RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1747
(68 letters)
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate
transferase; Reviewed.
Length = 307
Score = 75.2 bits (186), Expect = 3e-18
Identities = 24/39 (61%), Positives = 30/39 (76%)
Query: 10 MSKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQ 48
M K + VI+G T +GK+ L IE+AK+ NGEIISADSMQ
Sbjct: 1 MMKPKVIVIVGPTASGKTALAIELAKRLNGEIISADSMQ 39
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 66.1 bits (162), Expect = 6e-15
Identities = 20/38 (52%), Positives = 25/38 (65%)
Query: 11 SKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQ 48
K + VI G T +GK+ L I +AK+ GEIIS DSMQ
Sbjct: 1 KKPKLIVIAGPTASGKTALAIALAKRLGGEIISLDSMQ 38
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 56.0 bits (135), Expect = 3e-11
Identities = 22/34 (64%), Positives = 28/34 (82%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQ 48
+ VI G TG GKS+L +E+AK+ NGEIISADS+Q
Sbjct: 23 VIVISGPTGAGKSRLALELAKRLNGEIISADSVQ 56
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine
tRNA modification enzyme. Catalyzes the first step in
the modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 51.6 bits (124), Expect = 1e-09
Identities = 18/32 (56%), Positives = 25/32 (78%)
Query: 17 VILGSTGTGKSKLGIEIAKKFNGEIISADSMQ 48
++G T +GKS+L I++A+K N EIIS DSMQ
Sbjct: 3 FLMGPTASGKSQLSIQLAQKLNAEIISVDSMQ 34
>gnl|CDD|215399 PLN02748, PLN02748, tRNA dimethylallyltransferase.
Length = 468
Score = 50.7 bits (121), Expect = 3e-09
Identities = 23/45 (51%), Positives = 31/45 (68%), Gaps = 3/45 (6%)
Query: 12 KVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQ---GLKFL 53
K + V++G TG+GKSKL +++A F EII+ADSMQ GL L
Sbjct: 21 KAKVVVVMGPTGSGKSKLAVDLASHFPVEIINADSMQVYSGLDVL 65
>gnl|CDD|177823 PLN02165, PLN02165, adenylate isopentenyltransferase.
Length = 334
Score = 48.3 bits (115), Expect = 2e-08
Identities = 21/44 (47%), Positives = 32/44 (72%), Gaps = 3/44 (6%)
Query: 11 SKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQ---GLK 51
K + VI+G+TG+GKS+L +++A +F EII++D MQ GLK
Sbjct: 41 CKDKVVVIMGATGSGKSRLSVDLATRFPSEIINSDKMQVYDGLK 84
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 33.4 bits (76), Expect = 0.002
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISADSM 47
I +I G G+GKS L ++A+K +IS D +
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIPVISLDDL 33
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase
/ dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin
that induces shoot formation on host plants infected
with the Ti plasmid.
Length = 232
Score = 33.5 bits (77), Expect = 0.003
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQG 49
+++I G+T TGK+ I +AK+ +I D +Q
Sbjct: 3 LYLIWGATCTGKTAEAIALAKETGWPVIVLDRVQC 37
>gnl|CDD|184458 PRK14021, PRK14021, bifunctional shikimate
kinase/3-dehydroquinate synthase; Provisional.
Length = 542
Score = 32.5 bits (74), Expect = 0.007
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 10 MSKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADSM 47
++ P VI+G G GK+++G E+A+ AD
Sbjct: 3 PTRRPQAVIIGMMGAGKTRVGKEVAQMMRLPFADADVE 40
>gnl|CDD|238979 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 = 30.3 bits (69), Expect = 0.031
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISADSM 47
I V++G +G+GKS +G +A++ I D +
Sbjct: 1 IIVVMGVSGSGKSTVGKALAERLGAPFIDGDDL 33
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 30.1 bits (68), Expect = 0.044
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 16 FVILGSTGTGKSKLGIEIAKKFNGEIISADSM 47
FV++G G+GKS + +A + + I D +
Sbjct: 1 FVLMGVAGSGKSTIASALAHRLGAKFIEGDDL 32
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 29.2 bits (66), Expect = 0.098
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 14 PIFVIL-GSTGTGKSKLGIEIAKKFNGE---IISADSMQ 48
P+ V+L G G GK++L + ++ G I D ++
Sbjct: 12 PVAVLLGGQPGAGKTELARALLEELGGGNVVRIDPDELR 50
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 28.9 bits (65), Expect = 0.10
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 7/38 (18%)
Query: 2 KSSFLKVVMSKVPIFVILGSTGTGKSKLGIEIAKKFNG 39
+ F+K V ILG +GKS L ++A FN
Sbjct: 4 RPFFVKTV-------AILGGESSGKSTLVNKLANIFNT 34
>gnl|CDD|143485 cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Ornithine and Diaminopimelate
Decarboxylases, and Related Enzymes. This family
includes eukaryotic ornithine decarboxylase (ODC, EC
4.1.1.17), diaminopimelate decarboxylase (DapDC, EC
4.1.1.20), plant and prokaryotic biosynthetic arginine
decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine
decarboxylase (CANSDC), and ODC-like enzymes from
diverse bacterial species. These proteins are fold type
III PLP-dependent enzymes that catalyze essential steps
in the biosynthesis of polyamine and lysine. ODC and
ADC participate in alternative pathways of the
biosynthesis of putrescine, which is the precursor of
aliphatic polyamines in many organisms. ODC catalyzes
the direct synthesis of putrescine from L-ornithine,
while ADC converts L-arginine to agmatine, which is
hydrolysed to putrescine by agmatinase in a pathway that
exists only in plants and bacteria. DapDC converts
meso-2,6-diaminoheptanedioate to L-lysine, which is the
final step of lysine biosynthesis. CANSDC catalyzes the
decarboxylation of carboxynorspermidine, which is the
last step in the synthesis of norspermidine. The
PLP-dependent decarboxylases in this family contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. They exist as homodimers with active
sites that lie at the interface between the TIM barrel
domain of one subunit and the beta-sandwich domain of
the other subunit. Prokaryotic ornithine, lysine and
biodegradative arginine decarboxylases are fold type I
PLP-dependent enzymes and are not included in this
family.
Length = 368
Score = 28.8 bits (65), Expect = 0.12
Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 22 TGTGKSKLGIEIAKKFNGEIISADSMQGLKFLVECRVKLE-----LLRLKPD 68
TG KS IE A + I DS+ L+ L E KL LLR+ PD
Sbjct: 75 TGPAKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARILLRVNPD 126
>gnl|CDD|226463 COG3954, PrkB, Phosphoribulokinase [Energy production and
conversion].
Length = 289
Score = 28.7 bits (64), Expect = 0.16
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 10 MS-KVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQGLKF 52
MS K P+ + GS+G G + + K F I A ++G F
Sbjct: 1 MSAKHPVIAVTGSSGAGTTTTSLAFRKIFAQLNIHAAEVEGDSF 44
>gnl|CDD|223360 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 222
Score = 28.7 bits (65), Expect = 0.17
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 10 MSKVPIFVILGSTGTGKSKLGIEIAKKFN 38
M I I G G+GKS + +A+K
Sbjct: 1 MKAAIIIAIDGPAGSGKSTVAKILAEKLG 29
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 28.6 bits (64), Expect = 0.17
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 6 LKVVMSKV-PIFVILGS-TGTGKSKLGIEIAKKFN-GEIISADSMQ 48
L+ + P+ V++G +G GKS L +A + I+S D+++
Sbjct: 246 LRSIRRPPRPLHVLIGGVSGVGKSVLASALAYRLGITRIVSTDAVR 291
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 28.2 bits (63), Expect = 0.26
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISA 44
I I G G+GK+ + +A+K + ++ISA
Sbjct: 2 IITISGPPGSGKTTVAKILAEKLSLKLISA 31
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 28.0 bits (63), Expect = 0.28
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 20 GSTGTGKSKLGIEIAKKFNGEIISADS 46
G +G+GKS +G +A++ + I D
Sbjct: 2 GVSGSGKSTVGSALAERLGAKFIDGDD 28
>gnl|CDD|238981 cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48),
also known as uridine kinase or uridine-cytidine kinase
(UCK), catalyzes the reversible phosphoryl transfer
from ATP to uridine or cytidine to yield UMP or CMP. In
the primidine nucleotide-salvage pathway, this enzyme
combined with nucleoside diphosphate kinases further
phosphorylates UMP and CMP to form UTP and CTP. This
kinase also catalyzes the phosphorylation of several
cytotoxic ribonucleoside analogs such as
5-flurrouridine and cyclopentenyl-cytidine.
Length = 198
Score = 27.5 bits (62), Expect = 0.33
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGE---IISADS 46
I + G +G+GK+ + EI ++ IIS DS
Sbjct: 2 IGIA-GGSGSGKTTVAEEIIEQLGNPKVVIISQDS 35
>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 = 27.9 bits (62), Expect = 0.34
Identities = 14/29 (48%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 14 PIFV----ILGSTGTGKSKLGIEIAKKFN 38
P FV ILG TGKS L ++A FN
Sbjct: 159 PFFVKTVAILGGESTGKSTLVNKLAAVFN 187
>gnl|CDD|132173 TIGR03129, one_C_dehyd_B, formylmethanofuran dehydrogenase subunit
B. Members of this largely archaeal protein family are
subunit B of the formylmethanofuran dehydrogenase.
Nomenclature in some bacteria may reflect inclusion of
the formyltransferase described by TIGR03119 as part of
the complex, and therefore call this protein
formyltransferase/hydrolase complex Fhc subunit C. Note
that this model does not distinguish tungsten (FwdB)
from molybdenum-containing (FmdB) forms of this enzyme.
Length = 421
Score = 27.6 bits (62), Expect = 0.34
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 11 SKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADS 46
+K P+ ST + G+E+A+K I + S
Sbjct: 76 AKRPLIYGWSSTSCEAQRAGLELAEKLGAVIDNTAS 111
>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 = 27.7 bits (62), Expect = 0.37
Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 4/35 (11%)
Query: 17 VILGSTGTGKSKLGIEIAKKF-NGEIISADSMQGL 50
V++G++G+GKS K F E++S+D +GL
Sbjct: 12 VLVGASGSGKSTFA---RKHFKPTEVLSSDFCRGL 43
>gnl|CDD|226425 COG3910, COG3910, Predicted ATPase [General function prediction
only].
Length = 233
Score = 27.4 bits (61), Expect = 0.39
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 12 KVPIFVILGSTGTGKSKL--GIEIAKKFN 38
+ PI I G G+GKS L I FN
Sbjct: 36 RAPITFITGENGSGKSTLLEAIAAGMGFN 64
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 27.6 bits (62), Expect = 0.40
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 16 FVILGSTGTGKSKLGIEIAKKFN 38
+ILG G GKS L ++AKK
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKLG 25
>gnl|CDD|227341 COG5008, PilU, Tfp pilus assembly protein, ATPase PilU [Cell
motility and secretion / Intracellular trafficking and
secretion].
Length = 375
Score = 27.4 bits (61), Expect = 0.41
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 7 KVVMSKVPIFVILGSTGTGKS 27
+ ++K + +I+G+TG+GKS
Sbjct: 121 DLALAKRGLVIIVGATGSGKS 141
>gnl|CDD|238988 cd02030, NDUO42, NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42)
is a family of proteins that are highly similar to
deoxyribonucleoside kinases (dNK). Members of this
family have been identified as one of the subunits of
NADH:Ubiquinone oxioreductase (complex I), a
multi-protein complex located in the inner
mitochondrial membrane. The main function of the
complex is to transport electrons from NADH to
ubiquinone, which is accompanied by the translocation
of protons from the mitochondrial matrix to the inter
membrane space.
Length = 219
Score = 27.3 bits (61), Expect = 0.41
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 15 IFVILGSTGTGKSKLGIEIAKK 36
+ + G+ +GK KL E+A+K
Sbjct: 1 VITVDGNIASGKGKLAKELAEK 22
>gnl|CDD|213246 cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD. SbcCD
and other Mre11/Rad50 (MR) complexes are implicated in
the metabolism of DNA ends. They cleave ends sealed by
hairpin structures and are thought to play a role in
removing protein bound to DNA termini.
Length = 213
Score = 27.2 bits (61), Expect = 0.44
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 10 MSKVPIFVILGSTGTGKSKL 29
+ +F+I G TG GKS +
Sbjct: 25 LDNNGLFLICGPTGAGKSTI 44
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 27.2 bits (61), Expect = 0.49
Identities = 6/21 (28%), Positives = 13/21 (61%)
Query: 15 IFVILGSTGTGKSKLGIEIAK 35
+F++ G GTGK+ + + +
Sbjct: 3 VFLVTGGPGTGKTVVALNLFA 23
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 26.7 bits (60), Expect = 0.60
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 14 PIFVILGSTGTGKSKLGIEIAKKFNGEIISADS 46
I +I G G GK+ +G +AK + D
Sbjct: 1 NIVLI-GMMGAGKTTVGRLLAKALGLPFVDLDE 32
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family
for which functions are known are part of an
exonuclease complex with sbcD homologs. This complex is
involved in the initiation of recombination to regulate
the levels of palindromic sequences in DNA. This family
is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 1042
Score = 27.2 bits (60), Expect = 0.65
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 14 PIFVILGSTGTGKSKL 29
PIF+I G TG GK+ L
Sbjct: 27 PIFLICGKTGAGKTTL 42
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 27.0 bits (60), Expect = 0.71
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 16 FVILGSTGTGKSKLGIEIAKKFNGEII 42
VI+ TG GK+ + E + +
Sbjct: 58 GVIVLPTGAGKTVVAAEAIAELKRSTL 84
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 26.9 bits (60), Expect = 0.74
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 11 SKVPIFVILG-STGTGKSKLGIEIAKKFN-GEIISADS 46
SK PI +++G ++G G S + E+A + +I DS
Sbjct: 89 SKEPIIILIGGASGVGTSTIAFELASRLGIRSVIGTDS 126
>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 = 26.6 bits (59), Expect = 0.90
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 10 MSKVPIFVILGSTGTGKS 27
+ K+P +I G+TG+GKS
Sbjct: 35 LVKMPHLLIAGATGSGKS 52
>gnl|CDD|235492 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 26.3 bits (59), Expect = 1.1
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 10 MSKVPIFV-ILGSTGTGKSKLGIEIAKKFNGE---IISADS 46
M K PI + I G +G+GK+ + I ++ E +I DS
Sbjct: 2 MMKKPIIIGIAGGSGSGKTTVASTIYEELGDESIAVIPQDS 42
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 26.2 bits (58), Expect = 1.1
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 13 VPIFVILGSTGTGKSKLGIEIAKKFNGEIISAD 45
IF++ G G GK+ LG +A++ I D
Sbjct: 2 ARIFLV-GYMGAGKTTLGKALARELGLSFIDLD 33
>gnl|CDD|213261 cd03294, ABC_Pro_Gly_Betaine, ATP-binding cassette domain of the
osmoprotectant proline/glycine betaine uptake system.
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 = 26.1 bits (58), Expect = 1.2
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 15 IFVILGSTGTGKSKL 29
IFVI+G +G+GKS L
Sbjct: 52 IFVIMGLSGSGKSTL 66
>gnl|CDD|234579 PRK00023, cmk, cytidylate kinase; Provisional.
Length = 225
Score = 26.2 bits (59), Expect = 1.2
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 10 MSKVPIFVILGSTGTGKSKLGIEIAKKFN 38
M K + I G G+GK + +AKK
Sbjct: 1 MMKAIVIAIDGPAGSGKGTVAKILAKKLG 29
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 26.1 bits (58), Expect = 1.3
Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 10 MSKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADS 46
M K+ +++GS G+GKS L ++ +K N + D+
Sbjct: 1 MKKI---ILIGSGGSGKSTLARQLGEKLNIPVHHLDA 34
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 25.4 bits (56), Expect = 1.3
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 6 LKVVMSKVPIFVILGSTGTGKSKLGIEIA 34
++ S +FV+ G GTGK+ I
Sbjct: 3 VEAAASGRSLFVVDGGPGTGKTATAAAII 31
>gnl|CDD|110677 pfam01695, IstB_IS21, 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 = 26.1 bits (58), Expect = 1.3
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 16 FVILGSTGTGKSKLGIEIA 34
++LG G GK+ L +
Sbjct: 50 LLLLGPPGVGKTHLACALG 68
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 26.1 bits (57), Expect = 1.4
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 12 KVPIFVILGSTGTGKSKLGIEIAK 35
K PI ++G G GK+ LG IAK
Sbjct: 348 KGPILCLVGPPGVGKTSLGQSIAK 371
>gnl|CDD|226643 COG4175, ProV, ABC-type proline/glycine betaine transport system,
ATPase component [Amino acid transport and metabolism].
Length = 386
Score = 26.2 bits (58), Expect = 1.4
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 15 IFVILGSTGTGKSKL 29
IFVI+G +G+GKS L
Sbjct: 56 IFVIMGLSGSGKSTL 70
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 25.9 bits (58), Expect = 1.6
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISA 44
I I G G+GK+ + +A+K + +SA
Sbjct: 2 IITISGPPGSGKTTVARLLAEKLGLKHVSA 31
>gnl|CDD|180911 PRK07261, PRK07261, topology modulation protein; Provisional.
Length = 171
Score = 25.8 bits (57), Expect = 1.7
Identities = 9/32 (28%), Positives = 21/32 (65%)
Query: 17 VILGSTGTGKSKLGIEIAKKFNGEIISADSMQ 48
I+G +G+GKS L ++++ +N ++ D++
Sbjct: 4 AIIGYSGSGKSTLARKLSQHYNCPVLHLDTLH 35
>gnl|CDD|235335 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 25.4 bits (56), Expect = 1.9
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISAD 45
IF++ G G GKS +G ++A++ N E +D
Sbjct: 7 IFLV-GPMGAGKSTIGRQLAQQLNMEFYDSD 36
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 25.5 bits (56), Expect = 2.0
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 14 PIFVILGSTGTGKSKL 29
IF+I+G G GKS +
Sbjct: 26 GIFLIVGPNGAGKSSI 41
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 25.7 bits (57), Expect = 2.0
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFN 38
IF++ G GTGKS L +I ++F
Sbjct: 32 IFILKGGPGTGKSTLMKKIGEEFL 55
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 25.4 bits (56), Expect = 2.1
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 12 KVPIFVILGS-TGTGKSKLGIEIAKKFNGEI-ISADSM 47
K P+ +++G +G GKS + E+A++ IS DS+
Sbjct: 87 KRPLIILIGGASGVGKSTIAGELARRLGIRSVISTDSI 124
>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family.
This model represents a rather narrowly distributed
archaeal protein family in which members have a single
copy of the KaiC domain. This stands in contrast to the
circadian clock protein KaiC itself, with two copies of
the domain. Members are expected to have weak ATPase
activity, by homology to the
autokinase/autophosphorylase KaiC itself.
Length = 224
Score = 25.4 bits (56), Expect = 2.1
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 15 IFVILGSTGTGKSKLGIE 32
+ V++G GTGK+ ++
Sbjct: 18 VIVVIGEYGTGKTTFSLQ 35
>gnl|CDD|216796 pfam01935, DUF87, Domain of unknown function DUF87. The function
of this prokaryotic domain is unknown. It contains
several conserved aspartates and histidines that could
be metal ligands.
Length = 218
Score = 25.4 bits (56), Expect = 2.2
Identities = 10/12 (83%), Positives = 11/12 (91%)
Query: 16 FVILGSTGTGKS 27
F ILGSTG+GKS
Sbjct: 26 FAILGSTGSGKS 37
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 25.5 bits (56), Expect = 2.2
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 8 VVMSKVPIFVILGSTGTGKSKL 29
V + + + V+LG+TG+GKS L
Sbjct: 681 VSVPRGKLTVVLGATGSGKSTL 702
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 25.3 bits (55), Expect = 2.4
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 12 KVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADS 46
VPI++ G G+GKS L E+ + I+
Sbjct: 149 AVPIYLE-GGRGSGKSFLISELCDEGGQRIVEIHL 182
>gnl|CDD|173191 PRK14729, miaA, tRNA delta(2)-isopentenylpyrophosphate
transferase; Provisional.
Length = 300
Score = 25.2 bits (55), Expect = 2.4
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 10 MSKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQGLK 51
M + I I G T GKS + K EII+ DS+Q K
Sbjct: 1 MKENKIVFIFGPTAVGKSNILFHFPKGK-AEIINVDSIQVYK 41
>gnl|CDD|143438 cd07120, ALDH_PsfA-ACA09737, Pseudomonas putida aldehyde
dehydrogenase PsfA (ACA09737)-like. Included in this CD
is the aldehyde dehydrogenase (PsfA, locus ACA09737) of
Pseudomonas putida involved in furoic acid metabolism.
Transcription of psfA was induced in response to
2-furoic acid, furfuryl alcohol, and furfural.
Length = 455
Score = 25.4 bits (56), Expect = 2.6
Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 19/55 (34%)
Query: 8 VVMSKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQGLKFLVECRVKLEL 62
V V + GST TG++ I A + LK R+ LEL
Sbjct: 193 VASPDVDVISFTGSTATGRA--------------IMAAAAPTLK-----RLGLEL 228
>gnl|CDD|239162 cd02761, MopB_FmdB-FwdB, The MopB_FmdB-FwdB CD contains the
molybdenum/tungsten formylmethanofuran dehydrogenases,
subunit B (FmdB/FwdB), and other related proteins.
Formylmethanofuran dehydrogenase catalyzes the first
step in methane formation from CO2 in methanogenic
archaea and some eubacteria. Members of this CD belong
to the molybdopterin_binding (MopB) superfamily of
proteins.
Length = 415
Score = 25.0 bits (55), Expect = 2.9
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 11 SKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISADS 46
+K P+F LG+T + GIE+A+K I A S
Sbjct: 70 AKRPLFYGLGTTVCEAQRAGIELAEKLGAIIDHAAS 105
>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 = 24.9 bits (55), Expect = 2.9
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 16 FVILGSTGTGKSKLGIEIAKKFNG 39
+++G GTGKS+L +A +
Sbjct: 2 VLLVGPPGTGKSELAERLAAALSN 25
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 24.9 bits (55), Expect = 2.9
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 23 GTGKSKLGIEIAKKFNGEIISADS 46
G GKS +G +AK I D
Sbjct: 2 GAGKSTIGRLLAKALGLPFIDTDQ 25
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 25.1 bits (55), Expect = 3.2
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 16 FVILGSTGTGKSKLGIEIAKK 36
V+LG G GK+ L I I +
Sbjct: 108 LVLLGPPGVGKTHLAIAIGNE 128
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 24.8 bits (55), Expect = 3.3
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 5 FLKVVMSKVPIFVILGSTGTGKSKL 29
L+ ++ P+ V+ G+TG+GK++L
Sbjct: 133 TLEEAPAQFPLVVLGGNTGSGKTEL 157
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 25.0 bits (55), Expect = 3.4
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 16 FVILGSTGTGKS---KLGIEIAKKF-NGEIISADSMQGLKFLVE 55
+I+G TG GK+ + A K+ N +I++ D G +E
Sbjct: 439 TLIIGPTGAGKTVLLSFLLAQALKYGNPQIVAFDKDNGAYIFIE 482
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 25.0 bits (55), Expect = 3.5
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISA 44
+ I G G+GK+ + E+A+ +++SA
Sbjct: 2 VITISGLPGSGKTTVARELAEHLGLKLVSA 31
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 24.9 bits (55), Expect = 3.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNG 39
F+ LG TG GK++L +A+ G
Sbjct: 523 SFLFLGPTGVGKTELAKALAEALFG 547
>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 = 24.9 bits (55), Expect = 3.7
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 16 FVILGSTGTGKS 27
+I+G+TGTGK+
Sbjct: 18 ILIVGTTGTGKT 29
>gnl|CDD|237066 PRK12338, PRK12338, hypothetical protein; Provisional.
Length = 319
Score = 24.7 bits (54), Expect = 3.8
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 10 MSKVPIFVILGSTGTGKSKLGIEIAKKFN 38
M K + +I ++G GKS + E+A+ N
Sbjct: 1 MRKPYVILIGSASGIGKSTIASELARTLN 29
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 24.6 bits (55), Expect = 4.0
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 7 KVVMSKVPIFVILGSTGTGKS 27
+V + + I G +GTGK
Sbjct: 17 RVAPTDATVL-ITGESGTGKE 36
>gnl|CDD|223960 COG1029, FwdB, Formylmethanofuran dehydrogenase subunit B [Energy
production and conversion].
Length = 429
Score = 24.7 bits (54), Expect = 4.2
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 9 VMSKVPIFVILGSTGTGKSKLGIEIAKKFNGEI 41
V +K P+ ST +LGIE+A+K I
Sbjct: 77 VNAKRPLLYGWSSTSCEAQELGIELAEKLGAVI 109
>gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein. IVa2 protein can
interact with the adenoviral packaging signal and that
this interaction involves DNA sequences that have
previously been demonstrated to be required for
packaging. During the course of lytic infection, the
adenovirus major late promoter (MLP) is induced to high
levels after replication of viral DNA has started. IVa2
is a transcriptional activator of the major late
promoter.
Length = 370
Score = 24.6 bits (54), Expect = 4.4
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 10 MSKVP-IFVILGSTGTGKSKL 29
P I V+ G TG GKS+L
Sbjct: 83 YGLQPVIGVVYGPTGCGKSQL 103
>gnl|CDD|181884 PRK09469, glnA, glutamine synthetase; Provisional.
Length = 469
Score = 24.7 bits (54), Expect = 4.4
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 32 EIAKKFNGEIISADSMQGLKFLV 54
E+A +FN AD +Q K++V
Sbjct: 221 EVATRFNTMTKKADEIQIYKYVV 243
>gnl|CDD|215651 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 = 24.3 bits (54), Expect = 4.4
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 12 KVPIFVILGSTGTGKSKLGIEIAKKFNGEIIS 43
++ IF G +GTGK+ L IA+ +++
Sbjct: 17 RIGIF---GGSGTGKTVLLGMIARNAKADVVE 45
>gnl|CDD|237451 PRK13631, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 320
Score = 24.8 bits (54), Expect = 4.4
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 12 KVPIFVILGSTGTGKSKLGIEIAKKFNGEIISA 44
K I+ I+G++G+GKS L FNG I S
Sbjct: 51 KNKIYFIIGNSGSGKSTL----VTHFNGLIKSK 79
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 24.7 bits (54), Expect = 4.4
Identities = 8/34 (23%), Positives = 18/34 (52%)
Query: 12 KVPIFVILGSTGTGKSKLGIEIAKKFNGEIISAD 45
K+P+ V++ + T + I+ K + +I+ D
Sbjct: 417 KLPLLVLVDNGSTEEDIPAIKQLKAYGIDIVVVD 450
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 24.3 bits (53), Expect = 4.5
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 17 VILGSTGTGKSKLGIEIAKKFNGEIIS 43
+I G+ G+GK+ L E+A++ +
Sbjct: 2 LITGTPGSGKTTLAKELAERLGDVLRD 28
>gnl|CDD|201257 pfam00485, PRK, Phosphoribulokinase / Uridine kinase family. In
Arabidopsis the region carries two binding domains, a
phosphoribosylpyrophosphate-binding domain and, at the
very C-terminus, a uracil-binding domain.
Length = 197
Score = 24.6 bits (54), Expect = 4.6
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFNGEIISADSMQGLKFL 53
I + GS+G GK+ + F E + A ++G F
Sbjct: 1 IIGVTGSSGAGKTTVARTFVSIFGREGVPAAGIEGDSFH 39
>gnl|CDD|185352 PRK15455, PRK15455, PrkA family serine protein kinase; Provisional.
Length = 644
Score = 24.6 bits (54), Expect = 4.7
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 2 KSSF---LKVVMSKVPIFVILG 20
KSS LK +M +VPI+V+
Sbjct: 116 KSSLAERLKSLMERVPIYVLKA 137
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 24.4 bits (54), Expect = 4.7
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 4/24 (16%)
Query: 17 VILGSTGTGKS----KLGIEIAKK 36
+I G GTGK+ K+ E+ +
Sbjct: 59 LIYGPPGTGKTTTVKKVFEELEEI 82
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 24.4 bits (53), Expect = 5.4
Identities = 9/30 (30%), Positives = 19/30 (63%)
Query: 16 FVILGSTGTGKSKLGIEIAKKFNGEIISAD 45
F+ G TG GK+++ ++++K E++ D
Sbjct: 491 FLFAGPTGVGKTEVTVQLSKALGIELLRFD 520
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 24.1 bits (53), Expect = 5.5
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 15 IFVILGSTGTGKSKL 29
V+LG +G GK+
Sbjct: 28 FVVLLGPSGCGKTTT 42
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (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 = 24.3 bits (53), Expect = 5.8
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 16 FVILGSTGTGKSKL 29
F+I+GS GTGKS L
Sbjct: 3 FLIIGSAGTGKSCL 16
>gnl|CDD|237453 PRK13633, PRK13633, cobalt transporter ATP-binding subunit;
Provisional.
Length = 280
Score = 24.3 bits (53), Expect = 6.1
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 17 VILGSTGTGKSKLGIEIAKKFNGEIISAD 45
VILG G+GKS IAK N +I ++
Sbjct: 40 VILGRNGSGKST----IAKHMNALLIPSE 64
>gnl|CDD|184412 PRK13947, PRK13947, shikimate kinase; Provisional.
Length = 171
Score = 24.3 bits (53), Expect = 6.4
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 17 VILGSTGTGKSKLGIEIAKKFNGEIISADSM 47
V++G GTGK+ +G +A + I D
Sbjct: 5 VLIGFMGTGKTTVGKRVATTLSFGFIDTDKE 35
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 24.1 bits (52), Expect = 6.7
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 14 PIFVILGSTGTGKS 27
+ +I G G+GK+
Sbjct: 20 GLTLIYGPNGSGKT 33
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 23.9 bits (53), Expect = 7.2
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 7/28 (25%)
Query: 18 ILGSTGTGKSKL-----GIEIAKKFNGE 40
+LG G GKS L G++ K+F GE
Sbjct: 38 VLGLNGAGKSTLLRIMAGVD--KEFEGE 63
>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA.
Length = 193
Score = 24.1 bits (53), Expect = 7.3
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 15 IFVILGSTGTGKSKLGIEIAKKFN 38
+ V+ G+ G GKS L E+A+
Sbjct: 1 VIVVEGNIGAGKSTLAKELAEHLG 24
>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 = 24.1 bits (53), Expect = 7.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 15 IFVILGSTGTGKSKL 29
I ILG +G+GKS L
Sbjct: 36 ILAILGGSGSGKSTL 50
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation
of cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 217
Score = 23.9 bits (52), Expect = 7.4
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 14 PIFVILGSTGTGKSKLGIEIAKKFNGEIISADSM 47
I I G +G GKS + +A+K + + +M
Sbjct: 3 MIIAIDGPSGAGKSTVAKAVAEKLGYAYLDSGAM 36
>gnl|CDD|217156 pfam02634, FdhD-NarQ, FdhD/NarQ family. A pan-bacterial lineage of
proteins. Nitrate assimilation protein, NarQ, and FdhD
are required for formate dehydrogenase activity.
Structurally, they possess a deaminase fold with a
characteristic binding pocket, suggesting that they
might bind a nucleotide or related molecule
allosterically to regulate the formate dehydrogenase
catalytic subunit.
Length = 235
Score = 24.0 bits (53), Expect = 7.6
Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 4/33 (12%)
Query: 6 LKVVMSKVPIFVILGSTGTGKSKLGIEIAKKFN 38
K + +P+ V + + L +E+A++
Sbjct: 185 QKAARAGIPVLVSRSAP----TSLAVELAEELG 213
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 24.0 bits (53), Expect = 7.8
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 18 ILGSTGTGKSKL 29
+LG TG GKS L
Sbjct: 371 LLGRTGCGKSTL 382
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 23.9 bits (52), Expect = 7.8
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 11 SKVPIFVILGSTGTGKSKLGIEIAKKFNGE-----IISAD 45
KV + +++G +GKS L +A K II AD
Sbjct: 71 GKVGVVMVVGPVDSGKSTLTTYLANKLLARGRKVAIIDAD 110
>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 = 24.0 bits (53), Expect = 7.9
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 15 IFVILGSTGTGKSKL 29
I I+G +G+GKS L
Sbjct: 28 ILAIIGPSGSGKSTL 42
>gnl|CDD|180669 PRK06720, PRK06720, hypothetical protein; Provisional.
Length = 169
Score = 23.8 bits (51), Expect = 8.1
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 4/27 (14%)
Query: 1 MKSSFLK----VVMSKVPIFVILGSTG 23
+ SSF+K VV+S +PIF I+G+ G
Sbjct: 133 LTSSFMKQQEEVVLSDLPIFGIIGTKG 159
>gnl|CDD|237724 PRK14481, PRK14481, dihydroxyacetone kinase subunit DhaK;
Provisional.
Length = 331
Score = 24.0 bits (53), Expect = 8.3
Identities = 9/38 (23%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 28 KLGIEIAKKFNGEIISADSMQGLKFLVECRVKLELLRL 65
+ G+ +A+ G +++ M G + ++ ELL L
Sbjct: 282 ERGVTVARSLVGNYMTSLDMAGFSITL-LKLDDELLEL 318
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 23.6 bits (52), Expect = 8.6
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 10 MSKVPIFVILGSTGTGKSKLGIEIAKKFNGEIISAD 45
M K P V++G G GKS +G +AK+ + I D
Sbjct: 1 MLKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD 36
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 23.8 bits (52), Expect = 9.2
Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 7 KVVMSKVPIFVILGSTGTGK 26
KV S + I G +GTGK
Sbjct: 159 KVAPSDASVL-ITGESGTGK 177
>gnl|CDD|236269 PRK08462, PRK08462, biotin carboxylase; Validated.
Length = 445
Score = 23.5 bits (51), Expect = 9.8
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 7 KVVMSKVPIFVILGSTGTGKSKLGIEIAKKFNGEI 41
K VM + + VI GS G KS E AKK EI
Sbjct: 122 KEVMKRAGVPVIPGSDGALKS---YEEAKKIAKEI 153
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
0.321 0.139 0.376
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,270,983
Number of extensions: 243993
Number of successful extensions: 762
Number of sequences better than 10.0: 1
Number of HSP's gapped: 762
Number of HSP's successfully gapped: 119
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.6 bits)