RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2401
(363 letters)
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 554 bits (1430), Expect = 0.0
Identities = 196/364 (53%), Positives = 266/364 (73%), Gaps = 1/364 (0%)
Query: 1 MNLKCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKT 60
M LKCG++GLPNVGKSTLFNALTK A NYPFCTIEPN+G++ VPD RL L IVK
Sbjct: 1 MGLKCGIVGLPNVGKSTLFNALTKAGAEAANYPFCTIEPNVGVVPVPDPRLDKLAEIVKP 60
Query: 61 KKIFPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEIN 120
KKI PA I+ VDIAGLV GASKGEGLGN+FLA+IRE + ++HV+RCF+DD ITH+ G+++
Sbjct: 61 KKIVPATIEFVDIAGLVKGASKGEGLGNQFLANIREVDAIVHVVRCFEDDNITHVEGKVD 120
Query: 121 PIHDAEVIQTELILSDLAILEKYIDKENKKFFLKNEHSIELLKLLKRIIFNLNKSIPIRL 180
PI D E I TELIL+DL +EK +++ KK ++ + L+LL++++ +L + P R
Sbjct: 121 PIRDIETINTELILADLETVEKRLERLEKKAKGGDKEAKAELELLEKLLEHLEEGKPART 180
Query: 181 MSLNNEELMSIKFLNLLTIKPIIFVANVKENGF-KNNLLLDQLKIYAHNQNIPIIIICAK 239
+ L +EE +K L LLT KP+++VANV E+ N + +++ A + +++ICAK
Sbjct: 181 LELTDEEEKLLKSLQLLTAKPVLYVANVDEDDLADGNPYVKKVREIAAKEGAEVVVICAK 240
Query: 240 LEEEISDLNNIDKKFFLDNLGLKETKLNDLIRASFSLLDLRTYFTVGKKEIRAWTIPNGT 299
+E EI++L++ +K FL+ LGL+E+ L+ LIRA + LL L TYFT G KE+RAWTI GT
Sbjct: 241 IEAEIAELDDEEKAEFLEELGLEESGLDRLIRAGYELLGLITYFTAGPKEVRAWTIKKGT 300
Query: 300 TAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAGKIRSEGKKYLVEDGDILNF 359
TA QAAG+IHTD ++GFIRA ISY D + Y E G K AGK+R EGK Y+V+DGD+++F
Sbjct: 301 TAPQAAGVIHTDFEKGFIRAEVISYDDLIEYGSEAGAKEAGKVRLEGKDYIVQDGDVMHF 360
Query: 360 LFNI 363
FN+
Sbjct: 361 RFNV 364
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 447 bits (1153), Expect = e-158
Identities = 189/371 (50%), Positives = 250/371 (67%), Gaps = 9/371 (2%)
Query: 1 MNLKCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVK- 59
M+LK G++GLPNVGKSTLFNALTK NYPFCTIEPN+G++ VPD RL L IVK
Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTKAGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVKC 60
Query: 60 TKKIFPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEI 119
KI PA ++ VDIAGLV GASKGEGLGNKFL +IRE + +IHV+RCF D I H+ G++
Sbjct: 61 PPKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCFGDTDIEHVEGKV 120
Query: 120 NPIHDAEVIQTELILSDLAILEKYIDKENKKFFLKNEHSIEL---LKLLKRIIFNLNKSI 176
+P+ D E+I TELIL DL LEK ++ K+ + EL L LL ++ +L +
Sbjct: 121 DPVEDIEIINTELILWDLESLEKRWERLEKRAKAGKKLDKELKEELSLLGKLEEHLEEGK 180
Query: 177 PIR---LMSLNNEELMSIKFLNLLTIKPIIFVANVKENGFKN-NLLLDQLKIYAHNQNIP 232
P R L + E+L ++ LNLLT KP+++VANV E+ N N + +LK A +N
Sbjct: 181 PARGLDLSKWSEEDLEALASLNLLTAKPMLYVANVSEDDLANLNEYVKRLKELAAKENAE 240
Query: 233 IIIICAKLEEEISDLNNI-DKKFFLDNLGLKETKLNDLIRASFSLLDLRTYFTVGKKEIR 291
++ + A +E E+ +L + +K FL LG KE+ LN+LIRA + LL L+TYFT G KE+R
Sbjct: 241 VVPVSAAIELELRELADAEEKGEFLIELGQKESGLNELIRAGYGLLGLQTYFTAGVKEVR 300
Query: 292 AWTIPNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAGKIRSEGKKYLV 351
AWTI +G+ A AAG+IH D ++GFIRA ISY D + Y GE K AGK R EGK Y+V
Sbjct: 301 AWTIKDGSKAPDAAGVIHPDFEKGFIRAEVISYADLIHYGGEAAAKEAGKRRLEGKDYIV 360
Query: 352 EDGDILNFLFN 362
+DGD+++F FN
Sbjct: 361 QDGDVIHFKFN 371
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 417 bits (1073), Expect = e-145
Identities = 164/368 (44%), Positives = 237/368 (64%), Gaps = 6/368 (1%)
Query: 2 NLKCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTK 61
NLK G++GLPNVGKST FNAL K ++ AEN+PFCTI+PN + VPD+R L K K
Sbjct: 21 NLKMGIVGLPNVGKSTTFNALCKQQVPAENFPFCTIDPNTARVNVPDERFDWLCKHFKPK 80
Query: 62 KIFPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINP 121
I PA + + DIAGLV GAS+GEGLGN FL+HIR + + HV+R F+D+ ITH+ GEI+P
Sbjct: 81 SIVPAQLDITDIAGLVKGASEGEGLGNAFLSHIRAVDGIYHVVRAFEDEDITHVEGEIDP 140
Query: 122 IHDAEVIQTELILSDLAILEKYIDKENKKFFLKNE--HSIELLKLLKRIIFNLNKSIPIR 179
+ D E+I +ELIL DL +EK +D+ KK K + L +LK+++ L + P+R
Sbjct: 141 VRDLEIISSELILKDLEFVEKRLDELTKKRKKKKKKKEEKVELDVLKKVLEWLEEGKPVR 200
Query: 180 LMSLNNEELMSIKFLNLLTIKPIIFVANVKENGF--KNNLLLDQLKIY-AHNQNIPIIII 236
++E+ + LLT KP+I++ N+ E F + N L ++K + PII
Sbjct: 201 DGDWTDKEIEILNEYQLLTAKPMIYLVNMSEKDFIRQKNKWLAKIKEWVGEKGGGPIIPY 260
Query: 237 CAKLEEEISDLNNID-KKFFLDNLGLKETKLNDLIRASFSLLDLRTYFTVGKKEIRAWTI 295
A+ EEE+++L + + +K +L+ G+K++ L+ +I+ + LL+L +FT G E+R WTI
Sbjct: 261 SAEFEEELAELGSEEERKEYLEEYGIKQSMLDKIIKTGYKLLNLIHFFTAGPDEVRCWTI 320
Query: 296 PNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAGKIRSEGKKYLVEDGD 355
GT A QAAG+IH+D ++GFI A + Y+DFL E K GK R EGK Y+V+DGD
Sbjct: 321 QKGTKAPQAAGVIHSDFEKGFICAEVMKYEDFLELGSEAAVKAEGKYRQEGKDYVVQDGD 380
Query: 356 ILNFLFNI 363
I+ F FN+
Sbjct: 381 IIFFKFNV 388
>gnl|CDD|206687 cd01900, YchF, YchF GTPase. 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 = 369 bits (950), Expect = e-128
Identities = 142/274 (51%), Positives = 195/274 (71%), Gaps = 1/274 (0%)
Query: 5 CGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIF 64
G++GLPNVGKSTLFNALTK A NYPFCTIEPN+GI+ VPD+RL L IVK KKI
Sbjct: 1 IGIVGLPNVGKSTLFNALTKSNAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKIV 60
Query: 65 PAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIHD 124
PA I+ VDIAGLV GASKGEGLGNKFL+HIRE + + HV+RCF+DD ITH+ G ++P+ D
Sbjct: 61 PATIEFVDIAGLVKGASKGEGLGNKFLSHIREVDAIAHVVRCFEDDDITHVEGSVDPVRD 120
Query: 125 AEVIQTELILSDLAILEKYIDKENKKFFLKNEHSIELLKLLKRIIFNLNKSIPIRLMSLN 184
E+I TELIL+DL +EK +++ KK ++ + E L+LL++I +L + P R + L
Sbjct: 121 IEIINTELILADLETIEKRLERLEKKAKSGDKEAKEELELLEKIKEHLEEGKPARTLELT 180
Query: 185 NEELMSIKFLNLLTIKPIIFVANVKENGF-KNNLLLDQLKIYAHNQNIPIIIICAKLEEE 243
+EE+ +K L LLT KP+I+VANV E+ + N + +++ A + +I I AKLE E
Sbjct: 181 DEEIKILKSLQLLTAKPVIYVANVSEDDLIRGNNKVLKVREIAAKEGAEVIPISAKLEAE 240
Query: 244 ISDLNNIDKKFFLDNLGLKETKLNDLIRASFSLL 277
+++L+ + FL+ LGL+E+ L+ LIRA + LL
Sbjct: 241 LAELDEEEAAEFLEELGLEESGLDKLIRAGYELL 274
>gnl|CDD|129200 TIGR00092, TIGR00092, GTP-binding protein YchF. This predicted
GTP-binding protein is found in a single copy in every
complete bacterial genome, and is found in Eukaryotes. A
more distantly related protein, separated from this
model, is found in the archaea. It is known to bind GTP
and double-stranded nucleic acid. It is suggested to
belong to a nucleoprotein complex and act as a
translation factor [Unknown function, General].
Length = 368
Score = 325 bits (834), Expect = e-110
Identities = 178/369 (48%), Positives = 237/369 (64%), Gaps = 7/369 (1%)
Query: 1 MNLKCGLIGLPNVGKSTLFNALTKLKIS-AENYPFCTIEPNIGIIEVPDKRLKHLNNIVK 59
M L G++GLPNVGKSTLF A T L + A N PF TIEPN G++ D RL L +K
Sbjct: 1 MGLSGGIVGLPNVGKSTLFAATTNLLGNEAANPPFTTIEPNAGVVNPSDPRLDLLAIYIK 60
Query: 60 TKKIFPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEI 119
+K+ P + VDIAGLV GASKGEGLGN+FLA+IRE +I+ HV+RCF+DD I H+
Sbjct: 61 PEKVPPTTTEFVDIAGLVGGASKGEGLGNQFLANIREVDIIQHVVRCFEDDIIHHVGNVD 120
Query: 120 NPIHDAEVIQTELILSDLAILEKYIDKENKKFFLKNEHSIELLKLLKRIIFNLNKSIPIR 179
+P D E+I EL+ +D ++EK I + K + E L LL+ I+ LN R
Sbjct: 121 DPRDDFEIIDEELLKADEFLVEKRIGRSKKS-AEGGKDKKEELLLLEIILPLLNGGQMAR 179
Query: 180 LMSLNNEELMSIKFLNLLTIKPIIFVANVKENGFKN---NLLLDQLKIYAHNQNIPIII- 235
+ L+ EEL+ IK LNLLT KPII +ANV E+ +N N LL I A+++ P ++
Sbjct: 180 HVDLSKEELILIKSLNLLTKKPIILIANVSEDYLRNLNNNYLLIVEWIAAYSKGDPKVVF 239
Query: 236 ICAKLEEEISDLNNIDKKFFLDNLGLKETK-LNDLIRASFSLLDLRTYFTVGKKEIRAWT 294
+CA E E+S+L++ +++ FL LGL E+ LN +IRA + LL L +FT GK+E+RAWT
Sbjct: 240 VCALEESELSELDDEERQEFLQKLGLTESAGLNIIIRARYKLLLLSFFFTGGKEEVRAWT 299
Query: 295 IPNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAGKIRSEGKKYLVEDG 354
G A QAAGIIHTD + GFI A IS+ DF+ K QG K G +R EGK Y+V+DG
Sbjct: 300 RKGGWAAPQAAGIIHTDFETGFIAAEVISWDDFIYKKSSQGAKKGGLMRLEGKYYVVDDG 359
Query: 355 DILNFLFNI 363
D+L F FN+
Sbjct: 360 DVLFFAFNV 368
>gnl|CDD|203386 pfam06071, YchF-GTPase_C, Protein of unknown function (DUF933).
This domain is found at the C terminus of the YchF
GTP-binding protein and is possibly related to the
ubiquitin-like and MoaD/ThiS superfamilies.
Length = 84
Score = 151 bits (385), Expect = 3e-46
Identities = 51/84 (60%), Positives = 63/84 (75%)
Query: 279 LRTYFTVGKKEIRAWTIPNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKN 338
L T+FT G KE+RAWTI GTTA QAAG+IH+D ++GFIRA ISY D + Y E K
Sbjct: 1 LITFFTAGPKEVRAWTIRKGTTAPQAAGVIHSDFEKGFIRAEVISYDDLIEYGSEAKAKE 60
Query: 339 AGKIRSEGKKYLVEDGDILNFLFN 362
AGK+R EGK Y+V+DGDI++F FN
Sbjct: 61 AGKLRLEGKDYIVQDGDIIHFRFN 84
>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 = 141 bits (357), Expect = 6e-42
Identities = 45/83 (54%), Positives = 57/83 (68%)
Query: 279 LRTYFTVGKKEIRAWTIPNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKN 338
L ++FT G E+RAWTI GT A QAAG+IHTD ++GFIRA + Y+D + E K
Sbjct: 1 LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKYEDLVELGSEAAAKE 60
Query: 339 AGKIRSEGKKYLVEDGDILNFLF 361
AGK R EGK Y+V+DGDI+ F F
Sbjct: 61 AGKYRQEGKDYVVQDGDIIFFKF 83
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. 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 = 167
Score = 115 bits (291), Expect = 3e-31
Identities = 50/137 (36%), Positives = 77/137 (56%), Gaps = 23/137 (16%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIFP 65
GL+GLPNVGKSTL +ALT K+ +YPF T+EPN+G+ E D
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEFGD----------------G 44
Query: 66 AIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIHDA 125
I+++D+ GL+ GAS+G GLG + LAH+ +++++HVI +D +P+ D
Sbjct: 45 VDIQIIDLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASEDCV-------GDPLEDQ 97
Query: 126 EVIQTELILSDLAILEK 142
+ + E+ S L + K
Sbjct: 98 KTLNEEVSGSFLFLKNK 114
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 114 bits (288), Expect = 1e-28
Identities = 70/233 (30%), Positives = 112/233 (48%), Gaps = 43/233 (18%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGI----IEVPDKRLKH-----LNN 56
GL+G PNVGKST FNA T + NYPF TI+PN+G+ +E P K L
Sbjct: 5 GLVGKPNVGKSTFFNAATLADVEIANYPFTTIDPNVGVAYVRVECPCKELGVKCNPRNGK 64
Query: 57 IVKTKKIFPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKI--TH 114
+ + P ++L+D+AGLV GA +G GLGN+FL +R+ + +IHV+ D T
Sbjct: 65 CIDGTRFIP--VELIDVAGLVPGAHEGRGLGNQFLDDLRQADALIHVV-----DASGSTD 117
Query: 115 ISGEI------NPIHDAEVIQTELILSDLAILEKYIDKENKKFFLKNEHSIELLKLLKRI 168
G +P+ D + ++ EL + ILEK +K ++K + ++ + L
Sbjct: 118 EEGNPVEPGSHDPVEDIKFLEEELDMWIYGILEKNWEKFSRKAQAEKF---DIEEALAEQ 174
Query: 169 I--FNLNK----------SIPIRLMSLNNEELMSIKFLNLLTI--KPIIFVAN 207
+ +N+ +P +E+L ++ L KP++ AN
Sbjct: 175 LSGLGINEEHVKEALRELGLPEDPSKWTDEDL--LELARELRKISKPMVIAAN 225
Score = 35.9 bits (84), Expect = 0.030
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 17/62 (27%)
Query: 295 IPNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAGKIRSEGKKYLVEDG 354
+P G+TA A IHTDI GF+ A+ +A R G+ Y ++DG
Sbjct: 345 LPKGSTARDLAYKIHTDIGEGFLYAI-----------------DARTKRRIGEDYELKDG 387
Query: 355 DI 356
D+
Sbjct: 388 DV 389
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. 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 = 110 bits (277), Expect = 1e-27
Identities = 74/231 (32%), Positives = 117/231 (50%), Gaps = 39/231 (16%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGI----IEVPDKRLKHLNN----- 56
GL+G PNVGKST FNA T + NYPF TI+PN+G+ +E P K L N
Sbjct: 2 GLVGKPNVGKSTFFNAATLADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYGK 61
Query: 57 IVKTKKIFPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKD------- 109
+ K+ P ++L+D+AGLV GA +G+GLGN+FL +R+ +++IHV+ D
Sbjct: 62 CIDGKRYVP--VELIDVAGLVPGAHEGKGLGNQFLDDLRDADVLIHVV----DASGGTDA 115
Query: 110 DKITHISGEINPIHDAEVIQTELILSDLAILEKYIDK-ENKKFFLKNEHSIELLKLLKRI 168
+ +G +P+ D E ++ E+ + ILE+ +K K K + L + L
Sbjct: 116 EGNGVETGGYDPLEDIEFLENEIDMWIYGILERNWEKIVRKAKAEKTDIVEALSEQLS-- 173
Query: 169 IFNLNKSI----------PIRLMSLNNEELMSIKFLNLLTI--KPIIFVAN 207
F +N+ + P L ++E+L ++ L KP++ AN
Sbjct: 174 GFGVNEDVVIEALEELELPADLSKWDDEDL--LRLARELRKRRKPMVIAAN 222
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 109 bits (274), Expect = 4e-27
Identities = 53/139 (38%), Positives = 77/139 (55%), Gaps = 27/139 (19%)
Query: 6 GLIGLPNVGKSTLFNALT--KLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKI 63
GL+GLPN GKSTL +A++ K KI+ +YPF T+ PN+G++ V D R
Sbjct: 161 GLVGLPNAGKSTLISAVSAAKPKIA--DYPFTTLVPNLGVVRVDDGR------------- 205
Query: 64 FPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIH 123
+ DI GL+ GAS+G GLG++FL HI T +++H+I +D +PI
Sbjct: 206 ---SFVIADIPGLIEGASEGAGLGHRFLKHIERTRVLLHLIDISPED-------GSDPIE 255
Query: 124 DAEVIQTELILSDLAILEK 142
D E+I+ EL + EK
Sbjct: 256 DYEIIRNELKKYSPELAEK 274
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. 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 = 104 bits (261), Expect = 8e-27
Identities = 57/139 (41%), Positives = 83/139 (59%), Gaps = 29/139 (20%)
Query: 6 GLIGLPNVGKSTLFNALT--KLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKI 63
GL+GLPN GKSTL +A++ K KI+ +YPF T+ PN+G++ V D R + V
Sbjct: 4 GLVGLPNAGKSTLLSAISNAKPKIA--DYPFTTLVPNLGVVRVDDGR-----SFV----- 51
Query: 64 FPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIH 123
+ DI GL+ GAS+G+GLG++FL HI T +++HVI D +SGE +P+
Sbjct: 52 ------IADIPGLIEGASEGKGLGHRFLRHIERTRVLLHVI----D-----LSGEDDPVE 96
Query: 124 DAEVIQTELILSDLAILEK 142
D E I+ EL + + EK
Sbjct: 97 DYETIRNELEAYNPGLAEK 115
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 102 bits (257), Expect = 1e-24
Identities = 60/200 (30%), Positives = 88/200 (44%), Gaps = 56/200 (28%)
Query: 6 GLIGLPNVGKSTLFNALT--KLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKI 63
GL+GLPN GKSTL +A++ K KI+ +YPF T+ PN+G++ V + V
Sbjct: 163 GLVGLPNAGKSTLLSAVSAAKPKIA--DYPFTTLVPNLGVVRVDGG-----ESFV----- 210
Query: 64 FPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIH 123
+ DI GL+ GAS+G GLG +FL HI T +++HVI D +PI
Sbjct: 211 ------VADIPGLIEGASEGVGLGLRFLRHIERTRVLLHVIDLSPID-------GRDPIE 257
Query: 124 DAEVIQTEL---------------------ILSD--LAILEKYIDKENKKFF------LK 154
D + I+ EL L + L L+K + + L
Sbjct: 258 DYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALT 317
Query: 155 NEHSIELLKLLKRIIFNLNK 174
E ELL+ L ++
Sbjct: 318 REGLDELLRALAELLEETKA 337
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 99.8 bits (250), Expect = 8e-24
Identities = 49/139 (35%), Positives = 76/139 (54%), Gaps = 30/139 (21%)
Query: 6 GLIGLPNVGKSTLFNALT--KLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKI 63
GL+GLPN GKSTL +A++ K KI+ +YPF T+ PN+G++ V D + + V
Sbjct: 162 GLVGLPNAGKSTLISAVSAAKPKIA--DYPFTTLHPNLGVVRVDDYK-----SFV----- 209
Query: 64 FPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIH 123
+ DI GL+ GAS+G GLG++FL HI T +++H++ D P+
Sbjct: 210 ------IADIPGLIEGASEGAGLGHRFLKHIERTRLLLHLVDIEAVD----------PVE 253
Query: 124 DAEVIQTELILSDLAILEK 142
D + I+ EL + +K
Sbjct: 254 DYKTIRNELEKYSPELADK 272
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 100 bits (252), Expect = 1e-23
Identities = 57/141 (40%), Positives = 80/141 (56%), Gaps = 31/141 (21%)
Query: 6 GLIGLPNVGKSTLFNALT--KLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKI 63
GL+G PNVGKSTL + ++ K KI+ NY F T+ PN+G++E D R + V
Sbjct: 162 GLVGFPNVGKSTLLSVVSNAKPKIA--NYHFTTLVPNLGVVETDDGR-----SFV----- 209
Query: 64 FPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEI--NP 121
+ DI GL+ GAS+G GLG++FL HI T +++HVI D +SG +P
Sbjct: 210 ------MADIPGLIEGASEGVGLGHQFLRHIERTRVIVHVI----D-----MSGSEGRDP 254
Query: 122 IHDAEVIQTELILSDLAILEK 142
I D E I EL L + +LE+
Sbjct: 255 IEDYEKINKELKLYNPRLLER 275
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 90.7 bits (226), Expect = 6e-20
Identities = 45/129 (34%), Positives = 71/129 (55%), Gaps = 27/129 (20%)
Query: 6 GLIGLPNVGKSTLFNALT--KLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKI 63
GL+G P+ GKS+L +AL+ K KI+ +YPF T+ PN+G+++ D R
Sbjct: 163 GLVGFPSAGKSSLISALSAAKPKIA--DYPFTTLVPNLGVVQAGDTRFT----------- 209
Query: 64 FPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIH 123
+ D+ GL+ GAS+G+GLG FL HI +++HV+ C T G +P+
Sbjct: 210 ------VADVPGLIPGASEGKGLGLDFLRHIERCAVLVHVVDC-----ATLEPGR-DPLS 257
Query: 124 DAEVIQTEL 132
D + ++ EL
Sbjct: 258 DIDALEAEL 266
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 89.9 bits (224), Expect = 6e-20
Identities = 47/127 (37%), Positives = 70/127 (55%), Gaps = 23/127 (18%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIFP 65
GL+GLPN GKST A++ K +YPF T+ PN+G++ V D+R + V
Sbjct: 163 GLLGLPNAGKSTFIRAVSAAKPKVADYPFTTLVPNLGVVRVDDER-----SFV------- 210
Query: 66 AIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIHDA 125
+ DI GL+ GAS+G GLG +FL H+ +++H+I I I G +P+ +A
Sbjct: 211 ----VADIPGLIEGASEGAGLGIRFLKHLERCRVLLHLI------DIAPIDGS-DPVENA 259
Query: 126 EVIQTEL 132
+I EL
Sbjct: 260 RIIINEL 266
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 80.0 bits (198), Expect = 2e-18
Identities = 41/130 (31%), Positives = 66/130 (50%), Gaps = 23/130 (17%)
Query: 4 KCGLIGLPNVGKSTLFNALTKLKIS-AENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKK 62
+ L+G PNVGKSTL NALT K++ +YP T +P +G++ + +
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGRQ------------- 47
Query: 63 IFPAIIKLVDIAGLVSGASKGEGLG--NKFLAHIRETNIVIHVI--RCFKDDKITHISGE 118
I LVD GL+ GAS+G+G+ N+FL IRE ++++ V+ + I E
Sbjct: 48 -----IILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEE 102
Query: 119 INPIHDAEVI 128
+ + +I
Sbjct: 103 LEKLPKKPII 112
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (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 = 75.7 bits (187), Expect = 8e-16
Identities = 32/106 (30%), Positives = 52/106 (49%), Gaps = 17/106 (16%)
Query: 5 CGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIF 64
L+G P+VGKSTL + LT K Y F T+ G++E
Sbjct: 3 VALVGFPSVGKSTLLSKLTNTKSEVAAYEFTTLTCVPGVMEYKG---------------- 46
Query: 65 PAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDD 110
A I+L+D+ G++ GAS G+G G + +A R ++++ V+ K +
Sbjct: 47 -AKIQLLDLPGIIEGASDGKGRGRQVIAVARTADLILIVLDATKPE 91
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 76.2 bits (188), Expect = 2e-15
Identities = 84/362 (23%), Positives = 143/362 (39%), Gaps = 78/362 (21%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIFP 65
L+G P+VGKSTL N LT K +YPF T+EP G++E
Sbjct: 67 ALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEPVPGMLEYKG----------------- 109
Query: 66 AIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRCFKDDKITHISGEINPIHDA 125
A I+L+D+ G++ GAS G G G + L+ R +++I V+ F+D H
Sbjct: 110 AQIQLLDLPGIIEGASSGRGRGRQVLSVARNADLIIIVLDVFEDP------------HHR 157
Query: 126 EVIQTELILSDLAILEKYIDKENKKFFLKNEHSIELLKLLKRIIFNLNKSIPIRLMSLNN 185
++I+ E L D+ I ++K +K K+ + + L L+
Sbjct: 158 DIIERE--LEDVGI---RLNKRPPDVTIK-----------KKESGGIRINGTGPLTHLDE 201
Query: 186 EELMSIKFLNLLTIKPIIFVANVKENGFKNNLLLDQLK--IYAHNQNIPIIIICAKL--- 240
+ + +I L I A+V + ++ LD L + + P + + K+
Sbjct: 202 DTVRAI--LREYRIHN----ADVL---IREDVTLDDLIDALEGNRVYKPALYVVNKIDLP 252
Query: 241 -EEEISDLNNIDKKFFLDNLGLKETKLNDLIRASFSLLDLRTYFTVGKKEIRAWT----I 295
EE+ L + K L++L + +L L +T E + +
Sbjct: 253 GLEELERLARKPNSVPIS--AKKGINLDELKERIWDVLGLIRVYTKPPGEEPDFDEPLIL 310
Query: 296 PNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAGKIRSEGKKYLVEDGD 355
G+T IH D+ F A + K K+ G+ G +++ED D
Sbjct: 311 RRGSTVGDVCRKIHRDLVENFRYAR-VWGKSV---------KHPGQ--RVGLDHVLEDED 358
Query: 356 IL 357
I+
Sbjct: 359 IV 360
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 56.1 bits (136), Expect = 1e-09
Identities = 22/102 (21%), Positives = 34/102 (33%), Gaps = 17/102 (16%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISA-ENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIF 64
+ G PNVGKS+L NAL + P T +P E+
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLG-------------- 46
Query: 65 PAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIRC 106
+ L+D GL G + ++V+ V+
Sbjct: 47 --PVVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDS 86
>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 = 48.2 bits (115), Expect = 1e-07
Identities = 22/94 (23%), Positives = 31/94 (32%), Gaps = 29/94 (30%)
Query: 279 LRTYFTVGKK-----------EIRAWTIPNGTTAEQAAGIIHTDIKRGFIRALTISYKDF 327
L + V + GTT A IH D+++GFI A+
Sbjct: 1 LIPVYPVKNIHTFTNGSGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVG------ 54
Query: 328 LLYKGEQGCKNAGKIRSEGKKYLVEDGDILNFLF 361
G+ R EGK ++ DIL F
Sbjct: 55 ------------GRRRLEGKDVILGKNDILKFKT 76
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane
protein. The N terminus contains a P-loop motif
suggesting that iron transport may be ATP dependent.
Length = 159
Score = 48.2 bits (116), Expect = 6e-07
Identities = 20/46 (43%), Positives = 29/46 (63%)
Query: 7 LIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLK 52
L+G PNVGK+TLFNALT + N+P T+E G ++ K ++
Sbjct: 2 LVGNPNVGKTTLFNALTGARQKVGNWPGVTVEKKEGEFKLGGKEIE 47
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of
the cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 48.3 bits (116), Expect = 1e-06
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 3 LKCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLK 52
+ L+G PNVGK+TLFNALT + N+P T+E G + ++
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQHVGNWPGVTVEKKEGTFKYKGYEIE 50
>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 = 44.6 bits (106), Expect = 1e-06
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 22/81 (27%)
Query: 281 TYFTVGKKEIRAWTIPNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAG 340
FT A +P G TA A IHTD+ +GFI AL G
Sbjct: 2 IIFTPDG---SAVELPKGATAMDFALKIHTDLGKGFIGAL-----------------VNG 41
Query: 341 KIRSEGKKYLVEDGDILNFLF 361
++ Y ++DGD ++ +
Sbjct: 42 QL--VDLSYTLQDGDTVSIVT 60
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 48.4 bits (116), Expect = 4e-06
Identities = 20/52 (38%), Positives = 28/52 (53%)
Query: 1 MNLKCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLK 52
L L+G PNVGK+TLFNALT N+P T+E G ++ ++
Sbjct: 2 KKLTVALVGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIE 53
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 45.9 bits (109), Expect = 4e-06
Identities = 23/100 (23%), Positives = 43/100 (43%), Gaps = 18/100 (18%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISA-ENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIF 64
++G VGKS+L NAL ++ + P T +P++ + E+ ++K
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVK------------ 48
Query: 65 PAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVI 104
+ LVD GL G G +R ++++ V+
Sbjct: 49 ---LVLVDTPGLDEFG--GLGREELARLLLRGADLILLVV 83
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 46.5 bits (111), Expect = 1e-05
Identities = 18/42 (42%), Positives = 21/42 (50%)
Query: 9 GLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKR 50
G PNVGKS+L LT K YPF T ++G E R
Sbjct: 175 GYPNVGKSSLVRKLTTAKPEVAPYPFTTKGIHVGHFERGYLR 216
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 46.4 bits (111), Expect = 1e-05
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 24/103 (23%)
Query: 7 LIGLPNVGKSTLFNALTKLKIS-AENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIFP 65
++G PNVGKSTLFN LT +I+ + P T + G E +
Sbjct: 8 IVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGRE--------------- 52
Query: 66 AIIKLVDIAGLVSGASKGEGLG----NKFLAHIRETNIVIHVI 104
L+D GL G + L + L I E ++++ V+
Sbjct: 53 --FILIDTGGLDDG--DEDELQELIREQALIAIEEADVILFVV 91
Score = 35.2 bits (82), Expect = 0.041
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 3 LKCGLIGLPNVGKSTLFNALTK 24
+K +IG PNVGKS+L NA+
Sbjct: 179 IKIAIIGRPNVGKSSLINAILG 200
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 46.5 bits (111), Expect = 1e-05
Identities = 20/45 (44%), Positives = 26/45 (57%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKR 50
L+G N GKSTLFNALT + + F T++P IE+ D R
Sbjct: 196 ALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDGR 240
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus,
defects in NOG1 can lead to defects in 60S biogenesis.
The S. cerevisiae NOG1 gene is essential for cell
viability, and mutations in the predicted G motifs
abrogate function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 44.5 bits (106), Expect = 2e-05
Identities = 18/42 (42%), Positives = 22/42 (52%)
Query: 9 GLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKR 50
G PNVGKS+L N LT+ K YPF T +G + R
Sbjct: 7 GYPNVGKSSLVNKLTRAKPEVAPYPFTTKSLFVGHFDYKYLR 48
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to
other GTPases, it is likely that an ancient gene
duplication, rather than a fusion of evolutionarily
distinct GTPases, gave rise to this family. Although
the exact function of these proteins has not been
elucidated, studies have revealed that the E. coli EngA
homolog, Der, and Neisseria gonorrhoeae EngA are
essential for cell viability. A recent report suggests
that E. coli Der functions in ribosome assembly and
stability.
Length = 157
Score = 44.0 bits (105), Expect = 2e-05
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 7 LIGLPNVGKSTLFNALTKLKIS-AENYP 33
++G PNVGKSTLFN LT + + + P
Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVSDTP 29
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 43.5 bits (103), Expect = 3e-05
Identities = 31/103 (30%), Positives = 40/103 (38%), Gaps = 16/103 (15%)
Query: 4 KCGLIGLPNVGKSTLFNALTKLKIS-AENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKK 62
K ++G PNVGKSTL N L KIS E P T +IE K K
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYK---------- 52
Query: 63 IFPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETNIVIHVIR 105
L+D AG + + +R +IVI V+
Sbjct: 53 -----FNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLD 90
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 42.4 bits (101), Expect = 1e-04
Identities = 21/45 (46%), Positives = 28/45 (62%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKR 50
L+G N GKSTLFNALT + AE+ F T++P I++P R
Sbjct: 45 ALVGYTNAGKSTLFNALTGADVLAEDQLFATLDPTTRRIKLPGGR 89
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 43.2 bits (103), Expect = 1e-04
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKR 50
L+G N GKSTLFNALT + A + F T++P +++PD
Sbjct: 193 ALVGYTNAGKSTLFNALTGADVYAADQLFATLDPTTRRLDLPDGG 237
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 42.3 bits (101), Expect = 2e-04
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 7 LIGLPNVGKSTLFNALTKLKIS 28
++G PNVGKSTLFN LT + +
Sbjct: 6 IVGRPNVGKSTLFNRLTGKRDA 27
Score = 36.2 bits (85), Expect = 0.026
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 2 NLKCGLIGLPNVGKSTLFNALTK 24
+K +IG PNVGKS+L NAL
Sbjct: 173 PIKIAIIGRPNVGKSSLINALLG 195
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 42.0 bits (100), Expect = 3e-04
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 7 LIGLPNVGKSTLFNALTKLKIS-AENYP 33
++G PNVGKSTLFN LT + + + P
Sbjct: 4 IVGRPNVGKSTLFNRLTGKRDAIVSDTP 31
Score = 35.5 bits (83), Expect = 0.040
Identities = 14/22 (63%), Positives = 16/22 (72%)
Query: 3 LKCGLIGLPNVGKSTLFNALTK 24
+K +IG PNVGKSTL NAL
Sbjct: 173 IKIAIIGRPNVGKSTLVNALLG 194
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 41.6 bits (99), Expect = 3e-04
Identities = 18/31 (58%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 1 MNLKCG---LIGLPNVGKSTLFNALTKLKIS 28
M K G ++G PNVGKSTL NAL KIS
Sbjct: 1 MGFKSGFVAIVGRPNVGKSTLLNALVGQKIS 31
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 42.0 bits (99), Expect = 3e-04
Identities = 18/42 (42%), Positives = 28/42 (66%)
Query: 7 LIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPD 48
L+G N GKSTLFN +T+ ++ A + F T++P + I+V D
Sbjct: 202 LVGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVAD 243
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 41.6 bits (98), Expect = 5e-04
Identities = 18/30 (60%), Positives = 21/30 (70%)
Query: 9 GLPNVGKSTLFNALTKLKISAENYPFCTIE 38
G PNVGKSTLFNALT + N+P T+E
Sbjct: 1 GNPNVGKSTLFNALTGANQTVGNWPGVTVE 30
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except
some eubacteria. It binds to the 16S ribosomal RNA
(rRNA) of the 30S subunit and appears to play a role in
the assembly of the 30S subunit, possibly by
chaperoning the 16S rRNA. It also contacts several
assembly elements of the 30S subunit. Era couples cell
growth with cytokinesis and plays a role in cell
division and energy metabolism. Homologs have also been
found in eukaryotes. Era contains two domains: the
N-terminal GTPase domain and a C-terminal domain KH
domain that is critical for RNA binding. Both domains
are important for Era function. Era is functionally
able to compensate for deletion of RbfA, a cold-shock
adaptation protein that is required for efficient
processing of the 16S rRNA.
Length = 168
Score = 39.8 bits (94), Expect = 5e-04
Identities = 18/28 (64%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 4 KCG---LIGLPNVGKSTLFNALTKLKIS 28
K G +IG PNVGKSTL NAL KIS
Sbjct: 2 KSGFVAIIGRPNVGKSTLLNALVGQKIS 29
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 39.3 bits (92), Expect = 0.002
Identities = 34/150 (22%), Positives = 51/150 (34%), Gaps = 24/150 (16%)
Query: 3 LKCGLIGLPNVGKSTLFNAL--------------TKLKISAENYPFCTIEPNIGIIEVPD 48
++G PNVGKSTL N L T+ +IS T I I+ P
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGI---HTTGASQIIFIDTPG 57
Query: 49 KRL-KHLNNIVKTKKIFPAIIKLVDIAGLVSGASKGEGLGNKFLAHIRETN-----IVIH 102
KH N + K+ A I VD+ V + + G G L ++
Sbjct: 58 FHEKKHSLNRLMMKEARSA-IGGVDLILFVVDSDQWNGDGEFVLTKLQNLKRPVVLTRNK 116
Query: 103 VIRCFKDDKITHISGEINPIHDAEVIQTEL 132
+ FKD + I +++
Sbjct: 117 LDNKFKDKLLPLIDKYAILEDFKDIVPISA 146
>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 = 36.1 bits (84), Expect = 0.003
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 17/66 (25%)
Query: 292 AWTIPNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAGKIRSEGKKYLV 351
A+ +P G+TA A IHTDI GF+ A+ +A R G+ Y +
Sbjct: 24 AFLLPKGSTARDLAYAIHTDIGDGFLHAI-----------------DARTGRRVGEDYEL 66
Query: 352 EDGDIL 357
+ D++
Sbjct: 67 KHRDVI 72
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 39.3 bits (92), Expect = 0.003
Identities = 25/76 (32%), Positives = 32/76 (42%), Gaps = 17/76 (22%)
Query: 3 LKCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKK 62
L GLIG PN GK+TLFN LT + N+ T+E G D +
Sbjct: 4 LTIGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKEGQFSTTDHQ------------ 51
Query: 63 IFPAIIKLVDIAGLVS 78
+ LVD+ G S
Sbjct: 52 -----VTLVDLPGTYS 62
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. 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 = 140
Score = 37.2 bits (87), Expect = 0.004
Identities = 26/73 (35%), Positives = 30/73 (41%), Gaps = 21/73 (28%)
Query: 6 GLIGLPNVGKSTLFNAL-TKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIF 64
GL+G PNVGKS+L NAL K+S + P T KH I
Sbjct: 86 GLVGYPNVGKSSLINALVGSKKVSVSSTPGKT---------------KHFQTIFLEPG-- 128
Query: 65 PAIIKLVDIAGLV 77
I L D GLV
Sbjct: 129 ---ITLCDCPGLV 138
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 38.6 bits (91), Expect = 0.004
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 7 LIGLPNVGKSTLFNALTK 24
+ G PNVGKS+L NAL
Sbjct: 220 IAGRPNVGKSSLLNALLG 237
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 38.3 bits (90), Expect = 0.004
Identities = 19/31 (61%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 1 MNLKCG---LIGLPNVGKSTLFNALTKLKIS 28
M K G +IG PNVGKSTL NAL KIS
Sbjct: 2 MKFKSGFVAIIGRPNVGKSTLLNALVGQKIS 32
>gnl|CDD|206751 cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly
permuted subfamily of the Ras GTPases. 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 = 37.3 bits (87), Expect = 0.004
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 14/59 (23%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKIF 64
G IG PNVGKS++ N L K+ C + P G +V I K+I+
Sbjct: 106 GFIGYPNVGKSSVINTLRSKKV-------CKVAPIPGETKV-------WQYITLMKRIY 150
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes.
TrmE contains a GTPase domain that forms a canonical
Ras-like fold. It functions a molecular switch GTPase,
and apparently uses a conformational change associated
with GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 36.7 bits (86), Expect = 0.005
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 7 LIGLPNVGKSTLFNALTK 24
+ G PNVGKS+L NAL
Sbjct: 8 IAGKPNVGKSSLLNALAG 25
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 37.8 bits (88), Expect = 0.007
Identities = 44/184 (23%), Positives = 71/184 (38%), Gaps = 23/184 (12%)
Query: 3 LKCGLIGLPNVGKSTLFNA-LTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTK 61
K ++G PNVGKS+L NA L + + + T + G E LN I
Sbjct: 204 FKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFE--------LNGI---- 251
Query: 62 KIFPAIIKLVDIAGLVSGASKGEGLG-NKFLAHIRETNIVIHVIRC----FKDDKITHIS 116
+IKL+D AG+ A E LG K I++ ++VI+V+ KDD +
Sbjct: 252 -----LIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDL 306
Query: 117 GEINPIHDAEVIQTELILSDLAILEKYIDKENKKFFLKNEHSIELLKLLKRIIFNLNKSI 176
+ + + +L ++ L + K L+ LL + I
Sbjct: 307 NKSKKPFILVLNKIDLKINSLEFFVSSKVLNSSNLSAKQLKIKALVDLLTQKINAFYSKE 366
Query: 177 PIRL 180
+ L
Sbjct: 367 RVEL 370
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. 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 all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 36.4 bits (85), Expect = 0.010
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 3 LKCGLIGLPNVGKSTLFNALTKLKI 27
L+ ++G+PNVGKSTL N L K+
Sbjct: 116 LRAMVVGIPNVGKSTLINRLRGKKV 140
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to
other GTPases, it is likely that an ancient gene
duplication, rather than a fusion of evolutionarily
distinct GTPases, gave rise to this family. Although
the exact function of these proteins has not been
elucidated, studies have revealed that the E. coli EngA
homolog, Der, and Neisseria gonorrhoeae EngA are
essential for cell viability. A recent report suggests
that E. coli Der functions in ribosome assembly and
stability.
Length = 174
Score = 35.5 bits (83), Expect = 0.020
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 2 NLKCGLIGLPNVGKSTLFNALTK 24
+K +IG PNVGKS+L NAL
Sbjct: 2 PIKIAIIGRPNVGKSSLLNALLG 24
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 36.0 bits (84), Expect = 0.024
Identities = 14/22 (63%), Positives = 16/22 (72%)
Query: 3 LKCGLIGLPNVGKSTLFNALTK 24
LK +IG PNVGKS+L NAL
Sbjct: 218 LKVVIIGRPNVGKSSLLNALLG 239
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. 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 = 171
Score = 34.9 bits (81), Expect = 0.028
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 6 GLIGLPNVGKSTLFNAL 22
G++G PNVGKS++ N+L
Sbjct: 120 GVVGYPNVGKSSVINSL 136
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 34.0 bits (79), Expect = 0.085
Identities = 14/20 (70%), Positives = 15/20 (75%)
Query: 8 IGLPNVGKSTLFNALTKLKI 27
IG+PNVGKSTL N L KI
Sbjct: 127 IGIPNVGKSTLINRLAGKKI 146
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 34.0 bits (79), Expect = 0.10
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 8 IGLPNVGKSTLFNALTKLKI 27
+G+PNVGKSTL N L K+
Sbjct: 124 VGIPNVGKSTLINRLAGKKV 143
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 33.5 bits (77), Expect = 0.13
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 6 GLIGLPNVGKSTLFNALTKLKI 27
G++G PNVGKSTL N L K+
Sbjct: 136 GVVGYPNVGKSTLINRLLGKKV 157
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 32.3 bits (74), Expect = 0.17
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 4 KCGLIGLPNVGKSTLFNALTK 24
G++G P VGKS++ NAL
Sbjct: 101 IVGVVGYPKVGKSSIINALKG 121
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 33.4 bits (77), Expect = 0.20
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 7 LIGLPNVGKSTLFNALT 23
L+G PNVGKS+L N L
Sbjct: 216 LVGKPNVGKSSLLNKLA 232
Score = 31.1 bits (71), Expect = 1.0
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 8 IGLPNVGKSTLFN 20
+G PNVGKSTL N
Sbjct: 44 VGRPNVGKSTLVN 56
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 32.6 bits (74), Expect = 0.25
Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 1/55 (1%)
Query: 3 LKCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNI 57
K ++G VGK+TL N L E YP + P +R L
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVG-DEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLW 59
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 32.8 bits (75), Expect = 0.28
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 7 LIGLPNVGKSTLFNALT 23
L+G PNVGKS+L N LT
Sbjct: 455 LVGRPNVGKSSLLNQLT 471
Score = 29.4 bits (66), Expect = 3.3
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 7 LIGLPNVGKSTLFN 20
++G PNVGKSTL N
Sbjct: 280 IVGRPNVGKSTLVN 293
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. 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 = 191
Score = 31.9 bits (73), Expect = 0.29
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 7 LIGLPNVGKSTLFNALTK 24
++G NVGKSTL NAL K
Sbjct: 130 VVGATNVGKSTLINALLK 147
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
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 = 180
Score = 31.8 bits (73), Expect = 0.29
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 3 LKCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGI--IEVPDKRLKHL 54
C ++G GKS L A S Y TI+P + +EVP + K+L
Sbjct: 5 FLCFVLGAKGSGKSALLQAFLGRSFSQNAYSP-TIKPRYAVNTVEVPGQE-KYL 56
>gnl|CDD|217243 pfam02824, TGS, TGS domain. The TGS domain is named after ThrRS,
GTPase, and SpoT. Interestingly, TGS domain was detected
also at the amino terminus of the uridine kinase from
the spirochaete Treponema pallidum (but not any other
organism, including the related spirochaete Borrelia
burgdorferi). TGS is a small domain that consists of ~50
amino acid residues and is predicted to possess a
predominantly beta-sheet structure. There is no direct
information on the functions 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 = 29.8 bits (68), Expect = 0.31
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 19/66 (28%)
Query: 295 IPNGTTAEQAAGIIHTDIKRGFIRALTISYKDFLLYKGEQGCKNAGKIRSEGKKYLVEDG 354
+P G+T E A IHTD+ + FI G K G+ G +++EDG
Sbjct: 13 LPRGSTPEDFAYAIHTDLGKKFI-----------------GAKVNGQRV--GLDHVLEDG 53
Query: 355 DILNFL 360
D++ +
Sbjct: 54 DVVEIV 59
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 31.8 bits (73), Expect = 0.35
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 7 LIGLPNVGKSTLFNALTKLKISAENYPFCTIEPN 40
+G NVGKSTL LT K+ P T +PN
Sbjct: 14 FVGRSNVGKSTLVRELTGKKVRVGKRPGVTRKPN 47
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA,
an essential protein involved in cell division control.
YihA and its orthologs are small proteins that
typically contain less than 200 amino acid residues and
consists of the GTPase domain only (some of the
eukaryotic homologs contain an N-terminal extension of
about 120 residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 31.7 bits (73), Expect = 0.35
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 7 LIGLPNVGKSTLFNALTKLK 26
G NVGKS+L NALT K
Sbjct: 4 FAGRSNVGKSSLINALTNRK 23
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component
of iron-siderophores, vitamin B12 and hemin
transporters and related proteins. 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 = 31.3 bits (72), Expect = 0.43
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 5 CGLIGLPN-VGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKI 63
G++G PN GKSTL L L ++P+ G I + K L L+ +KI
Sbjct: 28 VGILG-PNGAGKSTLLKTLAGL-----------LKPSSGEILLDGKDLASLSPKELARKI 75
Query: 64 --FPAIIKLVDIAGL 76
P ++L+ +A L
Sbjct: 76 AYVPQALELLGLAHL 90
>gnl|CDD|213186 cd03219, ABC_Mj1267_LivG_branched, ATP-binding cassette component
of branched chain amino acids transport system. 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 = 31.6 bits (73), Expect = 0.51
Identities = 12/20 (60%), Positives = 15/20 (75%), Gaps = 2/20 (10%)
Query: 5 CGLIGLPN-VGKSTLFNALT 23
GLIG PN GK+TLFN ++
Sbjct: 29 HGLIG-PNGAGKTTLFNLIS 47
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They generally show sequence conservation in the
region between the Walker A and B motifs (G1 and G3 box
motifs), to the exclusion of other GTPases. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 30.8 bits (70), Expect = 0.52
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 6 GLIGLPNVGKSTLFNALTKLKISA 29
GL+G GKS+L NAL +++A
Sbjct: 1 GLMGKTGAGKSSLCNALFGTEVAA 24
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted 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 = 146
Score = 30.4 bits (69), Expect = 0.66
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 6 GLIGLPNVGKSTLFNALTK 24
G++GLPNVGKS+ NAL
Sbjct: 95 GVVGLPNVGKSSFINALLN 113
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation
GTPase HydF. This model describes the family of the
[Fe] hydrogenase maturation protein HypF as
characterized in Chlamydomonas reinhardtii and found,
in an operon with radical SAM proteins HydE and HydG,
in numerous bacteria. It has GTPase activity, can bind
an 4Fe-4S cluster, and is essential for hydrogenase
activity [Protein fate, Protein modification and
repair].
Length = 391
Score = 31.3 bits (72), Expect = 0.78
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 6 GLIGLPNVGKSTLFNALT 23
G+ G N GKS+L NALT
Sbjct: 10 GIFGRRNAGKSSLINALT 27
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). 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 = 168
Score = 30.0 bits (68), Expect = 1.1
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 7 LIGLPNVGKSTLFNALTKLKIS-AENYPFC-------TIEPNIGIIEVPDKRLK 52
++GL N GK+T L + K ++NY T+ NIG IEV RL
Sbjct: 4 ILGLDNAGKTTF---LEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLM 54
>gnl|CDD|217147 pfam02618, YceG, YceG-like family. This family of proteins is
found in bacteria. Proteins in this family are typically
between 332 and 389 amino acids in length. This family
was previously incorrectly annotated and names as
aminodeoxychorismate lyase. The structure of Escherichia
coli yceG was solved by X-ray crystallography.
Length = 291
Score = 30.6 bits (70), Expect = 1.3
Identities = 15/69 (21%), Positives = 22/69 (31%), Gaps = 2/69 (2%)
Query: 269 LIRASFSLLDLRTYFTVGKKEIRAWTIPNGTTAEQAAGII--HTDIKRGFIRALTISYKD 326
++ S ++ GK TIP G T EQ A + IK+ A
Sbjct: 49 ELKPGMSAAEILEKLVSGKVVQYKVTIPEGLTLEQIAERLAKAGGIKKEEFLAALKDPAF 108
Query: 327 FLLYKGEQG 335
G+
Sbjct: 109 LEELGGKLP 117
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 29.9 bits (68), Expect = 1.4
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 7 LIGLPNVGKSTLFNALTKLK 26
G NVGKS+L NALT K
Sbjct: 29 FAGRSNVGKSSLINALTNQK 48
>gnl|CDD|188394 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit,
PQQ-dependent alcohol dehydrogenase system. Members of
this protein family are the ATP-binding subunit of an
ABC transporter system that is associated with PQQ
biosynthesis and PQQ-dependent alcohol dehydrogenases.
While this family shows homology to several efflux ABC
transporter subunits, the presence of a periplasmic
substrate-binding protein and association with systems
for catabolism of alcohols suggests a role in import
rather than detoxification [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 236
Score = 30.0 bits (68), Expect = 1.7
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 5 CGLIGLPNVGKSTLFNALTKLKISAE 30
L+G GKSTLF+ LT+L ++ E
Sbjct: 30 VALLGPNGAGKSTLFSLLTRLYVAQE 55
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members
commonly are called EngB based on homology to EngA, one
of several other GTPases of ribosome biogenesis.
Cutoffs as set find essentially all bacterial members,
but also identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about
80 percent of bacterial genomes [Protein synthesis,
Other].
Length = 178
Score = 29.4 bits (67), Expect = 1.9
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 7 LIGLPNVGKSTLFNALTKLK 26
G NVGKS+L NALT K
Sbjct: 23 FAGRSNVGKSSLINALTNRK 42
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 29.8 bits (68), Expect = 2.0
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 13/60 (21%)
Query: 5 CGLIGLPN-VGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDKRLKHLNNIVKTKKI 63
G++G PN GKSTL L L ++P G + + K + L+ KK+
Sbjct: 31 TGILG-PNGSGKSTLLKCLAGL-----------LKPKSGEVLLDGKDIASLSPKELAKKL 78
>gnl|CDD|239388 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 = 28.8 bits (65), Expect = 2.4
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 6 GLIGLPNVGKSTLFNALTK 24
G+ G+P GKSTL +AL
Sbjct: 3 GITGVPGAGKSTLIDALIT 21
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. 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 = 29.0 bits (66), Expect = 2.4
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 11/46 (23%)
Query: 4 KCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVPDK 49
+ GL+G GKSTL + +EP+ GI+
Sbjct: 28 RIGLVGRNGAGKSTLLKLIA-----------GELEPDEGIVTWGST 62
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 28.9 bits (66), Expect = 2.7
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 12 NVGKSTLFNALTKLK 26
NVGKS+L NALT K
Sbjct: 34 NVGKSSLINALTNRK 48
>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 = 3.8
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 6 GLIGLPNVGKSTLFNALTKL 25
G+ G+P GKSTL AL
Sbjct: 33 GITGVPGAGKSTLIEALGME 52
>gnl|CDD|151872 pfam11433, DUF3198, Protein of unknown function (DUF3198). Some
members in this family of proteins are annotated as
membrane proteins however this cannot be confirmed.
Currently, this archaeal family has no known function.
Length = 51
Score = 26.4 bits (58), Expect = 4.0
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 134 LSDLAILEKYIDKENKKFFLKNEHSIELLKLLKRIIFNLNKSIPIRL 180
L D E YI+ E+K F++N L L+R+ L KS I+L
Sbjct: 1 LKDTIDFESYINSESKSVFVRN------LTELERLAKRLGKSYEIQL 41
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase
is also found in Gram-positive bacteria, archaea, and
the roundworm C. elegans. It may have a more general,
but still unknown function. Mutations have also been
found that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase
activity of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein
interactions].
Length = 300
Score = 29.0 bits (65), Expect = 4.3
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 6 GLIGLPNVGKSTLFNALTKLKI 27
G+ G P GKSTL AL
Sbjct: 38 GITGTPGAGKSTLLEALGMELR 59
>gnl|CDD|236574 PRK09568, PRK09568, DNA primase large subunit; Reviewed.
Length = 306
Score = 28.6 bits (64), Expect = 5.3
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 108 KDDKITHISGEINPIHDAEVIQTEL----ILSDLAILEKYIDKENKKF--FLKNEHSIEL 161
+++ H P+ V T L IL+DL ++ KY KE K+F L+NE+ L
Sbjct: 50 SGEELPHYVSYNEPVL---VFYTTLLSLAILNDLRLIRKYAHKEAKQFKSLLQNENEENL 106
Query: 162 LKLLKRIIFNLNKS 175
L++ K + N+NK
Sbjct: 107 LEITKLLGLNINKC 120
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 28.4 bits (64), Expect = 5.9
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 7 LIGLPNVGKSTLFNAL 22
L+G VGKSTL NAL
Sbjct: 200 LLGSSGVGKSTLVNAL 215
>gnl|CDD|225324 COG2604, COG2604, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 594
Score = 28.5 bits (64), Expect = 6.0
Identities = 15/74 (20%), Positives = 27/74 (36%)
Query: 146 KENKKFFLKNEHSIELLKLLKRIIFNLNKSIPIRLMSLNNEELMSIKFLNLLTIKPIIFV 205
+ ++ K + E L+ + I N+ + MS+ E L L I I +
Sbjct: 497 LKLQEILEKVDSKSEKLEKISAKIDNIKELFDESKMSILQEILQPALHHIELNIARIYKL 556
Query: 206 ANVKENGFKNNLLL 219
+ F N L +
Sbjct: 557 NIKDKEDFLNKLYI 570
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 27.4 bits (61), Expect = 6.2
Identities = 25/110 (22%), Positives = 40/110 (36%), Gaps = 9/110 (8%)
Query: 4 KCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIGIIEVP-DKRLKHL---NNIVK 59
K +IG GKS+L + L + E + +EV D L ++ +
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 60 TKKIFPAIIKLVDIAGLVSGASKGEGLG-----NKFLAHIRETNIVIHVI 104
K +K D LV + E L +L ++R+ I VI
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVI 110
>gnl|CDD|223488 COG0411, LivG, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 250
Score = 27.9 bits (63), Expect = 6.8
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 2/21 (9%)
Query: 6 GLIGLPN-VGKSTLFNALTKL 25
GLIG PN GK+TLFN +T
Sbjct: 34 GLIG-PNGAGKTTLFNLITGF 53
>gnl|CDD|226888 COG4485, COG4485, Predicted membrane protein [Function unknown].
Length = 858
Score = 28.6 bits (64), Expect = 7.3
Identities = 25/122 (20%), Positives = 49/122 (40%), Gaps = 12/122 (9%)
Query: 161 LLKLLKRIIFNLNKSIPIRLMSLNNEELMSIKFLNLLTIKPIIFVANVKENGFKNNLLLD 220
++ F ++ + L L N + +LL IK I + GFK N
Sbjct: 526 SSSYYDKLGF-ISMGTNLNLRYLGNRINL----DSLLGIKYNISENPPDKYGFKKNSEHK 580
Query: 221 QLKIYAHNQNIPIIIICAKLEEEISDLNNIDKKFFLDNLGLKETKLNDLIRASFSLLDLR 280
+Y ++ ++PI + A + ++ ++KK LDN ++ LN L+ + +
Sbjct: 581 NNTLYENHYSLPIAVPSANIYNDV----KLNKKSTLDN---QQAMLNGLVSKNTTYFTHF 633
Query: 281 TY 282
Sbjct: 634 PA 635
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 28.2 bits (64), Expect = 8.4
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 6 GLIGLPN-VGKSTLFNALT 23
G+IG PN GKSTLF +T
Sbjct: 354 GIIG-PNGAGKSTLFKMIT 371
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. 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 = 231
Score = 27.7 bits (62), Expect = 8.4
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 11/72 (15%)
Query: 8 IGLPNVGKSTLFNAL----TKLKISAENYPFCTIEPN---IGIIEVPDKRLKHLNNIVKT 60
+G P VGKSTL +L TK +S P + + IE P+ +N+++
Sbjct: 45 VGPPGVGKSTLIRSLIKRYTKQNLSDIKGPITIVTGKKRRLTFIECPND----INSMIDV 100
Query: 61 KKIFPAIIKLVD 72
KI ++ L+D
Sbjct: 101 AKIADLVLLLID 112
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl)
small GTPases. 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 = 27.2 bits (61), Expect = 8.7
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 7/39 (17%)
Query: 4 KCGLIGLPNVGKSTLFNALTKLKISAENYPFCTIEPNIG 42
+ ++GL GK+T+ KLK T P IG
Sbjct: 1 RILMLGLDGAGKTTILY---KLK----LGEVVTTIPTIG 32
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 27.1 bits (61), Expect = 9.6
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 7 LIGLPNVGKSTLFNALTKLKISAENYPF 34
LIG+ GK+T+ L K A PF
Sbjct: 4 LIGMMGAGKTTVGRLLAK----ALGLPF 27
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.142 0.401
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,954,348
Number of extensions: 1953613
Number of successful extensions: 2333
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2269
Number of HSP's successfully gapped: 193
Length of query: 363
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 265
Effective length of database: 6,590,910
Effective search space: 1746591150
Effective search space used: 1746591150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.3 bits)