RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2657
(163 letters)
>gnl|CDD|193251 pfam12775, AAA_7, P-loop containing dynein motor region D3. the
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D3 and is an ATP binding
site.
Length = 272
Score = 263 bits (673), Expect = 5e-90
Identities = 109/164 (66%), Positives = 136/164 (82%), Gaps = 1/164 (0%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKP 60
M+L + +++PVML+GNAG+GKS+L+ L+SL P+ Y + +VPFN+YT+S MLQ VLEKP
Sbjct: 26 MDLLMERQRPVMLVGNAGTGKSVLVGDKLASLDPDAYLVKNVPFNYYTTSAMLQAVLEKP 85
Query: 61 LEKKAGRNFGPPGNKTMIYFVDDMNMPEVDAYGTVQPHTVIRQYMDYQHWYDRQKLSLKD 120
LEKKAGRN+GPPG K ++YF+DDMNMPEVDAYGTVQPHT+IRQ+MDY HWYDR KL+LK+
Sbjct: 86 LEKKAGRNYGPPGTKKLVYFIDDMNMPEVDAYGTVQPHTLIRQHMDYGHWYDRSKLTLKE 145
Query: 121 IHNIMFVSAMNPTSGSFTIEPRLQRHFYVFALRL-GLLRIGSIY 163
IHN +VS MNPT+GSFTI RLQRHF VFAL G + +IY
Sbjct: 146 IHNCQYVSCMNPTAGSFTINSRLQRHFCVFALSFPGQDALSTIY 189
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 46.9 bits (111), Expect = 1e-06
Identities = 37/149 (24%), Positives = 57/149 (38%), Gaps = 14/149 (9%)
Query: 7 KRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLEK--- 63
+ + G GSGK +L+ L S + F+ T + VLE+ E
Sbjct: 1493 TLRSYIYCGPPGSGKEMLMCPSLRS--ELITEVKYFNFSTCTMTPSKLSVLERETEYYPN 1550
Query: 64 -KAGRNFGPPGNKTMIYFVDDMNMPEVDAYGTVQPHTVI---RQYMDYQHWYDRQKLSLK 119
R + P K ++ F D++N+P Y P TVI R ++ Q ++ +S
Sbjct: 1551 TGVVRLYPKPVVKDLVLFCDEINLPYGFEYY---PPTVIVFLRPLVERQGFWSSIAVSWV 1607
Query: 120 DIHNIMFVSAMNP--TSGSFTIEPRLQRH 146
I I+ A NP G R R
Sbjct: 1608 TICGIILYGACNPGTDEGRVKYYERFIRK 1636
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 40.4 bits (95), Expect = 6e-05
Identities = 30/152 (19%), Positives = 51/152 (33%), Gaps = 31/152 (20%)
Query: 10 PVMLIGNAGSGKSIL---INKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLEKK-- 64
V+L+G G+GKS L + LS+ P LT T ++ + P
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTR----DTTEEDLKGRRNIDPGGASWV 56
Query: 65 ------AGRNFGPPGNKTMIYFVDDMNMPEVDAYGTVQPHTVIRQYMDYQHWY--DRQKL 116
A R I +D++N D ++ +D + + +L
Sbjct: 57 DGPLVRAAREGE-------IAVLDEINRANPDVLNSLLS------LLDERRLLLPEGGEL 103
Query: 117 SLKDIHNIMFVSAMNPTS-GSFTIEPRLQRHF 147
++ MNP G + P L+ F
Sbjct: 104 VKAAPDGFRLIATMNPLDRGLNELSPALRSRF 135
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 37.6 bits (88), Expect = 5e-04
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 8 RKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEK 59
+L G +GSGK+ L+ ++ LP P + T ++L+K+L
Sbjct: 4 AGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAP-SLGTPKDLLRKILRA 54
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 36.5 bits (84), Expect = 0.003
Identities = 13/40 (32%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 3 LFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSV 42
LF+ + K ++++G+ G GK+ L+N+++ PE Y T
Sbjct: 1 LFMKEFK-IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIG 39
>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 = 34.3 bits (78), Expect = 0.010
Identities = 24/160 (15%), Positives = 47/160 (29%), Gaps = 33/160 (20%)
Query: 7 KRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLEKKAG 66
+ ++++G GSGK+ L + L P + Y E + + + L
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGV------IYIDGEDILEEVLDQLLLIIV 54
Query: 67 RNFGPPG---------------NKTMIYFVDDMNMPEVDAYGTVQPHTVIRQYMDYQHWY 111
G K + +D E+ + + ++ +
Sbjct: 55 GGKKASGSGELRLRLALALARKLKPDVLILD-----EITSLLDAEQEALLLLLEEL---- 105
Query: 112 DRQKLSLKDIHNIMFVSAMNP--TSGSFTIEPRLQRHFYV 149
R L LK N+ + N G + R R +
Sbjct: 106 -RLLLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVL 144
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 35.0 bits (81), Expect = 0.010
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 8 RKPVMLIGNAGSGKSILINKMLSSLPPE 35
R+ VM+IG+ G+GKS+L M LP E
Sbjct: 50 RRHVMMIGSPGTGKSMLAKAMAELLPKE 77
>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 = 34.1 bits (78), Expect = 0.014
Identities = 21/114 (18%), Positives = 43/114 (37%), Gaps = 8/114 (7%)
Query: 11 VMLIGNAGSGKSILINKMLSSLPPET----YALTSVPFNFYTSSEMLQKVLEKPLEKKAG 66
V+L G +G+GK+ L+ ++L L A + P+ F + L + L + L +
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRELAAELL 86
Query: 67 RNFGPPGNKTMIYFVDDMN--MPEVDAYGTVQPHTVIRQYMDYQHWYDRQKLSL 118
++ + + ++ V+ +D W D + L L
Sbjct: 87 LLREALLAALGAELIEGLQDLVELLERLLARARPLVL--VLDDLQWADEESLDL 138
>gnl|CDD|182733 PRK10790, PRK10790, putative multidrug transporter
membrane\ATP-binding components; Provisional.
Length = 592
Score = 33.9 bits (78), Expect = 0.025
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPE 35
+NL +P R V L+G+ GSGKS L + ++ P
Sbjct: 360 INLSVPSRGFVALVGHTGSGKSTLASLLMGYYPLT 394
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is
also a nucleotide binding domain (NBD).
Length = 227
Score = 33.3 bits (77), Expect = 0.032
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSIL---INKMLSSLPPE 35
+L IPK + LIG +G GKS L +N++ +P
Sbjct: 20 SLDIPKGEITALIGPSGCGKSTLLRLLNRLNDLIPGA 56
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling
inter- mediates into the (bacterio)chlorophyll branch
in response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 33.3 bits (77), Expect = 0.036
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 11 VMLIGNAGSGKSILINKMLSSLPPETYA 38
+++IG GSGK++L ++ LPP T
Sbjct: 25 LLMIGPPGSGKTMLAKRLPGILPPLTEQ 52
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 32.6 bits (75), Expect = 0.080
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 7/38 (18%)
Query: 12 MLIGNAGSGKSILINKMLSSLPP-------ETYALTSV 42
+L+G G+GK++L +++ LPP E A+ S+
Sbjct: 202 LLVGPPGTGKTMLASRLPGLLPPLSIPEALEVSAIHSL 239
>gnl|CDD|224042 COG1117, PstB, ABC-type phosphate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 253
Score = 32.1 bits (74), Expect = 0.084
Identities = 16/30 (53%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSIL---INKM 28
NL IPK K LIG +G GKS L +N+M
Sbjct: 27 NLDIPKNKVTALIGPSGCGKSTLLRCLNRM 56
>gnl|CDD|188099 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding
protein. This model represents the ATP-binding protein
of a family of ABC transporters for inorganic
phosphate. In the model species Escherichia coli, a
constitutive transporter for inorganic phosphate, with
low affinity, is also present. The high affinity
transporter that includes this polypeptide is induced
when extracellular phosphate concentrations are low.
The proteins most similar to the members of this family
but not included appear to be amino acid transporters
[Transport and binding proteins, Anions].
Length = 247
Score = 31.9 bits (73), Expect = 0.089
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSIL---INKM 28
NL IPK + LIG +G GKS L +N+M
Sbjct: 21 NLDIPKNQVTALIGPSGCGKSTLLRSLNRM 50
>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 = 32.1 bits (74), Expect = 0.090
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
NL +PK + V ++G GSGKS L++ +L L
Sbjct: 25 NLEVPKGELVAIVGPVGSGKSSLLSALLGELEK 57
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 32.1 bits (73), Expect = 0.12
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLS 30
++ +P+ K +++G GSGKS L+ +LS
Sbjct: 680 SVSVPRGKLTVVLGATGSGKSTLLQSLLS 708
>gnl|CDD|213262 cd03295, ABC_OpuCA_Osmoprotection, ATP-binding cassette domain of
the osmoprotectant transporter. OpuCA is a the ATP
binding component of a bacterial solute transporter
that serves a protective role to cells growing in a
hyperosmolar environment. ABC (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 = 242
Score = 31.5 bits (72), Expect = 0.13
Identities = 13/32 (40%), Positives = 23/32 (71%), Gaps = 3/32 (9%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSI---LINKML 29
+NL I K + ++LIG +GSGK+ +IN+++
Sbjct: 20 LNLEIAKGEFLVLIGPSGSGKTTTMKMINRLI 51
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 31.2 bits (71), Expect = 0.14
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 7 KRKPVMLIGNAGSGKSILINKMLSSLP 33
+R+P++L G +G GKS + +L P
Sbjct: 1 QRRPIVLSGPSGVGKSHIKKALLDEYP 27
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 31.9 bits (72), Expect = 0.14
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
+NL IP V ++G G GK+ LI+ ML L
Sbjct: 636 INLEIPVGSLVAIVGGTGEGKTSLISAMLGELSH 669
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette
transport system involved in resistant to organic
solvents. 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 = 235
Score = 31.3 bits (72), Expect = 0.15
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPE 35
+L + + + + +IG +GSGKS L+ ++ L P+
Sbjct: 20 DLDVRRGEILAIIGPSGSGKSTLLRLIVGLLRPD 53
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 31.6 bits (72), Expect = 0.16
Identities = 15/34 (44%), Positives = 22/34 (64%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
+NL +P V ++G+ G GK+ LI+ ML LPP
Sbjct: 636 INLDVPVGSLVAIVGSTGEGKTSLISAMLGELPP 669
>gnl|CDD|131085 TIGR02030, BchI-ChlI, magnesium chelatase ATPase subunit I. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 337
Score = 31.4 bits (71), Expect = 0.18
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTS 49
+N+ PK VM++G+ G+GKS + + L++L PE A+ PFN S
Sbjct: 18 LNVIDPKIGGVMVMGDRGTGKSTAV-RALAALLPEIKAVAGCPFNSSPS 65
>gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein;
Provisional.
Length = 582
Score = 31.5 bits (72), Expect = 0.19
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
N IP K V L+G +GSGKS + N
Sbjct: 363 NFKIPAGKTVALVGRSGSGKSTIAN 387
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR proteins. 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 = 234
Score = 30.7 bits (70), Expect = 0.24
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
+L IP + V L+G +GSGKS L+N
Sbjct: 22 SLDIPAGETVALVGPSGSGKSTLVN 46
>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 = 31.1 bits (71), Expect = 0.24
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET 36
+ +P + V L+G +G+GKS L+N +L + P
Sbjct: 342 SFTVPPGERVALVGPSGAGKSTLLNLLLGFVDPTE 376
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 30.8 bits (70), Expect = 0.25
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 16/69 (23%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEML---QKVLE 58
+L I + V +IG+ G+GKS L+N + L P TS ++L V +
Sbjct: 26 SLEIAEGDFVTVIGSNGAGKSTLLNAIAGDLKP-------------TSGQILIDGVDVTK 72
Query: 59 KPLEKKAGR 67
K + K+A
Sbjct: 73 KSVAKRANL 81
>gnl|CDD|224052 COG1127, Ttg2A, ABC-type transport system involved in resistance
to organic solvents, ATPase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 263
Score = 30.6 bits (70), Expect = 0.26
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET 36
+L +P+ + + ++G +GSGKS L+ +L L P+
Sbjct: 28 DLDVPRGEILAILGGSGSGKSTLLRLILGLLRPDK 62
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members
of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 608
Score = 31.0 bits (70), Expect = 0.27
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 7 KRKPVMLIGNAGSGKSILINKMLSSLPPE 35
+++ V+LIG G GKS+L M LP E
Sbjct: 36 QKRNVLLIGEPGVGKSMLAKAMAELLPDE 64
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 30.0 bits (69), Expect = 0.30
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPE 35
+L I + V ++G +GSGKS L+ +L P
Sbjct: 22 SLTIKPGEKVAIVGPSGSGKSTLLKLLLRLYDPT 55
>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30). Rab30 subfamily.
Rab30 appears to be associated with the Golgi stack. It
is expressed in a wide variety of tissue types and in
humans maps to chromosome 11. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 169
Score = 30.3 bits (68), Expect = 0.31
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 11 VMLIGNAGSGKSILINKMLSSL-PPETYALTSVPFNFYT 48
++LIGNAG GK+ L+ + L PP A V F T
Sbjct: 10 IVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKT 48
>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 = 30.3 bits (69), Expect = 0.31
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 5 IPKRKPVMLIGNAGSGKSILINKMLSS 31
R V ++G GKS LIN +L S
Sbjct: 122 AKYRGDVYVVGATNVGKSTLINALLKS 148
>gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein;
Provisional.
Length = 260
Score = 30.4 bits (69), Expect = 0.33
Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILI---NKMLSSLPPETYA 38
NL I K + IG +G GKS L+ N+M L PE A
Sbjct: 33 NLDIAKNQVTAFIGPSGCGKSTLLRTFNRMY-ELYPEQRA 71
>gnl|CDD|213235 cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain
of the bacitracin-resistance transporter. The BcrA
subfamily represents ABC transporters involved in
peptide antibiotic resistance. Bacitracin is a
dodecapeptide antibiotic produced by B. licheniformis
and B. subtilis. The synthesis of bacitracin is
non-ribosomally catalyzed by a multi-enzyme complex
BcrABC. Bacitracin has potent antibiotic activity
against gram-positive bacteria. The inhibition of
peptidoglycan biosynthesis is the best characterized
bacterial effect of bacitracin. The bacitracin
resistance of B. licheniformis is mediated by the ABC
transporter Bcr which is composed of two identical BcrA
ATP-binding subunits and one each of the integral
membrane proteins, BcrB and BcrC. B. subtilis cells
carrying bcr genes on high-copy number plasmids develop
collateral detergent sensitivity, a similar phenomenon
in human cells with overexpressed multi-drug resistance
P-glycoprotein.
Length = 208
Score = 30.3 bits (69), Expect = 0.34
Identities = 8/32 (25%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSL 32
++L + K + +G G+GK+ + K++ L
Sbjct: 19 ISLHVKKGEIYGFLGPNGAGKTTTM-KIILGL 49
>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 = 30.3 bits (69), Expect = 0.36
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
NL I K K +IG +GSGKS L+N
Sbjct: 18 NLTIEKGKMYAIIGESGSGKSTLLN 42
>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 = 30.3 bits (69), Expect = 0.39
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPE 35
N I + V ++G G+GK+ LIN ++ P+
Sbjct: 23 NFSIKPGETVAIVGPTGAGKTTLINLLMRFYDPQ 56
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 30.0 bits (68), Expect = 0.41
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 5 IPKRKPVMLIGNAGSGKSIL 24
IP+R V+L G G+GKSI
Sbjct: 20 IPERNVVLLSGGPGTGKSIF 39
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 30.3 bits (69), Expect = 0.42
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEK 59
NL I + + V +IG +G+GKS L+ + L+ L T + FN +++ K L K
Sbjct: 24 NLEINQGEMVAIIGPSGAGKSTLL-RSLNGLVDPTSG--EILFNGVQITKLKGKELRK 78
>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 = 30.4 bits (69), Expect = 0.43
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPE--TYALTSVPFNFYTSSEMLQKV 56
+L +P + V ++G +GSGKS L+ + L P L VP + E+ ++V
Sbjct: 355 SLDLPPGERVAILGPSGSGKSTLLATLAGLLDPLQGEVTLDGVPVSSLDQDEVRRRV 411
>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 = 30.3 bits (69), Expect = 0.43
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
NL I + L+G +G+GKS L+N +L L P
Sbjct: 341 NLTIKAGQLTALVGASGAGKSTLLNLLLGFLAP 373
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 30.2 bits (69), Expect = 0.43
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLP 33
N +P + + L+G +G+GK+ L+N +L LP
Sbjct: 370 NFTLPAGQRIALVGPSGAGKTSLLNALLGFLP 401
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 29.8 bits (67), Expect = 0.44
Identities = 27/155 (17%), Positives = 51/155 (32%), Gaps = 20/155 (12%)
Query: 3 LFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLE 62
L +P K ++L G G+GK+ L + + L PF + +S++L+ ++ L
Sbjct: 14 LELPPPKNLLLYGPPGTGKTTLARAIANEL-----FRPGAPFLYLNASDLLEGLVVAELF 68
Query: 63 K---KAGRNFGPPGNKTMIYFVDDMNMPEVDAYGTVQPHTVIRQYMDYQHWYDRQKLSLK 119
K + F+D+++ A + V+ D
Sbjct: 69 GHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALL--RVLETLND----------LRI 116
Query: 120 DIHNIMFVSAMNPTSGSFTIEPRLQRHFYVFALRL 154
D N+ + A N R + L
Sbjct: 117 DRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
>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 = 29.3 bits (66), Expect = 0.46
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 11 VMLIGNAGSGKSILINKMLSSLPPETY 37
V++IG+ GSGKS L+++++ P
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEP 28
>gnl|CDD|213257 cd03290, ABCC_SUR1_N, ATP-binding cassette domain of the
sulfonylurea receptor, subfamily C. The SUR domain 1.
The sulfonylurea receptor SUR is an ATP transporter of
the ABCC/MRP family with tandem ATPase binding domains.
Unlike other ABC proteins, it has no intrinsic transport
function, neither active nor passive, but associates
with the potassium channel proteins Kir6.1 or Kir6.2 to
form the ATP-sensitive potassium (K(ATP)) channel.
Within the channel complex, SUR serves as a regulatory
subunit that fine-tunes the gating of Kir6.x in response
to alterations in cellular metabolism. It constitutes a
major pharmaceutical target as it binds numerous drugs,
K(ATP) channel openers and blockers, capable of up- or
down-regulating channel activity.
Length = 218
Score = 29.6 bits (66), Expect = 0.53
Identities = 27/107 (25%), Positives = 43/107 (40%), Gaps = 19/107 (17%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKML-------------SSLPPETYALTSVPFNFY 47
+N+ IP + M++G G GKS L+ +L + E + N Y
Sbjct: 20 INIRIPTGQLTMIVGQVGCGKSSLLLAILGEMQTLEGKVHWSNKNESEPSFEATRSRNRY 79
Query: 48 TSSEMLQK--VLEKPLEKKAGRNFGPPGNKTMIYFVDDMN--MPEVD 90
+ + QK +L +E+ FG P NK V D P++D
Sbjct: 80 SVAYAAQKPWLLNATVEENI--TFGSPFNKQRYKAVTDACSLQPDID 124
>gnl|CDD|177020 CHL00081, chlI, Mg-protoporyphyrin IX chelatase.
Length = 350
Score = 30.0 bits (68), Expect = 0.59
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSE--MLQKVLE 58
+N+ PK VM++G+ G+GKS I + L L PE + PFN + S M +V E
Sbjct: 31 LNVIDPKIGGVMIMGDRGTGKSTTI-RALVDLLPEIEVVKDDPFNSHPSDPELMSDEVRE 89
Query: 59 K 59
Sbjct: 90 A 90
>gnl|CDD|234457 TIGR04075, bacter_Pnkp, polynucleotide kinase-phosphatase.
Members of this protein family are the bacterial
polynucleotide kinase-phosphatase (Pnkp) whose genes
occur paired with genes for the 3' terminal RNA ribose
2'-O-methyltransferase Hen1. All members of the seed
alignment belong to a cassette with the Hen1. The pair
acts in bacterial RNA repair. This enzyme performs
end-healing reactions on broken RNA, preparing from the
RNA ligase to close the break. The working hypothesis
is that the combination of Pnkp (RNA repair) and Hen1
(RNA modification) serves to first repair RNA damage
from ribotoxins and then perform a modification that
prevents the damage from recurring [Transcription, RNA
processing].
Length = 851
Score = 30.0 bits (68), Expect = 0.59
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKS 22
M + IP+ V+L+G +GSGKS
Sbjct: 1 MKITIPELSLVVLVGASGSGKS 22
>gnl|CDD|237393 PRK13477, PRK13477, bifunctional pantoate ligase/cytidylate kinase;
Provisional.
Length = 512
Score = 29.8 bits (68), Expect = 0.70
Identities = 12/22 (54%), Positives = 18/22 (81%), Gaps = 1/22 (4%)
Query: 2 NLFIPKRKPVMLI-GNAGSGKS 22
N+F+ KR+P++ I G AG+GKS
Sbjct: 277 NVFLMKRQPIIAIDGPAGAGKS 298
>gnl|CDD|172741 PRK14253, PRK14253, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 249
Score = 29.4 bits (66), Expect = 0.70
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSIL---INKM 28
+NL IP R+ LIG +G GKS L +N+M
Sbjct: 22 INLPIPARQVTALIGPSGCGKSTLLRCLNRM 52
>gnl|CDD|237457 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 29.3 bits (66), Expect = 0.70
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILI 25
++L IP+ L+G G+GKS L+
Sbjct: 24 LSLSIPEGSKTALLGPNGAGKSTLL 48
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 29.2 bits (66), Expect = 0.71
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 9 KPVMLIGNAGSGKSILINKM 28
K ++LIG+ GSGKS L ++
Sbjct: 2 KKIILIGSGGSGKSTLARQL 21
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated
with diverse processes in dividing and non-dividing
cells. They were first discovered in the budding yeast
S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 275
Score = 29.4 bits (67), Expect = 0.80
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 11 VMLIGNAGSGKSILINKMLSS 31
+M++G +G GKS IN + +
Sbjct: 7 IMVVGESGLGKSTFINTLFGT 27
>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 = 29.5 bits (67), Expect = 0.81
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 6/79 (7%)
Query: 9 KPVMLI-GNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLEKKAGR 67
K V L+ G G+GK+++ + + L T+ F + + L VL + L
Sbjct: 1 KAVFLVTGGPGTGKTVVALNLFAELSDSDLGRTA---VFLSGNHPLVLVLYEALAGDLKV 57
Query: 68 NFGP--PGNKTMIYFVDDM 84
+ I +
Sbjct: 58 RKKKLFRKPTSFINNLHKA 76
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 29.4 bits (66), Expect = 0.86
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 7/39 (17%)
Query: 11 VMLIGNAGSGKSILINKMLSSLPP-------ETYALTSV 42
++L G GSGK++L +++ LPP ET + S+
Sbjct: 214 LLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSL 252
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 29.0 bits (66), Expect = 0.88
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 12 MLIGNAGSGKSILINKMLSSLPPET 36
+L G +G GKS L+N + L +T
Sbjct: 168 VLAGQSGVGKSTLLNALAPDLELKT 192
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 29.0 bits (65), Expect = 0.90
Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 7/78 (8%)
Query: 5 IPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLEKK 64
+P+ V++ G G+GK+I + L E + + S E L +
Sbjct: 20 LPRGSVVLITGPPGTGKTIFALQFLYEGAREGE--PVLYVSTEESPEELLENARSF---- 73
Query: 65 AGRNFGPPGNKTMIYFVD 82
G + K + +D
Sbjct: 74 -GWDLEVYIEKGKLAILD 90
>gnl|CDD|184203 PRK13643, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 288
Score = 28.9 bits (64), Expect = 0.98
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKP 60
++L + K LIG+ GSGKS L+ + L P T +V +S+ +++ KP
Sbjct: 25 IDLEVKKGSYTALIGHTGSGKSTLLQHLNGLLQP-TEGKVTVGDIVVSSTSKQKEI--KP 81
Query: 61 LEKKAGRNFGPP 72
+ KK G F P
Sbjct: 82 VRKKVGVVFQFP 93
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 29.2 bits (66), Expect = 1.00
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 13 LIGNAGSGKSILINKMLSSLPPET 36
L+G +G GKS LIN +L L +T
Sbjct: 169 LLGQSGVGKSTLINALLPELNQKT 192
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and
chromosome partitioning / Cytoskeleton].
Length = 373
Score = 29.2 bits (66), Expect = 1.1
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 11 VMLIGNAGSGKSILINKMLSS 31
+M++G +G GK+ IN + +
Sbjct: 26 IMVVGESGLGKTTFINTLFGT 46
>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 = 28.8 bits (65), Expect = 1.1
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 8 RKPVMLIGNAGSGKSILINKMLSSLPPE 35
R ++ G GSGK+ L++ +L+ +PP+
Sbjct: 178 RLAFLVSGGTGSGKTTLLSALLALVPPD 205
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 28.8 bits (65), Expect = 1.1
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET---YALTSVPFNFYTSSEMLQKV 56
+L I K + V+LIG GSGKS L+ + L P + + + E+ QKV
Sbjct: 24 SLEIEKGERVLLIGPNGSGKSTLLKLLNGLLKPTSGEVLVDGLDTSSEKSLLELRQKV 81
>gnl|CDD|225438 COG2884, FtsE, Predicted ATPase involved in cell division [Cell
division and chromosome partitioning].
Length = 223
Score = 28.7 bits (65), Expect = 1.1
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
++ IPK + V L G +G+GKS L+ + P
Sbjct: 21 VSFHIPKGEFVFLTGPSGAGKSTLLKLIYGEERP 54
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the
KaiC domain (pfam06745) that occurs in two copies of
the circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 29.0 bits (65), Expect = 1.1
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 5 IPKRKPVMLIGNAGSGKSIL 24
IP+R V+L G G+GKSI
Sbjct: 18 IPERNVVLLSGGPGTGKSIF 37
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component
of iron-siderophores, vitamin B12 and hemin
transporters and related proteins. ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 28.6 bits (65), Expect = 1.2
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET 36
++L I + V ++G G+GKS L+ + L P +
Sbjct: 18 LSLSIEAGEIVGILGPNGAGKSTLLKTLAGLLKPSS 53
>gnl|CDD|226952 COG4586, COG4586, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 325
Score = 28.9 bits (65), Expect = 1.2
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSL 32
++ IPK + V +G G+GKS + KML+ L
Sbjct: 43 ISFEIPKGEIVGFLGANGAGKSTTL-KMLTGL 73
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 28.8 bits (65), Expect = 1.3
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 11 VMLIGNAGSGKSILINKMLSS 31
+M++G +G GK+ LIN + +
Sbjct: 7 LMVVGESGLGKTTLINTLFLT 27
>gnl|CDD|131367 TIGR02314, ABC_MetN, D-methionine ABC transporter, ATP-binding
protein. Members of this family are the ATP-binding
protein of the D-methionine ABC transporter complex.
Known members belong to the Proteobacteria.
Length = 343
Score = 28.7 bits (64), Expect = 1.4
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILI 25
++L +P + +IG +G+GKS LI
Sbjct: 24 VSLHVPAGQIYGVIGASGAGKSTLI 48
>gnl|CDD|213216 cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a
mitochondrial protein MTABC3 and related proteins.
MTABC3 (also known as ABCB6) is a mitochondrial
ATP-binding cassette protein involved in iron
homeostasis and one of four ABC transporters expressed
in the mitochondrial inner membrane, the other three
being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast
MDL1 (multidrug resistance-like protein 1) and MDL2
(multidrug resistance-like protein 2) transporters are
also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1
and is thought to have a role in resistance to
oxidative stress. Interestingly, subfamily B is more
closely related to the carboxyl-terminal component of
subfamily C than the two halves of ABCC molecules are
with one another.
Length = 238
Score = 28.3 bits (64), Expect = 1.5
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILIN 26
++L IP K V L+G++G GKS +++
Sbjct: 22 LSLTIPPGKTVALVGSSGCGKSTVVS 47
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I 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. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of 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 = 211
Score = 28.2 bits (64), Expect = 1.5
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
+L I K + V+++G GSGKS L+
Sbjct: 21 SLTIKKGEFVLIVGPNGSGKSTLLR 45
>gnl|CDD|184582 PRK14236, PRK14236, phosphate transporter ATP-binding protein;
Provisional.
Length = 272
Score = 28.5 bits (64), Expect = 1.5
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSIL---INKM 28
++ IPK + IG +G GKS L N+M
Sbjct: 45 SMRIPKNRVTAFIGPSGCGKSTLLRCFNRM 74
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides, Transport and
binding proteins, Other].
Length = 571
Score = 28.5 bits (64), Expect = 1.5
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
+L I + V L+G +GSGKS L+N
Sbjct: 352 SLVIEPGETVALVGRSGSGKSTLVN 376
>gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein;
Reviewed.
Length = 240
Score = 28.5 bits (64), Expect = 1.5
Identities = 14/31 (45%), Positives = 22/31 (70%), Gaps = 3/31 (9%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSIL---INKM 28
++L I + + V++IG +GSGKS L INK+
Sbjct: 20 IDLNIDQGEVVVIIGPSGSGKSTLLRCINKL 50
>gnl|CDD|184585 PRK14239, PRK14239, phosphate transporter ATP-binding protein;
Provisional.
Length = 252
Score = 28.2 bits (63), Expect = 1.6
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 13 LIGNAGSGKSIL---INKMLSSLPPETYALTSVPFN 45
LIG +GSGKS L IN+M + L PE S+ +N
Sbjct: 36 LIGPSGSGKSTLLRSINRM-NDLNPEVTITGSIVYN 70
>gnl|CDD|172749 PRK14261, PRK14261, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 253
Score = 28.3 bits (63), Expect = 1.6
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 5 IPKRKPVMLIGNAGSGKSILI---NKM 28
IPK + LIG +G GKS L+ N+M
Sbjct: 29 IPKNRVTALIGPSGCGKSTLLRCFNRM 55
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 28.4 bits (64), Expect = 1.6
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 10 PVMLI-GNAGSGKSILINKMLSSLPPETYA 38
PV +I G GSGK+ L+N +L++ + A
Sbjct: 2 PVTVITGFLGSGKTTLLNHLLANRDGKKIA 31
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 28.3 bits (64), Expect = 1.7
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
+ IPK + ++G GSGKS L+ + L P
Sbjct: 22 SFSIPKGEITGILGPNGSGKSTLLKCLAGLLKP 54
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block
in cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 28.1 bits (63), Expect = 1.7
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 10 PVMLI-GNAGSGKSILINKMLSSL 32
P +LI G GSGKS +N ++ SL
Sbjct: 39 PHLLIAGATGSGKSTFLNTLILSL 62
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling
protein DNA-binding domain. The plasmid conjugative
coupling protein TrwB forms hexamers from six
structurally very similar protomers. This hexamer
contains a central channel running from the cytosolic
pole (made up by the AADs) to the membrane pole ending
at the transmembrane pore shaped by 12 transmembrane
helices, rendering an overall mushroom-like structure.
The TrwB_AAD (all-alpha domain) domain appears to be
the DNA-binding domain of the structure. TrwB, a basic
integral inner-membrane nucleoside-triphosphate-binding
protein, is the structural prototype for the type IV
secretion system coupling proteins, a family of
proteins essential for macromolecular transport between
cells and export.
Length = 386
Score = 28.3 bits (64), Expect = 1.8
Identities = 7/28 (25%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 5 IPKRKPV---MLIGNAGSGKSILINKML 29
+P+R +++G G+GK+ + ++L
Sbjct: 9 LPRRSETQHILIVGTTGTGKTQALRELL 36
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 26.4 bits (59), Expect = 1.8
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 11 VMLIGNAGSGKSILINKMLSSLPPETYALTSVPFN 45
+L G +GSGKS LI+ + + L P V FN
Sbjct: 24 TLLTGPSGSGKSTLIDAIQTLLVPA----KRVAFN 54
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 28.4 bits (63), Expect = 1.9
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 5 IPKRKPVMLIGNAGSGKSILINKM 28
+ P+ L G GSGKS LI+++
Sbjct: 146 LKIAVPIYLEGGRGSGKSFLISEL 169
>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 = 1.9
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 5 IPKRKPVMLIGNAGSGKSILINKML 29
IP V++ G +GSGKS L+N+ L
Sbjct: 18 IPLNVLVVVTGVSGSGKSTLVNEGL 42
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 28.4 bits (63), Expect = 2.0
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 11 VMLIGNAGSGKSILINKMLSSLPP--ETYALTSVPFNFYTSSEMLQK 55
++LIG G+GK++L +++ LP AL S ++E +QK
Sbjct: 213 LLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQK 259
>gnl|CDD|237455 PRK13637, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 287
Score = 28.1 bits (63), Expect = 2.0
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILI 25
N+ I + V LIG+ GSGKS LI
Sbjct: 27 NIEIEDGEFVGLIGHTGSGKSTLI 50
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is
one of the Kai proteins among which direct
protein-protein association may be a critical process
in the generation of circadian rhythms in
cyanobacteria.
Length = 231
Score = 28.0 bits (63), Expect = 2.1
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 5 IPKRKPVMLIGNAGSGKSIL 24
IP+ + V++ G G+GK+I
Sbjct: 16 IPRGRVVLITGGPGTGKTIF 35
>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 = 27.6 bits (62), Expect = 2.2
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
+L + + V L+G GSGKS L+
Sbjct: 19 SLTLKAGEIVALVGPNGSGKSTLLR 43
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 27.5 bits (62), Expect = 2.2
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 13 LIGNAGSGKSILINKMLSSLPPET 36
L G +G GKS L+N +L L T
Sbjct: 40 LAGQSGVGKSTLLNALLPELDLRT 63
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 28.0 bits (63), Expect = 2.3
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 7 KRKPVMLIGNAGSGKSILINKML 29
K V L+G++G GKS L+N +L
Sbjct: 194 GGKTVALLGSSGVGKSTLVNALL 216
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 28.1 bits (63), Expect = 2.3
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 1 MNLFIPKRKPVMLI-GNAGSGKSILINKMLSSL 32
N + + LI G G+GK++L++ +L+
Sbjct: 428 FNFHVGEDVGHTLIIGPTGAGKTVLLSFLLAQA 460
>gnl|CDD|237452 PRK13632, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 271
Score = 28.0 bits (63), Expect = 2.3
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSL 32
+ I + + V ++G+ GSGKS I+K+L+ L
Sbjct: 29 SFEINEGEYVAILGHNGSGKST-ISKILTGL 58
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 27.9 bits (62), Expect = 2.3
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 8 RKPVMLIGNAGSGKSILINKMLSSLPPETYALT 40
R ++L G GSGK+ + ++S++PP+ +T
Sbjct: 162 RLTMLLCGPTGSGKTTMSKTLISAIPPQERLIT 194
>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 = 27.8 bits (62), Expect = 2.5
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 11 VMLIGNAGSGKSILINKMLSSL 32
++++G +GSGKS L+ + L
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRL 25
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 28.1 bits (63), Expect = 2.5
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 105 MDYQHWYD-----RQKLSLKDIHNIMFVSAMNPTSGSFTIEPR 142
Y W D + +S +D +VS++ SG+ IEP
Sbjct: 76 RGYSIWVDPRIEENEDISREDFDE--WVSSLEIYSGNKKIEPH 116
>gnl|CDD|224050 COG1125, OpuBA, ABC-type proline/glycine betaine transport
systems, ATPase components [Amino acid transport and
metabolism].
Length = 309
Score = 27.6 bits (62), Expect = 2.6
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 3/31 (9%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSIL---INKML 29
NL I + + ++LIG +GSGK+ IN+++
Sbjct: 21 NLTIEEGEFLVLIGPSGSGKTTTLKMINRLI 51
>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 = 27.7 bits (62), Expect = 2.6
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 11 VMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNF 46
V+L+G + SGK+ L K+ + T TS+ N
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRSTV--TSIEPNV 36
>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 27.9 bits (63), Expect = 2.8
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSIL 24
+L IP+ K V++ G +GSGKS L
Sbjct: 20 DLEIPRNKLVVITGLSGSGKSSL 42
Score = 26.8 bits (60), Expect = 6.5
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 5 IPKRKPVMLIGNAGSGKSILINKML 29
IP + G +GSGKS LIN L
Sbjct: 624 IPLGVFTCVTGVSGSGKSTLINDTL 648
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 27.7 bits (62), Expect = 2.9
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 6 PKRKPVMLIGNAGSGKSILINKMLSS 31
++ V ++G GKS LIN++L
Sbjct: 130 KRKIRVGVVGYPNVGKSTLINRLLGK 155
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 27.5 bits (62), Expect = 2.9
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSL 32
NL I + V ++G +GSGKS L+N +L L
Sbjct: 25 NLEIEAGEFVAIVGPSGSGKSTLLN-LLGGL 54
>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 = 27.4 bits (61), Expect = 2.9
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 13 LIGNAGSGKSILINKML--SSLPPETYALTSVPFNFYT 48
++G G GKS L+N +L T+ + Y
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYV 39
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 27.3 bits (61), Expect = 3.0
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 11 VMLIGNAGSGKSILINKMLSSLP 33
++++G GSGKS ++L L
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELG 24
>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 = 27.7 bits (62), Expect = 3.1
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSIL 24
++ IP+ K V++ G +GSGKS L
Sbjct: 16 DVEIPRDKLVVITGLSGSGKSSL 38
Score = 26.9 bits (60), Expect = 7.0
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKML 29
+ IP + G +GSGKS LIN L
Sbjct: 628 TVSIPLGLFTCITGVSGSGKSTLINDTL 655
>gnl|CDD|200134 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD 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 [Protein fate, Protein and
peptide secretion and trafficking].
Length = 544
Score = 27.7 bits (62), Expect = 3.2
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPE 35
++ + + + +IG +GSGKS L ++ PP
Sbjct: 337 ISFSLQAGEALAIIGPSGSGKSTLARLIVGIWPPT 371
>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 = 27.2 bits (61), Expect = 3.2
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 7 KRKPVMLIGNAGSGKSILINKMLSSLPPE 35
RK +++ G GSGK+ L+N +L+ +PP+
Sbjct: 24 ARKNILISGGTGSGKTTLLNALLAFIPPD 52
>gnl|CDD|237451 PRK13631, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 320
Score = 27.5 bits (61), Expect = 3.2
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 7 KRKPVMLIGNAGSGKSILIN 26
K K +IGN+GSGKS L+
Sbjct: 51 KNKIYFIIGNSGSGKSTLVT 70
>gnl|CDD|213237 cd03270, ABC_UvrA_I, ATP-binding cassette domain I 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 = 226
Score = 27.2 bits (61), Expect = 3.3
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSIL 24
++ IP+ K V++ G +GSGKS L
Sbjct: 15 DVDIPRNKLVVITGVSGSGKSSL 37
>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 = 26.9 bits (60), Expect = 3.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 11 VMLIGNAGSGKSILINKML 29
V L+G GKS LIN +
Sbjct: 2 VALVGRPNVGKSTLINALT 20
>gnl|CDD|189778 pfam00938, Lipoprotein_3, Lipoprotein. This family of
lipoproteins is Mycoplasma specific.
Length = 87
Score = 26.3 bits (58), Expect = 3.4
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 20 GKSILIN---KMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLEKKAGRNFGPPGNKT 76
GK LI K S P +T T++ + + S K+LEK L+ + + FG +K
Sbjct: 27 GKKNLITSLKKSYESNPKKT---TNLLLDAWKQSLEDGKILEKELDSRFAKAFGSGKSKE 83
Query: 77 MIY 79
+
Sbjct: 84 DVE 86
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 27.5 bits (61), Expect = 3.9
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSL 32
+NL I + + V LIG GSGKS L +L+ L
Sbjct: 342 INLTIKRGELVFLIGGNGSGKSTLA-MLLTGL 372
>gnl|CDD|172762 PRK14274, PRK14274, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 259
Score = 27.2 bits (60), Expect = 3.9
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILI---NKMLSSLP 33
+NL IP+ + +IG +G GKS I N M+ +P
Sbjct: 31 INLSIPENEVTAIIGPSGCGKSTFIKTLNLMIQMVP 66
>gnl|CDD|182561 PRK10575, PRK10575, iron-hydroxamate transporter ATP-binding
subunit; Provisional.
Length = 265
Score = 27.1 bits (60), Expect = 4.0
Identities = 15/29 (51%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKML 29
++L P K LIG+ GSGKS L+ KML
Sbjct: 30 LSLTFPAGKVTGLIGHNGSGKSTLL-KML 57
>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 = 27.3 bits (61), Expect = 4.0
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 11 VMLIGNAGSGKSILINKMLSSLPPETYALT 40
V ++G +GSGKS L+ + + P+ ++T
Sbjct: 367 VAILGRSGSGKSTLLQLLAGAWDPQQGSIT 396
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 27.3 bits (61), Expect = 4.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 7 KRKPVMLIGNAGSGKSILIN 26
K+ V L+GN GK+ L N
Sbjct: 2 KKLTVALVGNPNVGKTTLFN 21
>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 = 26.8 bits (60), Expect = 4.2
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
+ I + + +IG +GSGKS L +L L P
Sbjct: 22 SFSIEPGESLAIIGPSGSGKSTLARLILGLLRP 54
>gnl|CDD|213259 cd03292, ABC_FtsE_transporter, ATP-binding cassette domain of the
cell division transporter. FtsE is a hydrophilic
nucleotide-binding protein that binds FtsX to form a
heterodimeric ATP-binding cassette (ABC)-type
transporter that associates with the bacterial inner
membrane. The FtsE/X transporter is thought to be
involved in cell division and is important for assembly
or stability of the septal ring.
Length = 214
Score = 27.0 bits (60), Expect = 4.2
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET 36
+N+ I + V L+G +G+GKS L+ + P +
Sbjct: 20 INISISAGEFVFLVGPSGAGKSTLLKLIYKEELPTS 55
>gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding
protein. [Transport and binding proteins, Anions].
Length = 237
Score = 27.1 bits (60), Expect = 4.4
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILI 25
+NL +P V L+G +GSGKS L+
Sbjct: 19 VNLEVPTGSLVALLGPSGSGKSTLL 43
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 27.2 bits (61), Expect = 4.5
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET 36
+L IP + V ++G +GSGKS L+ +L P+
Sbjct: 493 SLEIPPGEKVAIVGRSGSGKSTLLKLLLGLYKPQQ 527
>gnl|CDD|191413 pfam05970, PIF1, PIF1-like helicase. This family includes
homologues of the PIF1 helicase, which inhibits
telomerase activity and is cell cycle regulated. This
family includes a large number of largely
uncharacterized plant proteins. This family includes a
P-loop motif that is involved in nucleotide binding.
Length = 364
Score = 27.3 bits (61), Expect = 4.5
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 15 GNAGSGKSILINKMLSSLPPE 35
G G+GK+ L + +SL
Sbjct: 29 GYGGTGKTYLWKALSASLRSR 49
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 27.1 bits (61), Expect = 4.5
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
NL + K + V ++G +G GKS L+
Sbjct: 23 NLSVEKGEFVAILGPSGCGKSTLLR 47
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 26.9 bits (60), Expect = 4.5
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 10 PVMLIGNAGSGKSILINKMLSSLP-PETYALTSVPFNFY 47
V+L G AGSGK+ L+ K+ + F
Sbjct: 2 TVILQGEAGSGKTTLLQKIALLWAQGKLPQDFDFVFFLP 40
>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 = 26.8 bits (60), Expect = 4.5
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
+L I K + + L G +G+GK+ L+ + +L P
Sbjct: 22 SLHIRKGEFLFLTGPSGAGKTTLLKLLYGALTP 54
>gnl|CDD|237809 PRK14738, gmk, guanylate kinase; Provisional.
Length = 206
Score = 27.0 bits (60), Expect = 4.5
Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 14/60 (23%)
Query: 9 KPVMLI--GNAGSGKSILINKMLSSLPPETYALTS------------VPFNFYTSSEMLQ 54
KP++++ G +G GK ++ +M P + +T+ V ++F T E +
Sbjct: 12 KPLLVVISGPSGVGKDAVLARMRERKLPFHFVVTATTRPKRPGEIDGVDYHFVTPEEFRE 71
>gnl|CDD|206650 cd01851, GBP, Guanylate-binding protein (GBP) family (N-terminal
domain). Guanylate-binding protein (GBP), N-terminal
domain. Guanylate-binding proteins (GBPs) define a
group of proteins that are synthesized after activation
of the cell by interferons. The biochemical properties
of GBPs are clearly different from those of Ras-like
and heterotrimeric GTP-binding proteins. They bind
guanine nucleotides with low affinity (micromolar
range), are stable in their absence and have a high
turnover GTPase. In addition to binding GDP/GTP, they
have the unique ability to bind GMP with equal affinity
and hydrolyze GTP not only to GDP, but also to GMP.
Furthermore, two unique regions around the base and the
phosphate-binding areas, the guanine and the phosphate
caps, respectively, give the nucleotide-binding site a
unique appearance not found in the canonical
GTP-binding proteins. The phosphate cap, which
constitutes the region analogous to switch I,
completely shields the phosphate-binding site from
solvent such that a potential GTPase-activating protein
(GAP) cannot approach.
Length = 224
Score = 26.9 bits (60), Expect = 4.6
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 9 KPVMLIGNAGSGKSILINKMLS 30
V + G+ SGKS L+N +
Sbjct: 8 VVVSVFGSQSSGKSFLLNHLFG 29
>gnl|CDD|226963 COG4604, CeuD, ABC-type enterochelin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 252
Score = 26.9 bits (60), Expect = 4.6
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET 36
+L IPK +IG G+GKS L++ M L ++
Sbjct: 21 SLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKDS 55
>gnl|CDD|131817 TIGR02770, nickel_nikD, nickel import ATP-binding protein NikD.
This family represents the NikD subunit of a
multisubunit nickel import ABC transporter complex.
Nickel, once imported, may be used in urease and in
certain classes of hydrogenase and superoxide
dismutase. NikD and NikE are homologous [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 230
Score = 26.9 bits (60), Expect = 4.8
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET 36
+NL + + + + L+G +GSGKS+ +L LPP
Sbjct: 5 LNLSLKRGEVLALVGESGSGKSLTCLAILGLLPPGL 40
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 26.9 bits (60), Expect = 4.9
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALT--SVPFNFYTSSEMLQKV 56
++L +P K LIG G GKS L+ L P++ + P + +S ++ +++
Sbjct: 21 LSLSLPTGKITALIGPNGCGKSTLLKCFARLLTPQSGTVFLGDKPISMLSSRQLARRL 78
>gnl|CDD|182336 PRK10253, PRK10253, iron-enterobactin transporter ATP-binding
protein; Provisional.
Length = 265
Score = 26.9 bits (59), Expect = 5.0
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 10/80 (12%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKP 60
+ + IP +IG G GKS L+ + LS L +T + + E +Q K
Sbjct: 26 LTVEIPDGHFTAIIGPNGCGKSTLL-RTLSRL------MTPAHGHVWLDGEHIQHYASKE 78
Query: 61 LEKKAG---RNFGPPGNKTM 77
+ ++ G +N PG+ T+
Sbjct: 79 VARRIGLLAQNATTPGDITV 98
>gnl|CDD|227250 COG4913, COG4913, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1104
Score = 27.3 bits (60), Expect = 5.1
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 8 RKPVMLIGNAGSGKSILINKMLSSLPPE 35
R+ +++ G +GSGKS LI+ + + L P+
Sbjct: 37 REGILVTGGSGSGKSTLIDAITAVLLPQ 64
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 26.1 bits (57), Expect = 5.1
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 11 VMLIGNAGSGKSILINK 27
+++ G GSGKS L K
Sbjct: 2 ILITGPPGSGKSTLAKK 18
>gnl|CDD|226637 COG4167, SapF, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 267
Score = 26.7 bits (59), Expect = 5.1
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 7 KRKPVMLIGNAGSGKSILINKMLSSLPPET 36
+ + + +IG GSGKS L KML+ + T
Sbjct: 38 EGQTLAIIGENGSGKSTLA-KMLAGMIEPT 66
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 26.8 bits (60), Expect = 5.2
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
+L + K + LIG G+GKS L+ +L L P
Sbjct: 24 SLSVEKGEITALIGPNGAGKSTLLKAILGLLKP 56
>gnl|CDD|188208 TIGR02323, CP_lyasePhnK, phosphonate C-P lyase system protein
PhnK. Members of this family are the PhnK protein of
C-P lyase systems for utilization of phosphonates.
These systems resemble phosphonatase-based systems in
having a three component ABC transporter, where
TIGR01097 is the permease, TIGR01098 is the
phosphonates binding protein, and TIGR02315 is the
ATP-binding cassette (ABC) protein. They differ,
however, in having, typically, ten or more additional
genes, many of which are believed to form a
membrane-associated complex. This protein (PhnK) and
the adjacent-encoded PhnL resemble transporter
ATP-binding proteins but are suggested, based on
mutatgenesis studies, to be part of this complex rather
than part of a transporter per se [Central intermediary
metabolism, Phosphorus compounds].
Length = 253
Score = 26.7 bits (59), Expect = 5.2
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 13 LIGNAGSGKSILINKMLSSLPPET 36
++G +GSGKS L+ + L P+
Sbjct: 34 IVGESGSGKSTLLGCLAGRLAPDH 57
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 26.8 bits (60), Expect = 5.3
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 6 PKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPF 44
K+ V ++G GKS LINK+L + +T+ PF
Sbjct: 153 NKKD-VYVVGVTNVGKSSLINKLLKQNNGDKDVITTSPF 190
>gnl|CDD|236997 PRK11831, PRK11831, putative ABC transporter ATP-binding protein
YrbF; Provisional.
Length = 269
Score = 26.7 bits (59), Expect = 5.3
Identities = 9/36 (25%), Positives = 21/36 (58%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPET 36
++L +P+ K ++G +G GK+ L+ + + P+
Sbjct: 26 ISLTVPRGKITAIMGPSGIGKTTLLRLIGGQIAPDH 61
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139)
is part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(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).
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.
Length = 222
Score = 26.6 bits (60), Expect = 5.3
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPP 34
++L +P+ + V L+G G+GK+ L+ ++ LPP
Sbjct: 19 VSLTVPEGEIVALLGRNGAGKTTLLKTIMGLLPP 52
>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 = 26.9 bits (60), Expect = 5.5
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 1 MNLFIPKRKPV---MLIGNAGSGKSILINKMLSSL 32
N + K + ++ G GSGK+ L+N +L+ +
Sbjct: 424 FNFHVRDAKVLGHTLIFGPTGSGKTTLLNFLLAQM 458
>gnl|CDD|237649 PRK14254, PRK14254, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 285
Score = 26.7 bits (59), Expect = 6.0
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 5 IPKRKPVMLIGNAGSGKSIL---INKM 28
IP+ + +IG +G GKS IN+M
Sbjct: 62 IPENQVTAMIGPSGCGKSTFLRCINRM 88
>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 = 26.8 bits (60), Expect = 6.1
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILI 25
+L I + V LIG +G+GKS L+
Sbjct: 21 SLSINPGEFVALIGPSGAGKSTLL 44
>gnl|CDD|237650 PRK14265, PRK14265, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 274
Score = 26.5 bits (58), Expect = 6.2
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILI---NKMLSSLP 33
++L IP +K + IG +G GKS L+ N+M +P
Sbjct: 39 VHLKIPAKKIIAFIGPSGCGKSTLLRCFNRMNDLIP 74
>gnl|CDD|184586 PRK14240, PRK14240, phosphate transporter ATP-binding protein;
Provisional.
Length = 250
Score = 26.6 bits (59), Expect = 6.3
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILI---NKM 28
+NL I + + LIG +G GKS + N+M
Sbjct: 22 INLDIEENQVTALIGPSGCGKSTFLRTLNRM 52
>gnl|CDD|223521 COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 316
Score = 26.8 bits (60), Expect = 6.4
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTS 41
+ + K + + ++G +GSGKS+L ++ LP +
Sbjct: 25 SFELKKGEILGIVGESGSGKSVLAKAIMGLLPKPNARIVG 64
>gnl|CDD|226641 COG4172, COG4172, ABC-type uncharacterized transport system,
duplicated ATPase component [General function
prediction only].
Length = 534
Score = 26.9 bits (60), Expect = 6.6
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 11 VMLIGNAGSGKSILINKMLSSLP--PETYALTSVPFN 45
+ L+G +GSGKS+ +L LP + S+ F+
Sbjct: 39 LALVGESGSGKSVTALSILGLLPSPAAAHPSGSILFD 75
>gnl|CDD|236863 PRK11153, metN, DL-methionine transporter ATP-binding subunit;
Provisional.
Length = 343
Score = 26.7 bits (60), Expect = 6.6
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILI 25
+L IP + +IG +G+GKS LI
Sbjct: 25 SLHIPAGEIFGVIGASGAGKSTLI 48
>gnl|CDD|237651 PRK14266, PRK14266, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 250
Score = 26.5 bits (58), Expect = 6.6
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILI---NKMLSSLP 33
+NL IPK LIG +G GKS I N+M +P
Sbjct: 22 VNLDIPKNSVTALIGPSGCGKSTFIRTLNRMNDLIP 57
>gnl|CDD|226969 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase
and permease components [General function prediction
only].
Length = 580
Score = 26.9 bits (60), Expect = 6.7
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 13 LIGNAGSGKSILINKMLSSLPP 34
+IG +GSGKS L ++ PP
Sbjct: 367 IIGPSGSGKSTLARLLVGIWPP 388
>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 = 10/25 (40%), Positives = 18/25 (72%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
+L +P + V ++G +G+GKS L+N
Sbjct: 19 DLTVPAGEIVAILGPSGAGKSTLLN 43
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 26.7 bits (59), Expect = 6.9
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 4 FIPKR------KPVMLIGNAGSGKSILINKMLSSL 32
IP+ K V ++G +GKS L+NK+ +
Sbjct: 152 HIPREVRPFFVKTVAILGGESTGKSTLVNKLAAVF 186
>gnl|CDD|224787 COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family
domains [General function prediction only].
Length = 436
Score = 26.5 bits (59), Expect = 7.0
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 11 VMLIGNAGSGKSIL 24
V L G AG+GK++L
Sbjct: 248 VSLGGKAGTGKTLL 261
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 26.3 bits (58), Expect = 7.2
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 9 KPVMLIGNAGSGKSILINKMLSSL 32
K V ++G SGKS L+NK+ +
Sbjct: 9 KTVAILGGESSGKSTLVNKLANIF 32
>gnl|CDD|215414 PLN02772, PLN02772, guanylate kinase.
Length = 398
Score = 26.7 bits (59), Expect = 7.3
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 9 KPVMLIGNAGSGKSILINKMLSSLP 33
KP+++ G +G GK LI+ ++ P
Sbjct: 136 KPIVISGPSGVGKGTLISMLMKEFP 160
>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 = 26.6 bits (59), Expect = 7.3
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 12 MLIGNAGSGKSILINKMLSS 31
M+IG G+GK+ I ++L+S
Sbjct: 46 MIIGTTGTGKTTQIRELLAS 65
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 26.6 bits (59), Expect = 7.5
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 9 KPVMLIGNAGSGKSIL----INKMLSSLPPE 35
+ +++IG GSGK+ L IN+M+ P E
Sbjct: 149 RNILVIGGTGSGKTTLVNAIINEMVIQDPTE 179
>gnl|CDD|184588 PRK14243, PRK14243, phosphate transporter ATP-binding protein;
Provisional.
Length = 264
Score = 26.3 bits (58), Expect = 8.3
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 3 LFIPKRKPVMLIGNAGSGKSILI---NKM 28
L IPK + IG +G GKS ++ N++
Sbjct: 31 LDIPKNQITAFIGPSGCGKSTILRCFNRL 59
>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 = 26.2 bits (58), Expect = 8.3
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 7 KRKPVMLIGNAGSGKSILINKMLSSLPPET 36
RK +++ G SGK+ L+N +L +PPE
Sbjct: 142 ARKSIIICGGTASGKTTLLNALLDFIPPEE 171
>gnl|CDD|237454 PRK13634, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 290
Score = 26.1 bits (58), Expect = 8.6
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPL 61
N+ IP V +IG+ GSGKS L+ + L P + +T ++ K L KPL
Sbjct: 27 NVSIPSGSYVAIIGHTGSGKSTLLQHLNGLLQPTSGTVTIG--ERVITAGKKNKKL-KPL 83
Query: 62 EKKAG 66
KK G
Sbjct: 84 RKKVG 88
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 25.8 bits (57), Expect = 8.7
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 11 VMLIGNAGSGKSILINKMLS-SLPPET 36
++LIG+ G GKS LI ++S P
Sbjct: 5 IVLIGDEGVGKSSLIMSLVSEEFPENV 31
>gnl|CDD|224588 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related
proteins [Cell division and chromosome partitioning].
Length = 858
Score = 26.3 bits (58), Expect = 8.8
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 11 VMLIGNAGSGKSILINKMLSSL 32
+++ G GSGKS+ +N M+ SL
Sbjct: 533 LLIAGATGSGKSVALNTMILSL 554
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain
of the nitrate and sulfonate transporters. NrtD and
SsuB are the ATP-binding subunits of the bacterial
ABC-type nitrate and sulfonate transport systems,
respectively. 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 = 220
Score = 25.9 bits (58), Expect = 8.8
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
+L + + + V L+G +G GKS L+
Sbjct: 24 SLSVEEGEFVALVGPSGCGKSTLLR 48
>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 = 25.9 bits (58), Expect = 9.0
Identities = 14/31 (45%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILINKMLSSL 32
+L I K + V ++G +GSGKS L+N +L L
Sbjct: 24 SLSIEKGEFVAIVGPSGSGKSTLLN-ILGGL 53
>gnl|CDD|173666 cd05575, STKc_SGK, Catalytic domain of the Protein Serine/Threonine
Kinase, Serum- and Glucocorticoid-induced Kinase.
Serine/Threonine Kinases (STKs), Serum- and
Glucocorticoid-induced Kinase (SGK) subfamily, catalytic
(c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The SGK subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. There are three
isoforms of SGK, named SGK1, SGK2, and SGK3 (also called
cytokine-independent survival kinase CISK). SGKs are
activated by insulin and growth factors via
phosphoinositide 3-kinase and PDK1. They activate ion
channels, ion carriers, and the Na-K-ATPase, as well as
regulate the activity of enzymes and transcription
factors. SGKs play important roles in transport, hormone
release, neuroexcitability, cell proliferation, and
apoptosis.
Length = 323
Score = 26.3 bits (58), Expect = 9.1
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 13/43 (30%)
Query: 27 KMLSSLPPETYALTSVPFNFYT--SSEMLQKVLEKPLEKKAGR 67
+ML LPP FY+ ++EM +L KPL K
Sbjct: 188 EMLYGLPP-----------FYSRDTAEMYDNILNKPLRLKPNI 219
>gnl|CDD|225913 COG3378, COG3378, Phage associated DNA primase [General function
prediction only].
Length = 517
Score = 26.2 bits (58), Expect = 9.2
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 8 RKPVMLIGNAGSGKSILIN 26
+K L G G+GKS ++
Sbjct: 230 QKLFWLYGPGGNGKSTFVD 248
>gnl|CDD|226482 COG3973, COG3973, Superfamily I DNA and RNA helicases [General
function prediction only].
Length = 747
Score = 26.4 bits (58), Expect = 9.2
Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 24/91 (26%)
Query: 6 PKRKPVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLEKKA 65
K K +++ G AGSGK+ T AL V + Y PL+ K
Sbjct: 224 EKNKILVVQGAAGSGKT-------------TIALHRVAYLLYGY--------RGPLQAKP 262
Query: 66 GRNFGPPGNKTMIYFVDDMNMPEVDAYGTVQ 96
GP N+ + ++ + +PE+ G VQ
Sbjct: 263 VLVLGP--NRVFLEYISRV-LPELGEEGVVQ 290
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 26.4 bits (59), Expect = 9.3
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 13 LIGNAGSGKSILINKMLSSLPPE 35
++G +GSGKS L ++ LP
Sbjct: 40 IVGESGSGKSTLALALMGLLPEG 62
>gnl|CDD|234400 TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa. This
model represents the N-terminal domain or EccCa subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 661
Score = 26.5 bits (59), Expect = 9.3
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 12 MLIGNAGSGKSILINKMLSSL----PPETYALTSVPF 44
+ IG GSGKS L+ ++ L PE L V F
Sbjct: 442 LCIGATGSGKSELLRTLVLGLAATHSPEQLNLVLVDF 478
>gnl|CDD|224055 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
permease components [Defense mechanisms].
Length = 567
Score = 26.2 bits (58), Expect = 9.3
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 2 NLFIPKRKPVMLIGNAGSGKSILIN 26
+ I + V ++G +GSGKS LI
Sbjct: 349 SFSIEPGEKVAIVGPSGSGKSTLIK 373
>gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit.
This model describes the ATP binding subunit of the
multisubunit cobalt transporter in bacteria and its
equivalents in archaea. The model is restricted to ATP
subunit that is a part of the cobalt transporter, which
belongs to the ABC transporter superfamily (ATP Binding
Cassette). The model excludes ATP binding subunit that
are associated with other transporters belonging to ABC
transporter superfamily. This superfamily includes two
groups, one which catalyze the uptake of small
molecules, including ions from the external milieu and
the other group which is engaged in the efflux of small
molecular weight compounds and ions from within the
cell. Energy derived from the hydrolysis of ATP drive
the both the process of uptake and efflux [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 190
Score = 25.8 bits (57), Expect = 9.4
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPETYALT 40
+N + + + L+G G+GKS L+ + L P++ A+
Sbjct: 11 LNFAAERGEVLALLGANGAGKSTLLLHLNGLLRPQSGAVL 50
>gnl|CDD|130252 TIGR01184, ntrCD, nitrate transport ATP-binding subunits C and D.
This model describes the ATP binding subunits of
nitrate transport in bacteria and archaea. This protein
belongs to the ATP-binding cassette (ABC) superfamily.
It is thought that the two subunits encoded by ntrC and
ntrD form the binding surface for interaction with ATP.
This model is restricted in identifying ATP binding
subunit associated with the nitrate transport. Nitrate
assimilation is aided by other proteins derived from
the operon which among others include products of ntrA
- a regulatory protein; ntrB - a hydropbobic
transmembrane permease and narB - a reductase
[Transport and binding proteins, Anions, Transport and
binding proteins, Other].
Length = 230
Score = 25.9 bits (57), Expect = 9.4
Identities = 14/32 (43%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSL 32
+NL I + + + LIG++G GKS L+N ++S L
Sbjct: 4 VNLTIQQGEFISLIGHSGCGKSTLLN-LISGL 34
>gnl|CDD|224445 COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and
metabolism].
Length = 167
Score = 25.7 bits (57), Expect = 9.6
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 31 SLPPETYALTSVPFNFYTSSEMLQKVLE 58
PE A+ + P F + E+ +K LE
Sbjct: 65 GARPELKAIEAPPNKFSSLKELFEKTLE 92
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 26.2 bits (57), Expect = 9.7
Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 16/86 (18%)
Query: 10 PVMLIGNAGSGKSILINKMLSSLPPETYALTSVPFNFYTSSEMLQKVLEKPLEKKAGRNF 69
PV L G AGSGK+ + ++ +L + FY + ++ + K G+
Sbjct: 121 PVFLKGGAGSGKNHIAEQIAEALDLD----------FYFMNAIMDEFELKGFIDANGKFH 170
Query: 70 GPPGNKTM----IYFVDDMN--MPEV 89
P + ++F+D+++ +PE
Sbjct: 171 ETPFYEAFKKGGLFFIDEIDASIPEA 196
>gnl|CDD|226620 COG4136, COG4136, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 213
Score = 25.9 bits (57), Expect = 9.8
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 1 MNLFIPKRKPVMLIGNAGSGKSILINKMLSSLPPE 35
+N I K + V L+G +G GKS L++ M+ +L +
Sbjct: 21 VNFTIAKGEIVTLMGPSGCGKSTLLSWMIGALAGQ 55
>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 = 25.8 bits (58), Expect = 9.9
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 11 VMLIGNAGSGKSILINKMLSSL 32
+L+G +G GKS L+N +L L
Sbjct: 88 SVLVGQSGVGKSTLLNALLPEL 109
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.138 0.413
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,533,612
Number of extensions: 773492
Number of successful extensions: 1292
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1292
Number of HSP's successfully gapped: 221
Length of query: 163
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 74
Effective length of database: 6,990,096
Effective search space: 517267104
Effective search space used: 517267104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.0 bits)