Query 027848
Match_columns 218
No_of_seqs 126 out of 484
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 16:08:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027848.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027848hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00501 BRIGHT BRIGHT, ARID 99.9 7.9E-28 1.7E-32 182.3 10.2 90 32-121 1-91 (93)
2 PF01388 ARID: ARID/BRIGHT DNA 99.9 1E-26 2.3E-31 174.7 8.2 90 29-118 2-92 (92)
3 KOG2744 DNA-binding proteins B 99.8 1.2E-18 2.7E-23 167.6 9.6 108 23-130 153-262 (512)
4 KOG2510 SWI-SNF chromatin-remo 99.1 6.3E-11 1.4E-15 113.3 6.8 91 31-128 291-382 (532)
5 PF00249 Myb_DNA-binding: Myb- 86.5 1.5 3.3E-05 28.9 4.2 39 65-114 10-48 (48)
6 PF09441 Abp2: ARS binding pro 73.8 5.4 0.00012 34.2 4.2 41 54-98 45-85 (175)
7 PF13921 Myb_DNA-bind_6: Myb-l 67.6 9.3 0.0002 25.9 3.7 36 66-114 8-43 (60)
8 cd00167 SANT 'SWI3, ADA2, N-Co 63.2 17 0.00037 22.0 4.0 36 66-113 9-44 (45)
9 smart00717 SANT SANT SWI3, AD 45.5 49 0.0011 20.1 4.0 26 84-114 22-47 (49)
10 PF10545 MADF_DNA_bdg: Alcohol 43.2 20 0.00044 25.0 2.2 38 81-118 24-64 (85)
11 PLN03212 Transcription repress 36.9 47 0.001 30.2 3.9 40 66-116 35-74 (249)
12 PF13873 Myb_DNA-bind_5: Myb/S 34.0 46 0.00099 23.6 2.8 53 62-115 14-70 (78)
13 PF06783 UPF0239: Uncharacteri 33.7 26 0.00057 26.9 1.5 14 163-176 19-32 (85)
14 PF05066 HARE-HTH: HB1, ASXL, 33.6 62 0.0013 22.8 3.4 34 37-80 3-36 (72)
15 PF05849 L-fibroin: Fibroin li 31.1 34 0.00074 31.0 2.0 48 137-184 1-51 (245)
16 PF13725 tRNA_bind_2: Possible 30.8 30 0.00065 25.8 1.4 21 78-98 78-98 (101)
17 smart00595 MADF subfamily of S 30.2 29 0.00062 25.1 1.2 42 79-120 23-65 (89)
18 PF12776 Myb_DNA-bind_3: Myb/S 28.3 86 0.0019 22.8 3.5 58 65-122 11-70 (96)
19 cd08797 Death_NFkB1_p105 Death 26.2 84 0.0018 23.6 3.1 14 84-97 16-29 (76)
20 PLN03091 hypothetical protein; 25.6 76 0.0016 31.3 3.5 40 66-116 24-63 (459)
21 cd07268 Glo_EDI_BRP_like_4 Thi 25.5 28 0.00061 29.3 0.5 51 26-76 3-53 (149)
22 PF04967 HTH_10: HTH DNA bindi 25.2 88 0.0019 21.7 2.9 39 74-114 14-52 (53)
23 TIGR01557 myb_SHAQKYF myb-like 24.7 97 0.0021 21.7 3.0 28 85-115 25-55 (57)
24 cd08798 Death_NFkB2_p100 Death 24.0 98 0.0021 23.3 3.1 15 83-97 15-29 (76)
25 cd08310 Death_NFkB-like Death 23.0 1E+02 0.0022 22.4 3.0 14 83-96 12-25 (72)
26 PRK02363 DNA-directed RNA poly 22.2 58 0.0013 26.6 1.7 63 36-108 4-69 (129)
27 cd01670 Death Death Domain: a 22.1 67 0.0014 22.5 1.8 15 84-98 11-25 (79)
28 PF02337 Gag_p10: Retroviral G 20.4 1.1E+02 0.0023 23.7 2.7 55 34-95 7-64 (90)
No 1
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=99.95 E-value=7.9e-28 Score=182.33 Aligned_cols=90 Identities=41% Similarity=0.699 Sum_probs=86.6
Q ss_pred CChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHH
Q 027848 32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY 110 (218)
Q Consensus 32 ~er~~Fl~~L~~F~~~rG~pl-~~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y 110 (218)
++++.|+++|.+||+++|+|+ ++|.|+|++||||+||.+|+++|||++||++++|.+||++||+|+++++++..||++|
T Consensus 1 ~~~~~F~~~L~~F~~~~g~~~~~~P~i~g~~vdL~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y 80 (93)
T smart00501 1 RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHY 80 (93)
T ss_pred CcHHHHHHHHHHHHHHcCCcCCcCCeECCEeCcHHHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHH
Confidence 478999999999999999998 7999999999999999999999999999999999999999999998899999999999
Q ss_pred HHhhHHHHhhh
Q 027848 111 LTLLYHYEQVH 121 (218)
Q Consensus 111 ~kyLl~YE~~~ 121 (218)
.+||+|||+++
T Consensus 81 ~k~L~~yE~~~ 91 (93)
T smart00501 81 ERYLLPFERFL 91 (93)
T ss_pred HHHhHHHHHHh
Confidence 99999999974
No 2
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=99.94 E-value=1e-26 Score=174.73 Aligned_cols=90 Identities=43% Similarity=0.721 Sum_probs=82.8
Q ss_pred cccCChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHH
Q 027848 29 DVSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLR 107 (218)
Q Consensus 29 ~~~~er~~Fl~~L~~F~~~rG~pl-~~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK 107 (218)
..+++++.|+++|++||+++|+++ ++|.++|++||||+||.+|+++|||++|+++++|.+||++||+++.+++.+..|+
T Consensus 2 ~~~~~~~~F~~~L~~f~~~~g~~~~~~P~i~g~~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~ 81 (92)
T PF01388_consen 2 ANTREREQFLEQLREFHESRGTPIDRPPVIGGKPVDLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLR 81 (92)
T ss_dssp SSCHHHHHHHHHHHHHHHHTTSSSSS-SEETTSE-SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHH
T ss_pred CcchHHHHHHHHHHHHHHHcCCCCCCCCcCCCEeCcHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHH
Confidence 345789999999999999999997 7999999999999999999999999999999999999999999998888888999
Q ss_pred HHHHHhhHHHH
Q 027848 108 KHYLTLLYHYE 118 (218)
Q Consensus 108 ~~Y~kyLl~YE 118 (218)
++|++||++||
T Consensus 82 ~~Y~~~L~~fE 92 (92)
T PF01388_consen 82 QHYEKYLLPFE 92 (92)
T ss_dssp HHHHHHTHHHH
T ss_pred HHHHHHhHhhC
Confidence 99999999998
No 3
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=99.76 E-value=1.2e-18 Score=167.58 Aligned_cols=108 Identities=46% Similarity=0.684 Sum_probs=97.7
Q ss_pred CCCCCCcccCChhHHHHHHHHHHhhcCCCCC-CCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCC-CCC
Q 027848 23 PLSSHEDVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSP-TTT 100 (218)
Q Consensus 23 p~~~~e~~~~er~~Fl~~L~~F~~~rG~pl~-~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~-~~t 100 (218)
|....+....+++.|+++|+.||+++|++++ +|+|+|+++|||+||.+|+++||+++|+..+.|++|...+.+|. +++
T Consensus 153 ~~~~~e~~~~~~eeF~~dl~~f~~~~~~~~~~iPii~~~~ldL~~Ly~lV~s~GG~~~V~~~k~Wrev~~~l~~pt~tiT 232 (512)
T KOG2744|consen 153 PLYETEGVPKSSEEFMEDLRRFMKKRGTKVKSIPIIGGQPLDLHWLYALVTSRGGLDEVTNKKLWREVIDGLNFPTPTIT 232 (512)
T ss_pred cccccccccccHHHHHHHHHHHHHHhCCcceeccccCCCcchHHHHHHHHhcCCchhHhhhhhhHHHHhccccCCCcccc
Confidence 3344455566999999999999999999995 99999999999999999999999999999999999999999999 999
Q ss_pred cHHHHHHHHHHHhhHHHHhhhhhhccCCCC
Q 027848 101 SASFVLRKHYLTLLYHYEQVHFFKMQGPPC 130 (218)
Q Consensus 101 ~as~~LK~~Y~kyLl~YE~~~~~~e~~~~~ 130 (218)
++++.|++.|.|+|++||+.+.+....+.+
T Consensus 233 saaf~lr~~y~K~L~~ye~~~~~~~~~pln 262 (512)
T KOG2744|consen 233 SAAFTLRKQYLKLLFEYECEFEKNRHVPLN 262 (512)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 999999999999999999998876553333
No 4
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=99.14 E-value=6.3e-11 Score=113.28 Aligned_cols=91 Identities=29% Similarity=0.437 Sum_probs=82.5
Q ss_pred cCChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHH
Q 027848 31 SKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKH 109 (218)
Q Consensus 31 ~~er~~Fl~~L~~F~~~rG~pl-~~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~ 109 (218)
..+++..+++|+.|++.+.+++ ..|.++.++||||+||..|.+.||+..|+++| +++|.-|| .++++.||++
T Consensus 291 qp~r~~wvDR~raF~ee~~Sp~t~~p~~gakPldl~rlYvsvke~gg~~~v~knk--rd~a~~lg-----ssaa~~l~k~ 363 (532)
T KOG2510|consen 291 QPERKEWVDRLRAFTEERASPMTNLPAVGAKPLDLYRLYVSVKEIGGLTQVNKNK--RDLATNLG-----SSAASSLKKQ 363 (532)
T ss_pred CcchhhHHHHHHHHHHhhcCcccccccccccchhHHHHHHHHHHhccceeeccch--hhhhhccc-----hHHHHHHHHH
Confidence 5689999999999999999999 58999999999999999999999999999999 99999888 5578899999
Q ss_pred HHHhhHHHHhhhhhhccCC
Q 027848 110 YLTLLYHYEQVHFFKMQGP 128 (218)
Q Consensus 110 Y~kyLl~YE~~~~~~e~~~ 128 (218)
|.+||+.||++...+++++
T Consensus 364 y~~~lf~fec~f~Rg~e~p 382 (532)
T KOG2510|consen 364 YIQYLFAFECKFERGEEPP 382 (532)
T ss_pred HHHHHHhhceeeeccCCCC
Confidence 9999999999866555543
No 5
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=86.47 E-value=1.5 Score=28.87 Aligned_cols=39 Identities=18% Similarity=0.307 Sum_probs=28.0
Q ss_pred hhhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027848 65 HVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (218)
Q Consensus 65 y~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y~kyL 114 (218)
-.|..+|...|.- .|..||..++ .+ -.+.+++..|.++|
T Consensus 10 ~~l~~~v~~~g~~-------~W~~Ia~~~~--~~--Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 10 EKLLEAVKKYGKD-------NWKKIAKRMP--GG--RTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHHSTTT-------HHHHHHHHHS--SS--STHHHHHHHHHHHT
T ss_pred HHHHHHHHHhCCc-------HHHHHHHHcC--CC--CCHHHHHHHHHhhC
Confidence 3466677766644 6999999999 21 23448999999886
No 6
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=73.84 E-value=5.4 Score=34.20 Aligned_cols=41 Identities=17% Similarity=0.290 Sum_probs=34.1
Q ss_pred CCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCCC
Q 027848 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPT 98 (218)
Q Consensus 54 ~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~ 98 (218)
+|.-+||..+.|.||..|.++-.- .=|.|.++|-+||..+.
T Consensus 45 pPkS~Gk~Fs~~~Lf~LI~k~~~k----eikTW~~La~~LGVepp 85 (175)
T PF09441_consen 45 PPKSDGKSFSTFTLFELIRKLESK----EIKTWAQLALELGVEPP 85 (175)
T ss_pred CCCcCCccchHHHHHHHHHHHhhh----hHhHHHHHHHHhCCCCC
Confidence 799999999999999999975432 23579999999998653
No 7
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=67.64 E-value=9.3 Score=25.88 Aligned_cols=36 Identities=14% Similarity=0.310 Sum_probs=23.5
Q ss_pred hhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027848 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (218)
Q Consensus 66 ~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y~kyL 114 (218)
.|-..|...|. .|..||..|| . - .+.+++..|.++|
T Consensus 8 ~L~~~~~~~g~--------~W~~Ia~~l~---~-R-t~~~~~~r~~~~l 43 (60)
T PF13921_consen 8 LLLELVKKYGN--------DWKKIAEHLG---N-R-TPKQCRNRWRNHL 43 (60)
T ss_dssp HHHHHHHHHTS---------HHHHHHHST---T-S--HHHHHHHHHHTT
T ss_pred HHHHHHHHHCc--------CHHHHHHHHC---c-C-CHHHHHHHHHHHC
Confidence 34555665543 5999999996 1 1 2348888888866
No 8
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=63.18 E-value=17 Score=22.05 Aligned_cols=36 Identities=14% Similarity=0.281 Sum_probs=24.1
Q ss_pred hhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHHHHh
Q 027848 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113 (218)
Q Consensus 66 ~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y~ky 113 (218)
.|...|...|- ..|..||+.++-- .+..+++.|.++
T Consensus 9 ~l~~~~~~~g~-------~~w~~Ia~~~~~r-----s~~~~~~~~~~~ 44 (45)
T cd00167 9 LLLEAVKKYGK-------NNWEKIAKELPGR-----TPKQCRERWRNL 44 (45)
T ss_pred HHHHHHHHHCc-------CCHHHHHhHcCCC-----CHHHHHHHHHHh
Confidence 45556666653 5799999998641 233788888765
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=45.54 E-value=49 Score=20.14 Aligned_cols=26 Identities=15% Similarity=0.382 Sum_probs=18.5
Q ss_pred CChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027848 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (218)
Q Consensus 84 k~W~eVa~~LGlp~~~t~as~~LK~~Y~kyL 114 (218)
+.|..||..++ +. .+..++..|.+++
T Consensus 22 ~~w~~Ia~~~~---~r--t~~~~~~~~~~~~ 47 (49)
T smart00717 22 NNWEKIAKELP---GR--TAEQCRERWNNLL 47 (49)
T ss_pred CCHHHHHHHcC---CC--CHHHHHHHHHHHc
Confidence 57999999987 11 2337888887764
No 10
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=43.21 E-value=20 Score=25.03 Aligned_cols=38 Identities=21% Similarity=0.262 Sum_probs=23.3
Q ss_pred cccCChHHHHhhhCC--CCC-CCcHHHHHHHHHHHhhHHHH
Q 027848 81 VAEKKWREVGAVFKF--SPT-TTSASFVLRKHYLTLLYHYE 118 (218)
Q Consensus 81 t~~k~W~eVa~~LGl--p~~-~t~as~~LK~~Y~kyLl~YE 118 (218)
.+++.|.+||..||. +.. +...-..|+..|.+.+...+
T Consensus 24 ~r~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~~~~ 64 (85)
T PF10545_consen 24 LREEAWQEIARELGKEFSVDDCKKRWKNLRDRYRRELKKIK 64 (85)
T ss_pred HHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 355689999999983 321 22223356666666655555
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=36.95 E-value=47 Score=30.18 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=26.6
Q ss_pred hhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHHHHhhHH
Q 027848 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYH 116 (218)
Q Consensus 66 ~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y~kyLl~ 116 (218)
.|...|.+.|. +.|..||..++...+ +.+.+.-|.+||.|
T Consensus 35 ~L~~lV~kyG~-------~nW~~IAk~~g~gRT----~KQCReRW~N~L~P 74 (249)
T PLN03212 35 ILVSFIKKEGE-------GRWRSLPKRAGLLRC----GKSCRLRWMNYLRP 74 (249)
T ss_pred HHHHHHHHhCc-------ccHHHHHHhhhcCCC----cchHHHHHHHhhch
Confidence 35566777663 369999999874322 22677888888744
No 12
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=34.02 E-value=46 Score=23.62 Aligned_cols=53 Identities=15% Similarity=0.204 Sum_probs=32.5
Q ss_pred cchhhhHHHHHhc---CcchhhcccCChHHHHhhhCC-CCCCCcHHHHHHHHHHHhhH
Q 027848 62 LDLHVLYVEATTR---GGYEKVVAEKKWREVGAVFKF-SPTTTSASFVLRKHYLTLLY 115 (218)
Q Consensus 62 VDLy~Ly~~V~~~---GGy~~Vt~~k~W~eVa~~LGl-p~~~t~as~~LK~~Y~kyLl 115 (218)
|++..-|..|..- ++.....++..|.+|+..+.- ++. .-...+++..|.++..
T Consensus 14 v~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~-~Rs~~~lkkkW~nlk~ 70 (78)
T PF13873_consen 14 VELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPG-KRSWKQLKKKWKNLKS 70 (78)
T ss_pred HHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHH
Confidence 4455555555543 222333445699999999974 333 3344499999887654
No 13
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=33.75 E-value=26 Score=26.94 Aligned_cols=14 Identities=57% Similarity=0.921 Sum_probs=12.1
Q ss_pred HHHHHhhhhhhhhH
Q 027848 163 LCLLLFGLFVGLIL 176 (218)
Q Consensus 163 ~~~~~~~~~~~~~~ 176 (218)
+.+..+|+|.|.|+
T Consensus 19 e~llRYGLf~GAIF 32 (85)
T PF06783_consen 19 ENLLRYGLFVGAIF 32 (85)
T ss_pred HHHHHHHHHHHHHH
Confidence 56778999999986
No 14
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=33.56 E-value=62 Score=22.81 Aligned_cols=34 Identities=21% Similarity=0.298 Sum_probs=21.5
Q ss_pred HHHHHHHHHhhcCCCCCCCeeCCeecchhhhHHHHHhcCcchhh
Q 027848 37 FWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKV 80 (218)
Q Consensus 37 Fl~~L~~F~~~rG~pl~~P~I~Gk~VDLy~Ly~~V~~~GGy~~V 80 (218)
|.+.-.+-+++.|.| +..-.++..+.++|++...
T Consensus 3 ~~eaa~~vL~~~~~p----------m~~~eI~~~i~~~~~~~~~ 36 (72)
T PF05066_consen 3 FKEAAYEVLEEAGRP----------MTFKEIWEEIQERGLYKKS 36 (72)
T ss_dssp HHHHHHHHHHHH-S-----------EEHHHHHHHHHHHHTS---
T ss_pred HHHHHHHHHHhcCCC----------cCHHHHHHHHHHhCCCCcc
Confidence 444555555555544 7888999999999999877
No 15
>PF05849 L-fibroin: Fibroin light chain (L-fibroin); InterPro: IPR008660 This family consists of several moth fibroin light chain (L-fibroin) proteins. Fibroin of Bombyx mori is secreted into the lumen of posterior silk gland (PSG) from the surrounding PSG cells as a molecular complex consisting of a heavy (H)-chain of approximately 350 kDa, a light (L)-chain of 25 kDa and a P25 of about 27 kDa. The H- and L-chains are disulphide-linked but P25 is associated with the H-L complex by non-covalent force [].; GO: 0005576 extracellular region
Probab=31.07 E-value=34 Score=30.98 Aligned_cols=48 Identities=25% Similarity=0.167 Sum_probs=39.7
Q ss_pred hhhhhhhhhhceecchhhhhHHHHHHHHHHHhhhhhh---hhHHHHHHHHH
Q 027848 137 EFLLVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVG---LILFITLQQLH 184 (218)
Q Consensus 137 ~~~~~~~y~~v~~~e~~~f~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ 184 (218)
|.....||+..|...++-+++.+-.-..-.-|++.+| +||..|+||+-
T Consensus 1 Psv~i~q~~~nei~~~~dnG~~iss~lid~af~lvDggd~~iyiL~~~qil 51 (245)
T PF05849_consen 1 PSVTINQYSDNEIPPDIDNGKPISSSLIDRAFDLVDGGDINIYILTLQQIL 51 (245)
T ss_pred CceeeeccccccCCCCCcCccchHHHHHHHHHHhhcCCCccHHHHHHHHHH
Confidence 4556778999999999999998866677778888877 79999999975
No 16
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=30.78 E-value=30 Score=25.84 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=14.0
Q ss_pred hhhcccCChHHHHhhhCCCCC
Q 027848 78 EKVVAEKKWREVGAVFKFSPT 98 (218)
Q Consensus 78 ~~Vt~~k~W~eVa~~LGlp~~ 98 (218)
.+|.+++.|.+||+++|++..
T Consensus 78 ~k~LQ~ksw~~~a~~l~l~g~ 98 (101)
T PF13725_consen 78 AKGLQGKSWEEVAKELGLPGR 98 (101)
T ss_dssp HHHCS---HHHHHHHCT-SSH
T ss_pred HHHHCCCCHHHHHHHcCCCCC
Confidence 357778999999999999853
No 17
>smart00595 MADF subfamily of SANT domain.
Probab=30.21 E-value=29 Score=25.08 Aligned_cols=42 Identities=21% Similarity=0.237 Sum_probs=28.9
Q ss_pred hhcccCChHHHHhhhCCCCC-CCcHHHHHHHHHHHhhHHHHhh
Q 027848 79 KVVAEKKWREVGAVFKFSPT-TTSASFVLRKHYLTLLYHYEQV 120 (218)
Q Consensus 79 ~Vt~~k~W~eVa~~LGlp~~-~t~as~~LK~~Y~kyLl~YE~~ 120 (218)
...+...|.+||..||.+.. |...=..|+..|.+.+...+..
T Consensus 23 ~~~r~~aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~~ 65 (89)
T smart00595 23 KEEKRKAWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQNG 65 (89)
T ss_pred hHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34455699999999998532 3333347888888877766653
No 18
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=28.28 E-value=86 Score=22.75 Aligned_cols=58 Identities=16% Similarity=0.217 Sum_probs=39.5
Q ss_pred hhhHHHHHhcCcc--hhhcccCChHHHHhhhCCCCCCCcHHHHHHHHHHHhhHHHHhhhh
Q 027848 65 HVLYVEATTRGGY--EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHF 122 (218)
Q Consensus 65 y~Ly~~V~~~GGy--~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y~kyLl~YE~~~~ 122 (218)
..++..-...|.. ...=+...|..|+.+|.-..+..-...++++.|..+=..|.....
T Consensus 11 l~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~ 70 (96)
T PF12776_consen 11 LDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKE 70 (96)
T ss_pred HHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566666 233344589999999996554433445899999988888888654
No 19
>cd08797 Death_NFkB1_p105 Death domain of the Nuclear Factor-KappaB1 precursor protein p105. Death Domain (DD) of the Nuclear Factor-KappaB1 (NF-kB1) precursor protein p105. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB1 (or p50) is produced from the processing of the precursor protein p105, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the classical (or canonical) NF-kB pathway. In the cytosol, p50 forms an inactive complex with RelA (or p65) and the Inhibitor of NF-kB (IkB). Activation is triggered by the phosphorylation and degradation of IkB, resulting in the active DNA-binding p50-RelA dimer to migrate to the nucleus. The classical pathway regulates the majority of genes activated by NF-kB including those encod
Probab=26.24 E-value=84 Score=23.58 Aligned_cols=14 Identities=14% Similarity=0.468 Sum_probs=12.0
Q ss_pred CChHHHHhhhCCCC
Q 027848 84 KKWREVGAVFKFSP 97 (218)
Q Consensus 84 k~W~eVa~~LGlp~ 97 (218)
..|+.+|++||+..
T Consensus 16 g~Wr~LA~kL~l~~ 29 (76)
T cd08797 16 KNWETLAQKLGLGI 29 (76)
T ss_pred CCHHHHHHHHCchh
Confidence 35999999999974
No 20
>PLN03091 hypothetical protein; Provisional
Probab=25.60 E-value=76 Score=31.26 Aligned_cols=40 Identities=18% Similarity=0.167 Sum_probs=26.9
Q ss_pred hhHHHHHhcCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHHHHhhHH
Q 027848 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYH 116 (218)
Q Consensus 66 ~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y~kyLl~ 116 (218)
+|...|.+.|- +.|..||..++...+ +.+.|.-|.+||.|
T Consensus 24 ~L~~~V~kyG~-------~nWs~IAk~~g~gRT----~KQCRERW~NyLdP 63 (459)
T PLN03091 24 KLLRHITKYGH-------GCWSSVPKQAGLQRC----GKSCRLRWINYLRP 63 (459)
T ss_pred HHHHHHHHhCc-------CCHHHHhhhhccCcC----cchHhHHHHhccCC
Confidence 56677887763 479999998874332 12567777777654
No 21
>cd07268 Glo_EDI_BRP_like_4 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=25.48 E-value=28 Score=29.33 Aligned_cols=51 Identities=14% Similarity=0.035 Sum_probs=41.8
Q ss_pred CCCcccCChhHHHHHHHHHHhhcCCCCCCCeeCCeecchhhhHHHHHhcCc
Q 027848 26 SHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGG 76 (218)
Q Consensus 26 ~~e~~~~er~~Fl~~L~~F~~~rG~pl~~P~I~Gk~VDLy~Ly~~V~~~GG 76 (218)
+|-++........++++.-+.+.|.-++.-.|+||+|-||+|..-+.-.|.
T Consensus 3 DHialR~n~~~~A~~w~~~l~~~G~llSen~INGRPI~l~~L~qPl~~~~~ 53 (149)
T cd07268 3 DHIALRVNENQTAERWKEGLLQCGELLSENEINGRPIALIKLEKPLQFAGW 53 (149)
T ss_pred ceEEEeeCCHHHHHHHHHHHHHhchhhhccccCCeeEEEEEcCCCceeCCc
Confidence 455555667778889999999999988889999999999999887765444
No 22
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=25.24 E-value=88 Score=21.69 Aligned_cols=39 Identities=23% Similarity=0.221 Sum_probs=31.2
Q ss_pred cCcchhhcccCChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027848 74 RGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (218)
Q Consensus 74 ~GGy~~Vt~~k~W~eVa~~LGlp~~~t~as~~LK~~Y~kyL 114 (218)
..||=.+-++-.=.++|++||++++ ..+..||+.-.|.+
T Consensus 14 ~~GYfd~PR~~tl~elA~~lgis~s--t~~~~LRrae~kli 52 (53)
T PF04967_consen 14 ELGYFDVPRRITLEELAEELGISKS--TVSEHLRRAERKLI 52 (53)
T ss_pred HcCCCCCCCcCCHHHHHHHhCCCHH--HHHHHHHHHHHHHh
Confidence 4677778888899999999999864 36778888877654
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=24.69 E-value=97 Score=21.66 Aligned_cols=28 Identities=7% Similarity=0.167 Sum_probs=19.6
Q ss_pred Ch---HHHHhhhCCCCCCCcHHHHHHHHHHHhhH
Q 027848 85 KW---REVGAVFKFSPTTTSASFVLRKHYLTLLY 115 (218)
Q Consensus 85 ~W---~eVa~~LGlp~~~t~as~~LK~~Y~kyLl 115 (218)
.| ..|++.++.+.- ...++++++++|-+
T Consensus 25 ~~a~pk~I~~~~~~~~l---T~~qV~SH~QKy~~ 55 (57)
T TIGR01557 25 DWATPKRILELMVVDGL---TRDQVASHLQKYRL 55 (57)
T ss_pred cccchHHHHHHcCCCCC---CHHHHHHHHHHHHc
Confidence 38 889999886541 12378888888754
No 24
>cd08798 Death_NFkB2_p100 Death domain of the Nuclear Factor-KappaB2 precursor protein p100. Death Domain (DD) of the Nuclear Factor-KappaB2 (NF-kB2) precursor protein p100. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB2 (or p52) is produced from the processing of the precursor protein p100, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the non-canonical NF-kB pathway. The p100 precursor is cytosolic and interacts with RelB. Upon phosphorylation by IKKalpha, p100 is processed to its 52kDa active, DNA binding form and the p52/RelB complex is translocated into the nucleus. The non-canonical pathway plays a role in adaptive immunity and lymphorganogenesis. In general, DDs are protein-protein interaction domains found i
Probab=23.99 E-value=98 Score=23.26 Aligned_cols=15 Identities=13% Similarity=0.452 Sum_probs=13.0
Q ss_pred cCChHHHHhhhCCCC
Q 027848 83 EKKWREVGAVFKFSP 97 (218)
Q Consensus 83 ~k~W~eVa~~LGlp~ 97 (218)
.+.|..+|++||+..
T Consensus 15 g~dW~~LA~kL~l~~ 29 (76)
T cd08798 15 DVPWMELAERLGLQS 29 (76)
T ss_pred CCCHHHHHHHHCcch
Confidence 568999999999863
No 25
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=22.98 E-value=1e+02 Score=22.38 Aligned_cols=14 Identities=21% Similarity=0.672 Sum_probs=12.5
Q ss_pred cCChHHHHhhhCCC
Q 027848 83 EKKWREVGAVFKFS 96 (218)
Q Consensus 83 ~k~W~eVa~~LGlp 96 (218)
.+.|..+|++||+.
T Consensus 12 ~~dWr~LA~~L~~~ 25 (72)
T cd08310 12 GCDWRELAQLLDLG 25 (72)
T ss_pred CCCHHHHHHHcCcH
Confidence 56899999999987
No 26
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=22.21 E-value=58 Score=26.56 Aligned_cols=63 Identities=8% Similarity=-0.022 Sum_probs=45.9
Q ss_pred HHHHHHHHHHhhcCCCCCCCeeCCeecchhhhHHHHHhcCcchhhcccCChHHHHhhhCCCCC---CCcHHHHHHH
Q 027848 36 VFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPT---TTSASFVLRK 108 (218)
Q Consensus 36 ~Fl~~L~~F~~~rG~pl~~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt~~k~W~eVa~~LGlp~~---~t~as~~LK~ 108 (218)
.+++.-..++..++.| +.++.|+..|.+..|+..-...++=.++...|.+... +++....||+
T Consensus 4 S~idvAy~iL~~~~~~----------m~f~dL~~ev~~~~~~s~e~~~~~iaq~YtdLn~DGRFi~lG~n~WgLr~ 69 (129)
T PRK02363 4 SLIEVAYEILKEKKEP----------MSFYDLVNEIQKYLGKSDEEIRERIAQFYTDLNLDGRFISLGDNKWGLRS 69 (129)
T ss_pred cHHHHHHHHHHHcCCc----------ccHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhccCCeeEcCCCceeccc
Confidence 4555566667666554 8899999999999998765555677788888888764 4555666776
No 27
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=22.09 E-value=67 Score=22.45 Aligned_cols=15 Identities=20% Similarity=0.558 Sum_probs=13.1
Q ss_pred CChHHHHhhhCCCCC
Q 027848 84 KKWREVGAVFKFSPT 98 (218)
Q Consensus 84 k~W~eVa~~LGlp~~ 98 (218)
+.|.++|+.||++..
T Consensus 11 ~~W~~la~~Lgl~~~ 25 (79)
T cd01670 11 KDWKKLARKLGLSDG 25 (79)
T ss_pred hHHHHHHHHhCCCHH
Confidence 679999999998853
No 28
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=20.44 E-value=1.1e+02 Score=23.68 Aligned_cols=55 Identities=16% Similarity=0.134 Sum_probs=34.0
Q ss_pred hhHHHHHHHHHHhhcCCCCCCCeeCCeecchhhhHHHHHhcCcchhhc---ccCChHHHHhhhCC
Q 027848 34 PIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVV---AEKKWREVGAVFKF 95 (218)
Q Consensus 34 r~~Fl~~L~~F~~~rG~pl~~P~I~Gk~VDLy~Ly~~V~~~GGy~~Vt---~~k~W~eVa~~LGl 95 (218)
++.|+..|+..++.||..++.. ||-+++..+.+..=.=... .-..|..|++.|.-
T Consensus 7 ~~~fv~~Lk~lLk~rGi~v~~~-------~L~~f~~~i~~~~PWF~~eG~l~~~~W~kvG~~l~~ 64 (90)
T PF02337_consen 7 KQPFVSILKHLLKERGIRVKKK-------DLINFLSFIDKVCPWFPEEGTLDLDNWKKVGEELKR 64 (90)
T ss_dssp HHHHHHHHHHHHHCCT----HH-------HHHHHHHHHHHHTT-SS--SS-HHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHcCeeecHH-------HHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHHHHHH
Confidence 3789999999999999887543 6677777776533221111 12479988888743
Done!