Query 027313
Match_columns 225
No_of_seqs 128 out of 485
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 08:04:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027313.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027313hhsearch_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 9E-28 1.9E-32 182.9 10.3 90 32-121 1-91 (93)
2 PF01388 ARID: ARID/BRIGHT DNA 99.9 1.4E-26 3E-31 174.9 8.0 89 30-118 3-92 (92)
3 KOG2744 DNA-binding proteins B 99.8 6.5E-19 1.4E-23 170.4 9.3 104 23-126 153-258 (512)
4 KOG2510 SWI-SNF chromatin-remo 99.2 1.7E-11 3.8E-16 117.6 6.2 92 31-129 291-383 (532)
5 PF00249 Myb_DNA-binding: Myb- 86.8 1.4 3.1E-05 29.2 4.2 38 66-114 11-48 (48)
6 PF09441 Abp2: ARS binding pro 73.8 5.4 0.00012 34.4 4.2 41 54-98 45-85 (175)
7 PF13921 Myb_DNA-bind_6: Myb-l 69.1 8.2 0.00018 26.3 3.7 36 66-114 8-43 (60)
8 cd00167 SANT 'SWI3, ADA2, N-Co 63.5 16 0.00036 22.2 4.0 36 66-113 9-44 (45)
9 smart00717 SANT SANT SWI3, AD 46.1 47 0.001 20.3 4.0 26 84-114 22-47 (49)
10 PF10545 MADF_DNA_bdg: Alcohol 46.1 18 0.00039 25.5 2.3 38 81-118 24-64 (85)
11 PF12776 Myb_DNA-bind_3: Myb/S 37.7 67 0.0014 23.5 4.3 60 66-125 12-73 (96)
12 PF13873 Myb_DNA-bind_5: Myb/S 37.6 37 0.00079 24.3 2.8 53 62-115 14-70 (78)
13 PLN03212 Transcription repress 37.5 46 0.00099 30.4 3.9 39 67-116 36-74 (249)
14 PF04744 Monooxygenase_B: Mono 36.4 31 0.00066 33.3 2.8 33 165-206 147-179 (381)
15 PF06783 UPF0239: Uncharacteri 33.0 28 0.0006 27.0 1.6 14 163-176 19-32 (85)
16 cd08797 Death_NFkB1_p105 Death 31.7 51 0.0011 24.9 2.8 15 83-97 15-29 (76)
17 PF05066 HARE-HTH: HB1, ASXL, 31.2 72 0.0016 22.6 3.4 43 37-90 3-45 (72)
18 PF13725 tRNA_bind_2: Possible 28.9 34 0.00073 25.7 1.4 20 79-98 79-98 (101)
19 smart00595 MADF subfamily of S 27.3 38 0.00082 24.6 1.4 41 80-120 24-65 (89)
20 PLN03091 hypothetical protein; 25.7 75 0.0016 31.5 3.5 40 66-116 24-63 (459)
21 cd08798 Death_NFkB2_p100 Death 25.6 73 0.0016 24.1 2.7 14 83-96 15-28 (76)
22 PF05849 L-fibroin: Fibroin li 24.5 56 0.0012 29.8 2.2 69 137-205 1-85 (245)
23 KOG3109 Haloacid dehalogenase- 23.9 41 0.00089 30.6 1.3 99 76-181 32-151 (244)
24 cd01670 Death Death Domain: a 23.2 62 0.0013 22.8 1.9 15 84-98 11-25 (79)
25 cd08310 Death_NFkB-like Death 22.9 1E+02 0.0022 22.5 3.0 14 83-96 12-25 (72)
26 PF04967 HTH_10: HTH DNA bindi 22.9 1E+02 0.0022 21.5 2.8 39 74-114 14-52 (53)
27 TIGR01557 myb_SHAQKYF myb-like 22.7 1.1E+02 0.0023 21.5 3.0 26 87-115 30-55 (57)
28 cd08802 Death_UNC5B Death doma 22.6 96 0.0021 23.8 2.9 14 83-96 20-33 (84)
29 PRK02363 DNA-directed RNA poly 20.7 66 0.0014 26.4 1.8 63 36-108 4-69 (129)
30 cd08799 Death_UNC5C Death doma 20.0 1.2E+02 0.0026 23.2 2.9 14 83-96 20-33 (84)
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=9e-28 Score=182.90 Aligned_cols=90 Identities=41% Similarity=0.699 Sum_probs=86.7
Q ss_pred CChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhccccChHHHHhhhCCCCCCCcHHHHHHHHH
Q 027313 32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY 110 (225)
Q Consensus 32 ~ere~Fl~~L~~F~~~rG~pl-k~P~I~GK~VDLy~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~Y 110 (225)
++++.|+++|.+||+.+|+|+ ++|.|+|++||||+||++|+++|||++||++++|.+||++||+|+++++++..||++|
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 7999999999999999999999999999999999999999999998889999999999
Q ss_pred HHhhHHHHHHH
Q 027313 111 LTLLYHYEQVH 121 (225)
Q Consensus 111 ~kyLlpYE~~~ 121 (225)
.+||+|||++.
T Consensus 81 ~k~L~~yE~~~ 91 (93)
T smart00501 81 ERYLLPFERFL 91 (93)
T ss_pred HHHhHHHHHHh
Confidence 99999999985
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=99.93 E-value=1.4e-26 Score=174.87 Aligned_cols=89 Identities=44% Similarity=0.730 Sum_probs=82.1
Q ss_pred ccCChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhccccChHHHHhhhCCCCCCCcHHHHHHH
Q 027313 30 VSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRK 108 (225)
Q Consensus 30 ~~~ere~Fl~~L~~F~~~rG~pl-k~P~I~GK~VDLy~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~ 108 (225)
..++++.|+++|.+||+++|+++ ++|.++|++||||+||++|+++|||++|+++++|.+||++||+++.+++.+..||+
T Consensus 3 ~~~~~~~F~~~L~~f~~~~g~~~~~~P~i~g~~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~ 82 (92)
T PF01388_consen 3 NTREREQFLEQLREFHESRGTPIDRPPVIGGKPVDLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQ 82 (92)
T ss_dssp SCHHHHHHHHHHHHHHHHTTSSSSS-SEETTSE-SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHH
T ss_pred cchHHHHHHHHHHHHHHHcCCCCCCCCcCCCEeCcHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHH
Confidence 35689999999999999999997 79999999999999999999999999999999999999999999988877889999
Q ss_pred HHHHhhHHHH
Q 027313 109 HYLTLLYHYE 118 (225)
Q Consensus 109 ~Y~kyLlpYE 118 (225)
+|++||++||
T Consensus 83 ~Y~~~L~~fE 92 (92)
T PF01388_consen 83 HYEKYLLPFE 92 (92)
T ss_dssp HHHHHTHHHH
T ss_pred HHHHHhHhhC
Confidence 9999999998
No 3
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=99.77 E-value=6.5e-19 Score=170.39 Aligned_cols=104 Identities=47% Similarity=0.710 Sum_probs=96.2
Q ss_pred CCCCCCcccCChhHHHHHHHHHHhhcCCCCC-CCeeCCeecchhhhHHHHHhcCcchhhccccChHHHHhhhCCCC-CCC
Q 027313 23 PLSSHEDVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSP-TTT 100 (225)
Q Consensus 23 P~~s~e~~~~ere~Fl~~L~~F~~~rG~plk-~P~I~GK~VDLy~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~-~~t 100 (225)
|....+....+++.|+++|+.||+.+|++++ +|+|+|+++|||+||.+|+++||+++|+.+++|++|...+++|+ +++
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 3344555667999999999999999999995 99999999999999999999999999999999999999999999 999
Q ss_pred cHHHHHHHHHHHhhHHHHHHHhhhcC
Q 027313 101 SASFVLRKHYLTLLYHYEQVHFFKMQ 126 (225)
Q Consensus 101 ~as~~LK~~Y~kyLlpYE~~~~~ge~ 126 (225)
++++.|++.|.|+|++||+.+.+...
T Consensus 233 saaf~lr~~y~K~L~~ye~~~~~~~~ 258 (512)
T KOG2744|consen 233 SAAFTLRKQYLKLLFEYECEFEKNRH 258 (512)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999999886644
No 4
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=99.20 E-value=1.7e-11 Score=117.62 Aligned_cols=92 Identities=29% Similarity=0.460 Sum_probs=84.9
Q ss_pred cCChhHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCcchhhccccChHHHHhhhCCCCCCCcHHHHHHHH
Q 027313 31 SKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKH 109 (225)
Q Consensus 31 ~~ere~Fl~~L~~F~~~rG~pl-k~P~I~GK~VDLy~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~ 109 (225)
..+++..+++|+.|++.+.+++ ..|.++.|+||||+||..|.++||+..|++++ +++|.-|| .++++.||++
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 4689999999999999999999 58999999999999999999999999999998 99999888 4578899999
Q ss_pred HHHhhHHHHHHHhhhcCCCC
Q 027313 110 YLTLLYHYEQVHFFKMQGPP 129 (225)
Q Consensus 110 Y~kyLlpYE~~~~~ge~~~~ 129 (225)
|.+||+.||+....|+++++
T Consensus 364 y~~~lf~fec~f~Rg~e~p~ 383 (532)
T KOG2510|consen 364 YIQYLFAFECKFERGEEPPP 383 (532)
T ss_pred HHHHHHhhceeeeccCCCCH
Confidence 99999999999888887655
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=86.79 E-value=1.4 Score=29.15 Aligned_cols=38 Identities=18% Similarity=0.311 Sum_probs=27.8
Q ss_pred hhHHHHHhcCcchhhccccChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027313 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (225)
Q Consensus 66 ~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~Y~kyL 114 (225)
.|...|...|.- .|..||..++ .+ -.+.+++.+|.++|
T Consensus 11 ~l~~~v~~~g~~-------~W~~Ia~~~~--~~--Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 11 KLLEAVKKYGKD-------NWKKIAKRMP--GG--RTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHSTTT-------HHHHHHHHHS--SS--STHHHHHHHHHHHT
T ss_pred HHHHHHHHhCCc-------HHHHHHHHcC--CC--CCHHHHHHHHHhhC
Confidence 456677766644 6999999999 22 23359999999886
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=73.82 E-value=5.4 Score=34.39 Aligned_cols=41 Identities=20% Similarity=0.319 Sum_probs=34.4
Q ss_pred CCeeCCeecchhhhHHHHHhcCcchhhccccChHHHHhhhCCCCC
Q 027313 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPT 98 (225)
Q Consensus 54 ~P~I~GK~VDLy~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~ 98 (225)
+|.-+||..+.|.||..|.++-.-+ -+.|.++|-+||..+.
T Consensus 45 pPkS~Gk~Fs~~~Lf~LI~k~~~ke----ikTW~~La~~LGVepp 85 (175)
T PF09441_consen 45 PPKSDGKSFSTFTLFELIRKLESKE----IKTWAQLALELGVEPP 85 (175)
T ss_pred CCCcCCccchHHHHHHHHHHHhhhh----HhHHHHHHHHhCCCCC
Confidence 7999999999999999999864432 3579999999998653
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=69.08 E-value=8.2 Score=26.30 Aligned_cols=36 Identities=14% Similarity=0.297 Sum_probs=23.7
Q ss_pred hhHHHHHhcCcchhhccccChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027313 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (225)
Q Consensus 66 ~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~Y~kyL 114 (225)
.|-..|...|. .|..||+.|| .. .+.+++..|.++|
T Consensus 8 ~L~~~~~~~g~--------~W~~Ia~~l~--~R---t~~~~~~r~~~~l 43 (60)
T PF13921_consen 8 LLLELVKKYGN--------DWKKIAEHLG--NR---TPKQCRNRWRNHL 43 (60)
T ss_dssp HHHHHHHHHTS---------HHHHHHHST--TS----HHHHHHHHHHTT
T ss_pred HHHHHHHHHCc--------CHHHHHHHHC--cC---CHHHHHHHHHHHC
Confidence 34555665553 5999999996 11 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=63.52 E-value=16 Score=22.24 Aligned_cols=36 Identities=14% Similarity=0.281 Sum_probs=24.2
Q ss_pred hhHHHHHhcCcchhhccccChHHHHhhhCCCCCCCcHHHHHHHHHHHh
Q 027313 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113 (225)
Q Consensus 66 ~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~Y~ky 113 (225)
.|...|...|- ..|..||+.++-. .+..+++.|.++
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 34555666653 5799999998642 234788888765
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=46.08 E-value=47 Score=20.34 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=18.8
Q ss_pred cChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027313 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (225)
Q Consensus 84 k~W~eVA~~LGlp~~~t~as~~LK~~Y~kyL 114 (225)
+.|..||..++-. .+..++..|.+++
T Consensus 22 ~~w~~Ia~~~~~r-----t~~~~~~~~~~~~ 47 (49)
T smart00717 22 NNWEKIAKELPGR-----TAEQCRERWNNLL 47 (49)
T ss_pred CCHHHHHHHcCCC-----CHHHHHHHHHHHc
Confidence 5799999998711 2347888887765
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=46.06 E-value=18 Score=25.46 Aligned_cols=38 Identities=24% Similarity=0.352 Sum_probs=22.1
Q ss_pred ccccChHHHHhhhC--CCCC-CCcHHHHHHHHHHHhhHHHH
Q 027313 81 VAEKKWREVGAVFK--FSPT-TTSASFVLRKHYLTLLYHYE 118 (225)
Q Consensus 81 t~~k~W~eVA~~LG--lp~~-~t~as~~LK~~Y~kyLlpYE 118 (225)
.+.+.|.+||..+| ++.. +...-..|+..|.+.+...+
T Consensus 24 ~r~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~~~~ 64 (85)
T PF10545_consen 24 LREEAWQEIARELGKEFSVDDCKKRWKNLRDRYRRELKKIK 64 (85)
T ss_pred HHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35668999999998 3321 22222355555555555544
No 11
>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=37.72 E-value=67 Score=23.47 Aligned_cols=60 Identities=15% Similarity=0.235 Sum_probs=40.6
Q ss_pred hhHHHHHhcCcc--hhhccccChHHHHhhhCCCCCCCcHHHHHHHHHHHhhHHHHHHHhhhc
Q 027313 66 VLYVEATTRGGY--EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKM 125 (225)
Q Consensus 66 ~LY~~V~~~GGy--~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~Y~kyLlpYE~~~~~ge 125 (225)
.++..-...|.. ...=+...|..|+.+|.-..+..-...++++.|...=..|..+.....
T Consensus 12 ~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l~~ 73 (96)
T PF12776_consen 12 DLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKELRN 73 (96)
T ss_pred HHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHHHc
Confidence 444555556666 233344589999999986544433445999999999999988765443
No 12
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=37.59 E-value=37 Score=24.27 Aligned_cols=53 Identities=15% Similarity=0.231 Sum_probs=32.4
Q ss_pred cchhhhHHHHHhc---CcchhhccccChHHHHhhhC-CCCCCCcHHHHHHHHHHHhhH
Q 027313 62 LDLHVLYVEATTR---GGYEKVVAEKKWREVGAVFK-FSPTTTSASFVLRKHYLTLLY 115 (225)
Q Consensus 62 VDLy~LY~~V~~~---GGy~~Vt~~k~W~eVA~~LG-lp~~~t~as~~LK~~Y~kyLl 115 (225)
|++..-|..|..- ++.....+...|.+|+..+. .++.. -...+++..|.++..
T Consensus 14 v~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~-Rs~~~lkkkW~nlk~ 70 (78)
T PF13873_consen 14 VELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGK-RSWKQLKKKWKNLKS 70 (78)
T ss_pred HHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCC-CCHHHHHHHHHHHHH
Confidence 4444555555543 22223334569999999996 44333 344599999988754
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=37.46 E-value=46 Score=30.44 Aligned_cols=39 Identities=15% Similarity=0.203 Sum_probs=26.2
Q ss_pred hHHHHHhcCcchhhccccChHHHHhhhCCCCCCCcHHHHHHHHHHHhhHH
Q 027313 67 LYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYH 116 (225)
Q Consensus 67 LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~Y~kyLlp 116 (225)
|...|.+.|. +.|..||..++...+ +.+.+.-|.+||.|
T Consensus 36 L~~lV~kyG~-------~nW~~IAk~~g~gRT----~KQCReRW~N~L~P 74 (249)
T PLN03212 36 LVSFIKKEGE-------GRWRSLPKRAGLLRC----GKSCRLRWMNYLRP 74 (249)
T ss_pred HHHHHHHhCc-------ccHHHHHHhhhcCCC----cchHHHHHHHhhch
Confidence 4456776663 369999999874322 23778888888754
No 14
>PF04744 Monooxygenase_B: Monooxygenase subunit B protein; InterPro: IPR006833 Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related []. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules []. These enzymes are composed of 3 subunits - A (IPR003393 from INTERPRO), B (IPR006833 from INTERPRO) and C (IPR006980 from INTERPRO) - and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain[]. The soluble regions of these enzymes derive primarily from the B subunit. This subunit forms two antiparallel beta-barrel-like structures and contains the mono- and di- nuclear copper metal centres [].; PDB: 3CHX_E 3RFR_A 3RGB_A 1YEW_A.
Probab=36.42 E-value=31 Score=33.34 Aligned_cols=33 Identities=36% Similarity=0.789 Sum_probs=23.2
Q ss_pred HHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCce
Q 027313 165 LLLFGLFVGLILFITLQQLHFLFTALRAGLAWLLWNIPRKGL 206 (225)
Q Consensus 165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 (225)
|+-||+ |+++|- |++..+ .|+||++|-.-|++.
T Consensus 147 LEtygl--~~v~~W-----h~~W~~--ig~aWl~~W~rrp~f 179 (381)
T PF04744_consen 147 LETYGL--GNVYFW-----HLFWMV--IGVAWLLYWVRRPMF 179 (381)
T ss_dssp TTTTTH--HHHHHH-----HHHHHH--HHHHHHHHHHSST-S
T ss_pred eeeccc--CceEee-----hhHHHH--HHHHHHHHHHhcccc
Confidence 566775 677764 666654 489999999988863
No 15
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=33.05 E-value=28 Score=26.96 Aligned_cols=14 Identities=57% Similarity=0.921 Sum_probs=12.2
Q ss_pred HHHHHhhhhhhhHH
Q 027313 163 LCLLLFGLFVGLIL 176 (225)
Q Consensus 163 ~~~~~~~~~~~~~~ 176 (225)
+.+..+|+|.|.|+
T Consensus 19 e~llRYGLf~GAIF 32 (85)
T PF06783_consen 19 ENLLRYGLFVGAIF 32 (85)
T ss_pred HHHHHHHHHHHHHH
Confidence 56789999999996
No 16
>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=31.75 E-value=51 Score=24.91 Aligned_cols=15 Identities=13% Similarity=0.497 Sum_probs=12.3
Q ss_pred ccChHHHHhhhCCCC
Q 027313 83 EKKWREVGAVFKFSP 97 (225)
Q Consensus 83 ~k~W~eVA~~LGlp~ 97 (225)
++.|+.+|++||+..
T Consensus 15 ~g~Wr~LA~kL~l~~ 29 (76)
T cd08797 15 DKNWETLAQKLGLGI 29 (76)
T ss_pred CCCHHHHHHHHCchh
Confidence 345999999999973
No 17
>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=31.21 E-value=72 Score=22.61 Aligned_cols=43 Identities=16% Similarity=0.235 Sum_probs=24.2
Q ss_pred HHHHHHHHHhhcCCCCCCCeeCCeecchhhhHHHHHhcCcchhhccccChHHHH
Q 027313 37 FWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVG 90 (225)
Q Consensus 37 Fl~~L~~F~~~rG~plk~P~I~GK~VDLy~LY~~V~~~GGy~~Vt~~k~W~eVA 90 (225)
|.+.-.+-+++.|. ++..-.++..|.++|++... .+..|..|+
T Consensus 3 ~~eaa~~vL~~~~~----------pm~~~eI~~~i~~~~~~~~~-~k~p~~~i~ 45 (72)
T PF05066_consen 3 FKEAAYEVLEEAGR----------PMTFKEIWEEIQERGLYKKS-GKTPEATIA 45 (72)
T ss_dssp HHHHHHHHHHHH-S-----------EEHHHHHHHHHHHHTS----GGGGGHHHH
T ss_pred HHHHHHHHHHhcCC----------CcCHHHHHHHHHHhCCCCcc-cCCHHHHHH
Confidence 34444455555554 47788899999999999876 233444444
No 18
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=28.88 E-value=34 Score=25.72 Aligned_cols=20 Identities=25% Similarity=0.423 Sum_probs=13.5
Q ss_pred hhccccChHHHHhhhCCCCC
Q 027313 79 KVVAEKKWREVGAVFKFSPT 98 (225)
Q Consensus 79 ~Vt~~k~W~eVA~~LGlp~~ 98 (225)
+|.+++.|.+||+++|++..
T Consensus 79 k~LQ~ksw~~~a~~l~l~g~ 98 (101)
T PF13725_consen 79 KGLQGKSWEEVAKELGLPGR 98 (101)
T ss_dssp HHCS---HHHHHHHCT-SSH
T ss_pred HHHCCCCHHHHHHHcCCCCC
Confidence 57778999999999999853
No 19
>smart00595 MADF subfamily of SANT domain.
Probab=27.31 E-value=38 Score=24.59 Aligned_cols=41 Identities=20% Similarity=0.216 Sum_probs=27.3
Q ss_pred hccccChHHHHhhhCCCCC-CCcHHHHHHHHHHHhhHHHHHH
Q 027313 80 VVAEKKWREVGAVFKFSPT-TTSASFVLRKHYLTLLYHYEQV 120 (225)
Q Consensus 80 Vt~~k~W~eVA~~LGlp~~-~t~as~~LK~~Y~kyLlpYE~~ 120 (225)
..+...|.+||..||.+.. |..-=..|+..|.+.+......
T Consensus 24 ~~r~~aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~~ 65 (89)
T smart00595 24 EEKRKAWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQNG 65 (89)
T ss_pred HHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4445699999999998532 3223347777777766666554
No 20
>PLN03091 hypothetical protein; Provisional
Probab=25.68 E-value=75 Score=31.47 Aligned_cols=40 Identities=18% Similarity=0.167 Sum_probs=26.9
Q ss_pred hhHHHHHhcCcchhhccccChHHHHhhhCCCCCCCcHHHHHHHHHHHhhHH
Q 027313 66 VLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYH 116 (225)
Q Consensus 66 ~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~Y~kyLlp 116 (225)
+|...|.+.|- +.|..||..++...+ +.+.|.-|.+||.|
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 46677877763 479999998874432 12667777777654
No 21
>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=25.57 E-value=73 Score=24.09 Aligned_cols=14 Identities=14% Similarity=0.475 Sum_probs=12.5
Q ss_pred ccChHHHHhhhCCC
Q 027313 83 EKKWREVGAVFKFS 96 (225)
Q Consensus 83 ~k~W~eVA~~LGlp 96 (225)
.+.|+.+|++||+.
T Consensus 15 g~dW~~LA~kL~l~ 28 (76)
T cd08798 15 DVPWMELAERLGLQ 28 (76)
T ss_pred CCCHHHHHHHHCcc
Confidence 56899999999986
No 22
>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=24.54 E-value=56 Score=29.79 Aligned_cols=69 Identities=23% Similarity=0.170 Sum_probs=50.5
Q ss_pred hhhhhhhhhcceecccchhhhHHHHHHHHHHhhhhhh---hHHHHHHHHHHHH-------------HHHHHHHHHHHHhh
Q 027313 137 EFLLVQQYLRVTCSEFFVFYHQILTRLCLLLFGLFVG---LILFITLQQLHFL-------------FTALRAGLAWLLWN 200 (225)
Q Consensus 137 ~~~~~~~y~~v~~~~~~~f~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~ 200 (225)
|.....||+..+...++-+++.|..-..-.-|++.+| +||..|+||+--= ..+--+.++=|-|-
T Consensus 1 Psv~i~q~~~nei~~~~dnG~~iss~lid~af~lvDggd~~iyiL~~~qil~DlA~qgD~~SQa~AvgqT~~~vgeLa~g 80 (245)
T PF05849_consen 1 PSVTINQYSDNEIPPDIDNGKPISSSLIDRAFDLVDGGDINIYILTLQQILNDLANQGDSASQASAVGQTIGIVGELAWG 80 (245)
T ss_pred CceeeeccccccCCCCCcCccchHHHHHHHHHHhhcCCCccHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHhcC
Confidence 4456778999999999999999977777778888887 7999999997510 11112345667788
Q ss_pred cCCCc
Q 027313 201 IPRKG 205 (225)
Q Consensus 201 ~~~~~ 205 (225)
||..+
T Consensus 81 ~pgda 85 (245)
T PF05849_consen 81 IPGDA 85 (245)
T ss_pred CCcch
Confidence 88654
No 23
>KOG3109 consensus Haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=23.94 E-value=41 Score=30.60 Aligned_cols=99 Identities=20% Similarity=0.217 Sum_probs=56.6
Q ss_pred cchhhccccChHHHHhhhCCCCCCCcHHHHHHHH-HHHhhH------------HHHHHHhhhcC---CCCCCCCCChhhh
Q 027313 76 GYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKH-YLTLLY------------HYEQVHFFKMQ---GPPCVPSGKFEFL 139 (225)
Q Consensus 76 Gy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~-Y~kyLl------------pYE~~~~~ge~---~~~~~p~~~~~~~ 139 (225)
|.+..++++-=.-...+||++... +..|+.. |.+|=. ++++++.+-.. -....|+..+..+
T Consensus 32 ~i~~~~~~nI~~f~~eklgi~~e~---a~~L~~~~yk~YG~t~aGL~~~~~~~d~deY~~~V~~~LPlq~LkPD~~LRnl 108 (244)
T KOG3109|consen 32 GIQLMMRNNIQEFFVEKLGISEEE---AEELRESLYKEYGLTMAGLKAVGYIFDADEYHRFVHGRLPLQDLKPDPVLRNL 108 (244)
T ss_pred hHHHHHHHHHHHHHHHHhCCChhh---hHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHhhccCcHhhcCCCHHHHHH
Confidence 455666677677788999998652 1233322 222322 22333222222 1113434333322
Q ss_pred hhhhhhcceecccchhhhHHHHH--HHHHHhhh---hhhhHHHHHHH
Q 027313 140 LVQQYLRVTCSEFFVFYHQILTR--LCLLLFGL---FVGLILFITLQ 181 (225)
Q Consensus 140 ~~~~y~~v~~~~~~~f~~~~~~~--~~~~~~~~---~~~~~~~~~~~ 181 (225)
+ .++-+.....|+++..-. +||.+.|+ |+|.|+|=|+.
T Consensus 109 L----L~l~~r~k~~FTNa~k~HA~r~Lk~LGieDcFegii~~e~~n 151 (244)
T KOG3109|consen 109 L----LSLKKRRKWIFTNAYKVHAIRILKKLGIEDCFEGIICFETLN 151 (244)
T ss_pred H----HhCccccEEEecCCcHHHHHHHHHHhChHHhccceeEeeccC
Confidence 2 255555578888887444 89999985 99999998886
No 24
>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=23.20 E-value=62 Score=22.76 Aligned_cols=15 Identities=20% Similarity=0.558 Sum_probs=13.1
Q ss_pred cChHHHHhhhCCCCC
Q 027313 84 KKWREVGAVFKFSPT 98 (225)
Q Consensus 84 k~W~eVA~~LGlp~~ 98 (225)
+.|..+|++||++..
T Consensus 11 ~~W~~la~~Lgl~~~ 25 (79)
T cd01670 11 KDWKKLARKLGLSDG 25 (79)
T ss_pred hHHHHHHHHhCCCHH
Confidence 689999999998854
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=22.92 E-value=1e+02 Score=22.53 Aligned_cols=14 Identities=21% Similarity=0.672 Sum_probs=12.5
Q ss_pred ccChHHHHhhhCCC
Q 027313 83 EKKWREVGAVFKFS 96 (225)
Q Consensus 83 ~k~W~eVA~~LGlp 96 (225)
.+.|+.+|++||+.
T Consensus 12 ~~dWr~LA~~L~~~ 25 (72)
T cd08310 12 GCDWRELAQLLDLG 25 (72)
T ss_pred CCCHHHHHHHcCcH
Confidence 56799999999987
No 26
>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=22.89 E-value=1e+02 Score=21.54 Aligned_cols=39 Identities=23% Similarity=0.221 Sum_probs=30.8
Q ss_pred cCcchhhccccChHHHHhhhCCCCCCCcHHHHHHHHHHHhh
Q 027313 74 RGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLL 114 (225)
Q Consensus 74 ~GGy~~Vt~~k~W~eVA~~LGlp~~~t~as~~LK~~Y~kyL 114 (225)
..||=.+-++-.=.+||+.||++++ ..+..||+.-.|.+
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 4677778888889999999999865 36678888777654
No 27
>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=22.74 E-value=1.1e+02 Score=21.54 Aligned_cols=26 Identities=4% Similarity=-0.008 Sum_probs=18.8
Q ss_pred HHHHhhhCCCCCCCcHHHHHHHHHHHhhH
Q 027313 87 REVGAVFKFSPTTTSASFVLRKHYLTLLY 115 (225)
Q Consensus 87 ~eVA~~LGlp~~~t~as~~LK~~Y~kyLl 115 (225)
..|++.++.+.- ...++++++++|-.
T Consensus 30 k~I~~~~~~~~l---T~~qV~SH~QKy~~ 55 (57)
T TIGR01557 30 KRILELMVVDGL---TRDQVASHLQKYRL 55 (57)
T ss_pred HHHHHHcCCCCC---CHHHHHHHHHHHHc
Confidence 889998887541 23488999988854
No 28
>cd08802 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, 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 activatio
Probab=22.58 E-value=96 Score=23.76 Aligned_cols=14 Identities=14% Similarity=0.506 Sum_probs=12.2
Q ss_pred ccChHHHHhhhCCC
Q 027313 83 EKKWREVGAVFKFS 96 (225)
Q Consensus 83 ~k~W~eVA~~LGlp 96 (225)
.+.|+.+|++||+.
T Consensus 20 g~DW~~LAekL~ld 33 (84)
T cd08802 20 GNDWRLLAQKLSMD 33 (84)
T ss_pred CCcHHHHHHHcCch
Confidence 34699999999998
No 29
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=20.72 E-value=66 Score=26.39 Aligned_cols=63 Identities=8% Similarity=-0.022 Sum_probs=44.5
Q ss_pred HHHHHHHHHHhhcCCCCCCCeeCCeecchhhhHHHHHhcCcchhhccccChHHHHhhhCCCCC---CCcHHHHHHH
Q 027313 36 VFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPT---TTSASFVLRK 108 (225)
Q Consensus 36 ~Fl~~L~~F~~~rG~plk~P~I~GK~VDLy~LY~~V~~~GGy~~Vt~~k~W~eVA~~LGlp~~---~t~as~~LK~ 108 (225)
++++.-..+++.+|.| +..+.|+..|++..|+..-...++=+++...|.+... +++....||.
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 4556666677766544 7889999999999998765555667777778877654 4555566666
No 30
>cd08799 Death_UNC5C Death domain found in Uncoordinated-5C. Death Domain (DD) found in Uncoordinated-5C (UNC5C). UNC5C is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5C plays a critical role in the development of spinal accesory motor neurons. Methylation of the UNC5C gene is associated with early stages of colorectal carcinogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, 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.
Probab=20.03 E-value=1.2e+02 Score=23.18 Aligned_cols=14 Identities=14% Similarity=0.537 Sum_probs=12.2
Q ss_pred ccChHHHHhhhCCC
Q 027313 83 EKKWREVGAVFKFS 96 (225)
Q Consensus 83 ~k~W~eVA~~LGlp 96 (225)
.+.|..+|++||+.
T Consensus 20 g~DWr~LAekLgl~ 33 (84)
T cd08799 20 GNDWRMLAHKLNLD 33 (84)
T ss_pred CCCHHHHHHHcCCH
Confidence 35699999999987
Done!