RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780226|ref|YP_003064639.1| translation-associated GTPase
[Candidatus Liberibacter asiaticus str. psy62]
(367 letters)
>gnl|CDD|30362 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 481 bits (1239), Expect = e-136
Identities = 214/373 (57%), Positives = 267/373 (71%), Gaps = 7/373 (1%)
Query: 1 MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAE 60
M K GI+GLPNVGKSTLFNALT+ A A+ ANYPFCTIEPN G V VPD R+ +LAEI +
Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTK-AGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVK 59
Query: 61 -SKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGR 119
+ P + FVDIAGLV+GASKGEGLGN+FL +IREVDAIIHV+RCF D +I HVEG+
Sbjct: 60 CPPKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCFGDTDIEHVEGK 119
Query: 120 IDPINDIETIETELMLSDLERLERLFEK-NKKYRNHKSEEIVLLQ--SIISSSLRLIEEG 176
+DP+ DIE I TEL+L DLE LE+ +E+ K+ + K + L + S++ +EEG
Sbjct: 120 VDPVEDIEIINTELILWDLESLEKRWERLEKRAKAGKKLDKELKEELSLLGKLEEHLEEG 179
Query: 177 KPVRSL-LESLDSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNA 235
KP R L L + + SLNLLTAKP+LY+ NVSE D N Y + ++ LA+++NA
Sbjct: 180 KPARGLDLSKWSEEDLEALASLNLLTAKPMLYVANVSEDDLANLNEYVKRLKELAAKENA 239
Query: 236 EMIIISAAIEAEISQLPE-EERALFMEELDISISGLELLIRSGYRLLDLITYFTVGPKET 294
E++ +SAAIE E+ +L + EE+ F+ EL SGL LIR+GY LL L TYFT G KE
Sbjct: 240 EVVPVSAAIELELRELADAEEKGEFLIELGQKESGLNELIRAGYGLLGLQTYFTAGVKEV 299
Query: 295 RAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYI 354
RAWTI G+ A AAGVIH DFEKGFIRA ISY D + GGE AAKEAGK R EGK+YI
Sbjct: 300 RAWTIKDGSKAPDAAGVIHPDFEKGFIRAEVISYADLIHYGGEAAAKEAGKRRLEGKDYI 359
Query: 355 VKDGDILHFRFNV 367
V+DGD++HF+FNV
Sbjct: 360 VQDGDVIHFKFNV 372
>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 = 412 bits (1061), Expect = e-115
Identities = 165/281 (58%), Positives = 207/281 (73%), Gaps = 11/281 (3%)
Query: 5 CGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDL 64
GI+GLPNVGKSTLFNALT+ A A+AANYPFCTIEPN G V VPD R+ KLAEI + K +
Sbjct: 1 IGIVGLPNVGKSTLFNALTK-AGAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKI 59
Query: 65 VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIN 124
VP + FVDIAGLV+GASKGEGLGN+FL+HIREVDAI HV+RCF+D++I HVEG +DP+
Sbjct: 60 VPATIEFVDIAGLVKGASKGEGLGNKFLSHIREVDAIAHVVRCFEDDDITHVEGSVDPVR 119
Query: 125 DIETIETELMLSDLERLERLFEK-NKKYRNHKSE---EIVLLQSIISSSLRLIEEGKPVR 180
DIE I TEL+L+DLE +E+ E+ KK ++ E E+ LL+ I +EEGKP R
Sbjct: 120 DIEIINTELILADLETVEKRLERLEKKAKSGDKEAKAELELLEKIKE----HLEEGKPAR 175
Query: 181 SLLESLDSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMIII 240
SL L + I I SL LLTAKP+LY+ NVSE D GN V+ +A+++ AE+I I
Sbjct: 176 SL--ELTEEEIEILNSLQLLTAKPVLYVANVSEDDLANGNNKVLKVREIAAKEGAEVIPI 233
Query: 241 SAAIEAEISQLPEEERALFMEELDISISGLELLIRSGYRLL 281
SA IEAE+++L EEE A F+EEL + SGL+ LIR+GY LL
Sbjct: 234 SAKIEAELAELDEEEAAEFLEELGLEESGLDRLIRAGYELL 274
>gnl|CDD|36704 KOG1491, KOG1491, KOG1491, Predicted GTP-binding protein (ODN
superfamily) [General function prediction only].
Length = 391
Score = 378 bits (971), Expect = e-105
Identities = 182/376 (48%), Positives = 238/376 (63%), Gaps = 12/376 (3%)
Query: 1 MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAE 60
K GI+GLPNVGKST FNALT+ + A AAN+PFCTI+PN V VPD R L I
Sbjct: 19 NNLKIGIVGLPNVGKSTFFNALTK-SKAGAANFPFCTIDPNEARVEVPDSRFDLLCPIYG 77
Query: 61 SKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRI 120
K VP ++ DIAGLV+GAS GEGLGN+FL+HIR VDAI HV+R F+D +IIHVEG +
Sbjct: 78 PKSKVPAFLTVYDIAGLVKGASAGEGLGNKFLSHIRHVDAIFHVVRAFEDTDIIHVEGGV 137
Query: 121 DPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSL------RLIE 174
DP+ DIE I+ EL L DLE LE+ EK +K + Q L +L++
Sbjct: 138 DPVRDIEIIQEELRLKDLEFLEKRLEKLEKKHKRTKSNLETKQLKFEYGLLEKVKEKLLD 197
Query: 175 EGKPVRSLLESLDSDAIPIFKSLNLLTAKPILYICNVSEHD-CKKGNIYTEAVQRLASQQ 233
KPVR E + + I I L LLTAKP +Y+ N+SEHD +K N ++ +
Sbjct: 198 GKKPVRP-KEKWNDEEIEILNKLFLLTAKPTVYLLNLSEHDYARKKNKKLPKIKEWVDEV 256
Query: 234 N--AEMIIISAAIEAEISQLPEEERALFMEELDISISGLELLIRSGYRLLDLITYFTVGP 291
+ +I+ SAA E+++ +L EEE +E+L S S L +I++GY L+LI +FT G
Sbjct: 257 SPGDVVIVFSAAFESQLFELYEEEAVKELEDLGDS-SALPKIIKTGYSALNLIVFFTCGE 315
Query: 292 KETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGK 351
E RAWTI +GT A +AAGVIH+DFEKGFI A + ++D+ E+A K AGK R GK
Sbjct: 316 DEVRAWTIRKGTKAPQAAGVIHSDFEKGFIMAEVMKFEDFKEYKSESACKAAGKYRQVGK 375
Query: 352 EYIVKDGDILHFRFNV 367
EYIV+DGDI+ F+FN
Sbjct: 376 EYIVEDGDIIFFKFNP 391
>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 = 180 bits (460), Expect = 5e-46
Identities = 92/275 (33%), Positives = 119/275 (43%), Gaps = 99/275 (36%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
++GLPNVGKSTL NALT A + ANYPF T+EPN G V VPD
Sbjct: 1 LVGLPNVGKSTLLNALTN-AKPKVANYPFTTLEPNLGVVEVPDG---------------- 43
Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPINDI 126
R+ DI GL+ GAS+G GLGNQFLAHIR DAI+HV+ +D++I G +DP+ D
Sbjct: 44 ARIQVADIPGLIEGASEGRGLGNQFLAHIRRADAILHVVDASEDDDI----GGVDPLEDY 99
Query: 127 ETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESL 186
E + EL L DLE + L KPV
Sbjct: 100 EILNAELKLYDLETILGLLTA-----------------------------KPV------- 123
Query: 187 DSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMIIISAAIEA 246
+Y+ N + D + E V+ LA ++ AE++ ISA E
Sbjct: 124 -------------------IYVLNKIDLDDAEELEE-ELVRELALEEGAEVVPISAKTEE 163
Query: 247 EISQLPEEERALFMEELDISISGLELLIRSGYRLL 281
GL+ LIR+ Y LL
Sbjct: 164 ----------------------GLDELIRAIYELL 176
>gnl|CDD|133440 cd04867, TGS_YchF_C, TGS_YchF_C: This subfamily represents TGS
domain-containing YchF GTP-binding protein, a
universally conserved GTPase whose function is unknown.
The N-terminal domain of the YchF protein belongs to the
Obg-like family of GTPases, and some members of the
family contain a C-terminal TGS domain. TGS is a small
domain of about 50 amino acid residues with a
predominantly beta-sheet structure. There is no direct
information on the function of the TGS domain, but its
presence in two types of regulatory proteins (the
GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 83
Score = 160 bits (406), Expect = 8e-40
Identities = 55/83 (66%), Positives = 67/83 (80%)
Query: 283 LITYFTVGPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKE 342
LI++FT GP E RAWTI +GT A +AAGVIHTDFEKGFIRA + Y+D V +G E AAKE
Sbjct: 1 LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKYEDLVELGSEAAAKE 60
Query: 343 AGKARDEGKEYIVKDGDILHFRF 365
AGK R EGK+Y+V+DGDI+ F+F
Sbjct: 61 AGKYRQEGKDYVVQDGDIIFFKF 83
>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 = 123 bits (312), Expect = 5e-29
Identities = 79/266 (29%), Positives = 122/266 (45%), Gaps = 40/266 (15%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGE----VAVPDPRMHKLAEIAES 61
G++G PN GKST FNA T A + ANYPF TI+PN G V P +
Sbjct: 2 GLVGKPNAGKSTFFNAATL-ADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYG 60
Query: 62 KD-----LVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKD------ 110
K VP + +D+AGLV GA +G+GLGN+FL +R+ DA+IHV+ D
Sbjct: 61 KCIDGKRYVPVEL--IDVAGLVPGAHEGKGLGNKFLDDLRDADALIHVV----DASGGTD 114
Query: 111 -ENIIHVEGRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIIS-S 168
E G DP+ DIE +E E+ + LE+ +EK R +E+ +++++
Sbjct: 115 AEGNGVETGGHDPLEDIEFLENEIDMWIYGILEKNWEKIV--RKADAEKTDIVEALSEQL 172
Query: 169 SLRLIEEGKPVRSLLESLDSDAIP-------IFKSLNLLT--AKPILYICNVSEHDCKKG 219
S + E V LE L+ + + L +KP++ N ++ +
Sbjct: 173 SGFGVNEKD-VIEALEELELPEDLSKWTDEDLLRLARALRKRSKPMVIAANKADIPDAEN 231
Query: 220 NIYTEAVQRLASQQNAEMIIISAAIE 245
NI ++ + ++ SA E
Sbjct: 232 NISKLRLKYP----DEIVVPTSAEAE 253
>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 = 95.9 bits (240), Expect = 1e-20
Identities = 53/138 (38%), Positives = 74/138 (53%), Gaps = 26/138 (18%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
G++GLPN GKSTL +A++ A + A+YPF T+ PN G V V D R
Sbjct: 4 GLVGLPNAGKSTLLSAISN-AKPKIADYPFTTLVPNLGVVRVDDGR-------------- 48
Query: 66 PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIND 125
DI GL+ GAS+G+GLG++FL HI ++HV+ D+ DP+ D
Sbjct: 49 --SFVVADIPGLIEGASEGKGLGHRFLRHIERTRLLLHVIDLSGDD---------DPVED 97
Query: 126 IETIETELMLSDLERLER 143
+TI EL L + E LE+
Sbjct: 98 YKTIRNELELYNPELLEK 115
>gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 96.0 bits (239), Expect = 2e-20
Identities = 50/130 (38%), Positives = 66/130 (50%), Gaps = 28/130 (21%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
G++GLPN GKSTL +A++ A + A+YPF T+ PN G V V
Sbjct: 163 GLVGLPNAGKSTLLSAVSA-AKPKIADYPFTTLVPNLGVVRVDGGE-------------- 207
Query: 66 PTRMSFV--DIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPI 123
SFV DI GL+ GAS+G GLG +FL HI ++HV+ + DPI
Sbjct: 208 ----SFVVADIPGLIEGASEGVGLGLRFLRHIERTRVLLHVIDLSPIDG-------RDPI 256
Query: 124 NDIETIETEL 133
D +TI EL
Sbjct: 257 EDYQTIRNEL 266
>gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function.
Length = 106
Score = 86.6 bits (215), Expect = 9e-18
Identities = 38/105 (36%), Positives = 51/105 (48%), Gaps = 18/105 (17%)
Query: 14 GKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVPTRMSFVD 73
GKSTL NALT A ++YP T +PN G V + ++ VD
Sbjct: 1 GKSTLINALTGKKRAIVSDYPGTTRDPNEGRVELDGKQII-----------------LVD 43
Query: 74 IAGLVRGASKGEG-LGNQFLAHIREVDAIIHVLRCFKDENIIHVE 117
G++ GASKGEG LGN+ L I E D I+HV+ + +E
Sbjct: 44 TPGIIEGASKGEGELGNRTLEAIEEADLILHVVDASEGLTEEDLE 88
>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 = 82.6 bits (205), Expect = 2e-16
Identities = 41/129 (31%), Positives = 57/129 (44%), Gaps = 30/129 (23%)
Query: 5 CGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDL 64
++G P+VGKSTL + LT T S A Y F T+ VP +K A+I
Sbjct: 3 VALVGFPSVGKSTLLSKLTNTKSE-VAAYEFTTLTC------VPGVLEYKGAKI------ 49
Query: 65 VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIN 124
+D+ G++ GA+ G+G G Q +A R D I+ VL K E
Sbjct: 50 -----QLLDLPGIIEGAADGKGRGRQVIAVARTADLILMVLDATKPE------------G 92
Query: 125 DIETIETEL 133
E +E EL
Sbjct: 93 HREILEREL 101
>gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 76.8 bits (189), Expect = 1e-14
Identities = 81/364 (22%), Positives = 139/364 (38%), Gaps = 78/364 (21%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
++G P+VGKSTL N LT T S + A+YPF T+EP G + +K A+I
Sbjct: 67 ALVGFPSVGKSTLLNKLTNTKS-EVADYPFTTLEPVPGMLE------YKGAQI------- 112
Query: 66 PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIND 125
+D+ G++ GAS G G G Q L+ R D II VL F+D
Sbjct: 113 ----QLLDLPGIIEGASSGRGRGRQVLSVARNADLIIIVLDVFEDP-------------- 154
Query: 126 IETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLES 185
+ +ER E N + ++ + + I L
Sbjct: 155 ----------HHRDIIERELEDVGIRLNKRPPDVTIKKKESGG----IRINGTGP--LTH 198
Query: 186 LDSDAI-PIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMII--ISA 242
LD D + I + + A +L +V+ D +A++ + A ++ I
Sbjct: 199 LDEDTVRAILREYRIHNAD-VLIREDVTLDD------LIDALEGNRVYKPALYVVNKIDL 251
Query: 243 AIEAEISQLPEEERALFME-ELDISISGLELLIRSGYRLLDLITYFT----VGPKETRAW 297
E+ +L + ++ + + I L+ L + +L LI +T P
Sbjct: 252 PGLEELERLARKPNSVPISAKKGI---NLDELKERIWDVLGLIRVYTKPPGEEPDFDEPL 308
Query: 298 TIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIVKD 357
+ RG+ IH D + F Y + G++ + G +++++D
Sbjct: 309 ILRRGSTVGDVCRKIHRDLVENF---------RYARVWGKSVKHPGQRV---GLDHVLED 356
Query: 358 GDIL 361
DI+
Sbjct: 357 EDIV 360
>gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN
superfamily) [General function prediction only].
Length = 366
Score = 73.4 bits (180), Expect = 9e-14
Identities = 36/102 (35%), Positives = 51/102 (50%), Gaps = 17/102 (16%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
G++G PN GKSTL NAL+R A + A+Y F T+ P+ G V D +A
Sbjct: 200 GLVGFPNAGKSTLLNALSR-AKPKVAHYAFTTLRPHIGTVNYDD---FSQITVA------ 249
Query: 66 PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRC 107
DI G++ GA +GLG +FL HI ++ V+
Sbjct: 250 -------DIPGIIEGAHMNKGLGYKFLRHIERCKGLLFVVDL 284
>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 = 69.7 bits (171), Expect = 1e-12
Identities = 19/101 (18%), Positives = 30/101 (29%), Gaps = 16/101 (15%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
+ G N GKS+L NAL A + P T +P +
Sbjct: 1 LFGRTNAGKSSLLNALLGQEVAIVSPVPGTTTDPVEYVWELGPLG--------------- 45
Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRC 107
+ +D G+ G + D I+ V+
Sbjct: 46 -PVVLIDTPGIDEAGGLGREREELARRVLERADLILFVVDA 85
>gnl|CDD|133441 cd04938, TGS_Obg-like, TGS_Obg-like: The C-terminal TGS domain of
Obg-like GTPases such as those present in DRG
(developmentally regulated GTP-binding protein), and
GTP-binding proteins Ygr210 and YchF. The TGS domain
(named after the ThrRS, GTPase, and SpoT proteins where
it occurs) is a small domain of about 50 amino acid
residues with a predominantly beta-sheet structure.
There is no direct information on the function of the
TGS domain, but its presence in two types of regulatory
proteins (the GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 76
Score = 61.7 bits (150), Expect = 4e-10
Identities = 26/94 (27%), Positives = 34/94 (36%), Gaps = 29/94 (30%)
Query: 283 LITYFTV-----------GPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDY 331
LI + V G + +GT A IH D EKGFI A+
Sbjct: 1 LIPVYPVKNIHTFTNGSGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVG------ 54
Query: 332 VAMGGENAAKEAGKARDEGKEYIVKDGDILHFRF 365
G+ R EGK+ I+ DIL F+
Sbjct: 55 ------------GRRRLEGKDVILGKNDILKFKT 76
>gnl|CDD|36699 KOG1486, KOG1486, KOG1486, GTP-binding protein DRG2 (ODN
superfamily) [Signal transduction mechanisms].
Length = 364
Score = 60.3 bits (146), Expect = 8e-10
Identities = 35/105 (33%), Positives = 52/105 (49%), Gaps = 18/105 (17%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
+IG P+VGKSTL + +T T S +AA+Y F T+ G +
Sbjct: 67 LIGFPSVGKSTLLSKITSTHS-EAASYEFTTLTCIPGVIHYNG----------------- 108
Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDE 111
+ +D+ G++ GAS+G+G G Q +A R D I+ VL K E
Sbjct: 109 ANIQLLDLPGIIEGASQGKGRGRQVIAVARTADLILMVLDATKSE 153
>gnl|CDD|36700 KOG1487, KOG1487, KOG1487, GTP-binding protein DRG1 (ODN
superfamily) [Signal transduction mechanisms].
Length = 358
Score = 51.9 bits (124), Expect = 3e-07
Identities = 41/130 (31%), Positives = 59/130 (45%), Gaps = 30/130 (23%)
Query: 4 KCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKD 63
+ G +G P+VGKSTL + LT T S + A Y F T+ VP +K A+I
Sbjct: 61 RVGFVGFPSVGKSTLLSKLTGTFS-EVAAYEFTTL------TTVPGVIRYKGAKIQ---- 109
Query: 64 LVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPI 123
+D+ G++ GA G+G G Q +A R + I VL K P+
Sbjct: 110 -------LLDLPGIIEGAKDGKGRGKQVIAVARTCNLIFIVLDVLK------------PL 150
Query: 124 NDIETIETEL 133
+ + IE EL
Sbjct: 151 SHKKIIEKEL 160
>gnl|CDD|133435 cd01616, TGS, The TGS domain, named after the ThrRS, GTPase, and
SpoT/RelA proteins where it occurs, is structurally
similar to ubiquitin. TGS is a small domain of about 50
amino acid residues with a predominantly beta-sheet
structure. There is no direct information on the
function of the TGS domain, but its presence in two
types of regulatory proteins (the GTPases and guanosine
polyphosphate phosphohydrolases/synthetases) suggests a
ligand (most likely nucleotide)-binding, regulatory
role.
Length = 60
Score = 50.0 bits (120), Expect = 1e-06
Identities = 21/82 (25%), Positives = 28/82 (34%), Gaps = 22/82 (26%)
Query: 284 ITYFTVGPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEA 343
+ FT A +P+G A A IHTD KGFI AL
Sbjct: 1 MIIFTPD---GSAVELPKGATAMDFALKIHTDLGKGFIGALVN----------------- 40
Query: 344 GKARDEGKEYIVKDGDILHFRF 365
+ Y ++DGD +
Sbjct: 41 --GQLVDLSYTLQDGDTVSIVT 60
>gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 49.0 bits (117), Expect = 2e-06
Identities = 30/101 (29%), Positives = 41/101 (40%), Gaps = 19/101 (18%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
I+G PNVGKSTLFN LT A ++ P T + G+ + +
Sbjct: 8 IVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDA-----------------EWLG 50
Query: 67 TRMSFVDIAGLVRGASK--GEGLGNQFLAHIREVDAIIHVL 105
+D GL G E + Q L I E D I+ V+
Sbjct: 51 REFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVV 91
Score = 35.5 bits (82), Expect = 0.025
Identities = 22/103 (21%), Positives = 35/103 (33%), Gaps = 19/103 (18%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61
K IIG PNVGKS+L NA+ ++ T + + +
Sbjct: 178 PIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDS------IDIEFERDGRKY--- 228
Query: 62 KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHV 104
+D AG+ R E + + + R + AI
Sbjct: 229 --------VLIDTAGIRRKGKITESV--EKYSVARTLKAIERA 261
>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 = 47.4 bits (114), Expect = 6e-06
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPD 49
++G PNVGK+TLFNALT A + N+P T+E G +
Sbjct: 1 LVGNPNVGKTTLFNALTG-ARQKVGNWPGVTVEKKEGRFKLGG 42
>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 = 47.4 bits (114), Expect = 7e-06
Identities = 16/28 (57%), Positives = 18/28 (64%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYP 34
I+G PNVGKSTLFN LT A + P
Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVEDTP 29
>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 = 46.0 bits (109), Expect = 2e-05
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
G + ++G+PNVGKSTL N L A+ N P
Sbjct: 115 GIRAMVVGIPNVGKSTLINRLRGKKVAKVGNKP 147
>gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 46.0 bits (109), Expect = 2e-05
Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 21/102 (20%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
++G PNVGK+TLFNALT A+ + N+P T+E G++ +
Sbjct: 7 ALVGNPNVGKTTLFNALTG-ANQKVGNWPGVTVEKKEGKLKYKGHEIE------------ 53
Query: 66 PTRMSFVDIAGL--VRGASKGEGLGNQFLAHIREVDAIIHVL 105
VD+ G + S+ E + FL + D I++V+
Sbjct: 54 -----IVDLPGTYSLTAYSEDEKVARDFLLE-GKPDLIVNVV 89
>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 = 44.4 bits (106), Expect = 5e-05
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 4 KCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSG 43
++G PNVGK+TLFNALT A N+P T+E G
Sbjct: 1 TIALVGNPNVGKTTLFNALTG-ARQHVGNWPGVTVEKKEG 39
>gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 44.1 bits (104), Expect = 6e-05
Identities = 36/136 (26%), Positives = 58/136 (42%), Gaps = 18/136 (13%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
++G N GKSTLFNALT A A+ F T++P + + + D R L + +
Sbjct: 196 ALVGYTNAGKSTLFNALT-GADVYVADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDL 254
Query: 66 PTRM--SF---------VDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENII 114
P + +F D+ V AS E L + V+ ++ + + II
Sbjct: 255 PHPLVEAFKSTLEEVKEADLLLHVVDASDPE-----ILEKLEAVEDVLAEIGA-DEIPII 308
Query: 115 HVEGRIDPINDIETIE 130
V +ID + D E +
Sbjct: 309 LVLNKIDLLEDEEILA 324
>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 = 44.1 bits (105), Expect = 6e-05
Identities = 19/31 (61%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37
I G PNVGKS+L N LTR A + A YPF T
Sbjct: 5 IAGYPNVGKSSLVNKLTR-AKPEVAPYPFTT 34
>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 = 43.2 bits (103), Expect = 1e-04
Identities = 16/23 (69%), Positives = 17/23 (73%), Gaps = 3/23 (13%)
Query: 3 FKCG---IIGLPNVGKSTLFNAL 22
FK G I+G PNVGKSTL NAL
Sbjct: 1 FKSGFVAIVGRPNVGKSTLLNAL 23
>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 = 41.3 bits (98), Expect = 4e-04
Identities = 14/23 (60%), Positives = 16/23 (69%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTR 24
G K I+G PNVGKS+L NAL
Sbjct: 1 GIKVVIVGKPNVGKSSLLNALAG 23
>gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 41.2 bits (96), Expect = 4e-04
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 1 MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
+ G++G PNVGKSTL N L A+ +N P
Sbjct: 131 RKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRP 164
>gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 40.5 bits (95), Expect = 6e-04
Identities = 31/110 (28%), Positives = 49/110 (44%), Gaps = 21/110 (19%)
Query: 1 MGFKCG---IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAE 57
M FK G IIG PNVGKSTL NAL + + P T +++
Sbjct: 2 MKFKSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTT--------------RNRIRG 47
Query: 58 IAESKDLVPTRMSFVDIAGLVRGASK-GEGLGNQFLAHIREVDAIIHVLR 106
I + + ++ FVD G+ + GE + + +++VD I+ V+
Sbjct: 48 IVTTDN---AQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVD 94
>gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 39.8 bits (93), Expect = 0.001
Identities = 16/33 (48%), Positives = 18/33 (54%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
G K IIG PNVGKS+L NAL A +
Sbjct: 217 GLKVVIIGRPNVGKSSLLNALLGRDRAIVTDIA 249
>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 = 39.3 bits (93), Expect = 0.002
Identities = 29/110 (26%), Positives = 41/110 (37%), Gaps = 38/110 (34%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
++G N GKSTLFNALT A A + F T+ DP +L +
Sbjct: 45 ALVGYTNAGKSTLFNALTG-ADVYAEDQLFATL----------DPTTRRL--------RL 85
Query: 66 PTRMSFV--DIAGLVRG------ASKGEGLGNQF---LAHIREVDAIIHV 104
P + D G +R + F L + E D ++HV
Sbjct: 86 PDGREVLLTDTVGFIRDLPHQLVEA--------FRSTLEEVAEADLLLHV 127
>gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 39.1 bits (91), Expect = 0.002
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37
+ G PNVGKS+L LT TA + A YPF T
Sbjct: 173 VAGYPNVGKSSLVRKLT-TAKPEVAPYPFTT 202
>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 = 38.8 bits (90), Expect = 0.002
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYP 34
G+IG PNVGKS++ NAL + N P
Sbjct: 104 GVIGYPNVGKSSVINALLNKLKLKVGNVP 132
>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 = 37.9 bits (88), Expect = 0.004
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 4 KCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
G++G PNVGKS+L N+L R+ + P
Sbjct: 119 TVGVVGFPNVGKSSLINSLKRSRACNVGATP 149
>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 = 37.4 bits (88), Expect = 0.007
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 2 GFKCGIIGLPNVGKSTLFNALT 23
+ IIG PNVGKS+L NAL
Sbjct: 2 PIRIAIIGRPNVGKSSLVNALL 23
>gnl|CDD|37695 KOG2484, KOG2484, KOG2484, GTPase [General function prediction
only].
Length = 435
Score = 36.9 bits (85), Expect = 0.008
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYP 34
GIIG PNVGKS++ N+L R + N P
Sbjct: 256 GIIGYPNVGKSSVINSLKRRKACNVGNVP 284
>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 = 36.8 bits (85), Expect = 0.009
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 3 FKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
K G++G PNVGKS++ NAL SA + P
Sbjct: 102 GKVGVVGYPNVGKSSIINALKGRHSASTSPSP 133
>gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control,
cell division, chromosome partitioning, Signal
transduction mechanisms].
Length = 379
Score = 35.8 bits (82), Expect = 0.022
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 17/73 (23%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
+IG PNVGKSTL N + + + T G + +
Sbjct: 76 AVIGAPNVGKSTLTNQMIGQKVSAVSRKVHTTRHRILGIITSGE---------------- 119
Query: 66 PTRMSFVDIAGLV 78
T++ F D GLV
Sbjct: 120 -TQLVFYDTPGLV 131
>gnl|CDD|35631 KOG0410, KOG0410, KOG0410, Predicted GTP binding protein [General
function prediction only].
Length = 410
Score = 35.4 bits (81), Expect = 0.028
Identities = 29/144 (20%), Positives = 53/144 (36%), Gaps = 23/144 (15%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
++G N GKSTL ALT+ A+ + F T++P +P L + +P
Sbjct: 183 VVGYTNAGKSTLIKALTK-AALYPNDRLFATLDPTLHSAHLPSGNFVLLTDTVGFISDLP 241
Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPINDI 126
LV L + E D ++HV+ +I H +
Sbjct: 242 I--------QLVAAFQAT-------LEEVAEADLLLHVV------DISHPNAEEQ-RETV 279
Query: 127 ETIETELMLSDLERLERLFEKNKK 150
+ ++ + +L+ + E + K
Sbjct: 280 LHVLNQIGVPSEPKLQNMIEVDNK 303
>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 = 34.4 bits (80), Expect = 0.050
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 7 IIGLPNVGKSTLFNALTRTAS-AQAANYPFCTIEPN 41
G NVGKS+L NALT A+ + P T N
Sbjct: 4 FAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLIN 39
>gnl|CDD|173737 cd07834, STKc_MAPK, Catalytic domain of the Serine/Threonine
Kinase, Mitogen-Activated Protein Kinase.
Serine/Threonine Kinases (STKs), Mitogen-Activated
Protein Kinase (MAPK) subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The MAPK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. MAPKs serve as important
mediators of cellular responses to extracellular
signals. They control critical cellular functions
including differentiation, proliferation, migration, and
apoptosis. They are also implicated in the pathogenesis
of many diseases including multiple types of cancer,
stroke, diabetes, and chronic inflammation. Typical MAPK
pathways involve a triple kinase core cascade comprising
of the MAPK, which is phosphorylated and activated by a
MAPK kinase (MAP2K or MKK), which itself is
phosphorylated and activated by a MAPK kinase kinase
(MAP3K or MKKK). Each cascade is activated either by a
small GTP-binding protein or by an adaptor protein,
which transmits the signal either directly to a MAP3K to
start the triple kinase core cascade or indirectly
through a mediator kinase, a MAP4K. There are three main
typical MAPK subfamilies: Extracellular signal-Regulated
Kinase (ERK), c-Jun N-terminal Kinase (JNK), and p38.
Some MAPKs are atypical in that they are not regulated
by MAP2Ks. These include MAPK4, MAPK6, NLK, and ERK7.
Length = 330
Score = 34.4 bits (80), Expect = 0.053
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 96 REVDAIIHVLRCFKDENIIHVEGRIDPINDIET-----IETELMLSDLERL 141
RE I +LR + ENII + I E I TELM +DL ++
Sbjct: 48 RE----IKLLRHLRHENIIGLL-DILRPPSPEDFNDVYIVTELMETDLHKV 93
>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 = 34.1 bits (78), Expect = 0.060
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 7 IIGLPNVGKSTLFNALTRT 25
++G NVGKSTL NAL +
Sbjct: 132 VVGATNVGKSTLINALLKK 150
>gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 34.2 bits (77), Expect = 0.065
Identities = 38/211 (18%), Positives = 63/211 (29%), Gaps = 15/211 (7%)
Query: 3 FKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL-----AE 57
FK ++G VGK+TL N L YP + + P R KL A
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVG--DEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAG 63
Query: 58 IAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVE 117
E + L P + +V ++ E E + L D I+ V
Sbjct: 64 QEEYRSLRPEYYRGANGILIVYDSTLRESSDE----LTEEWLEELREL-APDDVPILLVG 118
Query: 118 GRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGK 177
+ID ++ + E + + E + L + SL +
Sbjct: 119 NKIDLFDEQSSSE---EILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNE 175
Query: 178 PVRSLLESLDSDAIPIFKSLNLLTAKPILYI 208
+ LL L + + L +
Sbjct: 176 LFKELLRKLLEEIEKLVLKNELRQLDRLNNP 206
>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 = 33.6 bits (77), Expect = 0.081
Identities = 12/17 (70%), Positives = 15/17 (88%)
Query: 6 GIIGLPNVGKSTLFNAL 22
G++G PNVGKS+L NAL
Sbjct: 87 GLVGYPNVGKSSLINAL 103
>gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation,
ribosomal structure and biogenesis].
Length = 531
Score = 33.4 bits (76), Expect = 0.088
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTR 24
G + I+G PNVGKS+L NAL+R
Sbjct: 268 GLQIAIVGRPNVGKSSLLNALSR 290
>gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters..
Length = 180
Score = 33.1 bits (76), Expect = 0.11
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 5 CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL--AEIAES 61
GI+G PN GKSTL L ++P+SGE+ + + L E+A
Sbjct: 28 VGILG-PNGAGKSTLLKTLAG------------LLKPSSGEILLDGKDLASLSPKELARK 74
Query: 62 KDLVPTRMSFVDIAGL 77
VP + + +A L
Sbjct: 75 IAYVPQALELLGLAHL 90
>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 = 32.9 bits (75), Expect = 0.13
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYP 34
G IG PNVGKS++ N L + A P
Sbjct: 106 GFIGYPNVGKSSIINTLRSKKVCKVAPIP 134
>gnl|CDD|133439 cd01669, TGS_Ygr210_C, TGS_Ygr210_C: The C-terminal TGS domain of
Ygr210 GTP-binding protein which is a member of Obg-like
family of GTPases, and present in archaea. Several
Obg-like 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. TGS is a small domain of about 50
amino acid residues with a predominantly beta-sheet
structure. There is no direct information on the
function of the TGS domain, but its presence in two
types of regulatory proteins (the GTPases and guanosine
polyphosphate phosphohydrolases/synthetases) suggests a
ligand (most likely nucleotide)-binding, regulatory
role.
Length = 76
Score = 32.6 bits (75), Expect = 0.16
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 17/67 (25%)
Query: 296 AWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIV 355
A+ +P+G+ A+ A IHTD GF+ A+ +A R G++Y +
Sbjct: 24 AFLLPKGSTARDLAYAIHTDIGDGFLHAI-----------------DARTGRRVGEDYEL 66
Query: 356 KDGDILH 362
K D++
Sbjct: 67 KHRDVIK 73
>gnl|CDD|37696 KOG2485, KOG2485, KOG2485, Conserved ATP/GTP binding protein
[General function prediction only].
Length = 335
Score = 32.6 bits (74), Expect = 0.18
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 7 IIGLPNVGKSTLFNALTR-----TASAQAANYPFCTI 38
++G+PNVGKS+L NAL +A+ P T
Sbjct: 148 VVGVPNVGKSSLINALRNVHLRKKKAARVGAEPGVTR 184
>gnl|CDD|37634 KOG2423, KOG2423, KOG2423, Nucleolar GTPase [General function
prediction only].
Length = 572
Score = 31.5 bits (71), Expect = 0.36
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAV 47
G IG PNVGKS++ N L C + P GE V
Sbjct: 311 GFIGYPNVGKSSIINTLR--------KKKVCKVAPIPGETKV 344
>gnl|CDD|36638 KOG1424, KOG1424, KOG1424, Predicted GTP-binding protein MMR1
[General function prediction only].
Length = 562
Score = 31.1 bits (70), Expect = 0.43
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 6 GIIGLPNVGKSTLFNAL 22
G +G PNVGKS+ NAL
Sbjct: 318 GFVGYPNVGKSSTINAL 334
>gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 31.0 bits (70), Expect = 0.48
Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 8 IGLPNVGKSTLFNALT-RTASAQAANYPFCTIEPNSGEVA 46
G NVGKS+L NALT + A+ + P T N EV
Sbjct: 30 AGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVD 69
>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 = 30.2 bits (68), Expect = 0.84
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS 42
GI G+P GKSTL +AL A+ I+P+S
Sbjct: 3 GITGVPGAGKSTLIDALITALRARGKRVAVLAIDPSS 39
>gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 30.1 bits (68), Expect = 0.86
Identities = 26/111 (23%), Positives = 40/111 (36%), Gaps = 23/111 (20%)
Query: 5 CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKD 63
GI+G PN GKSTL L ++P SGEV + + L+ +K
Sbjct: 31 TGILG-PNGSGKSTLLKCLAG------------LLKPKSGEVLLDGKDIASLSPKELAKK 77
Query: 64 L--------VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLR 106
L P ++ ++ L R G G V+ + +L
Sbjct: 78 LAYVPQSPSAPFGLTVYELVLLGRYPHLG-LFGRPSKEDEEIVEEALELLG 127
>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 = 30.1 bits (68), Expect = 0.91
Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 12/54 (22%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL 55
G +IG GKSTL L +EP SG V + ++KL
Sbjct: 27 GEFVALIGPSGAGKSTLLRCLNG------------LVEPTSGSVLIDGTDINKL 68
>gnl|CDD|36703 KOG1490, KOG1490, KOG1490, GTP-binding protein CRFG/NOG1 (ODN
superfamily) [General function prediction only].
Length = 620
Score = 30.0 bits (67), Expect = 0.97
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37
+ G PNVGKS+ N +TR A + Y F T
Sbjct: 173 VCGYPNVGKSSFNNKVTR-ADDEVQPYAFTT 202
>gnl|CDD|143354 cd07849, STKc_ERK1_2_like, Catalytic domain of Extracellular
signal-Regulated Kinase 1 and 2-like Serine/Threonine
Kinases. Serine/Threonine Kinases (STKs), Extracellular
signal-regulated kinases 1 and 2 (ERK1/2) and Fus3
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. This
ERK1/2-like subfamily is part of a larger superfamily
that includes the catalytic domains of other protein
STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. This subfamily is composed of
the mitogen-activated protein kinases (MAPKs) ERK1,
ERK2, baker's yeast Fus3, and similar proteins. MAPK
pathways are important mediators of cellular responses
to extracellular signals. ERK1/2 activation is
preferentially by mitogenic factors, differentiation
stimuli, and cytokines, through a kinase cascade
involving the MAPK kinases MEK1/2 and a MAPK kinase
kinase from the Raf family. ERK1/2 have numerous
substrates, many of which are nuclear and participate in
transcriptional regulation of many cellular processes.
They regulate cell growth, cell proliferation, and cell
cycle progression from G1 to S phase. Although the
distinct roles of ERK1 and ERK2 have not been fully
determined, it is known that ERK2 can maintain most
functions in the absence of ERK1, and that the deletion
of ERK2 is embryonically lethal. The MAPK, Fus3,
regulates yeast mating processes including
mating-specific gene expression, G1 arrest, mating
projection, and cell fusion.
Length = 336
Score = 29.6 bits (67), Expect = 1.5
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 10/54 (18%)
Query: 95 IREVDAIIHVLRCFKDENIIHV-----EGRIDPINDIETIETELMLSDLERLER 143
+RE I +LR FK ENII + + ND+ ++ ELM +DL +L +
Sbjct: 51 LRE----IKILRRFKHENIIGILDIIRPPSFESFNDVYIVQ-ELMETDLYKLIK 99
>gnl|CDD|39443 KOG4242, KOG4242, KOG4242, Predicted myosin-I-binding protein [Cell
motility].
Length = 553
Score = 29.3 bits (65), Expect = 1.7
Identities = 15/71 (21%), Positives = 25/71 (35%)
Query: 248 ISQLPEEERALFMEELDISISGLELLIRSGYRLLDLITYFTVGPKETRAWTIPRGTNAQK 307
IS+L + L++ ELD+S +G + I + T + T+
Sbjct: 204 ISKLLIQSGRLWLTELDLSTNGGKDDIPRTLNKKAGTLVLFKLDRSTTGIRLDLLTSPLA 263
Query: 308 AAGVIHTDFEK 318
A F K
Sbjct: 264 AGRTTKLTFGK 274
>gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system
belong to the larger ATP-Binding Cassette (ABC)
transporter superfamily. The characteristic feature of
these transporters is the obligatory coupling of ATP
hydrolysis to substrate translocation. 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 = 269
Score = 29.4 bits (66), Expect = 1.9
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 13/66 (19%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
I+GL GKSTL + R IEP SG+V + + ++ E ++L
Sbjct: 55 IMGLSGSGKSTLLRCINR------------LIEPTSGKVLIDGQDIAAMSR-KELRELRR 101
Query: 67 TRMSFV 72
++S V
Sbjct: 102 KKISMV 107
>gnl|CDD|72980 cd03221, ABCF_EF-3, ABCF_EF-3 Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two
ATP nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions..
Length = 144
Score = 29.3 bits (66), Expect = 1.9
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 12/49 (24%)
Query: 1 MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPD 49
G + G++G GKSTL + +EP+ G V
Sbjct: 25 PGDRIGLVGRNGAGKSTLLKLIA------------GELEPDEGIVTWGS 61
>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 = 29.0 bits (65), Expect = 2.0
Identities = 19/98 (19%), Positives = 27/98 (27%), Gaps = 23/98 (23%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
++G VGK++L N E E + D
Sbjct: 1 VVGDSGVGKTSLLNR-------------LLGGEFVPEEYETTIIDFYS---KTIEVDGKK 44
Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHV 104
++ D AG R S + R D II V
Sbjct: 45 VKLQIWDTAGQERFRSLRR-------LYYRGADGIILV 75
>gnl|CDD|37772 KOG2561, KOG2561, KOG2561, Adaptor protein NUB1, contains UBA
domain [Posttranslational modification, protein
turnover, chaperones, Signal transduction mechanisms].
Length = 568
Score = 29.2 bits (65), Expect = 2.0
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 142 ERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESLDSDAIPIFKSLNLLT 201
ER + KKY N ++ V +S+ RL+ G E+L + I K+L+LL
Sbjct: 356 EREILERKKYGNTPMKKWVNPRSLE----RLVSMGYERELAAEALRRNENDIQKALDLLQ 411
>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 = 28.9 bits (65), Expect = 2.2
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 14/42 (33%)
Query: 5 CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEV 45
G+IG PN GK+TLFN ++ + P SG V
Sbjct: 29 HGLIG-PNGAGKTTLFNLISG------------FLRPTSGSV 57
>gnl|CDD|36138 KOG0920, KOG0920, KOG0920, ATP-dependent RNA helicase A [RNA
processing and modification].
Length = 924
Score = 28.7 bits (64), Expect = 2.5
Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 13/91 (14%)
Query: 108 FKDENIIHVEGRIDPINDIETIETELMLSD-LERLERLFEKNKKYRNHKSEEIVLLQSII 166
F +I + GR P+ E L D L + + E + + ++ L + +
Sbjct: 338 FGGCPVITIPGRTFPV-------KEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKL 390
Query: 167 SSS---LRLIEEGKPVRSLLESLDSDAIPIF 194
LIE+ + + E AI +F
Sbjct: 391 WEPEIDYDLIED--LIEYIDEREFEGAILVF 419
>gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system,
ATPase component [Amino acid transport and metabolism].
Length = 386
Score = 28.8 bits (64), Expect = 2.8
Identities = 28/94 (29%), Positives = 40/94 (42%), Gaps = 27/94 (28%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEV-------------AVPDPRMH 53
I+GL GKSTL L R IEP GE+ + + R
Sbjct: 59 IMGLSGSGKSTLVRLLNR------------LIEPTRGEILVDGKDIAKLSAAELRELRRK 106
Query: 54 KLAEIAESKDLVPTRMSFVDIA-GL-VRGASKGE 85
K++ + +S L+P R ++A GL V+G K E
Sbjct: 107 KISMVFQSFALLPHRTVLENVAFGLEVQGVPKAE 140
>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 28.4 bits (63), Expect = 3.1
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS 42
GI G+P GKSTL AL R + ++P+S
Sbjct: 55 GITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSS 91
>gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 28.3 bits (63), Expect = 3.3
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 10/63 (15%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFC---TIEPNSGEVAVPDPRMHKLAEIAESKD 63
I+G P GKSTL A A T + +A ++ + + +
Sbjct: 5 ILGPPGAGKSTL-------AKKLAKKLGLPHLDTGDILRAAIAERTELGEEIKKYIDKGE 57
Query: 64 LVP 66
LVP
Sbjct: 58 LVP 60
>gnl|CDD|133292 cd01892, Miro2, Miro2 subfamily. Miro (mitochondrial Rho)
proteins have tandem GTP-binding domains separated by a
linker region containing putative calcium-binding EF
hand motifs. Genes encoding Miro-like proteins were
found in several eukaryotic organisms. This CD
represents the putative GTPase domain in the C terminus
of Miro proteins. These atypical Rho GTPases have
roles in mitochondrial homeostasis and apoptosis. Most
Rho proteins contain a lipid modification site at the
C-terminus; however, Miro is one of few Rho subfamilies
that lack this feature.
Length = 169
Score = 28.3 bits (64), Expect = 3.3
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 3 FKCGIIGLPNVGKSTLFNAL 22
F C ++G GKS L A
Sbjct: 5 FLCFVLGAKGSGKSALLRAF 24
>gnl|CDD|73006 cd03247, ABCC_cytochrome_bd, The CYD subfamily implicated in
cytochrome bd biogenesis. The CydC and CydD proteins
are important for the formation of cytochrome bd
terminal oxidase of E. coli and it has been proposed
that they were necessary for biosynthesis of the
cytochrome bd quinol oxidase and for periplasmic c-type
cytochromes. CydCD were proposed to determine a
heterooligomeric complex important for heme export into
the periplasm or to be involved in the maintenance of
the proper redox state of the periplasmic space. In
Bacillus subtilius, the absence of CydCD does not affect
the presence of halo-cytochrome c in the membrane and
this observation suggests that CydCD proteins are not
involved in the export of heme in this organism..
Length = 178
Score = 28.2 bits (63), Expect = 3.6
Identities = 26/134 (19%), Positives = 54/134 (40%), Gaps = 25/134 (18%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61
G K ++G GKSTL LT ++P GE+ + +++
Sbjct: 28 GEKIALLGRSGSGKSTLLQLLTG------------DLKPQQGEITLDG------VPVSDL 69
Query: 62 KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHV----E 117
+ + + +S ++ + + LG +F R+ A+ +L +D I+ +
Sbjct: 70 EKALSSLISVLNQRPYLFDTTLRNNLGRRFSGGERQRLALARIL--LQDAPIVLLDEPTV 127
Query: 118 GRIDPINDIETIET 131
G +DPI + + +
Sbjct: 128 G-LDPITERQLLSL 140
>gnl|CDD|33698 COG3911, COG3911, Predicted ATPase [General function prediction
only].
Length = 183
Score = 28.0 bits (62), Expect = 3.7
Identities = 20/64 (31%), Positives = 25/64 (39%), Gaps = 2/64 (3%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS--GEVAVPDPRMHKLAEIAESKDL 64
+ G P GK+TL AL R A I S G A+P AE+ + L
Sbjct: 14 LTGGPGAGKTTLLAALARAGFATVEEAGRDIIALESAQGGTALPWTDPGAFAELVGLQRL 73
Query: 65 VPTR 68
TR
Sbjct: 74 RQTR 77
>gnl|CDD|146421 pfam03770, IPK, Inositol polyphosphate kinase. ArgRIII has has
been demonstrated to be an inositol polyphosphate
kinase.
Length = 184
Score = 28.3 bits (64), Expect = 3.8
Identities = 15/81 (18%), Positives = 22/81 (27%), Gaps = 19/81 (23%)
Query: 103 HVLRCFKDENIIH-----VEGRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSE 157
+ R E + + I L L+ L E + YR
Sbjct: 73 YYGRSLSAEEVKEALKRFFSNGKSLRRSKKLIPR--FLERLQELRNWLESQESYR----- 125
Query: 158 EIVLLQSIISSSLRLIEEGKP 178
SSSL + +G P
Sbjct: 126 -------FYSSSLLFVYDGDP 139
>gnl|CDD|36463 KOG1249, KOG1249, KOG1249, Predicted GTPases [General function
prediction only].
Length = 572
Score = 28.0 bits (62), Expect = 4.0
Identities = 28/115 (24%), Positives = 40/115 (34%), Gaps = 17/115 (14%)
Query: 8 IGLPNVGKSTLFNALTR-----------TASAQAANYPFCTIEPNSGEVAVPDP-RMHKL 55
+G NVGKSTLFNAL A +++P T+ V VP P R+
Sbjct: 219 VGATNVGKSTLFNALLESDLCSVNAPKLVDRATISDWPGTTLSLLKFPVLVPHPYRLGGR 278
Query: 56 -----AEIAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVL 105
+K + R G A +G F ++A+ L
Sbjct: 279 RKRLGVHSVSAKKDMGERDLLALETGDAGKAGPVAAVGRTFAGSEELINAMAKEL 333
>gnl|CDD|132953 cd06622, PKc_MAPKK_PBS2_like, Catalytic domain of fungal PBS2-like
dual-specificity MAP kinase kinases. Protein kinases
(PKs), MAP kinase kinase (MAPKK) subfamily, fungal
PBS2-like proteins, catalytic (c) domain. PKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine or tyrosine residues on protein
substrates. The MAPKK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein serine/threonine kinases, protein tyrosine
kinases, RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase. The
mitogen-activated protein (MAP) kinase signaling
pathways are important mediators of cellular responses
to extracellular signals. The pathways involve a triple
kinase core cascade comprising of the MAP kinase (MAPK),
which is phosphorylated and activated by a MAPK kinase
(MAPKK or MKK), which itself is phosphorylated and
activated by a MAPK kinase kinase (MAPKKK or MKKK).
Members of this group include the MAPKKs Polymyxin B
resistance protein 2 (PBS2) from Saccharomyces
cerevisiae, Wis1 from Schizosaccharomyces pombe, and
related proteins. PBS2 and Wis1 are components of
stress-activated MAPK cascades in budding and fission
yeast, respectively. PBS2 is the specific activator of
the MAPK Hog1, which plays a central role in the
response of budding yeast to stress including exposure
to arsenite and hyperosmotic environments. Wis1
phosphorylates and activates the MAPK Sty1 (also called
Spc1 or Phh1), which stimulates a transcriptional
response to a wide range of cellular insults through the
bZip transcription factors Atf1, Pcr1, and Pap1.
Length = 286
Score = 27.9 bits (62), Expect = 4.2
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 69 MSFVD---IAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDE-NIIH 115
M ++D + L G EG+ L I A++ L+ K+E NIIH
Sbjct: 78 MEYMDAGSLDKLYAGGVATEGIPEDVLRRI--TYAVVKGLKFLKEEHNIIH 126
>gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated
protein/mitoxantrone resistance protein, ABC superfamily
[Secondary metabolites biosynthesis, transport and
catabolism].
Length = 1381
Score = 27.9 bits (62), Expect = 4.3
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 12/46 (26%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAV 47
G K GI+G GKS+L AL R +EP GE+ +
Sbjct: 1166 GEKVGIVGRTGAGKSSLILALFR------------LVEPAEGEILI 1199
>gnl|CDD|143363 cd07858, STKc_TEY_MAPK_plant, Catalytic domain of the
Serine/Threonine Kinases, TEY Mitogen-Activated Protein
Kinases from Plants. Serine/Threonine Kinases (STKs),
Plant TEY Mitogen-Activated Protein Kinase (MAPK)
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The TEY
MAPK subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. MAPKs are important mediators of cellular
responses to extracellular signals. In plants, MAPKs are
associated with physiological, developmental, hormonal,
and stress responses. Some plants show numerous gene
duplications of MAPKs. Arabidopsis thaliana harbors at
least 20 MAPKs, named AtMPK1-20. There are two subtypes
of plant MAPKs based on the conserved phosphorylation
motif present in the activation loop, TEY and TDY. This
subfamily represents the TEY subtype and is further
subdivided into three groups (A, B, and C). Group A is
represented by AtMPK3, AtMPK6, Nicotiana tabacum BTF4
(NtNTF4), among others. They are mostly involved in
environmental and hormonal responses. AtMPK3 and AtMPK6
are also key regulators for stomatal development and
patterning. Group B is represented by AtMPK4, AtMPK13,
and NtNTF6, among others. They may be involved in both
cell division and environmental stress response. AtMPK4
also participates in regulating innate immunity. Group C
is represented by AtMPK1, AtMPK2, NtNTF3, Oryza sativa
MAPK4 (OsMAPK4), among others. They may also be involved
in stress responses. AtMPK1 and AtMPK2 are activated
following mechanical injury and in the presence of
stress chemicals such as jasmonic acid, hydrogen
peroxide and abscisic acid. OsMAPK4 is also called
OsMSRMK3 for Multiple Stress-Responsive MAPK3.
Length = 337
Score = 28.1 bits (63), Expect = 4.4
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 102 IHVLRCFKDENIIHVEGRIDPI-----NDIETIETELMLSDLERLER 143
I +LR EN+I ++ + P ND+ I ELM +DL ++ R
Sbjct: 55 IKLLRHLDHENVIAIKDIMPPPHREAFNDV-YIVYELMDTDLHQIIR 100
>gnl|CDD|37292 KOG2081, KOG2081, KOG2081, Nuclear transport regulator
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 559
Score = 28.0 bits (62), Expect = 4.8
Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 195 KSLNLLTAKPILYICNVSEHD--CKKGNIYTEAVQRLASQQNAEMIIISAAIEAEISQLP 252
K L A IC+ C ++ ++Q N E + I IS LP
Sbjct: 480 KRLASAAALAFHRICSACRVQMTCLIPSLLELIRSLDSTQINEEAACLLQGISLIISNLP 539
Query: 253 EEERALFMEEL 263
+ + +EEL
Sbjct: 540 AHKAKIALEEL 550
>gnl|CDD|147781 pfam05816, TelA, Toxic anion resistance protein (TelA). This
family consists of several prokaryotic TelA like
proteins. TelA and KlA are associated with tellurite
resistance and plasmid fertility inhibition.
Length = 333
Score = 27.9 bits (63), Expect = 5.0
Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 116 VEGRIDPI-NDIETIETELMLSDLERLERLFEKNKKY 151
V G+ID I ++E + EL+ D L++L++KN +Y
Sbjct: 96 VGGQIDKILVELEKGKDELL-KDNAMLDQLYDKNLEY 131
>gnl|CDD|110135 pfam01112, Asparaginase_2, Asparaginase.
Length = 296
Score = 27.8 bits (62), Expect = 5.2
Identities = 9/56 (16%), Positives = 19/56 (33%)
Query: 305 AQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIVKDGDI 360
A+ AA I +G + +++K + A ++G + I
Sbjct: 238 AEAAAKRITKALPRGSGGLIALNHKGEIGAPCNTTGMFRATATEDGTTLEYSEIGI 293
>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 = 27.7 bits (62), Expect = 5.6
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 6 GIIGLPNVGKSTLFNALT 23
GI G+P GKSTL AL
Sbjct: 33 GITGVPGAGKSTLIEALG 50
>gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 27.5 bits (61), Expect = 5.6
Identities = 27/145 (18%), Positives = 50/145 (34%), Gaps = 30/145 (20%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61
G + G++G GKSTL L +EP+SGEV P ++ +++
Sbjct: 29 GERIGLVGRNGAGKSTLLKILAG------------ELEPDSGEVTRPKG--LRVGYLSQE 74
Query: 62 KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRID 121
L P + + + E++ +L DE + +E ++
Sbjct: 75 PPLDPEKTVLDYVIEGFGELR----------ELLAELEEAYALLADPDDELLAELEALLE 124
Query: 122 PIN------DIETIETELMLSDLER 140
++ E L D +R
Sbjct: 125 ELDGWTLEARAEEALLGLGFPDEDR 149
>gnl|CDD|38920 KOG3716, KOG3716, KOG3716, Carnitine O-acyltransferase CPTI [Lipid
transport and metabolism].
Length = 764
Score = 27.6 bits (61), Expect = 5.6
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 311 VIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGK 351
++ TDF KGFI+ +S ++ M A + RD+GK
Sbjct: 540 LVFTDFGKGFIKKCGVSPDAFIQM-----ALQLAYYRDQGK 575
>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 = 27.3 bits (61), Expect = 6.5
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 6 GIIGLPNVGKSTLFNALT 23
++GL N GK+TL N +
Sbjct: 3 TLVGLQNSGKTTLVNVIA 20
>gnl|CDD|39796 KOG4596, KOG4596, KOG4596, Uncharacterized conserved protein
[Function unknown].
Length = 1936
Score = 27.3 bits (60), Expect = 7.1
Identities = 46/222 (20%), Positives = 80/222 (36%), Gaps = 58/222 (26%)
Query: 53 HKLAEIAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDA-IIHVLRCFKDE 111
H++ E +D T + F GNQ +AHI EV A II + +K
Sbjct: 1072 HEIYNWTELQDTSLTCIEF----------------GNQKIAHINEVHAAIILLTSKYKGI 1115
Query: 112 NIIHVEGRID----------PINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVL 161
+ EG +D ET E+ +L D +LE + +S
Sbjct: 1116 SDPEFEGLLDLWFPPNKPIPNAFLRETGESNQLLPDWLKLEMI----------RSVV--- 1162
Query: 162 LQSIISSSLRLIEE----------GKPVRS---LLESLDSDAIPIFKSL--NLLTAKPIL 206
Q ++ ++L + G PV S LL+ LD+ +P + +L+ +
Sbjct: 1163 -QRLVDAALIDLSPHQAQLFVQVFGMPVESMSKLLKMLDNAVMPDLDRIDHQILSKMYLA 1221
Query: 207 YICNVSEHDCKKGNIYTEAVQRLASQQNAEMIIISAAIEAEI 248
++ + + R+ SQ + + I+ EI
Sbjct: 1222 HLIEGQRMRGAQSGETL--INRIHSQMDNLLPFIAKEEPMEI 1261
>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the
ATP synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor
Rho.
Length = 213
Score = 27.0 bits (61), Expect = 7.9
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 3/33 (9%)
Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
G + GI G GK+ L L A A+
Sbjct: 15 GQRIGIFGGSGTGKTVL---LGMIARNAKADVV 44
>gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 27.2 bits (60), Expect = 8.1
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPN 41
++G GKS+L NAL + + + T
Sbjct: 44 LMGATGAGKSSLINALFQGEVKEVSKVGVGTDITT 78
>gnl|CDD|34791 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 27.1 bits (59), Expect = 8.3
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 3 FKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGE------VAVPDPRMHKLA 56
F ++G P GKSTL +L R + Q + I SG+ + P +H++
Sbjct: 70 FIVAVVGPPGTGKSTLIRSLVRRFTKQTIDEIRGPITVVSGKTRRITFLECPSD-LHQMI 128
Query: 57 EIAESKDLV 65
++A+ DLV
Sbjct: 129 DVAKIADLV 137
>gnl|CDD|133282 cd01882, BMS1, Bms1. Bms1 is an essential, evolutionarily
conserved, nucleolar protein. Its depletion interferes
with processing of the 35S pre-rRNA at sites A0, A1,
and A2, and the formation of 40S subunits. Bms1, the
putative endonuclease Rc11, and the essential U3 small
nucleolar RNA form a stable subcomplex that is believed
to control an early step in the formation of the 40S
subumit. The C-terminal domain of Bms1 contains a
GTPase-activating protein (GAP) that functions
intramolecularly. It is believed that Rc11 activates
Bms1 by acting as a guanine-nucleotide exchange factor
(GEF) to promote GDP/GTP exchange, and that activated
(GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Length = 225
Score = 26.9 bits (60), Expect = 8.3
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQ 29
++G P VGK+TL +L + + Q
Sbjct: 44 VVGPPGVGKTTLIKSLVKNYTKQ 66
>gnl|CDD|88298 cd05027, S-100B, S-100B: S-100B domain found in proteins similar to
S100B. S100B is a calcium-binding protein belonging to a
large S100 vertebrate-specific protein family within the
EF-hand superfamily of calcium-binding proteins. Note
that the S-100 hierarchy, to which this S-100B group
belongs, contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. S100B is most
abundant in glial cells of the central nervous system,
predominately in astrocytes. S100B is involved in signal
transduction via the inhibition of protein
phoshorylation, regulation of enzyme activity and by
affecting the calcium homeostasis. Upon calcium binding
the S100B homodimer changes conformation to expose a
hydrophobic cleft, which represents the interaction site
of S100B with its more than 20 known target proteins.
These target proteins include several cellular
architecture proteins such as tubulin and GFAP; S100B
can inhibit polymerization of these oligomeric
molecules. Furthermore, S100B inhibits the
phosphorylation of multiple kinase substrates including
the Alzheimer protein tau and neuromodulin (GAP-43)
through a calcium-sensitive interaction with the protein
substrates..
Length = 88
Score = 26.9 bits (59), Expect = 8.3
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 150 KYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESLDSD 189
K++ KSE L+ + +S L I+E + V ++E+LDSD
Sbjct: 24 KHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSD 63
>gnl|CDD|36919 KOG1707, KOG1707, KOG1707, Predicted Ras related/Rac-GTP binding
protein [Defense mechanisms].
Length = 625
Score = 26.9 bits (59), Expect = 9.0
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 3 FKCGIIGLPNVGKSTLFNAL 22
F+C ++G N GKS L +
Sbjct: 426 FQCFVVGPKNCGKSALLQSF 445
>gnl|CDD|99995 cd04299, GT1_Glycogen_Phosphorylase_like, This family is most
closely related to the oligosaccharide phosphorylase
domain family and other unidentified sequences.
Oligosaccharide phosphorylase catalyzes the breakdown of
oligosaccharides into glucose-1-phosphate units. They
are important allosteric enzymes in carbohydrate
metabolism. The members of this family are found in
bacteria and Archaea..
Length = 778
Score = 26.7 bits (60), Expect = 9.1
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 133 LMLSDLERLERL 144
L+L D ERL+RL
Sbjct: 495 LLLRDPERLKRL 506
>gnl|CDD|146089 pfam03280, Lipase_chap, Proteobacterial lipase chaperone protein.
Length = 195
Score = 26.8 bits (60), Expect = 9.1
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 225 AVQRLASQQNAEMIIIS--AAIEAEISQLPEEERA 257
A++RL +Q+ + + A I+QLPE+ R
Sbjct: 65 ALERLRIKQDPSLSDEQKARRLAALIAQLPEDLRE 99
>gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 26.9 bits (59), Expect = 9.6
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYP 34
IIG P VGK+TL + R S +
Sbjct: 142 IIGPPQVGKTTLLRDIARLLSDGINQFL 169
>gnl|CDD|30807 COG0459, GroL, Chaperonin GroEL (HSP60 family) [Posttranslational
modification, protein turnover, chaperones].
Length = 524
Score = 26.7 bits (59), Expect = 9.6
Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 12/94 (12%)
Query: 159 IVLLQSIISSSLRLIEEG-----------KPVRSLLESLDSDAIPIFKSLNLLTAKPILY 207
+VL +++ + +LI G V +E L A P+ S L
Sbjct: 89 VVLAGALLKEAEKLIAAGIHPTVIKRGYRLAVEKAVEELKEIAKPVSDSEEELKIAITSV 148
Query: 208 ICNVSEHDCKKGNIYTEAVQRLA-SQQNAEMIII 240
+ D + G + EAV+++ Q + + III
Sbjct: 149 ASKSANSDEEIGELVVEAVEKVGKEQSDLDGIII 182
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 0.136 0.383
Gapped
Lambda K H
0.267 0.0790 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,297,598
Number of extensions: 229035
Number of successful extensions: 1029
Number of sequences better than 10.0: 1
Number of HSP's gapped: 989
Number of HSP's successfully gapped: 139
Length of query: 367
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 272
Effective length of database: 4,210,882
Effective search space: 1145359904
Effective search space used: 1145359904
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 (26.0 bits)