RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1883
(81 letters)
>gnl|CDD|192200 pfam09058, L27_1, L27_1. The L27 domain is a protein interaction
module that exists in a large family of scaffold
proteins, functioning as an organisation centre of
large protein assemblies required for the establishment
and maintenance of cell polarity. L27 domains form
specific heterotetrameric complexes, in which each
domain contains three alpha-helices.
Length = 63
Score = 71.4 bits (175), Expect = 1e-18
Identities = 28/44 (63%), Positives = 35/44 (79%)
Query: 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALL 61
+ RAL+LLE+Y SKL+ D+ LRS+IERVI IF+S LFQALL
Sbjct: 6 DTQRALQLLEEYQSKLSQTGDRGLRSSIERVINIFQSDLFQALL 49
>gnl|CDD|197794 smart00569, L27, domain in receptor targeting proteins Lin-2 and
Lin-7.
Length = 53
Score = 31.7 bits (73), Expect = 0.004
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 8/43 (18%)
Query: 20 HRALELLEDYHSKLTDPSDKQ-LRSAIERVIRIFKSRLFQALL 61
R LELLE+ S L+ D Q LR R+ +S QALL
Sbjct: 1 QRLLELLEELQSLLSPSEDLQELR-------RLLQSPHLQALL 36
>gnl|CDD|215101 PLN00203, PLN00203, glutamyl-tRNA reductase.
Length = 519
Score = 26.6 bits (59), Expect = 1.6
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 13 LLNYLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRL 56
L +Y E RA EL E SK+ D K+ R A+E + R ++L
Sbjct: 437 LRSYAERIRAAEL-EKCLSKMGDDLTKKQRKAVEDLSRGIVNKL 479
>gnl|CDD|217123 pfam02585, PIG-L, GlcNAc-PI de-N-acetylase. Members of this family
are related to PIG-L an
N-acetylglucosaminylphosphatidylinositol de-N-acetylase
(EC:3.5.1.89) that catalyzes the second step in GPI
biosynthesis.
Length = 115
Score = 25.8 bits (57), Expect = 1.8
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 8/44 (18%)
Query: 18 EAHRALELL--EDYH------SKLTDPSDKQLRSAIERVIRIFK 53
EA A E+L E L + ++L +A+ R+IR +
Sbjct: 57 EARAAAEILGVERVIFLDLPDGGLREWDLEELLAALARLIREIR 100
>gnl|CDD|224295 COG1377, FlhB, Flagellar biosynthesis pathway, component FlhB
[Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 363
Score = 26.0 bits (58), Expect = 2.2
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 31 SKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQLGGAIGISVLGIF 76
K P+ K+LR A E+ ++ KSR + L G + + G +
Sbjct: 8 EKTEKPTPKKLRDAREKG-QVPKSRELTSAASLLVGFLLLFFFGSY 52
>gnl|CDD|224105 COG1184, GCD2, Translation initiation factor 2B subunit, eIF-2B
alpha/beta/delta family [Translation, ribosomal
structure and biogenesis].
Length = 301
Score = 25.8 bits (57), Expect = 2.4
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 19 AHRALELLEDYHSKLTDPSDKQLRSAIERVI-RIFKSR 55
A A E LE S P+ ++L AI + + K+R
Sbjct: 25 AIAAAEALEILASDSQAPTVEELIDAIRELSETLVKAR 62
>gnl|CDD|173839 cd01150, AXO, Peroxisomal acyl-CoA oxidase. Peroxisomal acyl-CoA
oxidases (AXO) catalyze the first set in the peroxisomal
fatty acid beta-oxidation, the alpha,beta
dehydrogenation of the corresponding trans-enoyl-CoA by
FAD, which becomes reduced. In a second oxidative
half-reaction, the reduced FAD is reoxidized by
molecular oxygen. AXO is generally a homodimer, but it
has been reported to form a different type of oligomer
in yeast. There are several subtypes of AXO's, based on
substrate specificity. Palmitoyl-CoA oxidase acts on
straight-chain fatty acids and prostanoids; whereas, the
closely related Trihydroxycoprostanoly-CoA oxidase has
the greatest activity for 2-methyl branched side chains
of bile precursors. Pristanoyl-CoA oxidase, acts on
2-methyl branched fatty acids. AXO has an additional
domain, C-terminal to the region with similarity to
acyl-CoA dehydrogenases, which is included in this
alignment.
Length = 610
Score = 25.8 bits (57), Expect = 2.4
Identities = 9/41 (21%), Positives = 21/41 (51%)
Query: 8 LSTYYLLNYLEAHRALELLEDYHSKLTDPSDKQLRSAIERV 48
S +L +AH +L+ +H + + D +R+ ++R+
Sbjct: 490 NSQVHLRCAAKAHTEYTVLQRFHESVEEIVDPSVRAVLKRL 530
>gnl|CDD|236932 PRK11564, PRK11564, stationary phase inducible protein CsiE;
Provisional.
Length = 426
Score = 25.7 bits (57), Expect = 2.8
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 28 DYHSKLTDPSDKQLRSAIERVIRIFK 53
D D++LR AI+R++ F+
Sbjct: 222 DPLRD-AHQRDRRLRQAIKRLVNRFR 246
>gnl|CDD|218980 pfam06299, DUF1045, Protein of unknown function (DUF1045). This
family consists of several hypothetical proteins from
Agrobacterium, Rhizobium and Brucella species. The
function of this family is unknown.
Length = 160
Score = 25.2 bits (56), Expect = 3.7
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 6/40 (15%)
Query: 26 LEDY--HSKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQ 63
+++ H LT D R A+E + F LL +
Sbjct: 104 FDEFRFHMTLTGRLDAAERPAVEAALA----ARFAPLLPE 139
>gnl|CDD|187751 cd09270, RNase_H2-B, Ribonuclease H2-B is a subunit of the
eukaryotic RNase H complex which cleaves RNA-DNA
hybrids. Ribonuclease H2B is one of the three proteins
of eukaryotic RNase H2 complex that is required for
nucleic acid binding and hydrolysis. RNase H is
classified into two families, type I (prokaryotic RNase
HI, eukaryotic RNase H1 and viral RNase H) and type II
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2/HII). RNase H endonucleolytically hydrolyzes an RNA
strand when it is annealed to a complementary DNA strand
in the presence of divalent cations, in DNA replication
and repair. The enzyme can be found in bacteria,
archaea, and eukaryotes. Most prokaryotic and eukaryotic
genomes contain multiple RNase H genes. Despite a lack
of evidence for homology from sequence comparisons, type
I and type II RNase H share a common fold and similar
steric configurations of the four acidic active-site
residues, suggesting identical or very similar catalytic
mechanisms. Eukaryotic RNase HII is active during
replication and is believed to play a role in removal of
Okazaki fragment primers and single ribonucleotides in
DNA-DNA duplexes. Eukaryotic RNase HII is functional
when it forms a complex with RNase H2B and RNase H2C
proteins. It is speculated that the two accessory
subunits are required for correct folding of the
catalytic subunit of RNase HII. Mutations in the three
subunits of human RNase HII cause neurological disorder.
Length = 211
Score = 25.3 bits (56), Expect = 3.9
Identities = 9/38 (23%), Positives = 12/38 (31%), Gaps = 5/38 (13%)
Query: 10 TYYLLNYLEAHRALEL-----LEDYHSKLTDPSDKQLR 42
+ LL L L+D L+ PS L
Sbjct: 75 LFLLLPILYKADNKFAGKFLTLDDILDDLSSPSSHLLE 112
>gnl|CDD|222071 pfam13359, DDE_4, DDE superfamily endonuclease. This family of
proteins are related to pfam00665 and are probably
endonucleases of the DDE superfamily. Transposase
proteins are necessary for efficient DNA transposition.
This domain is a member of the DDE superfamily, which
contain three carboxylate residues that are believed to
be responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction.
Length = 155
Score = 25.3 bits (56), Expect = 4.0
Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 40 QLRSAIERVIRIFKSRLFQAL 60
R +ERVI K R F+ L
Sbjct: 112 SARIHVERVIGRLKGR-FRIL 131
>gnl|CDD|176159 cd08470, PBP2_CrgA_like_1, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding domain. This CD represents the substrate
binding domain of an uncharacterized LysR-type
transcriptional regulator (LTTR) CrgA-like 1. The LTTRs
are acting as both auto-repressors and activators of
target promoters, controlling operons involved in a wide
variety of cellular processes such as amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to name a few. In contrast to the tetrameric
form of other LTTRs, CrgA from Neisseria meningitides
assembles into an octameric ring, which can bind up to
four 63-bp DNA oligonucleotides. Phylogenetic cluster
analysis showed that the CrgA-like regulators form a
subclass of the LTTRs that function as octamers. The
CrgA is an auto-repressor of its own gene and activates
the expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is increased
by MBL (alpha-methylene-gamma-butyrolactone), an inducer
of NADPH-quinone oxidoreductase. The structural
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 25.0 bits (55), Expect = 4.3
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 7 ELSTYYLLNYLEAHRALELLEDY 29
+L YY+ +L A R + +LEDY
Sbjct: 143 QLPDYYVDEHLAAGRLVPVLEDY 165
>gnl|CDD|234565 PRK00002, aroB, 3-dehydroquinate synthase; Reviewed.
Length = 358
Score = 25.1 bits (56), Expect = 4.6
Identities = 9/29 (31%), Positives = 10/29 (34%)
Query: 23 LELLEDYHSKLTDPSDKQLRSAIERVIRI 51
E LE L + L AI R I
Sbjct: 194 FEWLEANVDALLALDGEALEEAIARSCEI 222
>gnl|CDD|223014 PHA03231, PHA03231, glycoprotein BALF4; Provisional.
Length = 829
Score = 24.9 bits (55), Expect = 5.0
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 45 IERVIRIFKSRLFQAL------LGQLGGAIGISVLGIF 76
I+ VI ++ + L LG +G A+G V G+
Sbjct: 649 IDNVIDNDRNAFVRGLAEFMQGLGAVGKAVGNVVSGVA 686
>gnl|CDD|226900 COG4517, COG4517, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 109
Score = 24.8 bits (54), Expect = 5.0
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 6 KELSTYYLLNYLEAHRALELLEDYHSKL-TDPSDKQLRSAIERVIRIF 52
+ + + +L + E E + D HS L DPS+++L+ V R
Sbjct: 24 RCIISSHLWGFNEIS---EFVFDVHSGLVVDPSEEKLKHEFAGVKRSH 68
>gnl|CDD|212064 cd11495, SLC5sbd_NIS-like_u3, uncharacterized subgroup of the
Na(+)/iodide (NIS) cotransporter subfamily; putative
solute-binding domain. Proteins belonging to the same
subfamily as this uncharacterized subgroup include i)
NIS, which transports I-, and other anions including
ClO4-, SCN-, and Br-, ii) SMVT, which transports biotin,
pantothenic acid and lipoate, and iii) the
Na(+)/monocarboxylate cotransporters SMCT1 and 2. SMCT1
is a high-affinity transporter while SMCT2 is a
low-affinity transporter. This subgroup belongs to the
solute carrier 5 (SLC5) transporter family.
Length = 477
Score = 24.8 bits (55), Expect = 5.8
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 56 LFQALLGQLGGAI-GISVLGIF 76
LF L G GG + G+ +LGIF
Sbjct: 399 LFLKLTGLFGGGLAGLFLLGIF 420
>gnl|CDD|219193 pfam06824, DUF1237, Protein of unknown function (DUF1237). This
family contains a number of hypothetical proteins of
about 450 residues in length. Their function is unknown,
and most are bacterial. However, structurally this
family is part of the 6 hairpin glycosidase superfamily,
suggesting a glycosyl hydrolase function.
Length = 403
Score = 24.8 bits (55), Expect = 6.2
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 23 LELLEDYH--SKLTDPSDKQLRSAIERVIRIFK 53
L L Y + TD D++ A+E ++R+F+
Sbjct: 122 LRLAYLYWKATGDTDFFDEEWIKAVETILRVFE 154
>gnl|CDD|148359 pfam06711, DUF1198, Protein of unknown function (DUF1198). This
family consists of several bacterial proteins of around
150 residues in length which are specific to Escherichia
coli, Salmonella species and Yersinia pestis. The
function of this family is unknown.
Length = 148
Score = 24.4 bits (53), Expect = 6.3
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 1 MGPRKKELSTYYLLNYLEAH--RALELLEDYHSKLTDPSDKQLRSAIERVIR 50
MG + YL E H A ++L + + + D SD+ L+ +I+
Sbjct: 49 MGKTAGQEFIRYLERPDEEHLQNAAQVLLIWQTFIVDASDENLQLWRRLLIK 100
>gnl|CDD|223134 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy
production and conversion].
Length = 504
Score = 24.5 bits (54), Expect = 7.3
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 12 YLLNYLEAHRALELLEDYHSK--LTDPSDKQLRSAIERVIRIFK 53
LL YL + ELLE+ + L D + +L++AI+ + F
Sbjct: 459 ELLAYLRSDHK-ELLEEIRTTKELDDEIEAKLKAAIKEFKKTFA 501
>gnl|CDD|99967 cd03793, GT1_Glycogen_synthase_GSY2_like, Glycogen synthase, which
is most closely related to the GT1 family of
glycosyltransferases, catalyzes the transfer of a
glucose molecule from UDP-glucose to a terminal branch
of a glycogen molecule, a rate-limit step of glycogen
biosynthesis. GSY2, the member of this family in S.
cerevisiae, has been shown to possess glycogen synthase
activity.
Length = 590
Score = 24.6 bits (54), Expect = 7.4
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 39 KQLRSAIERVIRIFKSRLFQALL 61
KQLR + V RLF+A L
Sbjct: 362 KQLRDTVNSVKEKIGKRLFEAAL 384
>gnl|CDD|216050 pfam00665, rve, Integrase core domain. Integrase mediates
integration of a DNA copy of the viral genome into the
host chromosome. Integrase is composed of three domains.
The amino-terminal domain is a zinc binding domain
pfam02022. This domain is the central catalytic domain.
The carboxyl terminal domain that is a non-specific DNA
binding domain pfam00552. The catalytic domain acts as
an endonuclease when two nucleotides are removed from
the 3' ends of the blunt-ended viral DNA made by reverse
transcription. This domain also catalyzes the DNA strand
transfer reaction of the 3' ends of the viral DNA to the
5' ends of the integration site.
Length = 113
Score = 24.2 bits (53), Expect = 7.4
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 2/40 (5%)
Query: 19 AHRALELLEDYH--SKLTDPSDKQLRSAIERVIRIFKSRL 56
+ ELL++ + P + Q +ER R K L
Sbjct: 74 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 113
>gnl|CDD|239729 cd03760, proteasome_beta_type_4, proteasome beta type-4 subunit.
The 20S proteasome, multisubunit proteolytic complex, is
the central enzyme of nonlysosomal protein degradation
in both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis.Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 197
Score = 24.1 bits (53), Expect = 9.6
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 19 AHRALELLEDYHSKLTDPSDKQLRSAIERVIRI 51
A+ AL LL + K D ++++ R+ IE +++
Sbjct: 138 AYLALPLLREAWEKKPDLTEEEARALIEECMKV 170
>gnl|CDD|236448 PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
Length = 502
Score = 24.3 bits (54), Expect = 9.7
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 13 LLNYLEAHRALELLEDYHS--KLTDPSDKQLRSAIERVIRIFKS 54
LL YL ++ A +LLE+ L+D + +L++AIE + F +
Sbjct: 460 LLAYLRSNHA-DLLEEIRETKDLSDEIEAKLKAAIEEFKKTFAA 502
>gnl|CDD|185108 PRK15186, PRK15186, AraC family transcriptional regulator;
Provisional.
Length = 291
Score = 24.3 bits (52), Expect = 9.7
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 28 DYHSKLTDPSDKQLRSAIER-VIRIF 52
D+ + LT P+ K L + IE V R+F
Sbjct: 111 DFSAPLTKPTTKHLLAPIETGVARVF 136
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
0.324 0.142 0.409
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,300,737
Number of extensions: 351125
Number of successful extensions: 590
Number of sequences better than 10.0: 1
Number of HSP's gapped: 589
Number of HSP's successfully gapped: 38
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.0 bits)