RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17564
(109 letters)
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 89.3 bits (222), Expect = 3e-22
Identities = 39/104 (37%), Positives = 57/104 (54%), Gaps = 3/104 (2%)
Query: 1 MPLLQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYA 60
+PL Q+KQ YN MD+ ++REL +L K A + LD+++ SF +GYR K+ ASD V A
Sbjct: 320 IPLKQAKQKYNHMDMDLKRELRELLEKYAPKYGLDDIVFQSFVRTYGYRGKLSASDVVEA 379
Query: 61 MLALLESPVRILCRMDDVELENIPEYNQIFEHQEKKPSDCFLDA 104
+ ALLE + D E E+I E +++ F A
Sbjct: 380 VTALLEVGSKSPAGASDTEEEDIELLK---EKEDESWLSNFWRA 420
>gnl|CDD|223371 COG0294, FolP, Dihydropteroate synthase and related enzymes
[Coenzyme metabolism].
Length = 274
Score = 29.6 bits (67), Expect = 0.25
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 5/62 (8%)
Query: 22 PTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYAMLALLESPVRILCRMDDVELE 81
P +L+ +AA+ L+M G + +D V A+ L + + V E
Sbjct: 118 PALLAAVAAELGAPILLMHE----QGVPETMSINDLVAAVDMFLLARIEE-ALAAGVGRE 172
Query: 82 NI 83
I
Sbjct: 173 LI 174
>gnl|CDD|132588 TIGR03549, TIGR03549, YcaO domain protein. This family consists
of remarkably well-conserved proteins from gamma and
beta Proteobacteria, heavily skewed towards organisms
of marine environments. Its gene neighborhood is not
conserved. This family has an OsmC-like N-terminal
domain. It shares a YcaO domain, frequently associated
with ATP-dependent cyclodehydration for peptide
modification. The function is unknown. Fifteen of the
first sixteen members of this family are from
selenouridine-positive genomes, but this correlation
may not be meaningful.
Length = 718
Score = 29.0 bits (65), Expect = 0.47
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 12/56 (21%)
Query: 56 DYVYAMLALLESP-VRILCRMDDVELENI---------PE--YNQIFEHQEKKPSD 99
DY A AL + V++ C D+ ENI PE YNQIF+ Q + P D
Sbjct: 40 DYFLASSALCAAYFVKVYCNARDIPTENIRLSQNNIVDPEDRYNQIFKIQVELPED 95
>gnl|CDD|226587 COG4102, COG4102, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 418
Score = 27.5 bits (61), Expect = 1.5
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 7/64 (10%)
Query: 2 PLLQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYAM 61
P L++ QL+ + DL+ ++ + + AD + S L + S +
Sbjct: 361 PGLKAAQLFENRDLAPTADIRALYKGVLADW----FGVDSANLD---KIVFPLSALIKPD 413
Query: 62 LALL 65
L L+
Sbjct: 414 LGLI 417
>gnl|CDD|133056 cd06434, GT2_HAS, Hyaluronan synthases catalyze polymerization of
hyaluronan. Hyaluronan synthases (HASs) are
bi-functional glycosyltransferases that catalyze
polymerization of hyaluronan. HASs transfer both GlcUA
and GlcNAc in beta-(1,3) and beta-(1,4) linkages,
respectively to the hyaluronan chain using UDP-GlcNAc
and UDP-GlcUA as substrates. HA is made as a free
glycan, not attached to a protein or lipid. HASs do not
need a primer for HA synthesis; they initiate HA
biosynthesis de novo with only UDP-GlcNAc, UDP-GlcUA,
and Mg2+. Hyaluronan (HA) is a linear
heteropolysaccharide composed of (1-3)-linked
beta-D-GlcUA-beta-D-GlcNAc disaccharide repeats. It can
be found in vertebrates and a few microbes and is
typically on the cell surface or in the extracellular
space, but is also found inside mammalian cells.
Hyaluronan has several physiochemical and biological
functions such as space filling, lubrication, and
providing a hydrated matrix through which cells can
migrate.
Length = 235
Score = 26.8 bits (60), Expect = 2.4
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 41 SFTLLHGYRTKIQASDYVYAM 61
+ L HGY+T Q + Y
Sbjct: 193 RYVLSHGYKTVYQYTSEAYTE 213
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 26.8 bits (60), Expect = 2.9
Identities = 14/70 (20%), Positives = 30/70 (42%), Gaps = 14/70 (20%)
Query: 49 RTKIQASDYVYAM-------------LALLESPVRILCRMDDVELENIPEYNQIFEHQEK 95
K Q +DY A+ + LE + LC + D+ +N ++ + F+ +E+
Sbjct: 394 ELKSQLADYQQALDVQQTRAIQYQQAVQALER-AKQLCGLPDLTADNAEDWLEEFQAKEQ 452
Query: 96 KPSDCFLDAA 105
+ ++ L
Sbjct: 453 EATEELLSLE 462
>gnl|CDD|183283 PRK11706, PRK11706, TDP-4-oxo-6-deoxy-D-glucose transaminase;
Provisional.
Length = 375
Score = 26.7 bits (60), Expect = 2.9
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 4/20 (20%)
Query: 28 MAA---DHQL-DELIMPSFT 43
MAA D Q DE+IMPS+T
Sbjct: 61 MAALLLDIQPGDEVIMPSYT 80
>gnl|CDD|200596 cd10974, CE4_CDA_like_1, Putative catalytic domain of chitin
deacetylase-like proteins with additional chitin-binding
peritrophin-A domain (ChBD) and/or a low-density
lipoprotein receptor class A domain (LDLa). Chitin
deacetylases (CDAs, EC 3.5.1.41) are secreted
metalloproteins belonging to a family of extracellular
chitin-modifying enzymes that catalyze the
N-deacetylation of chitin, a beta-1,4-linked
N-acetylglucosamine polymer, to form chitosan, a polymer
of beta-(1,4)-linked d-glucosamine residues. CDAs have
been isolated and characterized from various bacterial
and fungal species and belong to the larger carbohydrate
esterase 4 (CE4) superfamily. This family includes many
CDA-like proteins mainly from insects, which contain a
putative CDA-like catalytic domain similar to the
catalytic NodB homology domain of CE4 esterases. In
addition to the CDA-like domain, family members contain
two additional domains, a chitin-binding peritrophin-A
domain (ChBD) and a low-density lipoprotein receptor
class A domain (LDLa), or have the ChBD domain but do
not have the LDLa domain.
Length = 269
Score = 26.1 bits (58), Expect = 4.4
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 68 PVRILCRMDD-VELENIPEYNQIFEHQEKKPSDC 100
P I DD + NI Y +IF + P+ C
Sbjct: 1 PQMITLTFDDAINDNNIELYKKIFNGKRNNPNGC 34
>gnl|CDD|219069 pfam06512, Na_trans_assoc, Sodium ion transport-associated.
Members of this family contain a region found
exclusively in eukaryotic sodium channels or their
subunits, many of which are voltage-gated. Members very
often also contain between one and four copies of
pfam00520 and, less often, one copy of pfam00612.
Length = 230
Score = 25.4 bits (56), Expect = 6.2
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 4/35 (11%)
Query: 73 CRMDDVELENIPEYNQIFEHQEKKPSDCFLDAAYC 107
+ E E I E + K+P DCF +
Sbjct: 159 LEPPEEEEEEIAEEEEE----VKEPEDCFPEGCVR 189
>gnl|CDD|237427 PRK13559, PRK13559, hypothetical protein; Provisional.
Length = 361
Score = 25.5 bits (56), Expect = 6.6
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 61 MLALLESPVRILCRMDDVELE 81
+ A+++S VR+ R DD L
Sbjct: 184 VFAVVDSIVRLTGRADDPSLY 204
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 25.6 bits (56), Expect = 6.8
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 65 LESPVRILCRMDDVELENIPEYNQIFEHQEKK 96
+ P RIL + D++ LE I ++ E +E K
Sbjct: 223 MRDPKRILVKKDELTLEGIRQFYVAVEKEEWK 254
>gnl|CDD|226393 COG3876, COG3876, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 409
Score = 25.1 bits (55), Expect = 8.8
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 2/42 (4%)
Query: 17 IRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYV 58
I E + L + + T HGYR QA + V
Sbjct: 55 INSEGKSSLDVLYEKEDCKLTAL--CTPEHGYRGAAQAGETV 94
>gnl|CDD|119343 cd06541, ASCH, ASC-1 homology or ASCH domain, a small beta-barrel
domain found in all three kingdoms of life. ASCH
resembles the RNA-binding PUA domain and may also
interact with RNA. ASCH has been proposed to function as
an RNA-binding domain during coactivation,
RNA-processing and the regulation of prokaryotic
translation. The domain has been named after the ASC-1
protein, the activating signal cointegrator 1 or thyroid
hormone receptor interactor protein 4 (TRIP4). ASC-1 is
conserved in many eukaryotes and has been suggested to
participate in a protein complex that interacts with
RNA. It has been shown that ASC-1 mediates the
interaction between various transciption factors and the
basal transcriptional machinery.
Length = 105
Score = 24.5 bits (53), Expect = 9.8
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 70 RILCRMDDVELENIPEYNQIFEHQEKK--PSDCFLDAAY 106
+ L + V++E +P N++ E QE+ D L
Sbjct: 44 QPLAIAEVVKVEIMPMVNELSEEQEQAEGEGDLTLLYEL 82
>gnl|CDD|221152 pfam11635, Med16, Mediator complex subunit 16. Mediator is a large
complex of up to 33 proteins that is conserved from
plants through fungi to humans - the number and
representation of individual subunits varying with
species. It is arranged into four different sections, a
core, a head, a tail and a kinase-activity part, and the
number of subunits within each of these is what varies
with species. Overall, Mediator regulates the
transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Med16 is one of the
subunits of the Tail portion of the Mediator complex and
is required for lipopolysaccharide gene-expression.
Several members including a human protein have one or
more WD40 domains on them, pfam00400.
Length = 744
Score = 25.1 bits (55), Expect = 9.9
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 33 QLDELIMPSFTLLHGYRTKIQASDYVYAMLAL 64
Q+D+ PS L H +D +L L
Sbjct: 146 QIDDQKPPSLFLRHILGETPDDTDPEGKLLQL 177
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
0.323 0.136 0.394
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,515,085
Number of extensions: 463261
Number of successful extensions: 386
Number of sequences better than 10.0: 1
Number of HSP's gapped: 386
Number of HSP's successfully gapped: 27
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 (22.0 bits)
S2: 53 (24.2 bits)