RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12097
(74 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 = 85.7 bits (213), Expect = 5e-22
Identities = 30/69 (43%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 1 MSQVNPPCTLEHPENQSRVDYIHNVA-SAHDFDYPPEFYDIAEELWKDKGVQACFERSNE 59
M +N P PEN+ I ++A A + PPE + + LWKD G+QAC++R NE
Sbjct: 55 METLNIP--YGDPENEKDAKKILSLAPRAEEGPLPPELAEAIKRLWKDPGIQACYDRRNE 112
Query: 60 YQLIDCAKY 68
YQL D AKY
Sbjct: 113 YQLNDSAKY 121
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 68.4 bits (168), Expect = 1e-15
Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 9 TLEHPENQSRVDYI---HNVASAHDFDYPPEFYDIAEELWKDKGVQACFERSNEYQLIDC 65
E PE+ + I N + P E + LWKD+G+Q C+ R NE+QL D
Sbjct: 82 PFEDPESILDIRIITEQFNKTDETENVLPKEIAKAIKALWKDEGIQECYRRRNEFQLNDS 141
Query: 66 AKY 68
A Y
Sbjct: 142 ASY 144
>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 = 63.0 bits (154), Expect = 1e-13
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 1 MSQVNPPCTLEHPENQSRVDYIHNVAS----AHDFDYPPEFYDIAEELWKDKGVQACFER 56
+ + + PEN+ + ++ + + E + +ELW D G+Q + R
Sbjct: 57 LENLEIESSNSKPENEEIAKKLKSILDSLLDVDETRFSEELAEDIKELWNDPGIQEVYNR 116
Query: 57 SNEYQLIDCAKY 68
SNE+QL D AKY
Sbjct: 117 SNEFQLSDSAKY 128
>gnl|CDD|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor;
Provisional.
Length = 231
Score = 27.5 bits (61), Expect = 0.52
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 35 PEFYDIAEELWKDKGVQACFERSNEYQLIDCAKYLVSL 72
P F +I+ EL + A E EY L++ A L SL
Sbjct: 118 PNFEEISAEL----NLTA--EEYQEYLLLENAGTLESL 149
>gnl|CDD|131051 TIGR01996, PTS-II-BC-sucr, PTS system, sucrose-specific IIBC
component. This model represents the fused enzyme II B
and C components of the sucrose-specific PTS sugar
transporter system. Sucrose is converted to
sucrose-6-phosphate in the process of translocation
into the cell. Some of these transporters lack their
own IIA domains and instead use the glucose IIA protein
(IIAglc or Crr). The exceptions to this rule are
Staphylococci, Streptococci, Lactococci, Lactobacilli,
etc. which contain their own A domain as a C-terminal
fusion. This family is closely related to the trehalose
transporting PTS IIBC enzymes and the B and C domains
of each are described by subfamily-domain level
TIGRFAMs models (TIGR00826 and TIGR00852,
respectively).
Length = 461
Score = 27.3 bits (61), Expect = 0.61
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 42 EELWKDKGVQACFERSNEYQLI 63
+ + GV+ F S +YQ+I
Sbjct: 42 KAIENLDGVKGTFFNSGQYQII 63
>gnl|CDD|212525 cd10001, HDAC_classII_APAH, Histone deacetylase class IIa. This
subfamily includes bacterial acetylpolyamine
amidohydrolase (APAH) as well as other Class II histone
deacetylase (HDAC) and related proteins. Deacetylases
of class II are Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine residues of histones
(EC 3.5.1.98) and possibly other proteins to yield
deacetylated histones/other proteins. Mycoplana ramosa
APAH exhibits broad substrate specificity and catalyzes
the deacetylation of polyamines such as putrescine,
spermidine, and spermine by cleavage of a non-peptide
amide bond.
Length = 298
Score = 27.1 bits (61), Expect = 0.76
Identities = 8/33 (24%), Positives = 10/33 (30%)
Query: 11 EHPENQSRVDYIHNVASAHDFDYPPEFYDIAEE 43
HPEN R + I + D E
Sbjct: 24 PHPENPERAEAILDALKRAGLGEVLPPRDFGLE 56
>gnl|CDD|216151 pfam00850, Hist_deacetyl, Histone deacetylase domain. Histones
can be reversibly acetylated on several lysine
residues. Regulation of transcription is caused in part
by this mechanism. Histone deacetylases catalyze the
removal of the acetyl group. Histone deacetylases are
related to other proteins.
Length = 300
Score = 26.4 bits (59), Expect = 1.2
Identities = 8/28 (28%), Positives = 11/28 (39%)
Query: 12 HPENQSRVDYIHNVASAHDFDYPPEFYD 39
HPEN R++ I + EF
Sbjct: 9 HPENPERLEAILELLKESGLLDRLEFIA 36
>gnl|CDD|181506 PRK08622, PRK08622, galactose-6-phosphate isomerase subunit LacB;
Reviewed.
Length = 171
Score = 26.1 bits (58), Expect = 1.5
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 11 EHPENQSRVDYIHNVASAHDFDYPPEFYDIAEELWKDKGV 50
EN+ ++ I ++ + P F+D E W D+G
Sbjct: 130 PTEENKKLIEKIDHLEKPNADQANPHFFDEFLEKW-DRGE 168
>gnl|CDD|237433 PRK13576, PRK13576, 3-dehydroquinate dehydratase; Provisional.
Length = 216
Score = 25.9 bits (57), Expect = 1.8
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 18 RVDYIHNVASAHDFDYPPEFYDIAEELWK 46
V Y + + S H FDY P ++ E + K
Sbjct: 99 NVPYDNKIVSIHYFDYLPTSEEVKEIVSK 127
>gnl|CDD|233303 TIGR01177, TIGR01177, TIGR01177 family protein. This family is
found exclusively in the Archaea [Hypothetical
proteins, Conserved].
Length = 329
Score = 25.9 bits (57), Expect = 2.0
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 17 SRVDYIHNVASAHDFDYPPEFYDIAEEL 44
R+ + H V ++D + YD L
Sbjct: 49 ERLAFTHEVGRSYDTCAAKDLYDFVAGL 76
>gnl|CDD|215558 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 26.0 bits (57), Expect = 2.2
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 15 NQSRVDYIHNVASAHDFDYPPE 36
+ +DYI NV + DFD+ PE
Sbjct: 23 DSPIIDYIINVLADEDFDFGPE 44
>gnl|CDD|236964 PRK11727, PRK11727, 23S rRNA mA1618 methyltransferase;
Provisional.
Length = 321
Score = 25.2 bits (56), Expect = 3.1
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 18 RVDYIHNVA 26
R DYIH++A
Sbjct: 91 RADYIHHLA 99
>gnl|CDD|233774 TIGR02195, heptsyl_trn_II, lipopolysaccharide heptosyltransferase
II. This family consists of examples of ADP-heptose:LPS
heptosyltransferase II, an enzyme of LPS inner core
region biosynthesis. LPS, composed of lipid A, a core
region, and O antigen, is found in the outer membrane of
Gram-negative bacteria [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 334
Score = 25.4 bits (56), Expect = 3.2
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 32 DYPPEFYDIAEELWKDKGVQACFERSNEYQLIDCAKYL 69
D+ P + AE + + CF+R Y C L
Sbjct: 283 DFTPPLSEKAEVIRLNLECSPCFKRDCPYGHHQCLIDL 320
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 25.2 bits (56), Expect = 3.2
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 7/28 (25%)
Query: 29 HDFDYPPEF-YDIAEELWKDKGVQACFE 55
H F+YP + Y WKD+ V+ CFE
Sbjct: 150 HAFNYPDKEVY------WKDETVEYCFE 171
>gnl|CDD|227069 COG4725, IME4, Transcriptional activator, adenine-specific DNA
methyltransferase [Signal transduction mechanisms /
Transcription].
Length = 198
Score = 25.3 bits (55), Expect = 3.5
Identities = 10/41 (24%), Positives = 13/41 (31%), Gaps = 1/41 (2%)
Query: 16 QSRVDYIHNVASAHDFDYPPEFYDIAEELWKDKGVQACFER 56
+ I ++ P E Y IAE L F R
Sbjct: 127 PPTISLIVSMTRETS-RKPDELYGIAERLAGTHAKLEIFGR 166
>gnl|CDD|227430 COG5099, COG5099, RNA-binding protein of the Puf family,
translational repressor [Translation, ribosomal
structure and biogenesis].
Length = 777
Score = 25.1 bits (55), Expect = 3.5
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 35 PEFYDIAEELWKDKGVQACFERSNEYQLIDCAKYLVSLVK 74
YD++ + + VQ C E N + + ++S K
Sbjct: 586 ENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSK 625
>gnl|CDD|215230 PLN02418, PLN02418, delta-1-pyrroline-5-carboxylate synthase.
Length = 718
Score = 25.1 bits (55), Expect = 3.6
Identities = 9/23 (39%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 8 CTLEHPEN-QSRVDYIHNVASAH 29
CT+E ++ + +D+IH SAH
Sbjct: 603 CTVEIVDDVHAAIDHIHRHGSAH 625
>gnl|CDD|235833 PRK06581, PRK06581, DNA polymerase III subunit delta'; Validated.
Length = 263
Score = 24.8 bits (54), Expect = 5.1
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 1/52 (1%)
Query: 3 QVNPPCTLEHPENQSRVDYIHNVASAHDFDYPPEFYDIAEELWKDKGVQACF 54
++N ++ H N+ +I +A D+ F ELW D
Sbjct: 142 KINVRSSILHAYNELYSQFIQPIADNKTLDFINRFTTKDRELWLDFI-DNLL 192
>gnl|CDD|235947 PRK07152, nadD, putative nicotinate-nucleotide adenylyltransferase;
Validated.
Length = 342
Score = 24.5 bits (54), Expect = 5.4
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 43 ELWKD-----KGVQ-ACFERSNEYQLIDCAKYLVSLVK 74
+ WK+ K VQ F+R + KY V L+K
Sbjct: 113 KKWKNIEEILKKVQIVVFKRKKNINKKNLKKYNVLLLK 150
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 24.7 bits (54), Expect = 6.4
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 28 AHDFD----YPPEFYDIAEELWKDKGVQACFER 56
AH+ D YP EFY+ E+ K V+ ER
Sbjct: 1137 AHNMDVVRYYPLEFYEATLEMADPKDVEDLIER 1169
>gnl|CDD|173641 cd05072, PTKc_Lyn, Catalytic domain of the Protein Tyrosine Kinase,
Lyn. Protein Tyrosine Kinase (PTK) family; Lyn kinase;
catalytic (c) domain. The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Lyn is a member of the
Src subfamily of proteins, which are cytoplasmic (or
non-receptor) tyr kinases. Src kinases contain an
N-terminal SH4 domain with a myristoylation site,
followed by SH3 and SH2 domains, a tyr kinase domain,
and a regulatory C-terminal region containing a
conserved tyr. They are activated by autophosphorylation
at the tyr kinase domain, but are negatively regulated
by phosphorylation at the C-terminal tyr by Csk
(C-terminal Src Kinase). Src proteins are involved in
signaling pathways that regulate cytokine and growth
factor responses, cytoskeleton dynamics, cell
proliferation, survival, and differentiation. Lyn is
expressed in B lymphocytes and myeloid cells. It
exhibits both positive and negative regulatory roles in
B cell receptor (BCR) signaling. Lyn, as well as Fyn and
Blk, promotes B cell activation by phosphorylating ITAMs
(immunoreceptor tyr activation motifs) in CD19 and in Ig
components of BCR. It negatively regulates signaling by
its unique ability to phosphorylate ITIMs
(immunoreceptor tyr inhibition motifs) in cell surface
receptors like CD22 and CD5. Lyn also plays an important
role in G-CSF receptor signaling by phosphorylating a
variety of adaptor molecules.
Length = 261
Score = 24.6 bits (53), Expect = 6.5
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 34 PPEFYDIAEELWKDK 48
P E YDI + WK+K
Sbjct: 230 PDELYDIMKTCWKEK 244
>gnl|CDD|232985 TIGR00463, gltX_arch, glutamyl-tRNA synthetase, archaeal and
eukaryotic family. The glutamyl-tRNA synthetases of the
eukaryotic cytosol and of the Archaea are more similar
to glutaminyl-tRNA synthetases than to bacterial
glutamyl-tRNA synthetases. This model models just the
eukaryotic cytosolic and archaeal forms of the enzyme.
In some eukaryotes, the glutamyl-tRNA synthetase is part
of a longer, multifunctional aminoacyl-tRNA ligase. In
many species, the charging of tRNA(gln) proceeds first
through misacylation with Glu and then transamidation.
For this reason, glutamyl-tRNA synthetases, including
all known archaeal enzymes (as of 2010) may act on both
tRNA(gln) and tRNA(glu) [Protein synthesis, tRNA
aminoacylation].
Length = 556
Score = 24.4 bits (53), Expect = 6.6
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 32 DYPPEFYDIAEELWKDKGVQACFERSNEYQ 61
D +YD +L + C R E++
Sbjct: 167 DRIETYYDYTRKLIEMGKAYVCDCRPEEFR 196
>gnl|CDD|232887 TIGR00232, tktlase_bact, transketolase, bacterial and yeast. This
model is designed to capture orthologs of bacterial
transketolases. The group includes two from the yeast
Saccharomyces cerevisiae but excludes dihydroxyactetone
synthases (formaldehyde transketolases) from various
yeasts and the even more distant mammalian
transketolases. Among the family of thiamine
diphosphate-dependent enzymes that includes
transketolases, dihydroxyacetone synthases, pyruvate
dehydrogenase E1-beta subunits, and
deoxyxylulose-5-phosphate synthases, mammalian and
bacterial transketolases seem not to be orthologous
[Energy metabolism, Pentose phosphate pathway].
Length = 653
Score = 24.3 bits (53), Expect = 6.8
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 31 FDYPPEFYDIAEELWKDKGVQA 52
F+ P E YD ++ K++G +A
Sbjct: 280 FEVPQEVYDHFQKTVKERGAKA 301
>gnl|CDD|226481 COG3972, COG3972, Superfamily I DNA and RNA helicases [General
function prediction only].
Length = 660
Score = 24.5 bits (53), Expect = 7.2
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 32 DYPPEFYDIAEELWKDK 48
D+P F D+ + KDK
Sbjct: 306 DFPQSFIDLCFMVTKDK 322
>gnl|CDD|218953 pfam06245, DUF1015, Protein of unknown function (DUF1015). Family
of proteins with unknown function found in archaea and
bacteria.
Length = 415
Score = 24.1 bits (53), Expect = 8.2
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 10 LEHPENQSRVDYIHNVASA 28
+E P R+DY+ +
Sbjct: 341 IEDPRTDKRIDYVGGIRGL 359
>gnl|CDD|153284 cd07600, BAR_Gvp36, The Bin/Amphiphysin/Rvs (BAR) domain of
Saccharomyces cerevisiae Golgi vesicle protein of 36
kDa and similar proteins. BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions including organelle biogenesis, membrane
trafficking or remodeling, and cell division and
migration. Proteomic analysis shows that Golgi vesicle
protein of 36 kDa (Gvp36) may be involved in vesicular
trafficking and nutritional adaptation. A Saccharomyces
cerevisiae strain deficient in Gvp36 shows defects in
growth, in actin cytoskeleton polarization, in
endocytosis, in vacuolar biogenesis, and in the cell
cycle. BAR domains form dimers that bind to membranes,
induce membrane bending and curvature, and may also be
involved in protein-protein interactions.
Length = 242
Score = 23.9 bits (52), Expect = 9.7
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 31 FDYPPEFYDIAEELWK 46
+DYPP + + K
Sbjct: 29 YDYPPNLTESISDFSK 44
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
0.318 0.134 0.424
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,667,577
Number of extensions: 269826
Number of successful extensions: 315
Number of sequences better than 10.0: 1
Number of HSP's gapped: 314
Number of HSP's successfully gapped: 27
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)