RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6249
(119 letters)
>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 = 213 bits (544), Expect = 1e-71
Identities = 81/105 (77%), Positives = 94/105 (89%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVIA 74
STLLS LT+T+SE A+YEFTTLTC+PGV+EYKGA IQLLDLPGIIEGA+ GKGRGRQVIA
Sbjct: 14 STLLSKLTNTKSEVAAYEFTTLTCVPGVMEYKGAKIQLLDLPGIIEGASDGKGRGRQVIA 73
Query: 75 VARTADLVLMMLDATKQDVQRGLLEKELESVGIRLNKKKPNIYFK 119
VARTADL+L++LDATK + QR +LE+ELE VGIRLNKK PN+ K
Sbjct: 74 VARTADLILIVLDATKPEGQREILERELEGVGIRLNKKPPNVTIK 118
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 170 bits (432), Expect = 4e-53
Identities = 64/105 (60%), Positives = 85/105 (80%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVIA 74
STLL+ LT+T+SE A Y FTTL +PG++EYKGA IQLLDLPGIIEGA+ G+GRGRQV++
Sbjct: 77 STLLNKLTNTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIEGASSGRGRGRQVLS 136
Query: 75 VARTADLVLMMLDATKQDVQRGLLEKELESVGIRLNKKKPNIYFK 119
VAR ADL++++LD + R ++E+ELE VGIRLNK+ P++ K
Sbjct: 137 VARNADLIIIVLDVFEDPHHRDIIERELEDVGIRLNKRPPDVTIK 181
>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 = 93.2 bits (232), Expect = 2e-25
Identities = 45/109 (41%), Positives = 68/109 (62%), Gaps = 7/109 (6%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYK-GANIQLLDLPGIIEGAAQGKGRGRQVI 73
STLLS LT + E ASY FTTL GV E+ G +IQ++DLPG+++GA++G+G G Q++
Sbjct: 11 STLLSALTSAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGASEGRGLGEQIL 70
Query: 74 AVARTADLVLMMLDATKQDVQRGL-----LEKELESVGIRLNKKKPNIY 117
A +DL+L ++DA++ V L L +E+ + L K KP +
Sbjct: 71 AHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFL-KNKPEMI 118
>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 = 69.4 bits (171), Expect = 4e-16
Identities = 37/111 (33%), Positives = 61/111 (54%), Gaps = 20/111 (18%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIP--GVIEYK-GANIQLLDLPGIIEGAAQGKGRG-- 69
STLLS +++ + + A Y FTTL +P GV+ G + + D+PG+IEGA++GKG G
Sbjct: 14 STLLSAISNAKPKIADYPFTTL--VPNLGVVRVDDGRSFVIADIPGLIEGASEGKGLGHR 71
Query: 70 --RQVIAVARTADLVLMMLDAT-----KQDVQRGLLEKELESVGIRLNKKK 113
R + RT ++L ++D + +D + + ELE+ L +K
Sbjct: 72 FLRH---IERT-RVLLHVIDLSGEDDPVEDYE--TIRNELEAYNPGLAEKP 116
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 69.9 bits (172), Expect = 3e-15
Identities = 34/106 (32%), Positives = 56/106 (52%), Gaps = 8/106 (7%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGAN-IQLLDLPGIIEGAAQGKGRGRQVI 73
STLLS ++ + + A Y FTTL GV+ G + D+PG+IEGA++G G G + +
Sbjct: 173 STLLSAVSAAKPKIADYPFTTLVPNLGVVRVDGGESFVVADIPGLIEGASEGVGLGLRFL 232
Query: 74 A-VARTADLVLMMLDATKQDVQRGL-----LEKELESVGIRLNKKK 113
+ RT L+ ++D + D + + + ELE +L +K
Sbjct: 233 RHIERTRVLLH-VIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKP 277
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 65.1 bits (160), Expect = 1e-13
Identities = 35/107 (32%), Positives = 60/107 (56%), Gaps = 10/107 (9%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGAN-IQLLDLPGIIEGAAQGKGRGRQVI 73
STLLS +++ + + A+Y FTTL GV+E + D+PG+IEGA++G G G Q +
Sbjct: 172 STLLSVVSNAKPKIANYHFTTLVPNLGVVETDDGRSFVMADIPGLIEGASEGVGLGHQFL 231
Query: 74 A-VARTADLVLMMLDATKQDVQRGLLE------KELESVGIRLNKKK 113
+ RT +++ ++D + + R +E KEL+ RL ++
Sbjct: 232 RHIERTR-VIVHVIDMSGSE-GRDPIEDYEKINKELKLYNPRLLERP 276
>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 = 62.8 bits (153), Expect = 1e-13
Identities = 32/110 (29%), Positives = 46/110 (41%), Gaps = 11/110 (10%)
Query: 15 STLLSTLTHTQ-SEAASYEFTTLTCIPGVIEYKGANI--QLLDLPGIIEGAAQGKGRGRQ 71
STLL+ L + S TT + VIE G LLD G + A + R
Sbjct: 15 STLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYRA 74
Query: 72 VIAVARTADLVLMMLDA----TKQDVQRGLLEKELES-VGIRLNKKKPNI 116
V + R D+V+++LD KQ + + ES V I L K ++
Sbjct: 75 VESSLRVFDIVILVLDVEEILEKQTKE---IIHHAESGVPIILVGNKIDL 121
>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 = 60.8 bits (148), Expect = 3e-13
Identities = 39/109 (35%), Positives = 61/109 (55%), Gaps = 16/109 (14%)
Query: 15 STLLSTLTHTQ-SEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKG--RGRQ 71
STL++ LT + + + Y TT I GV+ G I L+D PG+IEGA++GKG +
Sbjct: 13 STLINALTGAKVAIVSDYPGTTRDPILGVLGL-GRQIILVDTPGLIEGASEGKGVEGFNR 71
Query: 72 VIAVARTADLVLMMLDA----TKQDVQRGLLEKELESVGIR-----LNK 111
+ R ADL+L+++DA T+ D + + +ELE + + LNK
Sbjct: 72 FLEAIREADLILLVVDASEGLTEDDEE---ILEELEKLPKKPIILVLNK 117
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 62.4 bits (153), Expect = 1e-12
Identities = 33/103 (32%), Positives = 51/103 (49%), Gaps = 5/103 (4%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGAN-IQLLDLPGIIEGAAQGKGRGRQVI 73
STL+S ++ + + A Y FTTL GV+ + D+PG+IEGA++G G G + +
Sbjct: 172 STLISAVSAAKPKIADYPFTTLHPNLGVVRVDDYKSFVIADIPGLIEGASEGAGLGHRFL 231
Query: 74 A-VARTADLVLMMLDATKQDVQRG--LLEKELESVGIRLNKKK 113
+ RT L+L ++D D + ELE L K
Sbjct: 232 KHIERTR-LLLHLVDIEAVDPVEDYKTIRNELEKYSPELADKP 273
>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 = 61.7 bits (151), Expect = 2e-12
Identities = 31/106 (29%), Positives = 55/106 (51%), Gaps = 8/106 (7%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGAN-IQLLDLPGIIEGAAQGKGRGRQVI 73
STL+S ++ + + A Y FTTL GV+ + D+PG+IEGA++G G G + +
Sbjct: 171 STLISAVSAAKPKIADYPFTTLVPNLGVVRVDDGRSFVIADIPGLIEGASEGAGLGHRFL 230
Query: 74 A-VARTADLVLMMLDATKQDVQRGL-----LEKELESVGIRLNKKK 113
+ RT ++L ++D + +D + + EL+ L +K
Sbjct: 231 KHIERTR-VLLHLIDISPEDGSDPIEDYEIIRNELKKYSPELAEKP 275
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 52.6 bits (127), Expect = 3e-09
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIP--GVIEY-KGANIQLLDLPGIIEGAAQGKGRG-R 70
ST + ++ + + A Y FTTL +P GV+ + + D+PG+IEGA++G G G R
Sbjct: 173 STFIRAVSAAKPKVADYPFTTL--VPNLGVVRVDDERSFVVADIPGLIEGASEGAGLGIR 230
Query: 71 QVIAVARTADLVLMMLDATKQD 92
+ + R ++L ++D D
Sbjct: 231 FLKHLERCR-VLLHLIDIAPID 251
>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 = 50.3 bits (121), Expect = 6e-09
Identities = 28/103 (27%), Positives = 42/103 (40%), Gaps = 6/103 (5%)
Query: 15 STLLSTLT-HTQSEAASYEFTTLTCIPGVIE-YKGANIQLLDLPGIIEGAAQGKGRGRQV 72
S+LL+ L + TT + E + L+D PG+ E G+ R +
Sbjct: 11 SSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEGGLGRERVEEA 70
Query: 73 IAVARTADLVLMMLDATKQDVQRGLLEKELESVGIR----LNK 111
VA ADLVL+++D+ V+ L G LNK
Sbjct: 71 RQVADRADLVLLVVDSDLTPVEEEAKLGLLRERGKPVLLVLNK 113
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 48.8 bits (117), Expect = 7e-08
Identities = 33/116 (28%), Positives = 47/116 (40%), Gaps = 31/116 (26%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGI----------IEGAAQ 64
S+L+ LT + E A Y FTT G E IQ++D PG+ IE
Sbjct: 182 SSLVRKLTTAKPEVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLLDRPLEERNEIE---- 237
Query: 65 GKGRGRQVI-AVARTADLVLMMLDATKQ-----DVQRGLLEKELESVGIRLNKKKP 114
RQ I A+ A ++L + D ++ + Q LLE I+ K P
Sbjct: 238 -----RQAILALRHLAGVILFLFDPSETCGYSLEEQISLLE------EIKELFKAP 282
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 47.6 bits (114), Expect = 2e-07
Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIP--GVIEYKGANIQLLDLPGIIEGAAQGKGRGRQV 72
S+L+S L+ + + A Y FTTL +P GV++ + D+PG+I GA++GKG G
Sbjct: 173 SSLISALSAAKPKIADYPFTTL--VPNLGVVQAGDTRFTVADVPGLIPGASEGKGLGLDF 230
Query: 73 IA-VARTADLV 82
+ + R A LV
Sbjct: 231 LRHIERCAVLV 241
>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 = 46.0 bits (110), Expect = 3e-07
Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 20/88 (22%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGI----------IEGAAQ 64
S+L++ LT + E A Y FTT + G +YK Q++D PGI IE
Sbjct: 14 SSLVNKLTRAKPEVAPYPFTTKSLFVGHFDYKYLRWQVIDTPGILDRPLEERNTIE---- 69
Query: 65 GKGRGRQVI-AVARTADLVLMMLDATKQ 91
Q I A+A VL +D ++
Sbjct: 70 -----MQAITALAHLRAAVLFFIDPSET 92
>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 = 45.3 bits (108), Expect = 1e-06
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 24/99 (24%)
Query: 15 STLLSTLTHTQSEAASYEFTT------------------LTCIPGVIEYKGAN------I 50
ST + T E A+Y FTT L K + +
Sbjct: 12 STFFNAATLADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYGKCIDGKRYVPV 71
Query: 51 QLLDLPGIIEGAAQGKGRGRQVIAVARTADLVLMMLDAT 89
+L+D+ G++ GA +GKG G Q + R AD+++ ++DA+
Sbjct: 72 ELIDVAGLVPGAHEGKGLGNQFLDDLRDADVLIHVVDAS 110
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 44.9 bits (107), Expect = 1e-06
Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 24/95 (25%)
Query: 15 STLLSTLTHTQSEAASYEFTTL---------------------TCIPGVIEYKGANIQLL 53
STL + LT +E A+Y F T+ C P + A ++ +
Sbjct: 16 STLFNALTKAGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVKCPPKIRP---APVEFV 72
Query: 54 DLPGIIEGAAQGKGRGRQVIAVARTADLVLMMLDA 88
D+ G+++GA++G+G G + + R D ++ ++
Sbjct: 73 DIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRC 107
>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 = 43.6 bits (103), Expect = 3e-06
Identities = 30/107 (28%), Positives = 47/107 (43%), Gaps = 12/107 (11%)
Query: 15 STLLSTLTH-TQSEAASYEFTTLTCIPGVIEYKGA--NIQLLDLPGIIEGAAQGKGRGRQ 71
S+LL+ L E + TT V E + L+D PG+ E G GR
Sbjct: 11 SSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF--GGLGREEL 68
Query: 72 VIAVARTADLVLMMLDATKQ---DVQRGLLEKELESVGIR----LNK 111
+ R ADL+L+++D+T + + + L+ + L GI NK
Sbjct: 69 ARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNK 115
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 40.9 bits (97), Expect = 4e-05
Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 24/99 (24%)
Query: 15 STLLSTLTHTQSEAASYEFTT--------------------LTCIPGVIEYKGAN----I 50
ST + T E A+Y FTT + C P + +
Sbjct: 15 STFFNAATLADVEIANYPFTTIDPNVGVAYVRVECPCKELGVKCNPRNGKCIDGTRFIPV 74
Query: 51 QLLDLPGIIEGAAQGKGRGRQVIAVARTADLVLMMLDAT 89
+L+D+ G++ GA +G+G G Q + R AD ++ ++DA+
Sbjct: 75 ELIDVAGLVPGAHEGRGLGNQFLDDLRQADALIHVVDAS 113
>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 = 40.7 bits (96), Expect = 4e-05
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 10/72 (13%)
Query: 50 IQLLDLPGIIEGAAQGKGRGRQVIAVAR----TADLVLMMLDATKQDVQ---RGLLEKEL 102
+ ++D PGI+ G Q + RG AV R ADL+ ++ D K D+ R ++E+
Sbjct: 90 VTIVDTPGILSGEKQRQSRGYDFNAVCRWFAERADLIFLLFDPHKLDISDEFRRVIEQLK 149
Query: 103 ---ESVGIRLNK 111
+ I LNK
Sbjct: 150 GHESKIRIVLNK 161
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 38.9 bits (92), Expect = 2e-04
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 17/86 (19%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIE------------YKG-----ANIQLLDLPG 57
STL + LT +EAA+Y F T+ GV+ K A I+ +D+ G
Sbjct: 16 STLFNALTKAGAEAANYPFCTIEPNVGVVPVPDPRLDKLAEIVKPKKIVPATIEFVDIAG 75
Query: 58 IIEGAAQGKGRGRQVIAVARTADLVL 83
+++GA++G+G G Q +A R D ++
Sbjct: 76 LVKGASKGEGLGNQFLANIREVDAIV 101
>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 = 38.6 bits (90), Expect = 2e-04
Identities = 32/106 (30%), Positives = 49/106 (46%), Gaps = 9/106 (8%)
Query: 15 STLLSTLTHT-QSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRG-RQV 72
S+LL+ L ++ + + TT + G E G I+LLD GI E A + G +
Sbjct: 217 SSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIREHADFVERLGIEKS 276
Query: 73 IAVARTADLVLMMLDATKQDVQRGLLEKELESVGIRLNKKKPNIYF 118
+ ADLV+ +LDA++ L K+ + I LNK K
Sbjct: 277 FKAIKQADLVIYVLDASQP------LTKDDFLI-IDLNKSKKPFIL 315
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 35.8 bits (82), Expect = 0.002
Identities = 32/100 (32%), Positives = 52/100 (52%), Gaps = 5/100 (5%)
Query: 12 SHESTLLSTLTHTQSEAASYEF-TTLTCIPGVIEYKGANIQLLDLPGIIE-GAAQGKGRG 69
S +STLL+ + + + + TT + I G+I K + L D PGI E + K
Sbjct: 63 SGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFEPKGSLEKAMV 122
Query: 70 RQVIAVARTADLVLMMLDATKQ--DVQRGLLEKELESVGI 107
R + +ADLVL+++D+ K D+ +L+K L S+ I
Sbjct: 123 RCAWSSLHSADLVLLIIDSLKSFDDITHNILDK-LRSLNI 161
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 35.6 bits (83), Expect = 0.002
Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 8/105 (7%)
Query: 15 STLLSTLTHTQ-SEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGR--Q 71
STL + LT + + + T I G E+ G L+D G+ +G Q
Sbjct: 17 STLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLDDGDEDELQELIREQ 76
Query: 72 VIAVARTADLVLMMLDATKQDVQRGLLEKELESVGIRLNKKKPNI 116
+ AD++L ++D + G+ + E I KKP I
Sbjct: 77 ALIAIEEADVILFVVDG-----REGITPADEEIAKILRRSKKPVI 116
Score = 33.3 bits (77), Expect = 0.016
Identities = 26/96 (27%), Positives = 40/96 (41%), Gaps = 27/96 (28%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVI-------AVART------AD 80
TT I E G L+D GI R + I +VART AD
Sbjct: 212 TTRDSIDIEFERDGRKYVLIDTAGI---------RRKGKITESVEKYSVARTLKAIERAD 262
Query: 81 LVLMMLDATKQDVQRGLLEKELESVGIRLNKKKPNI 116
+VL+++DAT+ G+ E++L G+ + +
Sbjct: 263 VVLLVIDATE-----GISEQDLRIAGLIEEAGRGIV 293
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They generally show sequence conservation in the
region between the Walker A and B motifs (G1 and G3 box
motifs), to the exclusion of other GTPases. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 34.6 bits (80), Expect = 0.004
Identities = 19/58 (32%), Positives = 27/58 (46%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVIAVARTADLVLMMLDATKQ 91
TT V + G + LLDLPG+ E + + + ADLVL +LDA +
Sbjct: 31 TTRAAQAYVWQTGGDGLVLLDLPGVGERGRRDREYEELYRRLLPEADLVLWLLDADDR 88
>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 = 33.9 bits (79), Expect = 0.007
Identities = 32/92 (34%), Positives = 49/92 (53%), Gaps = 19/92 (20%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVI---AVART------ADLVLM 84
TT I EY G L+D GI + KG+ + I +V RT AD+VL+
Sbjct: 36 TTRDSIDVPFEYDGQKYTLIDTAGIRK-----KGKVTEGIEKYSVLRTLKAIERADVVLL 90
Query: 85 MLDA----TKQDVQ-RGLLEKELESVGIRLNK 111
+LDA T+QD++ GL+ +E +++ I +NK
Sbjct: 91 VLDASEGITEQDLRIAGLILEEGKALIIVVNK 122
>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 = 34.0 bits (79), Expect = 0.011
Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 19/92 (20%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVI---AVART------ADLVLM 84
TT I E G L+D GI + KG+ + + +V RT AD+VL+
Sbjct: 206 TTRDSIDIPFERNGKKYTLIDTAGI-----RRKGKVTEGVEKYSVLRTLKAIERADVVLL 260
Query: 85 MLDA----TKQDVQ-RGLLEKELESVGIRLNK 111
+LDA T+QD++ GL + +++ I +NK
Sbjct: 261 VLDATEGITEQDLRIAGLALEAGKALVIVVNK 292
Score = 28.2 bits (64), Expect = 0.93
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 41 GVIEYKGANIQLLDLPGIIEGAA--QGKGRGRQVIAVARTADLVLMMLDA 88
G E+ G L+D GI E + R Q AD++L ++D
Sbjct: 40 GDAEWGGREFILIDTGGIEEDDDGLDKQIR-EQAEIAIEEADVILFVVDG 88
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 33.4 bits (77), Expect = 0.018
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGI 58
+TL + LT + ++ T+ G ++YKG I+++DLPG
Sbjct: 17 TTLFNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPGT 60
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 31.4 bits (72), Expect = 0.080
Identities = 32/111 (28%), Positives = 45/111 (40%), Gaps = 20/111 (18%)
Query: 15 STLLSTLTHTQSEAA---SYEFTTLTCIPGVIEYKGANIQLLDLPGI------IEGAAQG 65
S+LL+ L + A TT I I G ++L+D GI +E G
Sbjct: 231 SSLLNALL--GRDRAIVTDIAGTTRDVIEEDINLNGIPVRLVDTAGIRETDDVVE--RIG 286
Query: 66 KGRGRQVIAVARTADLVLMMLDATKQDVQRGLLEKELESVGIR----LNKK 112
R ++ I ADLVL +LDA++ + L EL LNK
Sbjct: 287 IERAKKAIE---EADLVLFVLDASQPLDKEDLALIELLPKKKPIIVVLNKA 334
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 30.9 bits (70), Expect = 0.10
Identities = 13/50 (26%), Positives = 22/50 (44%)
Query: 45 YKGANIQLLDLPGIIEGAAQGKGRGRQVIAVARTADLVLMMLDATKQDVQ 94
Y G N+ L D PG+ +G + + DLVL ++ A + +
Sbjct: 84 YDGENLVLWDTPGLGDGKDKDAEHRQLYRDYLPKLDLVLWLIKADDRALG 133
>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 = 30.5 bits (70), Expect = 0.15
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 31/81 (38%)
Query: 15 STLLSTLTHTQSEAASYEFTTL------------------------TCIPGVIEYKGANI 50
STL + LT + +EAA+Y F T+ +P IE+
Sbjct: 12 STLFNALTKSNAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKIVPATIEF----- 66
Query: 51 QLLDLPGIIEGAAQGKGRGRQ 71
+D+ G+++GA++G+G G +
Sbjct: 67 --VDIAGLVKGASKGEGLGNK 85
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 30.0 bits (69), Expect = 0.26
Identities = 29/93 (31%), Positives = 43/93 (46%), Gaps = 21/93 (22%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVI---AVART------ADLVLM 84
TT I E G L+D GI KG+ + + +V RT AD+VL+
Sbjct: 207 TTRDSIDTPFERDGQKYTLIDTAGIRR-----KGKVTEGVEKYSVIRTLKAIERADVVLL 261
Query: 85 MLDAT----KQDVQR--GLLEKELESVGIRLNK 111
++DAT +QD R GL + ++ I +NK
Sbjct: 262 VIDATEGITEQD-LRIAGLALEAGRALVIVVNK 293
>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 = 29.3 bits (67), Expect = 0.31
Identities = 12/44 (27%), Positives = 23/44 (52%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGI 58
+TL + LT + + ++ T+ G + G I+++DLPG
Sbjct: 11 TTLFNALTGARQKVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGT 54
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 29.5 bits (67), Expect = 0.32
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGI-IEGAAQGKGRGRQVIAVARTADLVLMMLDATKQ 91
TT I G++ A I +D PGI A G+ + + + DL+L ++DA +
Sbjct: 40 TTRNRIRGIVTTDNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEG 98
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 29.5 bits (67), Expect = 0.39
Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 17/88 (19%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIE------------YK-----GANIQLLDLPG 57
ST + L Q A ++ F T+ + +K A + + D+ G
Sbjct: 35 STTFNALCKQQVPAENFPFCTIDPNTARVNVPDERFDWLCKHFKPKSIVPAQLDITDIAG 94
Query: 58 IIEGAAQGKGRGRQVIAVARTADLVLMM 85
+++GA++G+G G ++ R D + +
Sbjct: 95 LVKGASEGEGLGNAFLSHIRAVDGIYHV 122
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 28.6 bits (64), Expect = 0.82
Identities = 18/40 (45%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 57 GIIEGAAQGKGR-GRQVIAVARTADLVLMMLDATKQDVQR 95
GI E AA+ R G V+AVAR DL LDA + R
Sbjct: 51 GIGEAAAEQFARRGATVVAVARREDL----LDAVADRITR 86
>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 = 28.2 bits (64), Expect = 0.82
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 41 GVIEYKGANIQLLDLPGI 58
G +YKG I+++DLPG
Sbjct: 40 GTFKYKGYEIEIVDLPGT 57
>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 = 27.8 bits (63), Expect = 1.0
Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 3/51 (5%)
Query: 41 GVIEYKGANIQLLDLPGIIEGAA--QGKGRGRQVIAVARTADLVLMMLDAT 89
G E+ G L+D GI + R Q AD++L ++D
Sbjct: 38 GEAEWGGREFILIDTGGIEPDDEGISKEIR-EQAEIAIEEADVILFVVDGR 87
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 27.6 bits (62), Expect = 1.3
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 13/71 (18%)
Query: 49 NIQLLDLPGIIEGAAQGKGRGRQVIAVARTADLVLMMLDA----TKQDVQRGLLEKELES 104
+ L+D PG+ A G + AD++L ++DA + + L +E++
Sbjct: 102 GLTLVDTPGLDSVA---VGDQDLTEEYIKPADIILAVVDANHDLSTSEALF--LAREVDP 156
Query: 105 VGIR----LNK 111
G R L K
Sbjct: 157 NGKRTIGVLTK 167
>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
Length = 287
Score = 27.3 bits (61), Expect = 1.9
Identities = 20/61 (32%), Positives = 25/61 (40%), Gaps = 13/61 (21%)
Query: 54 DLPG---IIEGAAQGKGRGRQVIAVARTADLVLMMLDATKQDVQRGLLEK---ELESVGI 107
D G +I GAA G G I A LVL DVQ+ L++ EL + G
Sbjct: 3 DFAGKVAVITGAASGFGLAFARIGAALGMKLVLA-------DVQQDALDRAVAELRAQGA 55
Query: 108 R 108
Sbjct: 56 E 56
>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 = 27.3 bits (61), Expect = 2.0
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 73 IAVARTADLVLMMLDA 88
I VA+ ADLVL+++D
Sbjct: 98 IDVAKIADLVLLLIDG 113
>gnl|CDD|187609 cd05351, XR_like_SDR_c, xylulose reductase-like, classical (c)
SDRs. Members of this subgroup include proteins
identified as L-xylulose reductase (XR) and carbonyl
reductase; they are members of the SDR family. XR,
catalyzes the NADP-dependent reduction of L-xyulose and
other sugars. Tetrameric mouse carbonyl reductase is
involved in the metabolism of biogenic and xenobiotic
carbonyl compounds. This subgroup also includes
tetrameric chicken liver D-erythrulose reductase, which
catalyzes the reduction of D-erythrulose to D-threitol.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser).
Length = 244
Score = 27.0 bits (60), Expect = 2.0
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 10/45 (22%)
Query: 48 ANIQLLDLPGIIEGAAQGKGR---------GRQVIAVART-ADLV 82
+ ++ GA +G GR G +V+AV+RT ADL
Sbjct: 1 MELDFAGKRALVTGAGKGIGRATVKALAKAGARVVAVSRTQADLD 45
>gnl|CDD|226683 COG4230, COG4230, Delta 1-pyrroline-5-carboxylate dehydrogenase
[Energy production and conversion].
Length = 769
Score = 27.4 bits (61), Expect = 2.0
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 58 IIEGAAQGKGRGRQVIAVARTADLVLMMLDATKQDVQRGL 97
I+ GA G R VI A D+V + +AT+ DV++ L
Sbjct: 117 IVNGAPVAGGEPRPVINPADPDDIVGTVTEATEADVEQAL 156
>gnl|CDD|176249 cd08289, MDR_yhfp_like, Yhfp putative quinone oxidoreductases.
yhfp putative quinone oxidoreductases (QOR). QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 326
Score = 26.9 bits (60), Expect = 2.3
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 50 IQLLDLPGIIEGAAQGKGRGRQVIAV 75
I L +LP ++ QG+ GR V+ +
Sbjct: 301 ITLDELPEALKQILQGRVTGRTVVKL 326
>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 = 27.0 bits (60), Expect = 2.4
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGI 58
STL + LT ++ T+ G + ++G +I+++DLPGI
Sbjct: 8 STLFNALTGANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGI 51
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 26.8 bits (60), Expect = 2.6
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 58 IIEGAAQGKGRGRQVIAVARTADLVL 83
++ GAAQG GRG + A A A +VL
Sbjct: 12 VVTGAAQGIGRGVALRAAAEGARVVL 37
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 27.0 bits (61), Expect = 2.7
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 83 LMMLDATKQDVQRGLLEKELESVGIRLNK 111
L+++D + + E LE I +NK
Sbjct: 315 LVLVDLRSKGLTGKEAEAALEEANITVNK 343
>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 = 26.7 bits (60), Expect = 2.9
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVIAVART----ADLVLMMLDAT 89
TT I G+ A I +D PGI + K G +++ A + DLVL ++DA+
Sbjct: 37 TTRNRIRGIYTDDDAQIIFVDTPGIHK---PKKKLGERMVKAAWSALKDVDLVLFVVDAS 93
Query: 90 K 90
+
Sbjct: 94 E 94
>gnl|CDD|129605 TIGR00514, accC, acetyl-CoA carboxylase, biotin carboxylase
subunit. This model represents the biotin carboxylase
subunit found usually as a component of acetyl-CoA
carboxylase. Acetyl-CoA carboxylase is designated EC
6.4.1.2 and this component, biotin carboxylase, has its
own designation, EC 6.3.4.14. Homologous domains are
found in eukaryotic forms of acetyl-CoA carboxylase and
in a number of other carboxylases (e.g. pyruvate
carboxylase), but seed members and trusted cutoff are
selected so as to exclude these. In some systems, the
biotin carboxyl carrier protein and this protein (biotin
carboxylase) may be shared by different
carboxyltransferases. However, this model is not
intended to identify the biotin carboxylase domain of
propionyl-coA carboxylase. The model should hit the full
length of proteins, except for chloroplast transit
peptides in plants. If it hits a domain only of a longer
protein, there may be a problem with the identification
[Fatty acid and phospholipid metabolism, Biosynthesis].
Length = 449
Score = 26.6 bits (59), Expect = 3.5
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 15/78 (19%)
Query: 38 CIPG---VIEYKGANIQL---LDLPGIIEGAAQGKGRGRQVIAVARTADLVLMMLDATKQ 91
C+PG ++E + N+++ + P II+ A G GRG + V R D ++ + T+
Sbjct: 130 CVPGSDGLVEDEEENVRIAKRIGYPVIIKATAGGGGRG---MRVVREPDELVKSISMTRA 186
Query: 92 DVQRGL------LEKELE 103
+ + +EK +E
Sbjct: 187 EAKAAFGNDGVYIEKYIE 204
>gnl|CDD|236307 PRK08591, PRK08591, acetyl-CoA carboxylase biotin carboxylase
subunit; Validated.
Length = 451
Score = 26.3 bits (59), Expect = 3.9
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 3/36 (8%)
Query: 56 PGIIEGAAQGKGRGRQVIAVARTADLVLMMLDATKQ 91
P II+ A G GRG + V RT + +
Sbjct: 154 PVIIKATAGGGGRG---MRVVRTEAELEKAFSMARA 186
>gnl|CDD|181188 PRK07985, PRK07985, oxidoreductase; Provisional.
Length = 294
Score = 26.5 bits (58), Expect = 4.2
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 45 YKGANIQLLDLPGIIEGAAQGKGRGRQVIAVART-ADLVLMMLDATKQDVQ 94
Y G+ +L D ++ G G GR IA AR AD+ + L ++D Q
Sbjct: 41 YVGSG-RLKDRKALVTGGDSGIGRA-AAIAYAREGADVAISYLPVEEEDAQ 89
>gnl|CDD|239170 cd02769, MopB_DMSOR-BSOR-TMAOR, The MopB_DMSOR-BSOR-TMAOR CD
contains dimethylsulfoxide reductase (DMSOR), biotin
sulfoxide reductase (BSOR), trimethylamine N-oxide
reductase (TMAOR) and other related proteins. DMSOR
always catalyzes the reduction of DMSO to
dimethylsulfide, but its cellular location and
oligomerization state are organism-dependent. For
example, in Rhodobacter sphaeriodes and Rhodobacter
capsulatus, it is an 82-kDa monomeric soluble protein
found in the periplasmic space; in E. coli, it is
membrane-bound and exists as a heterotrimer. BSOR
catalyzes the reduction of biotin sulfixode to biotin,
and is unique among Mo enzymes because no additional
auxiliary proteins or cofactors are required. TMAOR is
similar to DMSOR, but its only natural substrate is
TMAO. Members of this CD belong to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 609
Score = 26.1 bits (58), Expect = 5.1
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 56 PGIIEGAAQGKGRGRQVIAVARTADLVL 83
QG+ I VAR AD++L
Sbjct: 364 AAPPPALPQGRNPVSSFIPVARIADMLL 391
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 26.2 bits (59), Expect = 5.2
Identities = 37/116 (31%), Positives = 51/116 (43%), Gaps = 33/116 (28%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPG----VIE----YKGANIQLLDLPGI------IE 60
S+LL+ L E A +T I G VIE G ++L+D GI +E
Sbjct: 229 SSLLNALL--GEERA-----IVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRETDDEVE 281
Query: 61 GAAQGKGRGRQVIAVARTADLVLMMLDATKQDVQRGLLEKELESVGIRLNKKKPNI 116
G R R+ I ADLVL++LDA+ L E++ E + K KP I
Sbjct: 282 --KIGIERSREAIE---EADLVLLVLDAS-----EPLTEEDDEI--LEELKDKPVI 325
>gnl|CDD|218571 pfam05378, Hydant_A_N, Hydantoinase/oxoprolinase N-terminal region.
This family is found at the N-terminus of the pfam01968
family.
Length = 175
Score = 25.7 bits (57), Expect = 5.4
Identities = 9/38 (23%), Positives = 18/38 (47%)
Query: 39 IPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQVIAVA 76
+ ++ G I+ LD + E + K G + +AV+
Sbjct: 116 VDERVDADGEVIKPLDEEAVREALKELKDAGVEAVAVS 153
>gnl|CDD|187642 cd08937, DHB_DH-like_SDR_c,
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase (DHB DH)-like, classical (c) SDR. DHB DH
(aka 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate
dehydrogenase) catalyzes the NAD-dependent conversion
of 1,2-dihydroxycyclohexa-3,4-diene carboxylate to a
catechol. This subgroup also contains Pseudomonas
putida F1 CmtB, 2,3-dihydroxy-2,3-dihydro-p-cumate
dehydrogenase, the second enzyme in the pathway for
catabolism of p-cumate catabolism. This subgroup shares
the glycine-rich NAD-binding motif of the classical
SDRs and shares the same catalytic triad; however, the
upstream Asn implicated in cofactor binding or
catalysis in other SDRs is generally substituted by a
Ser. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 256
Score = 26.0 bits (57), Expect = 5.7
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 58 IIEGAAQGKGRGRQVIAVARTADLVLMMLDATKQDVQRGLLE 99
++ GAAQG GRG A ++L+ +V +L
Sbjct: 8 VVTGAAQGIGRGVAERLAGEGARVLLVDRSELVHEVLAEILA 49
>gnl|CDD|235097 PRK02999, PRK02999, malate synthase G; Provisional.
Length = 726
Score = 25.9 bits (58), Expect = 6.9
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 4/22 (18%)
Query: 60 EGAAQGKG----RGRQVIAVAR 77
GA +GKG RG +VIA AR
Sbjct: 152 GGAEKGKGYNPVRGAKVIAYAR 173
>gnl|CDD|226540 COG4054, McrB, Methyl coenzyme M reductase, beta subunit [Coenzyme
metabolism].
Length = 447
Score = 25.6 bits (56), Expect = 7.5
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 40 PGVIEYKGANIQ-LLDLPGIIEG 61
P ++Y GANI LL +P +EG
Sbjct: 168 PQTVDYMGANIATLLGIPQKLEG 190
>gnl|CDD|151819 pfam11379, DUF3182, Protein of unknown function (DUF3182). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 355
Score = 25.7 bits (57), Expect = 7.8
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 67 GRGRQVIAVARTADLVLMMLDATKQDVQRGLLEKELESV 105
GRG+QV+A A D L LD + +LE++L+
Sbjct: 149 GRGQQVVADADALDAALAALDDRELAAHGLVLEEDLDQP 187
>gnl|CDD|181305 PRK08226, PRK08226, short chain dehydrogenase; Provisional.
Length = 263
Score = 25.5 bits (56), Expect = 8.7
Identities = 11/53 (20%), Positives = 22/53 (41%)
Query: 58 IIEGAAQGKGRGRQVIAVARTADLVLMMLDATKQDVQRGLLEKELESVGIRLN 110
+I GA QG G G + A+L+L+ + + + L + + +
Sbjct: 10 LITGALQGIGEGIARVFARHGANLILLDISPEIEKLADELCGRGHRCTAVVAD 62
>gnl|CDD|202394 pfam02783, MCR_beta_N, Methyl-coenzyme M reductase beta subunit,
N-terminal domain. Methyl-coenzyme M reductase (MCR) is
the enzyme responsible for microbial formation of
methane. It is a hexamer composed of 2 alpha
(pfam02249), 2 beta (this family), and 2 gamma
(pfam02240) subunits with two identical nickel
porphinoid active sites. The N-terminal domain has an
alpha/beta ferredoxin-like fold.
Length = 182
Score = 25.1 bits (55), Expect = 9.1
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 40 PGVIEYKGANIQ-LLDLPGIIEG 61
P ++Y G NI LL +P +EG
Sbjct: 160 PQTVDYMGGNIATLLGIPQKLEG 182
>gnl|CDD|238370 cd00728, malate_synt_G, Malate synthase G (MSG), monomeric enzyme
present in some bacteria. In general, malate synthase
catalyzes the Claisen condensation of glyoxylate and
acetyl-CoA to malyl-CoA , which hydrolyzes to malate and
CoA. This reaction is part of the glyoxylate cycle,
which allows certain organisms to derive their carbon
requirements from two-carbon compounds, by bypassing the
two carboxylation steps of the citric acid cycle.
Length = 712
Score = 25.4 bits (56), Expect = 9.2
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 4/22 (18%)
Query: 60 EGAAQGKG----RGRQVIAVAR 77
GA +GKG RG +VIA AR
Sbjct: 144 NGAERGKGYNPVRGAKVIAYAR 165
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 0.135 0.373
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,706,100
Number of extensions: 490775
Number of successful extensions: 592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 568
Number of HSP's successfully gapped: 89
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
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: 53 (24.2 bits)