RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14605
(139 letters)
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 52.5 bits (126), Expect = 2e-10
Identities = 24/51 (47%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 14 YCEVCQQ---GGEIILCDTCPRAYHLCCLDPELDET--PEGKWSCPRCVSD 59
YC VC + GE++LCD C R +HL CL P L+ PEG+W CP C
Sbjct: 1 YCAVCGKVDDDGELLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPECKPK 51
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet
known if PHD fingers have a common molecular function.
Several reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is
a ubiquitin ligase have been refuted as these domains
were RING fingers misidentified as PHD fingers.
Length = 47
Score = 48.7 bits (116), Expect = 5e-09
Identities = 24/47 (51%), Positives = 30/47 (63%), Gaps = 4/47 (8%)
Query: 14 YCEVCQQ---GGEIILCDTCPRAYHL-CCLDPELDETPEGKWSCPRC 56
YC VC + GGE++ CD C R YH C P L+E P+GKW CP+C
Sbjct: 1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
>gnl|CDD|240069 cd04718, BAH_plant_2, BAH, or Bromo Adjacent Homology domain,
plant-specific sub-family with unknown function. BAH
domains are found in a variety of proteins playing
roles in transcriptional silencing and the remodeling
of chromatin. It is assumed that in most or all of
these instances the BAH domain mediates protein-protein
interactions.
Length = 148
Score = 41.4 bits (97), Expect = 2e-05
Identities = 17/35 (48%), Positives = 21/35 (60%)
Query: 34 YHLCCLDPELDETPEGKWSCPRCVSDGPPETASPP 68
+HLCCL P L E PEG W CP C + ++A P
Sbjct: 2 FHLCCLRPPLKEVPEGDWICPFCEVEKSGQSAMPQ 36
>gnl|CDD|213032 cd11672, ADDz, ADDz for ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger
domain. The ADDz zinc finger domain is present in the
chromatin-associated proteins
cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2
type transcription factor protein. The Dnmt3 family
includes two active DNA methyltransferases, Dnmt3a and
-3b, and one regulatory factor Dnmt3l. DNA methylation
is an important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The ADDz domain is a
PHD-like zinc finger motif that contains two parts, a
C2-C2 and a PHD-like zinc finger. PHD zinc finger
domains have been identified in more than 40 proteins
that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif.
Length = 120
Score = 38.0 bits (89), Expect = 2e-04
Identities = 24/61 (39%), Positives = 28/61 (45%), Gaps = 14/61 (22%)
Query: 12 QDYCEVCQQGGEIILCDT--CPRAY------HLCC---LDPELDETPEGKWSCPRCVSDG 60
Q YC +C GGE+ILCD C R Y L D LDE P WSC C+ +
Sbjct: 47 QSYCTICCGGGEVILCDNESCCRVYCTACLDFLVGPGTYDKVLDEDP---WSCYLCLPES 103
Query: 61 P 61
Sbjct: 104 K 104
>gnl|CDD|213033 cd11725, ADDz_Dnmt3, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 (Dnmt3). Dnmt3 is a de
novo DNA methyltransferase family that includes two
active enzymes Dnmt3a and -3b and one regulatory factor
Dnmt3l. The ADDz domain of Dnmt3 is located in the
C-terminal region of Dnmt3, which is an active catalytic
domain in Dnmt3a and -b, but lacks some residues for
enzymatic activity in Dnmt3l. DNA methylation is an
important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The ADDz_Dnmt3
domain is a PHD-like zinc finger motif that contains two
parts, a C2-C2 and a PHD-like zinc finger. PHD zinc
finger domains have been identified in more than 40
proteins that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif.
Length = 126
Score = 36.8 bits (86), Expect = 6e-04
Identities = 22/59 (37%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 12 QDYCEVCQQGGEIILCDT--CPRAYHLCCLDPELDET------PEGKWSCPRCVSDGPP 62
Q YC +C GGE+ILCD C R Y CLD + E WSC C+ +
Sbjct: 47 QSYCTICCGGGEVILCDNESCCRVYCTACLDILVGPGTYDKVLLEDPWSCYLCLPESKQ 105
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 37.2 bits (86), Expect = 0.001
Identities = 22/48 (45%), Positives = 28/48 (58%), Gaps = 8/48 (16%)
Query: 14 YCEVCQQG--GEIILCDT--CPRA-YHLCCLDPELDETPEGKWSCPRC 56
YC CQQ G+++ CD C R +HL C+ L E P+GKW CP C
Sbjct: 223 YC-FCQQVSYGQMVACDNANCKREWFHLECVG--LKEPPKGKWYCPEC 267
>gnl|CDD|213034 cd11726, ADDz_ATRX, ADDz domain of ATRX (alpha-thalassemia/mental
retardation, X-linked). ADDz_ATRX is a PHD-like zinc
finger domain of ATRX, which belongs to the SNF2 family
of chromatin remodeling proteins. ATRX is a large
chromatin-associated nuclear protein with two domains,
ADDz_ATRX at the N-terminus, followed by a C-terminal
ATPase/helicase domain. The ADDz_ATRX domain recognizes
a specific methylated histone, and this interaction is
required for heterochromatin localization of the ATRX
protein. Missense mutations in either of the two ATRX
domains lead to the X-linked alpha-thalassemia and
mental retardation syndrome; however the mutations in
the ADDz_ATRX domain produce a more severe disease
phenotype that may also relate to disturbing unknown
functions or interaction sites of this domain. The ADDz
domain is also present in chromatin-associated proteins
cytosine-5-methyltransferase 3 (Dnmt3); it is a PHD-like
zinc finger motif that contains two parts, a C2-C2 and a
PHD-like zinc finger. PHD zinc finger domains have been
identified in more than 40 proteins that are mainly
involved in chromatin mediated transcriptional control;
the classical PHD zinc finger has a C4-H-C3 motif that
spans about 50-80 amino acids. In ADDz, the conserved
histidine residue of the PHD finger is replaced by a
cysteine, and an additional zinc finger C2-C2 like motif
is located about twenty residues upstream of the C4-C-C3
motif.
Length = 127
Score = 35.0 bits (81), Expect = 0.003
Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 14 YCEVCQQGGEIILCDTCPRAYHLCC----LDPEL--DETPEGKWSCPRC 56
YC C +GGE+I CD+CP A+ C L E + E KW C C
Sbjct: 58 YCRWCGEGGELICCDSCPNAFCKKCIKRNLGREELSEIEDEDKWKCFVC 106
>gnl|CDD|213036 cd11728, ADDz_Dnmt3b, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 b (Dnmt3b).
ADDz_Dnmt3b is an active catalytic domain of Dnmt3b.
Dnmt3b is a member of the Dnmt3 family and is a de novo
DNA methyltransferases that has an N-terminal variable
region followed by a conserved PWWP region and the
cysteine-rich ADDz domain. DNA methylation is an
important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The
methyltransferase activity of Dnmt3a is not only
responsible for the establishment of DNA methylation
pattern, but is also essential for the inheritance of
these patterns during mitosis. Dnmt3b is ubiquitously
expressed in most adult tissues. The ADDz_Dnmt3 domain
is a PHD-like zinc finger motif that contains two parts,
a C2-C2 and a PHD-like zinc finger. PHD zinc finger
domains have been identified in more than 40 proteins
that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif. A knockout of Dnmt3b has
been shown to be lethal in the mouse model.
Length = 150
Score = 30.1 bits (68), Expect = 0.18
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 11 HQDYCEVCQQGGEIILCD--TCPRAYHLCCLDPELDETPEGK------WSCPRC 56
+Q YC VC +G E++LC +C R + + CLD + WSC C
Sbjct: 59 YQSYCTVCCEGRELLLCSNASCCRCFCVECLDVLVGPGTSANAKEQEPWSCYMC 112
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 30.7 bits (69), Expect = 0.22
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 18 CQQGGEIILCDTCPRAYHLCCLDPELDETPEGKWSCPRCV 57
+ I+ CD C H C + PEG W C +C+
Sbjct: 204 NENSNAIVFCDGCEICVHQSCYG--IQFLPEGFWLCRKCI 241
>gnl|CDD|223800 COG0728, MviN, Uncharacterized membrane protein, putative virulence
factor [General function prediction only].
Length = 518
Score = 29.6 bits (67), Expect = 0.52
Identities = 8/20 (40%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 118 ARIYGQMARQILLALFLGTG 137
+RI G R +L+A G G
Sbjct: 23 SRILG-FVRDVLIAAAFGAG 41
>gnl|CDD|222368 pfam13771, zf-HC5HC2H, PHD-like zinc-binding domain. The members
of this family are annotated as containing PHD domain,
but the zinc-binding region here is not typical of PHD
domains. The conformation here is a well-conserved
cysteine-histidine rich region spanning 90 residues,
where the Cys and His are arranged as
HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.
Length = 89
Score = 27.7 bits (62), Expect = 0.81
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 15 CEVCQQGGEIILCD--TCPRAYHLCC 38
C +C++ G I C C RA+H+ C
Sbjct: 39 CSLCKKKGACIGCCVKNCRRAFHVTC 64
>gnl|CDD|172646 PRK14158, PRK14158, heat shock protein GrpE; Provisional.
Length = 194
Score = 28.0 bits (62), Expect = 1.3
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 58 SDGPPETASPPAEEVKEKEVLCAFLKFQSAKDIDLAIQRGHWERRRYDRD--REKEKKEK 115
+ G PE A P A + KE+ A +AK+ + A + R R D + R++ +KEK
Sbjct: 26 AQGKPEAAQPVAAADRIKELEEAL----AAKEAEAAANWDKYLRERADLENYRKRVQKEK 81
Query: 116 EEARIYG 122
EE YG
Sbjct: 82 EELLKYG 88
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 28.5 bits (64), Expect = 1.4
Identities = 10/52 (19%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 88 KDIDLAIQRGHWERRRYDRDREKEKKEKEEARIYGQMARQIL--LALFLGTG 137
+I LA+ + + Y + +E +E+++ + + +I LA L
Sbjct: 445 NEIRLALMEVARKLKLYLSRKRREMEERKKRKTIEKYLPEIAKKLAEILEKP 496
>gnl|CDD|213035 cd11727, ADDz_Dnmt3l, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 like (Dnmt3l). Dnmt3l
is a regulator of DNA methylation, which acts by
recognizing unmethylated histone H3 tails and
interacting with Dnmt3a to stimulate its de novo DNA
methylation activity. The ADDz_Dnmt3l domain is located
in the C-terminal region of Dnmt3l that otherwise lacks
some residues required for DNA methyltransferase
activity. DNA methylation is an important epigenetic
mechanism involved in diverse biological processes such
as embryonic development, gene expression, and genomic
imprinting. Dnmt3l is also associating with HDAC1 and
acts as a transcriptional repressor. The ADDz_Dnmt3l
domain is a PHD-like zinc finger motif that contains
two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc
finger domains have been identified in more than 40
proteins that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional
zinc finger C2-C2 like motif is located about twenty
residues upstream of the C4-C-C3 motif.
Length = 149
Score = 27.8 bits (62), Expect = 1.4
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 11 HQDYCEVCQQGGEIILCDT--CPRAYHLCCLD 40
+Q YC +C G +++C+ C R Y C+D
Sbjct: 59 YQSYCSICCSGETLLICENPDCTRCYCFECVD 90
>gnl|CDD|152107 pfam11671, Apis_Csd, Complementary sex determiner protein. This
family of proteins represents the complementary sex
determiner in the honeybee. In the honeybee, the
mechanism of sex determination depends on the csd gene
which produces an SR-type protein. Males are homozygous
while females are homozygous for the csd gene.
Heterozygosity generates an active protein which
initiates female development.
Length = 146
Score = 27.4 bits (60), Expect = 2.2
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 101 RRRYDRDREKEKKEKEEARIYGQ 123
R+RY R RE+E+K + Y +
Sbjct: 3 RKRYSRSREREQKSYKNENSYRE 25
>gnl|CDD|185558 PTZ00329, PTZ00329, eukaryotic translation initiation factor 1A;
Provisional.
Length = 155
Score = 27.1 bits (60), Expect = 2.5
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 96 RGHWERRRYDRDREKEKKE---KEEARIYGQMAR 126
+G RRR D E EK+E KEE + Y Q+ R
Sbjct: 7 KGGKNRRRGKNDNEGEKRELVFKEEGQEYAQVLR 40
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and
plant flowering time control protein FCA. This
subfamily corresponds to the RRM1 and RRM2 domains of
the CUGBP1 and ETR-3-like factors (CELF) as well as
plant flowering time control protein FCA. CELF, also
termed BRUNOL (Bruno-like) proteins, is a family of
structurally related RNA-binding proteins involved in
regulation of pre-mRNA splicing in the nucleus, and
control of mRNA translation and deadenylation in the
cytoplasm. The family contains six members: CELF-1
(also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP),
CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2,
NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1,
CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5)
and CELF-6 (BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both, sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 26.0 bits (58), Expect = 3.1
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 79 CAFLKFQSAKDIDLAIQRGH 98
CAF+KF S ++ AI+ H
Sbjct: 43 CAFVKFSSREEAQKAIEALH 62
>gnl|CDD|223898 COG0828, RpsU, Ribosomal protein S21 [Translation, ribosomal
structure and biogenesis].
Length = 67
Score = 25.7 bits (57), Expect = 3.1
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 100 ERRRYDRDREKEKKEKEEAR 119
ER Y++ EK K++K AR
Sbjct: 34 EREFYEKPSEKRKRKKAAAR 53
>gnl|CDD|151199 pfam10706, Aminoglyc_resit, Aminoglycoside-2''-adenylyltransferase.
This family is conserved in Bacteria. It confers
resistance to kanamycin, gentamicin, and tobramycin. The
protein is also produced by plasmids in various
bacterial species and confers resistance to essentially
all clinically available aminoglycosides except
streptomycin, and it eliminates the synergism between
aminoglycosides and cell-wall active agents.
Length = 174
Score = 26.8 bits (59), Expect = 3.3
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 9 TEHQDYCEVCQQGGEIILCDTCPRAYHLCCLDPELDETPEGKWSCP 54
TE DY + Q G ++ C+ R E++ P G SCP
Sbjct: 69 TEQTDYGFLAQSQGILLDCEPAVRIDD----AYEIEGLPPG--SCP 108
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 27.2 bits (61), Expect = 3.6
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 88 KDIDLAIQRGHWERRRYDRDREKEKKEKEEARIYGQ----MARQILLALFLG 135
K+I LA+Q + ++Y + KE++ K++A+ + + +AR+ LA L
Sbjct: 442 KEIRLALQEVARKLKKYLSRKRKEEEAKKKAKTFEKYIPEIARK--LAEILE 491
>gnl|CDD|213037 cd11729, ADDz_Dnmt3a, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 a (Dnmt3a). Dnmt3a is
a member of the Dnmt3 family and is a protein with de
novo DNA methyltransferase activity. Dnmt3 family
members are Dnmt3a, Dnmt3b, and Dnmt3l the non-enzymatic
regulatory factor. Dnmt3a is recruited by Dnmt3l to
unmethylated histone H3 and methylates the target.
Dnmt3a has a variable region at the N-terminus, followed
by a conserved PWWP region and the cysteine-rich ADDz
domain. ADDz_Dnmt3a is an active catalytic domain of
Dnmt3a. DNA methylation is an important epigenetic
mechanism involved in diverse biological processes such
as embryonic development, gene expression, and genomic
imprinting. The methyltransferase activity of Dnmt3a is
not only responsible for the establishment of DNA
methylation pattern, but is also essential for the
inheritance of these patterns during mitosis. The
ADDz_Dnmt3 domain is a PHD-like zinc finger motif that
contains two parts, a C2-C2 and a PHD-like zinc finger.
PHD zinc finger domains have been identified in more
than 40 proteins that are mainly involved in chromatin
mediated transcriptional control; the classical PHD zinc
finger has a C4-H-C3 motif that spans about 50-80 amino
acids. In ADDz, the conserved histidine residue of the
PHD finger is replaced by a cysteine, and an additional
zinc finger C2-C2 like motif is located about twenty
residues upstream of the C4-C-C3 motif. A knockout of
Dnmt3a has been shown to be lethal in the mouse model.
Length = 137
Score = 26.3 bits (58), Expect = 4.5
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 12/60 (20%)
Query: 11 HQDYCEVCQQGGEIILC--DTCPRAYHLCCLDPELDETP--------EGKWSCPRCVSDG 60
+Q YC +C G E+++C + C R + + C+D L P E W+C C G
Sbjct: 56 YQSYCTICCGGREVLMCGNNNCCRCFCVECVD--LLVGPGAAQAAIKEDPWNCYMCGHKG 113
>gnl|CDD|223295 COG0217, COG0217, Uncharacterized conserved protein [Function
unknown].
Length = 241
Score = 26.4 bits (59), Expect = 4.9
Identities = 6/29 (20%), Positives = 17/29 (58%)
Query: 110 KEKKEKEEARIYGQMARQILLALFLGTGD 138
K ++ + ++I+ ++ ++I +A G D
Sbjct: 14 KAAQDAKRSKIFTKLIKEITVAAKQGGPD 42
>gnl|CDD|215343 PLN02638, PLN02638, cellulose synthase A (UDP-forming), catalytic
subunit.
Length = 1079
Score = 26.8 bits (59), Expect = 5.1
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 14/63 (22%)
Query: 15 CEVCQQG------GE-IILCDTCPRAYHLC--CLDPELDETPEGKWSCPRCVSDGPPETA 65
C++C GE + CD C A+ +C C + E +G SCP+C +
Sbjct: 20 CQICGDNVGKTVDGEPFVACDVC--AFPVCRPCYEYE---RKDGNQSCPQCKTKYKRHKG 74
Query: 66 SPP 68
SP
Sbjct: 75 SPA 77
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease,
contains DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 26.6 bits (59), Expect = 5.7
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 6 DLQTEHQDYCEVCQQGGEIILCDTCPR 32
DL + C C+ G + + DTCP
Sbjct: 47 DLFASFEIPCPKCRGKGTVTVYDTCPE 73
>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein. Circoviruses
are small circular single stranded viruses. This family
is the capsid protein from viruses such as porcine
circovirus and beak and feather disease virus. These
proteins are about 220 amino acids long.
Length = 237
Score = 26.3 bits (58), Expect = 6.4
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 96 RGHWERRRYDRDREKEKKEKEEARIYG-QMARQILLALFLGTGD 138
R HW RR R ++ RIY ++ RQ +F GTG
Sbjct: 18 RRHWRRRYRRRRLHINRRRHRTNRIYTFRLTRQFKFTIFKGTGS 61
>gnl|CDD|162743 TIGR02172, Fb_sc_TIGR02172, Fibrobacter succinogenes paralogous
family TIGR02172. This model describes a paralogous
family of five proteins, likely to be enzymes, in the
rumen bacterium Fibrobacter succinogenes S85. Members
show homology to proteins described by pfam01636, a
phosphotransferase enzyme family associated with
resistance to aminoglycoside antibiotics. However,
members of this family score below the current trusted
and noise cutoffs for pfam01636.
Length = 226
Score = 25.9 bits (57), Expect = 7.9
Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 45 ETPEGKWSCPRCVSDGP---PETASPPAEEVKEKEVL-CAFLKFQSAKD 89
E GK S R +SD P E A AE K+ C FQS K+
Sbjct: 74 ELIVGKRSFSRIISDNPSRLEEIAKIFAEMAKKLHSTKCDTSTFQSYKE 122
>gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin)
oxidoreductase, homodimeric. This model represents a
single chain form of pyruvate:ferredoxin (or flavodoxin)
oxidoreductase. This enzyme may transfer electrons to
nitrogenase in nitrogen-fixing species. Portions of this
protein are homologous to gamma subunit of the four
subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.
Length = 1165
Score = 26.3 bits (58), Expect = 8.1
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 93 AIQRGHWERRRYDRDREKEKKE 114
A++ G+W RY+ ++ K
Sbjct: 1087 AVESGYWPLYRYNPRLAEQGKN 1108
>gnl|CDD|212510 cd11724, TP_methylase_like, Uncharacterized subfamily of S-AdoMet
dependent tetrapyrrole methylases. TP-methylases use
S-AdoMet (S-adenosyl-L-methionine or SAM) in the
methylation of diverse substrates. Most members catalyze
various methylation steps in cobalamin (vitamin B12)
biosynthesis, other members like Diphthine synthase and
Ribosomal RNA small subunit methyltransferase I (RsmI)
act on other substrates. The function of this subfamily
is not known.
Length = 255
Score = 25.7 bits (57), Expect = 8.5
Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 8/72 (11%)
Query: 60 GPPETASPPAEEVKEKEVLCA----FLKFQSAKDIDLAIQRGHWERRRYDRDREKEKKEK 115
P E A+ +K K VL F + +L + R + EK+++ +
Sbjct: 32 CPKEIVKRFADYLKGKPVLEDPWKLFWHYGGKPWENLE----AEKSPREAFEEEKKRQRE 87
Query: 116 EEARIYGQMARQ 127
E ++ + Q
Sbjct: 88 EFVKVIREALAQ 99
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
0.319 0.137 0.438
Gapped
Lambda K H
0.267 0.0598 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,244,566
Number of extensions: 644180
Number of successful extensions: 1010
Number of sequences better than 10.0: 1
Number of HSP's gapped: 996
Number of HSP's successfully gapped: 55
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
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 (21.8 bits)
S2: 54 (24.9 bits)