RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4648
(116 letters)
>gnl|CDD|153426 cd07997, WGR_PARP, WGR domain of poly(ADP-ribose) polymerases. The
WGR domain is found in a variety of eukaryotic
poly(ADP-ribose) polymerases (PARPs). It has been called
WGR after the most conserved central motif of the
domain. The domain typically occurs together with a
catalytic PARP domain, and is between 70 and 80 residues
in length. It has been proposed to function as a nucleic
acid binding domain. PARPs catalyze the NAD(+)-dependent
synthesis of ADP-ribose polymers and their addition to
various nuclear proteins and histones. Higher eukaryotes
contain several PARPs and there may be up to 17 human
PARP-like proteins, with three of them (PARP-1, PARP-2,
and PARP-3) containing a WGR domain. The synthesis of
poly-ADP-ribose requires multiple enzymatic activities
for initiation, trans-ADP-ribosylation, elongation,
branching, and release of the polymer from the enzyme.
Poly-ADP-ribosylation was thought to be a reversible
post-translational covalent modification that serves as
a regulatory mechanism for protein substrates. However,
it is now known that it plays important roles in many
cellular processes including maintenance of genomic
stability, transcriptional regulation, energy
metabolism, cell death and survival, among others.
Length = 102
Score = 28.8 bits (65), Expect = 0.32
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 92 TDMSNNTNSTKKSQIIHSDNHDM 114
TD+SNN N K QI+ S +
Sbjct: 17 TDISNNNNKFYKIQILESKGPNT 39
>gnl|CDD|215647 pfam00002, 7tm_2, 7 transmembrane receptor (Secretin family). This
family is known as Family B, the secretin-receptor
family or family 2 of the G-protein-coupled receptors
(GCPRs).They have been described in many animal species,
but not in plants, fungi or prokaryotes. Three distinct
sub-families are recognised. Subfamily B1 contains
classical hormone receptors, such as receptors for
secretin and glucagon, that are all involved in
cAMP-mediated signalling pathways. Subfamily B2 contains
receptors with long extracellular N-termini, such as the
leukocyte cell-surface antigen CD97 ;
calcium-independent receptors for latrotoxin, and
brain-specific angiogenesis inhibitors amongst others.
Subfamily B3 includes Methuselah and other Drosophila
proteins. Other than the typical seven-transmembrane
region, characteristic structural features include an
amino-terminal extracellular domain involved in ligand
binding, and an intracellular loop (IC3) required for
specific G-protein coupling.
Length = 239
Score = 28.7 bits (65), Expect = 0.48
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 20 LALIMGLTWSVGLFA-GYIDNEPLWYAFIALNTLQGVFI 57
L ++G+TW + LFA + Y F LN+ QG F+
Sbjct: 201 LLPLLGITWILFLFAPEDDVSIVFLYLFAILNSFQGFFV 239
>gnl|CDD|222819 PHA01077, PHA01077, putative lower collar protein.
Length = 251
Score = 27.8 bits (61), Expect = 1.4
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 11/79 (13%)
Query: 36 YIDNEPLW---YAFIALNTLQGVFIFLAFTCTNKMIRNLFKSSSSINRPIRPASFSCSNT 92
++D E AF + V I T++ N+ SSS + + ++ F+ N
Sbjct: 81 FLDREINRQTVEAFGM--QVITVCI------THEDYLNVVYSSSEVEKYLQSQGFTEHNE 132
Query: 93 DMSNNTNSTKKSQIIHSDN 111
D +NNT+ T DN
Sbjct: 133 DTTNNTDETSNQNATSLDN 151
>gnl|CDD|227064 COG4720, COG4720, Predicted membrane protein [Function unknown].
Length = 177
Score = 26.2 bits (58), Expect = 3.4
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 18 VRLALIMGLTWSVG--LFAGYIDNEPLWYAFIALNT 51
+ L +++GL VG L A Y+D A + T
Sbjct: 108 IWLGIVLGLAIMVGWYLLAPYLDYLGWAEALGKIGT 143
>gnl|CDD|219445 pfam07517, SecA_DEAD, SecA DEAD-like domain. SecA protein binds to
the plasma membrane where it interacts with proOmpA to
support translocation of proOmpA through the membrane.
SecA protein achieves this translocation, in association
with SecY protein, in an ATP dependent manner. This
domain represents the N-terminal ATP-dependent helicase
domain, which is related to the pfam00270.
Length = 381
Score = 26.3 bits (59), Expect = 3.5
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 3 EITASSSTQRDFRLYVRLALIMGLT 27
+ AS + Q FRLY +LA G+T
Sbjct: 349 QTLASITYQNFFRLYPKLA---GMT 370
>gnl|CDD|233882 TIGR02474, pec_lyase, pectate lyase, PelA/Pel-15E family. Members
of this family are isozymes of pectate lyase (EC
4.2.2.2), also called polygalacturonic transeliminase
and alpha-1,4-D-endopolygalacturonic acid lyase [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 290
Score = 26.3 bits (58), Expect = 3.6
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 38 DNEPLWYAFIALNTLQGVF 56
+ LW F L+T + F
Sbjct: 239 GAKVLWARFYDLDTNRPFF 257
>gnl|CDD|224500 COG1584, COG1584, Predicted membrane protein [Function unknown].
Length = 207
Score = 25.4 bits (56), Expect = 6.8
Identities = 19/53 (35%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 20 LALIMGLTWSVGLFAGYIDNEPLWYAFIALNTLQGVFIFLAFTCTNKMIRNLF 72
LALI+ + GY+D PL A L G+F L F T K R L
Sbjct: 94 LALILLMPK--LGILGYLDPAPLANALGWYLILWGIFTLLMFIGTLKSTRALQ 144
>gnl|CDD|217862 pfam04051, TRAPP, Transport protein particle (TRAPP) component.
TRAPP plays a key role in the targeting and/or fusion of
ER-to-Golgi transport vesicles with their acceptor
compartment. TRAPP is a large multimeric protein that
contains at least 10 subunits. This family contains many
TRAPP family proteins. The Bet3 subunit is one of the
better characterized TRAPP proteins and has a dimeric
structure with hydrophobic channels. The channel
entrances are located on a putative membrane-interacting
surface that is distinctively flat, wide and decorated
with positively charged residues. Bet3 is proposed to
localise TRAPP to the Golgi.
Length = 148
Score = 25.2 bits (56), Expect = 7.4
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 37 IDNEPLWYAFIALNTLQGVFIFLAFTC 63
IDN+ F+ L +L F C
Sbjct: 85 IDNDNPLSQFVELPPDYSGLNYLNFLC 111
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 25.3 bits (55), Expect = 8.5
Identities = 11/51 (21%), Positives = 19/51 (37%)
Query: 63 CTNKMIRNLFKSSSSINRPIRPASFSCSNTDMSNNTNSTKKSQIIHSDNHD 113
C + + R S SS R S +++ S +T K+ I +
Sbjct: 122 CHDAVSRLERNSYSSAARRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRS 172
>gnl|CDD|234350 TIGR03766, TIGR03766, conserved hypothetical integral membrane
protein. Models TIGR03110, TIGR03111, and TIGR03112
describe a three-gene system found in several
Gram-positive bacteria, where TIGR03110 (XrtG) is
distantly related to a putative transpeptidase,
exosortase (TIGR02602). This model describes a small
clade that correlates by both gene clustering and
phyletic pattern, although imperfectly, to the three
gene system. Both this narrow clade, and the larger set
of full-length homologous integral membrane proteins,
have an especially well-conserved region near the
C-terminus with an invariant tyrosine. The function is
unknown.
Length = 483
Score = 25.3 bits (56), Expect = 9.0
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 13 DFRLYVRLALIMGLTWSVGLFAGYIDNEPLWYAFIALNTLQGVFIFL 59
DFR + I+ L + + N+ + L + G F+FL
Sbjct: 408 DFRFIAQFIWILSL---GIIIFAWFRNKDDKSLVLRL-AIFGGFLFL 450
>gnl|CDD|216766 pfam01889, DUF63, Membrane protein of unknown function DUF63.
Proteins found in Archaebacteria of unknown function.
These proteins are probably transmembrane proteins.
Length = 272
Score = 25.3 bits (56), Expect = 9.0
Identities = 11/73 (15%), Positives = 26/73 (35%), Gaps = 2/73 (2%)
Query: 4 ITASSSTQRDFRLYVRLALIMGLTWSVGLFAGYIDNEP--LWYAFIALNTLQGVFIFLAF 61
+ S + + Y +L +GL ++ + NE + +A+ L V L +
Sbjct: 102 LLISGKLFKAGKDYYKLFAAVGLILALINLGLLLVNEKITHPWVLVAVVGLVSVATALIY 161
Query: 62 TCTNKMIRNLFKS 74
+ ++
Sbjct: 162 LLAKPLKLSIMTD 174
>gnl|CDD|219516 pfam07690, MFS_1, Major Facilitator Superfamily.
Length = 346
Score = 25.5 bits (56), Expect = 9.4
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 19 RLALIMGLTWSVGLFAGYIDNEPLWYAFIALNTLQGVFIFLAFTCTNKMIRNLFK 73
R+ LI L +++GL + + + L LQG+ F +I + F
Sbjct: 63 RVLLIGLLLFALGLLLLLFASS--LWLLLVLRVLQGLGGGALFPAAAALIADWFP 115
>gnl|CDD|204272 pfam09618, Cas_Csy4, CRISPR-associated protein (Cas_Csy4). CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) is a widespread family of prokaryotic direct
repeats with spacers of unique sequence between
consecutive repeats. This protein family, typified by
YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas)
family strictly associated with the Ypest subtype of
CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas
Subtype Ypest protein 4.
Length = 182
Score = 24.9 bits (55), Expect = 9.5
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 7 SSSTQRDFRLYVRLALIMGLTWSVGLFAGY 36
S ST + FRL++ + GLF Y
Sbjct: 143 SLSTGQRFRLFIEQKELQPEP-VSGLFNSY 171
>gnl|CDD|220594 pfam10136, SpecificRecomb, Site-specific recombinase. Members of
this family of bacterial proteins are found in various
putative site-specific recombinase transmembrane
proteins.
Length = 647
Score = 25.2 bits (56), Expect = 9.7
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 21 ALIMG-LTWSVGLFAGYIDNEPLWYAF 46
A I G L + L AG+ DN W+ +
Sbjct: 477 AAITGVLLFLSSLIAGWADN---WFVY 500
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
0.323 0.133 0.397
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,484,998
Number of extensions: 451587
Number of successful extensions: 638
Number of sequences better than 10.0: 1
Number of HSP's gapped: 636
Number of HSP's successfully gapped: 52
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)