RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2924
(225 letters)
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 331 bits (851), Expect = e-114
Identities = 137/235 (58%), Positives = 166/235 (70%), Gaps = 12/235 (5%)
Query: 1 MARTQKNKATAGHLGLLKARIAKLRRELITPKGGGGGPGEGFDVAKTGDARIGFVGFPSV 60
+ART KNKAT H+GLLKA++A+LR EL K GG G GF V K+GDA + VGFPSV
Sbjct: 15 IARTPKNKATEHHIGLLKAKLAELREELEKRKSKSGGGGSGFAVKKSGDATVALVGFPSV 74
Query: 61 GKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQV 120
GKSTLL+ L SEVA Y FTTL VPG ++YKGA+IQLLDLPGIIEGA G+GRGRQV
Sbjct: 75 GKSTLLNKLTNTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIEGASSGRGRGRQV 134
Query: 121 IAVARTCSLIFIVLDVLKPLGHKKLIEHELEGFGLRLNKEPPN------------IDNQV 168
++VAR LI IVLDV + H+ +IE ELE G+RLNK PP+ I+
Sbjct: 135 LSVARNADLIIIVLDVFEDPHHRDIIERELEDVGIRLNKRPPDVTIKKKESGGIRINGTG 194
Query: 169 PQSELDLDTVKTILSEYRIHNADITLRYDATSDDLIDVVEGNRIYVPCIYLLNKI 223
P + LD DTV+ IL EYRIHNAD+ +R D T DDLID +EGNR+Y P +Y++NKI
Sbjct: 195 PLTHLDEDTVRAILREYRIHNADVLIREDVTLDDLIDALEGNRVYKPALYVVNKI 249
>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 = 314 bits (806), Expect = e-110
Identities = 123/186 (66%), Positives = 143/186 (76%), Gaps = 12/186 (6%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEG 109
AR+ VGFPSVGKSTLLS L SEVAAYEFTTLT VPG ++YKGAKIQLLDLPGIIEG
Sbjct: 1 ARVALVGFPSVGKSTLLSKLTNTKSEVAAYEFTTLTCVPGVMEYKGAKIQLLDLPGIIEG 60
Query: 110 AKDGKGRGRQVIAVARTCSLIFIVLDVLKPLGHKKLIEHELEGFGLRLNKEPPN------ 163
A DGKGRGRQVIAVART LI IVLD KP G ++++E ELEG G+RLNK+PPN
Sbjct: 61 ASDGKGRGRQVIAVARTADLILIVLDATKPEGQREILERELEGVGIRLNKKPPNVTIKKK 120
Query: 164 ------IDNQVPQSELDLDTVKTILSEYRIHNADITLRYDATSDDLIDVVEGNRIYVPCI 217
I + VP ++LD TVK IL EY+IHNAD+ +R D T DDLIDV+EGNR+Y+PC+
Sbjct: 121 KKGGINITSTVPLTKLDEKTVKAILREYKIHNADVLIREDITVDDLIDVIEGNRVYIPCL 180
Query: 218 YLLNKI 223
Y+ NKI
Sbjct: 181 YVYNKI 186
>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 = 97.4 bits (243), Expect = 1e-25
Identities = 47/162 (29%), Positives = 65/162 (40%), Gaps = 20/162 (12%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAGVY-SEVAAYEFTTLTTVPGCIKYKG--AKIQLLDLPG 105
+ +I VG P+VGKSTLL+ L G S TT V I+ G K LLD G
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 106 IIEGAKDGKGRGRQVIAVARTCSLIFIVLDVLKPL-GHKKLIEHELE-GFGLRLNKEPPN 163
+ + R V + R ++ +VLDV + L K I H E G + L +
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKID 120
Query: 164 ID---------------NQVPQSELDLDTVKTILSEYRIHNA 190
+ N P L +T K I S ++I A
Sbjct: 121 LRDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFKIVEA 162
>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 = 94.8 bits (236), Expect = 1e-24
Identities = 47/115 (40%), Positives = 67/115 (58%), Gaps = 6/115 (5%)
Query: 53 GFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYK-GAKIQLLDLPGIIEGAK 111
G VG P+VGKSTLLS L E+A+Y FTTL G ++ G IQ++DLPG+++GA
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGAS 60
Query: 112 DGKGRGRQVIAVARTCSLIFIVLDVLK-----PLGHKKLIEHELEGFGLRLNKEP 161
+G+G G Q++A LI V+D + PL +K + E+ G L L +P
Sbjct: 61 EGRGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKP 115
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 90.7 bits (226), Expect = 1e-21
Identities = 41/118 (34%), Positives = 68/118 (57%), Gaps = 6/118 (5%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAK-IQLLDLPGIIE 108
A +G VG P+ GKSTLLS ++ ++A Y FTTL G ++ G + + D+PG+IE
Sbjct: 160 ADVGLVGLPNAGKSTLLSAVSAAKPKIADYPFTTLVPNLGVVRVDGGESFVVADIPGLIE 219
Query: 109 GAKDGKGRGRQVIA-VARTCSLIFIV----LDVLKPLGHKKLIEHELEGFGLRLNKEP 161
GA +G G G + + + RT L+ ++ +D P+ + I +ELE + +L ++P
Sbjct: 220 GASEGVGLGLRFLRHIERTRVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKP 277
>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 = 85.9 bits (214), Expect = 4e-21
Identities = 44/120 (36%), Positives = 66/120 (55%), Gaps = 12/120 (10%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYK-GAKIQLLDLPGIIE 108
A +G VG P+ GKSTLLS ++ ++A Y FTTL G ++ G + D+PG+IE
Sbjct: 1 ADVGLVGLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDDGRSFVIADIPGLIE 60
Query: 109 GAKDGKGRG----RQVIAVARTCSLIFIVLDV---LKPLGHKKLIEHELEGFGLRLNKEP 161
GA +GKG G R + RT L+ V+D+ P+ + I +ELE + L ++P
Sbjct: 61 GASEGKGLGHRFLRH---IERTRVLLH-VIDLSGEDDPVEDYETIRNELEAYNPGLAEKP 116
>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 = 84.4 bits (210), Expect = 2e-19
Identities = 38/118 (32%), Positives = 66/118 (55%), Gaps = 6/118 (5%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAK-IQLLDLPGIIE 108
A +G VG P+ GKSTL+S ++ ++A Y FTTL G ++ + + D+PG+IE
Sbjct: 158 ADVGLVGLPNAGKSTLISAVSAAKPKIADYPFTTLVPNLGVVRVDDGRSFVIADIPGLIE 217
Query: 109 GAKDGKGRGRQVIA-VARTCSLIFIV----LDVLKPLGHKKLIEHELEGFGLRLNKEP 161
GA +G G G + + + RT L+ ++ D P+ ++I +EL+ + L ++P
Sbjct: 218 GASEGAGLGHRFLKHIERTRVLLHLIDISPEDGSDPIEDYEIIRNELKKYSPELAEKP 275
>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 = 77.3 bits (191), Expect = 2e-18
Identities = 43/118 (36%), Positives = 62/118 (52%), Gaps = 10/118 (8%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGV-YSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEG 109
R+ VG P+VGKSTL++ L G + V+ Y TT + G + G +I L+D PG+IEG
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGL-GRQIILVDTPGLIEG 59
Query: 110 AKDGKG--RGRQVIAVARTCSLIFIVLDVLKPLG-HKKLIEHELEGFGLR-----LNK 159
A +GKG + + R LI +V+D + L + I ELE + LNK
Sbjct: 60 ASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 80.5 bits (200), Expect = 6e-18
Identities = 39/108 (36%), Positives = 63/108 (58%), Gaps = 3/108 (2%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAK-IQLLDLPGIIE 108
A +G VG P+ GKSTL+S ++ ++A Y FTTL G ++ K + D+PG+IE
Sbjct: 159 ADVGLVGLPNAGKSTLISAVSAAKPKIADYPFTTLHPNLGVVRVDDYKSFVIADIPGLIE 218
Query: 109 GAKDGKGRGRQVIA-VARTCSLIFIV-LDVLKPLGHKKLIEHELEGFG 154
GA +G G G + + + RT L+ +V ++ + P+ K I +ELE +
Sbjct: 219 GASEGAGLGHRFLKHIERTRLLLHLVDIEAVDPVEDYKTIRNELEKYS 266
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 80.9 bits (201), Expect = 7e-18
Identities = 43/119 (36%), Positives = 66/119 (55%), Gaps = 8/119 (6%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAK-IQLLDLPGIIE 108
A +G VGFP+VGKSTLLS ++ ++A Y FTTL G ++ + + D+PG+IE
Sbjct: 159 ADVGLVGFPNVGKSTLLSVVSNAKPKIANYHFTTLVPNLGVVETDDGRSFVMADIPGLIE 218
Query: 109 GAKDGKGRGRQVIA-VARTCSLIFIVLDVLK-----PLGHKKLIEHELEGFGLRLNKEP 161
GA +G G G Q + + R +I V+D+ P+ + I EL+ + RL + P
Sbjct: 219 GASEGVGLGHQFLRHIER-TRVIVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERP 276
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 69.9 bits (172), Expect = 4e-14
Identities = 37/113 (32%), Positives = 63/113 (55%), Gaps = 10/113 (8%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVP--GCIKYKGAK-IQLLDLPGI 106
A +G +G P+ GKST + ++ +VA Y FTTL VP G ++ + + D+PG+
Sbjct: 160 ADVGLLGLPNAGKSTFIRAVSAAKPKVADYPFTTL--VPNLGVVRVDDERSFVVADIPGL 217
Query: 107 IEGAKDGKGRG-RQVIAVARTCSLIFIV----LDVLKPLGHKKLIEHELEGFG 154
IEGA +G G G R + + R L+ ++ +D P+ + ++I +ELE +
Sbjct: 218 IEGASEGAGLGIRFLKHLERCRVLLHLIDIAPIDGSDPVENARIIINELEKYS 270
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 66.0 bits (162), Expect = 1e-12
Identities = 48/141 (34%), Positives = 72/141 (51%), Gaps = 14/141 (9%)
Query: 36 GGPGEGFDVA---KTGDARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVP--GC 90
G PGE D+ K+ A +G VGFPS GKS+L+S L+ ++A Y FTTL VP G
Sbjct: 144 GEPGEERDLVLELKS-VADVGLVGFPSAGKSSLISALSAAKPKIADYPFTTL--VPNLGV 200
Query: 91 IKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCSLIFIVLDVL------KPLGHKK 144
++ + + D+PG+I GA +GKG G + C+++ V+D PL
Sbjct: 201 VQAGDTRFTVADVPGLIPGASEGKGLGLDFLRHIERCAVLVHVVDCATLEPGRDPLSDID 260
Query: 145 LIEHELEGFGLRLNKEPPNID 165
+E EL + L+ + D
Sbjct: 261 ALEAELAAYAPALDGDLGLGD 281
>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 = 59.6 bits (145), Expect = 2e-11
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 53 GFVGFPSVGKSTLLSTLAG-VYSEVAAYEFTTLTTVPGCI-KYKGAKIQLLDLPGIIEGA 110
G P+VGKS+LL+ L G V+ TT V + L+D PG+ E
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEG 60
Query: 111 KDGKGRGRQVIAVARTCSLIFIVLD 135
G+ R + VA L+ +V+D
Sbjct: 61 GLGRERVEEARQVADRADLVLLVVD 85
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 58.7 bits (143), Expect = 3e-10
Identities = 33/106 (31%), Positives = 49/106 (46%), Gaps = 22/106 (20%)
Query: 51 RIGFVGFPSVGKSTLLS--TLAGVYSEVAAYEFTTL------TTVPGC------IKYKGA 96
+IG VG P+VGKSTL + T AG E+A Y F T+ VP C K
Sbjct: 4 KIGIVGLPNVGKSTLFNALTKAGA--EIANYPFCTIEPNVGVVYVPDCRLDELAEIVKCP 61
Query: 97 K------IQLLDLPGIIEGAKDGKGRGRQVIAVARTCSLIFIVLDV 136
++ +D+ G+++GA G+G G + + R I V+
Sbjct: 62 PKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRC 107
>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 = 54.9 bits (133), Expect = 1e-09
Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 56 GFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
G+P+VGKS+L++ L EVA Y FTT + G YK + Q++D PGI
Sbjct: 7 GYPNVGKSSLVNKLTRAKPEVAPYPFTTKSLFVGHFDYKYLRWQVIDTPGI 57
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 55.8 bits (135), Expect = 2e-09
Identities = 21/53 (39%), Positives = 32/53 (60%)
Query: 56 GFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIE 108
G+P+VGKS+L+ L EVA Y FTT G + +IQ++D PG+++
Sbjct: 175 GYPNVGKSSLVRKLTTAKPEVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLLD 227
>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 = 54.0 bits (130), Expect = 3e-09
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 53 GFVGFPSVGKSTLLSTLAGV-YSEVAAYEFTTL--TTVPGCIKYKGAKIQLLDLPGIIEG 109
VG VGKS+LL+ L G EV+ TT + K+ L+D PG+ E
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 110 AKDGKGRGRQVIAVARTCSLIFIVLDV 136
G GR + R LI +V+D
Sbjct: 61 --GGLGREELARLLLRGADLILLVVDS 85
>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 = 54.5 bits (132), Expect = 6e-09
Identities = 53/226 (23%), Positives = 84/226 (37%), Gaps = 56/226 (24%)
Query: 52 IGFVGFPSVGKSTLLS--TLAGVYSEVAAYEFTT------------------LTTVPGCI 91
IG VG P+VGKST + TLA V E+A Y FTT L
Sbjct: 1 IGLVGKPNVGKSTFFNAATLADV--EIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPR 58
Query: 92 KYKGAK------IQLLDLPGIIEGAKDGKGRGRQVIAVARTCSLIFIVLDV--------- 136
K ++L+D+ G++ GA +GKG G Q + R ++ V+D
Sbjct: 59 YGKCIDGKRYVPVELIDVAGLVPGAHEGKGLGNQFLDDLRDADVLIHVVDASGGTDAEGN 118
Query: 137 -LKPLGHK-----KLIEHEL-EGFGLRLNKEPPNIDNQVPQSELDLD-TVKTILS----- 183
++ G+ + +E+E+ L + I + + D+ + LS
Sbjct: 119 GVETGGYDPLEDIEFLENEIDMWIYGILERNWEKIVRKAKAEKTDIVEALSEQLSGFGVN 178
Query: 184 EYRIHNADITLRYDA-----TSDDLIDVVEGNRIYV-PCIYLLNKI 223
E + A L A +DL+ + R P + NK
Sbjct: 179 EDVVIEALEELELPADLSKWDDEDLLRLARELRKRRKPMVIAANKA 224
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 55.0 bits (133), Expect = 6e-09
Identities = 22/56 (39%), Positives = 34/56 (60%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
+ VG P+VGK+TL + L G +V + T+ G +KYKG +I+++DLPG
Sbjct: 5 TVALVGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPGT 60
>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 = 49.8 bits (120), Expect = 7e-08
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 54 FVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
VG P+VGK+TL + L G +V + T+ G K G +I+++DLPG
Sbjct: 2 LVGNPNVGKTTLFNALTGARQKVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGT 54
>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 = 49.8 bits (120), Expect = 1e-07
Identities = 23/56 (41%), Positives = 32/56 (57%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
I VG P+VGK+TL + L G V + T+ G KYKG +I+++DLPG
Sbjct: 2 TIALVGNPNVGKTTLFNALTGARQHVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGT 57
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 46.7 bits (112), Expect = 3e-06
Identities = 31/95 (32%), Positives = 43/95 (45%), Gaps = 28/95 (29%)
Query: 51 RIGFVGFPSVGKSTLLS--TLAGVYSEVAAYEFTT--------------------LTTVP 88
IG VG P+VGKST + TLA V E+A Y FTT + P
Sbjct: 3 TIGLVGKPNVGKSTFFNAATLADV--EIANYPFTTIDPNVGVAYVRVECPCKELGVKCNP 60
Query: 89 GCIKYKGAK----IQLLDLPGIIEGAKDGKGRGRQ 119
K ++L+D+ G++ GA +G+G G Q
Sbjct: 61 RNGKCIDGTRFIPVELIDVAGLVPGAHEGRGLGNQ 95
>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 = 44.4 bits (105), Expect = 2e-05
Identities = 32/95 (33%), Positives = 48/95 (50%), Gaps = 8/95 (8%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGV-YSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEG 109
++ VG P+VGKS+LL+ L + V+ + TT V G + G I+LLD GI E
Sbjct: 205 KLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIREH 264
Query: 110 A----KDGKGRGRQVIAVARTCSLIFIVLDVLKPL 140
A + G + + I + L+ VLD +PL
Sbjct: 265 ADFVERLGIEKSFKAI---KQADLVIYVLDASQPL 296
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 43.5 bits (103), Expect = 3e-05
Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYS-EVAAYEFTTLTTVPGCIKYK-GAKIQLLDLPGII 107
R+G VG+P+VGKSTL++ L G + + TT K I LLD PGII
Sbjct: 134 RVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGI----QWIKLDDGIYLLDTPGII 188
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 42.7 bits (102), Expect = 6e-05
Identities = 32/108 (29%), Positives = 46/108 (42%), Gaps = 31/108 (28%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTL------------------------TT 86
+ G VG P+VGKSTL + L +E A Y F T+
Sbjct: 4 KCGIVGLPNVGKSTLFNALTKAGAEAANYPFCTIEPNVGVVPVPDPRLDKLAEIVKPKKI 63
Query: 87 VPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCSLIFIVL 134
VP A I+ +D+ G+++GA G+G G Q +A R I V+
Sbjct: 64 VP-------ATIEFVDIAGLVKGASKGEGLGNQFLANIREVDAIVHVV 104
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 42.2 bits (100), Expect = 1e-04
Identities = 27/100 (27%), Positives = 44/100 (44%), Gaps = 17/100 (17%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTL------TTVPG------CIKYKGAKI 98
++G VG P+VGKST + L + F T+ VP C +K I
Sbjct: 23 KMGIVGLPNVGKSTTFNALCKQQVPAENFPFCTIDPNTARVNVPDERFDWLCKHFKPKSI 82
Query: 99 -----QLLDLPGIIEGAKDGKGRGRQVIAVARTCSLIFIV 133
+ D+ G+++GA +G+G G ++ R I+ V
Sbjct: 83 VPAQLDITDIAGLVKGASEGEGLGNAFLSHIRAVDGIYHV 122
>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 = 40.3 bits (95), Expect = 1e-04
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 12/64 (18%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKY-----KGAKIQLLDL 103
+A IG VG+P+VGKS+L++ L G S+ ++++ PG K+ I L D
Sbjct: 82 EATIGLVGYPNVGKSSLINALVG--SKK-----VSVSSTPGKTKHFQTIFLEPGITLCDC 134
Query: 104 PGII 107
PG++
Sbjct: 135 PGLV 138
>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 = 2e-04
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 56 GFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
G P+VGKSTL + L G V + T+ G + ++G I+++DLPGI
Sbjct: 1 GNPNVGKSTLFNALTGANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGI 51
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 41.0 bits (97), Expect = 2e-04
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 55 VGFPSVGKSTLLSTLAGV-YSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAKDG 113
VG P+VGKSTL + L G + V+ T + G ++ G + L+D G+ +G +D
Sbjct: 9 VGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLDDGDEDE 68
Query: 114 KGRGR--QVIAVARTCSLIFIVLDV 136
Q + +I V+D
Sbjct: 69 LQELIREQALIAIEEADVILFVVDG 93
Score = 36.8 bits (86), Expect = 0.006
Identities = 27/109 (24%), Positives = 49/109 (44%), Gaps = 29/109 (26%)
Query: 51 RIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
+I +G P+VGKS+L++ + G + S++A TT ++ + G K L+D GI
Sbjct: 180 KIAIIGRPNVGKSSLINAILGEERVIVSDIAG---TTRDSIDIEFERDGRKYVLIDTAGI 236
Query: 107 IEGAKDGKGRGRQVI-------AVART------CSLIFIVLDVLKPLGH 142
R + I +VART ++ +V+D + +
Sbjct: 237 ---------RRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISE 276
>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 = 39.4 bits (93), Expect = 4e-04
Identities = 23/63 (36%), Positives = 30/63 (47%), Gaps = 16/63 (25%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGV-YSEVAAYEFTTLTTVPG------CIKYKGAKIQLLDL 103
R VG P+VGKSTL++ L G ++V PG I+ I+LLD
Sbjct: 117 RAMVVGIPNVGKSTLINRLRGKKVAKVGN--------KPGVTRGQQWIRIGP-NIELLDT 167
Query: 104 PGI 106
PGI
Sbjct: 168 PGI 170
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 40.5 bits (94), Expect = 4e-04
Identities = 39/133 (29%), Positives = 62/133 (46%), Gaps = 7/133 (5%)
Query: 55 VGFPSVGKSTLLSTLAG-VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIE--GAK 111
+G P+ GKSTLL+ + G S V TT + + G I K ++ L D PGI E G+
Sbjct: 58 IGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFEPKGSL 117
Query: 112 DGKGRGRQVIAVARTCSLIFIVLDVLKPLGHKKLIEHELEGFGLRLNKEPPNIDNQVPQS 171
+ K R + + L+ +++D LK I H + LN P + N++
Sbjct: 118 E-KAMVRCAWSSLHSADLVLLIIDSLKSFDD---ITHNILDKLRSLNIVPIFLLNKIDIE 173
Query: 172 ELDLDTVKTILSE 184
L+ +K L+E
Sbjct: 174 SKYLNDIKAFLTE 186
>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 = 39.0 bits (92), Expect = 6e-04
Identities = 32/113 (28%), Positives = 54/113 (47%), Gaps = 17/113 (15%)
Query: 51 RIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
+I +G P+VGKS+LL+ L G + S++A TT ++ +Y G K L+D GI
Sbjct: 4 KIAIIGRPNVGKSSLLNALLGEERVIVSDIAG---TTRDSIDVPFEYDGQKYTLIDTAGI 60
Query: 107 IEGAKDGKGRGRQVIAVART------CSLIFIVLDVLKPLGH--KKLIEHELE 151
+ K G + +V RT ++ +VLD + + ++ LE
Sbjct: 61 RKKGK--VTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQDLRIAGLILE 111
>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 = 38.6 bits (91), Expect = 0.001
Identities = 33/127 (25%), Positives = 58/127 (45%), Gaps = 26/127 (20%)
Query: 51 RIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
+I +G P+VGKSTL++ L G + S++A TT ++ + G K L+D GI
Sbjct: 174 KIAIIGRPNVGKSTLVNALLGEERVIVSDIAG---TTRDSIDIPFERNGKKYTLIDTAGI 230
Query: 107 IEGAKDGKGRGRQVI---AVART------CSLIFIVLDVLKPLGH--KKLIEHELE---G 152
KG+ + + +V RT ++ +VLD + + ++ LE
Sbjct: 231 RR-----KGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQDLRIAGLALEAGKA 285
Query: 153 FGLRLNK 159
+ +NK
Sbjct: 286 LVIVVNK 292
Score = 30.9 bits (71), Expect = 0.51
Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 4/85 (4%)
Query: 55 VGFPSVGKSTLLSTLAGV-YSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAK-- 111
VG P+VGKSTL + L G + V+ T G ++ G + L+D GI E
Sbjct: 5 VGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEEDDDGL 64
Query: 112 DGKGRGRQVIAVARTCSLIFIVLDV 136
D + R Q +I V+D
Sbjct: 65 DKQIR-EQAEIAIEEADVILFVVDG 88
>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 = 0.002
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 18/63 (28%)
Query: 52 IGFVGFPSVGKSTLLSTL--------AGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDL 103
+GF+G+P+VGKS++++TL A + E +++ TL +I L+D
Sbjct: 105 VGFIGYPNVGKSSVINTLRSKKVCKVAPIPGETKVWQYITLMK----------RIYLIDC 154
Query: 104 PGI 106
PG+
Sbjct: 155 PGV 157
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 37.6 bits (87), Expect = 0.003
Identities = 28/109 (25%), Positives = 37/109 (33%), Gaps = 11/109 (10%)
Query: 46 KTGDARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKY---KGAKIQLLD 102
+ +I +G VGK+TLL+ L G Y T P + K+QL D
Sbjct: 2 FMKEFKIVVLGDGGVGKTTLLNRLVG-DEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 103 LPGIIEGAKDGKGRGRQVIAVARTCSLIFIVLDVLKPLGHKKLIEHELE 151
G E R + I IV D +L E LE
Sbjct: 61 TAGQEEYRSLRPEYYRG-------ANGILIVYDSTLRESSDELTEEWLE 102
>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 = 35.8 bits (83), Expect = 0.005
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
R+G VG P+VGKS+ ++ L + T + +K +I L D PGI
Sbjct: 93 RVGVVGLPNVGKSSFINALLNKFKLKVGS-IPGTTKLQQDVKL-DKEIYLYDTPGI 146
>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 = 36.1 bits (84), Expect = 0.006
Identities = 22/62 (35%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 54 FVGFPSVGKSTLLSTLAGVYSEV--AAYEFTTLTT--VPGC----IKYK-GAKIQLLDLP 104
VG +VGKSTL++ L A LT +PG IK G +L D P
Sbjct: 130 VVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIPLGEGKKLYDTP 189
Query: 105 GI 106
GI
Sbjct: 190 GI 191
>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 = 36.2 bits (84), Expect = 0.008
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 51 RIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
+ +G P+VGKSTLL+ L G + S A TT + G ++I +D PG
Sbjct: 2 FVAILGRPNVGKSTLLNQLHGQKISITSPKAQ---TTRNRISGIHTTGASQIIFIDTPGF 58
Query: 107 IE 108
E
Sbjct: 59 HE 60
>gnl|CDD|213187 cd03220, ABC_KpsT_Wzt, ATP-binding cassette component of
polysaccharide transport system. The KpsT/Wzt ABC
transporter subfamily is involved in extracellular
polysaccharide export. Among the variety of
membrane-linked or extracellular polysaccharides
excreted by bacteria, only capsular polysaccharides,
lipopolysaccharides, and teichoic acids have been shown
to be exported by ABC transporters. A typical system is
made of a conserved integral membrane and an ABC. In
addition to these proteins, capsular polysaccharide
exporter systems require two 'accessory' proteins to
perform their function: a periplasmic (E.coli) or a
lipid-anchored outer membrane protein called OMA
(Neisseria meningitidis and Haemophilus influenza) and
a cytoplasmic membrane protein MPA2.
Length = 224
Score = 35.6 bits (83), Expect = 0.010
Identities = 17/32 (53%), Positives = 22/32 (68%), Gaps = 2/32 (6%)
Query: 42 FDVAKTGDARIGFVGFPSVGKSTLLSTLAGVY 73
F+V + G+ RIG +G GKSTLL LAG+Y
Sbjct: 43 FEVPR-GE-RIGLIGRNGAGKSTLLRLLAGIY 72
>gnl|CDD|206740 cd09913, EHD, Eps15 homology domain (EHD), C-terminal domain.
Dynamin-like C-terminal Eps15 homology domain (EHD)
proteins regulate endocytic events; they have been
linked to a number of Rab proteins through their
association with mutual effectors, suggesting a
coordinate role in endocytic regulation. Eukaryotic EHDs
comprise four members (EHD1-4) in mammals and single
members in Caenorhabditis elegans (Rme-1), Drosophila
melanogaster (Past1) as well as several eukaryotic
parasites. EHD1 regulates trafficking of multiple
receptors from the endocytic recycling compartment (ERC)
to the plasma membrane; EHD2 regulates trafficking from
the plasma membrane by controlling Rac1 activity; EHD3
regulates endosome-to-Golgi transport, and preserves
Golgi morphology; EHD4 is involved in the control of
trafficking at the early endosome and regulates exit of
cargo toward the recycling compartment as well as late
endocytic pathway. Rme-1, an ortholog of human EHD1,
controls the recycling of internalized receptors from
the endocytic recycling compartment to the plasma
membrane. In D. melanogaster, deletion of the Past1 gene
leads to infertility as well as premature death of adult
flies. Arabidopsis thaliana also has homologs of EHD
proteins (AtEHD1 and AtEHD2), possibly involved in
regulating endocytosis and signaling.
Length = 241
Score = 35.7 bits (83), Expect = 0.011
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 97 KIQLLDLPGIIEGAKDGKGRGRQVIAVAR----TCSLIFIVLDVLKP 139
+ ++D PGI+ G K + RG AV R LIF++ D K
Sbjct: 89 SVTIVDTPGILSGEKQRQSRGYDFNAVCRWFAERADLIFLLFDPHKL 135
>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 = 35.1 bits (82), Expect = 0.011
Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 4/85 (4%)
Query: 55 VGFPSVGKSTLLSTLAGVYSE-VAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAK-- 111
VG P+VGKSTL + L G V+ T G ++ G + L+D GI +
Sbjct: 3 VGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGIEPDDEGI 62
Query: 112 DGKGRGRQVIAVARTCSLIFIVLDV 136
+ R Q +I V+D
Sbjct: 63 SKEIR-EQAEIAIEEADVILFVVDG 86
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 35.3 bits (82), Expect = 0.017
Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 48 GDARIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDL 103
G R+ VG P+VGKS+LL+ LAG V +VA TT+ V I+ G + +D
Sbjct: 210 GPRRVALVGKPNVGKSSLLNKLAGEERSVVDDVAG---TTVDPVDSLIELGGKTWRFVDT 266
Query: 104 PGI 106
G+
Sbjct: 267 AGL 269
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 34.8 bits (81), Expect = 0.024
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 14/59 (23%)
Query: 55 VGFPSVGKSTLLSTLAG-VYSEVAAYEFTTLTTVPGCIKYK-----GAKIQLLDLPGII 107
+G P+VGKSTL++ LAG ++ PG K + G ++LLD PGI+
Sbjct: 127 IGIPNVGKSTLINRLAGKKIAKTGNR--------PGVTKAQQWIKLGKGLELLDTPGIL 177
>gnl|CDD|224057 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport
system, ATPase component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 249
Score = 34.5 bits (80), Expect = 0.029
Identities = 15/32 (46%), Positives = 22/32 (68%), Gaps = 2/32 (6%)
Query: 42 FDVAKTGDARIGFVGFPSVGKSTLLSTLAGVY 73
F++ K G+ R+G +G GKSTLL +AG+Y
Sbjct: 48 FEIYK-GE-RVGIIGHNGAGKSTLLKLIAGIY 77
>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 = 34.0 bits (78), Expect = 0.042
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 45 AKTGDA-RIGFVGFPSVGKSTLLSTL 69
TG+A R+G G P GKSTLL L
Sbjct: 29 PYTGNAHRVGITGTPGAGKSTLLEAL 54
>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 = 33.6 bits (78), Expect = 0.042
Identities = 26/84 (30%), Positives = 33/84 (39%), Gaps = 25/84 (29%)
Query: 16 LLKARIAKLRRELITPKGGGGGPGEGFDVAKT-----------GDARIGFVGFPSVGKST 64
L++ RIAKLR+EL E V K G + VG+ + GKST
Sbjct: 10 LIRERIAKLRKEL-----------E--KVKKQRELQRARRKRSGVPTVALVGYTNAGKST 56
Query: 65 LLSTLAGVYSEVAAYEFTTL-TTV 87
L + L G F TL T
Sbjct: 57 LFNALTGADVLAEDQLFATLDPTT 80
>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 = 33.6 bits (78), Expect = 0.050
Identities = 32/100 (32%), Positives = 47/100 (47%), Gaps = 17/100 (17%)
Query: 52 IGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTL------TTVPG------CIKYKGAKI- 98
IG VG P+VGKSTL + L +E A Y F T+ VP K KI
Sbjct: 1 IGIVGLPNVGKSTLFNALTKSNAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKIV 60
Query: 99 ----QLLDLPGIIEGAKDGKGRGRQVIAVARTCSLIFIVL 134
+ +D+ G+++GA G+G G + ++ R I V+
Sbjct: 61 PATIEFVDIAGLVKGASKGEGLGNKFLSHIREVDAIAHVV 100
>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 = 32.7 bits (75), Expect = 0.054
Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 1/88 (1%)
Query: 53 GFVGFPSVGKSTLLSTLAGV-YSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAK 111
G +G GKS+L + L G + V TT + G + LLDLPG+ E +
Sbjct: 1 GLMGKTGAGKSSLCNALFGTEVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPGVGERGR 60
Query: 112 DGKGRGRQVIAVARTCSLIFIVLDVLKP 139
+ + L+ +LD
Sbjct: 61 RDREYEELYRRLLPEADLVLWLLDADDR 88
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 33.9 bits (78), Expect = 0.064
Identities = 18/55 (32%), Positives = 27/55 (49%)
Query: 52 IGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
IG +G P+ GK+TL + L G V + T+ G ++ L+DLPG
Sbjct: 6 IGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKEGQFSTTDHQVTLVDLPGT 60
>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 = 33.1 bits (76), Expect = 0.073
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 45 AKTGDA-RIGFVGFPSVGKSTLLSTL 69
TG A R+G G P GKSTL+ L
Sbjct: 24 PLTGRAHRVGITGVPGAGKSTLIEAL 49
>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 = 0.082
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIK----YKGA-KIQLLDL 103
+G VG+P VGKS++++ L G +S + + PG K + KI L+D
Sbjct: 99 PVIVGVVGYPKVGKSSIINALKGRHSA----STSPIPGSPGYTKGIQLVRIDSKIYLIDT 154
Query: 104 PGI 106
PG+
Sbjct: 155 PGV 157
>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 = 32.9 bits (76), Expect = 0.092
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 14/59 (23%)
Query: 55 VGFPSVGKSTLLSTLAGVYS-EVAAYEFTTLTTVPGCIKYK-----GAKIQLLDLPGII 107
VG P+VGKSTL++ LAG +V PG K + ++LLD PGI+
Sbjct: 124 VGIPNVGKSTLINRLAGKKVAKVGNR--------PGVTKGQQWIKLSDGLELLDTPGIL 174
>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 = 32.0 bits (74), Expect = 0.11
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAG 71
RIG VG GKSTLL +AG
Sbjct: 26 GDRIGLVGRNGAGKSTLLKLIAG 48
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 33.0 bits (76), Expect = 0.11
Identities = 13/24 (54%), Positives = 13/24 (54%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAGV 72
RI VG GKSTLL LAG
Sbjct: 348 GDRIAIVGPNGAGKSTLLKLLAGE 371
Score = 28.0 bits (63), Expect = 4.7
Identities = 14/23 (60%), Positives = 14/23 (60%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGV 72
RIG VG GKSTLL LAG
Sbjct: 30 ERIGLVGRNGAGKSTLLKILAGE 52
>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 = 32.2 bits (74), Expect = 0.11
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 14/62 (22%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYS-EVAAYEFTTLTTVPGCIK-----YKGAKIQLLDLP 104
+G VG+P+VGKS+++++L + V A PG K + ++LLD P
Sbjct: 118 TVGVVGYPNVGKSSVINSLKRSRACNVGA--------TPGVTKSMQEVHLDKHVKLLDSP 169
Query: 105 GI 106
G+
Sbjct: 170 GV 171
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 32.9 bits (76), Expect = 0.13
Identities = 29/100 (29%), Positives = 49/100 (49%), Gaps = 18/100 (18%)
Query: 51 RIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
++ +G P+VGKS+LL+ L G + +++A TT + I G ++L+D GI
Sbjct: 219 KVVIIGRPNVGKSSLLNALLGRDRAIVTDIAG---TTRDVIEEDINLNGIPVRLVDTAGI 275
Query: 107 ------IEGAKDGKGRGRQVIAVARTCSLIFIVLDVLKPL 140
+E + G R ++ I L+ VLD +PL
Sbjct: 276 RETDDVVE--RIGIERAKKAIE---EADLVLFVLDASQPL 310
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 31.6 bits (71), Expect = 0.14
Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 3/84 (3%)
Query: 52 IGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAK 111
I VG P GK+TL LA E+ + I + LL + G + +
Sbjct: 5 ILIVGPPGSGKTTLARALAR---ELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 112 DGKGRGRQVIAVARTCSLIFIVLD 135
G+ R R +A+AR ++LD
Sbjct: 62 SGELRLRLALALARKLKPDVLILD 85
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 32.5 bits (74), Expect = 0.16
Identities = 27/108 (25%), Positives = 43/108 (39%), Gaps = 17/108 (15%)
Query: 44 VAKTGDARIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQ 99
+ +G R+ VG P+VGKS+LL+ L V +++A TT V ++ G
Sbjct: 445 LTPSGLRRVALVGRPNVGKSSLLNQLTHEERAVVNDLAG---TTRDPVDEIVEIDGEDWL 501
Query: 100 LLDLPGIIEGAKDGKG-------RGRQVIAVARTCSLIFIVLDVLKPL 140
+D GI G R + I L + D +P+
Sbjct: 502 FIDTAGIKRRQHKLTGAEYYSSLRTQAAI---ERSELALFLFDASQPI 546
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 31.9 bits (74), Expect = 0.21
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 51 RIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
+I +G P+VGKS+L++ L G + S++A TT ++ + G K L+D GI
Sbjct: 175 KIAIIGRPNVGKSSLINALLGEERVIVSDIAG---TTRDSIDTPFERDGQKYTLIDTAGI 231
>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD
family. Members of this protein family have two copies
of the ABC transporter ATP-binding cassette, but are
found outside the common ABC transporter operon
structure that features integral membrane permease
proteins and substrate-binding proteins encoded next to
the ATP-binding cassette (ABC domain) protein. The
member protein ChvD from Agrobacterium tumefaciens was
identified as both a candidate to interact with VirB8,
based on yeast two-hybrid analysis, and as an apparent
regulator of VirG. The general function of this protein
family is unknown.
Length = 552
Score = 31.8 bits (73), Expect = 0.25
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAGV 72
A+IG +G GKSTLL +AGV
Sbjct: 31 GAKIGVLGLNGAGKSTLLRIMAGV 54
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 31.5 bits (72), Expect = 0.32
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 45 AKTGDA-RIGFVGFPSVGKSTLLSTL 69
+TG+A IG G P GKSTL+ L
Sbjct: 46 PRTGNAHVIGITGVPGAGKSTLIEAL 71
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 31.4 bits (72), Expect = 0.33
Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 8/96 (8%)
Query: 51 RIGFVGFPSVGKSTLLSTLAG----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI 106
+ +G P+VGKSTLL+ L G + S TT + G + A+I +D PGI
Sbjct: 8 FVAIIGRPNVGKSTLLNALVGQKISIVSPKPQ---TTRNRIRGIVTTDNAQIIFVDTPGI 64
Query: 107 -IEGAKDGKGRGRQVIAVARTCSLIFIVLDVLKPLG 141
G+ + + + LI V+D + G
Sbjct: 65 HKPKHALGELMNKAARSALKDVDLILFVVDADEGWG 100
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 31.3 bits (71), Expect = 0.33
Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 1/89 (1%)
Query: 52 IGFVGFPSVGKSTLLSTL-AGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGA 110
+ +G GKS+L++ L G EV+ T T + Y G + L D PG+ +G
Sbjct: 42 VLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGLGDGK 101
Query: 111 KDGKGRGRQVIAVARTCSLIFIVLDVLKP 139
+ L+ ++
Sbjct: 102 DKDAEHRQLYRDYLPKLDLVLWLIKADDR 130
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.5 bits (72), Expect = 0.34
Identities = 25/80 (31%), Positives = 35/80 (43%), Gaps = 20/80 (25%)
Query: 16 LLKARIAKLRRELITPKGGGGGPGEGFDVA---------KTGDARIGFVGFPSVGKSTLL 66
++ RIAKL+REL E + A ++G + VG+ + GKSTL
Sbjct: 161 RIRRRIAKLKREL-----------ENVEKAREPRRKKRSRSGIPLVALVGYTNAGKSTLF 209
Query: 67 STLAGVYSEVAAYEFTTLTT 86
+ L G VA F TL
Sbjct: 210 NALTGADVYVADQLFATLDP 229
>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 = 30.5 bits (70), Expect = 0.37
Identities = 38/135 (28%), Positives = 60/135 (44%), Gaps = 18/135 (13%)
Query: 51 RIGFV---GFPSVGKSTLLSTLAGVYSEVAAYEF---TTLTTVPGCIKYKGAKIQLLDLP 104
+ GFV G P+VGKSTLL+ L G +++ TT + G A+I +D P
Sbjct: 2 KSGFVAIIGRPNVGKSTLLNALVG--QKISIVSPKPQTTRNRIRGIYTDDDAQIIFVDTP 59
Query: 105 GIIEG-AKDGKGRGRQVIAVARTCSLIFIVLDVLKPLGHK-KLIEHELEGFG----LRLN 158
GI + K G+ + + + L+ V+D + +G + I L+ L LN
Sbjct: 60 GIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTPVILVLN 119
Query: 159 KEPPNIDNQVPQSEL 173
K ID + +L
Sbjct: 120 K----IDLVKDKEDL 130
>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 = 30.0 bits (68), Expect = 0.48
Identities = 10/25 (40%), Positives = 11/25 (44%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSE 75
IG G P GKSTL+ L
Sbjct: 1 VIGITGVPGAGKSTLIDALITALRA 25
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 30.9 bits (71), Expect = 0.49
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAGV 72
A+IG +G GKSTLL +AGV
Sbjct: 33 GAKIGVLGLNGAGKSTLLRIMAGV 56
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.8 bits (68), Expect = 0.59
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 51 RIGFVGFPSVGKSTLLSTLA 70
RI G PS GK+TLL LA
Sbjct: 1 RIVITGGPSTGKTTLLEALA 20
>gnl|CDD|184713 PRK14502, PRK14502, bifunctional mannosyl-3-phosphoglycerate
synthase/mannosyl-3 phosphoglycerate phosphatase;
Provisional.
Length = 694
Score = 30.7 bits (69), Expect = 0.62
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 143 KKLIEHELEGF-GLRLNKEPPNIDNQVPQSELDLDTVKTILSEY 185
+K+IE +L G GL E P I P ++DL I+ +Y
Sbjct: 345 RKMIETQLAGIEGLESGPEIPQIKLIPPPQKMDLPKFSAIIEKY 388
>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 = 30.1 bits (69), Expect = 0.77
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 26/73 (35%)
Query: 16 LLKARIAKLRRELITPKGGGGGPGEGFDVAKTGD----AR-------IGFVGFPSVGKST 64
L++ RIA+L++EL V K + R + VG+ + GKST
Sbjct: 158 LIRERIAQLKKELE-------------KVEKQRERQRRRRKRADVPTVALVGYTNAGKST 204
Query: 65 LLSTL--AGVYSE 75
L + L A VY+
Sbjct: 205 LFNALTGADVYAA 217
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 30.0 bits (69), Expect = 0.77
Identities = 14/24 (58%), Positives = 17/24 (70%), Gaps = 3/24 (12%)
Query: 51 RIGFV---GFPSVGKSTLLSTLAG 71
+ GFV G P+VGKSTLL+ L G
Sbjct: 4 KSGFVAIVGRPNVGKSTLLNALVG 27
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 30.2 bits (69), Expect = 0.77
Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 46 KTGDA-RIGFVGFPSVGKSTLLSTL 69
TG+A RIG G P VGKST + L
Sbjct: 52 HTGNALRIGITGVPGVGKSTFIEAL 76
>gnl|CDD|176736 cd08321, Pyrin_ASC-like, Pyrin Death Domain found in ASC. Pyrin
Death Domain found in ASC (Apoptosis-associated
speck-like protein containing a CARD) and similar
proteins. ASC is an adaptor molecule that functions in
the assembly of the 'inflammasome', a multiprotein
platform, which is responsible for caspase-1 activation
and regulation of IL-1beta maturation. ASC contains two
domains from the Death Domain (DD) superfamily, an
N-terminal pyrin-like domain and a C-terminal Caspase
activation and recruitment domain (CARD). Through these
2 domains, ASC serves as an adaptor for inflammasome
integrity and oligomerizes to form supramolecular
assemblies. Other members of this subfamily are
associated with ATPase domains and their function
remains unknown. In general, Pyrin is a subfamily of the
DD superfamily and functions in several signaling
pathways. DDs are protein-protein interaction domains
found in a variety of domain architectures. Their common
feature is that they form homodimers by self-association
or heterodimers by associating with other members of the
DD superfamily including CARD and Death Effector Domain
(DED). They serve as adaptors in signaling pathways and
can recruit other proteins into signaling complexes.
Length = 82
Score = 28.3 bits (64), Expect = 0.89
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 134 LDVLKPLGHKKLIEHELEGFGLRLNKEPPNIDNQVPQSELD----LDTVKTILSEYRIHN 189
LD L+ L E EL+ F +L P ++P+ EL+ +D V ++ Y
Sbjct: 5 LDALE-----DLEEDELKKFKWKLRDIPLEGFPRIPRGELENADRVDLVDKMVQFYGEEY 59
Query: 190 A-DITLR 195
A ++T++
Sbjct: 60 AVEVTVK 66
>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 = 30.1 bits (68), Expect = 0.92
Identities = 36/153 (23%), Positives = 57/153 (37%), Gaps = 36/153 (23%)
Query: 53 GFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIK--------------YKGAK- 97
G VG P+VGKSTL + + AA TT+ Y +
Sbjct: 6 GIVGLPNVGKSTLFAATTNLLGNEAANPP--FTTIEPNAGVVNPSDPRLDLLAIYIKPEK 63
Query: 98 -----IQLLDLPGIIEGAKDGKGRGRQVIAVARTCSLIFIVLDVLKPLGHKKLIEHELEG 152
+ +D+ G++ GA G+G G Q +A R +I V+ + +I H
Sbjct: 64 VPPTTTEFVDIAGLVGGASKGEGLGNQFLANIREVDIIQHVVRCFE----DDIIHHV--- 116
Query: 153 FGLRLNKEPPNIDNQVPQSEL---DLDTVKTIL 182
N + P D ++ EL D V+ +
Sbjct: 117 ----GNVDDPRDDFEIIDEELLKADEFLVEKRI 145
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 180
Score = 29.5 bits (67), Expect = 0.98
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSE-VAAYEFTTLTTVPGCIKYKGAK--IQLLDLPG 105
+I +G SVGKS+L T+ V V +Y T T I YKG + ++++D G
Sbjct: 3 KIAVLGSRSVGKSSL--TVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAG 58
>gnl|CDD|185364 PRK15467, PRK15467, ethanolamine utilization protein EutP;
Provisional.
Length = 158
Score = 29.2 bits (65), Expect = 1.2
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYS---EVAAYEF 81
RI FVG GK+TL + L G Y+ + A EF
Sbjct: 3 RIAFVGAVGAGKTTLFNALQGNYTLARKTQAVEF 36
>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 = 28.5 bits (64), Expect = 1.3
Identities = 18/94 (19%), Positives = 29/94 (30%), Gaps = 15/94 (15%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYK-----GAKIQLLDLPG 105
++ +G GKS+LLS L G E T + + + D G
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLA---VDTLEVDGDTGLLNIWDFGG 57
Query: 106 IIEGAKDGKGRGRQVIAVARTCSLIFIVLDVLKP 139
E + I + I +V D+
Sbjct: 58 REELKFE-------HIIFMKWADAILLVYDLTDR 84
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 28.8 bits (65), Expect = 1.9
Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 16/71 (22%)
Query: 51 RIGFVGFPSVGKSTLLSTL---AGVYSEVAAYEFT-------------TLTTVPGCIKYK 94
+G +G GK+TL +L G + T T+ T ++
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 95 GAKIQLLDLPG 105
+I +D PG
Sbjct: 61 KRRINFIDTPG 71
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 28.8 bits (65), Expect = 2.5
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSE 75
VG GKSTLL+ L G +
Sbjct: 349 LTALVGASGAGKSTLLNLLLGFLAP 373
>gnl|CDD|235666 PRK06002, fliI, flagellum-specific ATP synthase; Validated.
Length = 450
Score = 28.8 bits (65), Expect = 2.8
Identities = 12/21 (57%), Positives = 13/21 (61%)
Query: 51 RIGFVGFPSVGKSTLLSTLAG 71
RIG VGKSTLL+ LA
Sbjct: 167 RIGIFAGSGVGKSTLLAMLAR 187
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.5 bits (65), Expect = 2.8
Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 20/97 (20%)
Query: 55 VGFPSVGKSTLLSTLAG-----VYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGI--- 106
G P+VGKS+LL+ L G V +++A TT + I G ++L+D GI
Sbjct: 221 AGRPNVGKSSLLNALLGEERAIV-TDIAG---TTRDVIEEHINLDGIPLRLIDTAGIRET 276
Query: 107 ---IEGAKDGKGRGRQVIAVARTCSLIFIVLDVLKPL 140
+E K G R R+ I A L+ +VLD +PL
Sbjct: 277 DDEVE--KIGIERSREAIEEA---DLVLLVLDASEPL 308
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 28.4 bits (64), Expect = 3.0
Identities = 21/68 (30%), Positives = 29/68 (42%), Gaps = 13/68 (19%)
Query: 54 FVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAKDG 113
G P GK+TL +AG + F L+ V +K DL IIE A+
Sbjct: 53 LWGPPGTGKTTLARLIAGTTN----AAFEALSAVTSGVK---------DLREIIEEARKN 99
Query: 114 KGRGRQVI 121
+ GR+ I
Sbjct: 100 RLLGRRTI 107
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 28.0 bits (63), Expect = 3.3
Identities = 20/57 (35%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPG 105
I FVG +VGKSTL+ L G V T Y L DLPG
Sbjct: 9 KPEIVFVGRSNVGKSTLVRELTGKKVRVGKRPGVTRKP----NHYDWGDFILTDLPG 61
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 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 N-terminal
GTPase domain 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 = 168
Score = 27.7 bits (62), Expect = 3.3
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAG 71
D RI +G VGKS+L+ +L
Sbjct: 2 DVRIVLIGDEGVGKSSLIMSLVS 24
>gnl|CDD|220597 pfam10139, Virul_Fac, Putative bacterial virulence factor.
Members of this family of prokaryotic proteins include
various putative virulence factor effector proteins.
Their exact function is, as yet, unknown.
Length = 852
Score = 28.5 bits (64), Expect = 3.6
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 52 IGFVGFPSVGKSTLLSTLAG 71
+GF G GKS L+S LA
Sbjct: 46 VGFFGPSQAGKSYLISALAA 65
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 28.2 bits (63), Expect = 3.6
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAG 71
+RIG +G GKSTL+ LAG
Sbjct: 339 SRIGLLGRNGAGKSTLIKLLAG 360
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 28.5 bits (64), Expect = 3.7
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 14/72 (19%)
Query: 54 FVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAK-- 111
VG P VGK+ ++ LA +E E K AKI LD+ ++ G K
Sbjct: 207 LVGEPGVGKTAIVEGLALRIAEGKVPER-----------LKNAKIYSLDMGTLLAGTKYR 255
Query: 112 -DGKGRGRQVIA 122
D + R + V++
Sbjct: 256 GDFEERLKAVVS 267
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 27.7 bits (63), Expect = 3.8
Identities = 11/19 (57%), Positives = 12/19 (63%), Gaps = 2/19 (10%)
Query: 54 FVGFPS-VGKSTLLSTLAG 71
VG S VGKSTLL+ L
Sbjct: 90 LVG-QSGVGKSTLLNALLP 107
>gnl|CDD|226360 COG3840, ThiQ, ABC-type thiamine transport system, ATPase
component [Coenzyme metabolism].
Length = 231
Score = 28.1 bits (63), Expect = 3.8
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 42 FDVAKTGDARIGFVGFPSVGKSTLLSTLAG 71
FD+ + +G GKSTLL+ +AG
Sbjct: 18 FDLTVPAGEIVAILGPSGAGKSTLLNLIAG 47
>gnl|CDD|224800 COG1888, COG1888, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 97
Score = 26.9 bits (60), Expect = 3.9
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 26/94 (27%)
Query: 132 IVLDVLKPLGHKKLIE-----HELEGF-GLR-----LNKEPPNIDNQVPQSELDLDTVKT 180
+VLDVLKP ++E +LEG G+ ++ E N+ + + LD D ++
Sbjct: 8 LVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEE 67
Query: 181 ILSEY--RIHNADITLRYDATSDDLIDVVEGNRI 212
++ E IH+ D +VV G RI
Sbjct: 68 VIEELGGAIHSID-------------EVVAGKRI 88
>gnl|CDD|215558 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 28.3 bits (63), Expect = 3.9
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 49 DARIGFVGFPSVGKSTLLSTLAG 71
D+RI VG +GKST+L ++G
Sbjct: 535 DSRIAMVGPNGIGKSTILKLISG 557
>gnl|CDD|226952 COG4586, COG4586, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 325
Score = 28.1 bits (63), Expect = 4.1
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 42 FDVAKTGDARIGFVGFPSVGKSTLLSTLAG 71
F++ K +GF+G GKST L L G
Sbjct: 45 FEIPK--GEIVGFLGANGAGKSTTLKMLTG 72
>gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK;
Provisional.
Length = 258
Score = 28.0 bits (63), Expect = 4.1
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 11/57 (19%)
Query: 52 IGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIE 108
+G VG GK+TLL+ L+ L G + Y+ QL DL + E
Sbjct: 35 LGIVGESGSGKTTLLNALSAR-----------LAPDAGEVHYRMRDGQLRDLYALSE 80
>gnl|CDD|226865 COG4458, SrfC, Uncharacterized protein conserved in bacteria,
putative virulence factor [Function unknown].
Length = 821
Score = 28.3 bits (63), Expect = 4.4
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 52 IGFVGFPSVGKSTLLSTLAG 71
+GF G GKS L+S LA
Sbjct: 64 VGFFGPSQAGKSHLISALAA 83
>gnl|CDD|213265 cd03298, ABC_ThiQ_thiamine_transporter, ATP-binding cassette
domain of the thiamine transport system. Part of the
binding-protein-dependent transport system tbpA-thiPQ
for thiamine and TPP. Probably responsible for the
translocation of thiamine across the membrane. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
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 = 211
Score = 27.5 bits (61), Expect = 4.5
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 42 FDVAKTGDARIGFVGFPSVGKSTLLSTLAG 71
FD+ VG GKSTLL+ +AG
Sbjct: 17 FDLTFAQGEITAIVGPSGSGKSTLLNLIAG 46
>gnl|CDD|224079 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway
ATPase [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 441
Score = 27.9 bits (63), Expect = 4.8
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 51 RIGFVGFPSVGKSTLLSTLA 70
RIG VGKSTLL +A
Sbjct: 165 RIGIFAGSGVGKSTLLGMIA 184
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 27.8 bits (62), Expect = 4.9
Identities = 23/101 (22%), Positives = 42/101 (41%), Gaps = 17/101 (16%)
Query: 52 IGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAK 111
IG +G +GK+T + LAGV L TV YK I+
Sbjct: 28 IGILGPNGIGKTTFIKMLAGVLKPDEGDIEIELDTV----SYKPQYIK-----------A 72
Query: 112 DGKGRGRQVIA--VARTCSLIFIVLDVLKPLGHKKLIEHEL 150
D +G R +++ + + ++ KPL +++++ E+
Sbjct: 73 DYEGTVRDLLSSITKDFYTHPYFKTEIAKPLQIEQILDREV 113
>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 = 27.1 bits (61), Expect = 5.7
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 52 IGFVGFPSVGKSTLLSTLAG 71
+ F G +VGKS+L++ L
Sbjct: 2 VAFAGRSNVGKSSLINALTN 21
>gnl|CDD|236946 PRK11649, PRK11649, putative peptidase; Provisional.
Length = 439
Score = 27.7 bits (62), Expect = 6.0
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 16/51 (31%)
Query: 160 EPPNIDNQVPQSELDL----------------DTVKTILSEYRIHNADITL 194
+ D +PQ ELD DT+ +IL++Y I +DI+
Sbjct: 72 QAAQEDEAIPQDELDDKIAGEAGVHEYVVSTGDTLSSILNQYGIDMSDISQ 122
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 27.2 bits (61), Expect = 6.1
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAGVY 73
R+ +G GKSTLL L G+
Sbjct: 31 ERVLLIGPNGSGKSTLLKLLNGLL 54
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). 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 = 171
Score = 27.0 bits (61), Expect = 6.4
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYS 74
++ VG GKSTLL L +Y
Sbjct: 30 KVAIVGPSGSGKSTLLKLLLRLYD 53
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 27.2 bits (61), Expect = 6.4
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 52 IGFVGFPSVGKSTLLSTLAG 71
I F G +VGKS+L++ L
Sbjct: 27 IAFAGRSNVGKSSLINALTN 46
>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 = 26.7 bits (60), Expect = 6.7
Identities = 34/105 (32%), Positives = 49/105 (46%), Gaps = 16/105 (15%)
Query: 55 VGFPSVGKSTLLSTLAGVYSEVA---AYEFTTLTTVPGCIKYKGAKIQLLDLPGI----- 106
G P+VGKS+LL+ LAG + A TT + I G ++L+D G+
Sbjct: 9 AGKPNVGKSSLLNALAG--RDRAIVSDIAGTTRDVIEEEIDLGGIPVRLIDTAGLRETED 66
Query: 107 -IEGAKDGKGRGRQVIAVARTCSLIFIVLDVLKPLGHKKLIEHEL 150
IE K G R R+ I A L+ +V+D + L + L EL
Sbjct: 67 EIE--KIGIERAREAIEEA---DLVLLVVDASEGLDEEDLEILEL 106
>gnl|CDD|163508 TIGR03796, NHLM_micro_ABC1, NHLM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes a multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHLM, Nitrile Hydratase Leader
Microcin [Transport and binding proteins, Amino acids,
peptides and amines, Cellular processes, Biosynthesis of
natural products].
Length = 710
Score = 27.6 bits (62), Expect = 7.3
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 40 EGFDVAKTGDARIGFVGFPSVGKSTLLSTLAGVYS 74
E F + R+ VG GKST+ +AG+Y
Sbjct: 496 ENFSLTLQPGQRVALVGGSGSGKSTIAKLVAGLYQ 530
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 27.3 bits (61), Expect = 7.5
Identities = 22/103 (21%), Positives = 39/103 (37%), Gaps = 19/103 (18%)
Query: 52 IGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAK 111
IG +G +GK+T + LAGV L + YK I +
Sbjct: 370 IGILGPNGIGKTTFVKLLAGVIKPDEG-SEEDLK-----VSYKPQYI-----------SP 412
Query: 112 DGKGRGRQVIAVARTCSLI--FIVLDVLKPLGHKKLIEHELEG 152
D G ++ A + + +++KPL + L+E ++
Sbjct: 413 DYDGTVEDLLRSAIRSAFGSSYFKTEIVKPLNLEDLLERPVDE 455
>gnl|CDD|233918 TIGR02546, III_secr_ATP, type III secretion apparatus
H+-transporting two-sector ATPase. [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 422
Score = 27.3 bits (61), Expect = 7.5
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 51 RIGFVGFPSVGKSTLLSTLA 70
RIG VGKSTLL +A
Sbjct: 147 RIGIFAGAGVGKSTLLGMIA 166
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 26.8 bits (60), Expect = 7.6
Identities = 10/19 (52%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 54 FVGFPS-VGKSTLLSTLAG 71
G S VGKSTLL+ L
Sbjct: 40 LAG-QSGVGKSTLLNALLP 57
>gnl|CDD|236151 PRK08099, PRK08099, bifunctional DNA-binding transcriptional
repressor/ NMN adenylyltransferase; Provisional.
Length = 399
Score = 27.3 bits (61), Expect = 7.8
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 52 IGFVGFPSVGKSTLLSTLAGVYSEVAAYEF 81
+ +G S GKSTL++ LA +++ +A+E+
Sbjct: 222 VAILGGESSGKSTLVNKLANIFNTTSAWEY 251
>gnl|CDD|213212 cd03245, ABCC_bacteriocin_exporters, ATP-binding cassette domain of
bacteriocin exporters, subfamily C. Many
non-lantibiotic bacteriocins of lactic acid bacteria are
produced as precursors which have N-terminal leader
peptides that share similarities in amino acid sequence
and contain a conserved processing site of two glycine
residues in positions -1 and -2. A dedicated ATP-binding
cassette (ABC) transporter is responsible for the
proteolytic cleavage of the leader peptides and
subsequent translocation of the bacteriocins across the
cytoplasmic membrane.
Length = 220
Score = 26.8 bits (60), Expect = 7.9
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 11/52 (21%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLD 102
++ +G GKSTLL LAG+Y + G + G I+ LD
Sbjct: 32 KVAIIGRVGSGKSTLLKLLAGLYKPTS-----------GSVLLDGTDIRQLD 72
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 27.3 bits (61), Expect = 8.0
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAG 71
R+ +G GKSTLL+TLAG
Sbjct: 362 ERVAILGPSGSGKSTLLATLAG 383
>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 = 26.6 bits (60), Expect = 8.0
Identities = 10/12 (83%), Positives = 11/12 (91%)
Query: 61 GKSTLLSTLAGV 72
GKSTLL TLAG+
Sbjct: 37 GKSTLLKTLAGL 48
>gnl|CDD|237894 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 27.2 bits (61), Expect = 8.7
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 50 ARIGFVGFPSVGKSTLLSTLAG 71
R+ +G VGK+TLL TL G
Sbjct: 346 ERLAIIGENGVGKTTLLRTLVG 367
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. 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 = 157
Score = 26.4 bits (59), Expect = 9.0
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 51 RIGFVGFPSVGKSTLLSTLAGVY 73
+ VG GKSTLL +AG+
Sbjct: 27 IVALVGPNGSGKSTLLRAIAGLL 49
>gnl|CDD|213183 cd03216, ABC_Carb_Monos_I, First domain of the ATP-binding
cassette component of monosaccharide transport system.
This family represents the domain I of the carbohydrate
uptake proteins that transport only monosaccharides
(Monos). The Carb_Monos family is involved in the
uptake of monosaccharides, such as pentoses (such as
xylose, arabinose, and ribose) and hexoses (such as
xylose, arabinose, and ribose), that cannot be broken
down to simple sugars by hydrolysis. Pentoses include
xylose, arabinose, and ribose. Important hexoses
include glucose, galactose, and fructose. In members of
the Carb_monos family, the single hydrophobic gene
product forms a homodimer while the ABC protein
represents a fusion of two nucleotide-binding domains.
However, it is assumed that two copies of the ABC
domains are present in the assembled transporter.
Length = 163
Score = 26.2 bits (59), Expect = 9.9
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 61 GKSTLLSTLAGVYS 74
GKSTL+ L+G+Y
Sbjct: 38 GKSTLMKILSGLYK 51
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
0.319 0.141 0.405
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: 11,594,392
Number of extensions: 1128960
Number of successful extensions: 1624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1582
Number of HSP's successfully gapped: 181
Length of query: 225
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 132
Effective length of database: 6,812,680
Effective search space: 899273760
Effective search space used: 899273760
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: 57 (26.2 bits)