RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14614
(92 letters)
>gnl|CDD|238033 cd00078, HECTc, HECT domain; C-terminal catalytic domain of a
subclass of Ubiquitin-protein ligase (E3). It binds
specific ubiquitin-conjugating enzymes (E2), accepts
ubiquitin from E2, transfers ubiquitin to substrate
lysine side chains, and transfers additional ubiquitin
molecules to the end of growing ubiquitin chains.
Length = 352
Score = 84.2 bits (209), Expect = 5e-21
Identities = 29/67 (43%), Positives = 44/67 (65%), Gaps = 1/67 (1%)
Query: 18 RPVALSDLESLDNEFHQSLLWIKEHDVTNEVLDLNFAVTEEI-FGQAKERELKPGGRNIA 76
+P++L DLE LD E ++SL + ++D + L+L F + + FG A ELKPGGR+I
Sbjct: 123 KPLSLEDLEELDPELYKSLKELLDNDGDEDDLELTFTIELDSSFGGAVTVELKPGGRDIP 182
Query: 77 VTEKNKK 83
VT +NK+
Sbjct: 183 VTNENKE 189
>gnl|CDD|214523 smart00119, HECTc, Domain Homologous to E6-AP Carboxyl Terminus
with. E3 ubiquitin-protein ligases. Can bind to E2
enzymes.
Length = 328
Score = 81.1 bits (201), Expect = 6e-20
Identities = 38/67 (56%), Positives = 47/67 (70%), Gaps = 1/67 (1%)
Query: 18 RPVALSDLESLDNEFHQSLLWIKEHDVTNEVLDLNFA-VTEEIFGQAKERELKPGGRNIA 76
+PV L DLESLD E ++SL W+ ++ T+E LDL F+ V FGQ K ELKPGG NI
Sbjct: 100 KPVTLHDLESLDPELYKSLKWLLLNNDTSEELDLTFSIVLTSEFGQVKVVELKPGGSNIP 159
Query: 77 VTEKNKK 83
VTE+NKK
Sbjct: 160 VTEENKK 166
>gnl|CDD|227354 COG5021, HUL4, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 872
Score = 76.7 bits (189), Expect = 5e-18
Identities = 33/67 (49%), Positives = 49/67 (73%)
Query: 17 SRPVALSDLESLDNEFHQSLLWIKEHDVTNEVLDLNFAVTEEIFGQAKERELKPGGRNIA 76
+PV+L DLESLD E ++SL+W+ +D+ +LDL F V ++ FG+++ EL P GRNI+
Sbjct: 636 GKPVSLVDLESLDPELYRSLVWLLNNDIDETILDLTFTVEDDSFGESRTVELIPNGRNIS 695
Query: 77 VTEKNKK 83
VT +NKK
Sbjct: 696 VTNENKK 702
>gnl|CDD|216035 pfam00632, HECT, HECT-domain (ubiquitin-transferase). The name
HECT comes from Homologous to the E6-AP Carboxyl
Terminus.
Length = 298
Score = 68.5 bits (168), Expect = 2e-15
Identities = 27/66 (40%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 18 RPVALSDLESLDNEFHQSLLWIKEHDVTNEVLDLNFAVTEEIFGQAKERELKPGGRNIAV 77
+P+ L DLE +D E ++SL + E D E L L F V+ E EL P G NI V
Sbjct: 73 KPITLEDLEEVDPELYRSLKSLLELDGDEEELCLTFTVSGEGE---GTIELIPNGSNIPV 129
Query: 78 TEKNKK 83
T +NK+
Sbjct: 130 TNENKE 135
>gnl|CDD|203189 pfam05175, MTS, Methyltransferase small domain. This domain is
found in ribosomal RNA small subunit methyltransferase C
as well as other methyltransferases .
Length = 170
Score = 31.0 bits (71), Expect = 0.042
Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 49 LDLNFAVTEEIFGQAKERELKPGGRNIAVTEKNKKYRT 86
++ V + A LKPGG V ++ Y +
Sbjct: 112 KATDYDVAQRFIAGAARH-LKPGGELWIVANRHLGYPS 148
>gnl|CDD|185722 cd08981, GH43_2, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes enzymes with
beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC
3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-),
alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase
(EC 3.2.1.99), xylanase (EC 3.2.1.8),
endo-alpha-L-arabinanase and galactan
1,3-beta-galactosidase (EC 3.2.1.145) activities. These
are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Many of the
enzymes in this family display both
alpha-L-arabinofuranosidase and beta-D-xylosidase
activity using aryl-glycosides as substrates. A common
structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 291
Score = 28.8 bits (65), Expect = 0.26
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 7/38 (18%)
Query: 3 RQRGTLV-VS------YSPHSSRPVALSDLESLDNEFH 33
+RGT + VS + PHS PV D LD +
Sbjct: 92 ERRGTAILVSDSPEGPFVPHSDGPVTPEDWMCLDGTLY 129
>gnl|CDD|236211 PRK08268, PRK08268, 3-hydroxy-acyl-CoA dehydrogenase; Validated.
Length = 507
Score = 27.1 bits (61), Expect = 1.2
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 49 LDLNFAVTEEIFGQ 62
LD+N AV E ++ Q
Sbjct: 241 LDVNHAVMESVYRQ 254
>gnl|CDD|226802 COG4359, COG4359, Uncharacterized conserved protein [Function
unknown].
Length = 220
Score = 26.3 bits (58), Expect = 2.1
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 15 HSSRPVALSDLE---SLDNEFHQSLLWIKEHDV 44
HSS L L +D F + + WIKEHD+
Sbjct: 58 HSSLEEILEFLLKDIKIDPGFKEFVEWIKEHDI 90
>gnl|CDD|218846 pfam05994, FragX_IP, Cytoplasmic Fragile-X interacting family.
CYFIP1/2 (Cytoplasmic fragile X mental retardation
interacting protein) like proteins for a highly
conserved protein family. The function of CYFIPs is
unclear, but CYFIP interaction with fragile X mental
retardation interacting protein (FMRP) involves the
domain of FMRP which also mediating homo- and
heteromerization.
Length = 815
Score = 26.6 bits (59), Expect = 2.3
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 26 ESLDNEFHQSLLWIKEH--DVTNEV 48
ESLD S LW +E D+ +
Sbjct: 221 ESLDKACDLSQLWFREFYLDLNKRI 245
>gnl|CDD|236185 PRK08205, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 583
Score = 25.7 bits (57), Expect = 3.5
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 47 EVLDLNFAV--TEEIFGQAKE--RELKPGGRNIAVTEKNKKYRT 86
+ +D N +V TEE QA LK + I V +K K++ T
Sbjct: 459 QSMDNNASVFRTEETLKQALTDIHALKERYKRITVQDKGKRFNT 502
>gnl|CDD|187685 cd09627, DOMON_murB_like, Domon-like domain of
UDP-N-acetylenolpyruvoylglucosamine reductase.
UDP-N-acetylenolpyruvoylglucosamine reductase (murB)
catalyzes an essential step in peptidoglycan
biosynthesis, the reduction of
UDP-N-acetylglucosamine-enolpyruvate to
UDP-N-acetylmuramate. A subset of these FAD-dependent
enzymes contains a C-terminal DOMON-like domain. DOMON
domains can be found in all three kindgoms of life and
are a diverse group of ligand binding domains that have
been shown to interact with sugars and hemes; initially
DOMON domains were suspected to confer protein-protein
interactions. The DOMON-like domain in murB may bind a
heme.
Length = 179
Score = 25.4 bits (56), Expect = 4.5
Identities = 16/61 (26%), Positives = 20/61 (32%), Gaps = 5/61 (8%)
Query: 2 YRQRGTLVVSYSPHSSRPVALSDLESLDNEFHQSLLWIKEHDVTNEVLDLNF-AVTEEIF 60
YRQR +S P D L +LL L+L AV E+
Sbjct: 98 YRQRLEGELSAEPPRIGLTRQPDDLRLGLRLDLALLP----PFVRGTLELGLTAVIEDGD 153
Query: 61 G 61
G
Sbjct: 154 G 154
>gnl|CDD|237277 PRK13026, PRK13026, acyl-CoA dehydrogenase; Reviewed.
Length = 774
Score = 25.3 bits (56), Expect = 5.5
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 15 HSSRPVALSDLES--LDNEFHQSLLWIKEHDVTNEVLDL 51
HS L+ E +DNE L + + D+ DL
Sbjct: 71 HSYPKPTLTAEEQAFIDNEVETLLTMLDDWDIVQNRKDL 109
>gnl|CDD|188448 TIGR03933, PIA_icaB, intercellular adhesin biosynthesis
polysaccharide N-deacetylase. A common motif in
bacterial biosynthesis of polysaccharide for export is
modification that follows polymerization. This model
describes a subfamily of polysaccharide N-deacetylases
that acts on poly-beta-1,6-N-acetyl-D-glyscosamine as
produced by Staphylococcus epidermidis and S. aureus.
The end product in these species is designated
polysaccharide intercellular adhesin (PIA), and this
gene designated icaB (intercellular adhesion protein B)
[Cell envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides, Cellular
processes, Pathogenesis].
Length = 245
Score = 25.2 bits (55), Expect = 5.6
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 8/38 (21%)
Query: 29 DNEFHQSLLWIKEHDVTNEVLDLNFAVTEEIFGQAKER 66
D+EF + W+K HD +T + F + KE+
Sbjct: 37 DSEFESQIKWLKAHDAK--------FLTLKEFIKYKEK 66
>gnl|CDD|180505 PRK06278, PRK06278, cobyrinic acid a,c-diamide synthase; Validated.
Length = 476
Score = 25.4 bits (56), Expect = 5.7
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 4/69 (5%)
Query: 19 PVALSDLES--LDNEFHQSLLWIKEHDVTNEVLDLNFAVTEEIFGQAKERELKPGGRNIA 76
+ S +E +++ + SLL K+ V E + LN EIF + K+ I
Sbjct: 358 SCSKSGIEGAFVESMAYYSLL--KKMGVKVEGIILNKVYNMEIFEKVKKIAENSNINLIG 415
Query: 77 VTEKNKKYR 85
V + + R
Sbjct: 416 VGKLKVEKR 424
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 25.2 bits (55), Expect = 6.9
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 66 RELKPGGRNIAVTEKN 81
RELKPG R IA + +
Sbjct: 422 RELKPGARPIACMDND 437
>gnl|CDD|148674 pfam07212, Hyaluronidase_1, Hyaluronidase protein (HylP). This
family consists of several phage associated
hyaluronidase proteins (EC:3.2.1.35) which seem to be
specific to Streptococcus pyogenes and Streptococcus
pyogenes bacteriophages. The substrate of hyaluronidase
is hyaluronic acid, a sugar polymer composed of
alternating N-acetylglucosamine and glucuronic acid
residues. Hyaluronic acid is found in the ground
substance of human connective tissue and the vitreous of
the eye and also is the sole component of the capsule of
group A streptococci. The capsule has been shown to be
an important virulence factor of this organism by virtue
of its ability to resist phagocytosis. Production by S.
pyogenes of both a hyaluronic acid capsule and
hyaluronidase enzymatic activity capable of destroying
the capsule is an interesting, yet-unexplained,
phenomenon.
Length = 273
Score = 24.6 bits (53), Expect = 8.6
Identities = 15/48 (31%), Positives = 22/48 (45%)
Query: 1 MYRQRGTLVVSYSPHSSRPVALSDLESLDNEFHQSLLWIKEHDVTNEV 48
+ RG VV YS + + L L + F+QS L++ TN V
Sbjct: 74 LSSSRGAGVVVYSNNDTSDGPLMSLRTGKETFNQSALFVDYKGTTNAV 121
>gnl|CDD|133404 cd04777, HTH_MerR-like_sg1, Helix-Turn-Helix DNA binding domain of
putative transcription regulators from the MerR
superfamily. Putative helix-turn-helix (HTH) MerR-like
transcription regulators (subgroup 1), N-terminal
domain. Based on sequence similarity, these proteins are
predicted to function as transcription regulators that
mediate responses to stress in eubacteria. They belong
to the MerR superfamily of transcription regulators that
promote transcription of various stress regulons by
reconfiguring the operator sequence located between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of two distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 107
Score = 24.3 bits (53), Expect = 8.6
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 29 DNEFHQSLLWIKEHDVTNEVLDLNFAV 55
D ++++S L K+ ++ E+ DL A+
Sbjct: 78 DQDYYKSFLKNKKDELEKEIEDLKKAI 104
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
0.314 0.131 0.378
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,541,311
Number of extensions: 363296
Number of successful extensions: 236
Number of sequences better than 10.0: 1
Number of HSP's gapped: 233
Number of HSP's successfully gapped: 23
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
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: 42 (22.0 bits)
S2: 53 (24.1 bits)