RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2279
(830 letters)
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 266 bits (682), Expect = 2e-78
Identities = 140/457 (30%), Positives = 211/457 (46%), Gaps = 48/457 (10%)
Query: 49 YKHLDSIS-RPTAYIRFI-EKNADELDEEVEYDMDEEDASWLNIMNEQRKISNLPPLAID 106
KH +FI + L V YD+DE D WL +NE I ++ +
Sbjct: 102 SKHAPMSEESHDEGKKFIDIEPPRGLFFSVIYDLDEYDTMWLRYLNE-SAIDE--NVSEE 158
Query: 107 TFELLMDRLEKECQFQMSHTQSQDI----IDDE--AVCCICNDGECQNSNVILFCDMCNL 160
FE+++ RLEKE F + + DE +C C +NSN I+FCD C +
Sbjct: 159 AFEIIVTRLEKEWFFFEHGLPDKHVEPIEPSDEFDDICTKCTSTHNENSNAIVFCDGCEI 218
Query: 161 AVHQDCYGVPYIPEGQWLCRRCLHTPSRAVDCVLCPNNGGAFKLTDRGAWAHVVCALWIP 220
VHQ CYG+ ++PEG WLCR+C++ + C CP++ GAFK T G W HV+CA++ P
Sbjct: 219 CVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGHVICAMFNP 278
Query: 221 EVRFANTVFLEPIDSIEAIPAARWKLTCYVCKQRGVGACIQCHKTNCYAAFHVTCAQQAG 280
E+ F + + +PID+I ++ ++RWKL C +CK+ G G CIQC NC A+HVTCA++AG
Sbjct: 279 ELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFG-GTCIQCSYFNCTRAYHVTCARRAG 337
Query: 281 LYMNMDTIRDHSGVEPVVVQKLAYCDAHTPPDVQHRPRLPAPSDEKLKNARLVLA---KK 337
+ I H+G+ + + C H P L EKL+ A K
Sbjct: 338 YFDL--NIYSHNGISYCIDHE-PLCRKHYPLGYGRMNGLRYFGYEKLRYKNPPTAIPRKV 394
Query: 338 RVSVPTVSI--------PTIPPERVQDIAQLISVPKKSQLMNRLI----AYWTIKRQLRN 385
R + P ++ P P + + K Q + I YW +KR+
Sbjct: 395 RAARPRATLFMKLCWKQPPATPSVLSRVEACDLKEKDRQDLPVNIFDICKYWEMKRKSEI 454
Query: 386 GVPLLRR--LQSSHQARRDEHCKIMSNTPENGNITELYHELKYWQCLRQDLERARLLCEL 443
G PL+ + S + D MS + E+ L QD + L E
Sbjct: 455 GGPLVILPDIVYSLKTLEDW----MSKR----RMREVAKAL-------QDQYQLLTLVES 499
Query: 444 VRKREKMKRELIKVTEACTMIKLNPLNSLL-LQLIDL 479
KR+ +K +L + + + P LL +++IDL
Sbjct: 500 TAKRQLLKCQLSNLRKKFLNLNYFPAQRLLQVKIIDL 536
>gnl|CDD|206003 pfam13832, zf-HC5HC2H_2, PHD-zinc-finger like domain.
Length = 109
Score = 169 bits (430), Expect = 1e-49
Identities = 57/119 (47%), Positives = 73/119 (61%), Gaps = 10/119 (8%)
Query: 190 VDCVLCPNNGGAFKLTDRGAWAHVVCALWIPEVRFANTVFLEPIDSIEAIPAARWKLTCY 249
+C LCP GGA K T G W HV+CA+++PEVRF N +EPID + IP RWKL C
Sbjct: 1 AECCLCPLRGGALKKTTDGRWVHVLCAIFVPEVRFGNGATMEPID-VSRIPKERWKLKCC 59
Query: 250 VCKQRGVGACIQCHKTNCYAAFHVTCAQQAGLYMNMDTIRDHSGVEPVVVQKLAYCDAH 308
CK+R GACIQC C +FHVTCA+ AG+YM ++ + +Q +AYC H
Sbjct: 60 FCKKRS-GACIQCSYGRCQTSFHVTCARAAGVYMEIEDWPN--------LQVIAYCQKH 109
>gnl|CDD|99900 cd05839, BR140_related, The PWWP domain is found in the BR140
family, which includes peregrin and BR140-like proteins
1 and 2. BR140 is the only family to contain the PWWP
domain at the C terminus, with PHD and bromo domains in
the N-terminal region. In myeloid leukemias, BR140 is
disrupted by chromosomal translocations, similar to
translocations of WHSC1 in lymphoid multiple myeloma.
The PWWP domain, named for a conserved Pro-Trp-Trp-Pro
motif, is a small domain consisting of 100-150 amino
acids. The PWWP domain is found in numerous proteins
that are involved in cell division, growth and
differentiation. Most PWWP-domain proteins seem to be
nuclear, often DNA-binding proteins, that function as
transcription factors regulating a variety of
developmental processes.
Length = 111
Score = 168 bits (427), Expect = 4e-49
Identities = 65/110 (59%), Positives = 78/110 (70%)
Query: 717 EQLQLVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVLFF 776
E L LVWAKCRGYP YPALII+P+MP + + P A A N E +YLVLFF
Sbjct: 2 EPLTLVWAKCRGYPSYPALIIDPKMPRDGVFHNGVPPDVLTLGEARAQNADERLYLVLFF 61
Query: 777 DTKRTWQWLPRNKLEPLGITDELDQIKLMESRKPADRKAVKKAYQEALVH 826
D KRTWQWLP +KLEPLG+ + LD++KL E RKP+ RKAV+KAY +AL H
Sbjct: 62 DNKRTWQWLPGDKLEPLGVDETLDKLKLKEGRKPSIRKAVQKAYDDALSH 111
>gnl|CDD|99944 cd05512, Bromo_brd1_like, Bromodomain; brd1_like subfamily. BRD1 is
a mammalian gene which encodes for a nuclear protein
assumed to be a transcriptional regulator. BRD1 has been
implicated with brain development and susceptibility to
schizophrenia and bipolar affective disorder.
Bromodomains are 110 amino acid long domains that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 98
Score = 154 bits (390), Expect = 3e-44
Identities = 53/98 (54%), Positives = 75/98 (76%)
Query: 468 PLNSLLLQLIDLIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLE 527
PL LL + +D ++ +DT +IF EPVD+ EVPDY D IKQPMD +TM K+++ +Y +LE
Sbjct: 1 PLEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLE 60
Query: 528 DFENDFNLMVENCLTYNEKDTIFYKAGIKMKQVGGALI 565
DFE DFNL++ NCL YN KDTIFY+A ++++ GGA++
Sbjct: 61 DFEADFNLIINNCLAYNAKDTIFYRAAVRLRDQGGAIL 98
>gnl|CDD|197636 smart00297, BROMO, bromo domain.
Length = 107
Score = 123 bits (310), Expect = 4e-33
Identities = 38/103 (36%), Positives = 57/103 (55%)
Query: 466 LNPLNSLLLQLIDLIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLS 525
L LL ++D + + FL+PV E PDY D+IK+PMDL T+ K++ +Y S
Sbjct: 5 QKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSS 64
Query: 526 LEDFENDFNLMVENCLTYNEKDTIFYKAGIKMKQVGGALINQA 568
+E+F DFNLM N TYN D+ YK K+++ + +
Sbjct: 65 VEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
>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 = 117 bits (295), Expect = 2e-31
Identities = 36/100 (36%), Positives = 48/100 (48%), Gaps = 13/100 (13%)
Query: 212 HVVCALWIPEVRFANTVFL--EPIDSIEAIPAARWKLTCYVCKQRGVGACIQCHKTNCYA 269
HV CALW PEV + P++ ++ R KL C +CK++G ACI C NC
Sbjct: 1 HVNCALWSPEVVQRGDDDMEGFPLEDVDKAVKRRRKLKCSLCKKKG--ACIGCCVKNCRR 58
Query: 270 AFHVTCAQQAGLYMNMDTIRDHSGVEPVVVQKLAYCDAHT 309
AFHVTCA++AG D + +YC H
Sbjct: 59 AFHVTCAREAGCLFQFDGDN---------GKFKSYCPKHR 89
>gnl|CDD|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily. Gcn5p
is a histone acetyltransferase (HAT) which mediates
acetylation of histones at lysine residues; such
acetylation is generally correlated with the activation
of transcription. Bromodomains are 110 amino acid long
domains, that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 101
Score = 113 bits (286), Expect = 5e-30
Identities = 41/90 (45%), Positives = 58/90 (64%)
Query: 468 PLNSLLLQLIDLIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLE 527
PL + L +++D +K + FLEPVD E PDY DVIK+PMDL+TM K++ Y++LE
Sbjct: 1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLE 60
Query: 528 DFENDFNLMVENCLTYNEKDTIFYKAGIKM 557
+F D L+ +NC YN DT +YK K+
Sbjct: 61 EFVADLKLIFDNCRLYNGPDTEYYKCANKL 90
>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain. Bromodomains are found in many
chromatin-associated proteins and in nuclear histone
acetyltransferases. They interact specifically with
acetylated lysine.
Length = 99
Score = 111 bits (279), Expect = 3e-29
Identities = 43/92 (46%), Positives = 56/92 (60%), Gaps = 2/92 (2%)
Query: 469 LNSLLLQLIDLIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLED 528
L SLL L L RD + FLEPVD E PDY +VIK PMDL+T+ K+K +Y SLE+
Sbjct: 5 LRSLLDALKKLK--RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEE 62
Query: 529 FENDFNLMVENCLTYNEKDTIFYKAGIKMKQV 560
FE D L+ N TYN + YK K++++
Sbjct: 63 FEADVRLIFSNAKTYNGPGSPIYKDAKKLEKL 94
>gnl|CDD|220792 pfam10513, EPL1, Enhancer of polycomb-like. This is a family of
EPL1 (Enhancer of polycomb-like) proteins. The EPL1
protein is a member of a histone acetyltransferase
complex which is involved in transcriptional activation
of selected genes.
Length = 145
Score = 110 bits (278), Expect = 2e-28
Identities = 46/98 (46%), Positives = 61/98 (62%), Gaps = 3/98 (3%)
Query: 24 VLEALQRSQE-AVTKLPEPCFKELDDYKHLDSI--SRPTAYIRFIEKNADELDEEVEYDM 80
+ + +Q +P P +E++DY + RP +YIRF EK+ +ELD VEYDM
Sbjct: 48 LQVPISAAQVAKKLYIPTPEAREIEDYDKPYAPKFKRPKSYIRFSEKSVEELDSGVEYDM 107
Query: 81 DEEDASWLNIMNEQRKISNLPPLAIDTFELLMDRLEKE 118
DEED +WL +NE+RK L PL+ D FE LMDRLEKE
Sbjct: 108 DEEDEAWLEELNEKRKEEGLAPLSEDDFEKLMDRLEKE 145
>gnl|CDD|99945 cd05513, Bromo_brd7_like, Bromodomain, brd7_like subgroup. The BRD7
gene encodes a nuclear protein that has been shown to
inhibit cell growth and the progression of the cell
cycle by regulating cell-cycle genes at the
transcriptional level. BRD7 has been identified as a
gene involved in nasopharyngeal carcinoma. The protein
interacts with acetylated histone H3 via its
bromodomain. Bromodomains are 110 amino acid long
domains that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 98
Score = 101 bits (253), Expect = 1e-25
Identities = 42/94 (44%), Positives = 57/94 (60%)
Query: 468 PLNSLLLQLIDLIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLE 527
PL L QLI ++ +D F PV P Y+ +IK PMD +TM K+K N Y S+E
Sbjct: 1 PLQKALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIE 60
Query: 528 DFENDFNLMVENCLTYNEKDTIFYKAGIKMKQVG 561
+F++DF LM EN + YN+ DTI+YKA K+ G
Sbjct: 61 EFKDDFKLMCENAMKYNKPDTIYYKAAKKLLHSG 94
>gnl|CDD|99932 cd05500, Bromo_BDF1_2_I, Bromodomain. BDF1/BDF2 like subfamily,
restricted to fungi, repeat I. BDF1 and BDF2 are yeast
transcription factors involved in the expression of a
wide range of genes, including snRNAs; they are required
for sporulation and DNA repair and protect histone H4
from deacetylation. Bromodomains are 110 amino acid long
domains, that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 103
Score = 90.8 bits (226), Expect = 7e-22
Identities = 33/74 (44%), Positives = 50/74 (67%), Gaps = 2/74 (2%)
Query: 489 FLEPVDVIE--VPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEK 546
FL PVD ++ +P Y +IK+PMDL T+ K+K+N Y S+E+F DFNLMV+NCLT+N
Sbjct: 25 FLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGP 84
Query: 547 DTIFYKAGIKMKQV 560
+ + G +++
Sbjct: 85 EHPVSQMGKRLQAA 98
>gnl|CDD|215921 pfam00439, Bromodomain, Bromodomain. Bromodomains are 110 amino
acid long domains, that are found in many chromatin
associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 84
Score = 88.2 bits (219), Expect = 3e-21
Identities = 35/84 (41%), Positives = 53/84 (63%)
Query: 473 LLQLIDLIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFEND 532
L++++ + + FLEPVD E PDY +VIK+PMDL+T+ K+K+ +Y SL +F D
Sbjct: 1 CLEILEDLMEHPLAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKD 60
Query: 533 FNLMVENCLTYNEKDTIFYKAGIK 556
L+ N +TYN +D+ YK K
Sbjct: 61 VELIFSNAITYNGEDSDIYKDAKK 84
>gnl|CDD|99930 cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_like subfamily,
repeat II. Human Brdt is a testis-specific member of the
BET subfamily of bromodomain proteins; the first
bromodomain in Brdt has been shown to be essential for
male germ cell differentiation. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 102
Score = 88.5 bits (220), Expect = 5e-21
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 488 IFLEPVDVI--EVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNE 545
F +PVD + DY D+IK PMDL+T+ K+ +Y ++F D LM NC YN
Sbjct: 23 PFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNP 82
Query: 546 KDTIFYKAGIKMKQV 560
D + K++ V
Sbjct: 83 PDHPVHAMARKLQDV 97
>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, Bromodomain. BDF1/BDF2 like subfamily,
restricted to fungi, repeat II. BDF1 and BDF2 are yeast
transcription factors involved in the expression of a
wide range of genes, including snRNAs; they are required
for sporulation and DNA repair and protect histone H4
from deacetylation. Bromodomains are 110 amino acid long
domains, that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 102
Score = 85.8 bits (213), Expect = 4e-20
Identities = 33/89 (37%), Positives = 57/89 (64%), Gaps = 4/89 (4%)
Query: 476 LIDLIKARDTG--DIFLEPVDVI--EVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFEN 531
L +L+K + + FL+PVD + +P+Y +IK+PMDL T++ K++ QY S ++FE
Sbjct: 9 LKELMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFER 68
Query: 532 DFNLMVENCLTYNEKDTIFYKAGIKMKQV 560
D L+ +NC T+N + T Y G ++++V
Sbjct: 69 DVRLIFKNCYTFNPEGTDVYMMGHQLEEV 97
>gnl|CDD|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like
subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was
identified as a novel human bromodomain gene by cDNA
library screening. The Drosophila homologue, Acf1, is
part of the CHRAC (chromatin accessibility complex) and
regulates ISWI-induced nucleosome remodeling.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 115
Score = 83.2 bits (206), Expect = 4e-19
Identities = 38/88 (43%), Positives = 50/88 (56%)
Query: 470 NSLLLQLIDLIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDF 529
S L QL+ I FL PV IEVPDY D+IK+PMDL T+ K+ +Y E+F
Sbjct: 14 LSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEF 73
Query: 530 ENDFNLMVENCLTYNEKDTIFYKAGIKM 557
+D L+ NC YN + T YKAG ++
Sbjct: 74 LSDIQLVFSNCFLYNPEHTSVYKAGTRL 101
>gnl|CDD|99894 cd05162, PWWP, The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes. The function of the PWWP
domain is still not known precisely; however, based on
the fact that other regions of PWWP-domain proteins are
responsible for nuclear localization and DNA-binding, is
likely that the PWWP domain acts as a site for
protein-protein binding interactions, influencing
chromatin remodeling and thereby regulating
transcriptional processes. Some PWWP-domain proteins
have been linked to cancer or other diseases; some are
known to function as growth factors.
Length = 87
Score = 81.7 bits (202), Expect = 7e-19
Identities = 38/109 (34%), Positives = 49/109 (44%), Gaps = 24/109 (22%)
Query: 716 FEQLQLVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVLF 775
F LVWAK +GYPW+PAL+++ PP+D E LVLF
Sbjct: 1 FRPGDLVWAKMKGYPWWPALVVD----------------PPKDSKKAKKKAKEGKVLVLF 44
Query: 776 FDTKRTWQWLPRNKLEPLGITDELDQIKLMESRKPADRKAVKKAYQEAL 824
F K T+ W+ +L+P E K + RK KKAY EAL
Sbjct: 45 FGDK-TFAWVGAERLKPFTEHKE-------SEAKQSKRKGFKKAYDEAL 85
>gnl|CDD|99935 cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BAZ2B_like
subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and
2B (BAZ2B) were identified as a novel human bromodomain
gene by cDNA library screening. BAZ2A is also known as
Tip5 (Transcription termination factor I-interacting
protein 5) and hWALp3. The proteins may play roles in
transcriptional regulation. Human Tip5 is part of a
complex termed NoRC (nucleolar remodeling complex),
which induces nucleosome sliding and may play a role in
the regulation of the rDNA locus. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 97
Score = 81.7 bits (202), Expect = 9e-19
Identities = 31/71 (43%), Positives = 48/71 (67%)
Query: 489 FLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDT 548
FLEPV+ VP Y +IK+PMD +T+ K+++ QY +LE+F D L+ +NC T+NE D+
Sbjct: 21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDS 80
Query: 549 IFYKAGIKMKQ 559
+AG M++
Sbjct: 81 EVGRAGHNMRK 91
>gnl|CDD|99957 cd05528, Bromo_AAA, Bromodomain; sub-family co-occurring with AAA
domains. Bromodomains are 110 amino acid long domains,
that are found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine. The structure(2DKW) in this alignment is an
uncharacterized protein predicted from analysis of cDNA
clones from human fetal liver.
Length = 112
Score = 81.2 bits (201), Expect = 2e-18
Identities = 37/98 (37%), Positives = 48/98 (48%), Gaps = 11/98 (11%)
Query: 488 IFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKD 547
F +PVD EVPDY ++IKQPMDL T+ K+ +QYL+ +DF D +L+V N L YN
Sbjct: 23 AFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDR 82
Query: 548 TIFYKAGIKMKQVGGALINQAAKTLNDAGFDQIGSILP 585
LI A L D I + L
Sbjct: 83 D-----------PADKLIRSRACELRDEVHAMIEAELD 109
>gnl|CDD|99943 cd05511, Bromo_TFIID, Bromodomain, TFIID-like subfamily. Human
TAFII250 (or TAF250) is the largest subunit of TFIID, a
large multi-domain complex, which initiates the assembly
of the transcription machinery. TAFII250 contains two
bromodomains that specifically bind to acetylated
histone H4. Bromodomains are 110 amino acid long
domains, that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 112
Score = 80.0 bits (198), Expect = 5e-18
Identities = 29/77 (37%), Positives = 48/77 (62%)
Query: 489 FLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDT 548
F PV+ +VPDY +IK+PMDL T+ K+ ++Y S E+F D L+V+N + YN D+
Sbjct: 21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80
Query: 549 IFYKAGIKMKQVGGALI 565
++ K +M ++ L+
Sbjct: 81 VYTKKAKEMLELAEELL 97
>gnl|CDD|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily. SPT7 is
a yeast protein that functions as a component of the
transcription regulatory histone acetylation (HAT)
complexes SAGA, SALSA, and SLIK. SAGA is involved in the
RNA polymerase II-dependent transcriptional regulation
of about 10% of all yeast genes. The SPT7 bromodomain
has been shown to weakly interact with acetylated
histone H3, but not H4. The human representative of this
subfamily is cat eye syndrome critical region protein 2
(CECR2). Bromodomains are 110 amino acid long domains,
that are found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 112
Score = 78.6 bits (194), Expect = 2e-17
Identities = 33/79 (41%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 489 FLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDT 548
FL V E PDY D+IK+PMDL TM K+K QY S +F +D NL+ +NCL YN +
Sbjct: 29 FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPS 88
Query: 549 IFYKA-GIKMKQVGGALIN 566
+ MK+ L+
Sbjct: 89 HPLRRHANFMKKKAEHLLK 107
>gnl|CDD|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V.
Polybromo is a nuclear protein of unknown function,
which contains 6 bromodomains. The human ortholog BAF180
is part of a SWI/SNF chromatin-remodeling complex, and
it may carry out the functions of Yeast Rsc-1 and Rsc-2.
It was shown that polybromo bromodomains bind to histone
H3 at specific acetyl-lysine positions. Bromodomains are
found in many chromatin-associated proteins and in
nuclear histone acetyltransferases. They interact
specifically with acetylated lysine, but not all the
bromodomains in polybromo may bind to acetyl-lysine.
Length = 105
Score = 76.6 bits (189), Expect = 7e-17
Identities = 29/64 (45%), Positives = 44/64 (68%)
Query: 497 EVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIK 556
E PDY DVIK+P+D+ + +K++ NQY SL+D +DF LM +N YNE D+ YK +
Sbjct: 35 EYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALT 94
Query: 557 MKQV 560
+++V
Sbjct: 95 LQKV 98
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 81.4 bits (201), Expect = 2e-16
Identities = 32/82 (39%), Positives = 46/82 (56%)
Query: 486 GDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNE 545
IFL E PDY ++IK PMDL T+ K+K +Y S E+F +D NLM +NC YN
Sbjct: 166 SSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNG 225
Query: 546 KDTIFYKAGIKMKQVGGALINQ 567
D+ Y ++++ LI +
Sbjct: 226 PDSSVYVDAKELEKYFLKLIEE 247
Score = 42.1 bits (99), Expect = 0.001
Identities = 29/70 (41%), Positives = 39/70 (55%)
Query: 489 FLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDT 548
FL PV EVPDY I+ PMDL+T K++ N Y E F D L +NC+ YN + T
Sbjct: 284 FLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVT 343
Query: 549 IFYKAGIKMK 558
+YK ++
Sbjct: 344 DYYKNANVLE 353
>gnl|CDD|222406 pfam13831, PHD_2, 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 = 33
Score = 68.8 bits (169), Expect = 6e-15
Identities = 19/33 (57%), Positives = 24/33 (72%)
Query: 150 NVILFCDMCNLAVHQDCYGVPYIPEGQWLCRRC 182
N +L C C++AVH CYGVP + +G WLCRRC
Sbjct: 1 NPLLVCSKCSVAVHASCYGVPELSDGPWLCRRC 33
>gnl|CDD|214603 smart00293, PWWP, domain with conserved PWWP motif. conservation
of Pro-Trp-Trp-Pro residues.
Length = 63
Score = 67.0 bits (164), Expect = 5e-14
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 16/79 (20%)
Query: 716 FEQLQLVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVLF 775
F+ LVWAK +G+PW+PAL+I+P+M I + E +Y VLF
Sbjct: 1 FKPGDLVWAKMKGFPWWPALVISPKMTPDNI---------------MKRKSDENLYPVLF 45
Query: 776 FDTKRTWQWLPRNKLEPLG 794
F K T W+P +KL PL
Sbjct: 46 FGDKDT-AWIPSSKLFPLT 63
>gnl|CDD|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily. Cbp (CREB
binding protein or CREBBP) is an acetyltransferase
acting on histone, which gives a specific tag for
transcriptional activation and also acetylates
non-histone proteins. CREBBP binds specifically to
phosphorylated CREB protein and augments the activity of
phosphorylated CREB to activate transcription of
cAMP-responsive genes. Bromodomains are 110 amino acid
long domains, that are found in many chromatin
associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 108
Score = 68.2 bits (167), Expect = 6e-14
Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 2/104 (1%)
Query: 469 LNSLLLQLIDLIKARDTGDIFLEPVD--VIEVPDYADVIKQPMDLTTMTNKVKANQYLSL 526
+L+ L L K F +PVD ++ +PDY D++K PMDL+T+ K+ QY
Sbjct: 5 RQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDP 64
Query: 527 EDFENDFNLMVENCLTYNEKDTIFYKAGIKMKQVGGALINQAAK 570
+ +D LM +N YN K + YK K+ +V I+ +
Sbjct: 65 WQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQEIDPVMQ 108
>gnl|CDD|99938 cd05506, Bromo_plant1, Bromodomain, uncharacterized subfamily
specific to plants. Might function as a global
transcription factor. Bromodomains are 110 amino acid
long domains, that are found in many chromatin
associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 99
Score = 66.6 bits (163), Expect = 2e-13
Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 488 IFLEPVDV--IEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNE 545
+F PVDV + +PDY D+IK+PMDL T+ K++ +Y S E+F D L N + YN
Sbjct: 20 VFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNP 79
Query: 546 KDTIFY 551
+
Sbjct: 80 PGNDVH 85
>gnl|CDD|99937 cd05505, Bromo_WSTF_like, Bromodomain; Williams syndrome
transcription factor-like subfamily (WSTF-like). The
Williams-Beuren syndrome deletion transcript 9 is a
putative transcriptional regulator. WSTF was found to
play a role in vitamin D-mediated transcription as part
of two chromatin remodeling complexes, WINAC and WICH.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 97
Score = 64.9 bits (158), Expect = 7e-13
Identities = 29/87 (33%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 479 LIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVE 538
++K R + F EPV E DY VI PMDL TM K Y S+++F +D L+
Sbjct: 12 ILKYRFSWP-FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFS 70
Query: 539 NCLTYNEKDTIFYKAGIKMKQVGGALI 565
N Y E + K +Q L+
Sbjct: 71 NAEKYYENGSYVLSCMRKTEQCCVNLL 97
>gnl|CDD|99929 cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like subfamily,
repeat I. Human Brdt is a testis-specific member of the
BET subfamily of bromodomain proteins; the first
bromodomain in Brdt has been shown to be essential for
male germ cell differentiation. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 107
Score = 65.1 bits (159), Expect = 8e-13
Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 489 FLEPVDVI--EVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEK 546
F +PVD + +PDY +IK PMDL T+ +++ N Y S + DFN M NC YN+
Sbjct: 26 FQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKP 85
>gnl|CDD|99954 cd05524, Bromo_polybromo_I, Bromodomain, polybromo repeat I.
Polybromo is a nuclear protein of unknown function,
which contains 6 bromodomains. The human ortholog BAF180
is part of a SWI/SNF chromatin-remodeling complex, and
it may carry out the functions of Yeast Rsc-1 and Rsc-2.
It was shown that polybromo bromodomains bind to histone
H3 at specific acetyl-lysine positions. Bromodomains are
found in many chromatin-associated proteins and in
nuclear histone acetyltransferases. They interact
specifically with acetylated lysine, but not all the
bromodomains in polybromo may bind to acetyl-lysine.
Length = 113
Score = 63.9 bits (156), Expect = 2e-12
Identities = 18/62 (29%), Positives = 35/62 (56%)
Query: 499 PDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIKMK 558
P+Y +V+ P+DL + K+K +Y ++D DF L++ N Y + D+ +K K+
Sbjct: 39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLW 98
Query: 559 QV 560
++
Sbjct: 99 EL 100
>gnl|CDD|99951 cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III.
Polybromo is a nuclear protein of unknown function,
which contains 6 bromodomains. The human ortholog BAF180
is part of a SWI/SNF chromatin-remodeling complex, and
it may carry out the functions of Yeast Rsc-1 and Rsc-2.
It was shown that polybromo bromodomains bind to histone
H3 at specific acetyl-lysine positions. Bromodomains are
found in many chromatin-associated proteins and in
nuclear histone acetyltransferases. They interact
specifically with acetylated lysine, but not all the
bromodomains in polybromo may bind to acetyl-lysine.
Length = 103
Score = 63.1 bits (154), Expect = 4e-12
Identities = 24/62 (38%), Positives = 36/62 (58%)
Query: 499 PDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIKMK 558
PDY IK P+ L + K+K +Y +LE+ E D NLM EN YN ++ YK K++
Sbjct: 37 PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQ 96
Query: 559 QV 560
++
Sbjct: 97 KL 98
>gnl|CDD|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily. Tif1
(transcription intermediary factor 1) is a member of the
tripartite motif (TRIM) protein family, which is
characterized by a particular domain architecture. It
functions by recruiting coactivators and/or corepressors
to modulate transcription. Vertebrate Tif1-gamma, also
labeled E3 ubiquitin-protein ligase TRIM33, plays a role
in the control of hematopoiesis. Its homologue in
Xenopus laevis, Ectodermin, has been shown to function
in germ-layer specification and control of cell growth
during embryogenesis. Bromodomains are 110 amino acid
long domains, that are found in many chromatin
associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 109
Score = 62.3 bits (152), Expect = 8e-12
Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 489 FLEPVDVIEVPDYADVIKQPMDLTTMTNKVK---ANQYLSLEDFENDFNLMVENCLTYNE 545
F EPV VP+Y +IK PMDL+ + K++ Y S E+F D LM +NC +NE
Sbjct: 25 FHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNE 83
Query: 546 KDTIFYKAGIKM 557
+D+ +AG ++
Sbjct: 84 EDSEVAQAGKEL 95
>gnl|CDD|99949 cd05518, Bromo_polybromo_IV, Bromodomain, polybromo repeat IV.
Polybromo is a nuclear protein of unknown function,
which contains 6 bromodomains. The human ortholog BAF180
is part of a SWI/SNF chromatin-remodeling complex, and
it may carry out the functions of Yeast Rsc-1 and Rsc-2.
It was shown that polybromo bromodomains bind to histone
H3 at specific acetyl-lysine positions. Bromodomains are
found in many chromatin-associated proteins and in
nuclear histone acetyltransferases. They interact
specifically with acetylated lysine, but not all the
bromodomains in polybromo may bind to acetyl-lysine.
Length = 103
Score = 61.3 bits (149), Expect = 1e-11
Identities = 22/65 (33%), Positives = 39/65 (60%)
Query: 487 DIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEK 546
D+F+E + PDY +I +P+DL T+ + ++ ++Y + E+ +DF LM N YNE+
Sbjct: 25 DLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEE 84
Query: 547 DTIFY 551
+ Y
Sbjct: 85 GSQVY 89
>gnl|CDD|99947 cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like subfamily, specific
to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related
matrix-associated actin-dependent regulator of chromatin
subfamily A member 2 is a global transcriptional
activator, which cooperates with nuclear hormone
receptors to boost transcriptional activation.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 107
Score = 61.7 bits (150), Expect = 1e-11
Identities = 20/64 (31%), Positives = 42/64 (65%)
Query: 497 EVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIK 556
E+P+Y ++I++P+D + +++ ++Y SLED E D L+ +N T+N + ++ Y+ I
Sbjct: 36 ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIV 95
Query: 557 MKQV 560
++ V
Sbjct: 96 LQSV 99
>gnl|CDD|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily.
WDR9 is a human gene located in the Down Syndrome
critical region-2 of chromosome 21. It encodes for a
nuclear protein containing WD40 repeats and two
bromodomains, which may function as a transcriptional
regulator involved in chromatin remodeling and play a
role in embryonic development. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 119
Score = 59.0 bits (143), Expect = 1e-10
Identities = 22/70 (31%), Positives = 38/70 (54%)
Query: 475 QLIDLIKARDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFN 534
+L++L+ + + F +PVD+++ PDY D+I PMDL T+ + Y +F D
Sbjct: 12 ELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVR 71
Query: 535 LMVENCLTYN 544
L+ N +Y
Sbjct: 72 LIFSNSKSYT 81
>gnl|CDD|99950 cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfamily, specific to
fungi. SNF2 is a yeast protein involved in
transcriptional activation, it is the catalytic
component of the SWI/SNF ATP-dependent chromatin
remodeling complex. The protein is essential for the
regulation of gene expression (both positive and
negative) of a large number of genes. The SWI/SNF
complex changes chromatin structure by altering
DNA-histone contacts within the nucleosome, which
results in a re-positioning of the nucleosome and
facilitates or represses the binding of gene-specific
transcription factors. Bromodomains are 110 amino acid
long domains, that are found in many chromatin
associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 103
Score = 58.1 bits (141), Expect = 2e-10
Identities = 30/98 (30%), Positives = 54/98 (55%), Gaps = 9/98 (9%)
Query: 472 LLLQLIDLIKA-----RDTG----DIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQ 522
L ++++ A +TG ++FLE PDY +IK+P+ L + +++
Sbjct: 1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRA 60
Query: 523 YLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIKMKQV 560
Y SLE+F DF+LM N TYN++ +I Y+ ++M++
Sbjct: 61 YKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKA 98
>gnl|CDD|99940 cd05508, Bromo_RACK7, Bromodomain, RACK7_like subfamily. RACK7
(also called human protein kinase C-binding protein) was
identified as a potential tumor suppressor genes, it
shares domain architecture with BS69/ZMYND11; both have
been implicated in the regulation of cellular
proliferation. Bromodomains are 110 amino acid long
domains, that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 99
Score = 57.0 bits (138), Expect = 5e-10
Identities = 22/62 (35%), Positives = 36/62 (58%)
Query: 483 RDTGDIFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLT 542
+ + FL+PVD+ + PDYA + +PMDL+T+ V+ Y S + F D ++ N +
Sbjct: 17 QPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAII 76
Query: 543 YN 544
YN
Sbjct: 77 YN 78
>gnl|CDD|99948 cd05517, Bromo_polybromo_II, Bromodomain, polybromo repeat II.
Polybromo is a nuclear protein of unknown function,
which contains 6 bromodomains. The human ortholog BAF180
is part of a SWI/SNF chromatin-remodeling complex, and
it may carry out the functions of Yeast Rsc-1 and Rsc-2.
It was shown that polybromo bromodomains bind to histone
H3 at specific acetyl-lysine positions. Bromodomains are
found in many chromatin-associated proteins and in
nuclear histone acetyltransferases. They interact
specifically with acetylated lysine, but not all the
bromodomains in polybromo may bind to acetyl-lysine.
Length = 103
Score = 56.7 bits (137), Expect = 6e-10
Identities = 26/62 (41%), Positives = 41/62 (66%)
Query: 499 PDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIKMK 558
PDY VIK+P+DL T+ ++++ Y S+ED E D +LMV+N T+NE + YK +K
Sbjct: 37 PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIK 96
Query: 559 QV 560
++
Sbjct: 97 KI 98
>gnl|CDD|99953 cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II in Rsc1/2_like
subfamily, specific to fungi. Rsc1 and Rsc2 are
components of the RSC complex (remodeling the structure
of chromatin), are essential for transcriptional
control, and have a specific domain architecture
including two bromodomains. The RSC complex has also
been linked to homologous recombination and
nonhomologous end-joining repair of DNA double strand
breaks. Bromodomains are 110 amino acid long domains,
that are found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 104
Score = 56.1 bits (136), Expect = 9e-10
Identities = 24/56 (42%), Positives = 30/56 (53%)
Query: 497 EVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYK 552
P+Y I P+ L + KVK +Y S + F ND NLM EN YNE D+ YK
Sbjct: 36 REPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYK 91
>gnl|CDD|99958 cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like
subfamily. WDR9 is a human gene located in the Down
Syndrome critical region-2 of chromosome 21. It encodes
for a nuclear protein containing WD40 repeats and two
bromodomains, which may function as a transcriptional
regulator involved in chromatin remodeling and play a
role in embryonic development. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 128
Score = 56.2 bits (136), Expect = 2e-09
Identities = 29/89 (32%), Positives = 48/89 (53%), Gaps = 3/89 (3%)
Query: 467 NPLNSLLLQLIDLIKARDTGDIFLEPVDVI-EVPDYADVIKQPMDLTTMTNKVKANQYLS 525
L S L +L+ ++ + F PVD+ PDY + + PMDL T+ ++++ Y S
Sbjct: 27 ERLISGLDKLLLSLQLEIA-EYFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRS 85
Query: 526 LEDFENDFNLMVENCLTYNEKDT-IFYKA 553
LE +D L++ N T+NE ++ I KA
Sbjct: 86 LEALRHDVRLILSNAETFNEPNSEIAKKA 114
>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 = 51.8 bits (124), Expect = 7e-09
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 137 VCCICNDGECQNSNVILFCDMCNLAVHQDCYGVPY---IPEGQWLCRRC 182
C +C G+ + +L CD C+ HQ C G P P+G+W C +C
Sbjct: 1 YCSVC--GKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
Score = 34.9 bits (80), Expect = 0.007
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 3/32 (9%)
Query: 247 TCYVCKQRGV-GACIQCHKTNCYAAFHVTCAQ 277
C VC + G +QC C +H TC
Sbjct: 1 YCSVCGKPDDGGELLQCDG--CDRWYHQTCLG 30
>gnl|CDD|99901 cd05840, SPBC215_ISWI_like, The PWWP domain is a component of the
S. pombe hypothetical protein SPBC215, as well as ISWI
complex protein 4. The ISWI (imitation switch) proteins
are ATPases responsible for chromatin remodeling in
eukaryotes, and SPBC215 is proposed to also bind
chromatin. The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes.
Length = 93
Score = 53.1 bits (128), Expect = 9e-09
Identities = 29/104 (27%), Positives = 48/104 (46%), Gaps = 18/104 (17%)
Query: 720 QLVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVLFFDTK 779
V AK +G+P +PA+++ +M P+ VL + Y V+FF
Sbjct: 5 DRVLAKVKGFPAWPAIVVPEEM-------------LPDSVLKGKKKKNKRTYPVMFFPDG 51
Query: 780 RTWQWLPRNKLEPLGITDELDQIKLMESRKPADRKAVKKAYQEA 823
+ W+P L+PL T+E K ++ K D++ KAY+ A
Sbjct: 52 -DYYWVPNKDLKPL--TEE-KIAKFLKKPKRKDKEL-IKAYKAA 90
>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 = 50.2 bits (120), Expect = 4e-08
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 137 VCCICNDGECQNSNVILFCDMCNLAVHQDCYGVPY----IPEGQWLCRRC 182
C +C G+ + +L CD C+ H C G P IPEG+W C C
Sbjct: 1 YCAVC--GKVDDDGELLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPEC 48
>gnl|CDD|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup. In
mammals, brd8 (bromodomain containing 8) interacts with
the thyroid hormone receptor in a ligand-dependent
fashion and enhances thyroid hormone-dependent
activation from thyroid response elements. Brd8 is
thought to be a nuclear receptor coactivator.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 104
Score = 48.9 bits (117), Expect = 4e-07
Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 489 FLEPVDVIEVPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDT 548
FL+PV P Y V+ +PMDL+T+ ++ S +F+ D LM +N + YN D
Sbjct: 24 FLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDH 83
Query: 549 IFYKAGIKMKQ 559
Y ++M++
Sbjct: 84 DVYLMAVEMQR 94
>gnl|CDD|216154 pfam00855, PWWP, PWWP domain. The PWWP domain is named after a
conserved Pro-Trp-Trp-Pro motif. The domain binds to
Histone-4 methylated at lysine-20, H4K20me, suggesting
that it is methyl-lysine recognition motif. Removal of
two conserved aromatic residues in a hydrophobic cavity
created by this domain within the full-lemgth protein,
Pdp1, abolishes the interaction o f the protein with
H4K20me3. In fission yeast, Set9 is the sole enzyme that
catalyzes all three states of H4K20me, and Set9-mediated
H4K20me is required for efficient recruitment of
checkpoint protein Crb2 to sites of DNA damage. The
methylation of H4K20 is involved in a diverse array of
cellular processes, such as organising higher-order
chromatin, maintaining genome stability, and regulating
cell-cycle progression.
Length = 74
Score = 45.8 bits (109), Expect = 2e-06
Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 22/89 (24%)
Query: 721 LVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVLFFDTKR 780
LVWAK +G+PW+PA I++ + I V FF
Sbjct: 7 LVWAKMKGFPWWPARIVSQKE------TPTSIRKDNR-------------VKVQFFGD-H 46
Query: 781 TWQWLPRNKLEPLGITDELDQIKLMESRK 809
W+ +L+PL ++++ RK
Sbjct: 47 KTAWVSPKRLKPL--DVDIEKFHKDRKRK 73
>gnl|CDD|99952 cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in Rsc1/2_like
subfamily, specific to fungi. Rsc1 and Rsc2 are
components of the RSC complex (remodeling the structure
of chromatin), are essential for transcriptional
control, and have a specific domain architecture
including two bromodomains. The RSC complex has also
been linked to homologous recombination and
nonhomologous end-joining repair of DNA double strand
breaks. Bromodomains are 110 amino acid long domains,
that are found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 106
Score = 44.6 bits (106), Expect = 1e-05
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 499 PDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIKMK 558
PDY +IK P+ L T+ ++ Y + ++F ND + N YN K ++ YK + ++
Sbjct: 38 PDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILE 95
Query: 559 Q 559
+
Sbjct: 96 K 96
>gnl|CDD|99933 cd05501, Bromo_SP100C_like, Bromodomain, SP100C_like subfamily. The
SP100C protein is a splice variant of SP100, a major
component of PML-SP100 nuclear bodies (NBs), which are
poorly understood. It is covalently modified by SUMO-1
and may play a role in processes at the chromatin level.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 102
Score = 42.8 bits (101), Expect = 4e-05
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 500 DYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIKMKQ 559
DY IK+PM L + ++ Y ++E F D L+ N + KD F + GI +++
Sbjct: 32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFY-KDDDFGQVGITLEK 90
Query: 560 V 560
Sbjct: 91 K 91
>gnl|CDD|99899 cd05838, WHSC1_related, The PWWP domain was first identified in the
WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a
protein implicated in Wolf-Hirschhorn syndrome (WHS).
When translocated, WHSC1 plays a role in lymphoid
multiple myeloma (MM) disease, also known as
plasmacytoma. WHCS1 proteins typically contain two
copies of the PWWP domain. The PWWP domain, named for a
conserved Pro-Trp-Trp-Pro motif, is a small domain
consisting of 100-150 amino acids. The PWWP domain is
found in numerous proteins that are involved in cell
division, growth and differentiation. Most PWWP-domain
proteins seem to be nuclear, often DNA-binding, proteins
that function as transcription factors regulating a
variety of developmental processes.
Length = 95
Score = 42.3 bits (100), Expect = 5e-05
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 25/111 (22%)
Query: 720 QLVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVLFFDTK 779
+VWAK + W+PA+I +P P ++ L + E + V+FF T
Sbjct: 5 DIVWAKLGNFRWWPAIICDP-------------REVPPNIQVLRHCIGE--FCVMFFGT- 48
Query: 780 RTWQWLPRNKLEPL--GITDELDQIKLMESRKPADRKAVKKAYQEA-LVHK 827
+ W+ R ++ P G +Q K S K +KA +EA L K
Sbjct: 49 HDYYWVHRGRVFPYQEGDKGFKEQTK---SYLA---KRFRKALEEASLAFK 93
>gnl|CDD|99898 cd05837, MSH6_like, The PWWP domain is present in MSH6, a mismatch
repair protein homologous to bacterial MutS. The PWWP
domain of histone-lysine N-methyltransferase, also known
as Nuclear SET domain-containing protein 3, is also
included. Mutations in MSH6 have been linked to
increased cancer susceptibility, particularly in
hereditary nonpolyposis colorectal cancer in humans.
The role of the PWWP domain in MSH6 is not clear; MSH6
orthologs found in S. cerevisiae, Caenorhabditis elegans
and Arabidopsis thaliana lack the PWWP domain. Histone
methyltransferases (HMTases) induce the
posttranslational methylation of lysine residues in
histones and play a role in apoptosis. In the HMTase
Whistle, the PWWP domain is necessary for HMTase
activity. The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes.
Length = 110
Score = 42.4 bits (100), Expect = 7e-05
Identities = 27/113 (23%), Positives = 44/113 (38%), Gaps = 15/113 (13%)
Query: 715 TFEQLQLVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVL 774
++ LVWAK GYPW+P ++ + PL + + Y V
Sbjct: 2 KYQVGDLVWAKVSGYPWWPCMVCSD--PLLGTYT---------KTKRNKRKPRQ--YHVQ 48
Query: 775 FFDTKRTWQWLPRNKLEPL--GITDELDQIKLMESRKPADRKAVKKAYQEALV 825
FF W+ L+P E ++ + + RKP +KA +KA +
Sbjct: 49 FFGDNPERAWISEKSLKPFKGSKQFESEKGEKFKVRKPNIKKARQKADIAIMQ 101
>gnl|CDD|99903 cd06080, MUM1_like, Mutated melanoma-associated antigen 1 (MUM-1)
is a melanoma-associated antigen (MAA). MUM-1 belongs
to the mutated or aberrantly expressed type of MAAs,
along with antigens such as CDK4, beta-catenin,
gp100-in4, p15, and N-acetylglucosaminyltransferase V.
It is highly expressed in several types of human
cancers. The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes.
Length = 80
Score = 37.0 bits (86), Expect = 0.003
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 716 FEQLQLVWAKCRGYPWYPALIINPQM 741
FE+ LVWAK +GYPW+PA+I +
Sbjct: 1 FEKNDLVWAKIQGYPWWPAVIKSISR 26
>gnl|CDD|99895 cd05834, HDGF_related, The PWWP domain is an essential part of the
Hepatoma Derived Growth Factor (HDGF) family of
proteins, and is necessary for DNA binding by HDGF. This
family of endogenous nuclear-targeted mitogens includes
HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2,
HPR3, HPR4, respectively) and lens epithelium-derived
growth factor, LEDGF. Members of the HDGF family have
been linked to human diseases, and HDGF is a prognostic
factor in several types of cancer. The PWWP domain,
named for a conserved Pro-Trp-Trp-Pro motif, is a small
domain consisting of 100-150 amino acids. The PWWP
domain is found in numerous proteins that are involved
in cell division, growth and differentiation. Most
PWWP-domain proteins seem to be nuclear, often
DNA-binding, proteins that function as transcription
factors regulating a variety of developmental processes.
Length = 83
Score = 35.3 bits (82), Expect = 0.011
Identities = 23/73 (31%), Positives = 28/73 (38%), Gaps = 23/73 (31%)
Query: 720 QLVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVLFFDTK 779
LV+AK +GYP +PA + P PP Y PVY FF T
Sbjct: 7 DLVFAKVKGYPAWPARVDEP-----------EDWKPP------GKKY--PVY---FFGTH 44
Query: 780 RTWQWLPRNKLEP 792
T +L L P
Sbjct: 45 ET-AFLKPEDLFP 56
>gnl|CDD|99955 cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-family. ASH1
(absent, small, or homeotic 1) is a member of the
trithorax-group in Drosophila melanogaster, an
epigenetic transcriptional regulator of HOX genes.
Drosophila ASH1 has been shown to methylate specific
lysines in histones H3 and H4. Mammalian ASH1 has been
shown to methylate histone H3. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 106
Score = 36.2 bits (84), Expect = 0.011
Identities = 14/63 (22%), Positives = 31/63 (49%)
Query: 498 VPDYADVIKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAGIKM 557
PDY + I P+DL+T+ ++ Y + E F++D + N Y + + + ++
Sbjct: 38 NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRL 97
Query: 558 KQV 560
++
Sbjct: 98 RKA 100
>gnl|CDD|99926 cd05494, Bromodomain_1, Bromodomain; uncharacterized subfamily.
Bromodomains are found in many chromatin-associated
proteins and in nuclear histone acetyltransferases. They
interact specifically with acetylated lysine.
Length = 114
Score = 36.3 bits (84), Expect = 0.011
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 474 LQLIDLIKARDTGDIFLEPVD--VIEVPDYADVIKQPMDLTTMTN 516
L+ + + + FLEPV+ PDY DVIK+PM T N
Sbjct: 9 LRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVN 53
>gnl|CDD|99897 cd05836, N_Pac_NP60, The PWWP domain is an essential part of the
cytokine-like nuclear factor n-pac protein, or NP60,
which enhances the activity of MAP2K4 and MAP2K6 kinases
to phosphorylate p38-alpha. In a variety of cell lines,
NP60 has been shown to localize to the nucleus. In
addition to the PWWP domain, NP60 also contains an
AT-hook and a C-terminal NAD-binding domain. The PWWP
domain, named for a conserved Pro-Trp-Trp-Pro motif, is
a small domain consisting of 100-150 amino acids. The
PWWP domain is found in numerous proteins that are
involved in cell division, growth and differentiation.
Most PWWP-domain proteins seem to be nuclear, often
DNA-binding proteins, that function as transcription
factors regulating a variety of developmental processes.
Length = 86
Score = 35.1 bits (81), Expect = 0.018
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 19/72 (26%)
Query: 721 LVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPEDVLALANNYTEPVYLVLFFDTKR 780
LVWAK +G+P +P I+ PP+D+ + V FF +
Sbjct: 6 LVWAKMKGFPPWPGRIVK----------------PPKDLKKPRGK--AKCFFVFFFGS-E 46
Query: 781 TWQWLPRNKLEP 792
W+ ++P
Sbjct: 47 NHAWIKEENIKP 58
>gnl|CDD|99896 cd05835, Dnmt3b_related, The PWWP domain is an essential component
of DNA methyltransferase 3 B (Dnmt3b) which is
responsible for establishing DNA methylation patterns
during embryogenesis and gametogenesis. In
tumorigenesis, DNA methylation by Dnmt3b is known to
play a role in the inactivation of tumor suppressor
genes. In addition, a point mutation in the PWWP domain
of Dnmt3b has been identified in patients with ICF
syndrome (immunodeficiency, centromeric instability, and
facial anomalies), a rare autosomal recessive disorder
characterized by hypomethylation of classical satellite
DNA. The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes.
Length = 87
Score = 34.3 bits (79), Expect = 0.029
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 720 QLVWAKCRGYPWYPALII 737
LVW K +G+PW+P ++
Sbjct: 5 DLVWGKIKGFPWWPGRVV 22
>gnl|CDD|237996 cd00029, C1, Protein kinase C conserved region 1 (C1) .
Cysteine-rich zinc binding domain. Some members of this
domain family bind phorbol esters and diacylglycerol,
some are reported to bind RasGTP. May occur in tandem
arrangement. Diacylglycerol (DAG) is a second messenger,
released by activation of Phospholipase D. Phorbol
Esters (PE) can act as analogues of DAG and mimic its
downstream effects in, for example, tumor promotion.
Protein Kinases C are activated by DAG/PE, this
activation is mediated by their N-terminal conserved
region (C1). DAG/PE binding may be phospholipid
dependent. C1 domains may also mediate DAG/PE signals in
chimaerins (a family of Rac GTPase activating proteins),
RasGRPs (exchange factors for Ras/Rap1), and Munc13
isoforms (scaffolding proteins involved in exocytosis).
Length = 50
Score = 30.9 bits (70), Expect = 0.19
Identities = 7/31 (22%), Positives = 10/31 (32%)
Query: 136 AVCCICNDGECQNSNVILFCDMCNLAVHQDC 166
C +C L C C + H+ C
Sbjct: 12 TFCDVCRKSIWGLFKQGLRCSWCKVKCHKKC 42
>gnl|CDD|99924 cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like sub-family.
ZMYND11 or BS69 is a ubiquitously expressed nuclear
protein that has been shown to associate with chromatin.
It interacts with chromatin remodeling factors and might
play a role in chromatin remodeling and gene expression.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 109
Score = 32.0 bits (73), Expect = 0.30
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 505 IKQPMDLTTMTNKVKANQYLSLEDFENDFNLMVENCLTYNEKDTIFYKAG 554
I +D+ + K+ + +Y SLE+F+ D L++ N ++ D+ Y A
Sbjct: 43 IHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAA 92
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 33.7 bits (77), Expect = 0.41
Identities = 26/166 (15%), Positives = 49/166 (29%), Gaps = 19/166 (11%)
Query: 593 NSSDVVHMEETSKAENNKQEEKKNSTDVVMGMSSKDTKNFKSPEITTRKRHGNKKKGAQE 652
++ + N++ + SK I + H NK + +
Sbjct: 252 ELEYSEKGKDHHHSHNHQHHSIGINNHHSKHADSK------LQTIEVIENHSNKSRPSSS 305
Query: 653 ELSVP-ESDSFKVYRSGGELKGEAFDSAEEGGEDGEENSSCSECSSSCDSSDSESGSSVS 711
+ E+ S + G + ++ SA+ + +S S S+ +GS S
Sbjct: 306 STNGSKETTSNSSSAAAGSIGSKSSKSAKHSNRNKSNSSPKSHSSA--------NGSVPS 357
Query: 712 GSHTFEQLQLVWAKCRGYPWYPALIINPQMPLGYIHNGVPIPSPPE 757
S + + + K A G NG PE
Sbjct: 358 SSVSDNESK---QKRASKSSSGARDSKKDAS-GMSANGTVENCIPE 399
>gnl|CDD|197661 smart00335, ANX, Annexin repeats.
Length = 53
Score = 30.1 bits (69), Expect = 0.44
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 796 TDELDQIKLMESRKPADRKAVKKAYQEA 823
TDE I+++ SR A +A+K+AY++
Sbjct: 2 TDEKTLIEILASRSNAQLQAIKQAYKKR 29
>gnl|CDD|202976 pfam04340, DUF484, Protein of unknown function, DUF484. This
family consists of several proteins of uncharacterized
function.
Length = 219
Score = 32.8 bits (75), Expect = 0.45
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 10/80 (12%)
Query: 379 IKRQLRNGVPL----LRRLQSSHQARRDEHCKIMSNTPENGNITELYHELKYWQCLRQDL 434
+ Q N V L L RL+ + + +M N N L+ L+ DL
Sbjct: 34 LPHQPANTVSLVERQLARLRERIRELEERLAALMDNARAN---DRLFDRTHR---LQLDL 87
Query: 435 ERARLLCELVRKREKMKREL 454
AR L +++R+ + REL
Sbjct: 88 LDARSLEDVLRRVDASAREL 107
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 33.6 bits (76), Expect = 0.48
Identities = 26/121 (21%), Positives = 43/121 (35%), Gaps = 11/121 (9%)
Query: 3 ICSKEDFEHEYGQASSDNRQLVLEALQRSQEAVTKLPEPCFKELDDYKHLDSISRPTAYI 62
I E E +L + E + +LP K + S + Y
Sbjct: 552 IGPLEARELGIELLRKLLSPFILRRTKEDVEVLKELPP---KIEKVLECELSEEQRELYE 608
Query: 63 RFI---EKNADELDEEVEYDMDE-----EDASWLNIMNEQRKISNLPPLAIDTFELLMDR 114
+ EKN L++ + D DE + + L ++ R+I N P L + E DR
Sbjct: 609 ALLEGAEKNQQLLEDLEKADSDENRIGDSELNILALLTRLRQICNHPALVDEGLEATFDR 668
Query: 115 L 115
+
Sbjct: 669 I 669
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 33.7 bits (77), Expect = 0.56
Identities = 33/187 (17%), Positives = 64/187 (34%), Gaps = 36/187 (19%)
Query: 545 EKDTIFYKAGIKMKQVGGA------LINQAAKTLNDAGFDQIGSIL------PGTSAKGV 592
A I + +NQ K+L+D D+ + G + G
Sbjct: 54 VLRDEGKHANILYNSILCNQKKHASFLNQR-KSLDDDDDDEFDFLYEDDEDDAGNATSGE 112
Query: 593 NSSD------VVHMEETSKAENNKQEEKKNSTDVVMGMSSKDTKNFKSPEITTRKRHGNK 646
+S+D + +E + ++ + S D +S +++ ++ +
Sbjct: 113 SSTDDDSLLELPDRDEDA-DTQANNDQTNDFDQDDSSNSQTDQGLKQSVNLSSAEKLIEE 171
Query: 647 KKGAQEELSVPESDSFKVYRSGGELKGEAFDSAEEGGEDGEENSSCSECSSSCDSSDSES 706
KKG ++FK Y G + EA +A++GG+ S S + SD +
Sbjct: 172 KKG-------QTENTFKFYNFGND-GEEA--AAKDGGK------SKSSDPGPLNDSDGQG 215
Query: 707 GSSVSGS 713
S
Sbjct: 216 DDGDPES 222
>gnl|CDD|219594 pfam07816, DUF1645, Protein of unknown function (DUF1645). These
sequences are derived from a number of hypothetical
plant proteins. The region in question is approximately
270 amino acids long. Some members of this family are
annotated as yeast pheromone receptor proteins AR781 but
no literature was found to support this.
Length = 191
Score = 32.5 bits (74), Expect = 0.63
Identities = 17/72 (23%), Positives = 22/72 (30%), Gaps = 7/72 (9%)
Query: 649 GAQEELSVPESDSFKVYRSGGELK-------GEAFDSAEEGGEDGEENSSCSECSSSCDS 701
S +F R L+ G + DS + E S C SS +
Sbjct: 30 DRGRVGSPRSESAFAPARLRRALRSLSPERGGGSSDSESTDEGELEGVPPSSYCVSSSPA 89
Query: 702 SDSESGSSVSGS 713
S S SS S
Sbjct: 90 SSSRKSSSTGSS 101
>gnl|CDD|119362 cd06545, GH18_3CO4_chitinase, The Bacteroides thetaiotaomicron
protein represented by pdb structure 3CO4 is an
uncharacterized bacterial member of the family 18
glycosyl hydrolases with homologs found in
Flavobacterium, Stigmatella, and Pseudomonas.
Length = 253
Score = 32.8 bits (75), Expect = 0.65
Identities = 18/73 (24%), Positives = 22/73 (30%), Gaps = 17/73 (23%)
Query: 510 DLTTMTNKVKANQYLSLEDFENDFNLMVENCL-----------------TYNEKDTIFYK 552
D T Q+ S +D ND N E L YN TI K
Sbjct: 164 DATGPWWGDNPGQHSSYDDAVNDLNYWNERGLASKDKLVLGLPFYGYGFYYNGIPTIRNK 223
Query: 553 AGIKMKQVGGALI 565
+ GG +I
Sbjct: 224 VAFAKQNYGGVMI 236
>gnl|CDD|215738 pfam00130, C1_1, Phorbol esters/diacylglycerol binding domain (C1
domain). This domain is also known as the Protein
kinase C conserved region 1 (C1) domain.
Length = 53
Score = 29.7 bits (67), Expect = 0.66
Identities = 9/30 (30%), Positives = 12/30 (40%)
Query: 138 CCICNDGECQNSNVILFCDMCNLAVHQDCY 167
C C + L C C L VH+ C+
Sbjct: 14 CDHCGEFLWGLGKQGLKCSWCGLNVHKRCH 43
>gnl|CDD|99902 cd05841, BS69_related, The PWWP domain is part of BS69 protein, a
nuclear protein that specifically binds adenoviral E1A
and Epstein-Barr viral EBNA2 proteins, suppressing their
transactivation functions. BS69 is a multi-domain
protein, containing bromo, PHD, PWWP, and MYND domains.
The specific role of the PWWP domain within BS69 is not
clearly identified, but BS69 functions in chromatin
remodeling, consistent with other PWWP-containing
proteins. The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes.
Length = 83
Score = 29.7 bits (67), Expect = 1.2
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 720 QLVWAKCRGYPWYPA 734
+LVWAK +G+P++PA
Sbjct: 11 ELVWAKLKGFPYWPA 25
>gnl|CDD|225701 COG3159, COG3159, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 218
Score = 31.2 bits (71), Expect = 1.6
Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 10/86 (11%)
Query: 372 RLIAYWTIKRQLRNGVPL----LRRLQSSHQARRDEHCKIMSNTPENGNITELYHELKYW 427
L+ + + V L L RL++ + +E +M N N L++ L
Sbjct: 25 ELLEELRLPHPVAGTVSLVERQLARLRNRIRELEEELAALMENARAN---ERLFYRLHAL 81
Query: 428 QCLRQDLERARLLCELVRKREKMKRE 453
Q DL AR L +L+R+ ++
Sbjct: 82 Q---LDLLDARSLDDLLRRVDRSWAR 104
>gnl|CDD|131480 TIGR02427, protocat_pcaD, 3-oxoadipate enol-lactonase. Members of
this family are 3-oxoadipate enol-lactonase. Note that
the substrate is known as 3-oxoadipate enol-lactone,
2-oxo-2,3-dihydrofuran-5-acetate,
4,5-Dihydro-5-oxofuran-2-acetate, and
5-oxo-4,5-dihydrofuran-2-acetate. The enzyme the
catalyzes the fourth step in the protocatechuate
degradation to beta-ketoadipate and then to succinyl-CoA
and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate,
and vanillate all can be converted in one step to
protocatechuate. This enzyme also acts in catechol
degradation. In genomes that catabolize both catechol
and protocatechuate, two forms of this enzyme may be
found. All members of the seed alignment for this model
were chosen from within protocatechuate degradation
operons of at least three genes of the pathway, from
genomes with the complete pathway through
beta-ketoadipate [Energy metabolism, Other].
Length = 251
Score = 31.2 bits (71), Expect = 2.0
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 327 LKNARLVLAKKRVSVPTVSI-----PTIPPERVQDIAQLIS 362
+++A ++VPT+ I + PPE V++IA L+
Sbjct: 180 IRDADFRDRLGAIAVPTLCIAGDQDGSTPPELVREIADLVP 220
>gnl|CDD|201070 pfam00191, Annexin, Annexin. This family of annexins also includes
giardin that has been shown to function as an annexin.
Length = 66
Score = 28.6 bits (65), Expect = 2.1
Identities = 9/27 (33%), Positives = 19/27 (70%)
Query: 796 TDELDQIKLMESRKPADRKAVKKAYQE 822
TDE I+++ +R A +A+++AY++
Sbjct: 15 TDEDTLIRILATRSNAQLQAIREAYKK 41
>gnl|CDD|219267 pfam07007, DUF1311, Protein of unknown function (DUF1311). This
family consists of several bacterial proteins of around
120 residues in length. Members of this family contain
four highly conserved cysteine residues. The function of
this family is unknown.
Length = 84
Score = 29.0 bits (65), Expect = 2.1
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 368 QLMNRLIAYWTIKRQLRNGVPLLRRLQSSHQARRDEHCK 406
+N AY + L + LR+ Q + RD C
Sbjct: 24 AELNA--AYQALLAALPDAKAALRKAQRAWLKYRDAECA 60
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 31.3 bits (72), Expect = 2.8
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 64 FIEKNADE-------LDEEVEYDMDEEDASWLNIMNEQRKISNLPPLAIDTFELLMDRLE 116
F++ NA+E EE++ D DEE+ N + S LP ++ F+ L + +
Sbjct: 173 FVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYK 232
Query: 117 K 117
K
Sbjct: 233 K 233
>gnl|CDD|204386 pfam10049, DUF2283, Protein of unknown function (DUF2283).
Members of this family of hypothetical bacterial
proteins have no known function.
Length = 50
Score = 27.5 bits (62), Expect = 3.2
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 59 TAYIRFIEKN---ADELDEEVEYDMDEED 84
YIR + ++E+D + D DE+
Sbjct: 11 ALYIRLSDSPIVESEEIDPGIILDYDEDG 39
>gnl|CDD|197519 smart00109, C1, Protein kinase C conserved region 1 (C1) domains
(Cysteine-rich domains). Some bind phorbol esters and
diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Length = 50
Score = 27.4 bits (61), Expect = 3.6
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 136 AVCCICNDGECQNSNVILFCDMCNLAVHQDC 166
CC+C + L C C + H+ C
Sbjct: 12 TFCCVCRKSIWGSFKQGLRCSECKVKCHKKC 42
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 30.1 bits (68), Expect = 3.9
Identities = 14/47 (29%), Positives = 19/47 (40%)
Query: 670 ELKGEAFDSAEEGGEDGEENSSCSECSSSCDSSDSESGSSVSGSHTF 716
L E S+ + ED E S+ S DSES S+ S +
Sbjct: 13 PLGNELSPSSSDETEDCSEESTDSWSDMYEGLKDSESSSNSVPSLSL 59
>gnl|CDD|212164 cd11650, AT4G37440_like, Uncharacterized protein domain conserved
in plants. This domain contains an extensive protein
sequence fragment that appears conserved in a number of
plant proteins, including the gene product of
Arabidopsis thaliana locus AT4G37440, which has been
identified in transcriptional profiling as expressed at
different levels in white cabbage cultivars.
Length = 253
Score = 30.1 bits (68), Expect = 4.3
Identities = 14/49 (28%), Positives = 16/49 (32%), Gaps = 6/49 (12%)
Query: 669 GELKGEAFDSAEEGGEDGEENSSCSECSSSCDSSDSESGSSVSGSHTFE 717
GE S + D +E SSS SDS S G E
Sbjct: 12 GETTVRDNASEGDEDGDA------TESSSSFGDSDSASEDDSGGDADTE 54
>gnl|CDD|216101 pfam00755, Carn_acyltransf, Choline/Carnitine o-acyltransferase.
Length = 590
Score = 30.3 bits (69), Expect = 4.5
Identities = 6/26 (23%), Positives = 8/26 (30%)
Query: 153 LFCDMCNLAVHQDCYGVPYIPEGQWL 178
V D YG+ Y G +
Sbjct: 534 TDIGGGFGPVVDDGYGICYNINGDRI 559
>gnl|CDD|215560 PLN03076, PLN03076, ARF guanine nucleotide exchange factor
(ARF-GEF); Provisional.
Length = 1780
Score = 30.6 bits (69), Expect = 4.7
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 9/66 (13%)
Query: 653 ELSVPESDSFKVYRSGGELKGEAFDSAEEGGEDGEENSSCSECSSSCDSSDSESGSSVSG 712
+L +P+ S K K +A ++ E G N + E DS SE S S
Sbjct: 556 QLRLPDPASLK--------KLDAVENNLEPGSLPVANGNGDENGEGSDSH-SELSSETSD 606
Query: 713 SHTFEQ 718
+ T EQ
Sbjct: 607 AATIEQ 612
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 30.3 bits (68), Expect = 5.4
Identities = 16/40 (40%), Positives = 18/40 (45%)
Query: 681 EGGEDGEENSSCSECSSSCDSSDSESGSSVSGSHTFEQLQ 720
E +SS S S S SDSES SS S S E +
Sbjct: 392 EPAASSSGSSSSSSGSESSSGSDSESESSSSDSEENEPPR 431
>gnl|CDD|238936 cd01977, Nitrogenase_VFe_alpha, Nitrogenase_VFe_alpha -like:
Nitrogenase VFe protein, alpha subunit like. This group
contains proteins similar to the alpha subunits of, the
VFe protein of the vanadium-dependent (V-) nitrogenase
and the FeFe protein of the iron only (Fe-) nitrogenase
Nitrogenase catalyzes the ATP-dependent reduction of
dinitrogen (N2) to ammonia. In addition to V- and Fe-
nitrogenases there is a molybdenum (Mo)-dependent
nitrogenase which is the most widespread and best
characterized of these systems. These systems consist
of component 1 (VFe protein, FeFe protein or, MoFe
protein respectively) and, component 2 (Fe protein).
MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases
are alpha2beta2delta2 hexamers. The alpha and beta
subunits of VFe and FeFe are similar to the alpha and
beta subunits of MoFe. For MoFe each alphabeta pair
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein which
has a practically identical structure in all three
systems, it contains a single [4Fe-4S] cluster.
Electrons are transferred from the [4Fe-4S] cluster of
the Fe protein to the P-cluster of the MoFe and in turn
to FeMoCo, the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the
Mo-nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 415
Score = 30.1 bits (68), Expect = 5.7
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 2/48 (4%)
Query: 90 IMNEQRKISNLPPLAIDT--FELLMDRLEKECQFQMSHTQSQDIIDDE 135
I NE +K +P L +D FE + L K F +++ +I +E
Sbjct: 224 IANELKKRYGIPRLDVDGFGFEYCAESLRKIGAFFGIEDRAEAVIAEE 271
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 29.9 bits (67), Expect = 5.8
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 14/62 (22%)
Query: 128 SQDIIDDEAVCCICNDGE------CQNSNVILFCDMCNLA-VHQDCYGVPYIPEGQWLCR 180
S+D + E + C C C N+N C H +C G+ P+G+W C
Sbjct: 213 SEDNSEGEELYCFCQQVSYGQMVACDNAN-------CKREWFHLECVGLKEPPKGKWYCP 265
Query: 181 RC 182
C
Sbjct: 266 EC 267
>gnl|CDD|221845 pfam12906, RINGv, RING-variant domain.
Length = 47
Score = 26.6 bits (59), Expect = 5.9
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 138 CCICNDGECQNSNVILFCDMC---NLAVHQDC 166
C IC +GE ++ +I C C VHQ C
Sbjct: 1 CRICLEGEEEDEPLIRPC-RCRGSLKYVHQSC 31
>gnl|CDD|191716 pfam07263, DMP1, Dentin matrix protein 1 (DMP1). This family
consists of several mammalian dentin matrix protein 1
(DMP1) sequences. The dentin matrix acidic
phosphoprotein 1 (DMP1) gene has been mapped to human
chromosome 4q21. DMP1 is a bone and teeth specific
protein initially identified from mineralised dentin.
DMP1 is primarily localised in the nuclear compartment
of undifferentiated osteoblasts. In the nucleus, DMP1
acts as a transcriptional component for activation of
osteoblast-specific genes like osteocalcin. During the
early phase of osteoblast maturation, Ca(2+) surges into
the nucleus from the cytoplasm, triggering the
phosphorylation of DMP1 by a nuclear isoform of casein
kinase II. This phosphorylated DMP1 is then exported out
into the extracellular matrix, where it regulates
nucleation of hydroxyapatite. DMP1 is a unique molecule
that initiates osteoblast differentiation by
transcription in the nucleus and orchestrates
mineralised matrix formation extracellularly, at later
stages of osteoblast maturation. The DMP1 gene has been
found to be ectopically expressed in lung cancer
although the reason for this is unknown.
Length = 514
Score = 30.0 bits (67), Expect = 6.4
Identities = 32/135 (23%), Positives = 56/135 (41%), Gaps = 22/135 (16%)
Query: 601 EETSKAE---NNKQEEKKNSTDVVM---------GMSSKDTKNFKSPEITTRKRHGNKKK 648
EE + E +N E K +ST+ S +D++ +S E + + + +
Sbjct: 276 EEDGRGELDDSNTMEVKSDSTENAGLSQSREHSRSESQEDSEENQSQEDSQEVQDPSSES 335
Query: 649 GAQEELSVPESDSFKVYRSGGELKGEAFDSAEEGGEDGEENSSC----------SECSSS 698
+ +L E+ S E +G+ D+ ED E++ S SE S+
Sbjct: 336 SQEADLPSQENSSESQEEVVSESRGDNPDNTTSHSEDQEDSESSEEDSLDTPSSSESQST 395
Query: 699 CDSSDSESGSSVSGS 713
+ +DSES S+S S
Sbjct: 396 EEQADSESNESLSSS 410
>gnl|CDD|227192 COG4855, COG4855, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 76
Score = 27.1 bits (60), Expect = 7.8
Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 7/32 (21%)
Query: 243 RW--KLTCYVCKQRG-----VGACIQCHKTNC 267
RW + CY C + G VG CI C C
Sbjct: 3 RWSNMMKCYDCAEEGKDTDAVGICIVCGMGLC 34
>gnl|CDD|216209 pfam00946, Mononeg_RNA_pol, Mononegavirales RNA dependent RNA
polymerase. Members of the Mononegavirales including
the Paramyxoviridae, like other non-segmented negative
strand RNA viruses, have an RNA-dependent RNA polymerase
composed of two subunits, a large protein L and a
phosphoprotein P. This is a protein family of the L
protein. The L protein confers the RNA polymerase
activity on the complex. The P protein acts as a
transcription factor.
Length = 1065
Score = 29.9 bits (68), Expect = 8.0
Identities = 19/101 (18%), Positives = 28/101 (27%), Gaps = 25/101 (24%)
Query: 121 FQMSHTQSQDIIDDEAVCCICN-DGE--CQN---SNVILFCDMCNLAVHQDCYGVPYIPE 174
+S + QD + E V C D C N F + + + YG+P +
Sbjct: 584 LTLSQSGVQDDDNYEIVSCFITTDLSKYCLNWRYETTAPFAQVLD-----ELYGLPSLFS 638
Query: 175 GQWLCRR------------CLHTPSRAVDCVLCPNNGGAFK 203
WL R +D PN
Sbjct: 639 --WLHLRFEKSTIYVGDPHNPPDLDNHIDLDNVPNGDIFIV 677
>gnl|CDD|233617 TIGR01884, cas_HTH, CRISPR locus-related DNA-binding protein. Most
but not all examples of this family are associated with
CRISPR loci, a combination of DNA repeats and
characteristic proteins encoded near the repeat cluster.
The C-terminal region of this protein is homologous to
DNA-binding helix-turn-helix domains with predicted
transcriptional regulatory activity [Regulatory
functions, DNA interactions, Mobile and extrachromosomal
element functions, Other].
Length = 203
Score = 28.9 bits (65), Expect = 8.3
Identities = 13/89 (14%), Positives = 30/89 (33%), Gaps = 4/89 (4%)
Query: 480 IKARDTGD--IFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKAN-QYLSLEDFENDFNLM 536
I ++ GD I ++ V + ++ + N V+ + + L+D +
Sbjct: 20 IGIKEEGDLVILVKSPIVDGARRAVESLRAIIS-DLYGNLVEGTIKEIELKDVPLALRQI 78
Query: 537 VENCLTYNEKDTIFYKAGIKMKQVGGALI 565
+ E I +G + L+
Sbjct: 79 SDIIKEEPEPGVIINLSGGMRILILILLL 107
>gnl|CDD|233339 TIGR01278, DPOR_BchB, light-independent protochlorophyllide
reductase, B subunit. Alternate name: dark
protochlorophyllide reductase This enzyme describes the
B subunit of the dark form protochlorophyllide
reductase, a nitrogenase-like enzyme. This subunit shows
homology to the nitrogenase molybdenum-iron protein. It
catalyzes a step in bacteriochlorophyll biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 511
Score = 29.4 bits (66), Expect = 8.8
Identities = 29/93 (31%), Positives = 40/93 (43%), Gaps = 13/93 (13%)
Query: 431 RQDLER---ARLLCELVRKREKMKRELIKVTEACTMIKLNPLNSLLLQLIDLIKARDTGD 487
R+DL R RL+ + R ++ K +LI VT +CT S LLQ DL
Sbjct: 62 RRDLARGSQTRLVDTVRRVDDRFKPDLIVVTPSCT--------SSLLQE-DLGNLAAAAG 112
Query: 488 IFLEPVDVIEVPDYADVIKQPMDLTTMTNKVKA 520
+ V V +V Y Q D T+T V+
Sbjct: 113 LDKSKVIVADVNAYRRKENQAAD-RTLTQLVRR 144
>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 = 27.5 bits (61), Expect = 8.9
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 249 YVCKQRGVGACI--QCHKTNCYAAFHVTCAQQAGLYMNMDTIRDHSG 293
YVCK +G G C + H+ C A C + MN D ++ G
Sbjct: 43 YVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVG---MNKDAVQHERG 86
>gnl|CDD|236558 PRK09545, znuA, high-affinity zinc transporter periplasmic
component; Reviewed.
Length = 311
Score = 29.2 bits (66), Expect = 9.0
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 21/60 (35%)
Query: 322 PSD-EKLKNARLV----------LAKKRVSVPTVSIPTIPPERVQDIAQLISVPKKSQLM 370
PSD ++L++A LV L K + +P + IAQL V K LM
Sbjct: 65 PSDVKRLQSADLVVWVGPEMEAFLEK--------PVSKLPENKQVTIAQLPDV--KPLLM 114
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 0.403
Gapped
Lambda K H
0.267 0.0891 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 41,950,919
Number of extensions: 4119366
Number of successful extensions: 3924
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3888
Number of HSP's successfully gapped: 96
Length of query: 830
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 725
Effective length of database: 6,280,432
Effective search space: 4553313200
Effective search space used: 4553313200
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 (21.7 bits)
S2: 63 (27.8 bits)