RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5652
(92 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 31.2 bits (71), Expect = 0.007
Identities = 12/19 (63%), Positives = 17/19 (89%)
Query: 51 MKRHIRTHTGERPFKCEFC 69
++RH+RTHTGE+P+KC C
Sbjct: 2 LRRHMRTHTGEKPYKCPVC 20
>gnl|CDD|214384 CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
Length = 296
Score = 30.3 bits (69), Expect = 0.090
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 20 HCKRCSNM--PRPDSSHLYVCFKCGYH--QYNSDR 50
C+ C + + S + +C +CGYH +SDR
Sbjct: 40 QCENCYGLNYKKFLKSKMNICEQCGYHLKMSSSDR 74
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 29.2 bits (66), Expect = 0.17
Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 13/43 (30%)
Query: 29 RPDSSHLYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAH 71
R + ++VC CGY TH GE P C C
Sbjct: 128 RLEEGKVWVCPVCGY-------------THEGEAPEVCPICGA 157
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 28.5 bits (63), Expect = 0.47
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 35 LYVCFKCGYHQYNSDRMKRHIRTHTGERPFKCEFCAHSATSKSNLKMHIMVKHQN 89
C C + + RHIR+HTGE+P +C + + L++ ++ +
Sbjct: 33 PDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHH 87
>gnl|CDD|235547 PRK05654, PRK05654, acetyl-CoA carboxylase subunit beta;
Validated.
Length = 292
Score = 28.3 bits (64), Expect = 0.51
Identities = 7/12 (58%), Positives = 10/12 (83%)
Query: 33 SHLYVCFKCGYH 44
++L VC KCG+H
Sbjct: 44 ANLNVCPKCGHH 55
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 27.4 bits (60), Expect = 1.1
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 60 GERPFKCEF--CAHSATSKSNLKMHIMVKHQN 89
+P+KC C +++ LK H++ HQN
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQN 377
>gnl|CDD|197822 smart00661, RPOL9, RNA polymerase subunit 9.
Length = 52
Score = 25.8 bits (57), Expect = 1.2
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 21 CKRCSNMPRP---DSSHLYVCFKCGYHQ 45
C +C NM P +VC KCGY +
Sbjct: 3 CPKCGNMLYPREGKEKRRFVCRKCGYEE 30
>gnl|CDD|227293 COG4957, COG4957, Predicted transcriptional regulator
[Transcription].
Length = 148
Score = 26.9 bits (60), Expect = 1.3
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 37 VCFKCGYHQYNSDRMKRHIRTHTGERP 63
+C + G ++ S +KRH+ TH G P
Sbjct: 78 ICLEDG-KKFKS--LKRHLTTHYGLTP 101
>gnl|CDD|223848 COG0777, AccD, Acetyl-CoA carboxylase beta subunit [Lipid
metabolism].
Length = 294
Score = 26.9 bits (60), Expect = 1.5
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 21 CKRCSNMP-RPD-SSHLYVCFKCGYH 44
C C M R + S+L VC KCG+H
Sbjct: 31 CPSCGEMLYRKELESNLKVCPKCGHH 56
>gnl|CDD|162723 TIGR02137, HSK-PSP, phosphoserine phosphatase/homoserine
phosphotransferase bifunctional protein. This protein
is has been characterized as both a phosphoserine
phosphatase and a phosphoserine:homoserine
phosphotransferase. In Pseudomonas aeruginosa, where the
characterization was done, a second phosphoserine
phosphatase (SerB) and a second homoserine kinase (thrB)
are found, but in Fibrobacter succinogenes neither are
present. This enzyme is a member of the haloacid
dehalogenase (HAD) superfamily, specifically part of
subfamily IB by virtue of the presence of an alpha
helical domain in between motifs I and II of the HAD
domain. The closest homologs to this family are
monofunctional phosphoserine phosphatases (TIGR00338).
Length = 203
Score = 26.4 bits (58), Expect = 2.3
Identities = 16/71 (22%), Positives = 23/71 (32%), Gaps = 12/71 (16%)
Query: 4 IFCRQLLPMDADFILGHCKRCSNMPRPDSSHL----YVCFKCGYHQYNSDRMKRHIRTHT 59
+ C +L D+D ++G+ R + R Y G YN M H
Sbjct: 109 LLCHKLEIDDSDRVVGYQLRQKDPKRQSVIAFKSLYYRVIAAG-DSYNDTTMLS--EAHA 165
Query: 60 GERPFKCEFCA 70
G F A
Sbjct: 166 G-----ILFHA 171
>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit
M/Transcription elongation factor TFIIS
[Transcription].
Length = 113
Score = 25.9 bits (57), Expect = 2.5
Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 21 CKRCSNM---PRPDSSHLYVCFKCGYHQYNSDRMK 52
C +C ++ + D VC KCGY + S++
Sbjct: 5 CPKCGSLLYPKKDDEGGKLVCRKCGYEEEASNKKV 39
>gnl|CDD|131452 TIGR02399, salt_tol_Pase, glucosylglycerol 3-phosphatase. Proteins
in this family are glucosylglycerol-phosphate
phosphatase, with the gene symbol stpA (Salt Tolerance
Protein A). A motif characteristic of acid phosphatases
is found, but otherwise this family shows little
sequence similarity to other phosphatases. This enzyme
acts on the glucosylglycerol phosphate, product of
glucosylglycerol phosphate synthase and immediate
precursor of the osmoprotectant glucosylglycerol.
Length = 389
Score = 26.3 bits (58), Expect = 2.6
Identities = 8/37 (21%), Positives = 13/37 (35%)
Query: 51 MKRHIRTHTGERPFKCEFCAHSATSKSNLKMHIMVKH 87
+ + I TG P F A +++ KH
Sbjct: 245 LNKFIYDSTGIAPLGRNFNFRDAPKSHQELLNLCKKH 281
>gnl|CDD|218591 pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein.
This family consists of several ROS/MUCR
transcriptional regulator proteins. The ros chromosomal
gene is present in octopine and nopaline strains of
Agrobacterium tumefaciens as well as in Rhizobium
meliloti. This gene encodes a 15.5-kDa protein that
specifically represses the virC and virD operons in the
virulence region of the Ti plasmid and is necessary for
succinoglycan production. Sinorhizobium meliloti can
produce two types of acidic exopolysaccharides,
succinoglycan and galactoglucan, that are
interchangeable for infection of alfalfa nodules. MucR
from Sinorhizobium meliloti acts as a transcriptional
repressor that blocks the expression of the exp genes
responsible for galactoglucan production therefore
allowing the exclusive production of succinoglycan.
Length = 130
Score = 25.6 bits (57), Expect = 2.8
Identities = 9/24 (37%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 37 VCFKCGYHQYNSDRMKRHIRTHTG 60
+C + G ++ + +KRH+RTH G
Sbjct: 72 ICLEDG-KKFKT--LKRHLRTHHG 92
>gnl|CDD|238184 cd00296, SIR2, SIR2 superfamily 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. Also included in this
superfamily is a group of uncharacterized Sir2-like
proteins which lack certain key catalytic residues and
conserved zinc binding cysteines.
Length = 222
Score = 25.8 bits (57), Expect = 3.0
Identities = 8/36 (22%), Positives = 12/36 (33%), Gaps = 3/36 (8%)
Query: 2 VCIFCRQLLP---MDADFILGHCKRCSNMPRPDSSH 34
C C + P + C +C + RPD
Sbjct: 115 RCTSCGKEYPRDEVLEREKPPRCPKCGGLLRPDVVD 150
>gnl|CDD|175986 cd04019, C2C_MCTP_PRT_plant, C2 domain third repeat found in
Multiple C2 domain and Transmembrane region Proteins
(MCTP); plant subset. MCTPs are involved in Ca2+
signaling at the membrane. Plant-MCTPs are composed of
a variable N-terminal sequence, four C2 domains, two
transmembrane regions (TMRs), and a short C-terminal
sequence. It is one of four protein classes that are
anchored to membranes via a transmembrane region; the
others being synaptotagmins, extended synaptotagmins,
and ferlins. MCTPs are the only membrane-bound C2 domain
proteins that contain two functional TMRs. MCTPs are
unique in that they bind Ca2+ but not phospholipids. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the third C2
repeat, C2C, and has a type-II topology.
Length = 150
Score = 25.7 bits (57), Expect = 3.5
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 6/22 (27%)
Query: 34 HLYVCFKCGYH------QYNSD 49
HL +C GYH Y+SD
Sbjct: 126 HLRLCLDGGYHVLDESTHYSSD 147
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 25.8 bits (57), Expect = 3.7
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 14/53 (26%)
Query: 23 RCSNMPRPDSS-HLYVCFKCGYH---QYNSDRMKRHIRTHTGERPFKCEFCAH 71
R S RP ++ C KCG + + R+ E P +CE C
Sbjct: 117 RASE-VRPRLKKAVFECPKCGREVEVEQSEFRV---------EPPRECENCGK 159
>gnl|CDD|129606 TIGR00515, accD, acetyl-CoA carboxylase, carboxyl transferase,
beta subunit. The enzyme acetyl-CoA carboxylase
contains a biotin carboxyl carrier protein or domain, a
biotin carboxylase, and a carboxyl transferase. This
model represents the beta chain of the carboxyl
transferase for cases in which the architecture of the
protein is as in E. coli, in which the
carboxyltransferase portion consists of two
non-identical subnits, alpha and beta [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 285
Score = 25.5 bits (56), Expect = 5.0
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 33 SHLYVCFKCGYH 44
+L VC KC +H
Sbjct: 43 RNLEVCPKCDHH 54
>gnl|CDD|217897 pfam04106, APG5, Autophagy protein Apg5. Apg5 is directly
required for the import of aminopeptidase I via the
cytoplasm-to-vacuole targeting pathway.
Length = 195
Score = 25.3 bits (56), Expect = 5.6
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 14 ADFIL-GHCKRCSNMPRPDSSHLYVCFKCG-YHQYNS 48
ADF+ G K N+ + DS L+ + +
Sbjct: 59 ADFLRNGTSKVIMNLSKADSKQLWKSVVNHNFDDFWR 95
>gnl|CDD|226060 COG3529, COG3529, Predicted nucleic-acid-binding protein
containing a Zn-ribbon domain [General function
prediction only].
Length = 66
Score = 24.4 bits (53), Expect = 5.8
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 16 FILG-HCKRCS-----NMPRPDSSHLYVCFKCGYHQYNSDR-MKRHIRTH 58
FI G C C M R ++ + C KCG+H +D+ ++ H+R +
Sbjct: 7 FIAGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMREADKEVRTHVRKN 56
>gnl|CDD|179247 PRK01211, PRK01211, dihydroorotase; Provisional.
Length = 409
Score = 25.2 bits (55), Expect = 6.8
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 43 YHQYNSDRMKRH------IRTHTGERPFKCEFCAHSATSKSNLKMHIM 84
+H S+ +++H +R H RP +CE A +LK I+
Sbjct: 165 FHAELSECLRKHQFESKNLRDHDLARPIECEIKAVKYVKNLDLKTKII 212
>gnl|CDD|238699 cd01408, SIRT1, SIRT1: Eukaryotic group (class1) which includes
human sirtuins SIRT1-3 and yeast Hst1-4; and are members
of the SIR2 family of proteins, silent information
regulator 2 (Sir2) enzymes which catalyze NAD+-dependent
protein/histone deacetylation. Sir2 proteins have been
shown to regulate gene silencing, DNA repair, 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 nuclear SIRT1 has been shown
to target the p53 tumor suppressor protein for
deacetylation to suppress DNA damage, and the
cytoplasmic SIRT2 homolog has been shown to target
alpha-tubulin for deacetylation for the maintenance of
cell integrity.
Length = 235
Score = 24.9 bits (55), Expect = 6.8
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 38 CFKCGYHQYNSDRMKRHIRTHTGERPFKCEFC 69
C KC H+Y D M+ I E P KC C
Sbjct: 119 CIKCK-HKYPGDWMREDIFNQ--EVP-KCPRC 146
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 25.0 bits (55), Expect = 8.1
Identities = 7/23 (30%), Positives = 8/23 (34%)
Query: 20 HCKRCSNMPRPDSSHLYVCFKCG 42
C C PD S C +C
Sbjct: 694 VCPDCGAEVPPDESGRVECPRCD 716
>gnl|CDD|235290 PRK04351, PRK04351, hypothetical protein; Provisional.
Length = 149
Score = 24.4 bits (54), Expect = 9.3
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 24 CSNMPRPDSSHLYVCFKCGYHQYNSDRMKRHIRTH 58
C +P ++LY C CG QY KR I T
Sbjct: 101 CPPLPSQKKNYLYECQSCG-QQY---LRKRRINTK 131
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
0.331 0.139 0.479
Gapped
Lambda K H
0.267 0.0692 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,231,174
Number of extensions: 299572
Number of successful extensions: 487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 484
Number of HSP's successfully gapped: 49
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 53 (24.3 bits)