RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4260
(129 letters)
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 84.9 bits (210), Expect = 1e-20
Identities = 39/115 (33%), Positives = 55/115 (47%), Gaps = 17/115 (14%)
Query: 4 APAAATSTPSTPVSQAGATATATTP--------GNAESTLLMGDEYGRMVQNIVDMGYER 55
A A+ +P ++ +P +A STL++G E ++ I++MGYER
Sbjct: 111 AAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERETTIEEIMEMGYER 170
Query: 56 SAVTEALRASFNNPDRAVEYLITGIP---------AAVVGEEAPVAANEPQGNNI 101
V ALRA+FNNPDRAVEYL+TGIP A PQ ++
Sbjct: 171 EEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAASTAAATTETPQHGSV 225
>gnl|CDD|201355 pfam00627, UBA, UBA/TS-N domain. This small domain is composed
of three alpha helices. This family includes the
previously defined UBA and TS-N domains. The UBA-domain
(ubiquitin associated domain) is a novel sequence motif
found in several proteins having connections to
ubiquitin and the ubiquitination pathway. The structure
of the UBA domain consists of a compact three helix
bundle. This domain is found at the N terminus of EF-TS
hence the name TS-N. The structure of EF-TS is known
and this domain is implicated in its interaction with
EF-TU. The domain has been found in non EF-TS proteins
such as alpha-NAC and MJ0280.
Length = 37
Score = 49.4 bits (119), Expect = 2e-09
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 44 MVQNIVDMGYERSAVTEALRASFNNPDRAVEYL 76
+++ + +MG+ R +ALRA+ N +RAVEYL
Sbjct: 5 LIKQLREMGFSREEAKKALRATNGNVERAVEYL 37
>gnl|CDD|238116 cd00194, UBA, Ubiquitin Associated domain. The UBA domain is a
commonly occurring sequence motif in some members of
the ubiquitination pathway, UV excision repair
proteins, and certain protein kinases. Although its
specific role is so far unknown, it has been suggested
that UBA domains are involved in conferring protein
target specificity. The domain, a compact three helix
bundle, has a conserved GFP-loop and the proline is
thought to be critical for binding. The UBA domain is
distinct from the conserved three helical domain seen
in the N-terminus of EF-TS and eukaryotic NAC proteins.
Length = 38
Score = 49.0 bits (118), Expect = 2e-09
Identities = 14/35 (40%), Positives = 25/35 (71%)
Query: 43 RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77
++ +++MG+ R +ALRA+ NN +RAVE+L+
Sbjct: 3 EKLEQLLEMGFSREEARKALRATNNNVERAVEWLL 37
>gnl|CDD|197551 smart00165, UBA, Ubiquitin associated domain. Present in Rad23,
SNF1-like kinases. The newly-found UBA in p62 is known
to bind ubiquitin.
Length = 37
Score = 45.2 bits (108), Expect = 7e-08
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 45 VQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77
+ +++MG+ R +ALRA+ N +RA EYL+
Sbjct: 5 IDQLLEMGFSREEALKALRAANGNVERAAEYLL 37
>gnl|CDD|139961 PRK13901, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 196
Score = 28.6 bits (64), Expect = 0.78
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 35 LLMGDE-------YGRMVQNIVDMGYERSAVTEALRASFN 67
L+ DE + + Q+IV+MG++R V A++
Sbjct: 131 LVKNDELESSLFKFKELEQSIVNMGFDRKLVNSAIKEIML 170
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 28.3 bits (64), Expect = 1.4
Identities = 10/20 (50%), Positives = 11/20 (55%), Gaps = 2/20 (10%)
Query: 38 GDEYGRMVQNIVDMGY--ER 55
G+ Y M IVD GY ER
Sbjct: 222 GNRYVEMPLKIVDTGYGLER 241
>gnl|CDD|239578 cd03498, SQR_TypeB_2_TM, Succinate:quinone oxidoreductase
(SQR)-like Type B subfamily 2, transmembrane subunit;
composed of proteins with similarity to the SQRs of
Geobacter metallireducens and Corynebacterium
glutamicum. SQR catalyzes the oxidation of succinate to
fumarate coupled to the reduction of quinone to quinol.
C. glutamicum SQR reduces low potential quinones such as
menaquinone. SQR is also called succinate dehydrogenase
(Sdh) or Complex II and is part of the citric acid cycle
and the aerobic respiratory chain. SQR is composed of a
flavoprotein catalytic subunit, an iron-sulfur protein
and one or two hydrophobic transmembrane subunits.
Members of this subfamily are classified as Type B as
they contain one transmembrane subunit and two heme
groups. The heme and quinone binding sites reside in the
transmembrane subunit. The transmembrane subunit of
members of this subfamily is also called Sdh cytochrome
b558 subunit based on the Bacillus subtilis protein. The
structural arrangement allows efficient electron
transfer between the catalytic subunit, through
iron-sulfur centers, and the transmembrane subunit
containing the electron acceptor (quinone). The
reversible reduction of quinone is an essential feature
of respiration, allowing transfer of electrons between
respiratory complexes. Proteins in this subfamily from
G. metallireducens and G. sulfurreducens are
bifunctional enzymes with SQR and QFR activities.
Length = 209
Score = 27.6 bits (62), Expect = 1.5
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
+G + MG R V E L ASF P A Y++ +
Sbjct: 116 FGVVGPVSPPMGVGRGDVYELLVASFQQPWIAALYVLAMV 155
>gnl|CDD|219419 pfam07462, MSP1_C, Merozoite surface protein 1 (MSP1) C-terminus.
This family represents the C-terminal region of
merozoite surface protein 1 (MSP1) which are found in a
number of Plasmodium species. MSP-1 is a 200-kDa protein
expressed on the surface of the P. vivax merozoite.
MSP-1 of Plasmodium species is synthesised as a
high-molecular-weight precursor and then processed into
several fragments. At the time of red cell invasion by
the merozoite, only the 19-kDa C-terminal fragment
(MSP-119), which contains two epidermal growth
factor-like domains, remains on the surface. Antibodies
against MSP-119 inhibit merozoite entry into red cells,
and immunisation with MSP-119 protects monkeys from
challenging infections. Hence, MSP-119 is considered a
promising vaccine candidate.
Length = 574
Score = 28.0 bits (62), Expect = 1.5
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 4/77 (5%)
Query: 4 APAAATSTPS----TPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVT 59
P A + PS P +G+ + +T + S L G + Q + Y+ +
Sbjct: 273 TPPQADAAPSPLSVRPAGSSGSASGSTQIPTSGSVLGPGAAATELQQVVQLQNYDEEDDS 332
Query: 60 EALRASFNNPDRAVEYL 76
+ F N D E L
Sbjct: 333 LVVLPIFGNDDDDDEDL 349
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 27.9 bits (63), Expect = 1.7
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 4 APAAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQN 47
A AAA + P+ P + A A A A E T L G + +N
Sbjct: 88 AAAAAAAAPAAPPAAAAAAAPAAAAVEDEVTPLRG-AAAAVAKN 130
>gnl|CDD|182116 PRK09856, PRK09856, fructoselysine 3-epimerase; Provisional.
Length = 275
Score = 27.1 bits (60), Expect = 2.7
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 20 GATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNP 69
GA+ T PG + ++++I+D GYE E + N P
Sbjct: 213 GASDTHYIPGEGKMP------LRELMRDIIDRGYEGYCTVELVTMYMNEP 256
>gnl|CDD|206292 pfam14123, DUF4290, Domain of unknown function (DUF4290). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 200 and 221 amino
acids in length. There are two conserved sequence
motifs: EYGR and KLWD.
Length = 177
Score = 26.7 bits (60), Expect = 2.8
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 40 EYGRMVQNIVD 50
EYGR +Q +VD
Sbjct: 14 EYGRNIQKMVD 24
>gnl|CDD|217043 pfam02450, LACT, Lecithin:cholesterol acyltransferase.
Lecithin:cholesterol acyltransferase (LACT) is involved
in extracellular metabolism of plasma lipoproteins,
including cholesterol.
Length = 377
Score = 27.1 bits (60), Expect = 3.4
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 41 YGRMVQNIVDMGYERSAVTEAL----RASFNNPDR 71
+ ++V+N+V++GYER+ A R S D
Sbjct: 67 WHKVVKNLVNIGYERNKTVSAAPYDWRLSPAERDD 101
>gnl|CDD|202430 pfam02845, CUE, CUE domain. CUE domains have been shown to bind
ubiquitin. It has been suggested that CUE domains are
related to pfam00627 and this has been confirmed by the
structure of the domain. CUE domains also occur in two
protein of the IL-1 signal transduction pathway, tollip
and TAB2.
Length = 42
Score = 24.7 bits (55), Expect = 3.8
Identities = 9/38 (23%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 44 MVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG 79
M++ + +M + + L+AS N + A++ L+ G
Sbjct: 4 MLETLKEMFPDLDEEVIRAVLQASNGNVEAAIDALLEG 41
>gnl|CDD|221084 pfam11336, DUF3138, Protein of unknown function (DUF3138). This
family of proteins with unknown function appear to be
restricted to Proteobacteria.
Length = 514
Score = 26.4 bits (58), Expect = 5.1
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 4 APAAATSTPSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALR 63
PAAA Q+ A A A P + + L D+ +M + I + + ++T+A
Sbjct: 51 KPAAAGGGAK---IQSAAAAAAAAPSSDAAAALTNDDVTQMREQIANQSLKVDSLTDAAT 107
>gnl|CDD|200465 cd11326, AmyAc_Glg_debranch, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities: 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. In Escherichia coli, GlgX is
the debranching enzyme and malQ is the
4-alpha-glucanotransferase. TreX, an archaeal
glycogen-debranching enzyme has dual activities like
mammals and yeast, but is structurally similar to GlgX.
TreX exists in two oligomeric states, a dimer and
tetramer. Isoamylase (EC 3.2.1.68) is one of the
starch-debranching enzymes that catalyzes the hydrolysis
of alpha-1,6-glucosidic linkages specific in
alpha-glucans such as amylopectin or glycogen and their
beta-limit dextrins. The Alpha-amylase family comprises
the largest family of glycoside hydrolases (GH), with
the majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 433
Score = 25.9 bits (58), Expect = 7.1
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 35 LLMGDEYGR 43
LL GDE+GR
Sbjct: 382 LLAGDEFGR 390
>gnl|CDD|139173 PRK12713, flgJ, flagellar rod assembly protein/muramidase FlgJ;
Provisional.
Length = 339
Score = 25.9 bits (56), Expect = 8.3
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 4/75 (5%)
Query: 12 PSTPVSQAGATATATTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNP-D 70
P+ + A A G A L+ D G VQ E +A+ + LR+ N D
Sbjct: 111 PAAAAAGGDAAAARALAGTAAPAPLVRDLRGNYVQPDPAPRREVNALLDVLRS--NRARD 168
Query: 71 RAVEYLITGIPAAVV 85
RA+ G P+ VV
Sbjct: 169 RAMA-AAEGAPSHVV 182
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
0.308 0.124 0.338
Gapped
Lambda K H
0.267 0.0843 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,375,381
Number of extensions: 551466
Number of successful extensions: 592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 590
Number of HSP's successfully gapped: 37
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.0 bits)