RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1854
(110 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 = 50.3 bits (121), Expect = 2e-09
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 63 FGNLLKTETLVDCTIGADGQYLKAHKVVVSACSPYFQV 100
L + L D T+ + AHK V++ACSPYF+
Sbjct: 1 LNELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFKA 38
>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 = 36.9 bits (86), Expect = 3e-04
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 74 DCTIGADGQYLKAHKVVVSACSPYFQ 99
D T+ G+ AHK V++A SPYF+
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFK 26
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 32.3 bits (73), Expect = 0.031
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 55 HCNTLLQVFGNLLKTETLVDC--TIGADGQYLKAHKVVVSACSPYFQ 99
H ++ NLL + L D TIG DG+ +KAHK +++A S YF+
Sbjct: 8 HNRRVVSNISNLLDDDILCDVIITIG-DGEEIKAHKTILAAGSKYFR 53
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 30.0 bits (68), Expect = 0.25
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 17 KLETPPPKRVVAIFEALKR-----ETHWLSMKMDQQFRLKWNN---HCNTLLQVFGNLLK 68
L+ P +R+ AI EAL+R E H L+ K+D+ F K N L +V L
Sbjct: 422 ALKKPTDRRIFAIAEALRRGVSVDEIHELT-KIDRWFLHKIKNIVDLEEELEEVKLTELD 480
Query: 69 TETL 72
E L
Sbjct: 481 PELL 484
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 28.6 bits (64), Expect = 0.58
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 15/59 (25%)
Query: 17 KLETPPPKRVVAIFEALKRETHWLSMKMDQQFRL----KWNNHCNTLLQVFGNLLKTET 71
KL P P R+ AI+ A+K+ M +D+ L W L L+ E
Sbjct: 443 KLRVPNPDRIHAIYAAMKK-----GMTVDEIHELTFIDPW------FLTQLKELVDVEQ 490
>gnl|CDD|217231 pfam02787, CPSase_L_D3, Carbamoyl-phosphate synthetase large
chain, oligomerisation domain. Carbamoyl-phosphate
synthase catalyzes the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain.
Length = 122
Score = 27.2 bits (61), Expect = 1.3
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 17 KLETPPPKRVVAIFEALKR 35
KL P +R+ AI EAL+R
Sbjct: 4 KLRHPTDERLFAIAEALRR 22
>gnl|CDD|223092 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 879
Score = 27.2 bits (61), Expect = 1.9
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 2 LQEENKILEDPKSILKLETPPPKRVVAIFEALK 34
LQE+ +L++ S+LK+ +V + E LK
Sbjct: 710 LQEQEDLLKEIASLLKVPPELLPKVERLLEELK 742
>gnl|CDD|198164 smart01096, CPSase_L_D3, Carbamoyl-phosphate synthetase large
chain, oligomerisation domain. Carbamoyl-phosphate
synthase catalyses the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain.
Length = 124
Score = 26.3 bits (59), Expect = 2.5
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 17 KLETPPPKRVVAIFEALKR 35
+L TP +R+ I EAL+R
Sbjct: 4 ELRTPTDERLFYIAEALRR 22
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 26.6 bits (59), Expect = 3.5
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 2 LQEENKILEDPKSILKLETPP-PKRVVAIFEALK 34
L E+ L++ ILK+ PK++ FE K
Sbjct: 703 LNEQEDKLKELADILKVTPNELPKKIERFFEEWK 736
>gnl|CDD|204374 pfam10006, DUF2249, Uncharacterized conserved protein (DUF2249).
Members of this family of hypothetical bacterial
proteins have no known function.
Length = 69
Score = 25.2 bits (56), Expect = 4.0
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 21 PPPKRVVAIFEALKRETHWLSMKMDQQFRLKWNNH 55
PPP+ AIFEAL +++ + L N+H
Sbjct: 8 PPPEPHAAIFEALD------ALEPGETLEL-VNDH 35
>gnl|CDD|224369 COG1452, Imp, Organic solvent tolerance protein OstA [Cell envelope
biogenesis, outer membrane].
Length = 784
Score = 26.2 bits (58), Expect = 4.8
Identities = 5/28 (17%), Positives = 6/28 (21%)
Query: 80 DGQYLKAHKVVVSACSPYFQVSWDVVFC 107
D + C P W V
Sbjct: 153 DNDVTILKNATYTTCEPCDNPIWSVKAS 180
>gnl|CDD|172477 PRK13974, PRK13974, thymidylate kinase; Provisional.
Length = 212
Score = 25.8 bits (57), Expect = 4.9
Identities = 13/43 (30%), Positives = 17/43 (39%)
Query: 24 KRVVAIFEALKRETHWLSMKMDQQFRLKWNNHCNTLLQVFGNL 66
+RV F + E +W + DQ N TLL F N
Sbjct: 169 ERVAEGFALIAEERNWKVISADQSIETISNEIKETLLNNFSNK 211
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 25.8 bits (58), Expect = 5.4
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 17 KLETPPPKRVVAIFEALKR 35
+L+ P P+R+ I EA +R
Sbjct: 424 ELKEPTPERLFYIAEAFRR 442
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 0.136 0.432
Gapped
Lambda K H
0.267 0.0865 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,453,603
Number of extensions: 433142
Number of successful extensions: 376
Number of sequences better than 10.0: 1
Number of HSP's gapped: 376
Number of HSP's successfully gapped: 21
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
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: 41 (22.0 bits)
S2: 53 (23.9 bits)