RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy517
(138 letters)
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 32.4 bits (74), Expect = 0.063
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 61 QGSGTNRRTRSEDARWECPQCGK-RYKYSRGLAMHRRLECG--KEPMFHCPYCPQKC 114
S E R CP CG Y+ +R +CG EP++ CP C +
Sbjct: 653 DMSDEGGVIEVEVGRRRCPSCGTETYE-------NRCPDCGTHTEPVYVCPDCGAEV 702
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 29.9 bits (68), Expect = 0.41
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 13/64 (20%)
Query: 53 NVDSASEFQGSGTNRRTRSEDARWECPQCGKRYKYSRGLAMHRRLECG--KEPMFHCPYC 110
+++ A++++G+ E R +CP CGK Y R CG EP++ CP C
Sbjct: 609 DINKAAKYKGT-----IEVEIGRRKCPSCGKETFYRRC------PFCGTHTEPVYRCPRC 657
Query: 111 PQKC 114
+
Sbjct: 658 GIEV 661
>gnl|CDD|163618 cd00842, MPP_ASMase, acid sphingomyelinase and related proteins,
metallophosphatase domain. Acid sphingomyelinase
(ASMase) is a ubiquitously expressed phosphodiesterase
which hydrolyzes sphingomyelin in acid pH conditions to
form ceramide, a bioactive second messenger, as part of
the sphingomyelin signaling pathway. ASMase is
localized at the noncytosolic leaflet of biomembranes
(for example the luminal leaflet of endosomes, lysosomes
and phagosomes, and the extracellular leaflet of plasma
membranes). ASMase-deficient humans develop
Niemann-Pick disease. This disease is characterized by
lysosomal storage of sphingomyelin in all tissues.
Although ASMase-deficient mice are resistant to
stress-induced apoptosis, they have greater
susceptibility to bacterial infection. The latter
correlates with defective phagolysosomal fusion and
antibacterial killing activity in ASMase-deficient
macrophages. ASMase belongs to the metallophosphatase
(MPP) superfamily. MPPs are functionally diverse, but
all share a conserved domain with an active site
consisting of two metal ions (usually manganese, iron,
or zinc) coordinated with octahedral geometry by a cage
of histidine, aspartate, and asparagine residues. The
MPP superfamily includes: the phosphoprotein
phosphatases (PPPs), Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 296
Score = 29.6 bits (67), Expect = 0.50
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 7 RRQIVSQFFNHKHQ-VFSSWKEDINIDDMSHFITSSPSNAKPFHNNN 52
I QFF H H+ F + +D + + + +PS P+ NN
Sbjct: 247 SDTIAGQFFGHTHRDEFRVFYDDNDTGEPINVALIAPS-VTPYSGNN 292
>gnl|CDD|200589 cd10967, CE4_GLA_like_6s, Putative catalytic NodB homology domain
of gellan lyase and similar proteins. This family is
represented by the extracellular
polysaccharide-degrading enzyme, gellan lyase
(gellanase, EC 4.2.2.-), from Bacillus sp. The enzyme
acts on gellan exolytically and releases a
tetrasaccharide of glucuronyl-glucosyl-rhamnosyl-glucose
with unsaturated glucuronic acid at the nonreducing
terminus. The family also includes many uncharacterized
prokaryotic polysaccharide deacetylases, which show high
sequence similarity to Bacillus sp. gellan lyase.
Although their biological functions remain unknown, all
members of the family contain a conserved domain with a
6-stranded beta/alpha barrel, which is similar to the
catalytic NodB homology domain of rhizobial NodB-like
proteins, belonging to the larger carbohydrate esterase
4 (CE4) superfamily.
Length = 202
Score = 28.5 bits (64), Expect = 1.0
Identities = 4/29 (13%), Positives = 9/29 (31%)
Query: 83 KRYKYSRGLAMHRRLECGKEPMFHCPYCP 111
+ + +RG+ +P C
Sbjct: 115 RGFIAARGVGGGGNPPNPSDPPADPADCH 143
>gnl|CDD|224487 COG1571, COG1571, Predicted DNA-binding protein containing a
Zn-ribbon domain [General function prediction only].
Length = 421
Score = 28.5 bits (64), Expect = 1.0
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 66 NRRTRSE-DARWECPQCGKRYKYSRGLAMHRRLECGKE 102
R +S + C +CG R + + + R LE G E
Sbjct: 357 GGRMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVE 394
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.5 bits (63), Expect = 1.1
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 72 EDARWECPQCGKRYKYSRGLAMHR 95
+D + C C KRYK GL HR
Sbjct: 395 KDKPYRCEVCDKRYKNLNGLKYHR 418
Score = 27.4 bits (60), Expect = 3.3
Identities = 25/89 (28%), Positives = 37/89 (41%), Gaps = 16/89 (17%)
Query: 15 FNHKHQVFSSWKEDINIDDMSHF----ITSSPSNAKPFHNNN-NVDSASEFQGSGTNRRT 69
F HK + I+ +M T+S SN K H N+D+ S R
Sbjct: 291 FIHKSVGNKEIRGGISTGEMIDVRKLPCTNSSSNGKLAHGGERNIDTPS--------RML 342
Query: 70 RSEDAR-WECP--QCGKRYKYSRGLAMHR 95
+ +D + ++CP C K+YK GL H
Sbjct: 343 KVKDGKPYKCPVEGCNKKYKNQNGLKYHM 371
>gnl|CDD|238698 cd01407, SIR2-fam, SIR2 family of proteins includes silent
information regulator 2 (Sir2) enzymes which catalyze
NAD+-dependent protein/histone deacetylation, where the
acetyl group from the lysine epsilon-amino group is
transferred to the ADP-ribose moiety of NAD+, producing
nicotinamide and the novel metabolite
O-acetyl-ADP-ribose. Sir2 proteins, also known as
sirtuins, are found in all eukaryotes and many archaea
and prokaryotes and have been shown to regulate gene
silencing, DNA repair, metabolic enzymes, and life span.
The most-studied function, gene silencing, involves the
inactivation of chromosome domains containing key
regulatory genes by packaging them into a specialized
chromatin structure that is inaccessible to DNA-binding
proteins. The oligomerization state of Sir2 appears to
be organism-dependent, sometimes occurring as a monomer
and sometimes as a multimer.
Length = 218
Score = 28.3 bits (64), Expect = 1.2
Identities = 12/37 (32%), Positives = 14/37 (37%), Gaps = 5/37 (13%)
Query: 74 ARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYC 110
R C +CGK Y A R E + CP C
Sbjct: 108 FRVRCTKCGKEYPRDELQADIDREE-----VPRCPKC 139
>gnl|CDD|162444 TIGR01607, PST-A, Plasmodium subtelomeric family (PST-A). This
model represents a paralogous family of genes in
Plasmodium falciparum and Plasmodium yoelii which are
closely related to various phospholipases and
lysophospholipases of plants as well as generally being
related to the alpha/beta-fold superfamily of
hydrolases. These genes are preferentially located in
the subtelomeric regions of the chromosomes of both P.
falciparum and P. yoelii.
Length = 332
Score = 28.2 bits (63), Expect = 1.2
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 14 FFNHKHQVFSSWKEDINIDDMSHFITSSPSNAKP 47
F+N K + S KE ++DM H IT P N +
Sbjct: 292 FYN-KLSI--SNKELHTLEDMDHVITIEPGNEEV 322
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 27.5 bits (61), Expect = 1.4
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 3/51 (5%)
Query: 78 CPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVIHIKKKH 128
CP C + S L H R E CP C ++ + + H+ KKH
Sbjct: 76 CPLCLMPFSSSVSLKQHIRY---TEHSKVCPVCGKEFRNTDSTLDHVCKKH 123
>gnl|CDD|235058 PRK02654, PRK02654, putative inner membrane protein translocase
component YidC; Provisional.
Length = 375
Score = 27.6 bits (62), Expect = 2.1
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 20 QVFSSWKEDINIDDMSHF--ITSSPSNAK 46
Q F S ++I I D HF I S P K
Sbjct: 144 QPFKSKPQNIFITDGVHFPVIASLPGGTK 172
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 27.6 bits (62), Expect = 2.6
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 16/55 (29%)
Query: 76 WECPQCG-------KRYKYSRGLAMHRRLECGKEPMFHCPYCPQKC--HQKGNMV 121
CP CG +R K+ +G E + + CP+C H K M+
Sbjct: 201 VPCPHCGEEQELRWERLKWDKG-------EAPETARYVCPHCGCVIEEHHKRAML 248
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or more
acidic residues. The function of members of this family
is unknown.
Length = 104
Score = 26.5 bits (59), Expect = 3.1
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 12/33 (36%)
Query: 78 CPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYC 110
CP CGKR+ Y + K+P+ CP C
Sbjct: 12 CPTCGKRF-Y----------DLNKDPIV-CPKC 32
>gnl|CDD|223915 COG0846, SIR2, NAD-dependent protein deacetylases, SIR2 family
[Transcription].
Length = 250
Score = 26.9 bits (60), Expect = 3.2
Identities = 9/37 (24%), Positives = 12/37 (32%), Gaps = 5/37 (13%)
Query: 74 ARWECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYC 110
R C +CG +Y + P CP C
Sbjct: 121 KRVRCSKCGNQYYDEDVIKFIEDGL---IP--RCPKC 152
>gnl|CDD|224570 COG1656, COG1656, Uncharacterized conserved protein [Function
unknown].
Length = 165
Score = 26.7 bits (59), Expect = 3.2
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 56 SASEFQGSGTNRRTRSEDARWECPQCGKRY 85
S E + + R+ + + CP+CGK Y
Sbjct: 111 SREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140
>gnl|CDD|224297 COG1379, COG1379, PHP family phosphoesterase with a Zn ribbon
[General function prediction only].
Length = 403
Score = 27.1 bits (60), Expect = 3.9
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 67 RRTRSEDA---RWECPQCGKRYK 86
R E+A RW CP+CG + K
Sbjct: 254 TRYSLEEAKSLRWRCPKCGGKIK 276
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 24.1 bits (53), Expect = 5.1
Identities = 7/25 (28%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 105 FHCPYCPQKCHQKGNMVIHIKKKHP 129
+ C +CP K + H+K H
Sbjct: 1 YKCSHCPYSSTPK-KLERHLKLHHG 24
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.0 bits (52), Expect = 5.3
Identities = 5/22 (22%), Positives = 10/22 (45%)
Query: 105 FHCPYCPQKCHQKGNMVIHIKK 126
+ CP C + K + H++
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|115907 pfam07282, OrfB_Zn_ribbon, Putative transposase DNA-binding domain.
This putative domain is found at the C-terminus of a
large number of transposase proteins. This domain
contains four conserved cysteines suggestive of a zinc
binding domain. Given the need for transposases to bind
DNA as well as the large number of DNA-binding zinc
fingers we hypothesise this domain is DNA-binding.
Length = 69
Score = 25.2 bits (56), Expect = 5.5
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 11/51 (21%)
Query: 77 ECPQCGKRYKYSRGLAMHRRLECGKEPMFHCPYCPQKCHQKGNMVIHIKKK 127
C CG + K S R F CP C + N I+I K+
Sbjct: 30 TCSVCGHKNKESL----SGRT-------FKCPNCGFVADRDVNAAINILKR 69
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 201
Score = 26.1 bits (58), Expect = 5.8
Identities = 10/46 (21%), Positives = 17/46 (36%), Gaps = 12/46 (26%)
Query: 22 FSSW-----KEDINIDDMSHFIT-------SSPSNAKPFHNNNNVD 55
F W KE+INI++ F+ + +P +N
Sbjct: 143 FIGWFETSAKENINIEEAMRFLVKNILKNDKGLQSPEPDEDNVIDL 188
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 23.8 bits (51), Expect = 6.6
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 105 FHCPYCPQKCHQKGNMVIHIKKKH 128
F CP C + K + H++K H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|232935 TIGR00354, polC, DNA polymerase, archaeal type II, large subunit.
This model represents the large subunit, DP2, of a two
subunit novel Archaeal replicative DNA polymerase first
characterized for Pyrococcus furiosus. Structure of DP2
appears to be organized as a ~950 residue component
separated from a ~300 residue component by a ~150 residue
intein. The other subunit, DP1, has sequence similarity
to the eukaryotic DNA polymerase delta small subunit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 1095
Score = 26.4 bits (58), Expect = 7.4
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 7/49 (14%)
Query: 34 MSHFITSSPSNAKPFHNNNNVDSASEFQGSGTNRRTRSEDARWECPQCG 82
SHF+ N + F S E + + N + R +C +CG
Sbjct: 994 NSHFLPDIIGNLRAF-------SRQEVRCTKCNTKYRRIPLVGKCLKCG 1035
>gnl|CDD|215494 PLN02915, PLN02915, cellulose synthase A [UDP-forming], catalytic
subunit.
Length = 1044
Score = 26.0 bits (57), Expect = 8.2
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 78 CPQCGKRYKYSRGLA 92
CPQC RYK +G
Sbjct: 60 CPQCNTRYKRHKGCP 74
>gnl|CDD|143409 cd07090, ALDH_F9_TMBADH, NAD+-dependent
4-trimethylaminobutyraldehyde dehydrogenase, ALDH
family 9A1. NAD+-dependent,
4-trimethylaminobutyraldehyde dehydrogenase (TMABADH,
EC=1.2.1.47), also known as aldehyde dehydrogenase
family 9 member A1 (ALDH9A1) in humans, is a cytosolic
tetramer which catalyzes the oxidation of
gamma-aminobutyraldehyde involved in 4-aminobutyric
acid (GABA) biosynthesis and also oxidizes betaine
aldehyde (gamma-trimethylaminobutyraldehyde) which is
involved in carnitine biosynthesis.
Length = 457
Score = 25.7 bits (57), Expect = 9.1
Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 68 RTRSED-ARWECPQCGKRYKYSR 89
R R+++ AR E GK + +R
Sbjct: 55 RERNDEIARLETIDNGKPIEEAR 77
>gnl|CDD|215343 PLN02638, PLN02638, cellulose synthase A (UDP-forming), catalytic
subunit.
Length = 1079
Score = 26.0 bits (57), Expect = 9.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 72 EDARWECPQCGKRYKYSRG 90
+D CPQC +YK +G
Sbjct: 56 KDGNQSCPQCKTKYKRHKG 74
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
0.319 0.131 0.425
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,725,687
Number of extensions: 532808
Number of successful extensions: 744
Number of sequences better than 10.0: 1
Number of HSP's gapped: 739
Number of HSP's successfully gapped: 58
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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 (21.8 bits)
S2: 54 (24.7 bits)