RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy33
(214 letters)
>gnl|CDD|202161 pfam02214, K_tetra, K+ channel tetramerisation domain. The
N-terminal, cytoplasmic tetramerisation domain (T1) of
voltage-gated K+ channels encodes molecular determinants
for subfamily-specific assembly of alpha-subunits into
functional tetrameric channels. It is distantly related
to the BTB/POZ domain pfam00651.
Length = 92
Score = 84.9 bits (211), Expect = 9e-22
Identities = 34/94 (36%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 15 VKLNVGGSLHYTTIGTLTK-HDTMLRAMFSGRMEILTDSEGWVLIDRCGKHFGIILNFLR 73
V+LNVGG T+ TLT+ DT+L + R + D DR KHF ILNF R
Sbjct: 1 VRLNVGGKRFETSKSTLTRFPDTLLGRLLK-RCDFYDDDTNEYFFDRSPKHFETILNFYR 59
Query: 74 DGQVSLPENP-KDVAELLAEAKYYCITELT-DLC 105
G L + L E ++Y + EL +LC
Sbjct: 60 TG-GKLHRPEEVCLDSFLEELEFYGLGELAIELC 92
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 78.9 bits (195), Expect = 2e-19
Identities = 34/99 (34%), Positives = 47/99 (47%), Gaps = 3/99 (3%)
Query: 14 YVKLNVGGSLHYTTIGTLTKHDTMLRAMFSGRMEILTDSEGWVLIDRCGKHFGIILNFLR 73
V L VGG + L H +A+FS + SE L D + F +LNFL
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFKALFSSDFKESDKSE-IYLDDVSPEDFRALLNFLY 59
Query: 74 DGQVSLPENPKDVAELLAEAKYYCITELTDLCEQTIKRK 112
G++ LPE +V ELL A Y I L +LCE+ + +
Sbjct: 60 TGKLDLPEE--NVEELLELADYLQIPGLVELCEEFLLKL 96
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab) or
POZ (for Pox virus and Zinc finger) domain is present
near the N-terminus of a fraction of zinc finger
(pfam00096) proteins and in proteins that contain the
pfam01344 motif such as Kelch and a family of pox virus
proteins. The BTB/POZ domain mediates homomeric
dimerisation and in some instances heteromeric
dimerisation. The structure of the dimerised PLZF
BTB/POZ domain has been solved and consists of a tightly
intertwined homodimer. The central scaffolding of the
protein is made up of a cluster of alpha-helices flanked
by short beta-sheets at both the top and bottom of the
molecule. POZ domains from several zinc finger proteins
have been shown to mediate transcriptional repression
and to interact with components of histone deacetylase
co-repressor complexes including N-CoR and SMRT. The POZ
or BTB domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 35.3 bits (82), Expect = 0.004
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 65 FGIILNFLRDGQVSLPENPKDVAELLAEAKYYCITELTDLCEQTIK 110
F +L F+ G++ + E ++V +LLA A I L D CE+ +
Sbjct: 58 FEALLEFIYTGKLEITE--ENVDDLLALADKLQIPALIDKCEEFLI 101
>gnl|CDD|220322 pfam09626, DHC, Dihaem cytochrome c. Dihaem cytochrome c (DHC) is
a soluble c-type cytochrome that folds into two distinct
domains, each binding a single haem group and connected
by a small linker region. Despite little sequence
similarity, the N-terminal domain (residues 12-75) is a
class I type cytochrome c, that binds one of the haems,
but the domain surrounding the other haem is
structurally unique. DHC binds electrostatically to an
oxygen-binding protein, sphaeroides haem protein (SHP),
as a component of a conserved electron transfer pathway.
DHC acts as the physiological electron donor for SHP
during phototrophic growth. In certain species DHC is
found upstream of pfam01292.
Length = 118
Score = 28.5 bits (64), Expect = 1.2
Identities = 13/76 (17%), Positives = 23/76 (30%), Gaps = 17/76 (22%)
Query: 52 SEGW-VLIDRCGKHFG-----------IILNFLRDGQVSLPENPKDVAELLAEAKYYCIT 99
+ W ++ HFG +I +LR L + + + + E IT
Sbjct: 19 AASWRKIMADLDDHFGTDASLDPPTRALIWAYLRANAADLSGSRRKILRSVPEPVPLRIT 78
Query: 100 ELTDLCEQTIKRKQRE 115
E + E
Sbjct: 79 ES-----PYFRALHPE 89
>gnl|CDD|182059 PRK09752, PRK09752, adhesin; Provisional.
Length = 1250
Score = 29.3 bits (65), Expect = 1.9
Identities = 22/56 (39%), Positives = 28/56 (50%), Gaps = 9/56 (16%)
Query: 8 SGNPCQYVKLNV-GGSLHYTTIGTLTKH-DT----MLRAMFSGRMEILTDSEGWVL 57
+G Q + L V GG HYT G L +H DT + +FSGR D E W+L
Sbjct: 980 AGGDGQTLNLRVIGGDYHYTAAGQLAQHEDTSTVQLSGDLFSGRWG--DDGE-WML 1032
>gnl|CDD|212131 cd11666, GH38N_Man2A1, N-terminal catalytic domain of Golgi
alpha-mannosidase II and similar proteins; glycoside
hydrolase family 38 (GH38). This subfamily is
represented by Golgi alpha-mannosidase II (GMII, also
known as mannosyl-oligosaccharide 1,3- 1,6-alpha
mannosidase, EC 3.2.1.114, Man2A1), a monomeric,
membrane-anchored class II alpha-mannosidase existing in
the Golgi apparatus of eukaryotes. GMII plays a key role
in the N-glycosylation pathway. It catalyzes the
hydrolysis of the terminal of both alpha-1,3-linked and
alpha-1,6-linked mannoses from the high-mannose
oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield
GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which
is the committed step of complex N-glycan synthesis.
GMII is activated by zinc or cobalt ions and is strongly
inhibited by swainsonine. Inhibition of GMII provides a
route to block cancer-induced changes in cell surface
oligosaccharide structures. GMII has a pH optimum of
5.5-6.0, which is intermediate between those of acidic
(lysosomal alpha-mannosidase) and neutral (ER/cytosolic
alpha-mannosidase) enzymes. GMII is a retaining glycosyl
hydrolase of family GH38 that employs a two-step
mechanism involving the formation of a covalent glycosyl
enzyme complex; two carboxylic acids positioned within
the active site act in concert: one as a catalytic
nucleophile and the other as a general acid/base
catalyst.
Length = 344
Score = 28.8 bits (64), Expect = 2.5
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 33 KHDTMLRAMFSGRMEILTDSEGWVLIDRCGKHFGIILNFLRDGQVSLPEN 82
K D + R + +G++EI+T GWV+ D H+ +++ L +G L N
Sbjct: 66 KKDAVKRLIENGQLEIVTG--GWVMPDEATAHYFALIDQLIEGHQWLERN 113
>gnl|CDD|232843 TIGR00133, gatB, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase,
B subunit. The heterotrimer GatABC is responsible for
transferring the NH2 group that converts Glu to Gln, or
Asp to Asn after the Glu or Asp has been ligated to the
tRNA for Gln or Asn, respectively. In Lactobacillus,
GatABC is responsible only for tRNA(Gln). In the
Archaea, GatABC is responsible only for tRNA(Asn), while
GatDE is responsible for tRNA(Gln). In lineages that
include Thermus, Chlamydia, or Acidithiobacillus, the
GatABC complex catalyzes both [Protein synthesis, tRNA
aminoacylation].
Length = 478
Score = 28.1 bits (63), Expect = 3.8
Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 13/67 (19%)
Query: 64 HFGIILNFLRDGQVS----------LPENPKDVAELLAEAKYYCIT---ELTDLCEQTIK 110
++ +++G++S + EN D ++L+ E I+ EL + E+ IK
Sbjct: 373 DLAELIKLIKEGKISGKSAKQLIEEMLENGGDPSKLIEELGLEQISDEKELIKIIEEVIK 432
Query: 111 RKQRETE 117
+E E
Sbjct: 433 ENPKEVE 439
>gnl|CDD|218160 pfam04587, ADP_PFK_GK, ADP-specific Phosphofructokinase/Glucokinase
conserved region. In archaea a novel type of glycolytic
pathway exists that is deviant from the classical
Embden-Meyerhof pathway. This pathway utilises two novel
proteins: an ADP-dependent Glucokinase and an
ADP-dependent Phosphofructokinase. This conserved region
is present at the C-terminal of both these proteins.
Interestingly this family contains sequences from higher
eukaryotes..
Length = 444
Score = 28.2 bits (63), Expect = 4.0
Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 5/66 (7%)
Query: 60 RCGKHFGIILNFL---RDGQVSL--PENPKDVAELLAEAKYYCITELTDLCEQTIKRKQR 114
R G GI+ N L +V P K +AEL + E +L + + R
Sbjct: 93 RMGGQAGIMANLLAGLYGKKVIAYTPFLSKKLAELFLDNILVPTVENGELVLKHPREAYR 152
Query: 115 ETEPIC 120
+ +P
Sbjct: 153 DGDPDK 158
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 27.8 bits (62), Expect = 4.4
Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 12/60 (20%)
Query: 85 DVAELLAEAKYYCIT-ELTDLCEQTIKRKQRETEPICRVPLITSLKEEQLLLNATAKPVV 143
D+ LL E+ + CI LTD +Q +K + +NA PVV
Sbjct: 193 DLDTLLQESDFVCIILPLTDETHHLFGAEQ-----------FAKMKSSAIFINAGRGPVV 241
>gnl|CDD|237025 PRK11929, PRK11929, putative bifunctional
UDP-N-acetylmuramoylalanyl-D-glutamate--2,
6-diaminopimelate
ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-
alanine ligase; Provisional.
Length = 958
Score = 27.7 bits (62), Expect = 5.2
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 40 AMFSGRMEILTDSEGWVLIDRC 61
+GRM+ S G +ID
Sbjct: 821 QPVAGRMQRRRLSCGTRIIDDT 842
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
0.322 0.138 0.417
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,726,654
Number of extensions: 999840
Number of successful extensions: 889
Number of sequences better than 10.0: 1
Number of HSP's gapped: 884
Number of HSP's successfully gapped: 22
Length of query: 214
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 121
Effective length of database: 6,812,680
Effective search space: 824334280
Effective search space used: 824334280
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: 57 (25.7 bits)