RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7718
(184 letters)
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 182 bits (465), Expect = 1e-57
Identities = 73/163 (44%), Positives = 104/163 (63%), Gaps = 17/163 (10%)
Query: 20 VPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEGSAMEKSVSVGDNGNLYEEWL 79
+PVT+ITG+LG+GKTTLLN++L + KKIAVI+NEFGE + + D G EE +
Sbjct: 1 IPVTVITGFLGSGKTTLLNHLLANRDGKKIAVIVNEFGEVGIDGGA-LLSDTG---EEVV 56
Query: 80 ELKNGCLCCSVKDNGVKAIENLMLKRGKFDYILLETTGLADPGPIAKVFWLDKELGSDIY 139
EL NGC+CC+V+D+ + A+E L+ +R + D +++ETTGLADP P+ + F D EL +
Sbjct: 57 ELTNGCICCTVRDDLLPALERLLRRRDRPDRLVIETTGLADPAPVIQTFLTDPELADGVR 116
Query: 140 LDGIVTVVDCKHTIDVSFPDYFSIYLSILLSRLKELKVEQVHF 182
LDG+VTVVD H F + L + EL +Q+ F
Sbjct: 117 LDGVVTVVDAAH-----FLEG--------LDAIAELAEDQLAF 146
>gnl|CDD|239386 cd03112, CobW_like, The function of this protein family is unkown.
The amino acid sequence of YjiA protein in E. coli
contains several conserved motifs that characterizes it
as a P-loop GTPase. YijA gene is among the genes
significantly induced in response to DNA-damage caused
by mitomycin. YijA gene is a homologue of the CobW gene
which encodes the cobalamin synthesis protein/P47K.
Length = 158
Score = 167 bits (426), Expect = 8e-54
Identities = 72/138 (52%), Positives = 99/138 (71%), Gaps = 15/138 (10%)
Query: 21 PVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEGSAMEKSVSVGDN---GNLYEE 77
PVT++TG+LGAGKTTLLN+ILTEQH +KIAVI NEFGE V + DN + EE
Sbjct: 1 PVTVLTGFLGAGKTTLLNHILTEQHGRKIAVIENEFGE-------VGI-DNQLVVDTDEE 52
Query: 78 WLELKNGCLCCSVKDNGVKAI----ENLMLKRGKFDYILLETTGLADPGPIAKVFWLDKE 133
+E+ NGC+CC+V+ + ++A+ E L + FD I++ETTGLADPGP+A+ F++D+E
Sbjct: 53 IIEMNNGCICCTVRGDLIRALLDLLERLDAGKIAFDRIVIETTGLADPGPVAQTFFMDEE 112
Query: 134 LGSDIYLDGIVTVVDCKH 151
L LDG++T+VD KH
Sbjct: 113 LAERYLLDGVITLVDAKH 130
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 141 bits (357), Expect = 5e-43
Identities = 56/137 (40%), Positives = 85/137 (62%), Gaps = 15/137 (10%)
Query: 21 PVTIITGYLGAGKTTLLNYIL-TEQHDKKIAVILNEFGE----GSAMEKSVSVGDNGNLY 75
PVT++TG+LG+GKTTLL ++L + KIAVI+N+FGE + ++
Sbjct: 1 PVTVLTGFLGSGKTTLLEHLLEKNREGLKIAVIVNDFGETGIDAELLRET---------G 51
Query: 76 EEWLELKNGCLCCSVKDNGVKAIENLMLKRGKFDYILLETTGLADPGPIAKVFWLDKELG 135
+EL NGC+CC+++++ +E L+ + + D + +ETTGLA P P+A+ F EL
Sbjct: 52 ALIVELNNGCICCTLREDLSMVLEALLELKERLDLLFIETTGLACPAPVAQTFLSP-ELR 110
Query: 136 SDIYLDGIVTVVDCKHT 152
SD+ LDG+VTVVD T
Sbjct: 111 SDLGLDGVVTVVDVAET 127
>gnl|CDD|183183 PRK11537, PRK11537, putative GTP-binding protein YjiA; Provisional.
Length = 318
Score = 126 bits (319), Expect = 7e-36
Identities = 64/141 (45%), Positives = 88/141 (62%), Gaps = 13/141 (9%)
Query: 17 LQPVPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEGSAMEKSVSVGDN--GNL 74
+ P+ VT++TG+LGAGKTTLL +IL EQH KIAVI NEFGE VSV D G+
Sbjct: 1 MNPIAVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIENEFGE-------VSVDDQLIGDR 53
Query: 75 YEEWLELKNGCLCCSVKDNGVKAIENLM--LKRGK--FDYILLETTGLADPGPIAKVFWL 130
+ L NGC+CCS + A+ +L+ L +G FD +++E TG+ADPGPI + F+
Sbjct: 54 ATQIKTLTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFS 113
Query: 131 DKELGSDIYLDGIVTVVDCKH 151
+ L LDG++ +VD H
Sbjct: 114 HEVLCQRYLLDGVIALVDAVH 134
>gnl|CDD|233883 TIGR02475, CobW, cobalamin biosynthesis protein CobW. The family
of proteins identified by this model is generally found
proximal to the trimeric cobaltochelatase subunit CobN
which is essential for vitamin B12 (cobalamin)
biosynthesis. The protein contains an P-loop
nucleotide-binding loop in the N-terminal domain and a
histidine-rich region in the C-terminal portion
suggesting a role in metal binding, possibly as an
intermediary between the cobalt transport and chelation
systems. A broader CobW family is delineated by two PFAM
models which identify the N- and C-terminal domains
(pfam02492 and pfam07683) [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 341
Score = 124 bits (312), Expect = 1e-34
Identities = 60/131 (45%), Positives = 89/131 (67%), Gaps = 4/131 (3%)
Query: 20 VPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGE-GSAMEKSVSVGDNGNLYEEW 78
+PVTI+TG+LGAGKTTL+ ++L ++IAVI+NEFG+ G E + G G E
Sbjct: 4 IPVTIVTGFLGAGKTTLIRHLLQNAAGRRIAVIVNEFGDLGIDGEILKACGIEGCSEENI 63
Query: 79 LELKNGCLCCSVKDNGVKAIENLMLKRGKFDYILLETTGLADPGPIAKVF-WLDKELGSD 137
+EL NGC+CC+V D+ + + L+ +R + D+IL+ET+GLA P P+ + F W E+ S
Sbjct: 64 VELANGCICCTVADDFIPTMTKLLARRQRPDHILIETSGLALPKPLVQAFQW--PEIRSR 121
Query: 138 IYLDGIVTVVD 148
+ +DG+VTVVD
Sbjct: 122 VTVDGVVTVVD 132
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 34.4 bits (79), Expect = 0.024
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 24 IITGYLGAGKTTLLNYILT-------EQHDKKIAVILNEFGEGSAMEKSVSVGD 70
+I G G+GKTT L + E D I ++LN F EK +S+ D
Sbjct: 226 LILGAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLID 279
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 33.4 bits (77), Expect = 0.044
Identities = 15/50 (30%), Positives = 20/50 (40%)
Query: 15 AELQPVPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEGSAMEK 64
AE P+ ++ G GKT LL L E + VI + EK
Sbjct: 15 AERGTYPIIVVYGPRRCGKTALLREFLEELRELGYRVIYYDPLRREFEEK 64
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 33.1 bits (76), Expect = 0.065
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 23 TIITGYLGAGKTTLLNYILTE 43
T+I G G+GKTTLLN++L +
Sbjct: 437 TLIFGPTGSGKTTLLNFLLAQ 457
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The
conserved ATP-binding motifs common to Rad50 and the
ABC transporter family include the Walker A and Walker
B motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known
as the ABC signature sequence.
Length = 204
Score = 32.6 bits (75), Expect = 0.066
Identities = 24/73 (32%), Positives = 28/73 (38%), Gaps = 26/73 (35%)
Query: 21 PVTIITGYLGAGKTTL---LNYILT---------EQHDKKIAVILNEFGEGSAMEKSVSV 68
P+T+I G GAGKTT+ L Y LT HD K+ EG E V
Sbjct: 23 PLTLIVGQNGAGKTTIIEALKYALTGELPPNSKGGAHDPKL------IREG---EVRAQV 73
Query: 69 -----GDNGNLYE 76
NG Y
Sbjct: 74 KLAFENANGKKYT 86
>gnl|CDD|224044 COG1119, ModF, ABC-type molybdenum transport system, ATPase
component/photorepair protein PhrA [Inorganic ion
transport and metabolism].
Length = 257
Score = 32.7 bits (75), Expect = 0.086
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 24 IITGYLGAGKTTLLNYILTEQH--DKKIAVILNEFGEGS 60
I G GAGKTTLL+ + E + ++ FG+G
Sbjct: 61 AIVGPNGAGKTTLLSLLTGEHPPSSGDVTLLGRRFGKGE 99
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 32.2 bits (74), Expect = 0.11
Identities = 36/145 (24%), Positives = 57/145 (39%), Gaps = 26/145 (17%)
Query: 8 EVPDLVPAELQPVPVTIITGYLGAGKTTLLNYILTEQHDK-KIAVILNEFGEGSAMEKSV 66
D + + +P+ + G G+GKT L+ L D+ KIAVI +
Sbjct: 1 SKNDRLAEKNRPMLRIGVGGPPGSGKTALIEKTLRALKDEYKIAVITGDI---------Y 51
Query: 67 SVGDNGNLYEEW------LELKNGCLCCSVKDNGV-KAIENLMLKRGKFDYILLETTG-L 118
+ D L + +E G C + + +AIE L+L D + +E+ G L
Sbjct: 52 TKEDADRLRKLPGEPIIGVETGKG---CHLDASMNLEAIEELVLDFPDLDLLFIESVGNL 108
Query: 119 ADP-----GPIAKVFWLDKELGSDI 138
P G +V +D G DI
Sbjct: 109 VCPFSPDLGDHLRVVVIDVTEGEDI 133
>gnl|CDD|132060 TIGR03015, pepcterm_ATPase, putative secretion ATPase, PEP-CTERM
locus subfamily. Members of this protein are marked as
probable ATPases by the nucleotide binding P-loop motif
GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of
helicases, and extensive homology to ATPases of
MSHA-type pilus systems and to GspA proteins associated
with type II protein secretion systems [Protein fate,
Protein and peptide secretion and trafficking].
Length = 269
Score = 32.0 bits (73), Expect = 0.12
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 24 IITGYLGAGKTTLLNYIL--TEQHDKKIAVILN 54
+ITG +GAGKTTL+ +L +Q A ++N
Sbjct: 47 LITGEVGAGKTTLIRNLLKRLDQERVVAAKLVN 79
>gnl|CDD|132027 TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit,
DevA family. Members of this protein family are found
mostly in the Cyanobacteria, but also in the
Planctomycetes. Cyanobacterial examples are involved in
heterocyst formation, by which some fraction of members
of the colony undergo a developmental change and become
capable of nitrogen fixation. The DevBCA proteins are
thought export of either heterocyst-specific
glycolipids or an enzyme essential for formation of the
laminated layer found in heterocysts.
Length = 220
Score = 31.9 bits (73), Expect = 0.12
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 16 ELQPVPVTIITGYLGAGKTTLLNYI 40
E+ P + I+TG G+GKTTLL I
Sbjct: 27 EINPGEIVILTGPSGSGKTTLLTLI 51
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 31.8 bits (73), Expect = 0.16
Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 2/31 (6%)
Query: 24 IITGYLGAGKTTLLNYILTE--QHDKKIAVI 52
+++G G+GKTTLL +L E D++I I
Sbjct: 133 LVSGGTGSGKTTLLYALLNEINTDDERIVTI 163
>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 = 31.9 bits (73), Expect = 0.20
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 7 SEVPDLVPAELQPVPVTIITGYLGAGKTTLLNYIL 41
V + P + G GAGK+TLLN +L
Sbjct: 335 RPALRPVSFTVPPGERVALVGPSGAGKSTLLNLLL 369
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 31.1 bits (71), Expect = 0.21
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 23 TIITGYLGAGKTTLLNYILTE-QHDKKIAVI 52
+I+G G+GKTTLLN +L D++I I
Sbjct: 28 ILISGGTGSGKTTLLNALLAFIPPDERIITI 58
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 31.0 bits (71), Expect = 0.21
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 14/49 (28%)
Query: 24 IITGYLGAGKTTL-------LNY-------ILTEQHDKKIAVILNEFGE 58
++ G +GAGKTT+ L ++ ++ I I E GE
Sbjct: 3 VLIGMMGAGKTTVGRLLAKALGLPFVDLDELIEQRAGMSIPEIFAEEGE 51
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 30.9 bits (70), Expect = 0.24
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 14/48 (29%)
Query: 25 ITGYLGAGKTTL--------------LNYILTEQHDKKIAVILNEFGE 58
+ GY+GAGKTTL L++ + + K + I E GE
Sbjct: 6 LVGYMGAGKTTLGKALARELGLSFIDLDFFIENRFHKTVGDIFAERGE 53
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 31.3 bits (71), Expect = 0.29
Identities = 12/16 (75%), Positives = 13/16 (81%)
Query: 25 ITGYLGAGKTTLLNYI 40
ITG GAGKTTLL+ I
Sbjct: 35 ITGPTGAGKTTLLDAI 50
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 30.9 bits (70), Expect = 0.31
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 21 PVTIITGYLGAGKTTLLNYILTE--QHDKKIAVI 52
P +I G G+GK+TLL + ++ VI
Sbjct: 2 PNMLIVGPSGSGKSTLLKLLALRLLARGGRVIVI 35
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 31.1 bits (71), Expect = 0.31
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 5 SDSEVPDLVPAELQPVPVTIITGYLGAGKTTLLNYIL 41
D ++ +L AE P+PV + G GK+TL+N IL
Sbjct: 23 DDEDLAELEAAEGGPLPVVAVVGRPNVGKSTLVNRIL 59
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 261
Score = 30.6 bits (69), Expect = 0.34
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 20 VPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNE 55
+P+ I+TGY G+GKTT + E + VI E
Sbjct: 1 MPLIILTGYPGSGKTTFAKELAKELRQEIWRVIHLE 36
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 30.0 bits (67), Expect = 0.36
Identities = 28/152 (18%), Positives = 49/152 (32%), Gaps = 17/152 (11%)
Query: 22 VTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEGSAMEKSVSVGDNGNLYEEWLEL 81
V +I G G+GKTTL + E VI + G++ L
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYID-------------GEDILEEVLDQLL 50
Query: 82 KNGCLCCSVKDNGVKAIENL--MLKRGKFDYILL-ETTGLADPGPIAKVFWL-DKELGSD 137
+G + + ++ K D ++L E T L D A + L + L
Sbjct: 51 LIIVGGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLL 110
Query: 138 IYLDGIVTVVDCKHTIDVSFPDYFSIYLSILL 169
+ + +TV+ + P +
Sbjct: 111 LKSEKNLTVILTTNDEKDLGPALLRRRFDRRI 142
>gnl|CDD|200328 TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase.
Members of this protein family comprise a distinct
clade of putative ATPase associated with an integral
membrane complex likely to act in pilus formation,
secretion, or conjugal transfer. The association of most
members with a nearby gene for a DEAH-box helicase
suggests a role in conjugal transfer.
Length = 340
Score = 30.8 bits (70), Expect = 0.36
Identities = 11/30 (36%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 24 IITGYLGAGKTTLLNYILTEQH-DKKIAVI 52
+++G G+GKTTLL+ +L D++I ++
Sbjct: 182 LVSGGTGSGKTTLLSALLALVPPDERIVLV 211
>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 = 30.1 bits (69), Expect = 0.40
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 18 QPVPVTIITGYLGAGKTTLLNYILT 42
VP + GY AGK+TL N LT
Sbjct: 39 SGVPTVALVGYTNAGKSTLFNA-LT 62
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 29.9 bits (68), Expect = 0.48
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 13 VPAELQPVPVTIITGYLGAGKTTLLNYILTEQHDKKIAVI 52
P + +PV V ++ G GAGKT L +L E + I
Sbjct: 6 KPPQERPVAV-LLGGQPGAGKTELARALLEELGGGNVVRI 44
>gnl|CDD|235492 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 30.1 bits (69), Expect = 0.50
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 21 PVTI-ITGYLGAGKTTLLNYILTEQHDKKIAVI 52
P+ I I G G+GKTT+ + I E D+ IAVI
Sbjct: 6 PIIIGIAGGSGSGKTTVASTIYEELGDESIAVI 38
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 30.4 bits (69), Expect = 0.52
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 10 PDLVPAELQPVPVTIITGYLGAGKTTLLNYILTE--QHDKKIAVI 52
+ V V ++ G + +GK+TL Y+ + +K+A+I
Sbjct: 63 WESKSESAGKVGVVMVVGPVDSGKSTLTTYLANKLLARGRKVAII 107
>gnl|CDD|226425 COG3910, COG3910, Predicted ATPase [General function prediction
only].
Length = 233
Score = 29.7 bits (67), Expect = 0.60
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 9/42 (21%)
Query: 7 SEVPDLVPA--------ELQPVPVTIITGYLGAGKTTLLNYI 40
E P +PA E + P+T ITG G+GK+TLL I
Sbjct: 17 EEYPFSLPAFRHLEERLEFRA-PITFITGENGSGKSTLLEAI 57
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 29.2 bits (66), Expect = 0.61
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 22 VTIITGYLGAGKTTLLNYILTEQHDKKIAVI 52
+ ++TG G+GKTTLL + + ++++ +
Sbjct: 6 IGVLTGESGSGKTTLLRRLARQLPNRRVVYV 36
>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 = 29.7 bits (68), Expect = 0.63
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 23 TIITGYLGAGKTTLLNYILTE 43
I G +G+GK++LL+ +L E
Sbjct: 34 VAIVGPVGSGKSSLLSALLGE 54
>gnl|CDD|182829 PRK10908, PRK10908, cell division protein FtsE; Provisional.
Length = 222
Score = 29.8 bits (67), Expect = 0.65
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 17 LQPVPVTIITGYLGAGKTTLLNYI 40
++P + +TG+ GAGK+TLL I
Sbjct: 25 MRPGEMAFLTGHSGAGKSTLLKLI 48
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases
are sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and
tend to undergo disruption to form pseudogenes. A
unique feature of all eukaryotic and certain bacterial
KAP NTPases is the presence of two or four
transmembrane helices inserted into the P-loop NTPase
domain. These transmembrane helices anchor KAP NTPases
in the membrane such that the P-loop domain is located
on the intracellular side.
Length = 301
Score = 30.1 bits (68), Expect = 0.69
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 6/63 (9%)
Query: 12 LVPAELQPVPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEF------GEGSAMEKS 65
LV L P V + G G+GKT+ LN + E + + F G+ A+
Sbjct: 12 LVEPSLAPGFVIGLYGAWGSGKTSFLNLLEDELKEFPEEFHIVYFDPWLFSGQDDAVASL 71
Query: 66 VSV 68
++
Sbjct: 72 LAA 74
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 30.1 bits (68), Expect = 0.75
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 21 PVTIITGYLGAGKTTLLNYIL 41
+ +I G GAGK+++L+ I
Sbjct: 26 GIFLIVGPNGAGKSSILDAIT 46
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 29.4 bits (66), Expect = 0.77
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 21 PVTIITGYLGAGKTTLLN---YILTEQHDK 47
+T+I G G+GKTT+L+ + L + +
Sbjct: 20 GLTLIYGPNGSGKTTILDAIRWALYGKTSR 49
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 30.0 bits (68), Expect = 0.80
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 23 TIITGYLGAGKTTLLNYILTEQ 44
T+I G GAGKT LL+++L +
Sbjct: 439 TLIIGPTGAGKTVLLSFLLAQA 460
>gnl|CDD|139913 PRK13853, PRK13853, type IV secretion system protein VirB4;
Provisional.
Length = 789
Score = 29.8 bits (67), Expect = 0.81
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 11 DLVPAELQPVPVTIITGYLGAGKTTLLNYIL 41
D +P E V +T I G +G GKTTL+ +IL
Sbjct: 418 DYIPHE-HDVGMTAIFGPIGRGKTTLMTFIL 447
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related
to the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 30.0 bits (67), Expect = 0.84
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 14/44 (31%)
Query: 21 PVTIITGYLGAGKTTL---LNYILTEQ-----------HDKKIA 50
P+TI+ G GAGKTT+ L YI T HD K+A
Sbjct: 29 PLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVA 72
>gnl|CDD|227268 COG4932, COG4932, Predicted outer membrane protein [Cell envelope
biogenesis, outer membrane].
Length = 1531
Score = 29.8 bits (67), Expect = 0.91
Identities = 17/59 (28%), Positives = 22/59 (37%)
Query: 19 PVPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEGSAMEKSVSVGDNGNLYEE 77
PV TI A K T N + E D + E G+ E+ V N Y+E
Sbjct: 1411 PVDFTIEFNQEEALKVTKTNKLFIEFEDSIGNQLNAEEHTGNVGEEYVFKAKNPGHYKE 1469
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 29.1 bits (66), Expect = 0.98
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 22 VTIITGYLGAGKTTLLNYILTEQH 45
+++ G G GK+TLLN +L E
Sbjct: 37 TSVLAGQSGVGKSTLLNALLPELD 60
>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 = 29.4 bits (67), Expect = 1.0
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 18 QPVPVTIITGYLGAGKTTLLNYILTE 43
VP + GY AGK+TL N LT
Sbjct: 187 ADVPTVALVGYTNAGKSTLFNA-LTG 211
>gnl|CDD|223040 PHA03311, PHA03311, helicase-primase subunit BBLF4; Provisional.
Length = 782
Score = 29.5 bits (67), Expect = 1.1
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 2 DSDSDSEVPDLVPAELQPVPVTIITGYLGAGKTT 35
S+ D E P +P P V +ITG GAGK+T
Sbjct: 53 RSEFDPETPLDLPPPFLPFSVYLITGTAGAGKST 86
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the
form of molybdenum cofactor (Moco) which is associated
with the metabolism of nitrogen, carbon and sulfur by
redox active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe
and mog. The mob locus contains mobA and mobB genes.
MobB catalyzes the attachment of the guanine
dinucleotide to molybdopterin.
Length = 159
Score = 28.8 bits (65), Expect = 1.1
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 25 ITGYLGAGKTTLLNYI---LTEQHDKKIAVI 52
GY G+GKTTLL + L+ + ++AVI
Sbjct: 6 FVGYSGSGKTTLLEKLIPALSARG-LRVAVI 35
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 28.7 bits (65), Expect = 1.1
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 24 IITGYLGAGKTTLLNYILTEQHDK 47
+++G G GK+TLL +L E
Sbjct: 3 VLSGPSGVGKSTLLKRLLEEFDPN 26
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 29.0 bits (66), Expect = 1.1
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 7 SEVPDLVPAELQPV---PVTIITGYLGAGKTTLLNYILTEQH 45
S EL+P+ VT++ G G GK+TLLN + +
Sbjct: 148 SAKEGEGLDELKPLLAGKVTVLAGQSGVGKSTLLNALAPDLE 189
>gnl|CDD|224677 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 28.8 bits (65), Expect = 1.2
Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 25 ITGYLGAGKTTLLNYILTE--QHDKKIAVI 52
I GY +GKTTL+ ++ + ++A +
Sbjct: 7 IVGYKNSGKTTLIEKLVRKLKARGYRVATV 36
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 157
Score = 28.7 bits (65), Expect = 1.2
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 22 VTIITGYLGAGKTTLLNYIL 41
+ + G G+GK+TLL I
Sbjct: 27 IVALVGPNGSGKSTLLRAIA 46
>gnl|CDD|164822 PHA00547, PHA00547, hypothetical protein.
Length = 337
Score = 29.1 bits (65), Expect = 1.3
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 21 PVTIITGYLGAGKTTLLNYI 40
P+++I G LG GKT LL Y+
Sbjct: 76 PLSVIIGKLGTGKTLLLTYL 95
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD.
This model describes the DndB protein encoded by an
operon associated with a sulfur-containing modification
to DNA. The operon is sporadically distributed in
bacteria, much like some restriction enzyme operons.
DndD is described as a putative ATPase. The small
number of examples known so far include species from
among the Firmicutes, Actinomycetes, Proteobacteria,
and Cyanobacteria [DNA metabolism,
Restriction/modification].
Length = 650
Score = 29.3 bits (66), Expect = 1.4
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 19 PVPVTIITGYLGAGKTTLLNYI 40
P P+ +I G GAGKTTLL+ I
Sbjct: 27 PKPIILIGGLNGAGKTTLLDAI 48
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 28.7 bits (65), Expect = 1.6
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 22 VTIITGYLGAGKTTLLN 38
V ++ G G GKTT L
Sbjct: 20 VAVVQGPAGTGKTTSLK 36
>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 = 1.6
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 21 PVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFG 57
PV I G++ GKT+LL+ I +K V E G
Sbjct: 88 PVVTIMGHVDHGKTSLLDSI------RKTKVAQGEAG 118
>gnl|CDD|226426 COG3911, COG3911, Predicted ATPase [General function prediction
only].
Length = 183
Score = 28.3 bits (63), Expect = 1.6
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 22 VTIITGYLGAGKTTLLN 38
I+TG GAGKTTLL
Sbjct: 11 RFILTGGPGAGKTTLLA 27
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 28.2 bits (64), Expect = 1.7
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 14/49 (28%)
Query: 24 IITGYLGAGKTT-------LLNY-------ILTEQHDKKIAVILNEFGE 58
++ G++GAGK+T L Y ++ + K I I E GE
Sbjct: 8 VLIGFMGAGKSTIGRLLAKRLGYDFIDTDHLIEARAGKSIPEIFEEEGE 56
>gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model
describes glucan exporter ATP binding protein in
bacteria. It belongs to the larger ABC transporter
superfamily with the characteristic ATP binding motif.
The In general, this protein is in some ways implicated
in osmoregulation and suggested to participate in the
export of glucan from the cytoplasm to periplasm. The
cyclic beta-1,2-glucan in the bactrerial periplasmic
space is suggested to confer the property of high
osmolority. It has also been demonstrated that mutants
in this loci have lost functions of virulence and
motility. It is unclear as to how virulence and
osmoadaptaion are related [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 585
Score = 28.7 bits (64), Expect = 1.8
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 25 ITGYLGAGKTTLLNYILTEQHDKKIAVIL 53
I G GAGKTTL+N +L +D + IL
Sbjct: 366 IVGPTGAGKTTLIN-LLQRVYDPTVGQIL 393
>gnl|CDD|226628 COG4148, ModC, ABC-type molybdate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 352
Score = 28.8 bits (65), Expect = 1.8
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 22 VTIITGYLGAGKTTLLNYI 40
+T + G G+GKT+L+N I
Sbjct: 26 ITALFGPSGSGKTSLINMI 44
>gnl|CDD|213205 cd03238, ABC_UvrA, ATP-binding cassette domain of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is
a multistep ATP-dependent reaction that requires the
UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are
ATPases, with UvrA having two ATP binding sites, which
have the characteristic signature of the family of ABC
proteins, and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 176
Score = 28.1 bits (63), Expect = 1.8
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 8 EVPDLVPAELQPVPVTI-------ITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGE 58
V LQ + V+I +TG G+GK+TL+N L ++ L +F
Sbjct: 2 TVSGANVHNLQNLDVSIPLNVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSR 59
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme [General
function prediction only].
Length = 255
Score = 28.5 bits (64), Expect = 1.9
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 90 VKDNGVKAIENLMLKRGKFDYILLETTGLADPGPIAKVFWLDKELGSDIYL 140
V++ K LK G D I++ LAD G ++ L K G+ +YL
Sbjct: 73 VREYVPKI-----LKAGI-DVIVMSVGALADEGLRERLRELAKCGGARVYL 117
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 26.4 bits (59), Expect = 1.9
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 22 VTIITGYLGAGKTTLLNYILT 42
T++TG G+GK+TL++ I T
Sbjct: 23 GTLLTGPSGSGKSTLIDAIQT 43
>gnl|CDD|213246 cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD. SbcCD
and other Mre11/Rad50 (MR) complexes are implicated in
the metabolism of DNA ends. They cleave ends sealed by
hairpin structures and are thought to play a role in
removing protein bound to DNA termini.
Length = 213
Score = 28.4 bits (64), Expect = 2.0
Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 11/66 (16%)
Query: 16 ELQPVPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEGSAMEKSVSVGDNGNLY 75
L + +I G GAGK+T+L+ A+ +G+ + ++
Sbjct: 24 GLDNNGLFLICGPTGAGKSTILD-----------AITYALYGKTPRYGRQENLRSVFAPG 72
Query: 76 EEWLEL 81
E+ E+
Sbjct: 73 EDTAEV 78
>gnl|CDD|188353 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC
transporter, lactococcin 972 group. A gene pair with a
fairly wide distribution consists of a polypeptide
related to the lactococcin 972 (see TIGR01653) and
multiple-membrane-spanning putative immunity protein
(see TIGR01654). This model represents a small clade
within the ABC transporters that regularly are found
adjacent to these bacteriocin system gene pairs and are
likely serve as export proteins [Cellular processes,
Toxin production and resistance, Transport and binding
proteins, Unknown substrate].
Length = 206
Score = 28.4 bits (64), Expect = 2.0
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 25 ITGYLGAGKTTLLNYI-LTEQHDK 47
I G G+GK+TLLN I L E+ D
Sbjct: 29 IIGESGSGKSTLLNIIGLLEKFDS 52
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication,
recombination, and repair].
Length = 845
Score = 28.8 bits (65), Expect = 2.0
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 21 PVTIITGYLGAGKTTLLNYILTEQ 44
V II G G+GKTT L L E+
Sbjct: 66 QVVIIVGETGSGKTTQLPQFLLEE 89
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 28.7 bits (65), Expect = 2.0
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 25 ITGYLGAGKTTLLNYIL 41
+ G GAGKT+LLN +L
Sbjct: 381 LVGPSGAGKTSLLNALL 397
>gnl|CDD|216586 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that
catalyzes the phosphorylation of adenylylsulphate to
3'-phosphoadenylylsulfate. This domain contains an ATP
binding P-loop motif.
Length = 157
Score = 28.0 bits (63), Expect = 2.0
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 21 PVTI-ITGYLGAGKTTLLNYILTEQHDKKIAVIL 53
TI TG G+GK+T+ N + + + I+V +
Sbjct: 2 GCTIWFTGLSGSGKSTIANALERKLFAQGISVYV 35
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 27.9 bits (63), Expect = 2.1
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 22 VTIITGYLGAGKTTLLNYIL 41
V ++TG G GKTT+LN L
Sbjct: 4 VVVVTGVPGVGKTTVLNKAL 23
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 28.6 bits (64), Expect = 2.1
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 21 PVTIITGYLGAGKTTLLNYIL 41
++ITG G GKTT + +L
Sbjct: 161 NFSLITGGPGTGKTTTVARLL 181
>gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This
model describes FtsE, a member of the ABC transporter
ATP-binding protein family. This protein, and its
permease partner FtsX, localize to the division site.
In a number of species, the ftsEX gene pair is located
next to FtsY, the signal recognition particle-docking
protein [Cellular processes, Cell division].
Length = 214
Score = 28.0 bits (63), Expect = 2.2
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 25 ITGYLGAGKTTLLNYI 40
+TG GAGKTTLL +
Sbjct: 33 LTGPSGAGKTTLLKLL 48
>gnl|CDD|184491 PRK14079, recF, recombination protein F; Provisional.
Length = 349
Score = 28.2 bits (63), Expect = 2.3
Identities = 22/55 (40%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 11 DLVPAELQPVP-VTIITGYLGAGKTTLLNYI---LTEQHDKKIAVILNEFGEGSA 61
+L P L P VT + G AGKT LL I LT + L FGEG A
Sbjct: 13 NLAPPTLAFPPGVTAVVGENAAGKTNLLEAIYLALTGELPNGRLADLVRFGEGEA 67
>gnl|CDD|224201 COG1282, PntB, NAD/NADP transhydrogenase beta subunit [Energy
production and conversion].
Length = 463
Score = 28.5 bits (64), Expect = 2.4
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 24 IITGYLGAGKTTLLNYILTEQHDKK-IAVILNEFGEGSAMEKSVSVGD 70
II G L +L+YI+ ++ I+VI FG K S D
Sbjct: 253 IIAGSLVGSSGAILSYIMCRCMNRSFISVIAGGFGGEVGEVKEGSAED 300
>gnl|CDD|225586 COG3044, COG3044, Predicted ATPase of the ABC class [General
function prediction only].
Length = 554
Score = 28.3 bits (63), Expect = 2.4
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 12/51 (23%)
Query: 8 EVPDLVPAELQ----------PVP--VTIITGYLGAGKTTLLNYILTEQHD 46
E P+ +P E++ +P +T+ITG GKTTLL I +
Sbjct: 218 EAPESLPVEIELPNGKEVVGMGIPQGITLITGGNFHGKTTLLTAIERGVDN 268
>gnl|CDD|213222 cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of
the transporters involved in export of lipoprotein and
macrolide, and cell division protein. This family is
comprised of MJ0796 ATP-binding cassette,
macrolide-specific ABC-type efflux carrier (MacAB), and
proteins involved in cell division (FtsE), and release
of lipoproteins from the cytoplasmic membrane (LolCDE).
They are clustered together phylogenetically. MacAB is
an exporter that confers resistance to macrolides,
while the LolCDE system is not a transporter at all. An
FtsE null mutants showed filamentous growth and
appeared viable on high salt medium only, indicating a
role for FtsE in cell division and/or salt transport.
The LolCDE complex catalyzes the release of
lipoproteins from the cytoplasmic membrane prior to
their targeting to the outer membrane.
Length = 218
Score = 27.8 bits (63), Expect = 2.5
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 22 VTIITGYLGAGKTTLLNYI 40
I G G+GK+TLLN +
Sbjct: 32 FVAIVGPSGSGKSTLLNIL 50
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 27.7 bits (63), Expect = 2.5
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 24 IITGYLGAGKTTLLNYILTEQHD 46
+++G GAGK+TL+ +L +
Sbjct: 9 VLSGPSGAGKSTLVKALLERDPN 31
>gnl|CDD|183063 PRK11264, PRK11264, putative amino-acid ABC transporter
ATP-binding protein YecC; Provisional.
Length = 250
Score = 28.2 bits (63), Expect = 2.6
Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 16 ELQPVPVTIITGYLGAGKTTLLNYI-LTEQHD 46
E++P V I G G+GKTTLL I L EQ +
Sbjct: 25 EVKPGEVVAIIGPSGSGKTTLLRCINLLEQPE 56
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 28.5 bits (64), Expect = 2.6
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 19 PVPVTIITGYLGAGKTTLLN 38
P +T + G GAGKTTLLN
Sbjct: 788 PGTLTALMGASGAGKTTLLN 807
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 925
Score = 28.4 bits (64), Expect = 2.7
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 23 TIITGYLGAGKTTLLNYIL 41
T ITG G+GK+TL+N L
Sbjct: 637 TCITGVSGSGKSTLINDTL 655
>gnl|CDD|235450 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
Length = 288
Score = 28.1 bits (64), Expect = 2.7
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 15 AELQPVPVTIITGYLGAGKTTLLN 38
P+ + I+TG GAGK+ L
Sbjct: 1 MTAAPMRLVIVTGLSGAGKSVALR 24
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They
export degradative enzymes by using a type I protein
secretion system and lack an N-terminal signal peptide,
but contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and
an outer membrane protein (OMP). For the HlyA
transporter complex, HlyB (ABC transporter) and HlyD
(MFP) reside in the inner membrane of E. coli. The OMP
component is TolC, which is thought to interact with
the MFP to form a continuous channel across the
periplasm from the cytoplasm to the exterior. HlyB
belongs to the family of ABC transporters, which are
ubiquitous, ATP-dependent transmembrane pumps or
channels. The spectrum of transport substrates ranges
from inorganic ions, nutrients such as amino acids,
sugars, or peptides, hydrophobic drugs, to large
polypeptides, such as HlyA.
Length = 173
Score = 27.6 bits (62), Expect = 2.9
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 16 ELQPVPVTIITGYLGAGKTTLLNYIL 41
++P I G G+GK+TL IL
Sbjct: 24 SIEPGESLAIIGPSGSGKSTLARLIL 49
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 28.3 bits (63), Expect = 2.9
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 21 PVTIITGYLGAGKTTLLNYILTEQHDKK 48
P+ I G++ GKTTLL+ I Q +K
Sbjct: 245 PIVTILGHVDHGKTTLLDKIRKTQIAQK 272
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 27.6 bits (62), Expect = 3.0
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 14/43 (32%)
Query: 30 GAGKTTL-------LNY-------ILTEQHDKKIAVILNEFGE 58
GAGK+T+ L + ++ IA I E GE
Sbjct: 2 GAGKSTIGRLLAKALGLPFIDTDQEIEKRTGMSIAEIFEEEGE 44
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 27.1 bits (61), Expect = 3.0
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 21 PVTIITGYLGAGKTTLLNYILTEQHDKKIAVI 52
+ +ITG GKTTLL L E + I I
Sbjct: 3 KIIVITGPRQVGKTTLLLQFLKELLSENILYI 34
>gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK;
Provisional.
Length = 258
Score = 28.0 bits (63), Expect = 3.0
Identities = 15/30 (50%), Positives = 17/30 (56%), Gaps = 5/30 (16%)
Query: 11 DLVPAELQPVPVTIITGYLGAGKTTLLNYI 40
DL P E V I G G+GKTTLLN +
Sbjct: 28 DLYPGE-----VLGIVGESGSGKTTLLNAL 52
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an
all alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of
Type IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 28.1 bits (63), Expect = 3.0
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 23 TIITGYLGAGKTTLLNYILTE---QHDKKIAVILN 54
T+I G G GKTT + +L + D+ I N
Sbjct: 45 TMIIGTTGTGKTTQIRELLASIRARGDRAIIYDPN 79
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 27.0 bits (60), Expect = 3.0
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 22 VTIITGYLGAGKTTLLNYILTE--QHDKKIAVI 52
V ++TG G GKTTL + + K++ +I
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33
>gnl|CDD|225265 COG2401, COG2401, ABC-type ATPase fused to a predicted
acetyltransferase domain [General function prediction
only].
Length = 593
Score = 28.3 bits (63), Expect = 3.0
Identities = 18/53 (33%), Positives = 26/53 (49%)
Query: 16 ELQPVPVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEGSAMEKSVSV 68
E++P V + G GAGKTTLL IL Q + + G+ + +VS
Sbjct: 405 EIKPGDVVAVVGQSGAGKTTLLRMILGAQKGRGEEKYRPDSGKVEVPKNTVSA 457
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 27.9 bits (63), Expect = 3.5
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 6 DSEVPDLVPAELQPVP--VTIITGYLGAGKTTLLNYI 40
S + D +L P P VTI+ G++ GKT+LL+ I
Sbjct: 234 VSLLEDDDEEDLVPRPPVVTIM-GHVDHGKTSLLDAI 269
>gnl|CDD|237421 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 27.5 bits (62), Expect = 3.6
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 23 TIITGYLGAGKTTLL 37
++TG G+GKTTLL
Sbjct: 31 LVLTGPNGSGKTTLL 45
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport
and metabolism].
Length = 189
Score = 27.4 bits (61), Expect = 3.6
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 22 VTIITGYLGAGKTTLLNYILTEQHDKKI 49
V +ITG G GKTT+L L E KI
Sbjct: 6 VVVITGVPGVGKTTVLKIALKELVKHKI 33
>gnl|CDD|238981 cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48),
also known as uridine kinase or uridine-cytidine kinase
(UCK), catalyzes the reversible phosphoryl transfer
from ATP to uridine or cytidine to yield UMP or CMP. In
the primidine nucleotide-salvage pathway, this enzyme
combined with nucleoside diphosphate kinases further
phosphorylates UMP and CMP to form UTP and CTP. This
kinase also catalyzes the phosphorylation of several
cytotoxic ribonucleoside analogs such as
5-flurrouridine and cyclopentenyl-cytidine.
Length = 198
Score = 27.5 bits (62), Expect = 3.7
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 25 ITGYLGAGKTTLLNYILTEQHDKKIAVI 52
I G G+GKTT+ I+ + + K+ +I
Sbjct: 4 IAGGSGSGKTTVAEEIIEQLGNPKVVII 31
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 27.6 bits (62), Expect = 3.8
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 25 ITGYLGAGKTTLLNYILTE 43
I G GAGK+TLL + E
Sbjct: 353 IVGPNGAGKSTLLKLLAGE 371
>gnl|CDD|236750 PRK10751, PRK10751, molybdopterin-guanine dinucleotide
biosynthesis protein B; Provisional.
Length = 173
Score = 27.3 bits (61), Expect = 3.9
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 19 PVPVTIITGYLGAGKTTLL 37
+P+ I + G GKTTLL
Sbjct: 5 MIPLLAIAAWSGTGKTTLL 23
>gnl|CDD|225438 COG2884, FtsE, Predicted ATPase involved in cell division [Cell
division and chromosome partitioning].
Length = 223
Score = 27.6 bits (62), Expect = 4.0
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 25 ITGYLGAGKTTLLNYILTEQHDKKIAVILNEF 56
+TG GAGK+TLL I E+ + +++N
Sbjct: 33 LTGPSGAGKSTLLKLIYGEERPTRGKILVNGH 64
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 27.2 bits (61), Expect = 4.0
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 21 PVTI-ITGYLGAGKTTLLNYILTEQHDKKIAVIL 53
I TG G+GK+T+ N + + K V L
Sbjct: 23 GAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYL 56
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl)
small GTPases. Arf (ADP-ribosylation factor)/Arl
(Arf-like) small GTPases. Arf proteins are activators
of phospholipase D isoforms. Unlike Ras proteins they
lack cysteine residues at their C-termini and therefore
are unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a
unique structural device, interswitch toggle, that
implements front-back communication from N-terminus to
the nucleotide binding site. Arf-like (Arl) proteins
are close relatives of the Arf, but only Arl1 has been
shown to function in membrane traffic like the Arf
proteins. Arl2 has an unrelated function in the folding
of native tubulin, and Arl4 may function in the
nucleus. Most other Arf family proteins are so far
relatively poorly characterized. Thus, despite their
significant sequence homologies, Arf family proteins
may regulate unrelated functions.
Length = 158
Score = 27.2 bits (61), Expect = 4.1
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 24 IITGYLGAGKTTLLNYILTEQHDKKI 49
++ G GAGKTT+L + + I
Sbjct: 3 LMLGLDGAGKTTILYKLKLGEVVTTI 28
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 27.7 bits (62), Expect = 4.1
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 24 IITGYLGAGKTTLLNYILTE-QHDKKIAVI 52
II G +GKTTLLN +L +++I I
Sbjct: 147 IICGGTASGKTTLLNALLDFIPPEERIVTI 176
>gnl|CDD|226617 COG4133, CcmA, ABC-type transport system involved in cytochrome c
biogenesis, ATPase component [Posttranslational
modification, protein turnover, chaperones].
Length = 209
Score = 27.3 bits (61), Expect = 4.1
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 23 TIITGYLGAGKTTLL 37
ITG GAGKTTLL
Sbjct: 31 LQITGPNGAGKTTLL 45
>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 = 27.5 bits (62), Expect = 4.1
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 7/39 (17%)
Query: 10 PDLVPAELQPVPVTI-------ITGYLGAGKTTLLNYIL 41
P L V +TI I G +G+GK+TLL +L
Sbjct: 474 PGQETPALDNVSLTIRPGEKVAIIGRIGSGKSTLLKLLL 512
>gnl|CDD|237729 PRK14491, PRK14491, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MoeA;
Provisional.
Length = 597
Score = 27.7 bits (62), Expect = 4.3
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 19 PVPVTIITGYLGAGKTTLLNYILTEQHDK--KIAVI 52
+P+ Y G GKTTLL ++ E + + ++AVI
Sbjct: 9 SIPLLGFCAYSGTGKTTLLEQLIPELNQRGLRLAVI 44
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 27.7 bits (62), Expect = 4.3
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 4 DSDSEVPDLVPAELQPVPVTIITGYLGAGKTTLL 37
V D V +L P I G G+GK+TLL
Sbjct: 345 PGAPPVLDGVSLDLPPGERVAILGPSGSGKSTLL 378
>gnl|CDD|182993 PRK11144, modC, molybdate transporter ATP-binding protein;
Provisional.
Length = 352
Score = 27.5 bits (62), Expect = 4.3
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 22 VTIITGYLGAGKTTLLNYI 40
+T I G GAGKT+L+N I
Sbjct: 26 ITAIFGRSGAGKTSLINAI 44
>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 = 4.5
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 15 AELQPVPVTIITGYLGAGKTTLLNYIL 41
++ +T + G GAGK+TLLN +L
Sbjct: 342 LTIKAGQLTALVGASGAGKSTLLNLLL 368
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 27.6 bits (62), Expect = 4.5
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 22 VTIITGYLGAGKTTLLNYILTE 43
V ++TG G GKT + + E
Sbjct: 3 VFLVTGGPGTGKTVVALNLFAE 24
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 259
Score = 27.3 bits (61), Expect = 4.6
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 8 EVPDLVPAELQPVPVTIITGYLGAGKTTLL 37
+ D V +L+P V I G GAGK+TLL
Sbjct: 15 RLLDGVSLDLRPGEVLAILGPNGAGKSTLL 44
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 26.8 bits (59), Expect = 4.7
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 12 LVPAELQPVPVTIITGYLGAGKTTLLNYIL 41
L A P ++TG G GKT+LL +L
Sbjct: 16 LRRARSGGPPSVLLTGPSGTGKTSLLRELL 45
>gnl|CDD|172360 PRK13833, PRK13833, conjugal transfer protein TrbB; Provisional.
Length = 323
Score = 27.5 bits (61), Expect = 4.8
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 24 IITGYLGAGKTTLLNYILTE 43
+I+G G+GKTTL N ++ E
Sbjct: 148 VISGGTGSGKTTLANAVIAE 167
>gnl|CDD|213186 cd03219, ABC_Mj1267_LivG_branched, ATP-binding cassette component
of branched chain amino acids transport system. The
Mj1267/LivG ABC transporter subfamily is involved in
the transport of the hydrophobic amino acids leucine,
isoleucine and valine. MJ1267 is a branched-chain amino
acid transporter with 29% similarity to both the LivF
and LivG components of the E. coli branched-chain amino
acid transporter. MJ1267 contains an insertion from
residues 114 to 123 characteristic of LivG
(Leucine-Isoleucine-Valine) homologs. The
branched-chain amino acid transporter from E. coli
comprises a heterodimer of ABCs (LivF and LivG), a
heterodimer of six-helix TM domains (LivM and LivH),
and one of two alternative soluble periplasmic
substrate binding proteins (LivK or LivJ).
Length = 236
Score = 27.0 bits (61), Expect = 4.8
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 30 GAGKTTLLNYI 40
GAGKTTL N I
Sbjct: 36 GAGKTTLFNLI 46
>gnl|CDD|226592 COG4107, PhnK, ABC-type phosphonate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 258
Score = 27.4 bits (61), Expect = 4.8
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 13 VPAELQPVPVTIITGYLGAGKTTLLNYI 40
V +L P V I G G+GKTTLL I
Sbjct: 25 VSFDLYPGEVLGIVGESGSGKTTLLKCI 52
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 27.3 bits (61), Expect = 4.9
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 10 PDLVPAELQPVPVTIITGYLGAGKTTLLNYILTEQH 45
+ + L +T++ G G GK+TL+N +L E +
Sbjct: 155 LEELAELLAG-KITVLLGQSGVGKSTLINALLPELN 189
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase
is also found in Gram-positive bacteria, archaea, and
the roundworm C. elegans. It may have a more general,
but still unknown function. Mutations have also been
found that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase
activity of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein
interactions].
Length = 300
Score = 27.4 bits (61), Expect = 5.0
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 25 ITGYLGAGKTTLLNYILTE--QHDKKIAVI 52
ITG GAGK+TLL + E + ++AVI
Sbjct: 39 ITGTPGAGKSTLLEALGMELRRRGLRVAVI 68
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 26.6 bits (60), Expect = 5.1
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 25 ITGYLGAGKTTLLNYIL 41
+ G GAGK+TLL I
Sbjct: 31 LVGRNGAGKSTLLKLIA 47
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 27.1 bits (61), Expect = 5.1
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 22 VTIITGYLGAGKTTLLN 38
I G G+GK+TLLN
Sbjct: 33 FVAIVGPSGSGKSTLLN 49
>gnl|CDD|177093 CHL00194, ycf39, Ycf39; Provisional.
Length = 317
Score = 27.3 bits (61), Expect = 5.2
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 155 VSFPDYFSIYLSILLSRLKELKVEQV 180
+S DYF Y +L RLK++ EQV
Sbjct: 286 ISLEDYFQEYFERILKRLKDINYEQV 311
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the
ATP-binding cassette component of cobalt transport
system. Domain II of the ABC component of a cobalt
transport family found in bacteria, archaea, and
eukaryota. The transition metal cobalt is an essential
component of many enzymes and must be transported into
cells in appropriate amounts when needed. The CbiMNQO
family ABC transport system is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 205
Score = 26.8 bits (60), Expect = 5.3
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 22 VTIITGYLGAGKTTLL 37
+ +TG GAGKTTL
Sbjct: 28 IIALTGKNGAGKTTLA 43
>gnl|CDD|213201 cd03234, ABCG_White, White pigment protein homolog of ABCG
transporter subfamily. The White subfamily represents
ABC transporters homologous to the Drosophila white
gene, which acts as a dimeric importer for eye pigment
precursors. The eye pigmentation of Drosophila is
developed from the synthesis and deposition in the
cells of red pigments, which are synthesized from
guanine, and brown pigments, which are synthesized from
tryptophan. The pigment precursors are encoded by the
white, brown, and scarlet genes, respectively. Evidence
from genetic and biochemical studies suggest that the
White and Brown proteins function as heterodimers to
import guanine, while the White and Scarlet proteins
function to import tryptophan. However, a recent study
also suggests that White may be involved in the
transport of a metabolite, such as 3-hydroxykynurenine,
across intracellular membranes. Mammalian ABC
transporters belonging to the White subfamily (ABCG1,
ABCG5, and ABCG8) have been shown to be involved in the
regulation of lipid-trafficking mechanisms in
macrophages, hepatocytes, and intestinal mucosa cells.
ABCG1 (ABC8), the human homolog of the Drosophila white
gene is induced in monocyte-derived macrophages during
cholesterol influx mediated by acetylated low-density
lipoprotein. It is possible that human ABCG1 forms
heterodimers with several heterologous partners.
Length = 226
Score = 26.9 bits (60), Expect = 5.4
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 22 VTIITGYLGAGKTTLLNYILTEQHDKKI 49
V I G G+GKTTLL+ I
Sbjct: 35 VMAILGSSGSGKTTLLDAISGRVEGGGT 62
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 26.9 bits (60), Expect = 5.4
Identities = 13/19 (68%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 22 VTIITGYLGAGKTTLLNYI 40
VT+I G GAGK+TLLN I
Sbjct: 35 VTVI-GSNGAGKSTLLNAI 52
>gnl|CDD|221000 pfam11145, DUF2921, Protein of unknown function (DUF2921). This
eukaryotic family of proteins has no known function.
Length = 871
Score = 27.5 bits (61), Expect = 5.5
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 146 VVDCKHTIDVSFPDYFSIY-LSILLSRLKELKVEQVHF 182
V DC + + FP FSI SI++ + +F
Sbjct: 350 VGDCSLRLSLRFPTTFSIRDRSIVVGEIWSANTGPSNF 387
>gnl|CDD|213265 cd03298, ABC_ThiQ_thiamine_transporter, ATP-binding cassette
domain of the thiamine transport system. Part of the
binding-protein-dependent transport system tbpA-thiPQ
for thiamine and TPP. Probably responsible for the
translocation of thiamine across the membrane. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 211
Score = 27.1 bits (60), Expect = 5.6
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 22 VTIITGYLGAGKTTLLNYI 40
+T I G G+GK+TLLN I
Sbjct: 26 ITAIVGPSGSGKSTLLNLI 44
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 27.3 bits (61), Expect = 5.6
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 16 ELQPVPVTIITGYLGAGKTTLL 37
+L V T+ITG GAGK+T+L
Sbjct: 23 QLDKVKKTLITGKNGAGKSTML 44
>gnl|CDD|237422 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 27.0 bits (61), Expect = 5.6
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 16 ELQPVPVTIITGYLGAGKTTLL 37
L+P V I G GAGK+TLL
Sbjct: 24 TLRPGEVVAILGPNGAGKSTLL 45
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid
transport, and lantibiotic immunity. In bacteria and
archaea, these transporters usually include an
ATP-binding protein and one or two integral membrane
proteins. Eukaryotic systems of the ABCA subfamily
display ABC domains that are quite similar to this
family. The ATP-binding domain shows the highest
similarity between all members of the ABC transporter
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 173
Score = 26.6 bits (60), Expect = 5.6
Identities = 12/21 (57%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 25 ITGYLG---AGKTTLLNYILT 42
I G LG AGKTTL+ IL
Sbjct: 28 IYGLLGPNGAGKTTLIKIILG 48
>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 27.0 bits (61), Expect = 5.6
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 15 AELQPVP-VTIITGYLGAGKTTLL 37
+L+ P V ++ G G GKT LL
Sbjct: 17 LDLELSPGVNVLVGENGQGKTNLL 40
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family
for which functions are known are part of an
exonuclease complex with sbcD homologs. This complex is
involved in the initiation of recombination to regulate
the levels of palindromic sequences in DNA. This family
is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 1042
Score = 27.2 bits (60), Expect = 5.7
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 21 PVTIITGYLGAGKTTLLNYI 40
P+ +I G GAGKTTLL+ I
Sbjct: 27 PIFLICGKTGAGKTTLLDAI 46
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 26.8 bits (60), Expect = 5.8
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 14/46 (30%)
Query: 27 GYLGAGKTTL-------LNY-------ILTEQHDKKIAVILNEFGE 58
G++GAGK+T+ LN + ++ IA I E GE
Sbjct: 9 GFMGAGKSTIGRALAKALNLPFIDTDQEIEKRTGMSIAEIFEEEGE 54
>gnl|CDD|233598 TIGR01851, argC_other, N-acetyl-gamma-glutamyl-phosphate reductase,
uncommon form. This model represents the less common of
two related families of
N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme
catalyzing the third step or Arg biosynthesis from Glu.
The two families differ by phylogeny, similarity
clustering, and gap architecture in a multiple sequence
alignment [Amino acid biosynthesis, Glutamate family].
Length = 310
Score = 27.1 bits (60), Expect = 5.8
Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 12 LVPAELQPVPVTIITGYLGAGKTTLLNYILTEQHDKKIA 50
++PA+ P+ + ++GY G GK + +Y + +
Sbjct: 132 ILPADF-PITINAVSGYSGGGKAMIADYEQGSADNPSLQ 169
>gnl|CDD|131197 TIGR02142, modC_ABC, molybdenum ABC transporter, ATP-binding
protein. This model represents the ATP-binding
cassette (ABC) protein of the three subunit molybdate
ABC transporter. The three proteins of this complex are
homologous to proteins of the sulfate ABC transporter.
Molybdenum may be used in nitrogenases of
nitrogen-fixing bacteria and in molybdopterin
cofactors. In some cases, molybdate may be transported
by a sulfate transporter rather than by a specific
molybdate transporter [Transport and binding proteins,
Anions].
Length = 354
Score = 27.0 bits (60), Expect = 6.1
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 16 ELQPVPVTIITGYLGAGKTTLLNYI 40
L VT I G G+GKTTL+ I
Sbjct: 19 TLPGQGVTAIFGRSGSGKTTLIRLI 43
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 27.2 bits (61), Expect = 6.2
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 18 QPVPVTIITGYLGAGKTTLLN 38
+P+ + GY AGK+TL N
Sbjct: 190 SGIPLVALVGYTNAGKSTLFN 210
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP
kinase. This enzyme transfers a phosphate from ATP to
GMP, yielding ADP and GDP [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 26.7 bits (60), Expect = 6.4
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 22 VTIITGYLGAGKTTLLNYILTEQHD 46
+ +I+G GAGK+TL+ +L E +
Sbjct: 2 LIVISGPSGAGKSTLVKALLEEDPN 26
>gnl|CDD|213194 cd03227, ABC_Class2, ATP-binding cassette domain of
non-transporter proteins. ABC-type Class 2 contains
systems involved in cellular processes other than
transport. These families are characterized by the fact
that the ABC subunit is made up of duplicated, fused
ABC modules (ABC2). No known transmembrane proteins or
domains are associated with these proteins.
Length = 162
Score = 26.6 bits (59), Expect = 6.6
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 22 VTIITGYLGAGKTTLLN---YILTEQHDKKIAVILNEFGEGSA 61
+TIITG G+GK+T+L+ L + G A
Sbjct: 23 LTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVA 65
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP).
Signal recognition particle receptor, beta subunit
(SR-beta). SR-beta and SR-alpha form the heterodimeric
signal recognition particle (SRP or SR) receptor that
binds SRP to regulate protein translocation across the
ER membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC)
to the ER membrane via interaction with the SR, which
is localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been
observed in human colon cancer, suggesting it may play
a role in the development of this type of cancer.
Length = 202
Score = 26.5 bits (59), Expect = 6.6
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 21 PVTIITGYLGAGKTTLLNYILTEQH 45
P ++ G +GKT L + T +
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKV 25
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 26.6 bits (60), Expect = 6.7
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 22 VTIITGYLGAGKTTLLNYIL 41
+++ G G GK+TLLN +L
Sbjct: 87 TSVLVGQSGVGKSTLLNALL 106
>gnl|CDD|226360 COG3840, ThiQ, ABC-type thiamine transport system, ATPase
component [Coenzyme metabolism].
Length = 231
Score = 26.5 bits (59), Expect = 6.8
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 22 VTIITGYLGAGKTTLLNYI 40
+ I G GAGK+TLLN I
Sbjct: 27 IVAILGPSGAGKSTLLNLI 45
>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 = 26.3 bits (58), Expect = 6.9
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 25 ITGYLGAGKTTLLNYILTEQH 45
+ G G GK++LLN +L +
Sbjct: 2 VVGRGGVGKSSLLNALLGGEV 22
>gnl|CDD|224058 COG1135, AbcC, ABC-type metal ion transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 339
Score = 26.8 bits (60), Expect = 6.9
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 25 ITGYLGAGKTTLL 37
I GY GAGK+TLL
Sbjct: 37 IIGYSGAGKSTLL 49
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 27.0 bits (60), Expect = 7.3
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 20 VPVTIITGYLGAGKTTLLNYI 40
VP + GY AGK+TL N I
Sbjct: 197 VPTVSLVGYTNAGKSTLFNRI 217
>gnl|CDD|223315 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 26.5 bits (59), Expect = 7.3
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 25 ITGYLGAGKTTLLNYI 40
+TG +G+GK+T+ +
Sbjct: 7 LTGGIGSGKSTVAKIL 22
>gnl|CDD|172418 PRK13898, PRK13898, type IV secretion system ATPase VirB4;
Provisional.
Length = 800
Score = 27.0 bits (60), Expect = 7.6
Identities = 9/29 (31%), Positives = 21/29 (72%), Gaps = 3/29 (10%)
Query: 126 KVFWLDKELGSDIY---LDGIVTVVDCKH 151
++F+ DK+ G++I+ L+G+ TV++ +
Sbjct: 476 RMFFFDKDRGAEIFIRALNGVYTVIEPRL 504
Score = 26.7 bits (59), Expect = 8.7
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 23 TIITGYLGAGKTTLLNYILTE 43
T+I G GAGKT L+N++ +
Sbjct: 449 TLIIGPTGAGKTVLMNFLCAQ 469
>gnl|CDD|222997 PHA03132, PHA03132, thymidine kinase; Provisional.
Length = 580
Score = 27.0 bits (60), Expect = 7.7
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 27 GYLGAGKTTLLNYI 40
G +G GKTTLLN++
Sbjct: 264 GVMGVGKTTLLNHM 277
>gnl|CDD|213231 cd03264, ABC_drug_resistance_like, ABC-type multidrug transport
system, ATPase component. The biological function of
this family is not well characterized, but display ABC
domains similar to members of ABCA subfamily. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 211
Score = 26.4 bits (59), Expect = 7.8
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 30 GAGKTTLLNYILTEQ 44
GAGKTTL+ + T
Sbjct: 35 GAGKTTLMRILATLT 49
>gnl|CDD|131576 TIGR02524, dot_icm_DotB, Dot/Icm secretion system ATPase DotB.
Members of this protein family are the DotB component of
Dot/Icm secretion systems, as found in obligate
intracellular pathogens Legionella pneumophila and
Coxiella burnetii. While this system resembles type IV
secretion systems and has been called a form of type IV,
the liturature now seems to favor calling this the
Dot/Icm system. This family is most closely related to
TraJ proteins of plasmid transfer, rather than to
proteins of other type IV secretion systems.
Length = 358
Score = 26.9 bits (59), Expect = 7.9
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 5 SDSEVPDLVPAELQPVP-VTIITGYLGAGKTTLLNYILTE 43
S ++P + + P + ITG G+GK+TLL I+ E
Sbjct: 118 SKLDLPAAIIDAIAPQEGIVFITGATGSGKSTLLAAIIRE 157
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with
the signal sequence when it emerges from the ribosome.
SRP54 of the signal recognition particle has a
three-domain structure: an N-terminal helical bundle
domain, a GTPase domain, and the M-domain that binds
the 7s RNA and also binds the signal sequence. The
extreme C-terminal region is glycine-rich and lower in
complexity and poorly conserved between species. The
GTPase domain is evolutionary related to P-loop NTPase
domains found in a variety of other proteins.
Length = 197
Score = 26.2 bits (59), Expect = 7.9
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 30 GAGKTTL---LNYILTEQHDKKIAVI 52
G GKTT L L + KK+ ++
Sbjct: 11 GVGKTTTIAKLAARLKLKGGKKVLLV 36
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 25.0 bits (55), Expect = 8.1
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 25 ITGYLGAGKTTLLNYILTEQHDKKIAVILNE 55
ITG G+GK+T+ L EQ + V+L+E
Sbjct: 4 ITGGSGSGKSTVAK-KLAEQLGGRSVVVLDE 33
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 26.5 bits (59), Expect = 8.2
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 25 ITGYLGAGKTTLLNYILTE--QHDKKIAVI 52
ITG GAGK+TL+ + E + ++AV+
Sbjct: 56 ITGVPGAGKSTLIEALGRELRERGHRVAVL 85
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 26.7 bits (59), Expect = 8.3
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 22 VTIITGYLGAGKTTLLNYIL 41
V I+TG G GKTT+ I+
Sbjct: 340 VVILTGGPGTGKTTITRAII 359
>gnl|CDD|227297 COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF
[Intracellular trafficking and secretion].
Length = 355
Score = 26.5 bits (59), Expect = 8.3
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 23 TIITGYLGAGKTTLLNYILTE 43
+I+G G+GKTTLLN +
Sbjct: 176 ILISGGTGSGKTTLLNALSGF 196
>gnl|CDD|226459 COG3950, COG3950, Predicted ATP-binding protein involved in
virulence [General function prediction only].
Length = 440
Score = 26.8 bits (59), Expect = 8.4
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 17 LQPVPVTIITGYLGAGKTTLLNYI 40
TII G G+GKTT+L+ I
Sbjct: 21 FGESETTIIVGPNGSGKTTVLDAI 44
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 26.5 bits (59), Expect = 8.4
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 30 GAGKTTLLNYILTEQHDKKIAVIL 53
GAGKTTL+ + + V+L
Sbjct: 10 GAGKTTLIELLAERLEARGYEVVL 33
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 26.5 bits (59), Expect = 8.5
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 24 IITGYLGAGKTTLLNYILTEQHDKKIAVILNE 55
++TG G+GKTT L L+E + + +I E
Sbjct: 262 LVTGPTGSGKTTTLYAALSELNTPERNIITIE 293
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 26.5 bits (59), Expect = 8.7
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 25 ITGYLGAGKTTLLNYI 40
I G GAGK+TLLN I
Sbjct: 30 ILGPSGAGKSTLLNLI 45
>gnl|CDD|213238 cd03271, ABC_UvrA_II, ATP-binding cassette domain II of the
excision repair protein UvrA. Nucleotide excision
repair in eubacteria is a process that repairs DNA
damage by the removal of a 12-13-mer oligonucleotide
containing the lesion. Recognition and cleavage of the
damaged DNA is a multistep ATP-dependent reaction that
requires the UvrA, UvrB, and UvrC proteins. Both UvrA
and UvrB are ATPases, with UvrA having two ATP binding
sites, which have the characteristic signature of the
family of ABC proteins and UvrB having one ATP binding
site that is structurally related to that of helicases.
Length = 261
Score = 26.4 bits (59), Expect = 9.0
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 23 TIITGYLGAGKTTLLNYIL 41
T +TG G+GK++L+N L
Sbjct: 24 TCVTGVSGSGKSSLINDTL 42
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK)
catalyzes the phosphorylation of adenosine
5'-phosphosulfate to form 3'-phosphoadenosine
5'-phosphosulfate (PAPS). The end-product PAPS is a
biologically "activated" sulfate form important for the
assimilation of inorganic sulfate.
Length = 149
Score = 25.9 bits (58), Expect = 9.1
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 25 ITGYLGAGKTTLLNYILTEQHDKKIAVIL 53
+TG G+GK+T+ + + + V +
Sbjct: 4 LTGLSGSGKSTIARALEEKLFQRGRPVYV 32
>gnl|CDD|99819 cd05776, DNA_polB_alpha_exo, inactive DEDDy 3'-5' exonuclease
domain of eukaryotic DNA polymerase alpha, a family-B
DNA polymerase. The 3'-5' exonuclease domain of
eukaryotic DNA polymerase alpha. DNA polymerase alpha
is a family-B DNA polymerase with a catalytic subunit
that contains a DnaQ-like 3'-5' exonuclease domain. It
is one of the three DNA-dependent type B DNA polymerases
(delta and epsilon are the other two) that have been
identified as essential for nuclear DNA replication in
eukaryotes. DNA polymerase alpha is almost exclusively
required for the initiation of DNA replication and the
priming of Okazaki fragments during elongation. It
associates with DNA primase and is the only enzyme able
to start DNA synthesis de novo. The catalytic subunit
contains both polymerase and 3'-5' exonuclease domains,
but only exhibits polymerase activity. The 3'-5'
exonuclease domain contains three sequence motifs termed
ExoI, ExoII and ExoIII, without the four conserved
acidic residues that are crucial for metal binding and
catalysis. This explains why in most organisms, that no
specific repair role, other than check point control,
has been assigned to this enzyme. The exonuclease domain
may have a structural role.
Length = 234
Score = 26.4 bits (59), Expect = 9.3
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 159 DYFSIYLSILLSRLKELKVEQ 179
D L +LLSR++ELKV
Sbjct: 105 DLEGFDLDVLLSRIQELKVPH 125
>gnl|CDD|237727 PRK14489, PRK14489, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobA/MobB;
Provisional.
Length = 366
Score = 26.6 bits (59), Expect = 9.3
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 20 VPVTIITGYLGAGKTTLL 37
P+ + GY G GKTTLL
Sbjct: 205 PPLLGVVGYSGTGKTTLL 222
>gnl|CDD|213230 cd03263, ABC_subfamily_A, ATP-binding cassette domain of the
lipid transporters, subfamily A. The ABCA subfamily
mediates the transport of a variety of lipid compounds.
Mutations of members of ABCA subfamily are associated
with human genetic diseases, such as, familial
high-density lipoprotein (HDL) deficiency, neonatal
surfactant deficiency, degenerative retinopathies, and
congenital keratinization disorders. The ABCA1 protein
is involved in disorders of cholesterol transport and
high-density lipoprotein (HDL) biosynthesis. The ABCA4
(ABCR) protein transports vitamin A derivatives in the
outer segments of photoreceptor cells, and therefore,
performs a crucial step in the visual cycle. The ABCA
genes are not present in yeast. However, evolutionary
studies of ABCA genes indicate that they arose as
transporters that subsequently duplicated and that
certain sets of ABCA genes were lost in different
eukaryotic lineages.
Length = 220
Score = 26.3 bits (59), Expect = 9.3
Identities = 12/21 (57%), Positives = 13/21 (61%), Gaps = 4/21 (19%)
Query: 25 ITGYLG---AGKTTLLNYILT 42
I G LG AGKTT L +LT
Sbjct: 30 IFGLLGHNGAGKTTTLK-MLT 49
>gnl|CDD|217188 pfam02689, Herpes_Helicase, Helicase. This family consists of
Helicases from the Herpes viruses. Helicases are
responsible for the unwinding of DNA and are essential
for replication and completion of the viral life cycle.
Length = 801
Score = 26.5 bits (59), Expect = 9.4
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 2 DSDSDSEVPDLVPAELQPVPVTIITGYLGAGKTT 35
S D E P+ L P +ITG GAGK+T
Sbjct: 42 RSIFDPEDPEDPNFAL-PFSAYLITGTAGAGKST 74
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 26.3 bits (58), Expect = 9.5
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 30 GAGKTTL---LNYILTEQHDKKIAVI 52
G GKTT L L ++ KK+ +I
Sbjct: 13 GVGKTTTAVNLAAALAKRGGKKVLLI 38
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter
family is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 26.0 bits (58), Expect = 9.5
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 22 VTIITGYLGAGKTTLLN 38
+T I G GAGK+TLLN
Sbjct: 37 LTAIMGPSGAGKSTLLN 53
>gnl|CDD|236780 PRK10867, PRK10867, signal recognition particle protein;
Provisional.
Length = 433
Score = 26.6 bits (60), Expect = 9.7
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 17 LQPVPVTII--TGYLGAGKTTL---LNYILTEQHDKKIAVI 52
L P T+I G GAGKTT L L ++ KK+ ++
Sbjct: 95 LAAKPPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLV 135
>gnl|CDD|118101 pfam09565, RE_NgoFVII, NgoFVII restriction endonuclease. This
family includes the NgoFVII (recognises GCSGC but
cleavage site unknown) restriction endonuclease.
Length = 296
Score = 26.3 bits (58), Expect = 9.9
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 22 VTIITGYLGAGKTTLLNYILTEQHDKKIAVI 52
+ I +GY L+ ++ H KI +I
Sbjct: 11 LLIASGYASNMALEELDKLVENHHILKITLI 41
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 26.2 bits (58), Expect = 9.9
Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 14 PAELQPV---PVTIITGYLGAGKTTLLNYILTEQHDKKIAVILNEFGEG 59
EL +++ G G GK++L+N + +++ I ++ G G
Sbjct: 111 LKELIEALQNRISVFAGQSGVGKSSLINALDPSVK-QQVNDISSKLGLG 158
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain
of glucan transporter and related proteins, subfamily
C. Glucan exporter ATP-binding protein. In A.
tumefaciens cyclic beta-1, 2-glucan must be transported
into the periplasmic space to exert its action as a
virulence factor. This subfamily belongs to the
MRP-like family and is involved in drug, peptide, and
lipid export. The MRP-like family, similar to all ABC
proteins, have a common four-domain core structure
constituted by two membrane-spanning domains each
composed of six transmembrane (TM) helices and two
nucleotide-binding domains (NBD). ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 229
Score = 26.0 bits (58), Expect = 10.0
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 25 ITGYLGAGKTTLLNYIL 41
I G GAGKTTL+N ++
Sbjct: 34 IVGPTGAGKTTLINLLM 50
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 0.139 0.411
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,537,361
Number of extensions: 890659
Number of successful extensions: 1424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1414
Number of HSP's successfully gapped: 218
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
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: 56 (25.1 bits)