RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3274
(115 letters)
>gnl|CDD|206038 pfam13867, SAP30_Sin3_bdg, Sin3 binding region of histone
deacetylase complex subunit SAP30. This C-terminal
domain of the SAP30 proteins appears to be the binding
region for Sin3.
Length = 53
Score = 78.5 bits (194), Expect = 6e-21
Identities = 28/53 (52%), Positives = 40/53 (75%)
Query: 46 LQVNTLRRYKKYFKVTSRPGLNKAQLAETLLKHFKTIPVVEKDVLSFFFYTVK 98
L VNTLRRYK++FK+ +RP +K QLAE + KHF + P+ E++V++ F Y VK
Sbjct: 1 LGVNTLRRYKRHFKLVTRPNSSKEQLAEAVQKHFMSQPLDEQEVIAGFLYAVK 53
>gnl|CDD|206037 pfam13866, zf-SAP30, SAP30 zinc-finger. SAP30 is a subunit of
the histone deacetylase complex, and this domain is a
zinc-finger. Solution of the structure shows a novel
fold comprising two beta-strands and two alpha-helices
with the zinc organising centre showing remote
resemblance to the treble clef motif. In silico
analysis of the structure revealed a highly conserved
surface dominated by basic residues. NMR-based analysis
of potential ligands for the SAP30 zn-finger motif
indicated a strong preference for nucleic acid
substrates. The zinc-finger of SAP3 probably functions
as a double-stranded DNA-binding motif, thereby
expanding the known functions of both SAP30 and the
mammalian Sin3 co-repressor complex.
Length = 68
Score = 41.1 bits (96), Expect = 3e-06
Identities = 19/26 (73%), Positives = 24/26 (92%)
Query: 3 ARHIYICEYHKCLIQSVRNKRRRKDS 28
ARH+YIC++HK LIQSVRN+R+RK S
Sbjct: 43 ARHLYICDFHKNLIQSVRNRRKRKGS 68
>gnl|CDD|223059 PHA03367, PHA03367, single-stranded DNA binding protein;
Provisional.
Length = 1115
Score = 33.0 bits (76), Expect = 0.019
Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 4/86 (4%)
Query: 24 RRKDSEDDSNENDESPDVDLFQLQVNTLRRYKK--YFKVTSRPGLNKAQLAETLLKHFKT 81
R +D EDD N+ +E+P +QL N L K VT +K FK
Sbjct: 505 RFRDKEDDGNQREETPSYTYWQLNQNILEYLSKMGLIDVTGEDTKL-ITGIRDFVKVFKD 563
Query: 82 I-PVVEKDVLSFFFYTVKSNTNKLDQ 106
I +V+ +V F VK+N N +
Sbjct: 564 IDAIVDAEVSKFINEMVKNNINFRES 589
>gnl|CDD|218013 pfam04298, Zn_peptidase_2, Putative neutral zinc
metallopeptidase. Zinc metallopeptidase zinc binding
regions have been predicted in some family members by a
pattern match (Prosite:PS00142).
Length = 222
Score = 32.5 bits (75), Expect = 0.026
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 45 QLQVNTLRRYKKYFKVTSRPGLNKAQLAETLL 76
Q +V +KKY KV S G+ A++A +L
Sbjct: 18 QNKVK--STFKKYSKVRSSSGMTGAEVARRIL 47
>gnl|CDD|204116 pfam09013, YopH_N, YopH, N-terminal. The N-terminal domain of YopH
is a compact structure composed of four alpha-helices
and two beta-hairpins. Helices alpha-1 and alpha-3 are
parallel to each other and antiparallel to helices
alpha-2 and alpha-4. This domain targets YopH for
secretion from the bacterium and translocation into
eukaryotic cells, and has phosphotyrosyl peptide-binding
activity, allowing for recognition of p130Cas and
paxillin.
Length = 121
Score = 28.0 bits (62), Expect = 0.79
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 47 QVNTLRRYKKYFKVTSRPGLNKAQ--------LAETLLKHFKTIPVVEKDVLSFFFYTVK 98
+ LR K T+ GL A+ +L+H K + ++DV TVK
Sbjct: 21 CIGKLRGNVAANKETTFQGLTITSGARESEKAFAQEVLEHVKNTALNQEDVAKLLPSTVK 80
Query: 99 SNTNKLDQKNGNTGE 113
N N + ++G GE
Sbjct: 81 HNLNNFELRSGGNGE 95
>gnl|CDD|185539 PTZ00286, PTZ00286, 6-phospho-1-fructokinase; Provisional.
Length = 459
Score = 26.9 bits (60), Expect = 2.3
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 41 VDLFQLQVNTLRRYKKYFKVTSRPGLNKAQLAETLLKH 78
+ L V T+ R +SR G + + +TL++H
Sbjct: 138 IKLDPKDVKTIHRLGGTILGSSRGGFDPKVMVDTLIRH 175
>gnl|CDD|223015 PHA03232, PHA03232, DNA packaging protein UL32; Provisional.
Length = 586
Score = 26.6 bits (59), Expect = 4.0
Identities = 9/34 (26%), Positives = 15/34 (44%)
Query: 45 QLQVNTLRRYKKYFKVTSRPGLNKAQLAETLLKH 78
L +T R+ ++ + P L + T LKH
Sbjct: 369 ALARDTAPRFARFAGEDAEPDLALGPVLATTLKH 402
>gnl|CDD|146748 pfam04276, DUF443, Protein of unknown function (DUF443). Family of
uncharacterized proteins.
Length = 197
Score = 26.0 bits (58), Expect = 4.5
Identities = 15/62 (24%), Positives = 20/62 (32%), Gaps = 11/62 (17%)
Query: 49 NTLRRYKKYFKVTSRPGLNKAQLAETLLKHFKTIPVVEKDVLSFFFYTVKSNTNKLDQKN 108
N LR YF + S +N +L VL Y K K+ +N
Sbjct: 73 NLLRPLTDYFNIQSEKLINIIICIIVILG-----------VLILRLYINKKLKLKIYNRN 121
Query: 109 GN 110
N
Sbjct: 122 KN 123
>gnl|CDD|225348 COG2738, COG2738, Predicted Zn-dependent protease [General
function prediction only].
Length = 226
Score = 26.2 bits (58), Expect = 4.7
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 45 QLQVNTLRRYKKYFKVTSRPGLNKAQLAETLL 76
Q +V + YKKY KV + GL A++A +L
Sbjct: 21 QSKVKS--TYKKYSKVRASSGLTGAEVARMIL 50
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 26.0 bits (58), Expect = 5.5
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 51 LRRYKKYFKVTSRPGLNKAQLAETLLKHFKTIP 83
LRRYK K R +N AE LLK K +
Sbjct: 758 LRRYKGREKSAERQQVN----AEMLLKFAKELD 786
>gnl|CDD|148722 pfam07280, DUF1443, Protein of unknown function (DUF1443). This
family consists of several Baculovirus proteins of
around 55 residues in length. The function of this
family is unknown.
Length = 43
Score = 24.0 bits (53), Expect = 6.4
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 66 LNKAQLAETLLKHFKTIP 83
LN+ Q+ L +K IP
Sbjct: 19 LNRGQVRRLLYYQYKYIP 36
>gnl|CDD|192303 pfam09488, Osmo_MPGsynth, Mannosyl-3-phosphoglycerate synthase
(osmo_MPGsynth). This family consists of examples of
mannosyl-3-phosphoglycerate synthase (MPGS), which
together with mannosyl-3-phosphoglycerate phosphatase
(MPGP) EC:2.4.1.217, comprises a two-step pathway for
mannosylglycerate biosynthesis. Mannosylglycerate is a
compatible solute that tends to be restricted to extreme
thermophiles of archaea and bacteria. Note that in
Rhodothermus marinus, this pathway is one of two; the
other is condensation of GDP-mannose with D-glycerate by
mannosylglycerate synthase.
Length = 381
Score = 25.3 bits (56), Expect = 7.5
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 17/55 (30%)
Query: 12 HKCLIQSVRNKRRRKDSEDDSNENDESPDVDLFQLQVNTLRRYKKYFKVTSRPGL 66
H CLI V N R VD ++++V+ LR + + T RP +
Sbjct: 75 HDCLIIVVSNSSRE--------------PVDRYKMEVDLLRHFSRL---TRRPII 112
>gnl|CDD|215405 PLN02760, PLN02760, 4-aminobutyrate:pyruvate transaminase.
Length = 504
Score = 25.5 bits (56), Expect = 8.9
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 47 QVNTLRRYKKYFKVTSRPGLNKAQLAETLLKHFK 80
Q+N L Y ++ T++P L+ LA+ LL+ F
Sbjct: 117 QLNKLPFYHSFWNRTTKPSLD---LAKELLEMFT 147
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
0.316 0.132 0.376
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,558,103
Number of extensions: 456479
Number of successful extensions: 489
Number of sequences better than 10.0: 1
Number of HSP's gapped: 488
Number of HSP's successfully gapped: 22
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)