RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4404
(151 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 35.1 bits (81), Expect = 6e-04
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 55 HMRRHIRRHTGEKAFHCPHCEYRCSQ 80
++RRH+R HTGEK + CP C S
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 30.1 bits (68), Expect = 0.039
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 83 ALYNHLKRHTGEKPFKCTICSHKAAR 108
L H++ HTGEKP+KC +C +
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|227311 COG4977, COG4977, Transcriptional regulator containing an amidase
domain and an AraC-type DNA-binding HTH domain
[Transcription].
Length = 328
Score = 29.9 bits (68), Expect = 0.42
Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 19/75 (25%)
Query: 8 YCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEK 67
Y +RLE ++ LLE LS +++ C + ++ H R RR G
Sbjct: 269 YLRLRLER-ARRLLEQ----TRLSIAEIAVA-------CGF--SSASHFSRAFRRQFGLS 314
Query: 68 AFHCPHCEYRCSQQS 82
P EYR +S
Sbjct: 315 ----PS-EYRRRFRS 324
>gnl|CDD|238703 cd01412, SIRT5_Af1_CobB, SIRT5_Af1_CobB: Eukaryotic, archaeal and
prokaryotic group (class3) which includes human sirtuin
SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli
CobB; 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, metabolic enzymes, and life span.
CobB is a bacterial sirtuin that deacetylates acetyl-CoA
synthetase at an active site lysine to stimulate its
enzymatic activity. .
Length = 224
Score = 29.1 bits (66), Expect = 0.74
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 6 CQYCEVRLESNS---KELLEHCKTCKNLSRPDV 35
C C E+N +E L C C L RP V
Sbjct: 112 CSSCGYVGENNEEIPEEELPRCPKCGGLLRPGV 144
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.9 bits (57), Expect = 1.3
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 69 FHCPHCEYRCSQQSALYNHLKRH 91
+ CP C +SAL H++ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|198347 cd07769, FGGY_GK, Glycerol kinases; a subfamily of the FGGY family
of carbohydrate kinases. This subfamily includes
glycerol kinases (GK; EC 2.7.1.30) and glycerol
kinase-like proteins from all three kingdoms of living
organisms. Glycerol is an important intermediate of
energy metabolism and it plays fundamental roles in
several vital physiological processes. GKs are involved
in the entry of external glycerol into cellular
metabolism. They catalyze the rate-limiting step in
glycerol metabolism by transferring a phosphate from ATP
to glycerol thus producing glycerol 3-phosphate (G3P) in
the cytoplasm. Human GK deficiency, called
hyperglycerolemia, is an X-linked recessive trait
associated with psychomotor retardation, osteoporosis,
spasticity, esotropia, and bone fractures. Under
different conditions, GKs from different species may
exist in different oligomeric states. The monomer of GKs
is composed of two large domains separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain. The high affinity ATP binding site of GKs is
created only by a substrate-induced conformational
change. Based on sequence similarity, some GK-like
proteins from metazoa, which have lost their GK
enzymatic activity, are also included in this CD.
Members in this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 484
Score = 28.0 bits (63), Expect = 2.0
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 2/21 (9%)
Query: 80 QQSALYNHLKRHTGEKPFKCT 100
QQ+AL+ G+ KCT
Sbjct: 242 QQAALFGQGCFEAGDA--KCT 260
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and recognises
the first three GAG bases of the consensus in a manner
similar to that seen in other classical zinc finger-DNA
complexes. The second basic region forms a helix that
interacts in the major groove recognising the last G of
the consensus, while the first basic region wraps around
the DNA in the minor groove and recognises the A in the
fourth position of the consensus sequence.
Length = 54
Score = 26.1 bits (57), Expect = 2.2
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 90 RHTGEKPFKCTICSHKAARKDHMKRHLQLKH 120
+ E+P C IC + +++RHL+L+H
Sbjct: 18 KSQSEQPATCPICQAVIRQSRNLRRHLELRH 48
>gnl|CDD|222324 pfam13695, zf-3CxxC, Zinc-binding domain. This is a family with
several pairs of CxxC motifs possibly representing a
multiple zinc-binding region. Only one pair of
cysteines is associated with a highly conserved
histidine residue.
Length = 96
Score = 26.2 bits (58), Expect = 3.8
Identities = 16/56 (28%), Positives = 21/56 (37%), Gaps = 7/56 (12%)
Query: 24 CKTCKNLSRPDVSFKYVC-LYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRC 78
CK C+ L RP + YV + +C G S H + G PH C
Sbjct: 41 CKKCQRLERPYLDENYVERIAYRCYKWAGISVEKPPHSGKSKG------PHNRELC 90
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 27.2 bits (61), Expect = 4.1
Identities = 18/66 (27%), Positives = 23/66 (34%), Gaps = 18/66 (27%)
Query: 53 SDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKP----FKCTICSHKAAR 108
SD R ++ CPHC Q + LK GE P + C C
Sbjct: 194 SDQRRYYVP---------CPHCGEE---QELRWERLKWDKGEAPETARYVCPHCGCVIE- 240
Query: 109 KDHMKR 114
+H KR
Sbjct: 241 -EHHKR 245
>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 = 24.6 bits (54), Expect = 4.3
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 71 CPHCEYRCSQQSALYNHLKRH 91
CP C S++S L HL+ H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|223048 PHA03333, PHA03333, putative ATPase subunit of terminase;
Provisional.
Length = 752
Score = 27.1 bits (60), Expect = 4.6
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 12/60 (20%)
Query: 60 IRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLK 119
++ TG+ H +++C H + C C+ DH+ LK
Sbjct: 344 VKDETGKTLVHVIDQQFKC----------DAHAQDPGITC-PCN-DVFCPDHITVDEGLK 391
>gnl|CDD|176204 cd08242, MDR_like, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family, including threonine dehydrogenase.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class
I mammalian ADH. MDRs display a broad range of
activities and are distinguished from the smaller short
chain dehydrogenases (~ 250 amino acids vs. the ~ 350
amino acids of the MDR). The MDR proteins have 2
domains: a C-terminal NAD(P) binding-Rossmann fold
domain of a beta-alpha form and an N-terminal catalytic
domain with distant homology to GroES. The MDR group
includes various activities, including the founding
alcohol dehydrogenase (ADH), quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase,
and numerous others. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Active site zinc has a catalytic role, while structural
zinc aids in stability. ADH-like proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit. The active site
zinc is coordinated by a histidine, two cysteines, and
a water molecule. The second zinc seems to play a
structural role, affects subunit interactions, and is
typically coordinated by 4 cysteines.
Length = 319
Score = 26.4 bits (59), Expect = 6.1
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 3/27 (11%)
Query: 61 RRHTGEKAFHCPHCEYRCSQQSALYNH 87
+R GE C CEY C + LY H
Sbjct: 73 KRVVGEINIACGRCEY-C--RRGLYTH 96
>gnl|CDD|219599 pfam07832, Bse634I, Cfr10I/Bse634I restriction endonuclease.
Cfr10I and Bse634I are two Type II restriction
endonucleases. They exhibit a conserved tetrameric
architecture that is of functional importance, wherein
two dimers are arranged 'back-to-back' with their
putative DNA-binding clefts facing opposite directions.
These clefts are formed between two monomers that
interact, mainly via hydrophobic interactions supported
by a few hydrogen bonds, to form a U-shaped dimer. Each
monomer is folded to form a compact alpha-beta
structure, whose core is made up of a five-stranded
mixed beta-sheet.The monomer may be split into separate
N-terminal and C-terminal subdomains at a hinge located
in helix alpha3.
Length = 281
Score = 26.4 bits (58), Expect = 6.8
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 82 SALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLKHNADL 124
S LY L+ K I + R D R Q H A++
Sbjct: 171 SGLYKRLQGKVQPGEIKAAISLKTSLRPD---RRYQPLHEANV 210
>gnl|CDD|184731 PRK14536, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 490
Score = 26.4 bits (58), Expect = 6.8
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 35 VSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKA 68
+S KY L ++C H G DH+R H HT E A
Sbjct: 225 MSMKY--LGEQCDIHIGGVDHIRVH---HTNEIA 253
>gnl|CDD|128877 smart00615, EPH_lbd, Ephrin receptor ligand binding domain.
Length = 177
Score = 26.1 bits (58), Expect = 7.1
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 43 YQKCSYHTGNSDH--MRRHIRRHTGEKAF 69
YQ C+ GN ++ IRR ++ +
Sbjct: 40 YQVCNVQEGNQNNWLRTNFIRRRGAQRIY 68
>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 = 26.2 bits (58), Expect = 7.8
Identities = 13/37 (35%), Positives = 14/37 (37%), Gaps = 3/37 (8%)
Query: 4 VICQYCE---VRLESNSKELLEHCKTCKNLSRPDVSF 37
V C C R E +E C C L RPDV
Sbjct: 114 VRCTSCGKEYPRDEVLEREKPPRCPKCGGLLRPDVVD 150
>gnl|CDD|128804 smart00531, TFIIE, Transcription initiation factor IIE.
Length = 147
Score = 25.8 bits (57), Expect = 8.3
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 54 DHMRRHIRR----HTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTIC 102
D MR+ + T + CP+C+ + + A N L G F C C
Sbjct: 81 DKMRKRLEDKLEDETNNAYYKCPNCQSKYTFLEA--NQLLDMDGT--FTCPRC 129
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
0.324 0.134 0.434
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,205,128
Number of extensions: 587596
Number of successful extensions: 864
Number of sequences better than 10.0: 1
Number of HSP's gapped: 858
Number of HSP's successfully gapped: 62
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.6 bits)