RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12932
(107 letters)
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab)
or POZ (for Pox virus and Zinc finger) domain is
present near the N-terminus of a fraction of zinc
finger (pfam00096) proteins and in proteins that
contain the pfam01344 motif such as Kelch and a family
of pox virus proteins. The BTB/POZ domain mediates
homomeric dimerisation and in some instances
heteromeric dimerisation. The structure of the
dimerised PLZF BTB/POZ domain has been solved and
consists of a tightly intertwined homodimer. The
central scaffolding of the protein is made up of a
cluster of alpha-helices flanked by short beta-sheets
at both the top and bottom of the molecule. POZ domains
from several zinc finger proteins have been shown to
mediate transcriptional repression and to interact with
components of histone deacetylase co-repressor
complexes including N-CoR and SMRT. The POZ or BTB
domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 46.1 bits (110), Expect = 8e-08
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 25 LYQLLKMESMVDVTLKAEGEAFQAHRIILSASSPFFQN 62
L +L + + DVTL + F AH+ +L+A SP+F+
Sbjct: 1 LNELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFKA 38
Score = 45.7 bits (109), Expect = 1e-07
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 71 LYQLLKMESMVDVTLKAEGEAFQAHRIILSASSPFFQ 107
L +L + + DVTL + F AH+ +L+A SP+F+
Sbjct: 1 LNELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFK 37
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac.
Domain in Broad-Complex, Tramtrack and Bric a brac.
Also known as POZ (poxvirus and zinc finger) domain.
Known to be a protein-protein interaction motif found
at the N-termini of several C2H2-type transcription
factors as well as Shaw-type potassium channels. Known
structure reveals a tightly intertwined dimer formed
via interactions between N-terminal strand and helix
structures. However in a subset of BTB/POZ domains,
these two secondary structures appear to be missing. Be
aware SMART predicts BTB/POZ domains without the beta1-
and alpha1-secondary structures.
Length = 97
Score = 38.8 bits (91), Expect = 4e-05
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 36 DVTLKAEGEAFQAHRIILSASSPFFQN 62
DVTL G+ F AH+ +L+A SP+F+
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFKA 27
Score = 38.4 bits (90), Expect = 5e-05
Identities = 13/26 (50%), Positives = 19/26 (73%)
Query: 82 DVTLKAEGEAFQAHRIILSASSPFFQ 107
DVTL G+ F AH+ +L+A SP+F+
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFK 26
>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
Length = 534
Score = 30.9 bits (70), Expect = 0.10
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 34 MVDVTLKAEGEAFQAHRIILSASSPFFQNF 63
+ + G + H+IILS+SS +F+
Sbjct: 11 DESIIIVNGGGIIKVHKIILSSSSEYFKKM 40
Score = 28.6 bits (64), Expect = 0.52
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 80 MVDVTLKAEGEAFQAHRIILSASSPFF 106
+ + G + H+IILS+SS +F
Sbjct: 11 DESIIIVNGGGIIKVHKIILSSSSEYF 37
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 30.7 bits (70), Expect = 0.12
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 31 MESMVDVTLKAEGEAFQAHRIILS 54
+E MVD L EG+ +RI+ S
Sbjct: 221 LEHMVDTVLYFEGDRHSEYRILRS 244
Score = 30.7 bits (70), Expect = 0.12
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 77 MESMVDVTLKAEGEAFQAHRIILS 100
+E MVD L EG+ +RI+ S
Sbjct: 221 LEHMVDTVLYFEGDRHSEYRILRS 244
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 28.9 bits (66), Expect = 0.49
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 31 MESMVDVTLKAEGEAFQAHRII 52
+E MVD L EG+ +RI+
Sbjct: 219 LEHMVDTVLYFEGDRHSRYRIL 240
Score = 28.9 bits (66), Expect = 0.49
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 77 MESMVDVTLKAEGEAFQAHRII 98
+E MVD L EG+ +RI+
Sbjct: 219 LEHMVDTVLYFEGDRHSRYRIL 240
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 28.0 bits (63), Expect = 0.82
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 31 MESMVDVTLKAEGEAFQAHRII 52
+E MVD L EG+ +RI+
Sbjct: 231 LEHMVDTVLYFEGDRHSRYRIL 252
Score = 28.0 bits (63), Expect = 0.82
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 77 MESMVDVTLKAEGEAFQAHRII 98
+E MVD L EG+ +RI+
Sbjct: 231 LEHMVDTVLYFEGDRHSRYRIL 252
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 28.1 bits (62), Expect = 0.92
Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 28 LLKMESMVDVTLK-AEGEAFQAHRIILSASSPFFQ 61
LL + + DV + +GE +AH+ IL+A S +F+
Sbjct: 19 LLDDDILCDVIITIGDGEEIKAHKTILAAGSKYFR 53
Score = 28.1 bits (62), Expect = 0.92
Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 74 LLKMESMVDVTLK-AEGEAFQAHRIILSASSPFFQ 107
LL + + DV + +GE +AH+ IL+A S +F+
Sbjct: 19 LLDDDILCDVIITIGDGEEIKAHKTILAAGSKYFR 53
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 27.5 bits (61), Expect = 1.3
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 31 MESMVDVTLKAEGEAFQAHRIILSASSPF 59
+E MVD L EG+ RI+ S + F
Sbjct: 233 LEHMVDTVLYFEGDRDSRFRILRSVKNRF 261
Score = 27.5 bits (61), Expect = 1.3
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 77 MESMVDVTLKAEGEAFQAHRIILSASSPF 105
+E MVD L EG+ RI+ S + F
Sbjct: 233 LEHMVDTVLYFEGDRDSRFRILRSVKNRF 261
>gnl|CDD|237407 PRK13516, PRK13516, gamma-glutamyl:cysteine ligase; Provisional.
Length = 373
Score = 27.6 bits (62), Expect = 1.3
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 49 HRIILSASSPFFQ 61
H I LSASSP+ Q
Sbjct: 160 HFIALSASSPYVQ 172
Score = 27.6 bits (62), Expect = 1.3
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 95 HRIILSASSPFFQ 107
H I LSASSP+ Q
Sbjct: 160 HFIALSASSPYVQ 172
>gnl|CDD|188553 TIGR04038, tatD_link_rSAM, radical SAM protein, TatD
family-associated. Members of this family are radical
SAM proteins found in about 5 percent of microbial
genomes. A portion occur as gene fusions with, or
adjacent to, members of the TatD family of hydrolases
(pfam01026). The TatD family may have several paralogs
per genome, including TatD itself from E. coli (a
soluble protein not actually part of the twin-arginine
translocation complex), which appears to act in quality
control for TAT, directing turnover of misfolded TAT
substrates. The functions of TatD family hydrolases in
general (other than TatD itself, which may be
exceptional within its larger family), and of this
radical SAM domain protein modeled here, are unknown.
Length = 191
Score = 25.3 bits (56), Expect = 6.2
Identities = 6/11 (54%), Positives = 8/11 (72%)
Query: 10 FCMKWQNFQVH 20
FC K ++FQV
Sbjct: 24 FCPKHRDFQVK 34
>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 25.7 bits (57), Expect = 6.4
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 3/62 (4%)
Query: 37 VTLKAEGEAFQAHRII-LSASSPFFQNFQVHLAFELYQLLKMESMVDVTLKAEGEAFQAH 95
+ F R+I S P Q H+ +++ +L ++ V+V GE F
Sbjct: 54 AVTNPKNTVFSVKRLIGRKFSDPVVQRDIKHVPYKVVKLPNGDAGVEVRYL--GETFTPE 111
Query: 96 RI 97
+I
Sbjct: 112 QI 113
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea.
Length = 187
Score = 25.0 bits (55), Expect = 7.5
Identities = 13/46 (28%), Positives = 20/46 (43%)
Query: 39 LKAEGEAFQAHRIILSASSPFFQNFQVHLAFELYQLLKMESMVDVT 84
LK E F+A R+++ + S Q E+ +LL VT
Sbjct: 87 LKDAIEEFKAKRVVIDSVSGLLLMEQSTARLEIRRLLFALKRFGVT 132
>gnl|CDD|218626 pfam05536, Neurochondrin, Neurochondrin. This family contains
several eukaryotic neurochondrin proteins. Neurochondrin
induces hydroxyapatite resorptive activity in bone
marrow cells resistant to bafilomycin A1, an inhibitor
of macrophage- and osteoclast-mediated resorption.
Expression of the gene is localised to chondrocyte,
osteoblast, and osteocyte in the bone and to the
hippocampus and Purkinje cell layer of cerebellum in the
brain.
Length = 542
Score = 25.5 bits (56), Expect = 7.7
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 15 QNFQVHLAFELYQLLKMESMVDVTLKAEGEAFQAHRIILSASSPFFQNFQVHLAFELYQL 74
+F + A L LL K+ E +L+ + FQ + FEL L
Sbjct: 152 GSFGLEQALHLLLLLLSALDS----KSWTEKDLDLTAVLTRLAELFQVLEGTRKFELLDL 207
Query: 75 L 75
L
Sbjct: 208 L 208
>gnl|CDD|182654 PRK10695, PRK10695, hypothetical protein; Provisional.
Length = 859
Score = 25.2 bits (56), Expect = 8.2
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 47 QAHRIILSASSPFFQNFQVHL 67
QA IL A P++ +F +HL
Sbjct: 399 QA---ILQAHEPYWGDFNLHL 416
>gnl|CDD|233699 TIGR02050, gshA_cyan_rel, carboxylate-amine ligase, YbdK family.
This family represents a division of a larger family,
the other branch of which is predicted to act as
glutamate--cysteine ligase (the first of two enzymes in
glutathione biosynthesis) in the cyanobacteria. Species
containing this protein, however, are generally not
believe to make glutathione, and the function is
unknown.
Length = 287
Score = 25.0 bits (55), Expect = 8.6
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 49 HRIILSASSPFFQNFQVHLA---FELYQLLKMESMVDVTLKAEGEAFQAHRIILSAS 102
H + LSASSPF+Q F A ++Q + +AF+A+ L +
Sbjct: 148 HLLALSASSPFWQGFDTGYASYRRNIFQAWPTAGLPPAFGSW--DAFEAYFADLLET 202
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
0.327 0.133 0.382
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,154,494
Number of extensions: 404694
Number of successful extensions: 394
Number of sequences better than 10.0: 1
Number of HSP's gapped: 394
Number of HSP's successfully gapped: 36
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)