RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10782
(105 letters)
>gnl|CDD|214982 smart01026, Beach, Beige/BEACH domain. The BEACH domain was
described in the BEIGE protein (D1035670) and in the
highly homologous CHS protein. The BEACH domain is
usually followed by a series of WD repeats. The function
of the BEACH domain is unknown.
Length = 280
Score = 148 bits (377), Expect = 4e-46
Identities = 47/104 (45%), Positives = 70/104 (67%), Gaps = 8/104 (7%)
Query: 1 MAGRSYNDLMQYPVLPFILSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHYVNNYNYL 60
+AGRSYNDL QYPV P++L+DY S TLDL++P +FR+L KP+ + + + Y
Sbjct: 21 LAGRSYNDLTQYPVFPWVLADYTSETLDLSNPSTFRDLSKPIGALNPERLEFFYERYE-- 78
Query: 61 AREMCDAVGGVNQEPYHYGSHYSNSGTVLHFLVRIPPFTSMFLN 104
E+ D P+HYG+HYS++G VL++L+R+ PFT++FL
Sbjct: 79 --ELEDPD----IPPFHYGTHYSSAGIVLYYLIRLEPFTTLFLQ 116
>gnl|CDD|216896 pfam02138, Beach, Beige/BEACH domain.
Length = 274
Score = 131 bits (331), Expect = 3e-39
Identities = 45/104 (43%), Positives = 67/104 (64%), Gaps = 9/104 (8%)
Query: 1 MAGRSYNDLMQYPVLPFILSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHYVNNYNYL 60
+AGRS+NDL QYPV P++L+DY S TLDL DP ++R+L KP+ +++ + Y L
Sbjct: 21 LAGRSFNDLSQYPVFPWVLADYTSETLDLNDPSTYRDLSKPIGALNEERLKKFKERYEEL 80
Query: 61 AREMCDAVGGVNQEPYHYGSHYSNSGTVLHFLVRIPPFTSMFLN 104
P+HYGSHYS+ G+VLH+L+R+ PFT++ +
Sbjct: 81 D---------EVGPPFHYGSHYSSPGSVLHYLIRLEPFTTLHIE 115
>gnl|CDD|100117 cd06071, Beach, BEACH (Beige and Chediak-Higashi) domains,
implicated in membrane trafficking, are present in a
family of proteins conserved throughout eukaryotes. This
group contains human lysosomal trafficking regulator
(LYST), LPS-responsive and beige-like anchor (LRBA) and
neurobeachin. Disruption of LYST leads to
Chediak-Higashi syndrome, characterized by severe
immunodeficiency, albinism, poor blood coagulation and
neurologic problems. Neurobeachin is a candidate gene
linked to autism. LBRA seems to be upregulated in
several cancer types. It has been shown that the BEACH
domain itself is important for the function of these
proteins.
Length = 275
Score = 126 bits (320), Expect = 1e-37
Identities = 44/102 (43%), Positives = 64/102 (62%), Gaps = 8/102 (7%)
Query: 2 AGRSYNDLMQYPVLPFILSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHYVNNYNYLA 61
AGRS+NDL QYP+ P+++SDY S LDL DP ++R+L KP+ +K+ Y +
Sbjct: 22 AGRSFNDLSQYPIFPWVISDYTSEELDLNDPSTYRDLSKPIGALNKERLQLLKERYESDS 81
Query: 62 REMCDAVGGVNQEPYHYGSHYSNSGTVLHFLVRIPPFTSMFL 103
+ + P+HYGSHYSN VL++LVR+ PFT++ L
Sbjct: 82 DD--------SDPPFHYGSHYSNPAIVLYYLVRLEPFTTLHL 115
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 29.1 bits (66), Expect = 0.36
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 75 PYHYGSHYSNSGTVLHFLVRIPPFTS 100
PY YG S +G H LVRI PF S
Sbjct: 184 PYAYGYLKSETGV--HRLVRISPFDS 207
>gnl|CDD|165102 PHA02735, PHA02735, putative DNA polymerase type B; Provisional.
Length = 716
Score = 28.9 bits (64), Expect = 0.48
Identities = 14/46 (30%), Positives = 18/46 (39%)
Query: 14 VLPFILSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHYVNNYNY 59
P I S Y + DL DPK+ V DK+ SH +
Sbjct: 289 AAPDINSAYPAILADLPDPKTLNWKHYLNEVSDKEPFSHSAKHAGI 334
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 27.6 bits (62), Expect = 1.3
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 75 PYHYGSHYSNSGTVLHFLVRIPPFTSM 101
YG + +G H LVRI PF S
Sbjct: 59 ENAYGYLKTETGV--HRLVRISPFDSN 83
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 27.0 bits (60), Expect = 1.9
Identities = 13/26 (50%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 75 PYHYGSHYSNSGTVLHFLVRIPPFTS 100
PY YG S G H LVRI PF +
Sbjct: 184 PYAYGYLKSEQGV--HRLVRISPFDA 207
>gnl|CDD|129368 TIGR00267, TIGR00267, TIGR00267 family protein. This family of
uncharacterized proteins shows a low level of similarity
(possibly meaningful) to the predicted membrane protein
YLR220W, which is involved in calcium homeostatis. It
shows no similarity to any other characterized
protein.This family is represented in three of the first
four completed archaeal genomes, with two members in A.
fulgidus [Hypothetical proteins, Conserved].
Length = 169
Score = 26.7 bits (59), Expect = 2.0
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 13 PVLPFILSDYKSATL 27
PVLPF++ D +AT+
Sbjct: 106 PVLPFLVFDRMTATI 120
>gnl|CDD|72471 pfam09053, CagZ, CagZ. CagZ is a 23 kDa protein consisting of a
single compact L-shaped domain, composed of seven
alpha-helices that run antiparallel to each other. 70%
of the residues are in alpha-helix conformation and no
beta-sheet is present. CagZ is essential for the
translocation of the pathogenic protein CagA into host
cells.
Length = 198
Score = 27.0 bits (59), Expect = 2.0
Identities = 18/77 (23%), Positives = 32/77 (41%)
Query: 19 LSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHYVNNYNYLAREMCDAVGGVNQEPYHY 78
+ +Y ++ D DP+ F + + + +KN + YNYL + + QE
Sbjct: 31 IQNYATSLKDSNDPQDFLRRVQELRINMQKNFISFDAYYNYLNNLVLASYNRCKQEKTFA 90
Query: 79 GSHYSNSGTVLHFLVRI 95
S N T+ F+ I
Sbjct: 91 ESTIKNELTLGEFVAEI 107
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 25.4 bits (56), Expect = 6.6
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 11 QYPVLPFILSDYKSATLDLTDPKSFRNLKKPMAVQDK 47
+ P L F+L D+ D++ + RNL + + Q K
Sbjct: 80 ETPAL-FLLKDFNRFLNDISISRKLRNLSRILKTQPK 115
>gnl|CDD|200503 cd11242, Sema_6, The Sema domain, a protein interacting module, of
class 6 semaphorins (Sema6). Class 6 semaphorins
(Sema6s) are membrane associated semaphorins. There are
6 subfamilies named 6A to 6D. Sema6s bind to plexin As
in a neuropilin independent fashion. Sema6-plexin A
signaling plays important roles in lamina-specific axon
projections. Interactions between plexin A2, plexin A4,
and Sema6A control lamina-restricted projection of
hippocampal mossy fibers. Interactions between Sema6C,
Sema6D and plexin A1 shape the stereotypic trajectories
of sensory axons in the spinal cord. In addition to axon
targeting, Sema6D-plexin A1 interactions influence a
wide range of other biological processes. During cardiac
development, Sema6D attracts or repels endothelial cells
in the cardiac tube depending on the expression patterns
of specific coreceptors in addition to plexin A1.
Furthermore, Sema6D binds a receptor complex comprising
of plexin A1, Trem2 (triggering receptor expressed on
myeloid cells 2), and DAP12 on dendritic cells and
osteoclasts to mediate T-cell-DC interactions and to
control bone development, respectively. The Sema domain
is located at the N-terminus and contains four disulfide
bonds formed by eight conserved cysteine residues. It
serves as a receptor-recognition and -binding module.
Length = 465
Score = 25.6 bits (56), Expect = 6.7
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 83 SNSGTVLHFLVRIPPFTS 100
S +GTVL FL RI P S
Sbjct: 395 SEAGTVLKFLARIGPSGS 412
>gnl|CDD|223025 PHA03253, PHA03253, UL35; Provisional.
Length = 609
Score = 25.3 bits (55), Expect = 7.3
Identities = 20/48 (41%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 7 NDLMQYPVL-PFILSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHY 53
N +M+ VL F L D K LDL S NL KP DK HY
Sbjct: 270 NSIMENVVLVGFQLPDLKETILDLAALISNMNLVKP----DKDLFPHY 313
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small
guanosine triphosphatases (GTPases). Rab GTPases form
the largest family within the Ras superfamily. There
are at least 60 Rab genes in the human genome, and a
number of Rab GTPases are conserved from yeast to
humans. Rab GTPases are small, monomeric proteins that
function as molecular switches to regulate vesicle
trafficking pathways. The different Rab GTPases are
localized to the cytosolic face of specific
intracellular membranes, where they regulate distinct
steps in membrane traffic pathways. In the GTP-bound
form, Rab GTPases recruit specific sets of effector
proteins onto membranes. Through their effectors, Rab
GTPases regulate vesicle formation, actin- and
tubulin-dependent vesicle movement, and membrane
fusion. 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 mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular
organisms possess 5-20 Rab members, several have been
found to possess 60 or more Rabs; for many of these Rab
isoforms, homologous proteins are not found in other
organisms. 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. Since crystal structures often lack
C-terminal residues, the lipid modification site is not
available for annotation in many of the CDs in the
hierarchy, but is included where possible.
Length = 159
Score = 24.7 bits (55), Expect = 8.0
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 28 DLTDPKSFRNLKK 40
D+T+ +SF NL K
Sbjct: 81 DVTNRESFENLDK 93
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 0.134 0.404
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,320,817
Number of extensions: 425957
Number of successful extensions: 325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 322
Number of HSP's successfully gapped: 18
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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 (21.7 bits)
S2: 53 (24.1 bits)