RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2643
(134 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 33.5 bits (77), Expect = 0.002
Identities = 15/26 (57%), Positives = 21/26 (80%)
Query: 41 DMKKHTYIHTGEKPHKCVVCGKAFSQ 66
++++H HTGEKP+KC VCGK+FS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.9 bits (65), Expect = 0.11
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 69 NLITHLRKHTGYKPFSCGLCDKAF 92
NL H+R HTG KP+ C +C K+F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSF 24
Score = 28.5 bits (64), Expect = 0.12
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 14 LSTHLLIHSDTRPYPCQYCGKRFHQ 38
L H+ H+ +PY C CGK F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 35.4 bits (81), Expect = 0.005
Identities = 25/79 (31%), Positives = 34/79 (43%), Gaps = 2/79 (2%)
Query: 9 KRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVV--CGKAFSQ 66
S+ ST + + RP C C F + + +H HTGEKP +C C K+FS+
Sbjct: 16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSR 75
Query: 67 SSNLITHLRKHTGYKPFSC 85
L HLR H
Sbjct: 76 PLELSRHLRTHHNNPSDLN 94
Score = 29.3 bits (65), Expect = 0.56
Identities = 25/112 (22%), Positives = 45/112 (40%), Gaps = 11/112 (9%)
Query: 4 CGKTFKRSSTLSTHLLIHSDTRPYPCQY--CGKRFHQKSDMKKHTYIHTGEKPHK----- 56
CGK F R+ L H+L+H+ P + +F + + + +
Sbjct: 329 CGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSE 388
Query: 57 CVV--CGKAFSQSSNLITHLRKHTGYKP--FSCGLCDKAFQRKVDLRRHRES 104
+ C + F + SNL H+ H ++P C K+F R +L H++
Sbjct: 389 TLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKI 440
Score = 29.3 bits (65), Expect = 0.71
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 1 CKQCGKTFKRSSTLSTHLLIHSDTRPY------PCQYCGKRFHQKSDMKKHTYIHTGEKP 54
KQC +F RSS L+ HL + + P CGK F + +K+H +HT P
Sbjct: 292 SKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP 351
Query: 55 HKCV--VCGKAFSQSSN 69
K FS N
Sbjct: 352 AKEKLLNSSSKFSPLLN 368
Score = 27.7 bits (61), Expect = 2.1
Identities = 29/82 (35%), Positives = 38/82 (46%), Gaps = 7/82 (8%)
Query: 53 KPHKCVVCGKAFSQSSNLITHLRK--HTG--YKPFSCG--LCDKAFQRKVDLRRHRESQH 106
P K C +FS+SS L HLR H+G KPFSC LC K F R L+RH H
Sbjct: 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRH-ILLH 346
Query: 107 PGSPAQQHHISSTSMIETPESI 128
+ + ++S +P
Sbjct: 347 TSISPAKEKLLNSSSKFSPLLN 368
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 32.2 bits (73), Expect = 0.032
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 26 PYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHL-RKH 77
PY C C F +K+H I E C VCGK F + + + H+ +KH
Sbjct: 73 PYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHVCKKH 123
>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 = 28.5 bits (64), Expect = 0.12
Identities = 14/22 (63%), Positives = 16/22 (72%)
Query: 56 KCVVCGKAFSQSSNLITHLRKH 77
KC CGK+FS+ SNL HLR H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 27.3 bits (61), Expect = 0.31
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 1 CKQCGKTFKRSSTLSTHLLIH 21
C CGK+F R S L HL H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 25.0 bits (55), Expect = 2.5
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 29 CQYCGKRFHQKSDMKKHTYIH 49
C CGK F +KS++K+H H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 31.1 bits (71), Expect = 0.15
Identities = 14/65 (21%), Positives = 19/65 (29%), Gaps = 24/65 (36%)
Query: 1 CKQCGKTFKRSSTLSTH----LLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHK 56
C+ CG + + L +H T C YCG + P
Sbjct: 438 CRDCGYIAE-----CPNCDSPLTLHKATGQLRCHYCG---------------YQEPIPQS 477
Query: 57 CVVCG 61
C CG
Sbjct: 478 CPECG 482
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 30.8 bits (69), Expect = 0.17
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 4 CGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCGKA 63
C K +K + L H+L H + ++ H+ +K +KP++C VC K
Sbjct: 357 CNKKYKNQNGLKYHML-HG--------HQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR 407
Query: 64 FSQSSNLITHLRKHT 78
+ + L H RKH+
Sbjct: 408 YKNLNGLKYH-RKHS 421
Score = 29.3 bits (65), Expect = 0.56
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 21/77 (27%)
Query: 51 GEKPHKCVV--CGKAFSQSSNLITHLR---------------KHTGY----KPFSCGLCD 89
KP+KC V C K + + L H+ K + KP+ C +CD
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405
Query: 90 KAFQRKVDLRRHRESQH 106
K ++ L+ HR+ H
Sbjct: 406 KRYKNLNGLKYHRKHSH 422
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 28.9 bits (64), Expect = 0.18
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 55 HKCVVCGKAFSQSSNLITHLRKH 77
++C +CG+ + + ++ITHLRKH
Sbjct: 6 YECPICGEIYIKRKSMITHLRKH 28
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.4 bits (61), Expect = 0.37
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 27 YPCQYCGKRFHQKSDMKKHTYIH 49
Y C CGK F KS +++H H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.9 bits (57), Expect = 1.1
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 55 HKCVVCGKAFSQSSNLITHLRKH 77
++C CGK F S L H+R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 24.3 bits (53), Expect = 4.1
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 1 CKQCGKTFKRSSTLSTHLLIH 21
C +CGK FK S L H+ H
Sbjct: 3 CPECGKVFKSKSALREHMRTH 23
>gnl|CDD|236691 PRK10426, PRK10426, alpha-glucosidase; Provisional.
Length = 635
Score = 29.2 bits (66), Expect = 0.71
Identities = 24/112 (21%), Positives = 38/112 (33%), Gaps = 15/112 (13%)
Query: 11 SSTLSTHLLIHSDTRPYPCQYCGKR----FHQKSDMKKHTYI---HTGEKPHKCVVCGKA 63
S +S H L HSD Y + KR + + T + H G +P
Sbjct: 447 SLGMSGHGLHHSDIGGYTTLFGMKRTKELLLRWCEFSAFTPVMRTHEGNRPGDNW----Q 502
Query: 64 FSQSSNLITHLRK----HTGYKPFSCGLCDKAFQRKVDLRRHRESQHPGSPA 111
F + I H + T KP+ L +A + + + R + A
Sbjct: 503 FDSDAETIAHFARMTRVFTTLKPYLKELVAEAAKTGLPVMRPLFLHYEDDAA 554
>gnl|CDD|234777 PRK00481, PRK00481, NAD-dependent deacetylase; Provisional.
Length = 242
Score = 28.2 bits (64), Expect = 1.2
Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 9/48 (18%)
Query: 15 STHLL-IHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCG 61
S +++ +H C CG+ + +K +P +C CG
Sbjct: 110 SKNVIELHGSLLRARCTKCGQTYDLDEYLK--------PEPPRCPKCG 149
>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine
triphosphatases (GTPases)-like. Rho4 is a GTPase that
controls septum degradation by regulating secretion of
Eng1 or Agn1 during cytokinesis. Rho4 also plays a role
in cell morphogenesis. Rho4 regulates septation and cell
morphology by controlling the actin cytoskeleton and
cytoplasmic microtubules. The localization of Rho4 is
modulated by Rdi1, which may function as a GDI, and by
Rga9, which is believed to function as a GAP. In S.
pombe, both Rho4 deletion and Rho4 overexpression result
in a defective cell wall, suggesting a role for Rho4 in
maintaining cell wall integrity. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 197
Score = 27.3 bits (61), Expect = 2.4
Identities = 7/39 (17%), Positives = 13/39 (33%)
Query: 95 KVDLRRHRESQHPGSPAQQHHISSTSMIETPESITTQMH 133
K DLR+ + S ++ +SI +
Sbjct: 117 KTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAY 155
>gnl|CDD|214384 CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
Length = 296
Score = 27.2 bits (61), Expect = 2.9
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 1 CKQCGKTFKRSSTLSTHLLIHSDT 24
C+QCG K SS+ LLI T
Sbjct: 60 CEQCGYHLKMSSSDRIELLIDPGT 83
>gnl|CDD|239134 cd02669, Peptidase_C19M, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin
molecules from polyubiquinated peptides by cleavage of
isopeptide bonds. They hydrolyze bonds involving the
carboxyl group of the C-terminal Gly residue of
ubiquitin. The purpose of the de-ubiquitination is
thought to be editing of the ubiquitin conjugates,
which could rescue them from degradation, as well as
recycling of the ubiquitin. The ubiquitin/proteasome
system is responsible for most protein turnover in the
mammalian cell, and with over 50 members, family C19 is
one of the largest families of peptidases in the human
genome.
Length = 440
Score = 26.9 bits (60), Expect = 3.6
Identities = 16/54 (29%), Positives = 20/54 (37%), Gaps = 14/54 (25%)
Query: 2 KQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPH 55
K C S +LS + Y C CGK F + H Y H+ E H
Sbjct: 17 KVC------SVSLSNLNV-------YACLVCGKYFQGRGK-GSHAYTHSLEDNH 56
>gnl|CDD|172627 PRK14138, PRK14138, NAD-dependent deacetylase; Provisional.
Length = 244
Score = 26.7 bits (59), Expect = 4.5
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 35 RFHQKSDMKKHTYIHTGEKPHKCVVCGKAFSQSSNLITHLRKHTGYKPFSCG 86
R HQK+ KK +H + + CV CGK ++ ++I L K + C
Sbjct: 100 RLHQKAGSKKVIELHGNVEEYYCVRCGKRYT-VEDVIEKLEKSDVPRCDDCS 150
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 24.1 bits (53), Expect = 4.6
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 55 HKCVVCGKAFSQSSNLITHLRKH 77
H C VCGK FS L H + H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 26.1 bits (58), Expect = 4.7
Identities = 11/35 (31%), Positives = 13/35 (37%), Gaps = 13/35 (37%)
Query: 27 YPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCVVCG 61
+ C CG Y H GE P C +CG
Sbjct: 135 WVCPVCG-------------YTHEGEAPEVCPICG 156
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of
the virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA
plus-strand. lambda1 is an Orthoreovirus core protein,
VP3 is the homologous core protein in Aquareoviruses.
Length = 1166
Score = 26.3 bits (58), Expect = 6.4
Identities = 8/21 (38%), Positives = 9/21 (42%)
Query: 55 HKCVVCGKAFSQSSNLITHLR 75
+ C VC FS L H R
Sbjct: 74 YVCNVCMAEFSSMDQLAEHQR 94
>gnl|CDD|220438 pfam09845, DUF2072, Zn-ribbon containing protein (DUF2072). This
archaeal protein has no known function.
Length = 121
Score = 25.5 bits (56), Expect = 7.1
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 3/23 (13%)
Query: 54 PHKCVVCGKAFSQSSNLITHLRK 76
PH+C CGK F S T + K
Sbjct: 1 PHRCTKCGKIFEDGS---TEILK 20
>gnl|CDD|225899 COG3364, COG3364, Zn-ribbon containing protein [General function
prediction only].
Length = 112
Score = 25.3 bits (55), Expect = 7.5
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 54 PHKCVVCGKAFSQSSNLI 71
PH+C CG+ F S I
Sbjct: 2 PHQCTRCGEVFDDGSEEI 19
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 26.1 bits (57), Expect = 8.0
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 15/72 (20%)
Query: 1 CKQCGKTFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTYIHTGEKPHKCV-V 59
C +CG+ F RS HL GKR H K K ++++ H+ +
Sbjct: 241 CVKCGREFSRSKVFEYHLE-------------GKR-HCKEGQGKEEFVYSEYVLHRYLKY 286
Query: 60 CGKAFSQSSNLI 71
G S++ +L+
Sbjct: 287 LGDPVSETRSLV 298
>gnl|CDD|216497 pfam01429, MBD, Methyl-CpG binding domain. The Methyl-CpG
binding domain (MBD) binds to DNA that contains one or
more symmetrically methylated CpGs. DNA methylation in
animals is associated with alterations in chromatin
structure and silencing of gene expression. MBD has
negligible non-specific affinity for DNA. In vitro
foot-printing with MeCP2 showed the MBD can protect a
12 nucleotide region surrounding a methyl CpG pair.
MBDs are found in several Methyl-CpG binding proteins
and also DNA demethylase.
Length = 75
Score = 24.6 bits (54), Expect = 8.3
Identities = 8/24 (33%), Positives = 10/24 (41%)
Query: 60 CGKAFSQSSNLITHLRKHTGYKPF 83
GK F S LI +L K+
Sbjct: 38 TGKKFRSKSELIRYLEKNGDTSLK 61
>gnl|CDD|218911 pfam06147, DUF968, Protein of unknown function (DUF968). Family of
uncharacterized prophage proteins that are also found in
bacteria and eukaryotes.
Length = 200
Score = 25.7 bits (57), Expect = 8.3
Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 19/71 (26%)
Query: 53 KPHKCVVCGKAFSQSSNLITHLR-----KHTGYKPFSCGLCDKAFQRKVDLRRHRESQHP 107
K CV+CGK +LI H R KH LC R H + H
Sbjct: 126 KNRPCVICGKPADDLHHLIGHGRGRMGTKHHDLFVLP--LC----------REHHQELHR 173
Query: 108 GSPA--QQHHI 116
G + +++ +
Sbjct: 174 GVKSFEKKYGL 184
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
0.321 0.130 0.418
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,109,711
Number of extensions: 474053
Number of successful extensions: 556
Number of sequences better than 10.0: 1
Number of HSP's gapped: 544
Number of HSP's successfully gapped: 85
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.7 bits)