Query 029398
Match_columns 194
No_of_seqs 158 out of 1089
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 12:17:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029398.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029398hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 99.4 1.1E-13 2.3E-18 118.9 5.0 45 3-51 71-115 (238)
2 PLN03212 Transcription repress 99.2 5.1E-11 1.1E-15 104.3 6.6 46 3-52 87-132 (249)
3 PLN03091 hypothetical protein; 99.0 3E-10 6.4E-15 106.2 6.6 45 3-51 76-120 (459)
4 PF00249 Myb_DNA-binding: Myb- 98.6 3.2E-08 6.9E-13 65.3 3.6 37 3-39 10-48 (48)
5 PF13921 Myb_DNA-bind_6: Myb-l 98.6 4.1E-08 8.9E-13 66.9 2.6 40 3-42 7-46 (60)
6 smart00717 SANT SANT SWI3, AD 98.5 1.2E-07 2.6E-12 59.8 3.8 38 3-40 10-48 (49)
7 cd00167 SANT 'SWI3, ADA2, N-Co 98.4 4.4E-07 9.6E-12 56.5 4.1 36 3-38 8-44 (45)
8 PLN03212 Transcription repress 97.9 7.2E-06 1.6E-10 72.2 3.3 42 3-44 34-77 (249)
9 KOG0048 Transcription factor, 97.7 1.3E-05 2.8E-10 69.1 1.7 42 3-44 18-61 (238)
10 PLN03091 hypothetical protein; 97.5 4.3E-05 9.2E-10 72.1 2.4 42 3-44 23-66 (459)
11 KOG0049 Transcription factor, 95.2 0.021 4.6E-07 56.8 4.0 42 3-44 369-411 (939)
12 COG5147 REB1 Myb superfamily p 94.9 0.023 5.1E-07 54.8 3.6 40 3-42 81-120 (512)
13 KOG0050 mRNA splicing protein 94.8 0.025 5.4E-07 54.8 3.2 42 3-44 16-58 (617)
14 COG5147 REB1 Myb superfamily p 94.0 0.028 6.1E-07 54.3 1.7 40 3-42 29-69 (512)
15 KOG0051 RNA polymerase I termi 91.3 0.18 3.9E-06 49.7 3.3 39 3-42 393-431 (607)
16 PF13837 Myb_DNA-bind_4: Myb/S 89.1 0.31 6.8E-06 34.8 2.3 27 15-42 36-66 (90)
17 KOG0049 Transcription factor, 87.7 1.1 2.3E-05 45.2 5.5 40 3-42 421-461 (939)
18 KOG0457 Histone acetyltransfer 80.6 1.8 3.9E-05 41.3 3.6 35 4-38 82-117 (438)
19 KOG4282 Transcription factor G 77.9 3.2 6.8E-05 37.4 4.2 29 13-42 83-115 (345)
20 PF08281 Sigma70_r4_2: Sigma-7 77.5 5.5 0.00012 25.9 4.2 35 3-38 16-50 (54)
21 PF13873 Myb_DNA-bind_5: Myb/S 77.3 2.9 6.3E-05 29.4 3.0 26 16-42 41-71 (78)
22 smart00595 MADF subfamily of S 76.2 4.1 8.8E-05 29.1 3.6 26 15-42 29-54 (89)
23 PF10545 MADF_DNA_bdg: Alcohol 71.6 5.8 0.00013 27.4 3.4 33 15-48 28-61 (85)
24 PF12776 Myb_DNA-bind_3: Myb/S 71.2 6.4 0.00014 28.3 3.7 26 16-42 34-64 (96)
25 TIGR01557 myb_SHAQKYF myb-like 66.8 9.8 0.00021 26.3 3.7 36 3-38 12-53 (57)
26 KOG0050 mRNA splicing protein 63.4 6.3 0.00014 38.8 2.9 39 3-42 68-106 (617)
27 PF13137 DUF3983: Protein of u 60.8 4.8 0.0001 25.7 1.0 10 177-186 24-33 (34)
28 COG5114 Histone acetyltransfer 60.8 8.3 0.00018 36.1 3.0 35 4-38 73-108 (432)
29 TIGR02894 DNA_bind_RsfA transc 58.7 7.1 0.00015 32.8 2.0 29 16-45 33-61 (161)
30 PF08914 Myb_DNA-bind_2: Rap1 58.0 17 0.00037 25.8 3.6 40 3-42 11-60 (65)
31 KOG1279 Chromatin remodeling f 52.0 16 0.00036 35.6 3.6 37 3-39 262-298 (506)
32 PRK09647 RNA polymerase sigma 51.0 39 0.00085 28.0 5.3 45 4-50 145-189 (203)
33 PRK12535 RNA polymerase sigma 50.9 37 0.00079 27.9 5.1 50 4-55 140-189 (196)
34 COG5259 RSC8 RSC chromatin rem 49.8 15 0.00033 35.8 3.0 35 3-37 288-322 (531)
35 PF01388 ARID: ARID/BRIGHT DNA 48.2 35 0.00075 24.6 4.1 37 4-40 40-89 (92)
36 smart00501 BRIGHT BRIGHT, ARID 47.4 42 0.00092 24.5 4.5 38 4-41 36-86 (93)
37 PF11035 SnAPC_2_like: Small n 44.6 74 0.0016 29.7 6.4 42 3-45 31-75 (344)
38 PRK13923 putative spore coat p 41.0 34 0.00073 28.9 3.4 42 3-45 18-62 (170)
39 PF06599 DUF1139: Protein of u 40.7 15 0.00032 33.5 1.3 14 172-185 277-290 (309)
40 PF04545 Sigma70_r4: Sigma-70, 38.2 67 0.0015 20.5 3.9 36 4-40 11-46 (50)
41 PRK09637 RNA polymerase sigma 37.8 83 0.0018 25.3 5.2 45 4-50 113-157 (181)
42 PRK12516 RNA polymerase sigma 36.8 92 0.002 25.2 5.3 46 3-50 122-167 (187)
43 smart00005 DEATH DEATH domain, 35.6 38 0.00082 23.9 2.6 29 4-33 7-36 (88)
44 PRK04217 hypothetical protein; 35.2 1E+02 0.0023 24.0 5.1 42 4-47 49-90 (110)
45 cd08319 Death_RAIDD Death doma 34.4 44 0.00096 24.7 2.8 31 3-34 3-33 (83)
46 TIGR02960 SigX5 RNA polymerase 34.1 59 0.0013 28.3 4.0 38 3-42 148-185 (324)
47 cd08779 Death_PIDD Death Domai 33.8 29 0.00064 25.5 1.8 41 4-45 4-47 (86)
48 PRK11922 RNA polymerase sigma 33.0 61 0.0013 27.2 3.8 43 5-49 157-199 (231)
49 cd08317 Death_ank Death domain 32.2 44 0.00096 24.1 2.5 30 4-34 6-35 (84)
50 PRK12542 RNA polymerase sigma 30.9 1.1E+02 0.0023 24.4 4.7 45 4-50 129-173 (185)
51 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 30.3 53 0.0012 22.4 2.4 32 4-36 11-42 (50)
52 TIGR02959 SigZ RNA polymerase 28.8 2E+02 0.0043 22.7 6.0 46 3-50 106-151 (170)
53 PRK12511 RNA polymerase sigma 28.7 1.5E+02 0.0033 23.9 5.4 46 4-51 118-163 (182)
54 PRK11179 DNA-binding transcrip 28.6 93 0.002 24.6 4.0 38 4-42 14-51 (153)
55 PRK15328 invasion protein IagB 28.1 1.6E+02 0.0035 24.3 5.4 40 3-42 97-138 (160)
56 cd08318 Death_NMPP84 Death dom 27.4 65 0.0014 23.6 2.7 28 5-33 10-37 (86)
57 PRK12540 RNA polymerase sigma 26.0 1.7E+02 0.0037 23.6 5.2 46 4-51 118-163 (182)
58 PRK11169 leucine-responsive tr 25.7 83 0.0018 25.3 3.3 39 3-42 18-56 (164)
59 PF13404 HTH_AsnC-type: AsnC-t 23.6 1.3E+02 0.0029 19.2 3.3 33 4-37 8-40 (42)
60 PRK12546 RNA polymerase sigma 23.2 2E+02 0.0043 23.4 5.1 43 4-48 120-162 (188)
61 COG5118 BDP1 Transcription ini 23.1 1E+02 0.0022 29.8 3.7 40 3-42 374-413 (507)
62 cd08777 Death_RIP1 Death Domai 21.5 71 0.0015 23.6 2.0 29 6-35 6-34 (86)
63 cd01670 Death Death Domain: a 21.0 67 0.0015 22.0 1.6 28 5-33 2-29 (79)
64 PRK12533 RNA polymerase sigma 20.5 1.8E+02 0.004 24.4 4.5 47 3-51 140-186 (216)
65 cd08805 Death_ank1 Death domai 20.5 81 0.0018 23.4 2.1 31 5-35 7-39 (84)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.43 E-value=1.1e-13 Score=118.92 Aligned_cols=45 Identities=56% Similarity=0.870 Sum_probs=41.7
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhcC
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQNQ 51 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~~ 51 (194)
++|+++|+.+||||+.||++|||||||+|||+|+++|+|| +....
T Consensus 71 ~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~lkkk----l~~~~ 115 (238)
T KOG0048|consen 71 DLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHLKKK----LLKMG 115 (238)
T ss_pred HHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHHHHH----HHHcC
Confidence 6899999999999999999999999999999999999999 65544
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.16 E-value=5.1e-11 Score=104.26 Aligned_cols=46 Identities=52% Similarity=0.855 Sum_probs=41.6
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhcCc
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQNQK 52 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~~~ 52 (194)
++|+++|.+||++|+.||++|||||+++|||||+.+++++ ++....
T Consensus 87 ~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~----l~r~~i 132 (249)
T PLN03212 87 DLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKK----LLRQGI 132 (249)
T ss_pred HHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHH----HHhcCC
Confidence 5899999999999999999999999999999999999998 554443
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.05 E-value=3e-10 Score=106.19 Aligned_cols=45 Identities=51% Similarity=0.848 Sum_probs=41.4
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhcC
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQNQ 51 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~~ 51 (194)
++|+++|++||+||+.||++|||||+++|||||+.+|||+ +++.+
T Consensus 76 ~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKk----lr~~~ 120 (459)
T PLN03091 76 NLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKK----LRQRG 120 (459)
T ss_pred HHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHH----HHHcC
Confidence 5899999999999999999999999999999999999999 55544
No 4
>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=98.63 E-value=3.2e-08 Score=65.34 Aligned_cols=37 Identities=27% Similarity=0.404 Sum_probs=34.6
Q ss_pred HHHHHHHHccCCC-HHHHhccCC-CCChHHHHHHHHHhh
Q 029398 3 QVLYLINFAPFSR-WSAIAGRLP-GRTDNEIKNVWHTHL 39 (194)
Q Consensus 3 ~lLi~l~~e~Gnk-Ws~IA~~Lp-GRTdn~IKNrW~~~L 39 (194)
++|++++.+||.. |..||..+| |||..+|++||+.++
T Consensus 10 ~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 10 EKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred HHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5899999999988 999999999 999999999999864
No 5
>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=98.56 E-value=4.1e-08 Score=66.93 Aligned_cols=40 Identities=30% Similarity=0.499 Sum_probs=34.2
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
++|+++|.++|+.|..||+.|+.||..+|++||+..|+..
T Consensus 7 ~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~ 46 (60)
T PF13921_consen 7 ELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPK 46 (60)
T ss_dssp HHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTT
T ss_pred HHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCccc
Confidence 6899999999999999999995599999999999976544
No 6
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.51 E-value=1.2e-07 Score=59.84 Aligned_cols=38 Identities=32% Similarity=0.552 Sum_probs=35.4
Q ss_pred HHHHHHHHccC-CCHHHHhccCCCCChHHHHHHHHHhhH
Q 029398 3 QVLYLINFAPF-SRWSAIAGRLPGRTDNEIKNVWHTHLK 40 (194)
Q Consensus 3 ~lLi~l~~e~G-nkWs~IA~~LpGRTdn~IKNrW~~~Lr 40 (194)
++|+.++.++| ..|..||..|++||..+|++||+..++
T Consensus 10 ~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 10 ELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred HHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 58999999999 999999999999999999999998654
No 7
>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=98.39 E-value=4.4e-07 Score=56.54 Aligned_cols=36 Identities=28% Similarity=0.480 Sum_probs=33.8
Q ss_pred HHHHHHHHccC-CCHHHHhccCCCCChHHHHHHHHHh
Q 029398 3 QVLYLINFAPF-SRWSAIAGRLPGRTDNEIKNVWHTH 38 (194)
Q Consensus 3 ~lLi~l~~e~G-nkWs~IA~~LpGRTdn~IKNrW~~~ 38 (194)
++|++++.++| .+|..||+.+++|+..+|+++|...
T Consensus 8 ~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 8 ELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred HHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 57999999999 9999999999999999999999874
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.92 E-value=7.2e-06 Score=72.16 Aligned_cols=42 Identities=17% Similarity=0.259 Sum_probs=37.7
Q ss_pred HHHHHHHHccC-CCHHHHhccC-CCCChHHHHHHHHHhhHhhHH
Q 029398 3 QVLYLINFAPF-SRWSAIAGRL-PGRTDNEIKNVWHTHLKKKAA 44 (194)
Q Consensus 3 ~lLi~l~~e~G-nkWs~IA~~L-pGRTdn~IKNrW~~~Lrkr~~ 44 (194)
++|++++++|| ++|..||+++ +|||+++|+.||..+|+..+.
T Consensus 34 e~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~ 77 (249)
T PLN03212 34 EILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVK 77 (249)
T ss_pred HHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcc
Confidence 58999999999 6899999998 699999999999999876644
No 9
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.73 E-value=1.3e-05 Score=69.08 Aligned_cols=42 Identities=10% Similarity=-0.047 Sum_probs=38.6
Q ss_pred HHHHHHHHccCCC-HHHHhccCC-CCChHHHHHHHHHhhHhhHH
Q 029398 3 QVLYLINFAPFSR-WSAIAGRLP-GRTDNEIKNVWHTHLKKKAA 44 (194)
Q Consensus 3 ~lLi~l~~e~Gnk-Ws~IA~~Lp-GRTdn~IKNrW~~~Lrkr~~ 44 (194)
++|++++++||.+ |..||+.++ ||++++|+-||..+|+..++
T Consensus 18 ~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik 61 (238)
T KOG0048|consen 18 LTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLK 61 (238)
T ss_pred HHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence 5899999999955 999999999 99999999999999998844
No 10
>PLN03091 hypothetical protein; Provisional
Probab=97.55 E-value=4.3e-05 Score=72.10 Aligned_cols=42 Identities=14% Similarity=0.146 Sum_probs=37.0
Q ss_pred HHHHHHHHccC-CCHHHHhccC-CCCChHHHHHHHHHhhHhhHH
Q 029398 3 QVLYLINFAPF-SRWSAIAGRL-PGRTDNEIKNVWHTHLKKKAA 44 (194)
Q Consensus 3 ~lLi~l~~e~G-nkWs~IA~~L-pGRTdn~IKNrW~~~Lrkr~~ 44 (194)
++|++++.+|| .+|..||+.+ +||++++||.||+.+|+..++
T Consensus 23 e~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~Ik 66 (459)
T PLN03091 23 EKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLK 66 (459)
T ss_pred HHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCccc
Confidence 58999999999 5799999988 599999999999988876643
No 11
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.15 E-value=0.021 Score=56.84 Aligned_cols=42 Identities=17% Similarity=0.337 Sum_probs=37.7
Q ss_pred HHHHHHHHccCCC-HHHHhccCCCCChHHHHHHHHHhhHhhHH
Q 029398 3 QVLYLINFAPFSR-WSAIAGRLPGRTDNEIKNVWHTHLKKKAA 44 (194)
Q Consensus 3 ~lLi~l~~e~Gnk-Ws~IA~~LpGRTdn~IKNrW~~~Lrkr~~ 44 (194)
.+|+.++.+||.| |++|...+|||++.+|+.||+..|.++++
T Consensus 369 ~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K 411 (939)
T KOG0049|consen 369 VLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAK 411 (939)
T ss_pred HHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhc
Confidence 3789999999955 99999999999999999999998887754
No 12
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=94.93 E-value=0.023 Score=54.80 Aligned_cols=40 Identities=20% Similarity=0.218 Sum_probs=37.4
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
+.|++++.++|++|+.||..+|||++.+|.++|...+...
T Consensus 81 ~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~~~~~ 120 (512)
T COG5147 81 EQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNTLEDL 120 (512)
T ss_pred HHHHHHHHhcCchhhhhccccCccchHHHHHHHHHHhhhh
Confidence 5789999999999999999999999999999999877766
No 13
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=94.76 E-value=0.025 Score=54.84 Aligned_cols=42 Identities=26% Similarity=0.345 Sum_probs=37.9
Q ss_pred HHHHHHHHccC-CCHHHHhccCCCCChHHHHHHHHHhhHhhHH
Q 029398 3 QVLYLINFAPF-SRWSAIAGRLPGRTDNEIKNVWHTHLKKKAA 44 (194)
Q Consensus 3 ~lLi~l~~e~G-nkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~ 44 (194)
++|--.+..|| +.|+.|++.|+..+..+|++||..++...++
T Consensus 16 eilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~ 58 (617)
T KOG0050|consen 16 EVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIK 58 (617)
T ss_pred HHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHh
Confidence 56777899999 8899999999999999999999998888754
No 14
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=93.97 E-value=0.028 Score=54.28 Aligned_cols=40 Identities=25% Similarity=0.370 Sum_probs=35.3
Q ss_pred HHHHHHHHccC-CCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPF-SRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~G-nkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
+.|..++++|| +.|++||..|.-|++++|++||+.++...
T Consensus 29 e~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~ 69 (512)
T COG5147 29 EDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQ 69 (512)
T ss_pred hHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchh
Confidence 35677889999 77999999998899999999998877666
No 15
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=91.34 E-value=0.18 Score=49.70 Aligned_cols=39 Identities=21% Similarity=0.358 Sum_probs=35.1
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
+.|..+|.++|+.|..|++.| ||....|+-||..+.+..
T Consensus 393 eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 393 EELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred HHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 578999999999999999999 999999999999766544
No 16
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=89.09 E-value=0.31 Score=34.79 Aligned_cols=27 Identities=44% Similarity=0.757 Sum_probs=19.8
Q ss_pred CHHHHhccC----CCCChHHHHHHHHHhhHhh
Q 029398 15 RWSAIAGRL----PGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 15 kWs~IA~~L----pGRTdn~IKNrW~~~Lrkr 42 (194)
.|..||..| ..||..+|+++|+. |+++
T Consensus 36 ~w~~Ia~~l~~~G~~rt~~qc~~Kw~~-L~~~ 66 (90)
T PF13837_consen 36 VWKEIAEELAEHGYNRTPEQCRNKWKN-LKKK 66 (90)
T ss_dssp HHHHHHHHHHHHC----HHHHHHHHHH-HHHH
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHH-HHHH
Confidence 499999988 47999999999999 4555
No 17
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=87.66 E-value=1.1 Score=45.24 Aligned_cols=40 Identities=18% Similarity=0.189 Sum_probs=31.2
Q ss_pred HHHHHHHHccC-CCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPF-SRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~G-nkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
+.|+.++.+|| ..|..||..||.||+.+...|-...++.+
T Consensus 421 eqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k 461 (939)
T KOG0049|consen 421 EQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAK 461 (939)
T ss_pred HHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHHH
Confidence 57899999999 88999999999999976555444334333
No 18
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=80.57 E-value=1.8 Score=41.31 Aligned_cols=35 Identities=23% Similarity=0.304 Sum_probs=31.8
Q ss_pred HHHHHHHccC-CCHHHHhccCCCCChHHHHHHHHHh
Q 029398 4 VLYLINFAPF-SRWSAIAGRLPGRTDNEIKNVWHTH 38 (194)
Q Consensus 4 lLi~l~~e~G-nkWs~IA~~LpGRTdn~IKNrW~~~ 38 (194)
+|++....|| ..|..||.++..|+..+||.+|..+
T Consensus 82 lLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~ 117 (438)
T KOG0457|consen 82 LLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKH 117 (438)
T ss_pred HHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHH
Confidence 6889999999 8999999999889999999998753
No 19
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=77.95 E-value=3.2 Score=37.35 Aligned_cols=29 Identities=24% Similarity=0.319 Sum_probs=23.8
Q ss_pred CCCHHHHhccC----CCCChHHHHHHHHHhhHhh
Q 029398 13 FSRWSAIAGRL----PGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 13 GnkWs~IA~~L----pGRTdn~IKNrW~~~Lrkr 42 (194)
|+.|..||+.+ --||+.+||++|+.. +++
T Consensus 83 ~~~We~va~k~~~~g~~rs~~qck~K~~nl-~k~ 115 (345)
T KOG4282|consen 83 GPLWEEVARKMAELGYPRSPKQCKAKIENL-KKK 115 (345)
T ss_pred ccHHHHHHHHHHHhCCCCCHHHHHHHHHHH-HHH
Confidence 56699999965 478999999999994 555
No 20
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=77.46 E-value=5.5 Score=25.90 Aligned_cols=35 Identities=17% Similarity=0.339 Sum_probs=26.3
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTH 38 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~ 38 (194)
+.++.++-..|-.|..||..+ |.+.+.|+.+-+..
T Consensus 16 r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 16 REIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRA 50 (54)
T ss_dssp HHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 467788889999999999999 99999999976653
No 21
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=77.28 E-value=2.9 Score=29.42 Aligned_cols=26 Identities=38% Similarity=0.720 Sum_probs=22.0
Q ss_pred HHHHhccC-----CCCChHHHHHHHHHhhHhh
Q 029398 16 WSAIAGRL-----PGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 16 Ws~IA~~L-----pGRTdn~IKNrW~~~Lrkr 42 (194)
|..|+..| +.|+..++|..|.. ++..
T Consensus 41 W~~I~~~lN~~~~~~Rs~~~lkkkW~n-lk~~ 71 (78)
T PF13873_consen 41 WEEIAEELNALGPGKRSWKQLKKKWKN-LKSK 71 (78)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHH-HHHH
Confidence 99999988 47999999999998 4444
No 22
>smart00595 MADF subfamily of SANT domain.
Probab=76.21 E-value=4.1 Score=29.10 Aligned_cols=26 Identities=35% Similarity=0.736 Sum_probs=22.0
Q ss_pred CHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 15 RWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 15 kWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
-|..||..| |.+...|+.+|+. ||.+
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~-LR~~ 54 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKN-LRDR 54 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHH-HHHH
Confidence 399999999 5599999999999 4554
No 23
>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=71.62 E-value=5.8 Score=27.37 Aligned_cols=33 Identities=27% Similarity=0.498 Sum_probs=24.1
Q ss_pred CHHHHhccCCC-CChHHHHHHHHHhhHhhHHHHHH
Q 029398 15 RWSAIAGRLPG-RTDNEIKNVWHTHLKKKAAAVLK 48 (194)
Q Consensus 15 kWs~IA~~LpG-RTdn~IKNrW~~~Lrkr~~~~lk 48 (194)
-|..||..|.+ -+...|+.+|+. ||.+-++.++
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~-Lr~~y~~~~~ 61 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKN-LRDRYRRELK 61 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHH-HHHHHHHHHH
Confidence 39999999953 577889999999 5555344333
No 24
>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=71.21 E-value=6.4 Score=28.30 Aligned_cols=26 Identities=42% Similarity=0.802 Sum_probs=19.8
Q ss_pred HHHHhccCC---C--CChHHHHHHHHHhhHhh
Q 029398 16 WSAIAGRLP---G--RTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 16 Ws~IA~~Lp---G--RTdn~IKNrW~~~Lrkr 42 (194)
|..|+..|. | .+..+|||||+.+ |+.
T Consensus 34 w~~i~~~~~~~~~~~~t~~qlknk~~~l-k~~ 64 (96)
T PF12776_consen 34 WNNIAEEFNEKTGLNYTKKQLKNKWKTL-KKD 64 (96)
T ss_pred HHHHHHHHHHHhCCcccHHHHHHHHHHH-HHH
Confidence 999999883 3 3678899999984 444
No 25
>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=66.85 E-value=9.8 Score=26.32 Aligned_cols=36 Identities=11% Similarity=0.103 Sum_probs=29.0
Q ss_pred HHHHHHHHccCC-CH---HHHhccCC--CCChHHHHHHHHHh
Q 029398 3 QVLYLINFAPFS-RW---SAIAGRLP--GRTDNEIKNVWHTH 38 (194)
Q Consensus 3 ~lLi~l~~e~Gn-kW---s~IA~~Lp--GRTdn~IKNrW~~~ 38 (194)
++.++.+..+|- .| ..|+..+. +.|..+|+.|...+
T Consensus 12 ~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy 53 (57)
T TIGR01557 12 DRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKY 53 (57)
T ss_pred HHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 467889999995 99 99999874 33999999987654
No 26
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=63.35 E-value=6.3 Score=38.80 Aligned_cols=39 Identities=21% Similarity=0.318 Sum_probs=35.7
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
+.|+.+...+-+.|..||..+ ||+.++|-.|++.++-..
T Consensus 68 erlLhlakl~p~qwrtIa~i~-gr~~~qc~eRy~~ll~~~ 106 (617)
T KOG0050|consen 68 ERLLHLAKLEPTQWRTIADIM-GRTSQQCLERYNNLLDVY 106 (617)
T ss_pred HHHHHHHHhcCCccchHHHHh-hhhHHHHHHHHHHHHHHH
Confidence 468899999999999999998 999999999999988776
No 27
>PF13137 DUF3983: Protein of unknown function (DUF3983)
Probab=60.82 E-value=4.8 Score=25.65 Aligned_cols=10 Identities=50% Similarity=1.032 Sum_probs=8.5
Q ss_pred hHHHHHHhcC
Q 029398 177 FWYNILVTSG 186 (194)
Q Consensus 177 fwy~~f~~~~ 186 (194)
=|.|||+++|
T Consensus 24 AWRNiFvqag 33 (34)
T PF13137_consen 24 AWRNIFVQAG 33 (34)
T ss_pred HHHHHHHHcc
Confidence 4999999986
No 28
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=60.78 E-value=8.3 Score=36.10 Aligned_cols=35 Identities=23% Similarity=0.243 Sum_probs=31.4
Q ss_pred HHHHHHHccC-CCHHHHhccCCCCChHHHHHHHHHh
Q 029398 4 VLYLINFAPF-SRWSAIAGRLPGRTDNEIKNVWHTH 38 (194)
Q Consensus 4 lLi~l~~e~G-nkWs~IA~~LpGRTdn~IKNrW~~~ 38 (194)
+|++.-..+| ..|..||.++..|+...||.++...
T Consensus 73 lli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~ 108 (432)
T COG5114 73 LLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKM 108 (432)
T ss_pred HHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHH
Confidence 6788899999 8999999999999999999988653
No 29
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=58.65 E-value=7.1 Score=32.77 Aligned_cols=29 Identities=17% Similarity=0.350 Sum_probs=25.1
Q ss_pred HHHHhccCCCCChHHHHHHHHHhhHhhHHH
Q 029398 16 WSAIAGRLPGRTDNEIKNVWHTHLKKKAAA 45 (194)
Q Consensus 16 Ws~IA~~LpGRTdn~IKNrW~~~Lrkr~~~ 45 (194)
...+++.| +||.-+|.=|||..+||+-..
T Consensus 33 FeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 33 FEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred HHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 56788888 999999999999999988443
No 30
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=58.04 E-value=17 Score=25.83 Aligned_cols=40 Identities=15% Similarity=0.263 Sum_probs=26.3
Q ss_pred HHHHHHHHcc--------CCC-HHHHhccCC-CCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAP--------FSR-WSAIAGRLP-GRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~--------Gnk-Ws~IA~~Lp-GRTdn~IKNrW~~~Lrkr 42 (194)
++|++.+.++ ||+ |..++..-| ++|=...|+||...|+.+
T Consensus 11 ~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 11 AALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp HHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred HHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 4566666433 344 999999888 999999999999888877
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=51.99 E-value=16 Score=35.56 Aligned_cols=37 Identities=8% Similarity=0.022 Sum_probs=32.4
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHL 39 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~L 39 (194)
-||++.+.+||-.|.+||.++..||-.+|--++-.+-
T Consensus 262 lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 262 LLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred HHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 3799999999999999999999999999887776543
No 32
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=51.00 E-value=39 Score=27.98 Aligned_cols=45 Identities=16% Similarity=0.140 Sum_probs=34.7
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhc
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQN 50 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~ 50 (194)
.++.++...|-+-..||..| |-+.+.|+++++. .++++++.++..
T Consensus 145 ~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l~R-Ark~Lr~~l~~~ 189 (203)
T PRK09647 145 AAVVLCDIEGLSYEEIAATL-GVKLGTVRSRIHR-GRQQLRAALAAH 189 (203)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHH-HHHHHHHHHHHh
Confidence 45556667889999999999 9999999999887 466655555543
No 33
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=50.88 E-value=37 Score=27.88 Aligned_cols=50 Identities=8% Similarity=-0.043 Sum_probs=38.2
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhcCcccc
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQNQKANT 55 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~~~~~~ 55 (194)
.++.+.--.|-.-..||..| |.+.+.||++++. .++++|+.+.+.+....
T Consensus 140 ~v~~l~~~~g~s~~EIAe~l-gis~~tV~~~l~R-ar~~Lr~~l~~~~~~~~ 189 (196)
T PRK12535 140 EALILTQVLGYTYEEAAKIA-DVRVGTIRSRVAR-ARADLIAATATGQASAE 189 (196)
T ss_pred HHhhhHHHhCCCHHHHHHHh-CCCHHHHHHHHHH-HHHHHHHHhccccchhh
Confidence 45566667788899999999 9999999999876 46776666766665443
No 34
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=49.81 E-value=15 Score=35.77 Aligned_cols=35 Identities=11% Similarity=0.019 Sum_probs=31.8
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHH
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHT 37 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~ 37 (194)
.||++..++||--|.+||+++..||-.+|=-|+-.
T Consensus 288 ~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 288 LLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred HHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHc
Confidence 58999999999999999999999999999887765
No 35
>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=48.20 E-value=35 Score=24.59 Aligned_cols=37 Identities=19% Similarity=0.310 Sum_probs=25.8
Q ss_pred HHHHHHHccC--------CCHHHHhccCCC---CC--hHHHHHHHHHhhH
Q 029398 4 VLYLINFAPF--------SRWSAIAGRLPG---RT--DNEIKNVWHTHLK 40 (194)
Q Consensus 4 lLi~l~~e~G--------nkWs~IA~~LpG---RT--dn~IKNrW~~~Lr 40 (194)
.|..+|.+.| .+|..||+.|.- .+ ..++|..+..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 4666777776 569999999922 12 3568888887664
No 36
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=47.38 E-value=42 Score=24.46 Aligned_cols=38 Identities=18% Similarity=0.252 Sum_probs=26.8
Q ss_pred HHHHHHHccC--------CCHHHHhccCCCC-----ChHHHHHHHHHhhHh
Q 029398 4 VLYLINFAPF--------SRWSAIAGRLPGR-----TDNEIKNVWHTHLKK 41 (194)
Q Consensus 4 lLi~l~~e~G--------nkWs~IA~~LpGR-----Tdn~IKNrW~~~Lrk 41 (194)
.|..++.++| ++|..||..|.-. ....+|..+..+|..
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 4666677766 5799999998322 346688888877654
No 37
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=44.65 E-value=74 Score=29.70 Aligned_cols=42 Identities=31% Similarity=0.454 Sum_probs=32.3
Q ss_pred HHHHHHHHccCCC---HHHHhccCCCCChHHHHHHHHHhhHhhHHH
Q 029398 3 QVLYLINFAPFSR---WSAIAGRLPGRTDNEIKNVWHTHLKKKAAA 45 (194)
Q Consensus 3 ~lLi~l~~e~Gnk---Ws~IA~~LpGRTdn~IKNrW~~~Lrkr~~~ 45 (194)
+||.-|+..-|.. -..|++.|+||+..+|++.-.. ||.|+.+
T Consensus 31 ~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~-LK~rvar 75 (344)
T PF11035_consen 31 QLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQ-LKGRVAR 75 (344)
T ss_pred HHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHH-HHHHHHH
Confidence 5667777777855 4789999999999999986655 6666555
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=40.99 E-value=34 Score=28.95 Aligned_cols=42 Identities=14% Similarity=0.154 Sum_probs=30.6
Q ss_pred HHHHHHHHccCCCH---HHHhccCCCCChHHHHHHHHHhhHhhHHH
Q 029398 3 QVLYLINFAPFSRW---SAIAGRLPGRTDNEIKNVWHTHLKKKAAA 45 (194)
Q Consensus 3 ~lLi~l~~e~GnkW---s~IA~~LpGRTdn~IKNrW~~~Lrkr~~~ 45 (194)
+.+++...+-|.+- ..++..| +||.-+|.-||+..+|++-..
T Consensus 18 e~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 18 EVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred HHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 44555666666554 4556777 999999999999999977443
No 39
>PF06599 DUF1139: Protein of unknown function (DUF1139); InterPro: IPR009519 This family consists of several hypothetical Fijivirus proteins of unknown function.
Probab=40.69 E-value=15 Score=33.48 Aligned_cols=14 Identities=21% Similarity=0.942 Sum_probs=12.0
Q ss_pred CCCchhHHHHHHhc
Q 029398 172 GGGMDFWYNILVTS 185 (194)
Q Consensus 172 ~~~mdfwy~~f~~~ 185 (194)
+.+-||||+||.|+
T Consensus 277 ~~dvD~WY~lfmrt 290 (309)
T PF06599_consen 277 HTDVDYWYSLFMRT 290 (309)
T ss_pred CCCHHHHHHHHHHH
Confidence 44889999999986
No 40
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=38.18 E-value=67 Score=20.48 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=26.8
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhH
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLK 40 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lr 40 (194)
.++.++-.-|-.+..||..| |-+...|+.+-+..++
T Consensus 11 ~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 11 EVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALK 46 (50)
T ss_dssp HHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHH
Confidence 45555556778899999999 9999999987666443
No 41
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=37.79 E-value=83 Score=25.31 Aligned_cols=45 Identities=16% Similarity=-0.007 Sum_probs=34.2
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhc
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQN 50 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~ 50 (194)
.++.+.-..|-.+..||..| |-+...|+++... .++++++.+...
T Consensus 113 ~i~~l~~~~g~~~~EIA~~l-gis~~tV~~~l~R-ar~~Lr~~l~~~ 157 (181)
T PRK09637 113 EALRLTELEGLSQKEIAEKL-GLSLSGAKSRVQR-GRVKLKELLEGC 157 (181)
T ss_pred HHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHHHH-HHHHHHHHHHHc
Confidence 45556667889999999999 9999999999875 456655555543
No 42
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=36.79 E-value=92 Score=25.25 Aligned_cols=46 Identities=13% Similarity=0.075 Sum_probs=34.9
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhc
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQN 50 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~ 50 (194)
+.++.|....|-....||..| |-+.+.||+|-+. .++++++.++..
T Consensus 122 r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~R-ar~~Lr~~l~~~ 167 (187)
T PRK12516 122 REAIILVGASGFAYEEAAEIC-GCAVGTIKSRVNR-ARQRLQEILQIE 167 (187)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHH-HHHHHHHHHHhh
Confidence 346667777899999999999 9999999998776 456655555543
No 43
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=35.64 E-value=38 Score=23.87 Aligned_cols=29 Identities=21% Similarity=0.274 Sum_probs=20.6
Q ss_pred HHHHHHHc-cCCCHHHHhccCCCCChHHHHH
Q 029398 4 VLYLINFA-PFSRWSAIAGRLPGRTDNEIKN 33 (194)
Q Consensus 4 lLi~l~~e-~GnkWs~IA~~LpGRTdn~IKN 33 (194)
.|..+... +|..|..+|+.| |=++..|..
T Consensus 7 ~~~~l~~~~~g~~W~~la~~L-g~~~~~i~~ 36 (88)
T smart00005 7 KLAKLLDHPLGLDWRELARKL-GLSEADIDQ 36 (88)
T ss_pred HHHHHHcCccchHHHHHHHHc-CCCHHHHHH
Confidence 44555556 899999999999 555555544
No 44
>PRK04217 hypothetical protein; Provisional
Probab=35.22 E-value=1e+02 Score=24.01 Aligned_cols=42 Identities=14% Similarity=0.055 Sum_probs=32.2
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHH
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVL 47 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~l 47 (194)
.++.+...-|-....||+.| |-+...|+++|+. .+++++..+
T Consensus 49 eai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~R-ArkkLre~L 90 (110)
T PRK04217 49 EALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTS-ARKKVAQML 90 (110)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHH-HHHHHHHHH
Confidence 34566666778999999999 9999999999997 455544434
No 45
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. 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, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=34.40 E-value=44 Score=24.73 Aligned_cols=31 Identities=16% Similarity=0.225 Sum_probs=24.8
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHH
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNV 34 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNr 34 (194)
+-|..+...+|..|..+|.+| |=++..|...
T Consensus 3 ~~L~~la~~LG~~W~~Lar~L-gls~~~I~~i 33 (83)
T cd08319 3 RELNQLAQRLGPEWEQVLLDL-GLSQTDIYRC 33 (83)
T ss_pred HHHHHHHHHHhhhHHHHHHHc-CCCHHHHHHH
Confidence 347788899999999999999 7777766543
No 46
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=34.11 E-value=59 Score=28.29 Aligned_cols=38 Identities=13% Similarity=0.129 Sum_probs=30.7
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
+.++.|+...|-....||..| |.+.+.||+|-+. .+++
T Consensus 148 R~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~R-ar~~ 185 (324)
T TIGR02960 148 RAVLLLRDVLGWRAAETAELL-GTSTASVNSALQR-ARAT 185 (324)
T ss_pred hhHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHHHH-HHHH
Confidence 345667777889999999999 9999999998776 3555
No 47
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. 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
Probab=33.83 E-value=29 Score=25.50 Aligned_cols=41 Identities=27% Similarity=0.173 Sum_probs=27.2
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHH---HHHHHHHhhHhhHHH
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNE---IKNVWHTHLKKKAAA 45 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~---IKNrW~~~Lrkr~~~ 45 (194)
-|..+-.++|..|..+|++| |=++.. |+..+-.-++.++..
T Consensus 4 ~l~~ia~~LG~~Wk~lar~L-Glse~~Id~Ie~~~~~dl~eq~~~ 47 (86)
T cd08779 4 NLLSIAGRLGLDWQAIGLHL-GLSYRELQRIKYNNRDDLDEQIFD 47 (86)
T ss_pred HHHHHHHHHhHHHHHHHHHc-CCCHHHHHHHHHHCccCHHHHHHH
Confidence 47788899999999999999 544444 455443334444333
No 48
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=33.00 E-value=61 Score=27.18 Aligned_cols=43 Identities=14% Similarity=0.230 Sum_probs=32.6
Q ss_pred HHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHh
Q 029398 5 LYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQ 49 (194)
Q Consensus 5 Li~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~ 49 (194)
++.++-..|-....||..| |-+...||++.+. .++++|+.++.
T Consensus 157 i~~l~~~~g~s~~EIAe~l-gis~~tVk~~l~R-ar~kLr~~l~~ 199 (231)
T PRK11922 157 VFVLRVVEELSVEETAQAL-GLPEETVKTRLHR-ARRLLRESLAR 199 (231)
T ss_pred hheeehhcCCCHHHHHHHH-CcCHHHHHHHHHH-HHHHHHHHHHH
Confidence 4445555688899999999 9999999999886 45665555643
No 49
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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-associati
Probab=32.19 E-value=44 Score=24.09 Aligned_cols=30 Identities=27% Similarity=0.339 Sum_probs=23.8
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHH
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNV 34 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNr 34 (194)
.|..+.+.+|..|..+|++| |=++..|...
T Consensus 6 ~l~~ia~~lG~dW~~LAr~L-g~~~~dI~~i 35 (84)
T cd08317 6 RLADISNLLGSDWPQLAREL-GVSETDIDLI 35 (84)
T ss_pred hHHHHHHHHhhHHHHHHHHc-CCCHHHHHHH
Confidence 46677788999999999999 7777666554
No 50
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=30.92 E-value=1.1e+02 Score=24.43 Aligned_cols=45 Identities=9% Similarity=0.214 Sum_probs=33.5
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhc
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQN 50 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~ 50 (194)
.++.+.-..|-....||..| |-+...||++.+. .++++++.++..
T Consensus 129 ~i~~l~~~~g~s~~EIA~~l-gis~~tVk~~l~R-ar~~Lr~~l~~~ 173 (185)
T PRK12542 129 QVFKYKVFYNLTYQEISSVM-GITEANVRKQFER-ARKRVQNMIGGI 173 (185)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHH-HHHHHHHHHccc
Confidence 45566677888999999999 9999999998765 456644445433
No 51
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=30.28 E-value=53 Score=22.35 Aligned_cols=32 Identities=16% Similarity=0.125 Sum_probs=23.2
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHH
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWH 36 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~ 36 (194)
-.+++..++|-+-..||+++ ||+-+.|++.-+
T Consensus 11 aqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 11 AQIDVMHQLGMSLREISRRI-GRSRTCIRRYLK 42 (50)
T ss_dssp HHHHHHHHTT--HHHHHHHH-T--HHHHHHHHH
T ss_pred HHHHHHHHhchhHHHHHHHh-CccHHHHHHHhc
Confidence 45678889999999999999 999999988543
No 52
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=28.76 E-value=2e+02 Score=22.66 Aligned_cols=46 Identities=17% Similarity=0.042 Sum_probs=35.4
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhc
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQN 50 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~ 50 (194)
+.++.++-..|-.-..||..| |-+...|+++.+. .++++++.++..
T Consensus 106 r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~R-ar~~Lr~~l~~~ 151 (170)
T TIGR02959 106 REAIRLTELEGLSQQEIAEKL-GLSLSGAKSRVQR-GRKKLKELLETC 151 (170)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHH-HHHHHHHHHHHh
Confidence 456667777888899999999 9999999998876 456655555543
No 53
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=28.70 E-value=1.5e+02 Score=23.88 Aligned_cols=46 Identities=9% Similarity=-0.063 Sum_probs=34.7
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhcC
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQNQ 51 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~~ 51 (194)
.++.++-..|-....||..| |-+...||++.+. .++++++.+.+..
T Consensus 118 ~v~~L~~~eg~s~~EIA~~l-gis~~tV~~~l~R-ar~~Lr~~~~~~~ 163 (182)
T PRK12511 118 AALHLVAIEGLSYQEAAAVL-GIPIGTLMSRIGR-ARAALRAFEEGTG 163 (182)
T ss_pred HHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHHHH-HHHHHHHHHHhcC
Confidence 35556666789999999999 9999999999876 4556555565444
No 54
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=28.63 E-value=93 Score=24.64 Aligned_cols=38 Identities=11% Similarity=0.096 Sum_probs=28.3
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
+|..|+.----.|+.||+.+ |-+...|+.|++.+....
T Consensus 14 Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 14 ILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 44444444337899999999 999999999998854433
No 55
>PRK15328 invasion protein IagB; Provisional
Probab=28.06 E-value=1.6e+02 Score=24.26 Aligned_cols=40 Identities=13% Similarity=0.215 Sum_probs=28.2
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCC--hHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRT--DNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRT--dn~IKNrW~~~Lrkr 42 (194)
.+|..+...+|..|..|+.+=-|-. ....+.++...+.+.
T Consensus 97 ~~L~~~~~~~g~~~~alaaYNaG~~~~~~~~~~~Y~~kV~~~ 138 (160)
T PRK15328 97 SILSDMMKIYGYSWEAVGAYNAGTSPKRSDIRKRYAKKIWEN 138 (160)
T ss_pred HHHHHHHHHcCChHHhhhhccCCCCCCCCHHHHHHHHHHHHH
Confidence 3678889999999999998765433 334566666555555
No 56
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. 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. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.42 E-value=65 Score=23.57 Aligned_cols=28 Identities=21% Similarity=0.341 Sum_probs=22.2
Q ss_pred HHHHHHccCCCHHHHhccCCCCChHHHHH
Q 029398 5 LYLINFAPFSRWSAIAGRLPGRTDNEIKN 33 (194)
Q Consensus 5 Li~l~~e~GnkWs~IA~~LpGRTdn~IKN 33 (194)
|..+-..+|..|..+|+.| |=++..|..
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~~ 37 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIRA 37 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 3446678899999999999 888777654
No 57
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=26.03 E-value=1.7e+02 Score=23.56 Aligned_cols=46 Identities=17% Similarity=0.070 Sum_probs=33.5
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhcC
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQNQ 51 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~~ 51 (194)
.++.++...|-....||..| |-+...||.+-+. .++++++.+....
T Consensus 118 ~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l~R-Ar~~Lr~~l~~~~ 163 (182)
T PRK12540 118 EALILVGASGFSYEDAAAIC-GCAVGTIKSRVNR-ARSKLSALLYVDG 163 (182)
T ss_pred HHhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHH-HHHHHHHHHHhcc
Confidence 45556667888999999999 9999999998765 3555444455443
No 58
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=25.69 E-value=83 Score=25.29 Aligned_cols=39 Identities=8% Similarity=-0.010 Sum_probs=29.3
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
++|..|+.--.-.|+.||+.+ |-+...|+.|++.+.+..
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 344444444448899999999 999999999998855444
No 59
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=23.56 E-value=1.3e+02 Score=19.19 Aligned_cols=33 Identities=15% Similarity=0.299 Sum_probs=22.7
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHH
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHT 37 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~ 37 (194)
||-.++.----.|..||+.+ |=+...|..|++.
T Consensus 8 Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~r 40 (42)
T PF13404_consen 8 ILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHH
T ss_pred HHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHH
Confidence 34444444336799999998 9999999999875
No 60
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.18 E-value=2e+02 Score=23.38 Aligned_cols=43 Identities=14% Similarity=0.073 Sum_probs=32.5
Q ss_pred HHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHH
Q 029398 4 VLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLK 48 (194)
Q Consensus 4 lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk 48 (194)
.++.++...|-....||..| |-+...||++-+. .++++++.+.
T Consensus 120 ~v~~L~~~~g~s~~EIA~~L-giS~~tVk~~l~R-ar~~Lr~~l~ 162 (188)
T PRK12546 120 EALILVGASGFSYEEAAEMC-GVAVGTVKSRANR-ARARLAELLQ 162 (188)
T ss_pred HHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHH-HHHHHHHHHh
Confidence 45666667899999999999 9999999998776 3455444343
No 61
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=23.12 E-value=1e+02 Score=29.77 Aligned_cols=40 Identities=20% Similarity=0.190 Sum_probs=33.8
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhh
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKK 42 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr 42 (194)
++.+++-...|.-.+.|+..||.|.-.+||..|...-+++
T Consensus 374 ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~n 413 (507)
T COG5118 374 EKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKVN 413 (507)
T ss_pred HHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhhC
Confidence 4567777889999999999999999999999988755444
No 62
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=21.53 E-value=71 Score=23.57 Aligned_cols=29 Identities=28% Similarity=0.383 Sum_probs=23.9
Q ss_pred HHHHHccCCCHHHHhccCCCCChHHHHHHH
Q 029398 6 YLINFAPFSRWSAIAGRLPGRTDNEIKNVW 35 (194)
Q Consensus 6 i~l~~e~GnkWs~IA~~LpGRTdn~IKNrW 35 (194)
-.+-..+|..|..+|+.| |=++..|++.=
T Consensus 6 ~~l~~~lG~~Wk~lar~L-G~s~~eI~~ie 34 (86)
T cd08777 6 DLLRENLGKKWKRCARKL-GFTESEIEEID 34 (86)
T ss_pred HHHHHHHHHHHHHHHHHc-CCCHHHHHHHH
Confidence 345578899999999999 88999888753
No 63
>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=20.97 E-value=67 Score=22.00 Aligned_cols=28 Identities=29% Similarity=0.415 Sum_probs=19.9
Q ss_pred HHHHHHccCCCHHHHhccCCCCChHHHHH
Q 029398 5 LYLINFAPFSRWSAIAGRLPGRTDNEIKN 33 (194)
Q Consensus 5 Li~l~~e~GnkWs~IA~~LpGRTdn~IKN 33 (194)
+..+...+|+.|..+|+.| |=+...|..
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I~~ 29 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEIDQ 29 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHHHH
Confidence 3456678899999999999 444444443
No 64
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=20.53 E-value=1.8e+02 Score=24.38 Aligned_cols=47 Identities=11% Similarity=0.076 Sum_probs=34.0
Q ss_pred HHHHHHHHccCCCHHHHhccCCCCChHHHHHHHHHhhHhhHHHHHHhcC
Q 029398 3 QVLYLINFAPFSRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQNQ 51 (194)
Q Consensus 3 ~lLi~l~~e~GnkWs~IA~~LpGRTdn~IKNrW~~~Lrkr~~~~lk~~~ 51 (194)
+.++.++-..|-.-..||..| |=+.+.||.+-+. .++++++.+....
T Consensus 140 R~v~~L~y~eg~s~~EIAe~L-giS~~tVk~~L~R-Ar~~Lr~~l~~~~ 186 (216)
T PRK12533 140 REVLVLRELEDMSYREIAAIA-DVPVGTVMSRLAR-ARRRLAALLGGAS 186 (216)
T ss_pred HhHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHH-HHHHHHHHHcccc
Confidence 345566666788899999999 9999999998776 4566555454443
No 65
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=20.47 E-value=81 Score=23.41 Aligned_cols=31 Identities=19% Similarity=0.142 Sum_probs=21.1
Q ss_pred HHHHHHccCCCHHHHhccC--CCCChHHHHHHH
Q 029398 5 LYLINFAPFSRWSAIAGRL--PGRTDNEIKNVW 35 (194)
Q Consensus 5 Li~l~~e~GnkWs~IA~~L--pGRTdn~IKNrW 35 (194)
|..+-+.+|..|..+|+.| +...-+.|+.-.
T Consensus 7 l~~Ia~~LG~dW~~Lar~L~vs~~dI~~I~~e~ 39 (84)
T cd08805 7 MAVIREHLGLSWAELARELQFSVEDINRIRVEN 39 (84)
T ss_pred HHHHHHHhcchHHHHHHHcCCCHHHHHHHHHhC
Confidence 4556788999999999998 233333444443
Done!