RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12018
(148 letters)
>gnl|CDD|216695 pfam01780, Ribosomal_L37ae, Ribosomal L37ae protein family. This
ribosomal protein is found in archaebacteria and
eukaryotes. It contains four conserved cysteine residues
that may bind to zinc.
Length = 90
Score = 31.0 bits (71), Expect = 0.054
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 54 KKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVY 100
KK E Q +Y CP C G +++K A G++ C CGK +
Sbjct: 26 KKIEISQHAKYTCPFC---------GKDAVKRKAVGIWKCRKCGKTF 63
>gnl|CDD|240332 PTZ00255, PTZ00255, 60S ribosomal protein L37a; Provisional.
Length = 90
Score = 31.2 bits (71), Expect = 0.056
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 9/46 (19%)
Query: 54 KKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKV 99
KK E Q +Y CP C G ++K A G++ C C K
Sbjct: 27 KKIEISQHAKYFCPFC---------GKHAVKRQAVGIWRCKGCKKT 63
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 32.3 bits (74), Expect = 0.076
Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 9/46 (19%)
Query: 64 YQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRH 109
Y+CP+CP T + G S KP+ C CG HK TL RH
Sbjct: 82 YKCPKCPRPTCYQSYG--SSKPDNPP---CPGCG----HKMTLKRH 118
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 28.3 bits (64), Expect = 0.20
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 35 FACDVCGKEYQYYRNLYRHKKFEC 58
C VCGK + + L HKK C
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSHC 25
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 30.1 bits (68), Expect = 0.42
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 90 MYVCDICGKVYQHKRTLYRHKK 111
+Y C+ C K + K L RH K
Sbjct: 198 LYFCEFCLKFMKRKEQLQRHMK 219
>gnl|CDD|232904 TIGR00280, L37a, ribosomal protein L37a. This model finds
eukaryotic ribosomal protein L37a and its archaeal
orthologs. The nomeclature is tricky because eukaryotes
have proteins called both L37 and L37a [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 92
Score = 27.5 bits (61), Expect = 1.3
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 54 KKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVY 100
KK E Q+ +Y CP C G +++K + G++ C CG +
Sbjct: 27 KKIEIQQKAKYVCPFC---------GKKTVKRGSTGIWTCRKCGAKF 64
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 25.8 bits (57), Expect = 1.3
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 49 NLYRHKKFECGQEPRYQCPQCPYRTKQ 75
NL RH + G++P Y+CP C
Sbjct: 1 NLRRHMRTHTGEKP-YKCPVCGKSFSS 26
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 28.5 bits (64), Expect = 1.6
Identities = 18/67 (26%), Positives = 24/67 (35%), Gaps = 18/67 (26%)
Query: 33 GKFACDVCGKEYQYYRNLYRHKKFECG--QEPRYQCPQCPYRTKQKELGWESLKPNAYGM 90
G+ C CG E Y ++ +CG EP Y CP C + P+ G
Sbjct: 666 GRRRCPSCGTE------TYENRCPDCGTHTEPVYVCPDCGA----------EVPPDESGR 709
Query: 91 YVCDICG 97
C C
Sbjct: 710 VECPRCD 716
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.5 bits (56), Expect = 1.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 91 YVCDICGKVYQHKRTLYRHKK 111
Y C CGKV++ K L H +
Sbjct: 1 YRCPECGKVFKSKSALREHMR 21
Score = 24.0 bits (52), Expect = 5.8
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 120 FQCPQCPYRAKQKANLKTHLII 141
++CP+C K K+ L+ H+
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability
[RNA processing and modification].
Length = 1175
Score = 28.4 bits (63), Expect = 1.8
Identities = 10/38 (26%), Positives = 15/38 (39%), Gaps = 5/38 (13%)
Query: 9 RGKSRVLHWNSFMSWEGPFKPKLYGKFACDVCGKEYQY 46
G + +H M W G CD+C EY++
Sbjct: 35 SGSIKYIHRECLMEWMEC-----SGTKKCDICHYEYKF 67
>gnl|CDD|202726 pfam03691, UPF0167, Uncharacterized protein family (UPF0167).
The proteins in this family are about 200 amino acids
long and each contain 3 CXXC motifs.
Length = 177
Score = 27.3 bits (61), Expect = 2.2
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 37 CDVCGKEYQYYRNLYRHKKFECGQEPRYQCPQC 69
CD CG+ R F ++ Y CP C
Sbjct: 27 CDCCGQA----RGYVYTGPFYTVEDVEYLCPWC 55
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 27.9 bits (63), Expect = 2.3
Identities = 18/81 (22%), Positives = 26/81 (32%), Gaps = 23/81 (28%)
Query: 63 RYQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQC 122
R +CP C G E+ C CG H +YR + +C
Sbjct: 626 RRKCPSC---------GKETFYR------RCPFCG---THTEPVYR-CPRCGIEVEEDEC 666
Query: 123 PQCPYRA----KQKANLKTHL 139
+C K+K +LK
Sbjct: 667 EKCGREPTPYSKRKIDLKELY 687
>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed.
Length = 637
Score = 27.7 bits (62), Expect = 2.4
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 11/36 (30%)
Query: 64 YQCPQCPYRTKQKELGWESLKPNAYGMYVCDICGKV 99
Y CP C R ++ + G Y+C+ CG+V
Sbjct: 533 YLCPNCRKRVEEVD-----------GEYICEFCGEV 557
>gnl|CDD|237756 PRK14559, PRK14559, putative protein serine/threonine phosphatase;
Provisional.
Length = 645
Score = 27.7 bits (62), Expect = 2.6
Identities = 16/61 (26%), Positives = 18/61 (29%), Gaps = 19/61 (31%)
Query: 66 CPQCPYRTKQKELGWESLKPNAYGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCPQC 125
CPQC + PN C CG HK +CG E C
Sbjct: 4 CPQC-----------QFENPNNNRF--CQKCGTSLTHKPC------PQCGTEVPVDEAHC 44
Query: 126 P 126
P
Sbjct: 45 P 45
>gnl|CDD|216792 pfam01927, DUF82, Protein of unknown function DUF82. This
prokaryotic protein family has no known function. The
protein contains four conserved cysteines that may be
involved in metal binding or disulphide bridges.
Length = 146
Score = 26.8 bits (60), Expect = 3.6
Identities = 13/41 (31%), Positives = 16/41 (39%), Gaps = 6/41 (14%)
Query: 66 CPQC--PYRTKQKELGWESLKPNAYGMY----VCDICGKVY 100
C +C P KE + P Y Y C CG+VY
Sbjct: 93 CLKCNGPLEPVSKEEVAGRVPPYVYERYDEFWRCPKCGRVY 133
>gnl|CDD|224570 COG1656, COG1656, Uncharacterized conserved protein [Function
unknown].
Length = 165
Score = 26.7 bits (59), Expect = 3.6
Identities = 18/79 (22%), Positives = 25/79 (31%), Gaps = 9/79 (11%)
Query: 43 EYQYYRNLYRHKKFECGQEPRYQCPQC--PYRTKQKELGWESLKPNAYGM----YVCDIC 96
E Q L R +CP+C +E E + Y Y C C
Sbjct: 77 EEQLAEFLARLGLKPRLFPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKC 136
Query: 97 GKVY---QHKRTLYRHKKD 112
GK+Y H R + +
Sbjct: 137 GKIYWKGSHWRRMVERIVE 155
>gnl|CDD|224245 COG1326, COG1326, Uncharacterized archaeal Zn-finger protein
[General function prediction only].
Length = 201
Score = 26.7 bits (59), Expect = 4.0
Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 15/69 (21%)
Query: 59 GQEPRYQCPQCPYRTKQKELGWESLKPNAYG-MYVCDICGKVY----------QHKRTLY 107
+E +CP C +E+ E +K + C+ CG V+ + + +
Sbjct: 2 TEEIYIECPSC----GSEEVSHEVIKERGREPLVRCEECGTVHPAIIKTPKPVRVRVIVS 57
Query: 108 RHKKDECGQ 116
RH++ +
Sbjct: 58 RHEESFTKE 66
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 24.2 bits (53), Expect = 4.4
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 92 VCDICGKVYQHKRTLYRHKK 111
C CGK + K L RH +
Sbjct: 1 KCPDCGKSFSRKSNLKRHLR 20
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 24.1 bits (53), Expect = 5.0
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 64 YQCPQCPYRTKQKEL 78
Y+C CPY + K+L
Sbjct: 1 YKCSHCPYSSTPKKL 15
>gnl|CDD|227360 COG5027, SAS2, Histone acetyltransferase (MYST family) [Chromatin
structure and dynamics].
Length = 395
Score = 26.7 bits (59), Expect = 5.3
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 90 MYVCDICGKVYQHKRTLYRHKKDECGQ 116
+Y+C+ C K Y + +L RH+K +C
Sbjct: 158 VYICEFCLKYYGSQTSLVRHRK-KCSL 183
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
composed of two C4-type zinc fingers. DNA-binding
domain of Tailless (TLX) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which co-ordinates a single zinc atom. TLX
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. TLX is an orphan receptor that is expressed
by neural stem/progenitor cells in the adult brain of
the subventricular zone (SVZ) and the dentate gyrus
(DG). It plays a key role in neural development by
promoting cell cycle progression and preventing
apoptosis in the developing brain. Like other members of
the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX has a
central well conserved DNA-binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 92
Score = 25.5 bits (56), Expect = 5.4
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 88 YGMYVCDICGKVYQHKRTLYRHKKDECGQEPRFQCP 123
YG+Y CD C + KR++ R+++ C + + CP
Sbjct: 21 YGIYACDGCSGFF--KRSIRRNRQYVCKSKGQGGCP 54
Score = 25.5 bits (56), Expect = 5.9
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 30 KLYGKFACDVCGKEYQYYRNLYRHKKFECGQEPRYQCP 67
K YG +ACD C ++ R++ R++++ C + + CP
Sbjct: 19 KHYGIYACDGCSGFFK--RSIRRNRQYVCKSKGQGGCP 54
>gnl|CDD|219926 pfam08600, Rsm1, Rsm1-like. Rsm1 is a protein involved in mRNA
export from the nucleus.
Length = 91
Score = 25.5 bits (56), Expect = 7.1
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 78 LGWESLKPNAYGMYVCDIC 96
GW+ L G+ C C
Sbjct: 7 FGWDGLPDGRLGLASCGTC 25
>gnl|CDD|227812 COG5525, COG5525, Phage terminase, large subunit GpA [Replication,
recombination and repair].
Length = 611
Score = 26.2 bits (58), Expect = 8.6
Identities = 14/64 (21%), Positives = 20/64 (31%), Gaps = 9/64 (14%)
Query: 37 CDVCGKEYQYYR----NLYRHKKFECGQEPRYQCPQCPYRTKQKELG----WESLKPNAY 88
C CG E Q + + R K + QC C + K G + +
Sbjct: 230 CPHCG-EEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPKLNGRGVCLRTGEWIRD 288
Query: 89 GMYV 92
GM
Sbjct: 289 GMTW 292
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 26.2 bits (57), Expect = 9.2
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 11/79 (13%)
Query: 35 FACDV--CGKEYQYYRNLYRHKKFECGQEPRYQCPQCPYRTKQKELGWESLKPNAYGMYV 92
+ C V C K+Y+ L H Q + P + + KP Y
Sbjct: 350 YKCPVEGCNKKYKNQNGLKYHML-HGHQNQKLHENPSPEKM---NIFSAKDKP-----YR 400
Query: 93 CDICGKVYQHKRTLYRHKK 111
C++C K Y++ L H+K
Sbjct: 401 CEVCDKRYKNLNGLKYHRK 419
>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 = 9.2
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 120 FQCPQCPYRAKQKANLKTHLIIKH 143
F+CP C K LK HL H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
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 0.139 0.476
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,987,562
Number of extensions: 557215
Number of successful extensions: 677
Number of sequences better than 10.0: 1
Number of HSP's gapped: 672
Number of HSP's successfully gapped: 80
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
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 (21.9 bits)
S2: 54 (24.6 bits)