RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6924
(89 letters)
>gnl|CDD|215497 PLN02919, PLN02919, haloacid dehalogenase-like hydrolase family
protein.
Length = 1057
Score = 75.3 bits (185), Expect = 1e-17
Identities = 25/43 (58%), Positives = 32/43 (74%), Gaps = 1/43 (2%)
Query: 22 DFCTKQEWMNTTEPLSLNSHLKNKIVIMDFFTYCCINCMHILP 64
+F K +W+NT PL LK K+VI+DF+TYCCINCMH+LP
Sbjct: 399 EFPPKLDWLNTA-PLQFRRDLKGKVVILDFWTYCCINCMHVLP 440
>gnl|CDD|239310 cd03012, TlpA_like_DipZ_like, TlpA-like family, DipZ-like
subfamily; composed uncharacterized proteins containing
a TlpA-like TRX domain. Some members show domain
architectures similar to that of E. coli DipZ protein
(also known as DsbD). The only eukaryotic members of
the TlpA family belong to this subfamily. TlpA is a
disulfide reductase known to have a crucial role in the
biogenesis of cytochrome aa3.
Length = 126
Score = 70.0 bits (172), Expect = 4e-17
Identities = 23/43 (53%), Positives = 33/43 (76%), Gaps = 1/43 (2%)
Query: 22 DFCTKQEWMNTTEPLSLNSHLKNKIVIMDFFTYCCINCMHILP 64
+F +W+NT +PLSL L+ K+V++DF+TYCCINC+H LP
Sbjct: 2 EFEGILQWLNTDKPLSLAQ-LRGKVVLLDFWTYCCINCLHTLP 43
>gnl|CDD|239264 cd02966, TlpA_like_family, TlpA-like family; composed of TlpA,
ResA, DsbE and similar proteins. TlpA, ResA and DsbE
are bacterial protein disulfide reductases with
important roles in cytochrome maturation. They are
membrane-anchored proteins with a soluble TRX domain
containing a CXXC motif located in the periplasm. The
TRX domains of this family contain an insert,
approximately 25 residues in length, which correspond
to an extra alpha helix and a beta strand when compared
with TRX. TlpA catalyzes an essential reaction in the
biogenesis of cytochrome aa3, while ResA and DsbE are
essential proteins in cytochrome c maturation. Also
included in this family are proteins containing a
TlpA-like TRX domain with domain architectures similar
to E. coli DipZ protein, and the N-terminal TRX domain
of PilB protein from Neisseria which acts as a
disulfide reductase that can recylce methionine
sulfoxide reductases.
Length = 116
Score = 38.8 bits (91), Expect = 4e-05
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 34 EPLSLNSHLKNKIVIMDFFTYCCINCMHILPIPILIRHILEYKRTHIIKTFQI 86
+P+SL S LK K+V+++F+ C C +P + + + ++
Sbjct: 10 KPVSL-SDLKGKVVLVNFWASWCPPCRAEMP------ELEALAKEYKDDGVEV 55
>gnl|CDD|222448 pfam13905, Thioredoxin_8, Thioredoxin-like. Thioredoxins are
small enzymes that participate in redox reactions, via
the reversible oxidation of an active centre disulfide
bond.
Length = 94
Score = 30.0 bits (68), Expect = 0.057
Identities = 8/43 (18%), Positives = 14/43 (32%), Gaps = 6/43 (13%)
Query: 44 NKIVIMDFFTYCCINCMHILPIPILIRHILEYKRTHIIKTFQI 86
K+V++ F+ C C P + E +I
Sbjct: 1 GKVVLLYFWASWCPPCRAFTP------ELKELYEKLKKPKVEI 37
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 29.9 bits (66), Expect = 0.096
Identities = 11/41 (26%), Positives = 16/41 (39%)
Query: 25 TKQEWMNTTEPLSLNSHLKNKIVIMDFFTYCCINCMHILPI 65
T + S LK K V++DF+ C C P+
Sbjct: 13 TAASFEELDGAPLSLSELKGKPVLVDFWAPWCPPCRAEAPL 53
>gnl|CDD|173347 PTZ00051, PTZ00051, thioredoxin; Provisional.
Length = 98
Score = 26.4 bits (58), Expect = 1.5
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 44 NKIVIMDFFTYCCINCMHILP 64
N++VI+DF+ C C I P
Sbjct: 18 NELVIVDFYAEWCGPCKRIAP 38
>gnl|CDD|185721 cd08980, GH43_1, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes enzymes with
beta-xylosidase (EC 3.2.1.37) and
alpha-L-arabinofuranosidase (EC 3.2.1.55) and possibly
bifunctional xylosidase/arabinofuranosidase 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 = 288
Score = 25.6 bits (57), Expect = 3.2
Identities = 7/23 (30%), Positives = 9/23 (39%), Gaps = 4/23 (17%)
Query: 4 TGHCSFVPVP----LVAIFHGRD 22
GH SF P ++H R
Sbjct: 239 PGHNSFTKSPDGTEDWIVYHARP 261
>gnl|CDD|221288 pfam11882, DUF3402, Domain of unknown function (DUF3402). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 350 to 473 amino acids in length. This domain is
found associated with pfam07923.
Length = 402
Score = 25.4 bits (56), Expect = 4.8
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 43 KNKIVIMDFFTYCCINCMHILPIPIL 68
KN+I + FF+ C + + + L
Sbjct: 215 KNEIPNLSFFSECYLEARNPPELDEL 240
>gnl|CDD|233735 TIGR02121, Na_Pro_sym, sodium/proline symporter. This family
consists of the sodium/proline symporter (proline
permease) from a number of Gram-negative and
Gram-positive bacteria and from the archaeal genus
Methanosarcina. Using the related pantothenate permease
as an outgroup, candidate sequences from Bifidobacterium
longum and several from archaea are found to be outside
the clade defined by known proline permeases. These
sequences, scoring between 570 and -40, define the range
between trusted and noise cutoff scores [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 487
Score = 25.0 bits (55), Expect = 6.2
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 8 SFVPVPLVAIFHGRDFCTKQEWMNTTEPLSLN 39
+ V VP+VA+F+ F + P L+
Sbjct: 193 ALVLVPIVALFNLGGFGETLSAVAAINPHLLD 224
>gnl|CDD|239266 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c
Oxidase) family; composed of proteins similar to Sco1,
a membrane-anchored protein possessing a soluble domain
with a TRX fold. Members of this family are required
for the proper assembly of cytochrome c oxidase (COX).
They contain a metal binding motif, typically CXXXC,
which is located in a flexible loop. COX, the terminal
enzyme in the respiratory chain, is imbedded in the
inner mitochondrial membrane of all eukaryotes and in
the plasma membrane of some prokaryotes. It is composed
of two subunits, COX I and COX II. It has been proposed
that Sco1 specifically delivers copper to the CuA site,
a dinuclear copper center, of the COX II subunit.
Mutations in human Sco1 and Sco2 cause fatal infantile
hepatoencephalomyopathy and cardioencephalomyopathy,
respectively. Both disorders are associated with severe
COX deficiency in affected tissues. More recently, it
has been argued that the redox sensitivity of the
copper binding properties of Sco1 implies that it
participates in signaling events rather than
functioning as a chaperone that transfers copper to COX
II.
Length = 142
Score = 24.5 bits (54), Expect = 7.1
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 34 EPLSLNSHLKNKIVIMDF-FTYC 55
P++L S LK K V++ F +T+C
Sbjct: 13 RPVTL-SDLKGKPVLVYFGYTHC 34
>gnl|CDD|204101 pfam08936, CsoSCA, Carboxysome Shell Carbonic Anhydrase.
Carboxysome Shell Carbonic Anhydrase is a bacterial
carbonic anhydrase localised in the carboxysome, where
it converts bicarbonate ions to carbon dioxide for use
in carbon fixation. It contains three domains, these
being: (1) an N-terminal domain composed primarily of
four alpha-helices; (2) a catalytic domain containing a
tightly bound zinc ion and (3) a C-terminal domain with
weak structural similarity to the catalytic domain.
Length = 459
Score = 24.9 bits (55), Expect = 7.6
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 58 NCMHILPIPILIR 70
N LPIP+++R
Sbjct: 386 NVSRGLPIPVVVR 398
>gnl|CDD|239220 cd02890, PTase, Protein prenyltransferase (PTase) domain, beta
subunit (alpha 6 - alpha 6 barrel fold). The protein
prenyltransferase family of lipid-modifying enzymes
includes protein farnesyltransferase (FTase) and
geranylgeranyltransferase types I and II (GGTase-I and
GGTase-II). They catalyze the carboxyl-terminal
lipidation of Ras, Rab, and several other cellular
signal transduction proteins, facilitating membrane
associations and specific protein-protein interactions.
Prenyltransferases employ a Zn2+ ion to alkylate a thiol
group catalyzing the formation of thioether linkages
between the C1 atom of farnesyl (15-carbon by FTase) or
geranylgeranyl (20-carbon by GGTase-I, II) isoprenoid
lipids and cysteine residues at or near the C-terminus
of protein acceptors. FTase and GGTase-I prenylate the
cysteine in the terminal sequence, "CAAX"; and GGTase-II
prenylates both cysteines in the "CC" (or "CXC")
terminal sequence. These enzymes are heterodimeric with
both alpha and beta subunits required for catalytic
activity. In contrast to other prenyltransferases,
GGTase-II does not recognize its protein acceptor
directly but requires Rab to complex with REP (Rab
escort protein) before prenylation can occur. These
enzymes are found exclusively in eukaryotes.
Length = 286
Score = 24.5 bits (54), Expect = 8.6
Identities = 3/13 (23%), Positives = 8/13 (61%)
Query: 51 FFTYCCINCMHIL 63
+T+C + + +L
Sbjct: 176 GYTFCAVASLALL 188
>gnl|CDD|173023 PRK14558, pyrH, uridylate kinase; Provisional.
Length = 231
Score = 24.3 bits (53), Expect = 9.2
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 33 TEPLSLNSHLKNKIVIMDFFT 53
TE S+ I++++FF
Sbjct: 191 TEAFSICKKYGITILVINFFE 211
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
0.333 0.144 0.489
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,487,913
Number of extensions: 344786
Number of successful extensions: 491
Number of sequences better than 10.0: 1
Number of HSP's gapped: 489
Number of HSP's successfully gapped: 22
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 bits)
S2: 53 (24.2 bits)