RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2713
(143 letters)
>gnl|CDD|216591 pfam01591, 6PF2K, 6-phosphofructo-2-kinase. This enzyme occurs as
a bifunctional enzyme with fructose-2,6-bisphosphatase.
The bifunctional enzyme catalyzes both the synthesis and
degradation of fructose-2,6-bisphosphate, a potent
regulator of glycolysis. This enzyme contains a P-loop
motif.
Length = 219
Score = 135 bits (342), Expect = 6e-41
Identities = 61/134 (45%), Positives = 82/134 (61%), Gaps = 2/134 (1%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFRVDNTE 65
++ +VGLPARGKT ++ KL+RYL W +KVF+V YRR ++ Y+ ++ FR DN E
Sbjct: 10 KTLIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRRSAVKAYSDYEFFRPDNEE 69
Query: 66 GYNIRQLSAREAQEDATKWLKND-GEVAIIDGTTATMEKRKQIHDYFARKMGFKVLFVEL 124
G IR+ A A D +L + G+VAI D T T E+RK I D FA + G KV F+E
Sbjct: 70 GMKIREQCALAALNDVLAYLNEESGQVAIFDATNTTRERRKMILD-FAEENGLKVFFLES 128
Query: 125 IVQDEEILEHNIKQ 138
I D EI+ NIK
Sbjct: 129 ICDDPEIIARNIKL 142
>gnl|CDD|140343 PTZ00322, PTZ00322,
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase;
Provisional.
Length = 664
Score = 69.9 bits (171), Expect = 6e-15
Identities = 41/134 (30%), Positives = 67/134 (50%), Gaps = 9/134 (6%)
Query: 7 LVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFRVDNTEG 66
L+V +VGLP RGKT +A ++ RY W +S++F AYRR+ LE T
Sbjct: 216 LIVIMVGLPGRGKTYVARQIQRYFQWNGLQSRIFIHQAYRRR-LE---RRGGAVSSPTGA 271
Query: 67 YNIRQLSAREAQEDATKWLKNDGEVAIIDGTTATMEKR----KQIHDYFARKMGFKVLFV 122
+ A+ D T ++ VA++DGT T +R + I + +M +V+FV
Sbjct: 272 AEVEFRIAKAIAHDMTTFICKTDGVAVLDGTNTTHARRMALLRAIRETGLIRMT-RVVFV 330
Query: 123 ELIVQDEEILEHNI 136
E++ + E + N+
Sbjct: 331 EVVNNNSETIRRNV 344
>gnl|CDD|226986 COG4639, COG4639, Predicted kinase [General function prediction
only].
Length = 168
Score = 40.5 bits (95), Expect = 5e-05
Identities = 26/128 (20%), Positives = 47/128 (36%), Gaps = 17/128 (13%)
Query: 8 VVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFRVDNTEGY 67
+V L G GK+ A + ++ V S+ R + + + D
Sbjct: 4 LVVLRGASGSGKSTFAKENFL-------QNYVLSLDDLRLLLGVSASKENSQKND----- 51
Query: 68 NIRQLSAREAQEDATKWLKNDGEVAIIDGTTATMEKRKQIHDYFARKMGFKVLFVELIVQ 127
+L + + L+ G+ IID T E R+++ D A+ G+K+ +
Sbjct: 52 ---ELVWDILYKQLEQRLRR-GKFTIIDATNLRREDRRKLID-LAKAYGYKIYAIVFDTP 106
Query: 128 DEEILEHN 135
E L N
Sbjct: 107 LELCLARN 114
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 37.7 bits (88), Expect = 4e-04
Identities = 32/131 (24%), Positives = 49/131 (37%), Gaps = 14/131 (10%)
Query: 8 VVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFRVDNTEGY 67
++ +VGLP GK+ A +L R L V S R+ L + Y
Sbjct: 1 LILMVGLPGSGKSTFARRLLRELGAV-----VLSSDTLRK---RLRGDGP----PDISYY 48
Query: 68 NIRQLSAREAQEDATKWLKNDGEVAIIDGTTATMEKRKQIHDYFARKMGFKVLFVELIVQ 127
+ + + G I+D T + E+R ++ D AR+ G V V L
Sbjct: 49 ARASGRVYQRLLELAREALRAGRPVIVDATNLSREERARLID-LARRYGAPVRIVYLEA- 106
Query: 128 DEEILEHNIKQ 138
EE+L Q
Sbjct: 107 PEEVLRERNAQ 117
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only
detects a fraction of this vast family. The poorly
conserved N-terminal helix is missing from the
alignment.
Length = 148
Score = 33.9 bits (77), Expect = 0.012
Identities = 21/91 (23%), Positives = 31/91 (34%), Gaps = 6/91 (6%)
Query: 5 TPLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFRVDNT 64
V+ +VG P GKT LA L+R L + L+ +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGG---K 57
Query: 65 EGYNIRQLSAREAQEDATKWLKNDGEVAIID 95
+ +L R A A K +V I+D
Sbjct: 58 KASGSGELRLRLALALA---RKLKPDVLILD 85
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 34.4 bits (80), Expect = 0.013
Identities = 19/44 (43%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 5 TPLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSA--YR 46
P V+ +VGL GKT A KL++YL KV V+A YR
Sbjct: 99 PPTVILMVGLQGSGKTTTAGKLAKYL--KKKGKKVLLVAADTYR 140
>gnl|CDD|236780 PRK10867, PRK10867, signal recognition particle protein;
Provisional.
Length = 433
Score = 33.5 bits (78), Expect = 0.023
Identities = 20/43 (46%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSA--YR 46
P V+ +VGL GKT A KL++YL K KV V+A YR
Sbjct: 100 PTVIMMVGLQGAGKTTTAGKLAKYLK-KKKKKKVLLVAADVYR 141
>gnl|CDD|107249 cd01536, PBP1_ABC_sugar_binding_like, Periplasmic sugar-binding
domain of active transport systems that are members of
the type I periplasmic binding protein (PBP1)
superfamily. Periplasmic sugar-binding domain of active
transport systems that are members of the type I
periplasmic binding protein (PBP1) superfamily. The
members of this family function as the primary receptors
for chemotaxis and transport of many sugar based solutes
in bacteria and archaea. The sugar binding domain is
also homologous to the ligand-binding domain of
eukaryotic receptors such as glutamate receptor (GluR)
and DNA-binding transcriptional repressors such as LacI
and GalR. Moreover, this periplasmic binding domain,
also known as Venus flytrap domain, undergoes transition
from an open to a closed conformational state upon the
binding of ligands such as lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars.
This family also includes the periplasmic binding domain
of autoinducer-2 (AI-2) receptors such as LsrB and LuxP
which are highly homologous to periplasmic
pentose/hexose sugar-binding proteins.
Length = 267
Score = 31.9 bits (73), Expect = 0.081
Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 10/66 (15%)
Query: 61 VDNTEGYNIRQLSAREAQEDATKWLKNDGEVAIIDG---TTATMEKRKQIHDYFARKMGF 117
DN E R A E K L G+VAII+G ++ E+ K D
Sbjct: 101 TDNYEA-------GRLAGEYLAKLLGGKGKVAIIEGPPGSSNAQERVKGFRDALKEYPDI 153
Query: 118 KVLFVE 123
+++ V+
Sbjct: 154 EIVAVQ 159
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 30.3 bits (68), Expect = 0.15
Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 20/91 (21%)
Query: 8 VVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFRVDNTEGY 67
++ + G P GK+ LA KL+ L + + + D+ R +
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKL------------------GIPVISLDDLLREEGLAEL 42
Query: 68 NIRQLSAREAQEDATKWL--KNDGEVAIIDG 96
+ +L + + + + + + +IDG
Sbjct: 43 DDGELDDIDIDLELLEEILDELAKQEWVIDG 73
>gnl|CDD|233210 TIGR00959, ffh, signal recognition particle protein. This model
represents Ffh (Fifty-Four Homolog), the protein
component that forms the bacterial (and organellar)
signal recognition particle together with a 4.5S RNA.
Ffh is a GTPase homologous to eukaryotic SRP54 and also
to the GTPase FtsY (TIGR00064) that is the receptor for
the signal recognition particle [Protein fate, Protein
and peptide secretion and trafficking].
Length = 428
Score = 30.7 bits (70), Expect = 0.20
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSA--YR 46
P V+ +VGL GKT KL+ YL K KV V+ YR
Sbjct: 99 PTVILMVGLQGSGKTTTCGKLAYYLKKKQGK-KVLLVACDLYR 140
>gnl|CDD|240307 PTZ00187, PTZ00187, succinyl-CoA synthetase alpha subunit;
Provisional.
Length = 317
Score = 30.5 bits (69), Expect = 0.26
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 76 EAQEDATKWLKNDGE----VAIIDGTTATMEKR 104
A+E+A +W+KN+ V+ I G TA +R
Sbjct: 237 TAEEEAAEWIKNNPIKKPVVSFIAGITAPPGRR 269
>gnl|CDD|237728 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 30.0 bits (68), Expect = 0.34
Identities = 18/46 (39%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 4 FTPLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKH 49
F P +A G GKT L L R L S+ FSV Y KH
Sbjct: 3 FHPFEIAFCGYSGSGKTTLITALVRRL------SERFSVGYY--KH 40
>gnl|CDD|107296 cd06301, PBP1_rhizopine_binding_like, Periplasmic binding proteins
specific to rhizopines. Periplasmic binding proteins
specific to rhizopines, which are simple sugar-like
compounds produced in the nodules induced by the
symbiotic root nodule bacteria, such as Rhizobium and
Sinorhizobium. Rhizopine-binding-like proteins from
other bacteria are also included. Two inositol based
rhizopine compounds are known to date:
L-3-O-methly-scyllo-inosamine (3-O-MSI) and
scyllo-inosamine. Bacterial strains that can metabolize
rhizopine have a greater competitive advantage in
nodulation and rhizopine synthesis is regulated by
NifA/NtrA regulatory transcription activators which are
maximally expressed at the onset of nitrogen fixation in
bacteroids. The members of this group belong to the
pentose/hexose sugar-binding protein family of the type
I periplasmic binding protein superfamily.
Length = 272
Score = 29.9 bits (68), Expect = 0.41
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 76 EAQEDATKWLKNDGEVAIIDGT---TATMEKRKQIHDYFARKMGFKVLF 121
+A+ A K L G VAI+ G +A +++ K + + A+ KV+
Sbjct: 112 QAEYVADK-LGGKGNVAILMGPLGQSAQIDRTKGVEEVLAKYPDIKVVE 159
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK)
catalyzes the phosphorylation of adenosine
5'-phosphosulfate to form 3'-phosphoadenosine
5'-phosphosulfate (PAPS). The end-product PAPS is a
biologically "activated" sulfate form important for the
assimilation of inorganic sulfate.
Length = 149
Score = 29.4 bits (67), Expect = 0.44
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 8 VVALVGLPARGKTVLAHKLSRYL 30
V+ L GL GK+ +A L L
Sbjct: 1 VIWLTGLSGSGKSTIARALEEKL 23
>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 = 28.8 bits (65), Expect = 0.70
Identities = 28/136 (20%), Positives = 50/136 (36%), Gaps = 11/136 (8%)
Query: 5 TPLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSA--YRRKHLELYNSHDIFRVD 62
P+ V L G P GKT LA L L + V + R H Y ++ + D
Sbjct: 11 RPVAVLLGGQPGAGKTELARALLEELGGGN----VVRIDPDELRTYH-PDY--DELQKAD 63
Query: 63 NTEGYNIRQLSAREAQEDATKWLKNDGEVAIIDGTTATMEKRKQIHDYFARKMGFKVLFV 122
+ + Q A E + G I++GT + + +++ G++V V
Sbjct: 64 PKDASELTQPDASRWVEKLIDYAIERGYNIILEGTLRSPDVARKLARKLKAA-GYEVE-V 121
Query: 123 ELIVQDEEILEHNIKQ 138
++ E+ +
Sbjct: 122 YVVAVPPELSWLGVLD 137
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 28.4 bits (64), Expect = 0.86
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 18/54 (33%)
Query: 7 LVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFR 60
+V+ + GLP GKT +A +L+ +L L+L ++ IFR
Sbjct: 1 MVITISGLPGSGKTTVARELAEHLG------------------LKLVSAGTIFR 36
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 28.7 bits (65), Expect = 0.89
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYL 30
P V+ LVGL GKT KL+ YL
Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAYL 25
>gnl|CDD|216586 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that
catalyzes the phosphorylation of adenylylsulphate to
3'-phosphoadenylylsulfate. This domain contains an ATP
binding P-loop motif.
Length = 157
Score = 28.4 bits (64), Expect = 1.0
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYL 30
+ GL GK+ +A+ L R L
Sbjct: 2 GCTIWFTGLSGSGKSTIANALERKL 26
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 28.2 bits (64), Expect = 1.1
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 18/54 (33%)
Query: 7 LVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFR 60
+++ + G P GKT +A L+ L L+ ++ +IFR
Sbjct: 1 MIITISGPPGSGKTTVARLLAEKL------------------GLKHVSAGEIFR 36
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 28.2 bits (64), Expect = 1.5
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYL 30
P + LVGL GKT A KL+RY
Sbjct: 95 PQTIMLVGLQGSGKTTTAAKLARYF 119
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 28.1 bits (63), Expect = 1.6
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYLT 31
PLVV +VG P GK+ L L + T
Sbjct: 39 PLVVVVVGPPGVGKSTLIRSLIKRYT 64
>gnl|CDD|215427 PLN02796, PLN02796, D-glycerate 3-kinase.
Length = 347
Score = 28.2 bits (63), Expect = 1.7
Identities = 10/41 (24%), Positives = 16/41 (39%)
Query: 2 RQFTPLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSV 42
+ PLV+ + GKT L L T ++ S+
Sbjct: 96 DEIPPLVIGISAPQGCGKTTLVFALVYLFNATGRRAASLSI 136
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 27.6 bits (62), Expect = 1.8
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYL 30
V+ GL GK+ +A+ L L
Sbjct: 23 GAVIWFTGLSGSGKSTIANALEEKL 47
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 27.4 bits (61), Expect = 1.9
Identities = 25/125 (20%), Positives = 41/125 (32%), Gaps = 19/125 (15%)
Query: 9 VALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYNSHDIFRVDNTEGYN 68
+ + G P GKT LA +L+ + ++ L L +I +
Sbjct: 1 ILITGTPGSGKTTLAKELAE-----RLGDVLRDLAKEN--GLVLELDEEITDESKRLDED 53
Query: 69 IRQLSAREAQEDATKWLKNDGEVAIIDGTTATMEKRKQIHDYFARKMGFKVLFVELIVQD 128
+ E + +GE IIDG + ++FV L
Sbjct: 54 KLA-KLLDKLEKIIE-ELAEGENVIIDG----------HLAELELERFKDLVFVVLRADP 101
Query: 129 EEILE 133
EE+LE
Sbjct: 102 EELLE 106
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 28.2 bits (62), Expect = 2.0
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYLT 31
P +VA+VG P GK+ L L R T
Sbjct: 69 PFIVAVVGPPGTGKSTLIRSLVRRFT 94
>gnl|CDD|219839 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 27.6 bits (62), Expect = 2.1
Identities = 22/103 (21%), Positives = 41/103 (39%), Gaps = 16/103 (15%)
Query: 7 LVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRRKHLELYN-SHDIFRVDNTE 65
L++ L GLP+ GK+ A +L++YL + V +S E D ++ E
Sbjct: 1 LII-LTGLPSSGKSTRAKELAKYL--EEKGYDVIVISD------ESLGIESDDYKDSKKE 51
Query: 66 GYNIRQLSAREAQEDATKWLKNDGEVAIIDGTTATMEKRKQIH 108
+R + D +K + I+D R +++
Sbjct: 52 K-FLRGSLRSAVKRDLSK-----NTIVIVDSLNYIKGFRYELY 88
>gnl|CDD|220422 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members
of this family include various bacterial predicted ABC
class ATPases.
Length = 447
Score = 27.6 bits (62), Expect = 2.8
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 12 VGLPARGKTVLAHKLSRYLT 31
VGLPARG+ +L L
Sbjct: 129 VGLPARGRRILGRAAINILL 148
>gnl|CDD|236151 PRK08099, PRK08099, bifunctional DNA-binding transcriptional
repressor/ NMN adenylyltransferase; Provisional.
Length = 399
Score = 27.3 bits (61), Expect = 2.8
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 2 RQFTPLVVALVGLPARGKTVLAHKLSRY 29
R F VA++G + GK+ L +KL+
Sbjct: 215 RPFFVRTVAILGGESSGKSTLVNKLANI 242
>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 = 3.0
Identities = 8/31 (25%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 9 VALVGLPARGKTVLAHKLSRYLTW----TDH 35
+ L+G+ GKT + L++ L D
Sbjct: 2 IVLIGMMGAGKTTVGRLLAKALGLPFVDLDE 32
>gnl|CDD|239389 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 = 27.1 bits (61), Expect = 3.1
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 8 VVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFSV 42
V+ LVGL GKT A KL+ YL K K V
Sbjct: 2 VILLVGLQGVGKTTTAAKLALYL-----KKKGKKV 31
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 26.6 bits (59), Expect = 3.9
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 11 LVGLPARGKTVLAHKLSRYLTW----TDH 35
L GLP GKT L+++L+ TD
Sbjct: 5 LCGLPTVGKTSFGKALAKFLSLPFFDTDD 33
>gnl|CDD|225351 COG2746, COG2746, Aminoglycoside N3'-acetyltransferase [Defense
mechanisms].
Length = 251
Score = 27.0 bits (60), Expect = 4.1
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 53 YNSHDIFRVDNTEGYNIRQLSAREAQEDATKWLKNDG 89
Y D FR G + R + AR+ + A + L+ +G
Sbjct: 209 YELEDNFREGTVGGAHARLVDARDLVDIAVRALRREG 245
>gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated.
Length = 223
Score = 26.5 bits (59), Expect = 5.2
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 6 PLVVALVGLPARGKTVLAHKL 26
PL VA+ G+ A GKT A +L
Sbjct: 22 PLRVAIDGITASGKTTFADEL 42
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 26.1 bits (58), Expect = 5.3
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 8 VVALVGLPARGKTVLAHKLSRYLTWTDHKS-KVFSVSAYRR 47
V L G GKT L K++ L W K + F +
Sbjct: 2 TVILQGEAGSGKTTLLQKIA--LLWAQGKLPQDFDFVFFLP 40
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 25.7 bits (57), Expect = 6.4
Identities = 19/67 (28%), Positives = 26/67 (38%), Gaps = 10/67 (14%)
Query: 11 LVGLPARGKTVLAHKLSRYLTWTDHKSKVFSVSAYRR----KHLELYNSHDIFRVD---- 62
L G P GK+ LA L+R L K SV Y R + Y + +D
Sbjct: 3 LYGPPGCGKSTLAKYLARALLKHLGLPKKDSV--YSRNPDDDFWDGYTGQPVVIIDDFGQ 60
Query: 63 NTEGYNI 69
N +G +
Sbjct: 61 NPDGPSD 67
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein
(DRG). The developmentally regulated GTP-binding
protein (DRG) subfamily is an uncharacterized member of
the Obg family, an evolutionary branch of GTPase
superfamily proteins. GTPases act as molecular switches
regulating diverse cellular processes. DRG2 and DRG1
comprise the DRG subfamily in eukaryotes. In view of
their widespread expression in various tissues and high
conservation among distantly related species in
eukaryotes and archaea, DRG proteins may regulate
fundamental cellular processes. It is proposed that the
DRG subfamily proteins play their physiological roles
through RNA binding.
Length = 233
Score = 26.0 bits (58), Expect = 6.5
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 9 VALVGLPARGKTVLAHKLS 27
VALVG P+ GK+ L KL+
Sbjct: 3 VALVGFPSVGKSTLLSKLT 21
>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
Length = 282
Score = 26.3 bits (58), Expect = 6.7
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 13 GLPARGKTVLAHKLSRYLTWTDHKSKVFS 41
GLP GK+ A L+ L+ + +++
Sbjct: 10 GLPGFGKSTTAKMLNDILSQNGIEVELYL 38
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport
and metabolism].
Length = 189
Score = 25.8 bits (57), Expect = 6.9
Identities = 22/95 (23%), Positives = 33/95 (34%), Gaps = 16/95 (16%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYLTWTDHKSKVFS-VSAYRRKHLELYNSHDIFRVDNT 64
VV + G+P GKT + + L HK + + K L D
Sbjct: 4 RKVVVITGVPGVGKTTVLKIALKEL--VKHKIVNYGDLMLEIAKKKGLVEHRD------- 54
Query: 65 EGYNIRQLSA---REAQEDATKWLKNDGEVAIIDG 96
+R+L RE Q +A K + I+D
Sbjct: 55 ---EMRKLPLENQRELQAEAAKRIAEMALEIIVDT 86
>gnl|CDD|222144 pfam13458, Peripla_BP_6, Periplasmic binding protein. This family
includes a diverse range of periplasmic binding
proteins.
Length = 343
Score = 26.1 bits (58), Expect = 8.0
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 5/52 (9%)
Query: 71 QLSAREAQEDATKWLKNDGEVAIIDGTTATMEKRKQIHDYFARKMGFKVLFV 122
Q A A + + DG AI G T+ + + +K V +
Sbjct: 51 QSDPDRAAAAARRLVDQDGVDAIFGGLTSAV--ALAVAPVLEKK---GVPLI 97
>gnl|CDD|223315 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 25.7 bits (57), Expect = 9.0
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRY 29
L++ L G GK+ +A L+
Sbjct: 2 MLIIGLTGGIGSGKSTVAKILAEL 25
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 26.0 bits (58), Expect = 9.3
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 1 LRQFTPLVVALVGLPARGKTVLAHKLSRYLT 31
LR PL V + G P GKT K+ L
Sbjct: 50 LRGSRPLNVLIYGPPGTGKTTTVKKVFEELE 80
>gnl|CDD|237260 PRK12906, secA, preprotein translocase subunit SecA; Reviewed.
Length = 796
Score = 25.8 bits (57), Expect = 9.4
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 34 DHKSKVFSVS-AYRRKHLELYNSHDIFRVDNTE-GYNIRQ-LSAREAQEDATKWLKNDGE 90
D K+K S++ RK +L+ +++ +NT ++I Q L A ++ DGE
Sbjct: 264 DEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHIDQALRANYIMLKDIDYVVQDGE 323
Query: 91 VAIIDGTTA-TMEKRK 105
V I+D T ME R+
Sbjct: 324 VLIVDEFTGRVMEGRR 339
>gnl|CDD|238978 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 (57), Expect = 9.4
Identities = 7/26 (26%), Positives = 14/26 (53%)
Query: 8 VVALVGLPARGKTVLAHKLSRYLTWT 33
++A+ G GK+ +A L++ L
Sbjct: 1 IIAIDGPAGSGKSTVAKLLAKKLGLP 26
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with
the signal sequence when it emerges from the ribosome.
SRP54 of the signal recognition particle has a
three-domain structure: an N-terminal helical bundle
domain, a GTPase domain, and the M-domain that binds
the 7s RNA and also binds the signal sequence. The
extreme C-terminal region is glycine-rich and lower in
complexity and poorly conserved between species. The
GTPase domain is evolutionary related to P-loop NTPase
domains found in a variety of other proteins.
Length = 197
Score = 25.4 bits (57), Expect = 9.4
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 6 PLVVALVGLPARGKTVLAHKLSRYL 30
P V+ LVG GKT KL+ L
Sbjct: 1 PGVILLVGPNGVGKTTTIAKLAARL 25
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 0.134 0.390
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,359,432
Number of extensions: 650969
Number of successful extensions: 983
Number of sequences better than 10.0: 1
Number of HSP's gapped: 976
Number of HSP's successfully gapped: 79
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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 (24.3 bits)