RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16882
(318 letters)
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 46.6 bits (110), Expect = 8e-06
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 13 HVCAECGKAFVESSKLKRHQ--LVHTGE--KPFQCTFEGCGKRFSLDFNLRTHVRIHTGD 68
+C +F SS L RH + H+GE KPF C + CGK FS + L+ H+ +HT
Sbjct: 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349
Query: 69 RPYVCPFDGCNKKFAQSTNLKSH 91
P + KF+ N +
Sbjct: 350 SPAKEKLLNSSSKFSPLLNNEPP 372
Score = 43.9 bits (103), Expect = 6e-05
Identities = 27/82 (32%), Positives = 35/82 (42%)
Query: 10 PRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDR 69
PR C C +F L RH HTGEKP QC++ GC K FS L H+R H +
Sbjct: 31 PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNP 90
Query: 70 PYVCPFDGCNKKFAQSTNLKSH 91
+ S++ S
Sbjct: 91 SDLNSKSLPLSNSKASSSSLSS 112
Score = 33.1 bits (75), Expect = 0.17
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 46 EGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTH 95
C FS +L H+R HTG++P C + GC+K F++ L H+ TH
Sbjct: 37 PNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 36.6 bits (85), Expect = 5e-04
Identities = 15/26 (57%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 28 LKRHQLVHTGEKPFQCTFEGCGKRFS 53
L+RH HTGEKP++C CGK FS
Sbjct: 2 LRRHMRTHTGEKPYKCPV--CGKSFS 25
Score = 36.2 bits (84), Expect = 6e-04
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 57 NLRTHVRIHTGDRPYVCPFDGCNKKFAQ 84
NLR H+R HTG++PY CP C K F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPV--CGKSFSS 26
Score = 26.6 bits (59), Expect = 1.7
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 1 MRKHLHTH-GPRVHVCAECGKAFV 23
+R+H+ TH G + + C CGK+F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFS 25
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 40.5 bits (94), Expect = 9e-04
Identities = 20/80 (25%), Positives = 30/80 (37%), Gaps = 23/80 (28%)
Query: 33 LVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIH--------------------TGDRPYV 72
L KP++C EGC K++ L+ H +H D+PY
Sbjct: 342 LKVKDGKPYKCPVEGCNKKYKNQNGLKYH-MLHGHQNQKLHENPSPEKMNIFSAKDKPYR 400
Query: 73 CPFDGCNKKFAQSTNLKSHI 92
C C+K++ LK H
Sbjct: 401 CEV--CDKRYKNLNGLKYHR 418
Score = 34.7 bits (79), Expect = 0.065
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 67 GDRPYVCPFDGCNKKFAQSTNLKSHIL 93
+PY CP +GCNKK+ LK H+L
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHML 372
>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 = 30.4 bits (69), Expect = 0.081
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 14 VCAECGKAFVESSKLKRHQLVH 35
C +CGK+F S LKRH H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.5 bits (59), Expect = 1.4
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 72 VCPFDGCNKKFAQSTNLKSHILTH 95
CP C K F++ +NLK H+ TH
Sbjct: 1 KCP--DCGKSFSRKSNLKRHLRTH 22
Score = 25.4 bits (56), Expect = 4.3
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 46 EGCGKRFSLDFNLRTHVRIH 65
CGK FS NL+ H+R H
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.8 bits (62), Expect = 0.58
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 13 HVCAECGKAFVESSKLKRHQLVH 35
+ C ECGK F S L+ H H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 1.4
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 71 YVCPFDGCNKKFAQSTNLKSHILTH 95
Y CP C K F + L+ H+ TH
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
Score = 25.1 bits (55), Expect = 4.8
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 41 FQCTFEGCGKRFSLDFNLRTHVRIH 65
++C CGK F LR H+R H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
>gnl|CDD|222154 pfam13470, PIN_3, PIN domain. Members of this family of bacterial
domains are predicted to be RNases (from similarities to
5'-exonucleases).
Length = 86
Score = 28.3 bits (64), Expect = 1.4
Identities = 14/42 (33%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 100 LLKGLFSLKMCPHILDEMKRHDGGYEETLHI-----PSD-HV 135
L GLF + ILDE + E I P D HV
Sbjct: 27 ALAGLFEPLISAEILDEYEELVEPTELGALILPLPDPDDNHV 68
>gnl|CDD|190042 pfam01567, Hanta_G1, Hantavirus glycoprotein G1. The medium (M)
genome segment of hantaviruses (family Bunyaviridae)
encodes the two virion glycoproteins. G1 and G2, as a
precursor protein in the complementary sense RNA.
Length = 525
Score = 29.7 bits (67), Expect = 2.2
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 4/67 (5%)
Query: 102 KGLFSLKM-CPHILDEMKRHDGGYEETLHIPSDHVNTVYLEETQVLDDHDNS---KKYIQ 157
+ ++ LK+ CPH + + + G E +P V + E + D H +S +K+ Q
Sbjct: 1 RNVYELKIECPHTVGLGQGYVTGSVELPPVPLTEVEQLVPESSCNFDLHQSSTTIQKFTQ 60
Query: 158 QKFIKKE 164
+ KK
Sbjct: 61 VSWRKKA 67
>gnl|CDD|219230 pfam06925, MGDG_synth, Monogalactosyldiacylglycerol (MGDG)
synthase. This family represents a conserved region of
approximately 180 residues within plant and bacterial
monogalactosyldiacylglycerol (MGDG) synthase
(EC:2.4.1.46). In Arabidopsis, there are two types of
MGDG synthase which differ in their N-terminal portion:
type A and type B.
Length = 169
Score = 28.9 bits (65), Expect = 2.7
Identities = 23/153 (15%), Positives = 48/153 (31%), Gaps = 27/153 (17%)
Query: 95 HAKAKLLKGLFSLKMCPHILDEMKRHDGGYEETLHIPSDHVNTVYLEETQV--------- 145
+ A+ L+ F+ + + HD +E V YL +
Sbjct: 2 NQAAEALREAFNNEFGDEYQVVV--HDS-LKELNPFLLKFVLRSYLFLVKHSRLYRLLYY 58
Query: 146 -LDDHDNSKKYIQQ----------KFIKKEEPECQITTHHNMVQIDKSSRKWEQKQVQI- 193
+ K + + +K+ +P+ I+TH + S K + ++
Sbjct: 59 GTEPKIPHKSILAKLATFFARELAALLKEFQPDIIISTHPLPAAVPLSVLKSKGLLKRVL 118
Query: 194 -RTLEGEFSVT--MWASGGTDDDECSNPEFEQE 223
T+ +F W D + E ++E
Sbjct: 119 VVTVVTDFRTCHPFWLHPEIDRYYVPSKEVKKE 151
>gnl|CDD|132752 cd06954, NR_LBD_LXR, The ligand binding domain of Liver X
receptors, a family of nuclear receptors of
ligand-activated transcription factors. The ligand
binding domain of Liver X receptors: Liver X receptors
(LXRs) belong to a family of nuclear receptors of
ligand-activated transcription factors. LXRs operate as
cholesterol sensors which protect from cholesterol
overload by stimulating reverse cholesterol transport
from peripheral tissues to the liver and its excretion
in the bile. Oxidized cholesterol derivatives or
oxysterols were identified as specific ligands for LXRs.
Upon ligand binding a conformational change leads to
recruitment of co-factors, which stimulates expression
of target genes. Among the LXR target genes are several
genes involved in cholesterol efflux from peripheral
tissues such as the ATP-binding-cassette transporters
ABCA1, ABCG1 and ApoE. There are two LXR isoforms in
mammals, LXRalpha and LXRbeta. LXRalpha is expressed
mainly in the liver, intestine, kidney, spleen, and
adipose tissue, whereas LXRbeta is ubiquitously
expressed at lower level. Both LXRalpha and LXRbeta
function as heterodimers with the retinoid X receptor
(RX R) which may be activated by either LXR ligands or
9-cis retinoic acid, a specific RXR ligand. The LXR/RXR
complex binds to a liver X receptor response element
(LXRE) in the promoter region of target genes. LXR has
typical NR modular structure with a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and the ligand
binding domain (LBD) at the C-terminal.
Length = 236
Score = 28.6 bits (64), Expect = 3.4
Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 188 QKQVQIRTLEGEFSVTMWASGG-TDDDECSNPEFEQEHEYEDCILTEQEI----KHEPIP 242
Q+Q R+ E VT W G E F H E IL+ QEI K +P
Sbjct: 12 QQQCNKRSFEDVPKVTPWPEGQDPQSREARQQRF--AHFTELAILSVQEIVDFAKQ--LP 67
Query: 243 G-IDLSDPKQLA 253
G + L+ Q+A
Sbjct: 68 GFLTLTREDQIA 79
>gnl|CDD|181199 PRK08020, ubiF, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Reviewed.
Length = 391
Score = 28.4 bits (64), Expect = 5.8
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 110 CPHILDEMKRHDGGYEETL 128
CP L ++R D G+E TL
Sbjct: 132 CPASLQALQRDDDGWELTL 150
>gnl|CDD|227293 COG4957, COG4957, Predicted transcriptional regulator
[Transcription].
Length = 148
Score = 27.3 bits (61), Expect = 6.2
Identities = 12/27 (44%), Positives = 13/27 (48%), Gaps = 3/27 (11%)
Query: 14 VCAECGKAFVESSKLKRHQLVHTGEKP 40
+C E GK F LKRH H G P
Sbjct: 78 ICLEDGKKF---KSLKRHLTTHYGLTP 101
>gnl|CDD|215532 PLN02982, PLN02982, galactinol-raffinose
galactosyltransferase/ghydrolase, hydrolyzing O-glycosyl
compounds.
Length = 865
Score = 28.2 bits (63), Expect = 6.4
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 2 RKHLHTHGPRVHV--CAECGKAFVESSKLKRHQLVHTGEKPF 41
R LH G HV CAE G V++S VH + P+
Sbjct: 152 RSALHP-GEDGHVMICAESGSTKVKASSFNSIAYVHVSDNPY 192
>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 = 27.1 bits (61), Expect = 6.5
Identities = 13/28 (46%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 14 VCAECGKAFVESSK-LKRHQLVHTGEKP 40
+C E GK F K LKRH H G P
Sbjct: 72 ICLEDGKKF----KTLKRHLRTHHGLTP 95
>gnl|CDD|238765 cd01488, Uba3_RUB, Ubiquitin activating enzyme (E1) subunit UBA3.
UBA3 is part of the heterodimeric activating enzyme
(E1), specific for the Rub family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins. consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin(-like) by C-terminal adenylation, and
subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis. UBA3
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 291
Score = 28.1 bits (63), Expect = 6.8
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 148 DHDNSKKYIQQKFIKKEEPECQITTHHNMVQIDKSSRKWEQKQVQI 193
D K + KF+ P +T H +Q DK + Q + I
Sbjct: 49 DIGKPKAEVAAKFVNDRVPGVNVTPHFGKIQ-DKDEEFYRQFNIII 93
>gnl|CDD|181699 PRK09206, PRK09206, pyruvate kinase; Provisional.
Length = 470
Score = 28.1 bits (63), Expect = 7.3
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 279 ANEVVPNVQNNGSSGANSGNNL 300
NEV+ V NNG G N G NL
Sbjct: 139 GNEVICKVLNNGDLGENKGVNL 160
>gnl|CDD|237748 PRK14537, PRK14537, 50S ribosomal protein L20/unknown domain fusion
protein; Provisional.
Length = 230
Score = 27.6 bits (61), Expect = 7.4
Identities = 19/121 (15%), Positives = 47/121 (38%), Gaps = 5/121 (4%)
Query: 149 HDNSKKYIQQKFIKKEEPECQITTHHNMVQIDKSSRKWEQKQVQIRTLEGEFSVTMWASG 208
H + ++Q + K+ +T + + ++K + + S
Sbjct: 100 HLQPEVFVQYVELAKKFLSQFQSTTITKPKKVLINEVLQEKTINQNEEKTSLQNEKVLSP 159
Query: 209 GTDDDECSNPEFEQEHEYEDCILTEQEIKHEPIPGIDLSDPKQLAEFASVNNYRPGNNKI 268
+++ S+ E E + + + I+H + + L + K+LA+ + N+ NK+
Sbjct: 160 ELSEEK-SDSELETQPQKTQLKEKKPSIEHIDLSKMLLKELKKLAKEHKIPNF----NKL 214
Query: 269 K 269
K
Sbjct: 215 K 215
>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 = 24.5 bits (53), Expect = 9.3
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 71 YVCPFDGCNKKFAQSTNLKSHILTH 95
+ CP C K F+ LK H+ H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
Score = 24.5 bits (53), Expect = 9.5
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 13 HVCAECGKAFVESSKLKRHQLVH 35
C CGK+F LKRH H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
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
0.317 0.133 0.408
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,489,698
Number of extensions: 1411446
Number of successful extensions: 1169
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1161
Number of HSP's successfully gapped: 32
Length of query: 318
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 221
Effective length of database: 6,635,264
Effective search space: 1466393344
Effective search space used: 1466393344
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: 59 (26.7 bits)