 393
+ A+ ++ + P+I SA Y N+ + E
Sbjct: 183 LVKEAQAQ------DQYEEIRNFVKGTIADNAPIIPISAQLKY----------NIDVVLE 226
Query: 394 AILKYVPVHKDNSNNPLQLQII 415
I +P+ K + +P ++ +I
Sbjct: 227 YICTQIPIPKRDLTSPPRMIVI 248
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 32.9 bits (76), Expect = 0.65
Identities = 26/85 (30%), Positives = 36/85 (42%), Gaps = 15/85 (17%)
Query: 297 VDNVLLLIDAVEGPMPQTRFVTRKALKL----GFKPIVVVNKIDRSNARPEWVVDATFDL 352
VD +L+ A E P T + R L L G KPI+V+NKID + E
Sbjct: 81 VDQAVLVFAAKE-PDFSTDLLDR-FLVLAEANGIKPIIVLNKIDLLDDLEEA-------- 130
Query: 353 FDKLCATEEQLDFPVIYTSALHGYA 377
+L A + + V+ SA G
Sbjct: 131 -RELLALYRAIGYDVLELSAKEGEG 154
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 32.7 bits (75), Expect = 0.68
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 20/73 (27%)
Query: 222 GKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEK------ERGITIFSKNCSIEYNGT-- 273
GKTT I+ L S ++D EI+ + I +E +G
Sbjct: 35 GKTTFINTLFGTS------------LVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHL 82
Query: 274 RINIIDTPGHADF 286
+ +IDTPG DF
Sbjct: 83 NLTVIDTPGFGDF 95
>gnl|CDD|239666 cd03695, CysN_NodQ_II, CysN_NodQ_II: This subfamily represents the
domain II of the large subunit of ATP sulfurylase
(ATPS): CysN or the N-terminal portion of NodQ, found
mainly in proteobacteria and homologous to the domain II
of EF-Tu. Escherichia coli ATPS consists of CysN and a
smaller subunit CysD and CysN. ATPS produces
adenosine-5'-phosphosulfate (APS) from ATP and sulfate,
coupled with GTP hydrolysis. In the subsequent reaction
APS is phosphorylated by an APS kinase (CysC), to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for
use in amino acid (aa) biosynthesis. The Rhizobiaceae
group (alpha-proteobacteria) appears to carry out the
same chemistry for the sufation of a nodulation factor.
In Rhizobium meliloti, a the hererodimeric complex
comprised of NodP and NodQ appears to possess both ATPS
and APS kinase activities. The N and C termini of NodQ
correspond to CysN and CysC, respectively. Other
eubacteria, Archaea, and eukaryotes use a different ATP
sulfurylase, which shows no aa sequence similarity to
CysN or NodQ. CysN and the N-terminal portion of NodQ
show similarity to GTPases involved in translation, in
particular, EF-Tu and EF-1alpha.
Length = 81
Score = 30.2 bits (69), Expect = 0.84
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 429 GRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLIT 483
G I SG I+ +VV++ P K +++ I F G ++EA +G+ V +T
Sbjct: 20 GTIASGSIRVGDEVVVL--PSGK--TSRVKSIETFDG----ELDEAGAGESVTLT 66
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 31.6 bits (71), Expect = 1.5
Identities = 38/154 (24%), Positives = 68/154 (44%), Gaps = 25/154 (16%)
Query: 193 GAHLKYLRRIGIDKLTLDKNIA--IIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDS 250
G+ K + K++ K ++ II + GK+TL++ ++ + K + ++ +
Sbjct: 33 GSTSKLPLEVKFGKMSNQKTVSVCIIGRPNSGKSTLLNRIIGE-----KLSIVTPKVQTT 87
Query: 251 NEIEKERGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERI--------LSMVDNVLL 302
I GI I T++ + DTPG + G +E+ L D VLL
Sbjct: 88 RSIIT--GI--------ITLKDTQVILYDTPGIFEPKGSLEKAMVRCAWSSLHSADLVLL 137
Query: 303 LIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKID 336
+ID+++ T + K L PI ++NKID
Sbjct: 138 IIDSLKSFDDITHNILDKLRSLNIVPIFLLNKID 171
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 31.5 bits (72), Expect = 1.9
Identities = 42/172 (24%), Positives = 75/172 (43%), Gaps = 37/172 (21%)
Query: 210 DKNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIE 269
+A++ + + GKTTL + L +G +K N G+T+ K ++
Sbjct: 3 KLTVALVGNPNVGKTTLFNAL---TGANQKVGNWP-------------GVTVEKKEGKLK 46
Query: 270 YNGTRINIIDTPGHADFGG--EVERI------LSMVDNVLLLIDAVEGPMPQTRFVTRKA 321
Y G I I+D PG E E++ D ++ ++DA + + ++T +
Sbjct: 47 YKGHEIEIVDLPGTYSLTAYSEDEKVARDFLLEGKPDLIVNVVDATN--LERNLYLTLQL 104
Query: 322 LKLGFKPIVVVNKIDRSNARPEWV-VDATFDLFDKLCATEEQLDFPVIYTSA 372
L+LG I+ +N ID A+ + +D +KL + L PV+ T A
Sbjct: 105 LELGIPMILALNMIDE--AKKRGIRIDI-----EKL---SKLLGVPVVPTVA 146
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 30.6 bits (70), Expect = 2.0
Identities = 33/119 (27%), Positives = 46/119 (38%), Gaps = 23/119 (19%)
Query: 268 IEYNGTRINIIDTPGHADFGGE----VER--ILSMV---DNVLLLIDAVE--GPMPQTRF 316
+Y R +IDTPG D E +E I ++ VL ID E G + +
Sbjct: 42 FDYKYLRWQVIDTPGILDRPLEERNTIEMQAITALAHLRAAVLFFIDPSETCGYSIEEQL 101
Query: 317 VTRKALKLGFKP--IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSAL 373
K +K F IVV+NKID T + ++ E+ VI S L
Sbjct: 102 SLFKEIKPLFNKPVIVVLNKIDLL----------TEEDLSEIEKELEKEGEEVIKISTL 150
>gnl|CDD|206740 cd09913, EHD, Eps15 homology domain (EHD), C-terminal domain.
Dynamin-like C-terminal Eps15 homology domain (EHD)
proteins regulate endocytic events; they have been
linked to a number of Rab proteins through their
association with mutual effectors, suggesting a
coordinate role in endocytic regulation. Eukaryotic EHDs
comprise four members (EHD1-4) in mammals and single
members in Caenorhabditis elegans (Rme-1), Drosophila
melanogaster (Past1) as well as several eukaryotic
parasites. EHD1 regulates trafficking of multiple
receptors from the endocytic recycling compartment (ERC)
to the plasma membrane; EHD2 regulates trafficking from
the plasma membrane by controlling Rac1 activity; EHD3
regulates endosome-to-Golgi transport, and preserves
Golgi morphology; EHD4 is involved in the control of
trafficking at the early endosome and regulates exit of
cargo toward the recycling compartment as well as late
endocytic pathway. Rme-1, an ortholog of human EHD1,
controls the recycling of internalized receptors from
the endocytic recycling compartment to the plasma
membrane. In D. melanogaster, deletion of the Past1 gene
leads to infertility as well as premature death of adult
flies. Arabidopsis thaliana also has homologs of EHD
proteins (AtEHD1 and AtEHD2), possibly involved in
regulating endocytosis and signaling.
Length = 241
Score = 30.7 bits (70), Expect = 2.1
Identities = 29/158 (18%), Positives = 45/158 (28%), Gaps = 48/158 (30%)
Query: 222 GKTTLIDHLLRQSGTFRKNQNINAR--------IMDSNEIEKERGITI------------ 261
GK+T I++LL Q +M + G +
Sbjct: 11 GKSTFINYLLGQDYP---GLRTGPEPTTDRFTVVMHGEDDGTIPGNALVVDPDKPFRGLS 67
Query: 262 ------FSKNCSIEYNGT---RINIIDTPGHADFGGEVERIL-------------SMVDN 299
+K + I+DTPG GE +R D
Sbjct: 68 KFGNGFLNKFEGSTLPHPLLESVTIVDTPGILS--GEKQRQSRGYDFNAVCRWFAERADL 125
Query: 300 VLLLIDAVE-GPMPQTRFVTRKALKLGFKPIVVVNKID 336
+ LL D + + R V + K +V+NK D
Sbjct: 126 IFLLFDPHKLDISDEFRRVIEQLKGHESKIRIVLNKAD 163
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 30.8 bits (70), Expect = 2.6
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 23/107 (21%)
Query: 277 IIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLG---FKPIVVVN 333
I++T G EV+ I +M D L+++ G Q +K G I+V+N
Sbjct: 148 IVETVGVGQ--SEVD-IANMADTFLVVMIPGAGDDLQ-------GIKAGIMEIADIIVIN 197
Query: 334 KIDRSNARPEWVVDATFDLFDKLCATEEQLDF-----PVIYTSALHG 375
K DR A A +L L E PV+ TSAL G
Sbjct: 198 KADRKGAE-----KAARELRSALDLLREVWRENGWRPPVVTTSALEG 239
>gnl|CDD|239670 cd03699, lepA_II, lepA_II: This subfamily represents the domain II
of LepA, a GTP-binding protein localized in the
cytoplasmic membrane. The N-terminal domain of LepA
shares regions of homology to translation factors. In
terms of interaction with the ribosome, EF-G, EF-Tu and
IF2 have all been demonstrated to interact at
overlapping sites on the ribosome. Chemical protection
studies demonstrate that they all include the
universally conserved alpha-sarcin loop as part of their
binding site. These data indicate that LepA may bind to
this location on the ribosome as well. LepA has never
been observed in archaea, and eukaryl LepA is
organellar. LepA is therefore a true bacterial GTPase,
found only in the bacterial lineage.
Length = 86
Score = 28.2 bits (64), Expect = 3.5
Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 13/84 (15%)
Query: 419 YSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKA--KINQIRVFKGLDRVLVNEALS 476
Y Y G I + R+ G +K + M+ ++ ++ +F+ + +E +
Sbjct: 10 YDPYRGVIALVRVFDGTLKKGDKIRFMS------TGKEYEVEEVGIFR-PEMTPTDELSA 62
Query: 477 GDI-VLITGI---EEICIGSTICD 496
G + +I GI ++ +G TI
Sbjct: 63 GQVGYIIAGIKTVKDARVGDTITL 86
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 29.7 bits (68), Expect = 4.0
Identities = 23/106 (21%), Positives = 39/106 (36%), Gaps = 27/106 (25%)
Query: 298 DNVLLLIDAVEGPMPQTRFVTRKALK-LGF--KPIVVV-NKIDRSNARPEWVVDATFDLF 353
D +L ++DA + + + LK LG PI++V NKID +
Sbjct: 122 DLLLHVVDASDPDREEQIETVEEVLKELGADDIPIILVLNKIDLLDD------------- 168
Query: 354 DKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFEAILKYV 399
++L ++ SA G + L EAI + +
Sbjct: 169 EELEERLRAGRPDAVFISAKTGE----------GLDLLKEAIEELL 204
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 30.3 bits (69), Expect = 4.2
Identities = 29/86 (33%), Positives = 40/86 (46%), Gaps = 17/86 (19%)
Query: 268 IEYNGTRINIIDTPGHADFG----GEVER--ILSM--VDNVLL-LIDAVE----GPMPQT 314
E RI +IDTPG D E+ER IL++ + V+L L D E Q
Sbjct: 210 FERGYLRIQVIDTPGLLDRPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQI 269
Query: 315 RFVTRKALKLGFKP--IVVVNKIDRS 338
+ +K FK +VV+NKID +
Sbjct: 270 SL--LEEIKELFKAPIVVVINKIDIA 293
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to
be involved in plant resistance to bacteria.
Length = 211
Score = 29.9 bits (68), Expect = 4.3
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 255 KERGITIFSKNCSIEYNGTRINIIDTPG------HADFGG-EVERILSM----VDNVLLL 303
+ +G+T + S ++G IN+IDTPG DF E+ R L + VLL+
Sbjct: 31 RAQGVTKTCQLVSRTWDGRIINVIDTPGLFDLSVSNDFISKEIIRCLLLAEPGPHAVLLV 90
Query: 304 IDA 306
+
Sbjct: 91 LSL 93
>gnl|CDD|206651 cd01852, AIG1, AvrRpt2-Induced Gene 1 (AIG1). This group
represents Arabidoposis protein AIG1 (avrRpt2-induced
gene 1) that appears to be involved in plant resistance
to bacteria. The Arabidopsis disease resistance gene
RPS2 is involved in recognition of bacterial pathogens
carrying the avirulence gene avrRpt2. AIG1 exhibits
RPS2- and avrRpt1-dependent induction early after
infection with Pseudomonas syringae carrying avrRpt2.
This subfamily also includes IAN-4 protein, which has
GTP-binding activity and shares sequence homology with a
novel family of putative GTP-binding proteins: the
immuno-associated nucleotide (IAN) family. The
evolutionary conservation of the IAN family provides a
unique example of a plant pathogen response gene
conserved in animals. The IAN/IMAP subfamily has been
proposed to regulate apoptosis in vertebrates and
angiosperm plants, particularly in relation to cancer,
diabetes, and infections. The human IAN genes were
renamed GIMAP (GTPase of the immunity associated
proteins).
Length = 201
Score = 29.8 bits (68), Expect = 4.4
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 257 RGITIFSKNCSIEYNGTRINIIDTPG 282
G+T + S ++G R+N+IDTPG
Sbjct: 33 SGVTKTCQKESAVWDGRRVNVIDTPG 58
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 29.8 bits (68), Expect = 5.2
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 324 LGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGY 376
LG +P++V+NKID + D ++ + + V+ S+ G
Sbjct: 149 LGIEPLIVLNKIDLLD-------DEGRAFVNEQLDIYRNIGYRVLMVSSHTGE 194
>gnl|CDD|183784 PRK12838, PRK12838, carbamoyl phosphate synthase small subunit;
Reviewed.
Length = 354
Score = 29.5 bits (67), Expect = 6.8
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 9/47 (19%)
Query: 210 DKNIAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKE 256
+ NI I+ VD T + +R+ GT + A I +++
Sbjct: 102 EWNIPGISGVD---TRALVKHIREKGT------MKASITTTDDAHAF 139
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 27.8 bits (62), Expect = 7.9
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 5/62 (8%)
Query: 277 IIDTPGHADFGGEVERI-LSMVDNVLLLIDAVEGPMPQTRFVTRKALKL----GFKPIVV 331
+IDTP + + L D V+++ + R +T L+L VV
Sbjct: 38 LIDTPPGLGLLVLLCLLALLAADLVIIVTTPEALAVLGARRLTEVVLELAIEGLRPVGVV 97
Query: 332 VN 333
VN
Sbjct: 98 VN 99
>gnl|CDD|234621 PRK00082, hrcA, heat-inducible transcription repressor;
Provisional.
Length = 339
Score = 29.4 bits (67), Expect = 8.2
Identities = 8/31 (25%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 82 ITTETGDIEGKIIDFNKNI-PNSIEIIEKIL 111
+ T++G +E ++I+ + I P+ +E L
Sbjct: 153 LVTDSGRVENRVIELPEGISPSDLEEASNFL 183
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 29.3 bits (66), Expect = 8.7
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 277 IIDTPGH-ADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKI 335
I PGH +++ +L VD V+ ++DA + + + R + ++V+NK
Sbjct: 14 IQWFPGHMKKAKRQLKEVLKSVDVVVEVVDARDPLGTRNPELER--IVKEKPKLLVLNKA 71
Query: 336 D 336
D
Sbjct: 72 D 72
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.140 0.405
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: 41,917,630
Number of extensions: 4363504
Number of successful extensions: 4116
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3846
Number of HSP's successfully gapped: 241
Length of query: 793
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 688
Effective length of database: 6,280,432
Effective search space: 4320937216
Effective search space used: 4320937216
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: 63 (28.3 bits)