RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780648|ref|YP_003065061.1| GTPase ObgE [Candidatus
Liberibacter asiaticus str. psy62]
(335 letters)
>gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 436 bits (1124), Expect = e-123
Identities = 179/340 (52%), Positives = 243/340 (71%), Gaps = 6/340 (1%)
Query: 1 MKFLDEAKVYIRSGDGGAGGISFRREKFIEFGGPDGGSGGRGGDVWIQATSNLNTLIDFR 60
MKF+DE K+ +++GDGG G +SFRREKF+ GGPDGG GGRGG V +A NLNTLIDFR
Sbjct: 1 MKFVDEVKIEVKAGDGGNGCVSFRREKFVPKGGPDGGDGGRGGSVIFEADENLNTLIDFR 60
Query: 61 YQQHFKAQHGEKGMKRNRSGAKGEDVVLTVPVGTQVFEEDGISLICDLDQEGQRIILAPG 120
Y++HFKA++GE GM RNR+GAKG+D+V+ VPVGT V +ED L+ DL + GQR ++A G
Sbjct: 61 YKKHFKAENGENGMGRNRTGAKGKDLVIKVPVGTVVRDEDTGELLADLTEHGQRFLVAKG 120
Query: 121 GNGGFGNAHFKSSTNQAPYYANPGILGQEKIIWLKLKLIADIGIIGLPNAGKSTFLASVT 180
G GG GNAHFKSS N+AP +A PG G+E+ + L+LKL+AD+G++GLPNAGKST L++V+
Sbjct: 121 GRGGLGNAHFKSSVNRAPRFATPGEPGEERDLRLELKLLADVGLVGLPNAGKSTLLSAVS 180
Query: 181 RAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIKNAHQGAGIGDRFLKHTERTHV 239
AKPKIADYPFTTL PNLG+V+ +G + F++ADIPG+I+ A +G G+G RFL+H ERT V
Sbjct: 181 AAKPKIADYPFTTLVPNLGVVRVDGGESFVVADIPGLIEGASEGVGLGLRFLRHIERTRV 240
Query: 240 LLHIVSALEENVQ---AAYQCILDELSAYNSELRKKIEIVGLSQIDTV-DSDTLARKKNE 295
LLH++ + + YQ I +EL Y+ +L +K IV L++ID D + L K
Sbjct: 241 LLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDEEELEELKKA 300
Query: 296 LATQCGQVPFEF-SSITGHGIPQILECLHDKIFSIRGENE 334
LA G F S++T G+ ++L L + + + E E
Sbjct: 301 LAEALGWEVFYLISALTREGLDELLRALAELLEETKAEAE 340
>gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN
superfamily) [General function prediction only].
Length = 366
Score = 274 bits (702), Expect = 3e-74
Identities = 120/326 (36%), Positives = 185/326 (56%), Gaps = 8/326 (2%)
Query: 2 KFLDEAKVYIRSGDGGAGGISFRREKFIEFGGPDGGSGGRGGDVWIQATSNLNTLIDFRY 61
F+D+ +V I+ G GG+G SF R GGPDGG GG GG V+ A +
Sbjct: 40 NFIDKRRVRIKGGSGGSGASSFFRGYRRPRGGPDGGDGGNGGHVYFVAKPGAFKQLSHVG 99
Query: 62 QQHFKAQHGEKGMKRNRSGAKGEDVVLTVPVGTQVFEEDGISLICDLDQEGQRIILAPGG 121
+A +GE G + G+ + + VPVGT V + + L+ +L +EG R+I A GG
Sbjct: 100 SLI-QAPNGENGKSKMCHGSNAKHSEIRVPVGTVVKDIEQGKLVAELTKEGDRVIAARGG 158
Query: 122 NGGFGNAHFKSSTNQAPYYANPGILGQEKIIWLKLKLIADIGIIGLPNAGKSTFLASVTR 181
GG GN F S+ N++P ++ PG+ G+E++I L+LK IAD+G++G PNAGKST L +++R
Sbjct: 159 EGGKGNKFFLSNENRSPKFSKPGLNGEERVIELELKSIADVGLVGFPNAGKSTLLNALSR 218
Query: 182 AKPKIADYPFTTLYPNLGIV-KEGYKEFILADIPGIIKNAHQGAGIGDRFLKHTERTHVL 240
AKPK+A Y FTTL P++G V + + + +ADIPGII+ AH G+G +FL+H ER L
Sbjct: 219 AKPKVAHYAFTTLRPHIGTVNYDDFSQITVADIPGIIEGAHMNKGLGYKFLRHIERCKGL 278
Query: 241 LHIV---SALEENVQAAYQCILDELSAYNSELRKKIEIVGLSQIDTVDSDTLARKKNELA 297
L +V N Q +++EL Y L + ++ ++ID +++ + LA
Sbjct: 279 LFVVDLSGKQLRNPWQQLQLLIEELELYEKGLADRPALIVANKIDLPEAE--KNLLSSLA 336
Query: 298 TQCGQVP-FEFSSITGHGIPQILECL 322
+ S+ +G G+ ++L L
Sbjct: 337 KRLQNPHVVPVSAKSGEGLEELLNGL 362
>gnl|CDD|110047 pfam01018, GTP1_OBG, GTP1/OBG. The N-terminal domain of the
Spo0B-associated GTP-binding protein has the OBG fold,
which is formed by three glycine-rich regions inserted
into a small 8-stranded beta-sandwich these regions form
six left-handed collagen-like helices packed and
H-bonded together.
Length = 156
Score = 223 bits (571), Expect = 4e-59
Identities = 84/156 (53%), Positives = 112/156 (71%)
Query: 3 FLDEAKVYIRSGDGGAGGISFRREKFIEFGGPDGGSGGRGGDVWIQATSNLNTLIDFRYQ 62
F+D+ ++Y+ +G+GG G +SFRREK++ GGPDGG+GGRGGDV +A NL+TL+DFRY+
Sbjct: 1 FVDQVEIYVAAGNGGNGCVSFRREKYVPKGGPDGGNGGRGGDVIFEADENLDTLLDFRYK 60
Query: 63 QHFKAQHGEKGMKRNRSGAKGEDVVLTVPVGTQVFEEDGISLICDLDQEGQRIILAPGGN 122
+HFKA+ G+ G RN G GED+V+ VP GT V + D L+ DL GQR++ A GG
Sbjct: 61 KHFKAEDGKHGGSRNCHGKNGEDLVIKVPPGTVVLDLDNGELLADLVHHGQRLLAAKGGK 120
Query: 123 GGFGNAHFKSSTNQAPYYANPGILGQEKIIWLKLKL 158
GG GNA FKS N+AP YA G G+E+ I L+LKL
Sbjct: 121 GGLGNAAFKSPVNRAPGYALNGEPGEERDIRLELKL 156
>gnl|CDD|133298 cd01898, Obg, Obg subfamily. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members
of the subfamily contain two equally and highly
conserved domains, a C-terminal GTP binding domain and
an N-terminal glycine-rich domain.
Length = 170
Score = 220 bits (563), Expect = 5e-58
Identities = 78/170 (45%), Positives = 118/170 (69%), Gaps = 3/170 (1%)
Query: 160 ADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIK 218
AD+G++GLPNAGKST L++++ AKPKIADYPFTTL PNLG+V+ + + F++ADIPG+I+
Sbjct: 1 ADVGLVGLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDDGRSFVVADIPGLIE 60
Query: 219 NAHQGAGIGDRFLKHTERTHVLLHIVS-ALEENVQAAYQCILDELSAYNSELRKKIEIVG 277
A +G G+G RFL+H ERT +LLH++ + +++ Y+ I +EL YN EL +K IV
Sbjct: 61 GASEGKGLGHRFLRHIERTRLLLHVIDLSGDDDPVEDYKTIRNELELYNPELLEKPRIVV 120
Query: 278 LSQIDTVDSDTLARKKNELATQCGQVP-FEFSSITGHGIPQILECLHDKI 326
L++ID +D + L EL + P F S++TG G+ ++L L + +
Sbjct: 121 LNKIDLLDEEELFELLKELLKELWGKPVFPISALTGEGLDELLRKLAELL 170
>gnl|CDD|133281 cd01881, Obg_like, The Obg-like subfamily consists of five
well-delimited, ancient subfamilies, namely Obg, DRG,
YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg,
DRG, YyaF/YchF, and Ygr210) are characterized by a
distinct glycine-rich motif immediately following the
Walker B motif (G3 box). Obg/CgtA is an essential gene
that is involved in the initiation of sporulation and
DNA replication in the bacteria Caulobacter and
Bacillus, but its exact molecular role is unknown.
Furthermore, several OBG family members possess a
C-terminal RNA-binding domain, the TGS domain, which is
also present in threonyl-tRNA synthetase and in
bacterial guanosine polyphosphatase SpoT. Nog1 is a
nucleolar protein that might function in ribosome
assembly. The DRG and Nog1 subfamilies are ubiquitous
in archaea and eukaryotes, the Ygr210 subfamily is
present in archaea and fungi, and the Obg and YyaF/YchF
subfamilies are ubiquitous in bacteria and eukaryotes.
The Obg/Nog1 and DRG subfamilies appear to form one
major branch of the Obg family and the Ygr210 and YchF
subfamilies form another branch. No GEFs, GAPs, or GDIs
for Obg have been identified.
Length = 176
Score = 166 bits (422), Expect = 1e-41
Identities = 65/176 (36%), Positives = 102/176 (57%), Gaps = 13/176 (7%)
Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIKNAHQ 222
++GLPN GKST L ++T AKPK+A+YPFTTL PNLG+V+ +ADIPG+I+ A +
Sbjct: 1 LVGLPNVGKSTLLNALTNAKPKVANYPFTTLEPNLGVVEVPDGARIQVADIPGLIEGASE 60
Query: 223 GAGIGDRFLKHTERTHVLLHIVSALEE------NVQAAYQCILDELSAYNSE-----LRK 271
G G+G++FL H R +LH+V A E+ + Y+ + EL Y+ E L
Sbjct: 61 GRGLGNQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETILGLLTA 120
Query: 272 KIEIVGLSQIDTVDSDTLARKK-NELATQCGQVPFEFSSITGHGIPQILECLHDKI 326
K I L++ID D++ L + ELA + G S+ T G+ +++ +++ +
Sbjct: 121 KPVIYVLNKIDLDDAEELEEELVRELALEEGAEVVPISAKTEEGLDELIRAIYELL 176
>gnl|CDD|30362 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 95.6 bits (238), Expect = 2e-20
Identities = 39/108 (36%), Positives = 60/108 (55%), Gaps = 22/108 (20%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK----------EGYK----- 206
IGI+GLPN GKST ++T+A +IA+YPF T+ PN+G+V E K
Sbjct: 5 IGIVGLPNVGKSTLFNALTKAGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVKCPPKI 64
Query: 207 -----EFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSALEE 249
EF+ DI G++K A +G G+G++FL + ++H+V +
Sbjct: 65 RPAPVEFV--DIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCFGD 110
>gnl|CDD|133299 cd01899, Ygr210, Ygr210 subfamily. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210
and YyaF/YchF subfamilies appear to form one major
branch of the Obg-like family. Among eukaryotes, the
Ygr210 subfamily is represented only in fungi. These
fungal proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 91.9 bits (229), Expect = 2e-19
Identities = 39/109 (35%), Positives = 59/109 (54%), Gaps = 24/109 (22%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGI-----------------VKEG 204
IG++G PNAGKSTF + T A +IA+YPFTT+ PN+G+ + G
Sbjct: 1 IGLVGKPNAGKSTFFNAATLADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYG 60
Query: 205 Y----KEFI---LADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSA 246
K ++ L D+ G++ AH+G G+G++FL L+H+V A
Sbjct: 61 KCIDGKRYVPVELIDVAGLVPGAHEGKGLGNKFLDDLRDADALIHVVDA 109
>gnl|CDD|36704 KOG1491, KOG1491, KOG1491, Predicted GTP-binding protein (ODN
superfamily) [General function prediction only].
Length = 391
Score = 87.3 bits (216), Expect = 5e-18
Identities = 50/180 (27%), Positives = 82/180 (45%), Gaps = 28/180 (15%)
Query: 147 GQEKIIWLKLKLIADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIV----- 201
++K++ + IGI+GLPN GKSTF ++T++K A++PF T+ PN V
Sbjct: 8 EEKKVLLGRDGNNLKIGIVGLPNVGKSTFFNALTKSKAGAANFPFCTIDPNEARVEVPDS 67
Query: 202 -----KEGYKE------FI-LADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSALEE 249
Y F+ + DI G++K A G G+G++FL H + H+V A E+
Sbjct: 68 RFDLLCPIYGPKSKVPAFLTVYDIAGLVKGASAGEGLGNKFLSHIRHVDAIFHVVRAFED 127
Query: 250 N----VQAAY------QCILDELSAYNSE-LRKKIEIVGLSQIDTVDSDTLARKKNELAT 298
V+ + I +EL + E L K++E + T + + K E
Sbjct: 128 TDIIHVEGGVDPVRDIEIIQEELRLKDLEFLEKRLEKLEKKHKRTKSNLETKQLKFEYGL 187
>gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function.
Length = 106
Score = 83.5 bits (207), Expect = 8e-17
Identities = 38/98 (38%), Positives = 56/98 (57%), Gaps = 3/98 (3%)
Query: 171 GKSTFLASVT-RAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQGAG-IGD 228
GKST + ++T + + ++DYP TT PN G V+ K+ IL D PGII+ A +G G +G+
Sbjct: 1 GKSTLINALTGKKRAIVSDYPGTTRDPNEGRVELDGKQIILVDTPGIIEGASKGEGELGN 60
Query: 229 RFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYN 266
R L+ E ++LH+V A E + ILD L
Sbjct: 61 RTLEAIEEADLILHVVDASEG-LTEEDLEILDLLLELG 97
>gnl|CDD|133300 cd01900, YchF, YchF subfamily. YchF is a member of the Obg family,
which includes four other subfamilies of GTPases: Obg,
DRG, Ygr210, and NOG1. Obg is an essential gene that is
involved in DNA replication in C. crescentus and
Streptomyces griseus and is associated with the
ribosome. Several members of the family, including
YchF, possess the TGS domain related to the RNA-binding
proteins. Experimental data and genomic analysis
suggest that YchF may be part of a nucleoprotein complex
and may function as a GTP-dependent translational
factor.
Length = 274
Score = 82.1 bits (204), Expect = 2e-16
Identities = 46/138 (33%), Positives = 72/138 (52%), Gaps = 25/138 (18%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK----------EGYK----- 206
IGI+GLPN GKST ++T+A + A+YPF T+ PN+GIV E K
Sbjct: 1 IGIVGLPNVGKSTLFNALTKAGAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKIV 60
Query: 207 ----EFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSALE-ENVQAAYQCI--L 259
EF+ DI G++K A +G G+G++FL H + H+V E +++ + +
Sbjct: 61 PATIEFV--DIAGLVKGASKGEGLGNKFLSHIREVDAIAHVVRCFEDDDITHVEGSVDPV 118
Query: 260 DELSAYNSELRKK-IEIV 276
++ N+EL +E V
Sbjct: 119 RDIEIINTELILADLETV 136
>gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 81.4 bits (201), Expect = 3e-16
Identities = 48/150 (32%), Positives = 69/150 (46%), Gaps = 15/150 (10%)
Query: 159 IADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIK 218
A + ++G P+ GKST L +T K ++ADYPFTTL P G+++ + L D+PGII+
Sbjct: 63 DATVALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIE 122
Query: 219 NAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKK------ 272
A G G G + L R L+ IV + E+ I EL L K+
Sbjct: 123 GASSGRGRGRQVLS-VARNADLIIIVLDVFEDPH-HRDIIERELEDVGIRLNKRPPDVTI 180
Query: 273 -------IEIVGLSQIDTVDSDTLARKKNE 295
I I G + +D DT+ E
Sbjct: 181 KKKESGGIRINGTGPLTHLDEDTVRAILRE 210
>gnl|CDD|133296 cd01896, DRG, The developmentally regulated GTP-binding protein
(DRG) subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their
widespread expression in various tissues and high
conservation among distantly related species in
eukaryotes and archaea, DRG proteins may regulate
fundamental cellular processes. It is proposed that the
DRG subfamily proteins play their physiological roles
through RNA binding.
Length = 233
Score = 76.0 bits (188), Expect = 1e-14
Identities = 34/104 (32%), Positives = 55/104 (52%), Gaps = 4/104 (3%)
Query: 160 ADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKN 219
A + ++G P+ GKST L+ +T K ++A Y FTTL G+++ + L D+PGII+
Sbjct: 1 ARVALVGFPSVGKSTLLSKLTNTKSEVAAYEFTTLTCVPGVLEYKGAKIQLLDLPGIIEG 60
Query: 220 AHQGAGIGDRFLKHTERTHVLLHIV-SALEENVQAAYQCILDEL 262
A G G G + + RT L+ +V A + + + EL
Sbjct: 61 AADGKGRGRQVIA-VARTADLILMVLDATKPEGH--REILEREL 101
>gnl|CDD|133297 cd01897, 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 = 168
Score = 74.1 bits (183), Expect = 6e-14
Identities = 47/176 (26%), Positives = 81/176 (46%), Gaps = 28/176 (15%)
Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQG 223
I G PN GKS+ + +TRAKP++A YPFTT +G Y + + D PG++
Sbjct: 5 IAGYPNVGKSSLVNKLTRAKPEVAPYPFTTKSLFVGHFDYKYLRWQVIDTPGLL------ 58
Query: 224 AGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILD--ELSAY------------NSEL 269
DR L+ ER + + ++AL +++AA + D E Y
Sbjct: 59 ----DRPLE--ERNTIEMQAITAL-AHLRAAVLFLFDPSETCGYSLEEQLSLFEEIKPLF 111
Query: 270 RKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECLHDK 325
+ K IV L++ID + + L+ + E G+ + S++T G+ ++ +
Sbjct: 112 KNKPVIVVLNKIDLLTFEDLSEIEEEEE-LEGEEVLKISTLTEEGVDEVKNKACEL 166
>gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 70.7 bits (173), Expect = 5e-13
Identities = 46/170 (27%), Positives = 79/170 (46%), Gaps = 26/170 (15%)
Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQG 223
+ G PN GKS+ + +T AKP++A YPFTT ++G + GY + D PG++
Sbjct: 173 VAGYPNVGKSSLVRKLTTAKPEVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLL------ 226
Query: 224 AGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILD--ELSAYNSE-----------LR 270
DR L+ ER + + AL ++ + D E Y+ E L
Sbjct: 227 ----DRPLE--ERNEIERQAILAL-RHLAGVILFLFDPSETCGYSLEEQISLLEEIKELF 279
Query: 271 KKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILE 320
K +V +++ID D + L + + + G+ P + S+ G G+ ++ E
Sbjct: 280 KAPIVVVINKIDIADEEKLEEIEASVLEEGGEEPLKISATKGCGLDKLRE 329
>gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like. This
family includes several distinct subfamilies (TrmE/ThdF,
FeoB, YihA (EngG), 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 = 163
Score = 68.9 bits (169), Expect = 2e-12
Identities = 39/165 (23%), Positives = 70/165 (42%), Gaps = 12/165 (7%)
Query: 164 IIGLPNAGKSTFLASVTRAKP-KIADYPFTTLYPNLGIVKEGYK-EFILADIPGIIKNAH 221
+ G NAGKS+ L ++ + ++ P TT P + + G +L D PGI +
Sbjct: 1 LFGRTNAGKSSLLNALLGQEVAIVSPVPGTTTDPVEYVWELGPLGPVVLIDTPGIDEAGG 60
Query: 222 QGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLSQI 281
G + + ER ++L +V A + +L+ L K + ++ L++I
Sbjct: 61 LGREREELARRVLERADLILFVVDADLRAD-EEEEKLLELLRERG----KPV-LLVLNKI 114
Query: 282 DTVDSD----TLARKKNELATQCGQVPFEFSSITGHGIPQILECL 322
D + + L + L G S++TG GI ++ E L
Sbjct: 115 DLLPEEEEEELLELRLLILLLLLGLPVIAVSALTGEGIDELREAL 159
>gnl|CDD|36699 KOG1486, KOG1486, KOG1486, GTP-binding protein DRG2 (ODN
superfamily) [Signal transduction mechanisms].
Length = 364
Score = 65.3 bits (159), Expect = 2e-11
Identities = 36/113 (31%), Positives = 56/113 (49%), Gaps = 2/113 (1%)
Query: 160 ADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKN 219
A + +IG P+ GKST L+ +T + A Y FTTL G++ L D+PGII+
Sbjct: 63 ARVALIGFPSVGKSTLLSKITSTHSEAASYEFTTLTCIPGVIHYNGANIQLLDLPGIIEG 122
Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKK 272
A QG G G + + ++L ++ A + Q + + EL A L K+
Sbjct: 123 ASQGKGRGRQVIAVARTADLILMVLDATKSEDQR--EILEKELEAVGIRLNKR 173
>gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 57.5 bits (139), Expect = 5e-09
Identities = 47/173 (27%), Positives = 74/173 (42%), Gaps = 20/173 (11%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKI-ADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNA 220
+ IIG PN GKST L ++ K I + P TT GIV + I D PGI K
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGIHKPK 68
Query: 221 HQGAGIGDRFLKHTERT----HVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIV 276
H +G+ K ++L +V A +E + IL++L K I+
Sbjct: 69 HA---LGELMNKAARSALKDVDLILFVVDA-DEGWGPGDEFILEQLKK-----TKTPVIL 119
Query: 277 GLSQIDTVDSDTLARKKNELATQCGQVPF----EFSSITGHGIPQILECLHDK 325
+++ID V T+ K + +PF S++ G + +LE + +
Sbjct: 120 VVNKIDKVKPKTVLLKLIAFLKK--LLPFKEIVPISALKGDNVDTLLEIIKEY 170
>gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 56.8 bits (137), Expect = 8e-09
Identities = 40/176 (22%), Positives = 81/176 (46%), Gaps = 8/176 (4%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIKN- 219
+ ++G NAGKST ++T A +AD F TL P ++ ++ +L D G I++
Sbjct: 195 VALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDL 254
Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLS 279
H L+ + +LLH+V A + + + + D L+ ++ + I+ L+
Sbjct: 255 PHPLVEAFKSTLEEVKEADLLLHVVDASDPEILEKLEAVEDVLAEIGAD--EIPIILVLN 312
Query: 280 QIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECLHDKIFSIRGENEF 335
+ID ++ + + + + P S+ TG G+ + E + + + +R E
Sbjct: 313 KIDLLEDEEILAELERGSPN----PVFISAKTGEGLDLLRERIIELLSGLRTEVTL 364
>gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control,
cell division, chromosome partitioning, Signal
transduction mechanisms].
Length = 379
Score = 54.3 bits (130), Expect = 4e-08
Identities = 56/282 (19%), Positives = 93/282 (32%), Gaps = 70/282 (24%)
Query: 95 QVFEEDGISLICDLDQEGQRIILAPGGNGG-------FGNAHFKSSTNQAPYYANPGILG 147
EE G + L A FG + +++S P Y
Sbjct: 7 YEMEELGHMINTHLASSLFVFSSASTSTYRERVEKLFFGYSDWETSV--GPLYPAALESR 64
Query: 148 QEKIIWLKLKLIADIGIIGLPNAGKSTFLASVTRAKPKIA-DYPFTTLYPNLGIVKEGYK 206
E+ + + + +IG PN GKST + K TT + LGI+ G
Sbjct: 65 DEE----EAQKSLYVAVIGAPNVGKSTLTNQMIGQKVSAVSRKVHTTRHRILGIITSGET 120
Query: 207 EFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCI-------- 258
+ + D PG++ K R H+++ ++ + Q A C+
Sbjct: 121 QLVFYDTPGLVSK------------KMHRRHHLMMSVLQNPRDAAQNA-DCVVVVVDASA 167
Query: 259 ---------LDELSAY---------NSELRKKIEIVGLSQIDTVDSDTLARKKNELA--- 297
L L Y N + K + + L+ D + + LA+ K E+
Sbjct: 168 TRTPLHPRVLHMLEEYSKIPSILVMNKIDKLKQKRLLLNLKDLLTNGELAKLKLEVQEKF 227
Query: 298 ----------TQCGQVPFE----FSSITGHGIPQILECLHDK 325
T CG FE S++ G GI + + L +
Sbjct: 228 TDVPSDEKWRTICGWSHFERVFMVSALYGEGIKDLKQYLMSQ 269
>gnl|CDD|133363 cd04163, Era, Era subfamily. 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 = 52.8 bits (128), Expect = 1e-07
Identities = 46/175 (26%), Positives = 73/175 (41%), Gaps = 24/175 (13%)
Query: 162 IGIIGLPNAGKSTFLASVTRAK-----PKIADYPFTTLYPNLGIVKEGYKEFILADIPGI 216
+ I+G PN GKST L ++ K PK P TT GI + + I D PGI
Sbjct: 6 VAIVGRPNVGKSTLLNALVGQKISIVSPK----PQTTRNRIRGIYTDDDAQIIFVDTPGI 61
Query: 217 IKNAHQGAGIGDRFLKHTERT----HVLLHIVSALEENVQAAYQCILDELSAYNSELRKK 272
K + +G+R +K ++L +V A E + IL+ L
Sbjct: 62 HKPKKK---LGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEF-ILELLKKSK----TP 113
Query: 273 IEIVGLSQIDTV-DSDTLARKKNEL-ATQCGQVPFEFSSITGHGIPQILECLHDK 325
+ I+ L++ID V D + L +L F S++ G + ++LE +
Sbjct: 114 V-ILVLNKIDLVKDKEDLLPLLEKLKELGPFAEIFPISALKGENVDELLEEIVKY 167
>gnl|CDD|36703 KOG1490, KOG1490, KOG1490, GTP-binding protein CRFG/NOG1 (ODN
superfamily) [General function prediction only].
Length = 620
Score = 52.7 bits (126), Expect = 1e-07
Identities = 39/142 (27%), Positives = 65/142 (45%), Gaps = 11/142 (7%)
Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQG 223
+ G PN GKS+F VTRA ++ Y FTT +G + Y + + D PGI+
Sbjct: 173 VCGYPNVGKSSFNNKVTRADDEVQPYAFTTKLLLVGHLDYKYLRWQVIDTPGILDRP--- 229
Query: 224 AGIGDRFLKHTERTHVLLHIVSALEENVQAAYQC---ILDELSAYNS---ELRKKIEIVG 277
DR + + L H+ SA+ + + C + ++ Y+S K+ I+
Sbjct: 230 --EEDRNIIEMQIITALAHLRSAVLYFMDLSEMCGYSVAAQVKLYHSIKPLFANKVTILV 287
Query: 278 LSQIDTVDSDTLARKKNELATQ 299
L++ID + + L +K EL
Sbjct: 288 LNKIDAMRPEDLDQKNQELLQT 309
>gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 52.2 bits (125), Expect = 2e-07
Identities = 38/175 (21%), Positives = 74/175 (42%), Gaps = 27/175 (15%)
Query: 161 DIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIK-N 219
+ ++G PN GK+T ++T A K+ ++P T+ G +K E + D+PG
Sbjct: 5 TVALVGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPGTYSLT 64
Query: 220 AHQG-AGIGDRFLKHTERTHVLLHIVSA--LEENVQAAYQCILDELSAYNSELRKKIEIV 276
A+ + FL + +++++V A LE N+ Q + EL + I+
Sbjct: 65 AYSEDEKVARDFLL-EGKPDLIVNVVDATNLERNLYLTLQLL---------ELGIPM-IL 113
Query: 277 GLSQIDTVDSDTLARKKN------ELATQCGQVPFEFSSITGHGIPQILECLHDK 325
L+ ID A+K+ +L+ G + G G+ ++ + +
Sbjct: 114 ALNMID------EAKKRGIRIDIEKLSKLLGVPVVPTVAKRGEGLEELKRAIIEL 162
>gnl|CDD|36700 KOG1487, KOG1487, KOG1487, GTP-binding protein DRG1 (ODN
superfamily) [Signal transduction mechanisms].
Length = 358
Score = 49.2 bits (117), Expect = 1e-06
Identities = 32/86 (37%), Positives = 48/86 (55%), Gaps = 1/86 (1%)
Query: 159 IADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIK 218
A +G +G P+ GKST L+ +T ++A Y FTTL G+++ + L D+PGII+
Sbjct: 59 DARVGFVGFPSVGKSTLLSKLTGTFSEVAAYEFTTLTTVPGVIRYKGAKIQLLDLPGIIE 118
Query: 219 NAHQGAGIGDRFLKHTERTHVLLHIV 244
A G G G + + RT L+ IV
Sbjct: 119 GAKDGKGRGKQVIA-VARTCNLIFIV 143
>gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 44.8 bits (106), Expect = 4e-05
Identities = 40/162 (24%), Positives = 65/162 (40%), Gaps = 12/162 (7%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKI-ADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNA 220
+ I+G PN GKST +T + I +D P T G + +EFIL D G+
Sbjct: 6 VAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLDDGD 65
Query: 221 HQGAG--IGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGL 278
I ++ L E V+L +V E + A + I L R K ++ +
Sbjct: 66 EDELQELIREQALIAIEEADVILFVVDG-REGITPADEEIAKIL------RRSKKPVILV 118
Query: 279 SQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILE 320
++ +D+ E + P S+ G GI +L+
Sbjct: 119 --VNKIDNLKAEELAYEFYSLGFGEPVPISAEHGRGIGDLLD 158
Score = 41.7 bits (98), Expect = 3e-04
Identities = 43/190 (22%), Positives = 79/190 (41%), Gaps = 19/190 (10%)
Query: 147 GQEKIIWLKLKLIADIGIIGLPNAGKSTFLASVTRAKPKIA-DYPFTTLYPNLGIVKEGY 205
E+ + I IIG PN GKS+ + ++ + I D TT +
Sbjct: 166 PDEEEEEEEETDPIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDG 225
Query: 206 KEFILADIPGI-----IKNAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILD 260
++++L D GI I + + + R LK ER V+L ++ A E D
Sbjct: 226 RKYVLIDTAGIRRKGKITESVEKYSVA-RTLKAIERADVVLLVIDATEGI------SEQD 278
Query: 261 ELSAYNSELRKKIEIVGLSQIDTVDSD--TLARKKNELATQCGQVPFE----FSSITGHG 314
A E + ++ +++ D V+ D T+ K +L + + F S++TG G
Sbjct: 279 LRIAGLIEEAGRGIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQG 338
Query: 315 IPQILECLHD 324
+ ++ E + +
Sbjct: 339 LDKLFEAIKE 348
>gnl|CDD|133280 cd01879, FeoB, 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 = 158
Score = 44.3 bits (106), Expect = 4e-05
Identities = 43/172 (25%), Positives = 80/172 (46%), Gaps = 29/172 (16%)
Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGI--IKNAH 221
++G PN GK+T ++T A+ K+ ++P T+ G K G KE + D+PG +
Sbjct: 1 LVGNPNVGKTTLFNALTGARQKVGNWPGVTVEKKEGRFKLGGKEIEIVDLPGTYSLSPYS 60
Query: 222 QGAGIGDRFLKHTERTHVLLHIV--SALEENVQAAYQCILDELSAYNSELRKKIEIVGLS 279
+ + FL E+ +++++V + LE N+ Q + EL + +V L+
Sbjct: 61 EDEKVARDFL-LGEKPDLIVNVVDATNLERNLYLTLQLL---------ELGLPV-VVALN 109
Query: 280 QIDTVDSDTLARKK------NELATQCGQVP-FEFSSITGHGIPQILECLHD 324
ID A K+ ++L+ G VP S+ G GI ++ + + +
Sbjct: 110 MID------EAEKRGIKIDLDKLSELLG-VPVVPTSARKGEGIDELKDAIAE 154
>gnl|CDD|35631 KOG0410, KOG0410, KOG0410, Predicted GTP binding protein [General
function prediction only].
Length = 410
Score = 41.2 bits (96), Expect = 4e-04
Identities = 44/184 (23%), Positives = 75/184 (40%), Gaps = 27/184 (14%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIKN- 219
I ++G NAGKST + ++T+A D F TL P L +L D G I +
Sbjct: 181 IAVVGYTNAGKSTLIKALTKAALYPNDRLFATLDPTLHSAHLPSGNFVLLTDTVGFISDL 240
Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLS 279
Q L+ +LLH+V ++S N+E +++ + L+
Sbjct: 241 PIQLVAAFQATLEEVAEADLLLHVV----------------DISHPNAEEQRETVLHVLN 284
Query: 280 QIDTVDSDTLARK---KNELATQCGQVPFE------FSSITGHGIPQILECLHDKIFSIR 330
QI L N++ + +V E S++TG G+ ++L+ K+ S
Sbjct: 285 QIGVPSEPKLQNMIEVDNKIDYEEDEVEEEKNLDVGISALTGDGLEELLKAEETKVASET 344
Query: 331 GENE 334
+E
Sbjct: 345 TVDE 348
>gnl|CDD|145523 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 = 188
Score = 40.5 bits (96), Expect = 7e-04
Identities = 42/170 (24%), Positives = 75/170 (44%), Gaps = 29/170 (17%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGI--IKN 219
I ++G PN GK+T ++T A+ + ++P T+ G K E + D+PG +
Sbjct: 2 IALVGNPNVGKTTLFNALTGARQHVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGTYSLSP 61
Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSA--LEENVQAAYQCILDELSAYNSELRKKIEIVG 277
+ + +L E+ V++++V A LE N+ Q + EL + +V
Sbjct: 62 YSEEEKVARDYL-LEEKPDVIINVVDATNLERNLYLTLQLL---------ELGIPV-VVA 110
Query: 278 LSQIDTVDSDTLARKK------NELATQCGQVP-FEFSSITGHGIPQILE 320
L+ +D A KK +L+ G VP S+ G GI ++ +
Sbjct: 111 LNMMD------EAEKKGIKIDIKKLSELLG-VPVVPTSARKGEGIDELKD 153
>gnl|CDD|133279 cd01878, HflX, 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 = 38.6 bits (91), Expect = 0.002
Identities = 45/182 (24%), Positives = 76/182 (41%), Gaps = 38/182 (20%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNL-GIVKEGYKEFILADIPGIIKNA 220
+ ++G NAGKST ++T A D F TL P + +E +L D G I++
Sbjct: 44 VALVGYTNAGKSTLFNALTGADVYAEDQLFATLDPTTRRLRLPDGREVLLTDTVGFIRD- 102
Query: 221 HQGAGIGDRFLKHT----------ERTH--VLLHIVSA----LEENVQAAYQCILDELSA 264
L H E +LLH+V A EE ++ + +L EL A
Sbjct: 103 ----------LPHQLVEAFRSTLEEVAEADLLLHVVDASDPDYEEQIETVEK-VLKELGA 151
Query: 265 YNSELRKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECLHD 324
+ I+ L++ID +D + L + + S+ TG G+ ++LE + +
Sbjct: 152 ED-----IPMILVLNKIDLLDDEELEERLEAGRPDAVFI----SAKTGEGLDELLEAIEE 202
Query: 325 KI 326
+
Sbjct: 203 LL 204
>gnl|CDD|133258 cd00882, Ras_like_GTPase, 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 regulate
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 = 157
Score = 38.6 bits (90), Expect = 0.002
Identities = 29/166 (17%), Positives = 54/166 (32%), Gaps = 18/166 (10%)
Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFT--TLYPNLGIVKEGYKEFILADIPGIIKNAH 221
++G GK++ L + + +Y T Y V + + D G
Sbjct: 1 VVGDSGVGKTSLLNRLLGGEFVPEEYETTIIDFYSKTIEVDGKKVKLQIWDTAGQE---- 56
Query: 222 QGAGIGDRFLKHTER-THVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVG--- 277
+ R ++ + + + L + I +VG
Sbjct: 57 ----RFRSLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKI 112
Query: 278 -LSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECL 322
L + V + LA + LA + G FE S+ TG + ++ E L
Sbjct: 113 DLPEERVVSEEELAEQ---LAKELGVPYFETSAKTGENVEELFEEL 155
>gnl|CDD|133295 cd01895, EngA2, EngA2 subfamily. This 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 = 38.2 bits (90), Expect = 0.003
Identities = 28/93 (30%), Positives = 43/93 (46%), Gaps = 7/93 (7%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIA-DYPFTTLYPNLGIVKEGYKEFILADIPGIIKNA 220
I IIG PN GKS+ + ++ + I D TT + K++ L D GI +
Sbjct: 5 IAIIGRPNVGKSSLVNALLGEERVIVSDIAGTTRDSIDVPFEYDGKKYTLIDTAGIRRKG 64
Query: 221 HQGAGIGDRF-----LKHTERTHVLLHIVSALE 248
GI +++ LK ER V+L ++ A E
Sbjct: 65 KVEEGI-EKYSVLRTLKAIERADVVLLVIDATE 96
>gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 37.7 bits (87), Expect = 0.005
Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 146 LGQEKIIWLK----LKLIADIGIIGLPNAGKSTFL-ASVTRAKPKIADYPFTTLYPNLGI 200
L +EKI LK LK +G++G PN GKST + + + K ++ P TT
Sbjct: 115 LSEEKIKRLKKKGLLKRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIK 174
Query: 201 VKEGYKEFILADIPGII 217
+ +G L D PGII
Sbjct: 175 LDDG---IYLLDTPGII 188
>gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation,
ribosomal structure and biogenesis].
Length = 531
Score = 37.7 bits (87), Expect = 0.005
Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 20/184 (10%)
Query: 156 LKLIADIGIIGLPNAGKSTFLASVTRAKPKI-ADYPFTT---LYPNLGIVKEGYKEFILA 211
L+ I I+G PN GKS+ L +++R I + P TT + + + G L+
Sbjct: 265 LQSGLQIAIVGRPNVGKSSLLNALSREDRSIVSPVPGTTRDAIEAQVTV--NGVP-VRLS 321
Query: 212 DIPGIIKNAHQG-AGIG-DRFLKHTERTHVLLHIVSA----LEENVQAA--YQCILDELS 263
D GI + ++ G +G +R K ER V+L +V A E +++ A + L
Sbjct: 322 DTAGIREESNDGIEALGIERARKRIERADVILLVVDAEESDTESDLKIARILETEGVGLV 381
Query: 264 AYNSELRKKIEIVGLSQIDTV---DSDTLARKKNELATQCGQVPF--EFSSITGHGIPQI 318
+++ K+ I+ ++ D V T A P E S T G ++
Sbjct: 382 VIVNKMEKQRIILVANKSDLVSKIPEMTKIPVVYPSAEGRSVFPIVVEVSCTTKEGCERL 441
Query: 319 LECL 322
L
Sbjct: 442 STAL 445
>gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 36.7 bits (85), Expect = 0.010
Identities = 42/179 (23%), Positives = 69/179 (38%), Gaps = 19/179 (10%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKI-ADYPFTT---LYPNLGIVKEGYKEFILADIPGII 217
+ IIG PN GKS+ L ++ I D TT + ++ + G L D GI
Sbjct: 220 VVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDVIEEDINL--NGIP-VRLVDTAGIR 276
Query: 218 KNAHQGAGIG-DRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIV 276
+ IG +R K E ++L ++ A + + ++L+ +KK IV
Sbjct: 277 ETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDK-------EDLALIELLPKKKPIIV 329
Query: 277 GLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECLHDKIFSIRGENEF 335
L++ D V L +K S+ TG G+ + E + G E
Sbjct: 330 VLNKADLVSKIELESEKLANGDAI----ISISAKTGEGLDALREAIKQLFGKGLGNQEG 384
>gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 36.4 bits (84), Expect = 0.013
Identities = 38/190 (20%), Positives = 68/190 (35%), Gaps = 33/190 (17%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKP--KIADYPFTTLYPNLGIVKEGYKEFILADIPG---- 215
I G N GKS+ + ++T K + + P T N V + E L D+PG
Sbjct: 27 IAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVDD---ELRLVDLPGYGYA 83
Query: 216 ---IIKNAHQGAGIGDRFLKHTE--RTHVLLHIVSALEENVQAAYQCILDELSAYNSELR 270
I + K +L+ ++ + + +L EL
Sbjct: 84 KVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFLL--------ELG 135
Query: 271 KKIEIVGLSQIDTVDSDTLARKKNELATQCGQVP------FEFSSITGHGIPQILECLHD 324
+ +V L++ D + ++ N++A + + P FSS+ GI + L
Sbjct: 136 IPVIVV-LTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDE----LKA 190
Query: 325 KIFSIRGENE 334
KI E +
Sbjct: 191 KILEWLKEAK 200
>gnl|CDD|57927 cd01856, YlqF, YlqF. Proteins of the YlqF 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. The YlqF subfamily is represented in a
phylogenetically diverse array of bacteria (including
gram-positive bacteria, proteobacteria, Synechocystis,
Borrelia, and Thermotoga) and in all eukaryotes..
Length = 171
Score = 35.6 bits (82), Expect = 0.021
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 164 IIGLPNAGKSTFLASVTRAK-PKIADYPFTTLYPNLGIVKEGYKEFILADIPGI 216
++G+PN GKST + + K K+ + P T + +K ++L D PGI
Sbjct: 120 VVGIPNVGKSTLINRLRGKKVAKVGNKPGVT--KGIQWIKISPGIYLL-DTPGI 170
>gnl|CDD|57924 cd01849, YlqF_related_GTPase, YlqF-related GTPases. These proteins
are found in bacteria, eukaryotes, and archaea. They
all exhibit a circular permutation of the GTPase
signature motifs so that the order of the conserved G
box motifs is G4-G5-G1-G2-G3, with G4 and G5 being
permuted from the C-terminal region of proteins in the
Ras superfamily to the N-terminus of YlqF-related
GTPases..
Length = 155
Score = 33.8 bits (77), Expect = 0.075
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 161 DIGIIGLPNAGKSTFLASVTRA-KPKIADYP-FTTLYPNLGIVKEGYKEFILADIPGI 216
+G+IG PN GKS+ + ++ K K+ + P TT + + + L D PGI
Sbjct: 102 TVGVIGYPNVGKSSVINALLNKLKLKVGNVPGTTTSQQEVKLDNKIK----LLDTPGI 155
>gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 33.4 bits (75), Expect = 0.079
Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 2/59 (3%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYP-FTTLYPNLGIVKEGYK-EFILADIPGIIK 218
I ++G GK+T L + + P L P I + L D G +
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEE 66
>gnl|CDD|133371 cd04171, SelB, SelB subfamily. 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 = 164
Score = 33.3 bits (77), Expect = 0.089
Identities = 38/126 (30%), Positives = 52/126 (41%), Gaps = 30/126 (23%)
Query: 208 FILADIPG---IIKNAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCI--LDEL 262
FI D+PG IKN GAG D VLL V A +E + Q L+ L
Sbjct: 55 FI--DVPGHEKFIKNMLAGAGGID---------LVLL--VVAADEGIMP--QTREHLEIL 99
Query: 263 SAYNSELRKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVP------FEFSSITGHGIP 316
K+ +V L++ D VD D L + E+ F S++TG GI
Sbjct: 100 ELLGI---KRG-LVVLTKADLVDEDWLELVEEEIRELLAGTFLADAPIFPVSAVTGEGIE 155
Query: 317 QILECL 322
++ E L
Sbjct: 156 ELKEYL 161
>gnl|CDD|57928 cd01857, HSR1_MMR1, HSR1/MMR1. Human HSR1, is localized to the
human MHC class I region and is highly homologous to a
putative GTP-binding protein, MMR1 from mouse. These
proteins represent a new subfamily of GTP-binding
proteins that has only eukaryote members. This subfamily
shows a circular permutation of the GTPase signature
motifs so that the C-terminal strands 5, 6, and 7
(strand 6 contains the G4 box with sequence NKXD) are
relocated to the N terminus..
Length = 141
Score = 32.4 bits (74), Expect = 0.18
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 14/77 (18%)
Query: 147 GQEKIIWLKLKLIADIGIIGLPNAGKSTFL-ASVTRAKPKIADYP-----FTTLYPNLGI 200
G + + LK A IG++G PN GKS+ + A V + K ++ P F T++
Sbjct: 71 GIVVVFFSALKENATIGLVGYPNVGKSSLINALVGKKKVSVSATPGKTKHFQTIFLT--- 127
Query: 201 VKEGYKEFILADIPGII 217
L D PG++
Sbjct: 128 -----PTITLCDCPGLV 139
>gnl|CDD|57931 cd04178, Nucleostemin_like, Nucleostemin-like. Nucleostemin (NS)
is a nucleolar protein that functions as a regulator of
cell growth and proliferation in stem cells and in
several types of cancer cells, but is not expressed in
the differentiated cells of most mammalian adult
tissues. NS shuttles between the nucleolus and
nucleoplasm bidirectionally at a rate that is fast and
independent of cell type. Lowering GTP levels decreases
the nucleolar retention of NS, and expression of NS is
abruptly down-regulated during differentiation prior to
terminal cell division. Found only in eukaryotes, NS
consists of an N-terminal basic domain, a coiled-coil
domain, a GTP-binding domain, an intermediate domain,
and a C-terminal acidic domain. Experimental evidence
indicates that NS uses its GTP-binding property as a
molecular switch to control the transition between the
nucleolus and nucleoplasm, and this process involves
interaction between the basic, GTP-binding, and
intermediate domains of the protein..
Length = 172
Score = 32.1 bits (73), Expect = 0.22
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 162 IGIIGLPNAGKSTFLASVTRAK 183
+G++G PN GKS+ + S+ R++
Sbjct: 120 VGVVGFPNVGKSSLINSLKRSR 141
>gnl|CDD|133294 cd01894, EngA1, EngA1 subfamily. This 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 = 32.0 bits (74), Expect = 0.23
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 164 IIGLPNAGKSTFLASVTRAKPKI-ADYPFTT---LYPNLGIVKEGYKEFILADIPGIIKN 219
I+G PN GKST +T + I D P T +Y G + G +EFIL D GI +
Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVEDTPGVTRDRIY---GEAEWGGREFILIDTGGIEPD 58
Query: 220 A 220
Sbjct: 59 D 59
>gnl|CDD|57926 cd01855, YqeH, YqeH. YqeH is an essential GTP-binding protein.
Depletion of YqeH induces an excess initiation of DNA
replication, suggesting that it negatively controls
initiation of chromosome replication. The YqeH subfamily
is common in eukaryotes and sporadically present in
bacteria with probable acquisition by plants from
chloroplasts. Proteins of the YqeH 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..
Length = 190
Score = 31.8 bits (72), Expect = 0.26
Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 6/71 (8%)
Query: 152 IWLKLKLIADIGIIGLPNAGKSTF---LASVTRAKPKIADYPFTTLYPN--LGIVK-EGY 205
I K D+ ++G N GKST L K K+ D T+ P L ++K
Sbjct: 120 IKKLAKKGGDVYVVGATNVGKSTLINALLKKDNGKKKLKDLLTTSPIPGTTLDLIKIPLG 179
Query: 206 KEFILADIPGI 216
L D PGI
Sbjct: 180 NGKKLYDTPGI 190
>gnl|CDD|37695 KOG2484, KOG2484, KOG2484, GTPase [General function prediction
only].
Length = 435
Score = 31.1 bits (70), Expect = 0.46
Identities = 26/105 (24%), Positives = 39/105 (37%), Gaps = 16/105 (15%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAH 221
+GIIG PN GKS+ + S+ R K + ++ VK K+ L D PGI+
Sbjct: 255 VGIIGYPNVGKSSVINSLKRRKACNVG-NVPGVTRSMQEVK-LDKKIRLLDSPGIV---- 308
Query: 222 QGAGIGDRFLKHTERTHVLLHIVSALEENVQ--AAYQCILDELSA 264
E+ + L + + CIL S
Sbjct: 309 --------PPSIDEKDALALRNCIPIGKVADPVTPVSCILKRCSK 345
>gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 31.0 bits (70), Expect = 0.53
Identities = 28/119 (23%), Positives = 46/119 (38%), Gaps = 10/119 (8%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGY--KEFILADIPGIIKN 219
IG++G AGKST L + P + ++ GY +E L ++
Sbjct: 32 IGLVGRNGAGKSTLLKILAG-----ELEPDSGEVTRPKGLRVGYLSQEPPLDPEKTVLDY 86
Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGL 278
+G G L E + LL A + +L+EL + E R + ++GL
Sbjct: 87 VIEGFGELRELLAELEEAYALLADPDDEL---LAELEALLEELDGWTLEARAEEALLGL 142
>gnl|CDD|39822 KOG4622, KOG4622, KOG4622, Predicted nucleotide kinase [General
function prediction only].
Length = 291
Score = 30.9 bits (69), Expect = 0.55
Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 18/117 (15%)
Query: 159 IADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIK 218
IA + +IG+P AGKS+F + A + I + +F++ P K
Sbjct: 1 IALLALIGIPAAGKSSFCRKILGAHAALRVRH---------IEHLCFDDFLMDATPSADK 51
Query: 219 NAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEI 275
A + G RF H E+ +SA++E+ Q S + R I
Sbjct: 52 AAKEQRG---RFECHIEK------CISAIQEDTDWPPQVRRISSSGDYNSGRHIILC 99
>gnl|CDD|133364 cd04164, trmE, 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 = 157
Score = 30.5 bits (70), Expect = 0.59
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 164 IIGLPNAGKSTFL 176
I+G PN GKS+ L
Sbjct: 6 IVGKPNVGKSSLL 18
>gnl|CDD|36638 KOG1424, KOG1424, KOG1424, Predicted GTP-binding protein MMR1
[General function prediction only].
Length = 562
Score = 29.2 bits (65), Expect = 1.8
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 162 IGIIGLPNAGKSTFLAS-VTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGII 217
+G +G PN GKS+ + + V R K ++ P T + + L D PG++
Sbjct: 317 VGFVGYPNVGKSSTINALVGRKKVSVSSTPGKTKHFQTIFLSPSVC---LCDCPGLV 370
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase
enzyme and as a kinase, and phosphorylates periplasmic
binding proteins involved in the LAO (lysine, arginine,
ornithine)/AO transport systems.
Length = 267
Score = 28.9 bits (65), Expect = 1.9
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 19/68 (27%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAH 221
+GI G+P AGKST + ++ + + + G++ +LA P
Sbjct: 32 VGITGVPGAGKSTLIEALG-----------------MELRRRGHRVAVLAVDPS--SPFT 72
Query: 222 QGAGIGDR 229
G+ +GDR
Sbjct: 73 GGSILGDR 80
>gnl|CDD|133278 cd01876, YihA_EngB, The YihA (EngB) subfamily. This 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 = 29.0 bits (66), Expect = 2.1
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 162 IGIIGLPNAGKSTFLASVTRAK--PKIADYPFTTLYPNLGIVKEGYKEFILADIPG 215
I G N GKS+ + ++T K + + P T N V + +F L D+PG
Sbjct: 2 IAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLINFFNVND---KFRLVDLPG 54
>gnl|CDD|133360 cd04160, Arfrp1, Arfrp1 subfamily. Arfrp1 (Arf-related protein 1),
formerly known as ARP, is a membrane-associated Arf
family member that lacks the N-terminal myristoylation
motif. Arfrp1 is mainly associated with the trans-Golgi
compartment and the trans-Golgi network, where it
regulates the targeting of Arl1 and the GRIP
domain-containing proteins, golgin-97 and golgin-245,
onto Golgi membranes. It is also involved in the
anterograde transport of the vesicular stomatitis virus
G protein from the Golgi to the plasma membrane, and in
the retrograde transport of TGN38 and Shiga toxin from
endosomes to the trans-Golgi network. Arfrp1 also
inhibits Arf/Sec7-dependent activation of phospholipase
D. Deletion of Arfrp1 in mice causes embryonic
lethality at the gastrulation stage and apoptosis of
mesodermal cells, indicating its importance in
development.
Length = 167
Score = 28.8 bits (65), Expect = 2.1
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 164 IIGLPNAGKSTFL 176
I+GL NAGK+TFL
Sbjct: 4 ILGLDNAGKTTFL 16
>gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily. Arl9/Arl10 was
identified from a human cancer-derived EST dataset. No
functional information about the subfamily is available
at the current time, but crystal structures of human
Arl10b and Arl10c have been solved.
Length = 159
Score = 28.8 bits (65), Expect = 2.3
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 161 DIGIIGLPNAGKSTFLASVT 180
+I ++GL N+GK+T + +
Sbjct: 1 EITLVGLQNSGKTTLVNVIA 20
>gnl|CDD|133254 cd00878, Arf_Arl, Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 28.7 bits (65), Expect = 2.3
Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 7/39 (17%)
Query: 161 DIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLG 199
I I+GL AGK+T L K+ T P +G
Sbjct: 1 RILILGLDGAGKTTILY-------KLKLGEVVTTIPTIG 32
>gnl|CDD|35298 KOG0075, KOG0075, KOG0075, GTP-binding ADP-ribosylation factor-like
protein [General function prediction only].
Length = 186
Score = 28.4 bits (63), Expect = 2.7
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 148 QEKIIWLK---LKLIADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEG 204
++K++W+ K ++ ++GL N+GK+T + + A+ + + T+ N+ V +G
Sbjct: 6 RKKLVWICNSFWKEEMELSLVGLQNSGKTTLVNVI--ARGQYLEDMIPTVGFNMRKVTKG 63
Query: 205 YKEFILADIPG 215
L D+ G
Sbjct: 64 NVTIKLWDLGG 74
>gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta). SR-beta and SR-alpha form the
heterodimeric signal recognition particle (SRP or SR)
receptor that binds SRP to regulate protein
translocation across the ER membrane. Nascent
polypeptide chains are synthesized with an N-terminal
hydrophobic signal sequence that binds SRP54, a
component of the SRP. SRP directs targeting of the
ribosome-nascent chain complex (RNC) to the ER membrane
via interaction with the SR, which is localized to the
ER membrane. The RNC is then transferred to the
protein-conducting channel, or translocon, which
facilitates polypeptide translation across the ER
membrane or integration into the ER membrane. SR-beta
is found only in eukaryotes; it is believed to control
the release of the signal sequence from SRP54 upon
binding of the ribosome to the translocon. High
expression of SR-beta has been observed in human colon
cancer, suggesting it may play a role in the development
of this type of cancer.
Length = 203
Score = 28.4 bits (64), Expect = 3.0
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 17/61 (27%)
Query: 164 IIGLPNAGKSTFL---------ASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIP 214
++G ++GK+ ++VT +P +A + L +G K+F L D+P
Sbjct: 5 LLGPSDSGKTALFTKLTTGKYRSTVTSIEPNVATF-------ILNSEGKG-KKFRLVDVP 56
Query: 215 G 215
G
Sbjct: 57 G 57
>gnl|CDD|72978 cd03219, ABC_Mj1267_LivG_branched, The Mj1267/LivG ABC transporter
subfamily is involved in the transport of the
hydrophobic amino acids leucine, isoleucine and valine.
MJ1267 is a branched-chain amino acid transporter with
29% similarity to both the LivF and LivG components of
the E. coli branched-chain amino acid transporter.
MJ1267 contains an insertion from residues 114 to 123
characteristic of LivG (Leucine-Isoleucine-Valine)
homologs. The branched-chain amino acid transporter
from E. coli comprises a heterodimer of ABCs (LivF and
LivG), a heterodimer of six-helix TM domains (LivM and
LivH), and one of two alternative soluble periplasmic
substrate binding proteins (LivK or LivJ)..
Length = 236
Score = 28.1 bits (63), Expect = 3.9
Identities = 38/151 (25%), Positives = 58/151 (38%), Gaps = 41/151 (27%)
Query: 163 GIIGLPN-AGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAH 221
G+IG PN AGK+T ++ L P G V F DI G+ +
Sbjct: 30 GLIG-PNGAGKTTLFNLISGF-----------LRPTSGSVL-----FDGEDITGLPPHEI 72
Query: 222 QGAGIGDRFLKHTERTHVLLHIVSAL--EENVQAAYQC------ILDELSAYNSELRKK- 272
GIG RT + + L ENV A Q +L E R++
Sbjct: 73 ARLGIG--------RTFQIPRLFPELTVLENVMVAAQARTGSGLLLARARREEREARERA 124
Query: 273 ---IEIVGLSQIDTVDSDTLA---RKKNELA 297
+E VGL+ + + L+ +++ E+A
Sbjct: 125 EELLERVGLADLADRPAGELSYGQQRRLEIA 155
>gnl|CDD|146182 pfam03408, Foamy_virus_ENV, Foamy virus envelope protein.
Expression of the envelope (Env) glycoprotein is
essential for viral particle egress. This feature is
unique to the Spumavirinae, a subclass of the
Retroviridae.
Length = 985
Score = 27.8 bits (62), Expect = 3.9
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 272 KIEIVGLSQIDTVDSDTLARKKN 294
K ++GLSQ+ ++S+T+A N
Sbjct: 157 KERVLGLSQVVMINSETIANSAN 179
>gnl|CDD|33380 COG3580, COG3580, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 351
Score = 27.9 bits (62), Expect = 4.0
Identities = 26/128 (20%), Positives = 40/128 (31%), Gaps = 12/128 (9%)
Query: 204 GYKEFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHI--VSALEENVQAAYQCILDE 261
Y E I +IP + D K + + +E + A Q E
Sbjct: 119 SYPEVIKNNIPDLRDGVMYLYPFLDLENKELLKEQFYKVFKEIGLSKEENEEAVQKAWKE 178
Query: 262 LSAYNSELRKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILEC 321
Y ++RKK E V L + + E P+ F HGIP+ +
Sbjct: 179 GEEYREDIRKKGEEV-LKYLK---------ENGEKGVVLAGRPYHFDPEINHGIPEKINS 228
Query: 322 LHDKIFSI 329
I +
Sbjct: 229 RGIPILTE 236
>gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is unkown.
The protein sequences are similar to the ArgK protein in
E. coli. ArgK protein is a membrane ATPase which is
required for transporting arginine, ornithine and lysine
into the cells by the arginine and ornithine (AO system)
and lysine, arginine and ornithine (LAO) transport
systems..
Length = 148
Score = 27.9 bits (62), Expect = 4.6
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 162 IGIIGLPNAGKSTFLASVTRA 182
IGI G+P AGKST + ++ A
Sbjct: 2 IGITGVPGAGKSTLIDALITA 22
>gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 27.7 bits (61), Expect = 4.6
Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 9/74 (12%)
Query: 155 KLKLIADIG----IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFIL 210
++K A G IIG GK F + + A+ PF N E
Sbjct: 93 QIKAYAPSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAF--NCAAYSE---NLQE 147
Query: 211 ADIPGIIKNAHQGA 224
A++ G K A GA
Sbjct: 148 AELFGHEKGAFTGA 161
>gnl|CDD|35280 KOG0057, KOG0057, KOG0057, Mitochondrial Fe/S cluster exporter, ABC
superfamily [Intracellular trafficking, secretion, and
vesicular transport].
Length = 591
Score = 27.5 bits (61), Expect = 5.4
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 10/72 (13%)
Query: 110 QEGQRIILAPGGNGGFGNAHFKSSTNQAPYYANPGILGQEKIIWLKLKLIADIGIIGLPN 169
QE I GG+ F + HF Y +L K + + + I+G
Sbjct: 339 QEAALPIELFGGSIEFDDVHFS-------YGPKRKVL---KGVSFTIPKGEKVAIVGSNG 388
Query: 170 AGKSTFLASVTR 181
+GKST L + R
Sbjct: 389 SGKSTILRLLLR 400
>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 27.6 bits (61), Expect = 5.7
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 162 IGIIGLPNAGKSTFLASVTR 181
IGI G+P AGKST + ++ R
Sbjct: 54 IGITGVPGAGKSTLIEALGR 73
>gnl|CDD|37696 KOG2485, KOG2485, KOG2485, Conserved ATP/GTP binding protein
[General function prediction only].
Length = 335
Score = 27.6 bits (61), Expect = 5.7
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGI-VKEGYKEF-----ILADIPGII 217
++G+PN GKS+ + ++ + P + V E + L D PGI+
Sbjct: 148 VVGVPNVGKSSLINALRNVHLRKKKAARVGAEPGVTRRVSERIRISHRPPVYLIDTPGIL 207
Query: 218 KNAHQG 223
+
Sbjct: 208 VPSIVD 213
>gnl|CDD|73015 cd03256, ABC_PhnC_transporter, ABC-type phosphate/phosphonate
transport system. Phosphonates are a class of
organophosphorus compounds characterized by a chemically
stable carbon-to-phosphorus (C-P) bond. Phosphonates
are widespread among naturally occurring compounds in
all kingdoms of wildlife, but only procaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 241
Score = 27.1 bits (60), Expect = 6.8
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 162 IGIIGLPNAGKSTFLASVTR 181
+ +IG AGKST L +
Sbjct: 30 VALIGPSGAGKSTLLRCLNG 49
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2l1/Arl13 subfamily. Arl2l1
(Arl2-like protein 1) and Arl13 form a subfamily of the
Arf family of small GTPases. Arl2l1 was identified in
human cells during a search for the gene(s) responsible
for Bardet-Biedl syndrome (BBS). Like Arl6, the
identified BBS gene, Arl2l1 is proposed to have
cilia-specific functions. Arl13 is found on the X
chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 27.0 bits (60), Expect = 7.6
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKPK 185
+ +GL NAGK+T ++++ PK
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPK 25
>gnl|CDD|36145 KOG0927, KOG0927, KOG0927, Predicted transporter (ABC superfamily)
[General function prediction only].
Length = 614
Score = 26.8 bits (59), Expect = 7.7
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 4/38 (10%)
Query: 163 GIIGLPNAGKSTFLASVTR----AKPKIADYPFTTLYP 196
G+IG +GKSTFL ++ I Y +
Sbjct: 105 GLIGPNGSGKSTFLRAIAGREVPIPEHIDFYLLSREIE 142
>gnl|CDD|57930 cd01859, MJ1464, MJ1464. 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 = 156
Score = 26.8 bits (59), Expect = 8.5
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 162 IGIIGLPNAGKSTFLASVTR 181
+G++G PN GKS+ + ++
Sbjct: 104 VGVVGYPNVGKSSIINALKG 123
>gnl|CDD|72979 cd03220, ABC_KpsT_Wzt, ABC_KpsT_Wzt The KpsT/Wzt ABC transporter
subfamily is involved in extracellular polysaccharide
export. Among the variety of membrane-linked or
extracellular polysaccharides excreted by bacteria, only
capsular polysaccharides, lipopolysaccharides, and
teichoic acids have been shown to be exported by ABC
transporters. A typical system is made of a conserved
integral membrane and an ABC. In addition to these
proteins, capsular polysaccharide exporter systems
require two 'accessory' proteins to perform their
function: a periplasmic (E.coli) or a lipid-anchored
outer membrane protein called OMA (Neisseria
meningitidis and Haemophilus influenzae) and a
cytoplasmic membrane protein MPA2..
Length = 224
Score = 26.7 bits (59), Expect = 9.0
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 162 IGIIGLPNAGKSTFL 176
IG+IG AGKST L
Sbjct: 51 IGLIGRNGAGKSTLL 65
>gnl|CDD|31329 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport
system, ATPase component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 249
Score = 26.7 bits (59), Expect = 9.1
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 162 IGIIGLPNAGKSTFL 176
+GIIG AGKST L
Sbjct: 56 VGIIGHNGAGKSTLL 70
>gnl|CDD|57929 cd01858, NGP_1, NGP-1. Autoantigen NGP-1 (Nucleolar G-protein gene
1) has been shown to localize in the nucleolus and
nucleolar organizers in all cell types analyzed, which
is indicative of a function in ribosomal assembly. NGP-1
and its homologs show a circular permutation of the
GTPase signature motifs so that the C-terminal strands
5, 6, and 7 (strand 6 contains the G4 box with NKXD
motif) are relocated to the N terminus..
Length = 157
Score = 26.7 bits (59), Expect = 9.2
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 162 IGIIGLPNAGKSTFLASVTRAKP-KIADYPF-TTLYPNLGIVKEGYKEFILADIPGI 216
+G IG PN GKS+ + ++ K K+A P T ++ + ++K Y L D PG+
Sbjct: 105 VGFIGYPNVGKSSIINTLRSKKVCKVAPIPGETKVWQYITLMKRIY----LIDCPGV 157
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and
Arl8, like Arl4 and Arl7, are localized to the nucleus
and nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 26.5 bits (59), Expect = 9.8
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 4/22 (18%)
Query: 155 KLKLIADIGIIGLPNAGKSTFL 176
+ K+I I+GL NAGK+T L
Sbjct: 15 EYKVI----IVGLDNAGKTTIL 32
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.140 0.412
Gapped
Lambda K H
0.267 0.0656 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,096,663
Number of extensions: 218810
Number of successful extensions: 791
Number of sequences better than 10.0: 1
Number of HSP's gapped: 771
Number of HSP's successfully gapped: 80
Length of query: 335
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 241
Effective length of database: 4,232,491
Effective search space: 1020030331
Effective search space used: 1020030331
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 (21.7 bits)
S2: 58 (26.3 bits)