RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15138
(320 letters)
>gnl|CDD|206728 cd04165, GTPBP1_like, GTP binding protein 1 (GTPBP1)-like family
includes GTPBP2. Mammalian GTP binding protein 1
(GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
are GTPases whose specific functions remain unknown. In
mouse, GTPBP1 is expressed in macrophages, in smooth
muscle cells of various tissues and in some neurons of
the cerebral cortex; GTPBP2 tissue distribution appears
to overlap that of GTPBP1. In human leukemia and
macrophage cell lines, expression of both GTPBP1 and
GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The
chromosomal location of both genes has been identified
in humans, with GTPBP1 located in chromosome 22q12-13.1
and GTPBP2 located in chromosome 6p21-12. Human
glioblastoma multiforme (GBM), a highly-malignant
astrocytic glioma and the most common cancer in the
central nervous system, has been linked to chromosomal
deletions and a translocation on chromosome 6. The GBM
translocation results in a fusion of GTPBP2 and PTPRZ1,
a protein involved in oligodendrocyte differentiation,
recovery, and survival. This fusion product may
contribute to the onset of GBM.
Length = 224
Score = 228 bits (584), Expect = 9e-75
Identities = 90/116 (77%), Positives = 101/116 (87%), Gaps = 1/116 (0%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVGNDILGFDSV 263
RVAVVGNVDAGKSTLLGVLT GELDNGRG AR LFRHKHE+ESGRTSSV NDILGFDS
Sbjct: 1 RVAVVGNVDAGKSTLLGVLTQGELDNGRGKARLNLFRHKHEVESGRTSSVSNDILGFDSD 60
Query: 264 GNVVNKPEHGSLDW-VKICERSAKVITFIDLAGHERYLKTTVFGMTGHVPDFGMLM 318
G VVN P++ + V+ICE+S+KV+TFIDLAGHERYLKTTVFGMTG+ PD+ ML+
Sbjct: 61 GEVVNYPDNHLGELDVEICEKSSKVVTFIDLAGHERYLKTTVFGMTGYAPDYAMLV 116
Score = 117 bits (295), Expect = 1e-31
Identities = 54/69 (78%), Positives = 60/69 (86%), Gaps = 2/69 (2%)
Query: 37 DHSMLQSKVGANAGIVGMTKEHLGLALALSVPVFVVVTKIDMCPPNVLQDTLKLLVRILK 96
D++ML VGANAGI+GMTKEHLGLALAL VPVFVVVTKIDM P NVLQ+TLK L R+LK
Sbjct: 111 DYAMLV--VGANAGIIGMTKEHLGLALALKVPVFVVVTKIDMTPANVLQETLKDLKRLLK 168
Query: 97 SPGCRKVPV 105
SPG RK+PV
Sbjct: 169 SPGVRKLPV 177
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 148 bits (375), Expect = 1e-40
Identities = 69/205 (33%), Positives = 113/205 (55%), Gaps = 1/205 (0%)
Query: 113 TEEQFDLLQKKIKSLIDNGRGETIYDIGIGQDGGENGLKPDEYEASVATLQSLATTLEAD 172
E++ D L ++K ++ G GE +Y IG+ DG GL ++ S+ L+ LA + A
Sbjct: 29 KEDRLDRLAGQMKYRLEEGDGEAVYVIGVSDDGEPLGLSDEKLVESIEVLRELAREVGAS 88
Query: 173 CVLLRQRKLDNGLTGQYLLRKRVESQDFLEIRVAVVGNVDAGKSTLLGVLTHGELDNGRG 232
++R + +G + L+R++ E + V V G+VD GKSTL+GVL G LD+G G
Sbjct: 89 IYIVRVHEGTDGYVAEVLVRRKTEEAP-EHVLVGVAGHVDHGKSTLVGVLVTGRLDDGDG 147
Query: 233 HARQKLFRHKHEMESGRTSSVGNDILGFDSVGNVVNKPEHGSLDWVKICERSAKVITFID 292
R L KHE+E G ++ + + GFD V K + + +R+ K+++F+D
Sbjct: 148 ATRSYLDVQKHEVERGLSADISLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVD 207
Query: 293 LAGHERYLKTTVFGMTGHVPDFGML 317
GHE +L+TT+ G+ G D+G+L
Sbjct: 208 TVGHEPWLRTTIRGLLGQKVDYGLL 232
Score = 66.0 bits (161), Expect = 6e-12
Identities = 29/60 (48%), Positives = 41/60 (68%), Gaps = 2/60 (3%)
Query: 37 DHSMLQSKVGANAGIVGMTKEHLGLALALSVPVFVVVTKIDMCPPNVLQDTLKLLVRILK 96
D+ +L V A+ G+ MTKEHLG+ALA+ +PV VVVTKIDM P + Q ++ + +LK
Sbjct: 228 DYGLLV--VAADDGVTKMTKEHLGIALAMELPVIVVVTKIDMVPDDRFQGVVEEISALLK 285
>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 = 77.7 bits (192), Expect = 4e-17
Identities = 35/117 (29%), Positives = 46/117 (39%), Gaps = 27/117 (23%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQ--KLFRHKHEMESGRTSSVGNDILGFD 261
V V+G+VD GK+TL G L + R R+ L K E E G T G
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVV----- 55
Query: 262 SVGNVVNKPEHGSLDWVKICERSAKVITFIDLAGHERYLKTTVFGMTGHVPDFGMLM 318
+W K + I FID GHE + K TV G+ D +L+
Sbjct: 56 ------------EFEWPK------RRINFIDTPGHEDFSKETVRGLA--QADGALLV 92
Score = 63.1 bits (154), Expect = 6e-12
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVVVTKIDMCPPNVLQDTLKLLVRILKSPGCRKVP 104
V AN G+ T+EHL +ALA +P+ V V KID + L+ + +LK G +
Sbjct: 93 VDANEGVEPQTREHLNIALAGGLPIIVAVNKIDRVGEEDFDEVLREIKELLKLIGFTFLK 152
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 61.4 bits (150), Expect = 2e-11
Identities = 25/118 (21%), Positives = 41/118 (34%), Gaps = 27/118 (22%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTH--GELDNGRGHARQKLFRHKHEMESGRTSSVGNDILGF 260
+ ++G+VD GK+TL L + G + + L + K E E G T +
Sbjct: 4 RNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAV---- 59
Query: 261 DSVGNVVNKPEHGSLDWVKICERSAKVITFIDLAGHERYLKTTVFGMTGHVPDFGMLM 318
E ++I ID GH + K + G D +L+
Sbjct: 60 -------------------SFETKKRLINIIDTPGHVDFTKEMIRGA--SQADGAILV 96
Score = 50.2 bits (121), Expect = 2e-07
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVVVTKIDMCPPNVLQDTLKLLVRIL 95
V A G++ T+EHL LA L VP+ V + KID L++ ++ + R L
Sbjct: 97 VDAVEGVMPQTREHLLLAKTLGVPIIVFINKIDRVDDAELEEVVEEISREL 147
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 35.3 bits (81), Expect = 0.022
Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 1/66 (1%)
Query: 202 EIRVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVGN-DILGF 260
E ++ V+G+ GK+TLL L E G L K R + D G
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQ 64
Query: 261 DSVGNV 266
+ ++
Sbjct: 65 EEYRSL 70
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 34.9 bits (81), Expect = 0.023
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 33 ASPADHSMLQSKVGANAGIVGMTKEHLGLALALSVP-VFVVVTKIDMCPPNVLQDTLKLL 91
A D +L V A+ GI+ T+EHL + L + VV+TK D+ + L+ + +
Sbjct: 71 AGGIDAVLLV--VAADEGIMPQTREHLEILELLGIKKGLVVLTKADLVDEDRLELVEEEI 128
Query: 92 VRILKSPGCRKVPV 105
+ +L P+
Sbjct: 129 LELLAGTFLADAPI 142
Score = 33.0 bits (76), Expect = 0.100
Identities = 29/105 (27%), Positives = 41/105 (39%), Gaps = 33/105 (31%)
Query: 205 VAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVGNDILGFDSVG 264
+ G++D GK+TL+ LT E D R E + G T LGF
Sbjct: 2 IGTAGHIDHGKTTLIKALTGIETD-----------RLPEEKKRGITID-----LGF---- 41
Query: 265 NVVNKPEHGSLDWVKICERSAKVITFIDLAGHERYLKTTVFGMTG 309
LD K + FID+ GHE+++K + G G
Sbjct: 42 --------AYLDL-----PDGKRLGFIDVPGHEKFVKNMLAGAGG 73
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 34.8 bits (80), Expect = 0.060
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 3/95 (3%)
Query: 36 ADHSMLQSKVGANAGIVGMTKEHLGLALALSVP-VFVVVTKIDMCPPNVLQDTLKLLVRI 94
D ++L V A+ G++ T EHL + L +P VV+TK D ++ T + +I
Sbjct: 74 IDAALLV--VDADEGVMTQTGEHLAVLDLLGIPHTIVVITKADRVNEEEIKRTEMFMKQI 131
Query: 95 LKSPGCRKVPVMNCLISPTEEQFDLLQKKIKSLID 129
L S K + + T + L+K++K+L++
Sbjct: 132 LNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLLE 166
Score = 32.5 bits (74), Expect = 0.27
Identities = 25/107 (23%), Positives = 37/107 (34%), Gaps = 34/107 (31%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVGNDILGFDS 262
+ +A G+VD GK+TLL LT D R E + G T +G
Sbjct: 1 MIIATAGHVDHGKTTLLKALTGIAAD-----------RLPEEKKRGMTIDLGFAYFPLPD 49
Query: 263 VGNVVNKPEHGSLDWVKICERSAKVITFIDLAGHERYLKTTVFGMTG 309
+ FID+ GHE+++ + G G
Sbjct: 50 -----------------------YRLGFIDVPGHEKFISNAIAGGGG 73
>gnl|CDD|237422 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 33.6 bits (78), Expect = 0.091
Identities = 16/31 (51%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 205 VAVVGNVDAGKSTLLGVLTHGELDNGRGHAR 235
VA++G AGKSTLL L+ GEL G R
Sbjct: 31 VAILGPNGAGKSTLLRALS-GELSPDSGEVR 60
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 33.2 bits (77), Expect = 0.097
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 205 VAVVGNVDAGKSTLLG 220
+ V+G+VDAGKSTL G
Sbjct: 2 LVVIGHVDAGKSTLTG 17
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 33.5 bits (77), Expect = 0.15
Identities = 25/112 (22%), Positives = 42/112 (37%), Gaps = 22/112 (19%)
Query: 202 EIRVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVG-NDILGF 260
E+ + +VG+VD GK+TL LT D H E++ G + +G D
Sbjct: 4 EVNIGMVGHVDHGKTTLTKALTGVWTD-----------THSEELKRGISIRLGYADA--- 49
Query: 261 DSVGNVVNKPEHGSLDWVKICERSA------KVITFIDLAGHERYLKTTVFG 306
+ +C + ++F+D GHE + T + G
Sbjct: 50 -EIYKCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSG 100
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 33.4 bits (77), Expect = 0.16
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 203 IRVAVVGNVDAGKSTLLGVL 222
+ + +G+VDAGKSTL+G L
Sbjct: 8 LNLVFIGHVDAGKSTLVGRL 27
Score = 27.6 bits (62), Expect = 9.2
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 53 GMTKEHLGLALALSVP-VFVVVTKIDM 78
G T+EH LA L + + V V K+D+
Sbjct: 131 GQTREHAFLARTLGIKQLIVAVNKMDL 157
>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 = 32.4 bits (75), Expect = 0.19
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 192 RKRVESQDFLEIRVAVVGNVDAGKSTLLGVLT 223
+R S VA+VG +AGKSTL LT
Sbjct: 34 ARRKRSGVP---TVALVGYTNAGKSTLFNALT 62
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 33.1 bits (76), Expect = 0.19
Identities = 15/43 (34%), Positives = 18/43 (41%)
Query: 189 YLLRKRVESQDFLEIRVAVVGNVDAGKSTLLGVLTHGELDNGR 231
+ V VVG VD+GKSTL L + L GR
Sbjct: 60 ADTWESKSESAGKVGVVMVVGPVDSGKSTLTTYLANKLLARGR 102
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 32.2 bits (74), Expect = 0.21
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 204 RVAVVGNVDAGKSTLLGVLTH 224
R G+VD GKSTL+G L +
Sbjct: 1 RFITCGSVDDGKSTLIGRLLY 21
>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 = 32.0 bits (73), Expect = 0.22
Identities = 23/102 (22%), Positives = 33/102 (32%), Gaps = 38/102 (37%)
Query: 202 EIRVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVGNDILGFD 261
EI++ +VG+ + GKSTLL L K+ E + G T +
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLL-----------GNKIS--ITEYKPGTTRN--------- 38
Query: 262 SVGNVVNKPEHGSLDWVKICERSAKVITF--IDLAGHERYLK 301
+ E K F +D AG E Y
Sbjct: 39 --------------YVTTVIEEDGKTYKFNLLDTAGQEDYDA 66
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 32.8 bits (75), Expect = 0.27
Identities = 24/105 (22%), Positives = 37/105 (35%), Gaps = 34/105 (32%)
Query: 205 VAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVGNDILGFDSVG 264
+ G++D GK+TLL LT G D R E + G T +G +
Sbjct: 3 IGTAGHIDHGKTTLLKALTGGVTD-----------RLPEEKKRGITIDLGFYYRKLED-- 49
Query: 265 NVVNKPEHGSLDWVKICERSAKVITFIDLAGHERYLKTTVFGMTG 309
V+ FID+ GH ++ + G+ G
Sbjct: 50 ---------------------GVMGFIDVPGHPDFISNLLAGLGG 73
Score = 31.2 bits (71), Expect = 0.78
Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 7/100 (7%)
Query: 32 EASPADHSMLQSKVGANAGIVGMTKEHLGLALALSVP-VFVVVTKIDMCPPNVLQDTLKL 90
D+++L V A+ G++ T EHL + L + +V+TK D ++ +K
Sbjct: 70 GLGGIDYALLV--VAADEGLMAQTGEHLLILDLLGIKNGIIVLTKADRVDEARIEQKIK- 126
Query: 91 LVRILKSPGCRKVPVMNCLISPTEEQFDLLQKKIKSLIDN 130
+IL + T + L+ ++ L++
Sbjct: 127 --QILADLSLANAKIFKTSAK-TGRGIEELKNELIDLLEE 163
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 32.6 bits (75), Expect = 0.32
Identities = 17/30 (56%), Positives = 21/30 (70%), Gaps = 3/30 (10%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGE--LDNGR 231
RV +VG AGKSTL+ +L GE LD+GR
Sbjct: 31 RVCLVGRNGAGKSTLMKILN-GEVLLDDGR 59
>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 = 30.7 bits (70), Expect = 0.35
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGEL 227
RVA+VG + GKSTL+ LT ++
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKV 24
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 31.9 bits (74), Expect = 0.39
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 196 ESQDFLEIRVAVVGNVDAGKSTLL 219
E ++ I++A++G + GKS+L+
Sbjct: 167 EDEEDEPIKIAIIGRPNVGKSSLI 190
>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 = 32.1 bits (74), Expect = 0.40
Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 167 TTLEADCVLLRQR------KLDNGLTGQYLLRKRVESQDFLEIRVAVVGNVDAGKSTLLG 220
T LE D L+R+R +L+ + R+R + D VA+VG +AGKSTL
Sbjct: 150 TQLETDRRLIRERIAQLKKELEKVEKQRERQRRRRKRADVP--TVALVGYTNAGKSTLFN 207
Query: 221 VLT 223
LT
Sbjct: 208 ALT 210
>gnl|CDD|188098 TIGR00957, MRP_assoc_pro, multi drug resistance-associated protein
(MRP). This model describes multi drug
resistance-associated protein (MRP) in eukaryotes. The
multidrug resistance-associated protein is an integral
membrane protein that causes multidrug resistance when
overexpressed in mammalian cells. It belongs to ABC
transporter superfamily. The protein topology and
function was experimentally demonstrated by epitope
tagging and immunofluorescence. Insertion of tags in the
critical regions associated with drug efflux, abrogated
its function. The C-terminal domain seem to highly
conserved [Transport and binding proteins, Other].
Length = 1522
Score = 32.2 bits (73), Expect = 0.45
Identities = 17/33 (51%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 205 VAVVGNVDAGKSTLLGVLTHGELDNGRGHARQK 237
VAVVG V GKS+LL L E+D GH K
Sbjct: 667 VAVVGQVGCGKSSLLSALL-AEMDKVEGHVHMK 698
>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 = 31.6 bits (73), Expect = 0.48
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 196 ESQDFLEIRVAVVGNVDAGKSTLLGVLTHGE 226
E ++ I++A++G + GKSTL+ L GE
Sbjct: 166 EEEEDGPIKIAIIGRPNVGKSTLVNALL-GE 195
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 31.4 bits (72), Expect = 0.67
Identities = 12/20 (60%), Positives = 17/20 (85%)
Query: 203 IRVAVVGNVDAGKSTLLGVL 222
+ +AV+G+VD GKSTL+G L
Sbjct: 7 LNLAVIGHVDHGKSTLVGRL 26
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 30.7 bits (70), Expect = 0.69
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 7/72 (9%)
Query: 61 LALALSVPVFVVVTKIDMCPPNVLQDTLK-LLVRILKSPGCRKVPVMNCLISPTEEQF-- 117
L L +PV VV+TK D + L + + K P + ++ + ++
Sbjct: 130 FLLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQ----WVVLFSSLKKKGI 185
Query: 118 DLLQKKIKSLID 129
D L+ KI +
Sbjct: 186 DELKAKILEWLK 197
>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 = 30.6 bits (70), Expect = 0.69
Identities = 16/70 (22%), Positives = 24/70 (34%), Gaps = 2/70 (2%)
Query: 59 LGLALALSVPVFVVVTKIDMCPPNVLQDTLKLLVRILKSPGCRKVPVMNCLISPTEEQFD 118
L L +P +V+TK D + L LK + L P + S D
Sbjct: 103 LEFLEELGIPFLIVLTKADKLKKSELAKVLKKIKEELNLFNIL--PPVILFSSKKGTGID 160
Query: 119 LLQKKIKSLI 128
L+ I +
Sbjct: 161 ELRALIAEWL 170
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 31.4 bits (71), Expect = 0.70
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTH--GELD 228
I VA +G+VD GKST +G L + G +D
Sbjct: 8 INVAFIGHVDHGKSTTVGHLLYKCGAID 35
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 30.8 bits (70), Expect = 0.70
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVVVTKIDMCPPNVLQDTLKLLVRILKS 97
V A GI T E L + L P+ VV+ KID+ P + ++ + + L+
Sbjct: 99 VDAKKGIQTQTAECLVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKRLQK 151
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 31.4 bits (72), Expect = 0.70
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTH 224
+R G+VD GKSTL+G L +
Sbjct: 25 LRFITCGSVDDGKSTLIGRLLY 46
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 31.1 bits (71), Expect = 0.71
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTH 224
+R G+VD GKSTL+G L +
Sbjct: 7 LRFITCGSVDDGKSTLIGRLLY 28
>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 = 30.5 bits (70), Expect = 0.77
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 202 EIRVAVVGNVDAGKSTLL 219
I++A++G + GKS+LL
Sbjct: 2 PIKIAIIGRPNVGKSSLL 19
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 31.1 bits (71), Expect = 0.82
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 183 NGLTGQYLLRKRVESQDFLEI----RVAVVG-NVDAGKSTLLGVLTHGELDNGRGH 233
L+ Y R + L + R+ +VG N AGKSTLL +L GEL+ G
Sbjct: 7 ENLSLAYGDRP-LLENVSLTLNPGERIGLVGRNG-AGKSTLLKILA-GELEPDSGE 59
Score = 30.7 bits (70), Expect = 1.3
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 10/57 (17%)
Query: 187 GQYLLRK---RVESQDFLEIRVAVVGNVDAGKSTLLGVLTHGEL--DNGRGHARQKL 238
G+ LL+ R++ D R+A+VG AGKSTLL +L GEL +G + +
Sbjct: 334 GRLLLKDLSFRIDRGD----RIAIVGPNGAGKSTLLKLLA-GELGPLSGTVKVGETV 385
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 30.8 bits (70), Expect = 0.97
Identities = 26/111 (23%), Positives = 41/111 (36%), Gaps = 20/111 (18%)
Query: 202 EIRVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVG---NDIL 258
E+ + +VG+VD GK+TL L+ D RH E++ G T +G I
Sbjct: 10 EVNIGMVGHVDHGKTTLTKALSGVWTD-----------RHSEELKRGITIKLGYADAKIY 58
Query: 259 GFDSVGNVVNKPEHGSLDWVKICERSAK---VITFIDLAGHERYLKTTVFG 306
C + ++F+D GHE + T + G
Sbjct: 59 KCPECYRPECYTTEPK---CPNCGAETELVRRVSFVDAPGHETLMATMLSG 106
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 30.1 bits (69), Expect = 0.98
Identities = 14/24 (58%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 205 VAVVGNVDAGKSTLLGVLTHGELD 228
VA+VG V +GKS+LL L GEL+
Sbjct: 34 VAIVGPVGSGKSSLLSALL-GELE 56
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 259
Score = 30.4 bits (69), Expect = 1.0
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 205 VAVVGNVDAGKSTLLGVLTHGELDNGRG 232
+A++G AGKSTLL L+ GEL G
Sbjct: 30 LAILGPNGAGKSTLLKALS-GELSPDSG 56
>gnl|CDD|226355 COG3835, CdaR, Sugar diacid utilization regulator [Transcription /
Signal transduction mechanisms].
Length = 376
Score = 30.4 bits (69), Expect = 1.1
Identities = 26/141 (18%), Positives = 48/141 (34%), Gaps = 17/141 (12%)
Query: 61 LALALSVPVFVVVTKIDMCPPNVLQDTLKLLVRILKSPGCR----------KVPVMNCLI 110
L + LS P ++ + N L+ + R+++S R + V+ +
Sbjct: 153 LGIDLSKPRVAILVEG----YNEQLHNLQRMARLIQSSESRRNDVAILSLNERVVLKPAL 208
Query: 111 SPTEEQFDLLQKKIKSLI--DNGRGETIYDIGIGQDGGENGLKPDEYEASVATLQ-SLAT 167
S ++ K+I+ L+ G IG G YE++ TL+ L
Sbjct: 209 SAERWDREVHSKRIEKLLARAKAYGRLSLRIGAGNYFVGPDSLARSYESAKKTLEVGLKR 268
Query: 168 TLEADCVLLRQRKLDNGLTGQ 188
E+ +L L
Sbjct: 269 KPESRIYFYEDLRLPVLLDSL 289
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 30.7 bits (70), Expect = 1.2
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 202 EIRVAVVGNVDAGKSTLLGVLT 223
++ VA+VGN + GK+TL LT
Sbjct: 3 KLTVALVGNPNVGKTTLFNALT 24
>gnl|CDD|182569 PRK10584, PRK10584, putative ABC transporter ATP-binding protein
YbbA; Provisional.
Length = 228
Score = 30.1 bits (68), Expect = 1.2
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 185 LTGQYLLRKRVESQDFLEIRVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHE 244
LTG L+ KR E+ +A++G +GKSTLL +L LD+G + + H+
Sbjct: 26 LTGVELVVKRGET-------IALIGESGSGKSTLLAIL--AGLDDGSSGEVSLVGQPLHQ 76
Query: 245 M-ESGR 249
M E R
Sbjct: 77 MDEEAR 82
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 30.1 bits (68), Expect = 1.5
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVV-VTKIDMCPPNVLQDTLKLLVRILKS 97
V A G + T+EH+ LA + VP VV + K DM L + +++ VR L S
Sbjct: 106 VSATDGPMPQTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLS 159
>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 = 29.3 bits (66), Expect = 1.5
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 206 AVVGNVDAGKSTLLGVLTHGE 226
VVG GKS+LL L GE
Sbjct: 1 VVVGRGGVGKSSLLNALLGGE 21
>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 = 29.8 bits (68), Expect = 1.5
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 203 IRVAVVGNVDAGKSTLLGVLT 223
I +A+VGN + GK+TL LT
Sbjct: 1 ITIALVGNPNVGKTTLFNALT 21
>gnl|CDD|183055 PRK11247, ssuB, aliphatic sulfonates transport ATP-binding subunit;
Provisional.
Length = 257
Score = 29.6 bits (67), Expect = 1.6
Identities = 16/33 (48%), Positives = 18/33 (54%), Gaps = 6/33 (18%)
Query: 205 VAVVGNVDAGKSTLLGVL------THGELDNGR 231
VAVVG GKSTLL +L + GEL G
Sbjct: 41 VAVVGRSGCGKSTLLRLLAGLETPSAGELLAGT 73
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 30.2 bits (69), Expect = 1.7
Identities = 26/101 (25%), Positives = 36/101 (35%), Gaps = 39/101 (38%)
Query: 201 LEIR---VAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGR-TSSVGND 256
LE+R V ++G+VD GK+TLL + + G E+G T +G
Sbjct: 1 LELRPPVVTIMGHVDHGKTTLLDKIRKTNVAAG---------------EAGGITQHIGAY 45
Query: 257 ILGFDSVGNVVNKPEHGSLDWVKICERSAKVITFIDLAGHE 297
V + ITFID GHE
Sbjct: 46 Q--------------------VPLDVIKIPGITFIDTPGHE 66
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 29.9 bits (68), Expect = 2.0
Identities = 10/22 (45%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 119 LLQKKIKSLIDNG-RGETIYDI 139
LLQ+ + +L+DNG RG+ + D
Sbjct: 327 LLQEAVDALLDNGIRGQPMRDG 348
>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 = 29.5 bits (67), Expect = 2.1
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 204 RVAVVGNVDAGKSTLLGVL 222
+VA++G V +GKSTLL +L
Sbjct: 32 KVAIIGRVGSGKSTLLKLL 50
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 29.8 bits (67), Expect = 2.1
Identities = 14/23 (60%), Positives = 17/23 (73%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGE 226
RVA+VG + GKS+LL LTH E
Sbjct: 452 RVALVGRPNVGKSSLLNQLTHEE 474
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 29.0 bits (66), Expect = 2.3
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 59 LGLALALSVPVFVVVTKIDMCPPNVLQDTLKLLVRILK 96
+ +PV +V+TK D + L LK + + LK
Sbjct: 122 IEWLRERGIPVLIVLTKADKLKKSELNKQLKKIKKALK 159
>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 = 29.6 bits (67), Expect = 2.6
Identities = 15/29 (51%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGELDNGRG 232
RVA++G +GKSTLL L G LD +G
Sbjct: 363 RVAILGPSGSGKSTLLATLA-GLLDPLQG 390
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 29.3 bits (66), Expect = 2.8
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTH 224
+R G+VD GKSTL+G L H
Sbjct: 1 LRFLTCGSVDDGKSTLIGRLLH 22
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 28.1 bits (63), Expect = 2.9
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 204 RVAVVGNVDAGKSTLL 219
V VVG D+GK+TL+
Sbjct: 2 IVLVVGPKDSGKTTLI 17
>gnl|CDD|118011 pfam09474, Type_III_YscX, Type III secretion system YscX
(type_III_YscX). Members of this family are encoded
within bacterial type III secretion gene clusters. Among
all species with type III secretion, those with this
protein are found among those that target animal rather
than plant cells. The member of this family in Yersinia
was shown by mutation to be required for type III
secretion of Yops effector proteins and therefore is
believed to be part of the secretion machinery.
Length = 121
Score = 28.2 bits (63), Expect = 2.9
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 150 LKPDEYEASVATLQSLATT-----LEADCVLLRQRKLDNGL 185
L+P ++ ++ TL+ L L+A LL + D L
Sbjct: 70 LRPGDFRQALDTLRLLLQESGSPELQAAAELLESMQEDERL 110
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 29.0 bits (66), Expect = 3.1
Identities = 28/111 (25%), Positives = 47/111 (42%), Gaps = 20/111 (18%)
Query: 202 EIRVAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVGNDILGFD 261
E+ + +VG+VD GK+TL+ LT D RH E++ G T +G
Sbjct: 9 EVNIGMVGHVDHGKTTLVQALTGVWTD-----------RHSEELKRGITIRLGYADATIR 57
Query: 262 SVGNVVNKPEHGSLDWVKICERSA------KVITFIDLAGHERYLKTTVFG 306
+ +PE + + C + ++F+D GHE + T + G
Sbjct: 58 KCPD-CEEPEAYTTE--PKCPNCGSETELLRRVSFVDAPGHETLMATMLSG 105
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 29.2 bits (66), Expect = 3.2
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGELDNGRGHAR 235
+VA++G +GKSTLL +L G D +G
Sbjct: 366 KVAILGRSGSGKSTLLQLLA-GAWDPQQGSIT 396
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD 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. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 29.2 bits (66), Expect = 3.2
Identities = 16/29 (55%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGELDNGRG 232
RVA+VG AGKSTLL +L G +D G
Sbjct: 350 RVALVGPSGAGKSTLLNLLL-GFVDPTEG 377
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 29.2 bits (66), Expect = 3.3
Identities = 26/88 (29%), Positives = 37/88 (42%), Gaps = 21/88 (23%)
Query: 143 QDGGENGLK-PDEYEASVATLQSLATTLEADCVLLR------QRKLDNGLTGQYLLRKRV 195
+ GG G + P E + LE D +R +R+L+N + RK+
Sbjct: 140 RLGGGIGFRGPGETQ------------LETDRRRIRRRIAKLKRELENVEKAREPRRKKR 187
Query: 196 ESQDFLEIRVAVVGNVDAGKSTLLGVLT 223
VA+VG +AGKSTL LT
Sbjct: 188 SRSGIP--LVALVGYTNAGKSTLFNALT 213
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 28.9 bits (65), Expect = 3.4
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 203 IRVAVVGNVDAGKSTLLGVL 222
I + V+G+VD+GKST G L
Sbjct: 8 INLVVIGHVDSGKSTTTGHL 27
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 28.7 bits (65), Expect = 3.4
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVV-VTKIDMC 79
V A G + T+EHL LA + VP VV + K DM
Sbjct: 96 VSATDGPMPQTREHLLLARQVGVPYIVVFLNKADMV 131
>gnl|CDD|226647 COG4181, COG4181, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, ATPase component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 228
Score = 28.5 bits (64), Expect = 3.5
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 204 RVAVVGNVDAGKSTLLGVL 222
VA+VG +GKSTLL VL
Sbjct: 38 TVAIVGPSGSGKSTLLAVL 56
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 28.8 bits (65), Expect = 3.6
Identities = 19/39 (48%), Positives = 22/39 (56%), Gaps = 7/39 (17%)
Query: 204 RVAVVGNVDAGKSTLL----GVLT--HGELD-NGRGHAR 235
RVA++G AGKSTLL G LT G L NG+ H
Sbjct: 27 RVAILGPSGAGKSTLLNLIAGFLTPASGSLTLNGQDHTT 65
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 29.0 bits (66), Expect = 3.6
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 205 VAVVGNVDAGKSTLL 219
V V+G+VD GK+TLL
Sbjct: 9 VVVLGHVDHGKTTLL 23
>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 = 28.7 bits (65), Expect = 3.9
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 203 IRVAVVGNVDAGKSTLLGVLT 223
RVA+VG GKSTLL LT
Sbjct: 1 ARVALVGFPSVGKSTLLSKLT 21
>gnl|CDD|225010 COG2099, CobK, Precorrin-6x reductase [Coenzyme metabolism].
Length = 257
Score = 28.5 bits (64), Expect = 4.1
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 48 NAGIVGMTKEHLGLALALSVPVFVVVTKIDMCP-PNVLQDTLKLLVRIL 95
N+G G T E + A L +PV ++ ID + D L ++
Sbjct: 204 NSGGAGGTYEKIEAARELGIPVIMIERPIDYPAGFGDVTDLDAALAQLR 252
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 29.0 bits (65), Expect = 4.3
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVVVTKIDMCPPNVLQDTLK 89
V A+ G++ T E + A A +VP+ V + KID P D +K
Sbjct: 166 VAADDGVMPQTIEAISHAKAANVPIIVAINKIDK--PEANPDRVK 208
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 28.3 bits (64), Expect = 4.3
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 6/37 (16%)
Query: 61 LALALSV------PVFVVVTKIDMCPPNVLQDTLKLL 91
L LALSV P V+ K D+ L+ LK L
Sbjct: 151 LLLALSVQLRLGLPQIPVLNKADLLSEEELERILKWL 187
>gnl|CDD|221278 pfam11864, DUF3384, Domain of unknown function (DUF3384). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 422 to 486 amino acids in length. This domain is
found associated with pfam02145.
Length = 470
Score = 28.8 bits (65), Expect = 4.3
Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 9/65 (13%)
Query: 77 DMCPPNVLQD----TLKLLVRILKSPGCRKVP----VMNCLISPTE-EQFDLLQKKIKSL 127
D+ P + L+LL +K R + + + FDL + + L
Sbjct: 35 DLIDPEKPPEARRAGLELLTACIKRQDLRSPIERAEFFRVISDNSNPDDFDLRLEALIVL 94
Query: 128 IDNGR 132
DNGR
Sbjct: 95 TDNGR 99
>gnl|CDD|234189 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB
family. Type I protein secretion is a system in some
Gram-negative bacteria to export proteins (often
proteases) across both inner and outer membranes to the
extracellular medium. This is one of three proteins of
the type I secretion apparatus. Targeted proteins are
not cleaved at the N-terminus, but rather carry signals
located toward the extreme C-terminus to direct type I
secretion. This model is related to models TIGR01842 and
TIGR01846, and to bacteriocin ABC transporters that
cleave their substrates during export [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 694
Score = 28.7 bits (65), Expect = 4.4
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 204 RVAVVGNVDAGKSTLLGVL 222
+VA++G + +GKSTLL +L
Sbjct: 493 KVAIIGRIGSGKSTLLKLL 511
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 28.7 bits (65), Expect = 4.4
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 209 GNVDAGKSTLLGVLTH 224
G+VD GKSTL+G L H
Sbjct: 34 GSVDDGKSTLIGRLLH 49
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 28.7 bits (65), Expect = 4.5
Identities = 7/17 (41%), Positives = 14/17 (82%)
Query: 203 IRVAVVGNVDAGKSTLL 219
I++A++G + GKS+L+
Sbjct: 179 IKIAIIGRPNVGKSSLI 195
>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 = 27.8 bits (63), Expect = 4.6
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTH 224
I+V + G + GKS+LL L
Sbjct: 4 IKVVIAGKPNVGKSSLLNALAG 25
>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 = 27.8 bits (63), Expect = 4.9
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 11/64 (17%)
Query: 67 VPVFVVVTKIDMCPPNVLQDTLKLLVRILKS--PGCRKVPVMNCLISPTE-EQFDLLQKK 123
PV +V+ KID+ ++ L L+ LK P P IS + E D L +
Sbjct: 112 TPVILVLNKIDLVKD---KEDLLPLLEKLKELHPFAEIFP-----ISALKGENVDELLEY 163
Query: 124 IKSL 127
I
Sbjct: 164 IVEY 167
Score = 27.0 bits (61), Expect = 9.9
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 205 VAVVGNVDAGKSTLL 219
VA++G + GKSTLL
Sbjct: 6 VAIIGRPNVGKSTLL 20
>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 = 28.3 bits (64), Expect = 4.9
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 204 RVAVVGNVDAGKSTLLGVL------THGELD-NGR 231
R+ ++G AGKSTLL +L G + GR
Sbjct: 50 RIGLIGRNGAGKSTLLRLLAGIYPPDSGTVTVRGR 84
>gnl|CDD|219275 pfam07034, ORC3_N, Origin recognition complex (ORC) subunit 3
N-terminus. This family represents the N-terminus
(approximately 300 residues) of subunit 3 of the
eukaryotic origin recognition complex (ORC). Origin
recognition complex (ORC) is composed of six subunits
that are essential for cell viability. They collectively
bind to the autonomously replicating sequence (ARS) in a
sequence-specific manner and lead to the chromatin
loading of other replication factors that are essential
for initiation of DNA replication.
Length = 313
Score = 28.5 bits (64), Expect = 4.9
Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 5/76 (6%)
Query: 31 PEASPADHSMLQSKVGANAGIVGMTKEHLGLALALSVPVFVVVTKIDMCPPNVLQDTLKL 90
AD +++ + K++ +L S PV V++ + P VLQD
Sbjct: 146 GTVDVADEEEEARTEKSDSAVWYAKKKNFDSSLWRSPPVVVILKDFESFSPKVLQD---- 201
Query: 91 LVRILKSPGCRKVPVM 106
+ IL S +P +
Sbjct: 202 FILIL-SEYVSSLPFV 216
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 28.7 bits (65), Expect = 5.0
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 4/27 (14%)
Query: 201 LEI----RVAVVGNVDAGKSTLLGVLT 223
LEI +VA+VG +GKSTLL +L
Sbjct: 494 LEIPPGEKVAIVGRSGSGKSTLLKLLL 520
>gnl|CDD|182566 PRK10580, proY, putative proline-specific permease; Provisional.
Length = 457
Score = 28.6 bits (64), Expect = 5.2
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 43 SKVGANAGIVGMTKEHLGLALALSVPVFVVVT 74
++VG N +T +H+G+ A S+ FVV+T
Sbjct: 261 NQVGTNGSPFVLTFQHMGITFAASILNFVVLT 292
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 28.0 bits (63), Expect = 5.2
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 205 VAVVGNVDAGKSTLL 219
+AVVG+ AGKS++L
Sbjct: 1 IAVVGDQSAGKSSVL 15
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 27.9 bits (63), Expect = 5.3
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 204 RVAVVGNVDAGKSTLL 219
+AVVG AGKSTLL
Sbjct: 2 LLAVVGEFSAGKSTLL 17
>gnl|CDD|238054 cd00106, KISc, Kinesin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type), in some its is found in the middle (M-type),
or C-terminal (C-type). N-type and M-type kinesins are
(+) end-directed motors, while C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 328
Score = 28.4 bits (64), Expect = 5.8
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 287 VITFIDLAGHERYLKTTVFG 306
+ +DLAG ER KT G
Sbjct: 229 KLNLVDLAGSERAKKTGAEG 248
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.2 bits (64), Expect = 5.9
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTH 224
++V + G + GKS+LL L
Sbjct: 216 LKVVIAGRPNVGKSSLLNALLG 237
>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 = 28.0 bits (63), Expect = 5.9
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 68 PVFVVVTKIDMCPPNVLQDTLK 89
PV +V KID+ P +V + LK
Sbjct: 62 PVILVGNKIDLLPKDVKPNRLK 83
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 27.0 bits (60), Expect = 6.1
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 204 RVAVVGNVDAGKSTLLGVLTHGE 226
+V V+G+ +GKS+LL L GE
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGE 23
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 28.3 bits (63), Expect = 6.1
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVV-VTKIDMCPPNVLQDTLKLLVRILKS 97
V A G + TKEH+ LA + VP VV + K+D+ L + +++ +R L S
Sbjct: 155 VSAPDGPMPQTKEHILLARQVGVPSLVVFLNKVDVVDDEELLELVEMELRELLS 208
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 28.1 bits (63), Expect = 6.3
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 205 VAVVGNVDAGKSTLLGVLTHGELDNGRG 232
V V+G+ AGKSTLL + G+L G
Sbjct: 35 VTVIGSNGAGKSTLLNAIA-GDLKPTSG 61
>gnl|CDD|130529 TIGR01462, greA, transcription elongation factor GreA. The GreA
and GreB transcription elongation factors enable to
continuation of RNA transcription past template-encoded
arresting sites. Among the Proteobacteria, distinct
clades of GreA and GreB are found. GreA differs
functionally in that it releases smaller
oligonucleotides. Because members of the family outside
the Proteobacteria resemble GreA more closely than GreB,
the GreB clade (TIGR01461) forms a plausible outgroup
and the remainder of the GreA/B family, included in this
model, is designated GreA. In the Chlamydias and some
spirochetes, the region described by This model is found
as the C-terminal region of a much larger protein
[Transcription, Transcription factors].
Length = 151
Score = 27.6 bits (62), Expect = 6.6
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 113 TEEQFDLLQKKIKSLIDNGRGETIYDIGIGQDGG---ENGLKPDEYEA 157
T+E ++ L+++++ L R E +I ++ G EN EY A
Sbjct: 3 TQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENA----EYHA 46
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 28.0 bits (63), Expect = 7.0
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVV-VTKIDMCPPNVLQDTLKLLVRILKS 97
V A G + T+EH+ LA + VP VV + K+D+ L + +++ VR L S
Sbjct: 106 VAATDGPMPQTREHILLARQVGVPYLVVFLNKVDLVDDEELLELVEMEVRELLS 159
>gnl|CDD|131266 TIGR02211, LolD_lipo_ex, lipoprotein releasing system, ATP-binding
protein. This model represents LolD, a member of the
ABC transporter family (pfam00005). LolD is involved in
localization of lipoproteins in some bacteria. It works
with a transmembrane protein LolC, which in some species
is a paralogous pair LolC and LolE. Depending on whether
the residue immediately following the new, modified
N-terminal Cys residue, the nascent lipoprotein may be
carried further by LolA and LolB to the outer membrane,
or remain at the inner membrane. The top scoring
proteins excluded by this model include homologs from
the archaeal genus Methanosarcina [Protein fate, Protein
and peptide secretion and trafficking].
Length = 221
Score = 27.7 bits (62), Expect = 7.2
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 205 VAVVGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKHEMESGRTSSVGNDILGF 260
VA+VG+ +GKSTLL +L G LDN + ++ S + + N LGF
Sbjct: 34 VAIVGSSGSGKSTLLHLL--GGLDNPTSGEVLFNGQSLSKLSSNERAKLRNKKLGF 87
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 28.3 bits (64), Expect = 7.2
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 204 RVAVVGNVDAGKSTLLGVL 222
R+A+VG AGK++LL L
Sbjct: 378 RIALVGPSGAGKTSLLNAL 396
>gnl|CDD|184340 PRK13809, PRK13809, orotate phosphoribosyltransferase; Provisional.
Length = 206
Score = 27.5 bits (61), Expect = 7.9
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 143 QDGGENGLKPDEYE-ASVATLQSLATTLEADCVL 175
Q G L P + +SV T+ L +L + L
Sbjct: 158 QKGACQPLGPQGIKLSSVFTVPDLIKSLISYGKL 191
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 27.7 bits (63), Expect = 8.0
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 205 VAVVGNVDAGKSTLL 219
VA+VG + GKSTLL
Sbjct: 8 VAIVGRPNVGKSTLL 22
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 27.4 bits (62), Expect = 8.1
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 45 VGANAGIVGMTKEHLGLALALSVPVFVVVTKIDMCP 80
V A+ G++ T E + A A +VP+ V + KID
Sbjct: 80 VAADDGVMPQTIEAINHAKAANVPIIVAINKIDKPY 115
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 241
Score = 27.5 bits (62), Expect = 8.2
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 204 RVAVVGNVDAGKSTLLGVL 222
VA++G AGKSTLL L
Sbjct: 29 FVALIGPSGAGKSTLLRCL 47
>gnl|CDD|238663 cd01367, KISc_KIF2_like, Kinesin motor domain, KIF2-like group.
KIF2 is a protein expressed in neurons, which has been
associated with axonal transport and neuron development;
alternative splice forms have been implicated in
lysosomal translocation. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In this
subgroup the motor domain is found in the middle
(M-type) of the protein chain. M-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second (KIF2 may be slower). To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 322
Score = 27.6 bits (62), Expect = 8.3
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 288 ITFIDLAGHERY 299
++FIDLAG ER
Sbjct: 225 LSFIDLAGSERG 236
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 27.1 bits (61), Expect = 8.7
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 198 QDFLEIRVAV-VGNVDAGKSTLLGVLTHGELDNGRGHARQKLFRHKH 243
+ L+ + +V G GKSTLL L ELD G +KL R +H
Sbjct: 30 KPLLKGKTSVLAGQSGVGKSTLLNALL-PELDLRTGEISEKLGRGRH 75
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 27.6 bits (62), Expect = 9.3
Identities = 12/21 (57%), Positives = 13/21 (61%)
Query: 203 IRVAVVGNVDAGKSTLLGVLT 223
VA+VG GKSTLL LT
Sbjct: 64 ATVALVGFPSVGKSTLLNKLT 84
>gnl|CDD|223069 PHA03390, pk1, serine/threonine-protein kinase 1; Provisional.
Length = 267
Score = 27.5 bits (62), Expect = 9.4
Identities = 10/43 (23%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 160 ATLQSLATTLEADCVLLRQRKLDNGLTGQ-YLLRKRVESQDFL 201
+L L L+ +C ++++ KL +G G+ +L+ + + F+
Sbjct: 4 KSLSELVQFLK-NCEIVKKLKLIDGKFGKVSVLKHKPTQKLFV 45
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 27.2 bits (61), Expect = 9.4
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 11/49 (22%)
Query: 203 IRVAVVGNVDAGKSTLL----GVLT---HGELDNG----RGHARQKLFR 240
I + +G+V GK+TL+ GV T EL G+A K+++
Sbjct: 1 INIGTIGHVAHGKTTLVKALSGVWTVRHKEELKRNITIKLGYANAKIYK 49
>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 = 27.6 bits (62), Expect = 9.5
Identities = 23/71 (32%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 156 EASVATLQSLATTLEADCVLLRQRKLDNGLTGQYLLRKRVESQDFLEI----RVAVVGNV 211
E+ VAT S A+ + L+ +Y K S L I A+VG
Sbjct: 299 ESPVATPGSGEKAEVANEPPIEIS--LENLSFRYPDGKPALSDLNLTIKAGQLTALVGAS 356
Query: 212 DAGKSTLLGVL 222
AGKSTLL +L
Sbjct: 357 GAGKSTLLNLL 367
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 27.5 bits (62), Expect = 9.7
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 203 IRVAVVGNVDAGKSTLLGVLTH 224
++V ++G + GKS+LL L
Sbjct: 218 LKVVIIGRPNVGKSSLLNALLG 239
>gnl|CDD|233207 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein. [Transport and binding proteins,
Other].
Length = 617
Score = 27.7 bits (62), Expect = 9.8
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 205 VAVVGNVDAGKSTLLGVLTH 224
+AV+G+ AGK+TL+ L
Sbjct: 54 LAVMGSSGAGKTTLMNALAF 73
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 27.5 bits (62), Expect = 10.0
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 4/27 (14%)
Query: 201 LEI----RVAVVGNVDAGKSTLLGVLT 223
L+I +VA++G GKSTLL +LT
Sbjct: 361 LQIKAGEKVALLGRTGCGKSTLLQLLT 387
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
0.318 0.136 0.395
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,166,254
Number of extensions: 1561484
Number of successful extensions: 1894
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1883
Number of HSP's successfully gapped: 153
Length of query: 320
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 223
Effective length of database: 6,635,264
Effective search space: 1479663872
Effective search space used: 1479663872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)