RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780132|ref|YP_003064545.1| guanylate kinase [Candidatus
Liberibacter asiaticus str. psy62]
(186 letters)
>gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 111 bits (279), Expect = 1e-25
Identities = 56/176 (31%), Positives = 85/176 (48%), Gaps = 8/176 (4%)
Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKH 63
+ VL G SGVGK+T+ K + L + L V TTR+PR E +DY F+++ +F+
Sbjct: 6 LIVLSGPSGVGKSTLVKAL-LEDDKLRFSVSATTRKPRPGEVDGVDYFFVTEEEFEELIE 64
Query: 64 TGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAPP 123
F+E + YYG +E + + G D++L + QG +KK + V SIFI PP
Sbjct: 65 RDEFLEWAEYHGNYYGTSREPVEQALAEGKDVILDIDVQGALQVKKKMPNAV-SIFILPP 123
Query: 124 SEAELIQRRIKRREDIPFNLDPDL------FGKNHSYSFTIVNNHLPTACRQVGLI 173
S EL +R R D + L + + IVN+ L A ++ I
Sbjct: 124 SLEELERRLKGRGTDSEEVIARRLENAKKEISHADEFDYVIVNDDLEKALEELKSI 179
>gnl|CDD|73180 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines..
Length = 137
Score = 92.5 bits (230), Expect = 5e-20
Identities = 44/121 (36%), Positives = 64/121 (52%), Gaps = 2/121 (1%)
Query: 4 IFVLIGASGVGKTTIAKQVVLN-SEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62
+ VL G SGVGK+T+ K+++ V TTR+PR E +DY F+S+ +F+
Sbjct: 1 LIVLSGPSGVGKSTLLKRLLEEFDPNFGFSVSHTTRKPRPGEVDGVDYHFVSKEEFERLI 60
Query: 63 HTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAP 122
G F+E + YYG K + + G ++L + QG +KK Y D V SIFI P
Sbjct: 61 ENGEFLEWAEFHGNYYGTSKAAVEEALAEGKIVILEIDVQGARQVKKSYPDAV-SIFILP 119
Query: 123 P 123
P
Sbjct: 120 P 120
>gnl|CDD|144280 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 182
Score = 84.3 bits (209), Expect = 2e-17
Identities = 57/175 (32%), Positives = 80/175 (45%), Gaps = 10/175 (5%)
Query: 4 IFVLIGASGVGKTTIAKQVV-LNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62
VL G SGVGK+ I K ++ E V TTR PR E DY F+S+ + +
Sbjct: 3 PIVLSGPSGVGKSHIKKALLDEYPEKFGYSVSHTTRPPRPGEVDGKDYHFVSKEEMENDI 62
Query: 63 HTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAP 122
F+E + YYG KE I E G +L + QG+ L+K S+FI P
Sbjct: 63 SANEFLEHAEFNGNYYGTSKEAIEQIAESGKICILDVDIQGVKQLRKAEL-SPISVFIKP 121
Query: 123 PSEAELIQRRIKRR-----EDIPFNLDP--DLFGKNHSYSFTIVNNHLPTACRQV 170
PS L QRR+K R E I ++ F + + IVN+ L A +++
Sbjct: 122 PSLKVL-QRRLKGRGTEQEEKINKRMEAAEQEFQHYAEFDYIIVNDDLDEAYKKL 175
>gnl|CDD|35829 KOG0609, KOG0609, KOG0609, Calcium/calmodulin-dependent serine
protein kinase/membrane-associated guanylate kinase
[Signal transduction mechanisms].
Length = 542
Score = 75.0 bits (184), Expect = 1e-14
Identities = 49/179 (27%), Positives = 76/179 (42%), Gaps = 16/179 (8%)
Query: 6 VLIGASGVGKTTIAKQVV-LNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHT 64
VLIGA GVG+ + +++ LN + V TTR PR DE ++Y F+S+ + +
Sbjct: 344 VLIGAQGVGRRELKNKLIELNPDRFGTAVPHTTRPPRSDEVDGVEYHFVSKEEMEADIRA 403
Query: 65 GLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAPPS 124
G F+E + YG + + N + G +L + Q L L+ E + IFIAPPS
Sbjct: 404 GKFLEYGEYEGNLYGTSLDSVRNVIASGKICVLDVEPQALKVLRTA-EFKPYVIFIAPPS 462
Query: 125 EAELIQRRIKRRE--DIPFNLDPDLFGK------------NHSYSFTIVNNHLPTACRQ 169
EL R + + + H + IVN+ L R+
Sbjct: 463 LEELRALRKVAVMSTIVAKQFTDEDLQEIIDESARIEQQYGHYFDLIIVNSDLDKTFRE 521
>gnl|CDD|35926 KOG0707, KOG0707, KOG0707, Guanylate kinase [Nucleotide transport
and metabolism].
Length = 231
Score = 50.4 bits (120), Expect = 3e-07
Identities = 44/133 (33%), Positives = 57/133 (42%), Gaps = 6/133 (4%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVM---PVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62
VL G SGVGK+T+ K+ L E M V TTR PR E Y F + +F
Sbjct: 41 VLSGPSGVGKSTLLKR--LREELGGMFGFSVSHTTRTPRAGEVHGKHYHFSTTEEFLSMI 98
Query: 63 HTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAP 122
FIE YG + M G +L + QG+ P++ D + IFI P
Sbjct: 99 KNNEFIEFATFSGNKYGTSIAAVQRLMLSGKVCILDIDLQGVQPIRATSLDAIY-IFIKP 157
Query: 123 PSEAELIQRRIKR 135
PS L +R R
Sbjct: 158 PSIKILEERLRAR 170
>gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism].
Length = 218
Score = 32.9 bits (75), Expect = 0.047
Identities = 33/143 (23%), Positives = 55/143 (38%), Gaps = 12/143 (8%)
Query: 4 IFVLI-GASGVGKTTIAKQVV--LNSEYLVMPVG----VTTRRPRVDEKQYIDYRFISQS 56
I + I G SG GKTT+AK++ L E +V+ +E+ I+Y
Sbjct: 9 IIIGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDDYYKDQSHLPFEERNKINYDHPEAF 68
Query: 57 QFKG-WKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPL--KKLYED 113
+H + V Y Y +++ +G+ L ++L +
Sbjct: 69 DLDLLIEHLKDLKQGKPVDLPVYDYKTHTREPETIKVEPNDVVIV-EGILLLYDERLRDL 127
Query: 114 QVTSIFIAPPSEAELIQRRIKRR 136
IF+ ++ LI RRIKR
Sbjct: 128 MDLKIFVDTDADVRLI-RRIKRD 149
>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the
ATP synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor
Rho.
Length = 213
Score = 32.0 bits (74), Expect = 0.086
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 7 LIGASGVGKTTIAKQVVLNSEYLVMPV 33
+ G SG GKT + + N++ V+ V
Sbjct: 20 IFGGSGTGKTVLLGMIARNAKADVVEV 46
>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G
in the GTP form binds to the ribosome, primarily
through the interaction of its EF-Tu-like domain with
the 50S subunit. The binding of EF-G to the ribosome
in this manner stimulates the GTPase activity of EF-G.
On GTP hydrolysis, EF-G undergoes a conformational
change that forces its arm deeper into the A site on
the 30S subunit. To accommodate this domain, the
peptidyl-tRNA in the A site moves to the P site,
carrying the mRNA and the deacylated tRNA with it. The
ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation
of EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains
only bacterial members.
Length = 268
Score = 32.1 bits (74), Expect = 0.10
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 5 FVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDE 44
L+G SG GKTT+A+ ++ + G R V++
Sbjct: 2 IALVGHSGSGKTTLAEALLYAT-------GAIDRLGSVED 34
>gnl|CDD|30352 COG0003, ArsA, Predicted ATPase involved in chromosome
partitioning [Cell division and chromosome
partitioning].
Length = 322
Score = 31.1 bits (70), Expect = 0.20
Identities = 11/19 (57%), Positives = 11/19 (57%)
Query: 1 MAHIFVLIGASGVGKTTIA 19
M I G GVGKTTIA
Sbjct: 1 MTRIVFFTGKGGVGKTTIA 19
>gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 30.5 bits (69), Expect = 0.26
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 4 IFVLIGASGVGKTTIAKQV--VLNSEYLVMPVG 34
I L+G GVGKT++ K + L +++ + +G
Sbjct: 352 ILCLVGPPGVGKTSLGKSIAKALGRKFVRISLG 384
>gnl|CDD|133250 cd00154, Rab, Rab family. Rab GTPases form the largest family
within the Ras superfamily. There are at least 60 Rab
genes in the human genome, and a number of Rab GTPases
are conserved from yeast to humans. Rab GTPases are
small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways.
In the GTP-bound form, Rab GTPases recruit specific
sets of effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. 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 mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular
organisms possess 5-20 Rab members, several have been
found to possess 60 or more Rabs; for many of these Rab
isoforms, homologous proteins are not found in other
organisms. 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. Since crystal structures often lack
C-terminal residues, the lipid modification site is not
available for annotation in many of the CDs in the
hierarchy, but is included where possible.
Length = 159
Score = 30.5 bits (70), Expect = 0.27
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 5 FVLIGASGVGKTTIAKQ 21
VLIG SGVGKT++ +
Sbjct: 3 IVLIGDSGVGKTSLLLR 19
>gnl|CDD|30194 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits..
Length = 150
Score = 30.6 bits (69), Expect = 0.28
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 4 IFVLIGASGVGKTTIAKQVV--LNSEYL 29
I V++G SG GK+T+ K + L + ++
Sbjct: 1 IIVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|39131 KOG3928, KOG3928, KOG3928, Mitochondrial ribosome small subunit
component, mediator of apoptosis DAP3 [Translation,
ribosomal structure and biogenesis].
Length = 461
Score = 30.3 bits (68), Expect = 0.30
Identities = 24/143 (16%), Positives = 43/143 (30%), Gaps = 29/143 (20%)
Query: 5 FVLIGASGVGKTTIAKQVV---LNSEYLVMPV----GVTTRRPRVDEKQYIDYRFISQSQ 57
FVL G G GK+ Q V + ++L++ + T R + +
Sbjct: 182 FVLDGEPGTGKSIALAQAVHYAADQKWLILHIPYAELWTNGRKDYSYDSDLKGLWDQPLY 241
Query: 58 FKGW------KHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLY 111
K + + K +Y G PL ++
Sbjct: 242 AKKILKNFKKTNEPALKKQLKTSKDY----VWSKRESTLKG------------KPLVEIV 285
Query: 112 EDQVTSIFIAPPSEAELIQRRIK 134
E + SI AP + L++ +
Sbjct: 286 ETGIASIKNAPDAVGILLRELKR 308
>gnl|CDD|30108 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII myosins.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle..
Length = 767
Score = 30.4 bits (68), Expect = 0.32
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDE 44
+ +G SG GKTT K + EYL + G R V++
Sbjct: 90 IFLGRSGAGKTTSCKHAL---EYLALAAGSVDGRVSVEK 125
>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 = 30.2 bits (68), Expect = 0.37
Identities = 8/21 (38%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 2 AHIFVLIGASGVGKTTIAKQV 22
++ L G G GKTT+A+ +
Sbjct: 20 KNLL-LYGPPGTGKTTLARAI 39
>gnl|CDD|147659 pfam05610, DUF779, Protein of unknown function (DUF779). This
family consists of several bacterial proteins of
unknown function.
Length = 95
Score = 29.9 bits (68), Expect = 0.40
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 52 FISQSQFKGWKHTGLFIETTKVR 74
+IS+SQF+ WKHT L I+ R
Sbjct: 53 YISKSQFEYWKHTQLIIDVVPGR 75
>gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily
includes classical N-Ras, H-Ras, and K-Ras, as well as
R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1,
RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins
regulate cell growth, proliferation and
differentiation. Ras is activated by guanine
nucleotide exchange factors (GEFs) that release GDP and
allow GTP binding. Many RasGEFs have been identified.
These are sequestered in the cytosol until activation
by growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active GTP-bound Ras interacts with several effector
proteins: among the best characterized are the Raf
kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs
and NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not
available for annotation.
Length = 160
Score = 29.8 bits (68), Expect = 0.41
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 6 VLIGASGVGKTTIAKQVVLN---SEY 28
V++GA GVGK+ I Q V EY
Sbjct: 3 VVLGAGGVGKSAITIQFVKGTFVEEY 28
>gnl|CDD|133313 cd04113, Rab4, Rab4 subfamily. Rab4 has been implicated in
numerous functions within the cell. It helps regulate
endocytosis through the sorting, recycling, and
degradation of early endosomes. Mammalian Rab4 is
involved in the regulation of many surface proteins
including G-protein-coupled receptors, transferrin
receptor, integrins, and surfactant protein A.
Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. 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 = 161
Score = 29.9 bits (68), Expect = 0.47
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 5 FVLIGASGVGKTTIAKQVVLN 25
F++IG+SG GK+ + + V N
Sbjct: 3 FIIIGSSGTGKSCLLHRFVEN 23
>gnl|CDD|33366 COG3564, COG3564, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 116
Score = 29.2 bits (65), Expect = 0.63
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 52 FISQSQFKGWKHTGLFIETTKVR 74
+IS Q++ WKHT L I+ R
Sbjct: 67 YISGPQYEAWKHTQLIIDVVPGR 89
>gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.5 bits (66), Expect = 0.66
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 5 FVLIGASGVGKTTIAKQVV 23
+++G G GK+T+AK++
Sbjct: 3 ILILGPPGAGKSTLAKKLA 21
>gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease
PIM1/LON [Posttranslational modification, protein
turnover, chaperones].
Length = 906
Score = 29.1 bits (65), Expect = 0.67
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 4 IFVLIGASGVGKTTIAKQVV--LNSEYLVMPVG 34
I +G GVGKT+IAK + LN ++ VG
Sbjct: 440 ILCFVGPPGVGKTSIAKSIARALNRKFFRFSVG 472
>gnl|CDD|38419 KOG3209, KOG3209, KOG3209, WW domain-containing protein [General
function prediction only].
Length = 984
Score = 29.2 bits (65), Expect = 0.70
Identities = 31/117 (26%), Positives = 44/117 (37%), Gaps = 17/117 (14%)
Query: 20 KQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTGLFIETTKVRDEYYG 79
+Q + ++ YL V TTRR E + DY F + F + +G +E YYG
Sbjct: 55 QQSIRDNLYL-FQVPCTTRRIL--EGEVPDYSFSTVPIFLCLEVSGCLLEFGTYESNYYG 111
Query: 80 YLKEDINNPMEHGYDILLILTHQ---GLAPLKKLYEDQVTSIF------IAPPSEAE 127
K P E D ++LT Q + Y + S I P E E
Sbjct: 112 TPK-----PPECPADDDMMLTDQELLLPPNSAESYRKRTKSYSIMENAGITTPEEEE 163
>gnl|CDD|30888 COG0542, ClpA, ATPases with chaperone activity, ATP-binding subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 786
Score = 29.1 bits (65), Expect = 0.71
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 4 IFVLIGASGVGKTTIAKQV 22
F+ +G +GVGKT +AK +
Sbjct: 523 SFLFLGPTGVGKTELAKAL 541
Score = 27.2 bits (60), Expect = 2.6
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 6 VLIGASGVGKTTIA 19
VL+G GVGKT I
Sbjct: 195 VLVGEPGVGKTAIV 208
>gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 29.1 bits (66), Expect = 0.73
Identities = 19/72 (26%), Positives = 27/72 (37%), Gaps = 26/72 (36%)
Query: 3 HIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62
VL G SGVGK+T+ ++ L + G IS+ +G +
Sbjct: 36 KTSVLAGQSGVGKSTLLNALLPE---LDLRTGE-----------------ISEKLGRG-R 74
Query: 63 HTGLFIETTKVR 74
HT TT V
Sbjct: 75 HT-----TTHVE 81
>gnl|CDD|31047 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 29.0 bits (65), Expect = 0.79
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 1 MAHIFVLIGASGVGKTTIAKQV 22
VLIG G GK+TI + +
Sbjct: 1 RNMNIVLIGFMGAGKSTIGRAL 22
>gnl|CDD|34258 COG4639, COG4639, Predicted kinase [General function prediction
only].
Length = 168
Score = 28.8 bits (64), Expect = 0.81
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYL 29
M + VL GASG GK+T AK+ L + L
Sbjct: 1 MRILVVLRGASGSGKSTFAKENFLQNYVL 29
>gnl|CDD|112956 pfam04166, PdxA, Pyridoxal phosphate biosynthetic protein PdxA. In
Escherichia coli the coenzyme pyridoxal 5'-phosphate is
synthesized de novo by a pathway that is thought to
involve the condensation of
4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose,
catalysed by the enzymes PdxA and PdxJ, to form either
pyridoxine (vitamin B6) or pyridoxine 5'-phosphate.
Length = 299
Score = 28.8 bits (65), Expect = 0.82
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 87 NPMEHGYDILLILTH-QGLAPLKKLYEDQVTSIFIAPP 123
+ YD +L + H QGL PLK L D+ ++ + P
Sbjct: 229 PVLLGRYDAVLAMYHDQGLIPLKYLGFDRGVNVTLGLP 266
>gnl|CDD|147726 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 = 28.8 bits (65), Expect = 0.85
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 6 VLIGASGVGKTTIAKQVVL 24
+L G +G GKTT+ +++ L
Sbjct: 4 ILQGEAGSGKTTLLQKLAL 22
>gnl|CDD|144508 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 28.8 bits (65), Expect = 0.89
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 7 LIGASGVGKTTIAKQVV 23
++G GVGKTT+AKQ+
Sbjct: 24 IVGMGGVGKTTLAKQIY 40
>gnl|CDD|143853 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 29.0 bits (66), Expect = 0.89
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 5 FVLIGASGVGKTTIAKQVVLNS 26
VL+G GVGK+++ + N
Sbjct: 2 LVLVGDGGVGKSSLLIRFTQNK 23
>gnl|CDD|73020 cd03261, ABC_Org_Solvent_Resistant, ABC (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 = 28.9 bits (65), Expect = 0.96
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
I +IG SG GK+T+ + +V
Sbjct: 28 ILAIIGPSGSGKSTLLRLIV 47
>gnl|CDD|30188 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP..
Length = 154
Score = 28.6 bits (64), Expect = 0.99
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 6 VLIGASGVGKTTIAKQV 22
VLIG G GKTT+ + +
Sbjct: 3 VLIGMMGAGKTTVGRLL 19
>gnl|CDD|29990 cd01124, KaiC, KaiC is a circadian clock protein primarily found
in cyanobacteria KaiC is a RecA-like ATPase, having
both Walker A and Walker B motifs. A related protein is
found in archaea..
Length = 187
Score = 28.7 bits (64), Expect = 1.0
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 4 IFVLIGASGVGKTTIAKQVVLN 25
+L G G GKTT A Q +
Sbjct: 1 STLLSGGPGTGKTTFALQFLYA 22
>gnl|CDD|31324 COG1127, Ttg2A, ABC-type transport system involved in resistance
to organic solvents, ATPase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 263
Score = 28.6 bits (64), Expect = 1.1
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
I ++G SG GK+T+ + ++
Sbjct: 36 ILAILGGSGSGKSTLLRLIL 55
>gnl|CDD|31320 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 28.6 bits (64), Expect = 1.1
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 4 IFVLIGASGVGKTTIAK 20
L+G SG GK+T+A+
Sbjct: 319 TLGLVGESGSGKSTLAR 335
>gnl|CDD|36269 KOG1051, KOG1051, KOG1051, Chaperone HSP104 and related
ATP-dependent Clp proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 898
Score = 28.4 bits (63), Expect = 1.1
Identities = 30/104 (28%), Positives = 44/104 (42%), Gaps = 15/104 (14%)
Query: 5 FVLIGASGVGKTTIAKQV---VLNSEYLVMPVGVTTRRPRVDEKQYI-DYRFI-SQSQFK 59
F+ +G GVGKT +AK + V SE + R+D ++ + I S +
Sbjct: 594 FLFLGPDGVGKTELAKALAEYVFGSEENFI---------RLDMSEFQEVSKLIGSPPGYV 644
Query: 60 GWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQG 103
G + G E K R Y L E+I +ILL L +G
Sbjct: 645 GKEEGGQLTEAVK-RRPYSVVLFEEIEKAHPDVLNILLQLLDRG 687
>gnl|CDD|143797 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 28.3 bits (64), Expect = 1.3
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 7 LIGASGVGKTTIAKQV 22
L G G GKTT+AK V
Sbjct: 3 LYGPPGTGKTTLAKAV 18
>gnl|CDD|30990 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 28.4 bits (63), Expect = 1.4
Identities = 6/20 (30%), Positives = 13/20 (65%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
+ ++ G G GK+T+A+ +
Sbjct: 3 LVLVGGLPGSGKSTLARGLA 22
>gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis)
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. This domain architecture suggests a role for
YjeQ as a regulator of translation..
Length = 287
Score = 28.2 bits (63), Expect = 1.4
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 3 HIFVLIGASGVGKTTI 18
VL+G SGVGK+T+
Sbjct: 162 KTSVLVGQSGVGKSTL 177
>gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 28.0 bits (62), Expect = 1.4
Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 8/82 (9%)
Query: 2 AHIFVLI-GASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQY-------IDYRFI 53
+ VL+ GA+G GK+++ + V VGV T Y D +
Sbjct: 38 EPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGL 97
Query: 54 SQSQFKGWKHTGLFIETTKVRD 75
+ K +H L+ + D
Sbjct: 98 GDGKDKDAEHRQLYRDYLPKLD 119
>gnl|CDD|31609 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 28.0 bits (62), Expect = 1.4
Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 4 IFVLIGASGVGKTT-IAK 20
+ L+G +GVGKTT +AK
Sbjct: 205 VIALVGPTGVGKTTTLAK 222
>gnl|CDD|72971 cd00267, ABC_ATPase, 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 = 157
Score = 28.0 bits (62), Expect = 1.5
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 4 IFVLIGASGVGKTTIAKQV 22
I L+G +G GK+T+ + +
Sbjct: 27 IVALVGPNGSGKSTLLRAI 45
>gnl|CDD|38564 KOG3354, KOG3354, KOG3354, Gluconate kinase [Carbohydrate
transport and metabolism].
Length = 191
Score = 28.1 bits (62), Expect = 1.5
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 4 IFVLIGASGVGKTTIAKQV 22
+ V++G SG GK+TI K +
Sbjct: 14 VIVVMGVSGSGKSTIGKAL 32
>gnl|CDD|133258 cd00882, Ras_like_GTPase, 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
regulate 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 = 157
Score = 27.8 bits (62), Expect = 1.6
Identities = 7/17 (41%), Positives = 14/17 (82%)
Query: 7 LIGASGVGKTTIAKQVV 23
++G SGVGKT++ +++
Sbjct: 1 VVGDSGVGKTSLLNRLL 17
>gnl|CDD|30759 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 28.1 bits (63), Expect = 1.6
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 4 IFVLIGASGVGKTTIAK 20
I L+G +G GKTT+ K
Sbjct: 31 IVALLGRNGAGKTTLLK 47
>gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 27.9 bits (62), Expect = 1.6
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 3 HIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPR 41
I VL+G SGVGK+T+ ++ + R R
Sbjct: 165 KITVLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGR 203
>gnl|CDD|30189 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield
adenosine diphosphates (ADP). This enzyme is required
for the biosynthesis of ADP and is essential for
homeostasis of adenosine phosphates..
Length = 194
Score = 27.9 bits (62), Expect = 1.7
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
+L+G G GK T A+++
Sbjct: 1 RILLLGPPGSGKGTQAERLA 20
>gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 28.0 bits (61), Expect = 1.8
Identities = 12/43 (27%), Positives = 20/43 (46%)
Query: 5 FVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQY 47
V++G GVGKTT+ ++V + P + P + Y
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPY 50
>gnl|CDD|72976 cd03217, ABC_FeS_Assembly, ABC-type transport system involved in
Fe-S cluster assembly, ATPase component. Biosynthesis
of iron-sulfur clusters (Fe-S) depends on multiprotein
systems. The SUF system of E. coli and Erwinia
chrysanthemi is important for Fe-S biogenesis under
stressful conditions. The SUF system is made of six
proteins: SufC is an atypical cytoplasmic ABC-ATPase,
which forms a complex with SufB and SufD; SufA plays
the role of a scaffold protein for assembly of
iron-sulfur clusters and delivery to target proteins;
SufS is a cysteine desulfurase which mobilizes the
sulfur atom from cysteine and provides it to the
cluster; SufE has no associated function yet..
Length = 200
Score = 27.7 bits (62), Expect = 1.8
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLV 30
+ L+G +G GK+T+AK ++ + +Y V
Sbjct: 28 VHALMGPNGSGKSTLAKTIMGHPKYEV 54
>gnl|CDD|145019 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.
This family consists of various cobyrinic acid
a,c-diamide synthases. These include CbiA and CbiP from
S.typhimurium, and CobQ from R. capsulatus. These
amidases catalyse amidations to various side chains of
hydrogenobyrinic acid or cobyrinic acid a,c-diamide in
the biosynthesis of cobalamin (vitamin B12) from
uroporphyrinogen III. Vitamin B12 is an important
cofactor and an essential nutrient for many plants and
animals and is primarily produced by bacteria. The
family also contains dethiobiotin synthetases as well
as the plasmid partitioning proteins of the MinD/ParA
family.
Length = 212
Score = 27.8 bits (62), Expect = 1.9
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 4 IFVLIGASGVGKTTIA 19
I + GVGKTT+A
Sbjct: 1 IAIAGTKGGVGKTTLA 16
>gnl|CDD|33504 COG3709, COG3709, Uncharacterized component of phosphonate
metabolism [Inorganic ion transport and metabolism].
Length = 192
Score = 27.6 bits (61), Expect = 1.9
Identities = 28/145 (19%), Positives = 56/145 (38%), Gaps = 11/145 (7%)
Query: 1 MAHIFVLIGASGVGKTTI----AKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQS 56
M + ++G SG GK T+ ++ + +T E D+ +S++
Sbjct: 4 MGRLIAVVGPSGAGKDTLLDAARARLAGRPRLHFVRRVITRPADAGGE----DHDALSEA 59
Query: 57 QFKGWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVT 116
+F G F + + YG + +I+ + G +L+ + L ++ Y +
Sbjct: 60 EFNTRAGQGAFALSWQAHGLSYG-IPAEIDLWLAAGDVVLVNGSRAVLPQARRRYPQLLV 118
Query: 117 SIFIAPPS--EAELIQRRIKRREDI 139
A P L +R + RE+I
Sbjct: 119 VCITASPEVLAQRLAERGRESREEI 143
>gnl|CDD|31322 COG1125, OpuBA, ABC-type proline/glycine betaine transport
systems, ATPase components [Amino acid transport and
metabolism].
Length = 309
Score = 27.6 bits (61), Expect = 2.0
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 4 IFVLIGASGVGKTTIAKQV 22
VLIG SG GKTT K +
Sbjct: 29 FLVLIGPSGSGKTTTLKMI 47
>gnl|CDD|33052 COG3240, COG3240, Phospholipase/lecithinase/hemolysin [Lipid
metabolism / General function prediction only].
Length = 370
Score = 27.3 bits (60), Expect = 2.2
Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 6/73 (8%)
Query: 22 VVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTGLFIETTKVRDEYYGYL 81
V+ + + P G + Q + S + G I +R + Y L
Sbjct: 213 VMTLPDLSLTPAGKAYGTEAIQASQATIA--FNASLTSQLEQLGGNI----IRIDTYTLL 266
Query: 82 KEDINNPMEHGYD 94
KE + NP E G
Sbjct: 267 KEIMTNPAEFGLA 279
>gnl|CDD|73022 cd03263, ABC_subfamily_A, The ABCA subfamily mediates the
transport of a variety of lipid compounds. Mutations
of members of ABCA subfamily are associated with human
genetic diseases, such as, familial high-density
lipoprotein (HDL) deficiency, neonatal surfactant
deficiency, degenerative retinopathies, and congenital
keratinization disorders. The ABCA1 protein is
involved in disorders of cholesterol transport and
high-density lipoprotein (HDL) biosynthesis. The ABCA4
(ABCR) protein transports vitamin A derivatives in the
outer segments of photoreceptor cells, and therefore,
performs a crucial step in the visual cycle. The ABCA
genes are not present in yeast. However, evolutionary
studies of ABCA genes indicate that they arose as
transporters that subsequently duplicated and that
certain sets of ABCA genes were lost in different
eukaryotic lineages..
Length = 220
Score = 27.4 bits (61), Expect = 2.4
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 3 HIFVLIGASGVGKTTI 18
IF L+G +G GKTT
Sbjct: 29 EIFGLLGHNGAGKTTT 44
>gnl|CDD|133347 cd04147, Ras_dva, Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily
consists of a set of proteins characterized only in
Xenopus leavis, to date. In Xenopus Ras-dva expression
is activated by the transcription factor Otx2 and
begins during gastrulation throughout the anterior
ectoderm. Ras-dva expression is inhibited in the
anterior neural plate by factor Xanf1. Downregulation
of Ras-dva results in head development abnormalities
through the inhibition of several regulators of the
anterior neural plate and folds patterning, including
Otx2, BF-1, Xag2, Pax6, Slug, and Sox9. Downregulation
of Ras-dva also interferes with the FGF-8a signaling
within the anterior ectoderm. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 198
Score = 27.5 bits (61), Expect = 2.4
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 6 VLIGASGVGKTTIAKQVVLNS 26
V +GA+GVGKT + ++ + ++
Sbjct: 3 VFMGAAGVGKTALIQRFLYDT 23
>gnl|CDD|133271 cd01868, Rab11_like, Rab11-like. Rab11a, Rab11b, and Rab25 are
closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia.
Rab11/25 proteins seem to regulate recycling pathways
from endosomes to the plasma membrane and to the
trans-Golgi network. Furthermore, Rab11a is thought to
function in the histamine-induced fusion of
tubulovesicles containing H+, K+ ATPase with the plasma
membrane in gastric parietal cells and in
insulin-stimulated insertion of GLUT4 in the plasma
membrane of cardiomyocytes. Overexpression of Rab25 has
recently been observed in ovarian cancer and breast
cancer, and has been correlated with worsened outcomes
in both diseases. In addition, Rab25 overexpression has
also been observed in prostate cancer, transitional
cell carcinoma of the bladder, and invasive breast
tumor cells. 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 = 165
Score = 27.5 bits (62), Expect = 2.4
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 6 VLIGASGVGKTTI 18
VLIG SGVGK+ +
Sbjct: 7 VLIGDSGVGKSNL 19
>gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 27.5 bits (61), Expect = 2.6
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 3 HIFVLIGASGVGKTTIAK 20
I ++G +G GK+T+ K
Sbjct: 29 EITGILGPNGSGKSTLLK 46
>gnl|CDD|133249 cd00066, G-alpha, G protein alpha subunit. The alpha subunit of
G proteins contains the guanine nucleotide binding
site. The heterotrimeric GNP-binding proteins are
signal transducers that communicate signals from many
hormones, neurotransmitters, chemokines, and autocrine
and paracrine factors. Extracellular signals are
received by receptors, which activate the G proteins,
which in turn route the signals to several distinct
intracellular signaling pathways. The alpha subunit of
G proteins is a weak GTPase. In the resting state,
heterotrimeric G proteins are associated at the
cytosolic face of the plasma membrane and the alpha
subunit binds to GDP. Upon activation by a receptor GDP
is replaced with GTP, and the G-alpha/GTP complex
dissociates from the beta and gamma subunits. This
results in activation of downstream signaling pathways,
such as cAMP synthesis by adenylyl cyclase, which is
terminated when GTP is hydrolized and the heterotrimers
reconstitute.
Length = 317
Score = 27.1 bits (61), Expect = 2.7
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 7 LIGASGVGKTTIAKQ 21
L+GA GK+TI KQ
Sbjct: 5 LLGAGESGKSTILKQ 19
>gnl|CDD|39857 KOG4658, KOG4658, KOG4658, Apoptotic ATPase [Signal transduction
mechanisms].
Length = 889
Score = 27.2 bits (60), Expect = 2.8
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 7 LIGASGVGKTTIAKQV 22
+ G GVGKTT+A+Q+
Sbjct: 184 IYGMGGVGKTTLARQI 199
>gnl|CDD|30813 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 27.2 bits (60), Expect = 2.8
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 10/45 (22%)
Query: 7 LIGASGVGKTTIAKQVVLN----------SEYLVMPVGVTTRRPR 41
L+G G GKT +AK V S+++ M VGV R R
Sbjct: 188 LVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVR 232
>gnl|CDD|30672 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 27.1 bits (60), Expect = 2.8
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 13/61 (21%)
Query: 4 IFVLIGASGVGKTTIAKQVV--LNSE---------YLVMPVGVTTRRPRVDEKQYIDYRF 52
+ V+ G + GKT +A + L E Y + +G T +P ++E + +
Sbjct: 5 LIVIAGPTASGKTALAIALAKRLGGEIISLDSMQVYRGLDIG--TAKPSLEELAGVPHHL 62
Query: 53 I 53
I
Sbjct: 63 I 63
>gnl|CDD|73178 COG4608, AppF, ABC-type oligopeptide transport system, ATPase
component [Amino acid transport and metabolism].
Length = 268
Score = 27.1 bits (60), Expect = 2.8
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
L+G SG GK+T+ + ++
Sbjct: 41 TLGLVGESGCGKSTLGRLIL 60
>gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 27.1 bits (60), Expect = 2.8
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 6 VLIGASGVGKTTIAK 20
++G SG GK+T+ K
Sbjct: 503 AIVGRSGSGKSTLLK 517
>gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion..
Length = 99
Score = 27.0 bits (59), Expect = 2.9
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 4 IFVLIGASGVGKTTIA 19
+ V+ G GVGKTT+A
Sbjct: 1 VIVVTGKGGVGKTTLA 16
>gnl|CDD|33633 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and
metabolism].
Length = 352
Score = 27.2 bits (60), Expect = 2.9
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 4 IFVLIGASGVGKTTI 18
L+G SG GKTT+
Sbjct: 33 FVTLLGPSGCGKTTL 47
>gnl|CDD|177027 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 26.9 bits (60), Expect = 3.5
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 6 VLIGASGVGKTTIAK 20
+LIG GVGKT IA+
Sbjct: 204 ILIGEPGVGKTAIAE 218
>gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation,
ribosomal structure and biogenesis].
Length = 531
Score = 26.9 bits (59), Expect = 3.6
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTR 38
++G VGK+++ + +V PV TTR
Sbjct: 272 AIVGRPNVGKSSLLNALSREDRSIVSPVPGTTR 304
>gnl|CDD|73018 cd03259, ABC_Carb_Solutes_like, ABC Carbohydrate and Solute
Transporters-like subgroup. This family is comprised
of proteins involved in the transport of apparently
unrelated solutes and proteins specific for di- and
oligosaccharides and polyols. 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 = 213
Score = 27.0 bits (60), Expect = 3.6
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 4 IFVLIGASGVGKTTI 18
L+G SG GKTT+
Sbjct: 28 FLALLGPSGCGKTTL 42
>gnl|CDD|73005 cd03246, ABCC_Protease_Secretion, 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 = 26.7 bits (59), Expect = 3.7
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 6 VLIGASGVGKTTIAK 20
+IG SG GK+T+A+
Sbjct: 32 AIIGPSGSGKSTLAR 46
>gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 26.8 bits (59), Expect = 3.7
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 1 MAHIFVLIG-ASGVGKTTIAKQV 22
+ +LIG ASGVGK+TIA ++
Sbjct: 87 KRPLIILIGGASGVGKSTIAGEL 109
>gnl|CDD|133348 cd04148, RGK, RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir)
subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to
the beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins
cited in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal
extension is reported to be conserved among the family
and lack the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 221
Score = 26.6 bits (59), Expect = 3.9
Identities = 8/16 (50%), Positives = 14/16 (87%)
Query: 6 VLIGASGVGKTTIAKQ 21
V++G+ GVGK+++A Q
Sbjct: 4 VMLGSPGVGKSSLASQ 19
>gnl|CDD|30745 COG0396, SufC, ABC-type transport system involved in Fe-S cluster
assembly, ATPase component [Posttranslational
modification, protein turnover, chaperones].
Length = 251
Score = 26.7 bits (59), Expect = 3.9
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLV 30
+ ++G +G GK+T+A ++ + +Y V
Sbjct: 32 VHAIMGPNGSGKSTLAYTIMGHPKYEV 58
>gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug 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, simlar 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 = 26.5 bits (59), Expect = 4.0
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 6 VLIGASGVGKTTIAK 20
++G SG GK+T+ K
Sbjct: 32 AIVGPSGSGKSTLLK 46
>gnl|CDD|72983 cd03224, ABC_TM1139_LivF_branched, 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 (59), Expect = 4.0
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
I L+G +G GKTT+ K ++
Sbjct: 28 IVALLGRNGAGKTTLLKTIM 47
>gnl|CDD|35953 KOG0734, KOG0734, KOG0734, AAA+-type ATPase containing the
peptidase M41 domain [Posttranslational modification,
protein turnover, chaperones].
Length = 752
Score = 26.5 bits (58), Expect = 4.1
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 10/46 (21%)
Query: 6 VLIGASGVGKTTIAKQV----------VLNSEYLVMPVGVTTRRPR 41
+L+G G GKT +A+ V SE+ M VGV RR R
Sbjct: 341 LLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMFVGVGARRVR 386
>gnl|CDD|133265 cd01862, Rab7, Rab7 subfamily. Rab7 is a small Rab GTPase that
regulates vesicular traffic from early to late
endosomal stages of the endocytic pathway. The yeast
Ypt7 and mammalian Rab7 are both involved in transport
to the vacuole/lysosome, whereas Ypt7 is also required
for homotypic vacuole fusion. Mammalian Rab7 is an
essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components
to the lytic compartment. Mammalian Rab7 is also
proposed to function as a tumor suppressor. 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 = 172
Score = 26.5 bits (59), Expect = 4.3
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 6 VLIGASGVGKTTIAKQVV 23
+++G SGVGKT++ Q V
Sbjct: 4 IILGDSGVGKTSLMNQYV 21
>gnl|CDD|32641 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 26.6 bits (58), Expect = 4.3
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
+AH ++ G GVGKTTIA+
Sbjct: 37 IAHAYLFSGPRGVGKTTIAR 56
>gnl|CDD|31326 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 26.5 bits (58), Expect = 4.5
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 4 IFVLIGASGVGKTTIAK 20
IF L+G +G GKTT+ K
Sbjct: 33 IFGLLGPNGAGKTTLLK 49
>gnl|CDD|133263 cd01860, Rab5_related, Rab5-related subfamily. This subfamily
includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53
of yeast, and RabF of plants. The members of this
subfamily are involved in endocytosis and
endocytic-sorting pathways. In mammals, Rab5 GTPases
localize to early endosomes and regulate fusion of
clathrin-coated vesicles to early endosomes and fusion
between early endosomes. In yeast, Ypt51p family
members similarly regulate membrane trafficking through
prevacuolar compartments. 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 = 163
Score = 26.3 bits (59), Expect = 4.5
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 6 VLIGASGVGKTTIA 19
VL+G S VGK+++
Sbjct: 5 VLLGDSSVGKSSLV 18
>gnl|CDD|145101 pfam01767, Birna_VP3, Birnavirus VP3 protein. VP3 is a minor
structural component of the virus. The large RNA segment
of birnaviruses codes for a polyprotein
(N-VP2-VP4-VP3-C).
Length = 229
Score = 26.4 bits (58), Expect = 4.5
Identities = 25/100 (25%), Positives = 41/100 (41%), Gaps = 15/100 (15%)
Query: 49 DYRFISQSQFKGWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGL---A 105
YR S QFK + TG + D+Y Y+ I P + L + GL
Sbjct: 133 GYRGPSPGQFKYYLITGRDPDPG---DDYEDYIPPPITRPTDENKIRRLANSIYGLPHQE 189
Query: 106 PLKKLYEDQVTSIFIAP----PSEAE-----LIQRRIKRR 136
P + D+V +++ P++ + L+ RR+K R
Sbjct: 190 PAPDAFYDEVAAVYAENQGRGPNQEQMRDLRLLARRMKSR 229
>gnl|CDD|37566 KOG2355, KOG2355, KOG2355, Predicted ABC-type transport, ATPase
component/CCR4 associated factor [General function
prediction only, Transcription].
Length = 291
Score = 26.5 bits (58), Expect = 4.5
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMP--VGVTTRRPRVDE 44
+L+GA+G GKTT+ K +L+ +++V V V R D
Sbjct: 44 LLVGANGAGKTTLLK--ILSGKHMVGGGVVQVLGRSAFHDT 82
>gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 26.4 bits (58), Expect = 4.5
Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 3 HIFVLIGASGVGKTT-IAK 20
+ + +G +GVGKTT IAK
Sbjct: 140 FVILFVGVNGVGKTTTIAK 158
>gnl|CDD|73174 COG0470, HolB, ATPase involved in DNA replication [DNA replication,
recombination, and repair].
Length = 325
Score = 26.4 bits (57), Expect = 4.6
Identities = 30/146 (20%), Positives = 58/146 (39%), Gaps = 19/146 (13%)
Query: 1 MAHIFVLIGASGVGKTT----IAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQS 56
+ H + G GVGKTT +AK+++ + ++P G + + D+ ++ S
Sbjct: 23 LPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPS 82
Query: 57 QFKGWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGL------APLKKL 110
+ + ++ + +P+E GY +++I L A LK L
Sbjct: 83 DLRKIDI---------IVEQVRELAEFLSESPLEGGYKVVIIDEADKLTEDAANALLKTL 133
Query: 111 YEDQVTSIFIAPPSEAELIQRRIKRR 136
E + FI ++ I I+ R
Sbjct: 134 EEPPKNTRFILITNDPSKILPTIRSR 159
>gnl|CDD|38232 KOG3022, KOG3022, KOG3022, Predicted ATPase, nucleotide-binding
[Cell cycle control, cell division, chromosome
partitioning].
Length = 300
Score = 26.4 bits (58), Expect = 4.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 4 IFVLIGASGVGKTTIAKQVVL 24
I VL G GVGK+T+ + L
Sbjct: 50 ILVLSGKGGVGKSTVTVNLAL 70
>gnl|CDD|33436 COG3638, COG3638, ABC-type phosphate/phosphonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 26.3 bits (58), Expect = 4.7
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 6 VLIGASGVGKTTIAKQVV-----LNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQS 56
+IG SG GK+T+ + + + E L V +T + + K D I Q
Sbjct: 34 AIIGPSGAGKSTLLRSLNGLVDPTSGEILFNGVQITKLKGKELRKLRRDIGMIFQQ 89
>gnl|CDD|34241 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase
and permease components [General function prediction
only].
Length = 580
Score = 26.4 bits (58), Expect = 4.8
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 7 LIGASGVGKTTIAKQVV 23
+IG SG GK+T+A+ +V
Sbjct: 367 IIGPSGSGKSTLARLLV 383
>gnl|CDD|73016 cd03257, ABC_NikE_OppD_transporters, The ABC transporter
subfamily specific for the transport of dipeptides,
oligopeptides (OppD), and nickel (NikDE). The NikABCDE
system of E. coli belongs to this family and is
composed of the periplasmic binding protein NikA, two
integral membrane components (NikB and NikC), and two
ATPase (NikD and NikE). The NikABCDE transporter is
synthesized under anaerobic conditions to meet the
increased demand for nickel resulting from hydrogenase
synthesis. The molecular mechanism of nickel uptake in
many bacteria and most archaea is not known. Many
other members of this ABC family are also involved in
the uptake of dipeptides and oligopeptides. The
oligopeptide transport system (Opp) is a five-component
ABC transport composed of a membrane-anchored substrate
binding proteins (SRP), OppA, two transmembrane
proteins, OppB and OppC, and two ATP-binding domains,
OppD and OppF..
Length = 228
Score = 26.2 bits (58), Expect = 4.8
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 4 IFVLIGASGVGKTTIAK 20
L+G SG GK+T+A+
Sbjct: 33 TLGLVGESGSGKSTLAR 49
>gnl|CDD|37180 KOG1969, KOG1969, KOG1969, DNA replication checkpoint protein
CHL12/CTF18 [Energy production and conversion,
Replication, recombination and repair].
Length = 877
Score = 26.2 bits (57), Expect = 5.0
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRR 39
I +L G G+GKTT+A + + Y V+ + + R
Sbjct: 328 ILLLCGPPGLGKTTLAHVIAKQAGYSVVEINASDER 363
>gnl|CDD|35315 KOG0092, KOG0092, KOG0092, GTPase Rab5/YPT51 and related small G
protein superfamily GTPases [Intracellular trafficking,
secretion, and vesicular transport].
Length = 200
Score = 26.4 bits (58), Expect = 5.2
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 6 VLIGASGVGKTTIAKQVVLN 25
VL+G SGVGK+++ + V +
Sbjct: 9 VLLGDSGVGKSSLVLRFVKD 28
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyses 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 = 26.3 bits (59), Expect = 5.6
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 3 HIFVLIGASGVGKTTIAK 20
H ++IG G GKT +AK
Sbjct: 23 HNLLMIGPPGSGKTMLAK 40
>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family
includes the NTP binding domain of F1 and V1 H+ATPases,
DnaB and related helicases as well as bacterial RecA
and related eukaryotic and archaeal recombinases. This
group also includes bacterial conjugation proteins and
related DNA transfer proteins involved in type II and
type IV secretion..
Length = 165
Score = 26.2 bits (57), Expect = 5.6
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 6 VLIGASGVGKTTIAKQVVLN 25
++ G +G GKTT+A Q+ LN
Sbjct: 3 LVFGPTGSGKTTLALQLALN 22
>gnl|CDD|72988 cd03229, ABC_Class3, This class is comprised of all BPD (Binding
Protein Dependent) systems that are largely represented
in archaea and eubacteria and are primarily involved in
scavenging solutes from the environment. 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 = 178
Score = 26.3 bits (58), Expect = 5.7
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 3 HIFVLIGASGVGKTTI 18
I L+G SG GK+T+
Sbjct: 27 EIVALLGPSGSGKSTL 42
>gnl|CDD|133342 cd04142, RRP22, RRP22 subfamily. RRP22 (Ras-related protein on
chromosome 22) subfamily consists of proteins that
inhibit cell growth and promote caspase-independent
cell death. Unlike most Ras proteins, RRP22 is
down-regulated in many human tumor cells due to
promoter methylation. RRP22 localizes to the nucleolus
in a GTP-dependent manner, suggesting a novel function
in modulating transport of nucleolar components. Most
Ras proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid.
Lipid binding is essential for membrane attachment, a
key feature of most Ras proteins. Like most Ras family
proteins, RRP22 is farnesylated.
Length = 198
Score = 26.0 bits (57), Expect = 5.7
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 7 LIGASGVGKTTIAKQVVLN 25
++GA GVGKT I +Q +
Sbjct: 5 VLGAPGVGKTAIVRQFLAQ 23
>gnl|CDD|72989 cd03230, ABC_DR_subfamily_A, This family of ATP-binding proteins
belongs to a multisubunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid
transport, and lantibiotic immunity. In bacteria and
archaea, these transporters usually include an
ATP-binding protein and one or two integral membrane
proteins. Eukaryote systems of the ABCA subfamily
display ABC domains that are quite similar to this
family. The ATP-binding domain shows the highest
similarity between all members of the ABC transporter
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 173
Score = 26.1 bits (58), Expect = 6.0
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 4 IFVLIGASGVGKTTIAK 20
I+ L+G +G GKTT+ K
Sbjct: 28 IYGLLGPNGAGKTTLIK 44
>gnl|CDD|31321 COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 252
Score = 26.0 bits (57), Expect = 6.0
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
++G SG GK+T+A+ +
Sbjct: 35 TLGIVGESGSGKSTLARLLA 54
>gnl|CDD|72985 cd03226, ABC_cobalt_CbiO_domain2, Domain II of the ABC component
of a cobalt transport family found in bacteria,
archaea, and eukaryota. The transition metal cobalt is
an essential component of many enzymes and must be
transported into cells in appropriate amounts when
needed. The CbiMNQO family ABC transport system is
involved in cobalt transport in association with the
cobalamin (vitamin B12) biosynthetic pathways. Most
cobalt (Cbi) transport systems possess a separate CbiN
component, the cobalt-binding periplasmic protein, and
they are encoded by the conserved gene cluster cbiMNQO.
Both the CbiM and CbiQ proteins are integral
cytoplasmic membrane proteins, and the CbiO protein has
the linker peptide and the Walker A and B motifs
commonly found in the ATPase components of the ABC-type
transport systems..
Length = 205
Score = 26.0 bits (57), Expect = 6.1
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 4 IFVLIGASGVGKTTIAK 20
I L G +G GKTT+AK
Sbjct: 28 IIALTGKNGAGKTTLAK 44
>gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 26.0 bits (57), Expect = 6.1
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 6 VLIGASGVGKTTIAK 20
+LIG +G GK+T+ K
Sbjct: 34 LLIGPNGSGKSTLLK 48
>gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system,
ATPase component [Amino acid transport and metabolism].
Length = 386
Score = 26.1 bits (57), Expect = 6.2
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 4 IFVLIGASGVGKTTIAKQV 22
IFV++G SG GK+T+ + +
Sbjct: 56 IFVIMGLSGSGKSTLVRLL 74
>gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265.
Length = 168
Score = 26.0 bits (58), Expect = 6.3
Identities = 11/21 (52%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 3 HIFVLIGASGVGKTTIAKQVV 23
IF + G GVGKTT+ K+V+
Sbjct: 1 RIF-ITGPPGVGKTTLVKKVI 20
>gnl|CDD|32178 COG1995, PdxA, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 332
Score = 26.0 bits (57), Expect = 6.5
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 87 NPMEHGYDILLILTH-QGLAPLKKLYEDQVTSIFIAPP 123
YD +L + H QGL PLK L D+ ++ + P
Sbjct: 253 PAYLANYDAVLAMYHDQGLIPLKYLGFDRGVNVTLGLP 290
>gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the
membrane by an interaction between SRP and its cognated
receptor (SR). In mammals, SRP consists of six protein
subunits and a 7SL RNA. One of these subunits is a 54
kd protein (SRP54), which is a GTP-binding protein that
interacts with the signal sequence when it emerges from
the ribosome. SRP54 is a multidomain protein that
consists of an N-terminal domain, followed by a central
G (GTPase) domain and a C-terminal M domain..
Length = 173
Score = 25.9 bits (57), Expect = 6.7
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 3 HIFVLIGASGVGKTT-IAK--QVVLNSEYLVMPVGVTTRRP 40
+ +L+G GVGKTT AK + V+ V T RP
Sbjct: 1 TVILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRP 41
>gnl|CDD|73010 cd03251, ABCC_MsbA, 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 = 25.9 bits (57), Expect = 6.8
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 7 LIGASGVGKTTIAK 20
L+G SG GK+T+
Sbjct: 33 LVGPSGSGKSTLVN 46
>gnl|CDD|143879 pfam00102, Y_phosphatase, Protein-tyrosine phosphatase.
Length = 234
Score = 25.7 bits (57), Expect = 6.9
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 1/45 (2%)
Query: 21 QVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTG 65
V L SE T R + + R ++ + GW G
Sbjct: 103 TVTLVSEETKEA-DYTVRTLELSNSGDDESRTVTHFHYTGWPDHG 146
>gnl|CDD|109737 pfam00693, Herpes_TK, Thymidine kinase from herpesvirus.
Length = 279
Score = 25.7 bits (57), Expect = 6.9
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 9 GASGVGKTTIAKQVVLNSE 27
GA G+GKTT A+ + S
Sbjct: 1 GAHGIGKTTTARALAAASS 19
>gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system
belong to the larger ATP-Binding Cassette (ABC)
transporter superfamily. The characteristic feature of
these transporters is the obligatory coupling of ATP
hydrolysis to substrate translocation. 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 = 269
Score = 25.9 bits (57), Expect = 7.0
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 4 IFVLIGASGVGKTTI 18
IFV++G SG GK+T+
Sbjct: 52 IFVIMGLSGSGKSTL 66
>gnl|CDD|73019 cd03260, ABC_PstB_phosphate_transporter, 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. P stA 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 = 25.9 bits (57), Expect = 7.0
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 4 IFVLIGASGVGKTTI 18
I LIG SG GK+T+
Sbjct: 28 ITALIGPSGCGKSTL 42
>gnl|CDD|35305 KOG0082, KOG0082, KOG0082, G-protein alpha subunit (small G
protein superfamily) [Cell cycle control, cell
division, chromosome partitioning, Signal transduction
mechanisms].
Length = 354
Score = 25.9 bits (57), Expect = 7.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 5 FVLIGASGVGKTTIAKQV 22
+L+GA GK+TI KQ+
Sbjct: 36 LLLLGAGESGKSTIVKQM 53
>gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 26.0 bits (57), Expect = 7.1
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 4 IFVLIGASGVGKTT 17
VL+G SG GK+T
Sbjct: 31 FVVLLGPSGCGKST 44
>gnl|CDD|73052 cd03293, ABC_NrtD_SsuB_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 = 25.8 bits (57), Expect = 7.3
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 4 IFVLIGASGVGKTTI 18
L+G SG GK+T+
Sbjct: 32 FVALVGPSGCGKSTL 46
>gnl|CDD|35960 KOG0741, KOG0741, KOG0741, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 744
Score = 25.7 bits (56), Expect = 7.3
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEY 28
+L G G GKT +A ++ L+S++
Sbjct: 542 LLEGPPGSGKTALAAKIALSSDF 564
>gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands..
Length = 271
Score = 25.6 bits (56), Expect = 7.3
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTT 37
+ +L +GVGKTT ++ L L+ GV
Sbjct: 32 LIILTAGTGVGKTTFLREYAL---DLITQHGVRV 62
>gnl|CDD|35383 KOG0161, KOG0161, KOG0161, Myosin class II heavy chain
[Cytoskeleton].
Length = 1930
Score = 26.0 bits (57), Expect = 7.4
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYID 49
++ G SG GKT K+V+ +YL V ++ + E D
Sbjct: 172 LITGESGAGKTENTKKVI---QYLAS-VASSSTKKVKIEGTLED 211
>gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, 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 = 25.8 bits (57), Expect = 7.4
Identities = 5/15 (33%), Positives = 12/15 (80%)
Query: 6 VLIGASGVGKTTIAK 20
+++G +G GK+T+ +
Sbjct: 31 LIVGPNGSGKSTLLR 45
>gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 25.7 bits (56), Expect = 7.5
Identities = 20/153 (13%), Positives = 47/153 (30%), Gaps = 16/153 (10%)
Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDY----RFISQS 56
++ G +G GKT K V+ E V V Y + +
Sbjct: 41 RPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKV 100
Query: 57 QFKGWKHTGLFIETTKVRDEYYGYL---KEDINNPMEHGYDILLILTHQGLAPLKKLYED 113
G + + + ++++ ++ ++L L +
Sbjct: 101 PLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLR-----APGENKV 155
Query: 114 QVTSIFIAPPSE-AELIQRRIKRR---EDIPFN 142
+V+ I ++ + + + R+K +I F
Sbjct: 156 KVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFP 188
>gnl|CDD|37239 KOG2028, KOG2028, KOG2028, ATPase related to the helicase subunit
of the Holliday junction resolvase [Replication,
recombination and repair].
Length = 554
Score = 25.8 bits (56), Expect = 7.5
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 6 VLIGASGVGKTTIAKQVVLNSE 27
+L G G GKTT+A+ + S+
Sbjct: 166 ILWGPPGTGKTTLARLIASTSK 187
>gnl|CDD|30793 COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 316
Score = 25.9 bits (57), Expect = 7.6
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 4 IFVLIGASGVGKTTIAK 20
I ++G SG GK+ +AK
Sbjct: 33 ILGIVGESGSGKSVLAK 49
>gnl|CDD|31323 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase
component [Amino acid transport and metabolism].
Length = 240
Score = 25.8 bits (57), Expect = 7.8
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 3 HIFVLIGASGVGKTTI 18
+ V+IG SG GK+T+
Sbjct: 29 EVVVIIGPSGSGKSTL 44
>gnl|CDD|72986 cd03227, ABC_Class2, ABC-type Class 2 contains systems involved
in cellular processes other than transport. These
families are characterised by the fact that the ABC
subunit is made up of duplicated, fused ABC modules
(ABC2). No known transmembrane proteins or domains are
associated with these proteins..
Length = 162
Score = 25.7 bits (56), Expect = 8.0
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 3 HIFVLIGASGVGKTTIAKQVVL 24
+ ++ G +G GK+TI + L
Sbjct: 22 SLTIITGPNGSGKSTILDAIGL 43
>gnl|CDD|73298 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located
on the inner membrane of the cell. This ATP-driven
oxyanion pump catalyzes the extrusion of arsenite,
antimonite and arsenate. Maintenance of a low
intracellular concentration of oxyanion produces
resistance to the toxic agents. The pump is composed of
two subunits, the catalytic ArsA subunit and the
membrane subunit ArsB, which are encoded by arsA and
arsB genes respectively. Arsenic efflux in bacteria is
catalyzed by either ArsB alone or by ArsAB complex. The
ATP-coupled pump, however, is more efficient. ArsA is
composed of two homologous halves, A1 and A2, connected
by a short linker sequence..
Length = 217
Score = 25.6 bits (56), Expect = 8.0
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 4 IFVLIGASGVGKTTIA 19
+ G GVGKTTIA
Sbjct: 1 VIFFTGKGGVGKTTIA 16
>gnl|CDD|31413 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase
subunit [Posttranslational modification, protein
turnover, chaperones].
Length = 444
Score = 25.6 bits (56), Expect = 8.0
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 6 VLIGASGVGKTTIAKQV 22
++IG +GVGKT IA+++
Sbjct: 54 LMIGPTGVGKTEIARRL 70
>gnl|CDD|36143 KOG0925, KOG0925, KOG0925, mRNA splicing factor ATP-dependent RNA
helicase [RNA processing and modification].
Length = 699
Score = 25.7 bits (56), Expect = 8.0
Identities = 18/39 (46%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 3 HIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPR 41
I VL+G +G GKTT Q VL E L GV +PR
Sbjct: 63 QIIVLVGETGSGKTTQIPQFVLEYE-LSHLTGVACTQPR 100
>gnl|CDD|31624 COG1435, Tdk, Thymidine kinase [Nucleotide transport and
metabolism].
Length = 201
Score = 25.6 bits (56), Expect = 8.2
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 2/43 (4%)
Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVD 43
M + + G GKT + + M V V P +D
Sbjct: 3 MGWLEFIYGPMFSGKTEELLRRARRYKEAGMKVLVFK--PAID 43
>gnl|CDD|31330 COG1135, AbcC, ABC-type metal ion transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 339
Score = 25.6 bits (56), Expect = 8.3
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 4 IFVLIGASGVGKTTI 18
IF +IG SG GK+T+
Sbjct: 34 IFGIIGYSGAGKSTL 48
>gnl|CDD|133344 cd04144, Ras2, Ras2 subfamily. The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Ras proteins.
Length = 190
Score = 25.6 bits (56), Expect = 8.4
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 6 VLIGASGVGKTTIAKQVVLNS 26
V++G GVGKT + Q+ LN
Sbjct: 3 VVLGDGGVGKTALTIQLCLNH 23
>gnl|CDD|35304 KOG0081, KOG0081, KOG0081, GTPase Rab27, small G protein
superfamily [Intracellular trafficking, secretion, and
vesicular transport].
Length = 219
Score = 25.7 bits (56), Expect = 8.6
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 5 FVLIGASGVGKTTIAKQVV---LNSEYLVMPVGVTTRRPRV 42
F+ +G SGVGKT+ Q N+++ + VG+ R RV
Sbjct: 12 FLALGDSGVGKTSFLYQYTDGKFNTQF-ISTVGIDFREKRV 51
>gnl|CDD|73296 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor..
Length = 147
Score = 25.5 bits (56), Expect = 8.9
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 9 GASGVGKTTIAKQV 22
G +G GK+T+AK +
Sbjct: 6 GPAGSGKSTVAKLL 19
>gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 25.4 bits (55), Expect = 9.5
Identities = 7/17 (41%), Positives = 14/17 (82%)
Query: 2 AHIFVLIGASGVGKTTI 18
+ IF+++G +G GK++I
Sbjct: 25 SGIFLIVGPNGAGKSSI 41
>gnl|CDD|73300 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is
a homologue of the Fer4_NifH superfamily. Like the
other members of the superfamily, MRP contains a
ATP-binding domain at the N-termini. It is found in
bacteria as a membrane-spanning protein and functions
as a Na+/H+ antiporter..
Length = 169
Score = 25.4 bits (56), Expect = 9.6
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 4 IFVLIGASGVGKTTIAKQVVL 24
I V+ G GVGK+T+A + L
Sbjct: 2 IAVMSGKGGVGKSTVAVNLAL 22
>gnl|CDD|73015 cd03256, ABC_PhnC_transporter, ABC-type phosphate/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
procaryotic 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 = 25.5 bits (56), Expect = 9.7
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 6 VLIGASGVGKTTI 18
LIG SG GK+T+
Sbjct: 31 ALIGPSGAGKSTL 43
>gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 25.3 bits (56), Expect = 9.9
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 2 AHIFVLIGASGVGKTTIA 19
A +L+G GVGKT +A
Sbjct: 47 AENLLLLGPPGVGKTHLA 64
>gnl|CDD|31949 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 25.3 bits (55), Expect = 9.9
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 1 MAHIFVLIGASGVGKTTIAKQVV 23
M I ++G GKTT+ +++V
Sbjct: 1 MMKILGIVGYKNSGKTTLIEKLV 23
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.140 0.414
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,374,858
Number of extensions: 126665
Number of successful extensions: 781
Number of sequences better than 10.0: 1
Number of HSP's gapped: 772
Number of HSP's successfully gapped: 184
Length of query: 186
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 98
Effective length of database: 4,362,145
Effective search space: 427490210
Effective search space used: 427490210
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: 54 (24.6 bits)