RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12863
(150 letters)
>gnl|CDD|221621 pfam12529, Xylo_C, Xylosyltransferase C terminal. This domain
family is found in eukaryotes, and is typically between
169 and 183 amino acids in length. The family is found
in association with pfam02485. There is a single
completely conserved residue G that may be functionally
important. Xylosyltransferases are enzymes involved in
the biosynthesis of the glycosaminoglycan linker region
in proteoglycans.
Length = 142
Score = 72.4 bits (178), Expect = 5e-17
Identities = 23/57 (40%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 78 HLEVSSSYDQKEQMSRDFLHAIGPYSEPVLIHEW-LTLVTHNITYLWIDPTNVLAAV 133
+LEV + +D KEQ+ R+F +GP E VL+ W +T +WIDP NV+A
Sbjct: 86 NLEVGTDWDPKEQIFRNFGGLLGPNDELVLVQRWARGPDNLTVTVVWIDPLNVIADS 142
>gnl|CDD|203593 pfam07200, Mod_r, Modifier of rudimentary (Mod(r)) protein. This
family represents a conserved region approximately 150
residues long within a number of eukaryotic proteins
that show homology with Drosophila melanogaster
Modifier of rudimentary (Mod(r)) proteins. The
N-terminal half of Mod(r) proteins is acidic, whereas
the C-terminal half is basic, and both of these regions
are represented in this family. Members of this family
include the Vps37 subunit of the endosomal sorting
complex ESCRT-I, a complex involved in recruiting
transport machinery for protein sorting at the
multivesicular body (MVB). The yeast ESCRT-I complex
consists of three proteins (Vps23, Vps28 and Vps37).
The mammalian homologue of Vps37 interacts with Tsg101
(Pfam: PF05743) through its mod(r) domain and its
function is essential for lysosomal sorting of EGF
receptors.
Length = 150
Score = 29.2 bits (66), Expect = 0.50
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 45 NDFRSSDYSRLVATKGKQLYFARKFEPVVNQDIHLEVSSSYDQKEQMSRDFL 96
D + L+ + L F + V QD++LE + Q E ++ + L
Sbjct: 2 KDLSLDELKELLQDEDALLEFVLELPQV--QDLNLEKDALLAQNESLAEENL 51
>gnl|CDD|222879 PHA02563, PHA02563, DNA polymerase; Provisional.
Length = 630
Score = 29.7 bits (67), Expect = 0.51
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 60 GKQLYFARKFEPVVNQDIHLEVSSSYDQKEQMSRDFLHAIGPYSEPVLIH 109
G+ Y + ++ + +V+S Y M +A PY EP
Sbjct: 241 GRTWYNPKYIGKLIEEGYVYDVNSLY--PYVM----YNAKLPYGEPFYEK 284
>gnl|CDD|217062 pfam02485, Branch, Core-2/I-Branching enzyme. This is a family of
two different beta-1,6-N-acetylglucosaminyltransferase
enzymes, I-branching enzyme and core-2 branching enzyme
. I-branching enzyme is responsible for the production
of the blood group I-antigen during embryonic
development. Core-2 branching enzyme forms crucial
side-chain branches in O-glycans.
Length = 242
Score = 28.8 bits (65), Expect = 0.90
Identities = 8/36 (22%), Positives = 12/36 (33%), Gaps = 4/36 (11%)
Query: 14 IDNNLHITNWKRSLGCKCQYRHVVDWCGCSPNDFRS 49
++ L +W R YR C P D +
Sbjct: 209 VNRTLTYVDWSRGGCHPKTYR----PCDIGPEDLKR 240
>gnl|CDD|236530 PRK09466, metL, bifunctional aspartate kinase II/homoserine
dehydrogenase II; Provisional.
Length = 810
Score = 29.1 bits (66), Expect = 1.0
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 66 ARKFEPVVNQDIHLEVSSSYD 86
AR +PV DI L++ SY
Sbjct: 270 ARTLQPVSGSDIDLQLRCSYQ 290
>gnl|CDD|180367 PRK06046, PRK06046, alanine dehydrogenase; Validated.
Length = 326
Score = 28.1 bits (63), Expect = 2.0
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 65 FARKFEPVVNQDIHLEVSSSYDQKEQMSRDFLHAIGPYSEPVLIHEWLTLVTH 117
F + VV D+ + D +E D L P +PV+ EW+ TH
Sbjct: 170 FVERMSSVVGCDVTVAE----DIEEACDCDILVTTTPSRKPVVKAEWIKEGTH 218
>gnl|CDD|233075 TIGR00656, asp_kin_monofn, aspartate kinase, monofunctional class.
This model describes a subclass of aspartate kinases.
These are mostly Lys-sensitive and not fused to
homoserine dehydrogenase, unlike some Thr-sensitive and
Met-sensitive forms. Homoserine dehydrogenase is part of
Thr and Met but not Lys biosynthetic pathways. Aspartate
kinase catalyzes a first step in the biosynthesis from
Asp of Lys (and its precursor diaminopimelate), Met, and
Thr. In E. coli, a distinct isozyme is inhibited by each
of the three amino acid products. The Met-sensitive (I)
and Thr-sensitive (II) forms are bifunctional enzymes
fused to homoserine dehydrogenases and form
homotetramers, while the Lys-sensitive form (III) is a
monofunctional homodimer. The Lys-sensitive enzyme of
Bacillus subtilis resembles the E. coli form but is an
alpha 2/beta 2 heterotetramer, where the beta subunit is
translated from an in-phase alternative initiator at
Met-246. The protein slr0657 from Synechocystis PCC6803
is extended by a duplication of the C-terminal region
corresponding to the beta chain. Incorporation of a
second copy of the C-terminal domain may be quite common
in this subgroup of aspartokinases [Amino acid
biosynthesis, Aspartate family].
Length = 401
Score = 27.7 bits (62), Expect = 2.2
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 56 VATKGKQLYFARKFEPVVNQDIHLEVSSSYDQKE 89
+AT G ++ R EP + + +EV SS+D +E
Sbjct: 204 LATFGAKVLHPRTVEPAMRSGVPIEVRSSFDPEE 237
>gnl|CDD|227434 COG5103, CDC39, Cell division control protein, negative regulator of
transcription [Cell division and chromosome partitioning
/ Transcription].
Length = 2005
Score = 27.7 bits (61), Expect = 3.1
Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 3/69 (4%)
Query: 51 DYSRLVATKGKQLYFARKFEPVVNQ--DIHLEVSSSYDQKEQMSRDFLHAIGPYSEPVLI 108
+ + L+F R F ++ + D+ E +S + + A+ P P
Sbjct: 1604 AHRKRAEFVHNYLFF-RLFSRILIETLDVIDEDTSCFVNNRSVVYSIFEALQPSRFPGFT 1662
Query: 109 HEWLTLVTH 117
WL L++H
Sbjct: 1663 FAWLELLSH 1671
>gnl|CDD|130022 TIGR00947, 2A73, putative bicarbonate transporter, IctB family.
This family of proteins is suggested to transport
inorganic carbon (HCO3-), based on the phenotype of a
mutant of IctB in Synechococcus sp. strain PCC 7942.
Bicarbonate uptake is used by many photosynthetic
organisms including cyanobacteria. These organisms are
able to concentrate CO2/HCO3- against a greater than
ten-fold concentration gradient. Cyanobacteria may have
several such carriers operating with different
efficiencies. Note that homology to various O-antigen
ligases, with possible implications for mutant cell
envelope structure, might allow alternatives to the
interpretation of IctB as a bicarbonate transport
protein [Transport and binding proteins, Carbohydrates,
organic alcohols, and acids].
Length = 425
Score = 27.0 bits (60), Expect = 4.0
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 123 WIDPTNVLAAVTRV 136
W+DP +VLA TRV
Sbjct: 151 WVDPESVLAGTTRV 164
>gnl|CDD|128490 smart00193, PTN, Pleiotrophin / midkine family. Heparin-binding
domain family.
Length = 80
Score = 25.6 bits (56), Expect = 4.8
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 22 NWKRSLGCKCQYRHVVDWCGCSPN 45
NWK+ G C+Y+ W C N
Sbjct: 39 NWKKQFGADCKYK-FESWGECDAN 61
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 0.133 0.424
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,239,846
Number of extensions: 610153
Number of successful extensions: 430
Number of sequences better than 10.0: 1
Number of HSP's gapped: 429
Number of HSP's successfully gapped: 13
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
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 (24.8 bits)