RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6618
(109 letters)
>gnl|CDD|206639 cd00066, G-alpha, Alpha subunit of G proteins (guanine nucleotide
binding). 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 = 315
Score = 69.1 bits (170), Expect = 3e-15
Identities = 22/49 (44%), Positives = 38/49 (77%)
Query: 42 LRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFSNNERE 90
++I+H +GF+ E+ +++RPV+YSN +QS+ A+LRAM L+I + + E E
Sbjct: 20 MKILHGNGFSDEERREFRPVIYSNILQSMKALLRAMETLNIPYGDPENE 68
Score = 45.6 bits (109), Expect = 7e-07
Identities = 14/31 (45%), Positives = 24/31 (77%)
Query: 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRIL 31
I+H +GF+ E+ +++RPV+YSN +QS +L
Sbjct: 22 ILHGNGFSDEERREFRPVIYSNILQSMKALL 52
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 64.5 bits (158), Expect = 1e-13
Identities = 20/49 (40%), Positives = 35/49 (71%)
Query: 42 LRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFSNNERE 90
+RI+H GF+ E+ ++YRP++YSN ++S+ A++ AM L+I F + E
Sbjct: 41 MRILHGDGFSQEERREYRPLIYSNILESMKALVDAMEELNIPFEDPESI 89
Score = 43.3 bits (103), Expect = 4e-06
Identities = 12/31 (38%), Positives = 23/31 (74%)
Query: 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRIL 31
I+H GF+ E+ ++YRP++YSN ++S ++
Sbjct: 43 ILHGDGFSQEERREYRPLIYSNILESMKALV 73
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 57.3 bits (139), Expect = 4e-11
Identities = 23/49 (46%), Positives = 35/49 (71%)
Query: 42 LRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFSNNERE 90
++I+H GF+ E+ +QYR V+YSN I+SL +L A+ NL I SN++ E
Sbjct: 22 MKILHGGGFSDEEREQYRAVIYSNIIRSLKTLLEALENLEIESSNSKPE 70
Score = 41.1 bits (97), Expect = 3e-05
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRIL 31
I+H GF+ E+ +QYR V+YSN I+S +L
Sbjct: 24 ILHGGGFSDEEREQYRAVIYSNIIRSLKTLL 54
>gnl|CDD|173383 PTZ00089, PTZ00089, transketolase; Provisional.
Length = 661
Score = 31.6 bits (72), Expect = 0.064
Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 22/77 (28%)
Query: 32 GTFL-----------LSKWLELRII----HESGFTSEDFKQYRPVVYSNTIQSLVAILRA 76
TFL L+ +I H+S ED ++PV +A+LRA
Sbjct: 433 ATFLNFYGYALGAVRLAALSHHPVIYVATHDSIGLGEDGPTHQPV-------ETLALLRA 485
Query: 77 MPNLSISFSNNERETAG 93
PNL + + ET+G
Sbjct: 486 TPNLLVIRPADGTETSG 502
>gnl|CDD|236519 PRK09442, panF, sodium/panthothenate symporter; Provisional.
Length = 483
Score = 28.3 bits (64), Expect = 0.77
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 15 YRPVVYSNTIQSTVRILGTFLL 36
+R VV ++ +Q V ++GT +L
Sbjct: 178 FRAVVLTDALQGIVMLVGTVIL 199
>gnl|CDD|217801 pfam03934, T2SK, Type II secretion system (T2SS), protein K.
Members of this family are involved in the Type II
protein secretion system. The T2SK family includes
proteins such as ExeK, PulK, OutX and XcpX.
Length = 282
Score = 27.7 bits (62), Expect = 1.0
Identities = 19/67 (28%), Positives = 27/67 (40%), Gaps = 18/67 (26%)
Query: 41 ELRIIHESGFTSEDFKQYRPVV--YS--------NTIQSLVAILRAM-PNLSISFSN--- 86
ELR++ G T E + + RP V NT + V L A+ LS+S +
Sbjct: 157 ELRLV--LGVTPELYARLRPYVCALPTDRTPINVNTAPAEV--LAALFEGLSLSQAQRLL 212
Query: 87 NERETAG 93
R G
Sbjct: 213 AARPADG 219
>gnl|CDD|226625 COG4145, PanF, Na+/panthothenate symporter [Coenzyme metabolism].
Length = 473
Score = 27.3 bits (61), Expect = 1.4
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 12 FKQYRPVVYSNTIQSTVRILGTFLL 36
F +R VV ++TIQ V ++GT +L
Sbjct: 173 FGGFRAVVLTDTIQGLVMLIGTVVL 197
>gnl|CDD|181079 PRK07679, PRK07679, pyrroline-5-carboxylate reductase; Reviewed.
Length = 279
Score = 27.4 bits (61), Expect = 1.6
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 4/24 (16%)
Query: 62 VYSNTIQSL----VAILRAMPNLS 81
V +++I++L V I+RAMPN S
Sbjct: 102 VSTHSIRNLLQKDVPIIRAMPNTS 125
>gnl|CDD|212037 cd10327, SLC5sbd_PanF, Na(+)/pantothenate cotransporters: PanF of
Escherichia coli and related proteins; solute binding
domain. PanF catalyzes the Na+-coupled uptake of
extracellular pantothenate for coenzyme A biosynthesis
in cells. This subfamily belongs to the solute carrier 5
(SLC5) transporter family.
Length = 472
Score = 26.8 bits (60), Expect = 2.2
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 15 YRPVVYSNTIQSTVRILGTFLL 36
+R V ++ IQ V I+GT LL
Sbjct: 176 FRAVALTDAIQGIVMIIGTVLL 197
>gnl|CDD|219442 pfam07514, TraI_2, Putative helicase. Some members of this
family have been annotated as helicases.
Length = 326
Score = 26.9 bits (60), Expect = 2.5
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 23 TIQSTVRILGTFLLSKWLELRIIHESGFTSEDFKQ-YRPVV--YSNTIQSLVA 72
S +L T + LE RI G + EDF++ Y P + Y+ +Q L A
Sbjct: 4 APLSAEDLLATERRQELLE-RIWQNLGLSREDFERLYLPPIRRYAELVQLLPA 55
>gnl|CDD|214865 smart00861, Transket_pyr, Transketolase, pyrimidine binding domain.
Transketolase (TK) catalyzes the reversible transfer of
a two-carbon ketol unit from xylulose 5-phosphate to an
aldose receptor, such as ribose 5-phosphate, to form
sedoheptulose 7-phosphate and glyceraldehyde 3-
phosphate. This enzyme, together with transaldolase,
provides a link between the glycolytic and
pentose-phosphate pathways. TK requires thiamine
pyrophosphate as a cofactor. In most sources where TK
has been purified, it is a homodimer of approximately 70
Kd subunits. TK sequences from a variety of eukaryotic
and prokaryotic sources show that the enzyme has been
evolutionarily conserved. In the peroxisomes of
methylotrophic yeast Hansenula polymorpha, there is a
highly related enzyme, dihydroxy-acetone synthase (DHAS)
(also known as formaldehyde transketolase), which
exhibits a very unusual specificity by including
formaldehyde amongst its substrates.
Length = 136
Score = 26.3 bits (59), Expect = 2.5
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 68 QSLVAILRAMPNLSISFSNNERETAGL 94
A+LRA+P L + ++ E GL
Sbjct: 88 IEDEALLRAIPGLKVVAPSDPAEAKGL 114
>gnl|CDD|109527 pfam00474, SSF, Sodium:solute symporter family. Membership of this
family is supported by a significant blast score.
Length = 406
Score = 26.5 bits (59), Expect = 3.0
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 15 YRPVVYSNTIQSTVRILGTFLLSKWLELRIIHESGFTSEDFKQY 58
+ V +++TIQ+ + + GT +L + + HE G S ++Y
Sbjct: 140 FLAVSWTDTIQAVLMLFGTIILM----IIVFHEVGGYSSAVEKY 179
>gnl|CDD|217387 pfam03143, GTP_EFTU_D3, Elongation factor Tu C-terminal domain.
Elongation factor Tu consists of three structural
domains, this is the third domain. This domain adopts a
beta barrel structure. This the third domain is
involved in binding to both charged tRNA and binding to
EF-Ts pfam00889.
Length = 91
Score = 25.5 bits (57), Expect = 3.8
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 4/31 (12%)
Query: 3 HESGFTSEDFKQYRPVVYSNTIQSTVRILGT 33
H + F YRPV Y +T T + +
Sbjct: 17 HPTPI----FNGYRPVFYCHTADVTGKFILP 43
>gnl|CDD|131174 TIGR02119, panF, sodium/pantothenate symporter. Pantothenate
(vitamin B5) is a precursor of coenzyme A and is made
from aspartate and 2-oxoisovalerate in most bacteria
with completed genome sequences. However, some pathogens
must import pantothenate. This model describes PanF, a
sodium/pantothenate symporter, from a larger family of
Sodium/substrate symporters (pfam00474). Several species
that have this transporter appear to lack all enzymes of
pantothenate biosynthesis, namely Haemophilus
influenzae, Pasteurella multocida, Fusobacterium
nucleatum, and Borrelia burgdorferi [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pantothenate
and coenzyme A, Transport and binding proteins, Other].
Length = 471
Score = 25.8 bits (57), Expect = 5.0
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 12 FKQYRPVVYSNTIQSTVRILGTFLL 36
F +R V ++ IQ V GT +L
Sbjct: 174 FGGFRAVALTDAIQGIVMFTGTTIL 198
>gnl|CDD|233138 TIGR00813, sss, transporter, SSS family. The Solute:Sodium
Symporter (SSS) Family (TC 2.A.21) Members of the SSS
family catalyze solute:Na+ symport. The solutes
transported may be sugars, amino acids, nucleosides,
inositols, vitamins, urea or anions, depending on the
system. Members of the SSS family have been identified
in bacteria, archaea and animals, and all functionally
well characterized members catalyze solute uptake via
Na+ symport. Proteins of the SSS generally share a core
of 13 TMSs, but different members of the family may have
different numbers of TMSs. A 13 TMS topology with a
periplasmic N-terminus and a cytoplasmic C-terminus has
been experimentally determined for the proline:Na+
symporter, PutP, of E. coli [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 407
Score = 25.7 bits (57), Expect = 5.3
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 18 VVYSNTIQSTVRILGTFLLSKWLELRIIHESGFTSEDFKQYR 59
VV+++TIQ+ + ILGTF+L + E G ++
Sbjct: 139 VVWTDTIQAVIMILGTFILP----VFAFSEVGGLGTFVEKAS 176
>gnl|CDD|132916 cd07033, TPP_PYR_DXS_TK_like, Pyrimidine (PYR) binding domain of
1-deoxy-D-xylulose-5-phosphate synthase (DXS),
transketolase (TK), and related proteins. Thiamine
pyrophosphate (TPP) family, pyrimidine (PYR) binding
domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS),
transketolase (TK), and the beta subunits of the E1
component of the human pyruvate dehydrogenase complex
(E1- PDHc), subfamily. The PYR domain is found in many
key metabolic enzymes which use TPP (also known as
thiamine diphosphate) as a cofactor. TPP binds in the
cleft formed by a PYR domain and a PP domain. The PYR
domain, binds the aminopyrimidine ring of TPP, the PP
domain binds the diphosphate residue. A polar
interaction between the conserved glutamate of the PYR
domain and the N1' of the TPP aminopyrimidine ring is
shared by most TPP-dependent enzymes, and participates
in the activation of TPP. The PYR and PP domains have a
common fold, but do not share strong sequence
conservation. The PP domain is not included in this
sub-family. Like many TPP-dependent enzymes DXS and TK
are homodimers having a PYR and a PP domain on the same
subunit. TK has two active sites per dimer which lie
between PYR and PP domains of different subunits. For
DXS each active site is located at the interface of a
PYR and a PP domain from the same subunit. E1-PDHc is an
alpha2beta2 dimer-of-heterodimers having two active
sites but having the PYR and PP domains arranged on
separate subunits, the PYR domains on the beta subunits,
the PP domains on the alpha subunits. DXS is a
regulatory enzyme of the mevalonate-independent pathway
involved in terpenoid biosynthesis, it catalyzes a
transketolase-type condensation of pyruvate with
D-glyceraldehyde-3-phosphate to form
1-deoxy-D-xylulose-5-phosphate (DXP) and carbon dioxide.
TK catalyzes the transfer of a two-carbon unit from
ketose phosphates to aldose phosphates. In heterotrophic
organisms, TK provides a link between glycolysis and the
pentose phosphate pathway and provides precursors for
nucleotide, aromatic amino acid and vitamin
biosynthesis. TK also plays a central role in the Calvin
cycle in plants. PDHc catalyzes the irreversible
oxidative decarboxylation of pyruvate to produce
acetyl-CoA in the bridging step between glycolysis and
the citric acid cycle. This subfamily includes the beta
subunits of the E1 component of the acetoin
dehydrogenase complex (ADC) and the branched chain
alpha-keto acid dehydrogenase/2-oxoisovalerate
dehydrogenase complex (BCADC). ADC participates in the
breakdown of acetoin. BCADC catalyzes the oxidative
decarboxylation of 4-methyl-2-oxopentanoate,
3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate
during the breakdown of branched chain amino acids.
Length = 156
Score = 25.5 bits (57), Expect = 6.3
Identities = 6/12 (50%), Positives = 12/12 (100%)
Query: 71 VAILRAMPNLSI 82
+A+LRA+PN+++
Sbjct: 116 IALLRAIPNMTV 127
>gnl|CDD|235900 PRK06978, PRK06978, nicotinate-nucleotide pyrophosphorylase;
Provisional.
Length = 294
Score = 25.5 bits (56), Expect = 6.5
Identities = 9/18 (50%), Positives = 11/18 (61%), Gaps = 4/18 (22%)
Query: 89 RETAGLSGLHCGAPWFNS 106
RE A L CG PWF++
Sbjct: 60 REEAVL----CGVPWFDA 73
>gnl|CDD|225772 COG3232, HpaF, 5-carboxymethyl-2-hydroxymuconate isomerase [Amino
acid transport and metabolism].
Length = 127
Score = 25.0 bits (55), Expect = 6.9
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 77 MPNLSISFSNNERETAGLSGL 97
MP+L + +++N RE A L GL
Sbjct: 1 MPHLIMEYTDNLREEADLPGL 21
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 25.4 bits (56), Expect = 6.9
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 42 LRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFSNNER 89
+ I +S T E+ + PVV I +V+ +P ++ S +E+
Sbjct: 452 IAAIIQSKKTEEEKRLEVPVVTEEDIAEIVSAWTGIPVNKLTKSESEK 499
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 25.4 bits (57), Expect = 7.9
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 5/21 (23%)
Query: 36 LSKWLELRI-----IHESGFT 51
LS+WLEL I IHE F
Sbjct: 128 LSEWLELTIRRDGKIHEQEFE 148
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved
in the reorganization of the actin cytoskeleton in
response to external stimuli. They also have roles in
cell transformation by Ras in cytokinesis, in focal
adhesion formation and in the stimulation of
stress-activated kinase. These various functions are
controlled through distinct effector proteins and
mediated through a GTP-binding/GTPase cycle involving
three classes of regulating proteins: GAPs
(GTPase-activating proteins), GEFs (guanine nucleotide
exchange factors), and GDIs (guanine nucleotide
dissociation inhibitors). Most Rho 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 Rho proteins. Since crystal structures often lack
C-terminal residues, this feature is not available for
annotation in many of the CDs in the hierarchy.
Length = 171
Score = 24.8 bits (55), Expect = 9.0
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 11/62 (17%)
Query: 7 FTSEDF-KQYRPVVYSNTIQSTVRILG-TFLLSKWLELRIIHESGFTSEDFKQYRPVVYS 64
+T+ F +Y P V+ N + V + G L W +G E++ + RP+ Y
Sbjct: 20 YTTNKFPTEYVPTVFDNY-SANVTVDGKQVNLGLWDT------AGQ--EEYDRLRPLSYP 70
Query: 65 NT 66
T
Sbjct: 71 QT 72
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 0.135 0.402
Gapped
Lambda K H
0.267 0.0843 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,473,299
Number of extensions: 448217
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 35
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
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: 53 (24.0 bits)