RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6220
(101 letters)
>gnl|CDD|176881 cd08872, START_STARD11-like, Ceramide-binding START domain of
mammalian STARD11 and related domains. This subfamily
includes the steroidogenic acute regulatory protein
(StAR)-related lipid transfer (START) domains of
mammalian STARD11 and related domains. The START domain
family belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. STARD11 can mediate transfer of the natural
ceramide isomers, dihydroceramide and phytoceramide, as
well as ceramides having C14, C16, C18, and C20 chains.
They can also transfer diacylglycerol, but with a lower
efficiency. STARD11 is synthesized from two major
transcripts: a larger one encoding Goodpasture
antigen-binding protein (GPBP)/ceramide transporter long
form (CERTL); and a smaller one encoding
GPBPdelta26/CERT, which is deleted for 26 amino acids.
Both splicing variants mediate ceramide transfer from
the ER to the Golgi, in a non-vesicular manner. It is
likely that these two carry out different functions in
specific sub-cellular locations. These proteins have
roles in brain homeostasis and disease processes.
GPBP/CERTL exists in multiple isoforms originating from
alternative translation initiation sites and
post-translational modifications. Goodpasture syndrome
is a human disorder caused by antibodies directed
against the a3-chain of collagen type IV. GPBP/CERTL
binds and phosphorylates this antigen. The human gene
encoding STARD11 is referred to as COL4A3BP referring to
its collagen binding function. It is unknown whether the
ceramide-transfer function of GPBP/CERTL is related to
this collagen interaction. The expression of GPBP/CERTL
is elevated in these and other spontaneous autoimmune
disorders including cutaneous lupus erythematosus,
pemphigoid, and lichen planus. GPBL/CERTL contains an
N-terminal pleckstrin homology domain (PH), which
targets the protein to the Golgi, a middle region
containing two serine-rich domains (SR1, SR2), a FFAT
(two phenylalanine amino acids in an acidic tract) motif
which is involved in endoplasmic reticulum targeting,
and this C-terminal SMART domain. The shorter splicing
variant, CERT, lacks the SR2 domain.
Length = 235
Score = 107 bits (269), Expect = 2e-30
Identities = 35/79 (44%), Positives = 51/79 (64%), Gaps = 2/79 (2%)
Query: 21 TLEKMTVAETISEDTILFWQIHKSIWPVTQRDAVFWSHMTQVPDPSDRDAQNIWIVVNNS 80
TLE V ET+S+DT++F Q HK +WP QRDA+F SH+ ++P + +A + WIV N S
Sbjct: 84 TLENFHVVETLSQDTLIFHQTHKRVWPAAQRDALFVSHIRKIPALEEPNAHDTWIVCNFS 143
Query: 81 TDLDAYPVSRR--RVTQTV 97
D D+ P++ + R TV
Sbjct: 144 VDHDSAPLNNKCVRAKLTV 162
>gnl|CDD|176851 cd00177, START, Lipid-binding START domain of mammalian
STARD1-STARD15 and related proteins. This family
includes the steroidogenic acute regulatory protein
(StAR)-related lipid transfer (START) domains of
mammalian STARD1-STARD15, and related domains, such as
the START domain of the Arabidopsis homeobox protein
GLABRA 2. The mammalian STARDs are grouped into 8
subfamilies. This family belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. For some members of this family, specific lipids
that bind in this pocket are known; these include
cholesterol (STARD1/STARD3/ STARD4/STARD5),
25-hydroxycholesterol (STARD5), phosphatidylcholine
(STARD2/ STARD7/STARD10), phosphatidylethanolamine
(STARD10) and ceramides (STARD11). The START domain is
found either alone or in association with other domains.
Mammalian STARDs participate in the control of various
cellular processes including lipid trafficking between
intracellular compartments, lipid metabolism, and
modulation of signaling events. Mutation or altered
expression of STARDs is linked to diseases such as
cancer, genetic disorders, and autoimmune disease. The
Arabidopsis homeobox protein GLABRA 2 suppresses root
hair formation in hairless epidermal root cells.
Length = 193
Score = 47.7 bits (114), Expect = 6e-08
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 7/67 (10%)
Query: 21 TLEKMTVAETISEDTILFWQIHKSIWPVTQRDAVFWSHMTQVPDPSDRDAQNIWIVVNNS 80
E+ V E I E T + + K WPV+ RD V+ ++ D +++V+ S
Sbjct: 70 NFEEFEVIEEIDEHTDIIYYKTKPPWPVSPRDFVYLRRRRKLDD-------GTYVIVSKS 122
Query: 81 TDLDAYP 87
D D++P
Sbjct: 123 VDHDSHP 129
>gnl|CDD|216740 pfam01852, START, START domain.
Length = 205
Score = 30.8 bits (70), Expect = 0.075
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 9/71 (12%)
Query: 21 TLEKMTVAETISEDTILFWQIHKSIW--PVTQRDAVFWSHMTQVPDPSDRDAQNIWIVVN 78
+ E IS L + + + P++ RD VF + Q+ D +++V+
Sbjct: 75 DVRSAETLEVISSGGALQYYVAELQAPTPLSPRDFVFLRYWRQLGDGV-------YVIVD 127
Query: 79 NSTDLDAYPVS 89
S D +P S
Sbjct: 128 RSVDSPQFPPS 138
>gnl|CDD|185493 PTZ00167, PTZ00167, RNA polymerase subunit 8c; Provisional.
Length = 144
Score = 28.2 bits (63), Expect = 0.46
Identities = 17/88 (19%), Positives = 37/88 (42%), Gaps = 6/88 (6%)
Query: 1 MSPPFLFRSNETTATLDACATLEKMT--VAETISEDTILFWQIHKSIWPVTQRDAVFWSH 58
P LF ++D + E+++ A++ D L I+ ++PV ++ +++
Sbjct: 2 SLPSCLFEDRFVVRSVD-NSKFERVSRIKAKSTGFDAELILDINSDLFPVREKQSLYIGL 60
Query: 59 MTQVPDPSDRDAQNIWIVVNNSTDLDAY 86
Q+ D N+W + +D Y
Sbjct: 61 TNQLSSGPD---DNVWESSEPQSLMDQY 85
>gnl|CDD|197918 smart00850, LytTR, LytTr DNA-binding domain. This domain is
found in a variety of bacterial transcriptional
regulators. The domain binds to a specific DNA sequence
pattern.
Length = 96
Score = 27.9 bits (63), Expect = 0.48
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 18/73 (24%)
Query: 26 TVAETISE-----DTILFWQIHKSIWPVTQRDAVFWSHMTQVPDPSDRDAQNIWIVVNNS 80
V T+ E D F++IH+S V H+ ++ + ++++
Sbjct: 31 LVRGTLKELEERLDPDNFFRIHRSYI-------VNLDHIKEI----EPWFNGTYLLIL-- 77
Query: 81 TDLDAYPVSRRRV 93
+ + PVSRR +
Sbjct: 78 KNGEEVPVSRRYL 90
>gnl|CDD|152201 pfam11765, Hyphal_reg_CWP, Hyphally regulated cell wall protein
N-terminal. The proteins in this family are all fungal
and largely annotated as being hyphally regulated cell
wall proteins, and several are listed as the enzyme
EC:3.2.1.18. This enzyme is acetylneuraminyl hydrolase
or exo-alpha-sialidase, that hydrolyses glycosidic
linkages of terminal sialic acid residues in
oligosaccharides, glycoproteins, glycolipids, colominic
acid and synthetic substrates.
Length = 332
Score = 27.8 bits (62), Expect = 0.86
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 18 ACATLEKMTVAETISEDTILFWQIHKSIWPVTQRDAVFWS 57
A A L +A TI+E+ + I+ SI +T +WS
Sbjct: 3 ALALLLSAVLAVTITENKVDRGTINLSIGDITIESGAYWS 42
>gnl|CDD|176885 cd08876, START_1, Uncharacterized subgroup of the steroidogenic
acute regulatory protein (StAR)-related lipid transfer
(START) domain family. Functionally uncharacterized
subgroup of the START domain family. The START domain
family belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. For some mammalian members of the START family
(STARDs), it is known which lipids bind in this pocket;
these include cholesterol (STARD1, -3, -4, and -5),
25-hydroxycholesterol (STARD5), phosphatidylcholine
(STARD2, -7, and -10), phosphatidylethanolamine
(STARD10) and ceramides (STARD11). Mammalian STARDs
participate in the control of various cellular
processes, including lipid trafficking between
intracellular compartments, lipid metabolism, and
modulation of signaling events. Mutation or altered
expression of STARDs is linked to diseases such as
cancer, genetic disorders, and autoimmune disease.
Length = 195
Score = 27.2 bits (61), Expect = 1.1
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 7/70 (10%)
Query: 24 KMTVAETISEDTILFWQIHKSIWPVTQRDAVFWSHMTQVPDPSDRDAQNIWIVVNNSTDL 83
+ V + ++ + + WPV RD V S Q D D ++ I +
Sbjct: 75 ESRVLKRTDDNERSVYTVIDLPWPVKDRDMVLRSTTEQ-----DADDGSVTITLEA--AP 127
Query: 84 DAYPVSRRRV 93
+A P + V
Sbjct: 128 EALPEQKGYV 137
>gnl|CDD|131525 TIGR02472, sucr_P_syn_N, sucrose-phosphate synthase, putative,
glycosyltransferase domain. This family consists of the
N-terminal regions, or in some cases the entirety, of
bacterial proteins closely related to plant
sucrose-phosphate synthases (SPS). The C-terminal domain
(TIGR02471), found with most members of this family,
resembles both bona fide plant sucrose-phosphate
phosphatases (SPP) and the SPP-like domain of plant SPS.
At least two members of this family lack the SPP-like
domain, which may have binding or regulatory rather than
enzymatic activity by analogy to plant SPS. This enzyme
produces sucrose 6-phosphate and UDP from UDP-glucose
and D-fructose 6-phosphate, and may be encoded near the
gene for fructokinase.
Length = 439
Score = 26.6 bits (59), Expect = 2.2
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 64 DPSDRDAQNIWIVVNNSTDLDAYPVSRRRVTQTVL 98
P ++ N+ +V+ D+ +R V Q VL
Sbjct: 273 SPKLQEMANLVLVLGCRDDIRKMESQQREVLQKVL 307
>gnl|CDD|200251 TIGR03214, ura-cupin, putative allantoin catabolism protein. This
model represents a protein containing a tandem
arrangement of cupin domains (N-terminal part of
pfam07883 and C-terminal more distantly related to
pfam00190). This protein is found in the vicinity of
genes involved in the catabolism of allantoin, a
breakdown product of urate and sometimes of urate
iteslf. The distribution of pathway components in the
genomes in which this family is observed suggests that
the function is linked to the allantoate catabolism to
glyoxylate pathway (GenProp0686) since it is sometimes
found in genomes lacking any elements of the
xanthine-to-allantoin pathways (e.g. in Enterococcus
faecalis).
Length = 252
Score = 26.2 bits (58), Expect = 3.5
Identities = 11/64 (17%), Positives = 18/64 (28%), Gaps = 3/64 (4%)
Query: 23 EKMTVAETISEDTILFWQIHKSIWPVTQRDA--VFWSHMTQVPDPSDRDAQNIWIVVNNS 80
K T+ ED F K PV A + + + ++W
Sbjct: 106 SKWTLENAQDEDARFFL-YKKRYQPVEGLHAPEAVVGNERDIEPEAYEGMDDVWATTLLP 164
Query: 81 TDLD 84
+L
Sbjct: 165 KELA 168
>gnl|CDD|225818 COG3279, LytT, Response regulator of the LytR/AlgR family
[Transcription / Signal transduction mechanisms].
Length = 244
Score = 25.4 bits (56), Expect = 5.7
Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 23/86 (26%)
Query: 8 RSNETTATLDACATLEKMTVAETISEDTILFWQIHKSIWPVTQRDAVFWSHMTQVPDPSD 67
R ET TL LEK F + H+S V + + ++
Sbjct: 172 RDLETYLTLKE---LEKKL-------PPSGFIRCHRSYI-------VNLAKIKEI----R 210
Query: 68 RDAQNIWIVVNNSTDLDAYPVSRRRV 93
R ++++ + PVSRR +
Sbjct: 211 RWFNGLYLL--ILGNGCEVPVSRRYL 234
>gnl|CDD|165538 PHA03281, PHA03281, envelope glycoprotein E; Provisional.
Length = 642
Score = 25.4 bits (55), Expect = 6.8
Identities = 10/33 (30%), Positives = 13/33 (39%)
Query: 68 RDAQNIWIVVNNSTDLDAYPVSRRRVTQTVLQV 100
+ A WIVVN S D + VL+
Sbjct: 270 KAADPPWIVVNISEDFAELEFDPPDIEPGVLKF 302
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
0.319 0.128 0.396
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,853,571
Number of extensions: 373725
Number of successful extensions: 252
Number of sequences better than 10.0: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 18
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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 (24.1 bits)