Query 041956
Match_columns 119
No_of_seqs 110 out of 344
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 12:27:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041956.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041956hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01557 myb_SHAQKYF myb-like 99.9 3.2E-25 7E-30 144.3 6.3 56 46-101 1-56 (57)
2 PLN03162 golden-2 like transcr 99.9 7.4E-25 1.6E-29 187.8 7.9 60 43-103 232-291 (526)
3 PF00249 Myb_DNA-binding: Myb- 98.7 3.1E-08 6.7E-13 60.7 5.5 48 48-99 1-48 (48)
4 smart00717 SANT SANT SWI3, AD 96.8 0.0049 1.1E-07 35.2 5.4 45 49-98 2-46 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 96.8 0.005 1.1E-07 34.8 5.3 44 50-98 1-44 (45)
6 smart00426 TEA TEA domain. 96.4 0.004 8.7E-08 42.5 3.6 46 50-97 5-67 (68)
7 PF13921 Myb_DNA-bind_6: Myb-l 94.6 0.13 2.8E-06 31.9 5.2 41 51-97 1-41 (60)
8 PF01285 TEA: TEA/ATTS domain 93.7 0.058 1.3E-06 47.2 3.1 54 45-98 46-112 (431)
9 PF12776 Myb_DNA-bind_3: Myb/S 92.4 0.21 4.5E-06 33.3 3.6 51 50-100 1-63 (96)
10 KOG0457 Histone acetyltransfer 89.8 0.62 1.3E-05 41.3 5.0 51 46-101 70-120 (438)
11 PLN03212 Transcription repress 89.3 0.82 1.8E-05 37.9 5.1 50 46-99 23-72 (249)
12 KOG3841 TEF-1 and related tran 89.1 0.34 7.4E-06 42.8 2.8 59 46-104 74-147 (455)
13 PLN03212 Transcription repress 87.7 1.7 3.7E-05 36.0 5.9 49 46-100 76-128 (249)
14 PLN03091 hypothetical protein; 87.4 2.2 4.7E-05 38.2 6.7 48 47-100 66-117 (459)
15 KOG0724 Zuotin and related mol 85.9 0.31 6.6E-06 39.9 0.7 60 40-105 45-104 (335)
16 PLN03091 hypothetical protein; 85.7 1.6 3.5E-05 39.0 5.1 51 45-99 11-61 (459)
17 smart00501 BRIGHT BRIGHT, ARID 80.5 2.3 4.9E-05 28.9 3.2 44 54-98 33-83 (93)
18 KOG0048 Transcription factor, 77.6 5.9 0.00013 31.4 5.2 45 44-94 58-102 (238)
19 PF13837 Myb_DNA-bind_4: Myb/S 64.3 7.6 0.00016 25.2 2.6 58 48-105 1-74 (90)
20 COG5114 Histone acetyltransfer 61.9 12 0.00026 33.0 4.0 48 48-100 63-110 (432)
21 smart00351 PAX Paired Box doma 52.1 63 0.0014 23.2 5.9 43 50-100 17-59 (125)
22 PF00046 Homeobox: Homeobox do 51.9 40 0.00087 20.2 4.2 54 45-101 1-54 (57)
23 PF07384 DUF1497: Protein of u 50.6 18 0.00039 23.9 2.5 21 50-70 37-57 (59)
24 TIGR02894 DNA_bind_RsfA transc 49.7 14 0.0003 28.9 2.2 50 45-100 45-94 (161)
25 KOG0049 Transcription factor, 49.6 22 0.00048 34.0 3.9 43 46-93 358-400 (939)
26 PF00690 Cation_ATPase_N: Cati 47.4 27 0.00058 22.1 3.0 33 73-105 5-40 (69)
27 cd06171 Sigma70_r4 Sigma70, re 43.1 57 0.0012 17.9 4.3 27 72-101 27-53 (55)
28 PF06627 DUF1153: Protein of u 41.8 63 0.0014 23.2 4.4 40 48-94 30-69 (90)
29 PRK11923 algU RNA polymerase s 41.3 51 0.0011 24.1 4.0 45 54-101 127-181 (193)
30 PF08671 SinI: Anti-repressor 38.8 26 0.00056 20.3 1.7 19 77-96 9-27 (30)
31 PF08281 Sigma70_r4_2: Sigma-7 37.6 85 0.0018 18.5 4.0 26 72-100 27-52 (54)
32 TIGR02989 Sig-70_gvs1 RNA poly 37.6 77 0.0017 22.1 4.4 47 52-101 98-154 (159)
33 cd08783 Death_MALT1 Death doma 37.1 68 0.0015 23.3 4.0 49 46-98 35-84 (97)
34 PRK12541 RNA polymerase sigma 36.8 78 0.0017 22.4 4.3 43 56-101 103-155 (161)
35 PRK09640 RNA polymerase sigma 35.0 95 0.0021 22.7 4.7 49 49-100 118-176 (188)
36 PF13384 HTH_23: Homeodomain-l 34.5 89 0.0019 18.1 3.7 38 55-100 6-43 (50)
37 PF01325 Fe_dep_repress: Iron 33.3 60 0.0013 20.6 3.0 28 57-84 7-35 (60)
38 PF02201 SWIB: SWIB/MDM2 domai 32.9 41 0.00088 22.2 2.2 27 74-100 8-34 (76)
39 KOG1279 Chromatin remodeling f 32.2 83 0.0018 28.6 4.6 44 46-95 251-294 (506)
40 PF02762 Cbl_N3: CBL proto-onc 31.9 35 0.00076 24.3 1.8 18 85-102 8-25 (86)
41 PRK13919 putative RNA polymera 31.8 93 0.002 22.5 4.1 28 72-102 152-179 (186)
42 PF09274 ParG: ParG; InterPro 31.5 64 0.0014 22.4 3.0 27 41-67 31-57 (76)
43 PRK09642 RNA polymerase sigma 31.1 93 0.002 21.9 3.9 27 72-101 123-149 (160)
44 PRK09413 IS2 repressor TnpA; R 31.0 1.6E+02 0.0035 20.7 5.2 49 46-101 8-56 (121)
45 PF13601 HTH_34: Winged helix 30.7 33 0.00073 22.9 1.5 29 69-100 12-40 (80)
46 PF05534 HicB: HicB family; I 30.2 87 0.0019 19.5 3.2 24 44-67 17-40 (51)
47 cd00086 homeodomain Homeodomai 29.4 1.2E+02 0.0027 17.6 5.1 53 46-101 2-54 (59)
48 PF11740 KfrA_N: Plasmid repli 28.7 2E+02 0.0042 19.7 6.0 35 70-106 18-52 (120)
49 PRK12522 RNA polymerase sigma 28.6 89 0.0019 22.4 3.5 49 50-101 104-162 (173)
50 PF02954 HTH_8: Bacterial regu 28.4 1.3E+02 0.0028 17.5 4.2 34 58-98 9-42 (42)
51 PRK12530 RNA polymerase sigma 28.2 1E+02 0.0022 22.7 3.9 44 54-100 123-176 (189)
52 PRK06759 RNA polymerase factor 28.1 1.4E+02 0.003 20.7 4.4 45 54-101 95-149 (154)
53 TIGR02950 SigM_subfam RNA poly 27.9 1.8E+02 0.0038 20.1 4.9 43 56-101 96-148 (154)
54 PF01388 ARID: ARID/BRIGHT DNA 27.3 72 0.0016 21.0 2.7 44 54-98 37-87 (92)
55 PRK05803 sporulation sigma fac 27.0 1.4E+02 0.003 23.0 4.5 26 69-97 193-218 (233)
56 PF08127 Propeptide_C1: Peptid 26.8 48 0.001 20.1 1.6 35 55-96 1-35 (41)
57 PF11888 DUF3408: Protein of u 26.5 2.6E+02 0.0056 20.4 5.7 44 47-100 81-124 (136)
58 PF11767 SET_assoc: Histone ly 26.2 53 0.0011 21.9 1.8 28 82-109 8-35 (66)
59 TIGR02985 Sig70_bacteroi1 RNA 25.5 1.5E+02 0.0032 20.2 4.1 27 72-101 130-156 (161)
60 smart00344 HTH_ASNC helix_turn 24.7 2.1E+02 0.0046 19.0 4.7 43 53-101 2-44 (108)
61 PF14383 VARLMGL: DUF761-assoc 24.1 59 0.0013 19.6 1.6 21 69-89 10-30 (34)
62 TIGR02937 sigma70-ECF RNA poly 22.5 1.9E+02 0.0041 19.0 4.0 26 73-101 128-153 (158)
63 TIGR02960 SigX5 RNA polymerase 22.4 1.7E+02 0.0036 23.3 4.4 45 55-102 132-186 (324)
64 PF13412 HTH_24: Winged helix- 22.2 1.7E+02 0.0038 16.9 4.8 40 55-100 4-43 (48)
65 PRK09415 RNA polymerase factor 22.2 2E+02 0.0043 20.9 4.4 45 54-101 116-170 (179)
66 TIGR02983 SigE-fam_strep RNA p 21.9 1.7E+02 0.0037 20.5 3.9 27 72-101 127-153 (162)
67 PF01527 HTH_Tnp_1: Transposas 21.8 1.2E+02 0.0026 18.8 2.9 47 46-99 2-48 (76)
68 PF00196 GerE: Bacterial regul 21.6 1.5E+02 0.0032 17.9 3.2 27 72-101 19-45 (58)
69 smart00421 HTH_LUXR helix_turn 21.6 1.6E+02 0.0036 16.4 3.3 27 72-101 19-45 (58)
70 smart00389 HOX Homeodomain. DN 21.1 1.9E+02 0.004 16.8 4.7 52 46-100 2-53 (56)
71 PF14075 UBN_AB: Ubinuclein co 21.1 1.1E+02 0.0023 24.6 3.0 21 44-64 148-168 (214)
72 COG5118 BDP1 Transcription ini 20.9 1.8E+02 0.0038 26.4 4.5 43 45-93 362-404 (507)
73 KOG2983 Uncharacterized conser 20.7 79 0.0017 27.3 2.2 17 53-69 85-101 (334)
74 PRK09636 RNA polymerase sigma 20.2 2E+02 0.0044 22.8 4.4 48 54-104 104-161 (293)
75 KOG1785 Tyrosine kinase negati 20.2 57 0.0012 29.7 1.4 17 85-101 262-278 (563)
No 1
>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=99.92 E-value=3.2e-25 Score=144.33 Aligned_cols=56 Identities=55% Similarity=0.900 Sum_probs=54.0
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
|+|++||+|+|.+|++||+.||+.+.|+|+.|+++|++++||+.||+|||||||++
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 58999999999999999999998789999999999999999999999999999986
No 2
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.91 E-value=7.4e-25 Score=187.82 Aligned_cols=60 Identities=47% Similarity=0.798 Sum_probs=56.6
Q ss_pred cCCCCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhccc
Q 041956 43 RSKVPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRSKKI 103 (119)
Q Consensus 43 ~~kK~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~~~ 103 (119)
..||+||+||+|||++||+||++|| .++|+||+||++|+|+|||++||||||||||+.++
T Consensus 232 g~KKpRLrWTpELH~rFVeAV~qLG-~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk 291 (526)
T PLN03162 232 GKKKAKVDWTPELHRRFVHAVEQLG-VEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRR 291 (526)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHhC-cCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcc
Confidence 3679999999999999999999999 79999999999999999999999999999999644
No 3
>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=98.74 E-value=3.1e-08 Score=60.68 Aligned_cols=48 Identities=23% Similarity=0.313 Sum_probs=41.7
Q ss_pred ceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhh
Q 041956 48 RLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYR 99 (119)
Q Consensus 48 Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR 99 (119)
|..||++.+..|++||.++|.. .|+.|.+.|+ .+.|..||++|.++|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~---~W~~Ia~~~~-~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD---NWKKIAKRMP-GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT---HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCc---HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence 5689999999999999999932 5999999997 5899999999999985
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=96.85 E-value=0.0049 Score=35.23 Aligned_cols=45 Identities=11% Similarity=0.255 Sum_probs=38.5
Q ss_pred eecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhh
Q 041956 49 LRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMY 98 (119)
Q Consensus 49 l~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKY 98 (119)
-.||++....|+.++.++|- ..+..|...|+ +.|..+|+.+...+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~---~~w~~Ia~~~~--~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGK---NNWEKIAKELP--GRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCc---CCHHHHHHHcC--CCCHHHHHHHHHHH
Confidence 46999999999999999992 35899999985 78999999887654
No 5
>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=96.84 E-value=0.005 Score=34.82 Aligned_cols=44 Identities=14% Similarity=0.291 Sum_probs=38.0
Q ss_pred ecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhh
Q 041956 50 RWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMY 98 (119)
Q Consensus 50 ~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKY 98 (119)
.||++.+..|+.++..+|- ..+..|.+.|+ +.|..+|+.|.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~--~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELP--GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcC--CCCHHHHHHHHHHh
Confidence 4999999999999999992 35899999985 58999999987764
No 6
>smart00426 TEA TEA domain.
Probab=96.45 E-value=0.004 Score=42.47 Aligned_cols=46 Identities=22% Similarity=0.359 Sum_probs=31.3
Q ss_pred ecCHHHHHHHHHHHHHhCCCCCCchhh-----------------HHhhhCCCCCCHHHHHHhhhh
Q 041956 50 RWTPDLHRCFVQAVERLGGQERATPKL-----------------VLQLMNIKGLSIAHVKSHLQM 97 (119)
Q Consensus 50 ~WT~ELH~kFv~Av~~LGg~~~A~PK~-----------------IlelM~v~gLT~~~VkSHLQK 97 (119)
+|.+++-..|++|+..+- .....+-+ |...-| .-.|+.||.||+|.
T Consensus 5 vWp~~lE~Af~~aL~~~~-~~g~~kik~~~r~k~~gRNelIs~YI~~~tG-k~Rt~KQVsShIQv 67 (68)
T smart00426 5 VWSPDIEQAFQEALAIYP-PCGRRKIILSDEGKMYGRNELIARYIKLRTG-KTRTRKQVSSHIQV 67 (68)
T ss_pred cCcHHHHHHHHHHHHHcC-ccCcccchhhhcCcccchhHHHHHHHHHHhC-Cccchhhhcchhee
Confidence 699999999999999875 22111111 222222 35899999999995
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=94.57 E-value=0.13 Score=31.95 Aligned_cols=41 Identities=12% Similarity=0.291 Sum_probs=35.0
Q ss_pred cCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhh
Q 041956 51 WTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQM 97 (119)
Q Consensus 51 WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQK 97 (119)
||++.-...+.++..+|. .|+.|.+.|+ ..|..+|+.+...
T Consensus 1 WT~eEd~~L~~~~~~~g~----~W~~Ia~~l~--~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN----DWKKIAEHLG--NRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-----HHHHHHHST--TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc----CHHHHHHHHC--cCCHHHHHHHHHH
Confidence 999999999999999983 5999999985 6899999998888
No 8
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=93.71 E-value=0.058 Score=47.18 Aligned_cols=54 Identities=22% Similarity=0.343 Sum_probs=30.0
Q ss_pred CCCceecCHHHHHHHHHHHHHhCCCCCCchh----------hHHhhhCC---CCCCHHHHHHhhhhh
Q 041956 45 KVPRLRWTPDLHRCFVQAVERLGGQERATPK----------LVLQLMNI---KGLSIAHVKSHLQMY 98 (119)
Q Consensus 45 kK~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK----------~IlelM~v---~gLT~~~VkSHLQKY 98 (119)
....-+|++++...|++|+..+---..+.-+ -|.+.+.. ...|+.||.||+|..
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 3578899999999999999877411111111 02222211 358999999999998
No 9
>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=92.39 E-value=0.21 Score=33.28 Aligned_cols=51 Identities=14% Similarity=0.330 Sum_probs=36.3
Q ss_pred ecCHHHHHHHHHHHHHh---CCC------CCCchhhHHhhhCC---CCCCHHHHHHhhhhhhh
Q 041956 50 RWTPDLHRCFVQAVERL---GGQ------ERATPKLVLQLMNI---KGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 50 ~WT~ELH~kFv~Av~~L---Gg~------~~A~PK~IlelM~v---~gLT~~~VkSHLQKYR~ 100 (119)
+||++..+-||+.+-.. |.. .+..+..|++.++- -.+|..||++|++..|.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 59999999999988543 432 12345557766664 35789999999987665
No 10
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=89.80 E-value=0.62 Score=41.35 Aligned_cols=51 Identities=16% Similarity=0.156 Sum_probs=44.5
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
--...||.+.-..||+|++.+| . -.|..|.+.|| .-|.++++.|--|+...
T Consensus 70 i~~~~WtadEEilLLea~~t~G-~--GNW~dIA~hIG--tKtkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYG-F--GNWQDIADHIG--TKTKEECKEHYLKHFVN 120 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhC-C--CcHHHHHHHHc--ccchHHHHHHHHHHHhc
Confidence 4567899999999999999999 2 26999999999 47999999999998873
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=89.30 E-value=0.82 Score=37.90 Aligned_cols=50 Identities=12% Similarity=0.081 Sum_probs=41.4
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhh
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYR 99 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR 99 (119)
..|..||+|.-++-+++|+.+|. ..|+.|.+.|+ ++.|..|++-+-..|=
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~---~nW~~IAk~~g-~gRT~KQCReRW~N~L 72 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGE---GRWRSLPKRAG-LLRCGKSCRLRWMNYL 72 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCc---ccHHHHHHhhh-cCCCcchHHHHHHHhh
Confidence 45778999999999999999993 46999999886 5788888887766664
No 12
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=89.06 E-value=0.34 Score=42.83 Aligned_cols=59 Identities=20% Similarity=0.412 Sum_probs=39.3
Q ss_pred CCceecCHHHHHHHHHHHHHhC---CCC----CC-----chhhHHhhhCC---CCCCHHHHHHhhhhhhhcccc
Q 041956 46 VPRLRWTPDLHRCFVQAVERLG---GQE----RA-----TPKLVLQLMNI---KGLSIAHVKSHLQMYRSKKID 104 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LG---g~~----~A-----~PK~IlelM~v---~gLT~~~VkSHLQKYR~~~~~ 104 (119)
-.--+|+++.-+.|.+|+..+- +.+ .+ .-.-|...+.. ...|+.||.||.|..-.++.+
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~r 147 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLR 147 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHH
Confidence 4667999999999999998763 210 00 01123333333 568999999999987654433
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=87.71 E-value=1.7 Score=36.03 Aligned_cols=49 Identities=22% Similarity=0.183 Sum_probs=39.0
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHH----hhhhhhh
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKS----HLQMYRS 100 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkS----HLQKYR~ 100 (119)
-.+-.||.|.-..-++++..+|. .|..|...| +|.|-.+||. ||.|..+
T Consensus 76 I~kgpWT~EED~lLlel~~~~Gn----KWs~IAk~L--pGRTDnqIKNRWns~LrK~l~ 128 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGN----RWSLIAGRI--PGRTDNEIKNYWNTHLRKKLL 128 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccc----cHHHHHhhc--CCCCHHHHHHHHHHHHhHHHH
Confidence 34568999999999999999993 599999986 8999999984 4555433
No 14
>PLN03091 hypothetical protein; Provisional
Probab=87.37 E-value=2.2 Score=38.21 Aligned_cols=48 Identities=13% Similarity=0.117 Sum_probs=39.6
Q ss_pred CceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHH----hhhhhhh
Q 041956 47 PRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKS----HLQMYRS 100 (119)
Q Consensus 47 ~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkS----HLQKYR~ 100 (119)
.+-.||+|.-...++.+..+|. .|..|...| +|.|-.+||. +|.|+..
T Consensus 66 kKgpWT~EED~lLLeL~k~~Gn----KWskIAk~L--PGRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 66 KRGTFSQQEENLIIELHAVLGN----RWSQIAAQL--PGRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCc----chHHHHHhc--CCCCHHHHHHHHHHHHHHHHH
Confidence 3457999999999999999993 699999986 8999999984 4556533
No 15
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=85.93 E-value=0.31 Score=39.85 Aligned_cols=60 Identities=13% Similarity=0.045 Sum_probs=47.1
Q ss_pred ccccCCCCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhccccC
Q 041956 40 PYVRSKVPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRSKKIDD 105 (119)
Q Consensus 40 ~~~~~kK~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~~~~~ 105 (119)
+|...+...-+||++.|.+|.+|+-.. +..|..|.++.+. .+..++.+|.|+|..+....
T Consensus 45 a~~i~~~~~~~~t~~~~~~~~~~l~~~----~~~~~~~~~~~~~--~~~v~~~~~~~~~~p~~~~~ 104 (335)
T KOG0724|consen 45 ALAILDDDEPRRTPDSWDKFAEALPLE----KRLEDKIEEYIGL--VFDVNIRESGQKPFPKYGKS 104 (335)
T ss_pred HHHHHhccccccchhhhhHHHhcCccc----cccchhHHhhhhh--HHHHhhhhccCCCccccCcc
Confidence 566665556679999999999988554 3568899888765 78899999999999875554
No 16
>PLN03091 hypothetical protein; Provisional
Probab=85.68 E-value=1.6 Score=38.96 Aligned_cols=51 Identities=12% Similarity=0.147 Sum_probs=40.6
Q ss_pred CCCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhh
Q 041956 45 KVPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYR 99 (119)
Q Consensus 45 kK~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR 99 (119)
+..|..||+|.-++.+++|..+|. ..|+.|...|+ ++.|-.|++-+-..|-
T Consensus 11 klrKg~WTpEEDe~L~~~V~kyG~---~nWs~IAk~~g-~gRT~KQCRERW~NyL 61 (459)
T PLN03091 11 KLRKGLWSPEEDEKLLRHITKYGH---GCWSSVPKQAG-LQRCGKSCRLRWINYL 61 (459)
T ss_pred CCcCCCCCHHHHHHHHHHHHHhCc---CCHHHHhhhhc-cCcCcchHhHHHHhcc
Confidence 456678999999999999999993 47999999886 4678778776655443
No 17
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=80.53 E-value=2.3 Score=28.86 Aligned_cols=44 Identities=23% Similarity=0.390 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhCCCCC----CchhhHHhhhCCCCC---CHHHHHHhhhhh
Q 041956 54 DLHRCFVQAVERLGGQER----ATPKLVLQLMNIKGL---SIAHVKSHLQMY 98 (119)
Q Consensus 54 ELH~kFv~Av~~LGg~~~----A~PK~IlelM~v~gL---T~~~VkSHLQKY 98 (119)
+|+.-|. +|..+||.+. ..|+.|.+.|+++.- ...++++|-+||
T Consensus 33 dL~~Ly~-~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~ 83 (93)
T smart00501 33 DLYRLYR-LVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERY 83 (93)
T ss_pred cHHHHHH-HHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHH
Confidence 7888887 5888999653 569999999999742 245566666666
No 18
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=77.59 E-value=5.9 Score=31.40 Aligned_cols=45 Identities=18% Similarity=0.241 Sum_probs=37.4
Q ss_pred CCCCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHh
Q 041956 44 SKVPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSH 94 (119)
Q Consensus 44 ~kK~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSH 94 (119)
+.-.|-.||+|.-+.-++|-..+|- .|..|..+| ||.|-..||.|
T Consensus 58 P~ikrg~fT~eEe~~Ii~lH~~~GN----rWs~IA~~L--PGRTDNeIKN~ 102 (238)
T KOG0048|consen 58 PDLKRGNFSDEEEDLIIKLHALLGN----RWSLIAGRL--PGRTDNEVKNH 102 (238)
T ss_pred CCccCCCCCHHHHHHHHHHHHHHCc----HHHHHHhhC--CCcCHHHHHHH
Confidence 3344677999999999999999994 499999885 89999999855
No 19
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=64.34 E-value=7.6 Score=25.25 Aligned_cols=58 Identities=16% Similarity=0.314 Sum_probs=34.6
Q ss_pred ceecCHHHHHHHHHHHHH------hC--CCCC--CchhhHHhhhCCCC--CCHHHHHHhh----hhhhhccccC
Q 041956 48 RLRWTPDLHRCFVQAVER------LG--GQER--ATPKLVLQLMNIKG--LSIAHVKSHL----QMYRSKKIDD 105 (119)
Q Consensus 48 Rl~WT~ELH~kFv~Av~~------LG--g~~~--A~PK~IlelM~v~g--LT~~~VkSHL----QKYR~~~~~~ 105 (119)
|-.||++.-..|++++.. ++ +... ..++.|.+.|..-| .|..|++... .+||.-+...
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~~~ 74 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKDRN 74 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSSSS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 567999999999998877 21 2222 26888888776544 5888877553 5566544433
No 20
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=61.85 E-value=12 Score=32.99 Aligned_cols=48 Identities=15% Similarity=0.230 Sum_probs=41.9
Q ss_pred ceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 48 RLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 48 Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
.--|+.+.--.|++|.+-||- -.|..|...+| ..+.+.|++|-=||-.
T Consensus 63 ~e~WgadEEllli~~~~TlGl---GNW~dIadyiG--sr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGL---GNWEDIADYIG--SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCC---CcHHHHHHHHh--hhhhHHHHHHHHHHHh
Confidence 346999999999999999992 26999999999 5899999999888876
No 21
>smart00351 PAX Paired Box domain.
Probab=52.13 E-value=63 Score=23.15 Aligned_cols=43 Identities=16% Similarity=0.197 Sum_probs=35.5
Q ss_pred ecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 50 RWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 50 ~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
-++.++-.+||.++. +| .+...|.+.+++ ++.-|..-+++|+.
T Consensus 17 ~~s~~~R~riv~~~~--~G---~s~~~iA~~~gv---s~~tV~kwi~r~~~ 59 (125)
T smart00351 17 PLPDEERQRIVELAQ--NG---VRPCDISRQLCV---SHGCVSKILGRYYE 59 (125)
T ss_pred CCCHHHHHHHHHHHH--cC---CCHHHHHHHHCc---CHHHHHHHHHHHHH
Confidence 388999999999985 43 367889998876 88888888999986
No 22
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=51.91 E-value=40 Score=20.17 Aligned_cols=54 Identities=22% Similarity=0.166 Sum_probs=34.8
Q ss_pred CCCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 45 KVPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 45 kK~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
|++|..+|++- ...|+++.... ...+...+.++...-|||..+|..=.|.-|.+
T Consensus 1 kr~r~~~t~~q-~~~L~~~f~~~--~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 1 KRKRTRFTKEQ-LKVLEEYFQEN--PYPSKEEREELAKELGLTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSSSSHHH-HHHHHHHHHHS--SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHH-HHHHHHHHHHh--ccccccccccccccccccccccccCHHHhHHH
Confidence 46778888654 45566666655 23444555555444478999999888777654
No 23
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=50.56 E-value=18 Score=23.88 Aligned_cols=21 Identities=19% Similarity=0.673 Sum_probs=18.5
Q ss_pred ecCHHHHHHHHHHHHHhCCCC
Q 041956 50 RWTPDLHRCFVQAVERLGGQE 70 (119)
Q Consensus 50 ~WT~ELH~kFv~Av~~LGg~~ 70 (119)
.+..|+|+.|-+-|+.|||..
T Consensus 37 kfnqem~aefheri~klggk~ 57 (59)
T PF07384_consen 37 KFNQEMQAEFHERIKKLGGKN 57 (59)
T ss_pred HhhHHHHHHHHHHHHHhcccc
Confidence 478899999999999999853
No 24
>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=49.69 E-value=14 Score=28.95 Aligned_cols=50 Identities=22% Similarity=0.317 Sum_probs=37.5
Q ss_pred CCCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 45 KVPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 45 kK~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
....|||...+-..+.+||+.--- .+-.+++. ...||.++|=+-||.|..
T Consensus 45 AACGFRWNs~VRkqY~~~i~~AKk-qRk~~~~~-----~~~ltl~~vI~fLq~l~~ 94 (161)
T TIGR02894 45 AACGFRWNAYVRKQYEEAIELAKK-QRKELKRE-----AGSLTLQDVISFLQNLKT 94 (161)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHH-HHhccccC-----cccCCHHHHHHHHHHHHh
Confidence 478999999999999999987651 11111111 256999999999999985
No 25
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=49.63 E-value=22 Score=34.01 Aligned_cols=43 Identities=28% Similarity=0.305 Sum_probs=34.2
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHH
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKS 93 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkS 93 (119)
-..-.||++.-.+.++||..+||.+ |-+|.+. ||+.+..|.+-
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kd---w~k~R~~--vPnRSdsQcR~ 400 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKD---WAKVRQA--VPNRSDSQCRE 400 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccc---hhhHHHh--cCCccHHHHHH
Confidence 4567899999999999999999875 4555555 58888777763
No 26
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=47.40 E-value=27 Score=22.11 Aligned_cols=33 Identities=24% Similarity=0.415 Sum_probs=26.0
Q ss_pred chhhHHhhhCC---CCCCHHHHHHhhhhhhhccccC
Q 041956 73 TPKLVLQLMNI---KGLSIAHVKSHLQMYRSKKIDD 105 (119)
Q Consensus 73 ~PK~IlelM~v---~gLT~~~VkSHLQKYR~~~~~~ 105 (119)
+...+++.+++ .|||.++|...+++|=.+....
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~~~~G~N~l~~ 40 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERRKKYGPNELPE 40 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHHHHHSSSSTTT
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHHHhcccccccc
Confidence 45677778773 7999999999999997765533
No 27
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=43.07 E-value=57 Score=17.85 Aligned_cols=27 Identities=19% Similarity=0.237 Sum_probs=21.7
Q ss_pred CchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 72 ATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 72 A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
-+++.|.+.||+ +...|.+++++.+.+
T Consensus 27 ~~~~~ia~~~~~---s~~~i~~~~~~~~~~ 53 (55)
T cd06171 27 LSYEEIAEILGI---SRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHHHHHHH
Confidence 478999999875 889999888877653
No 28
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=41.84 E-value=63 Score=23.22 Aligned_cols=40 Identities=30% Similarity=0.335 Sum_probs=25.7
Q ss_pred ceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHh
Q 041956 48 RLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSH 94 (119)
Q Consensus 48 Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSH 94 (119)
--||+..--...|.|| .||. -..-+.|.-.+||.+.+.+-
T Consensus 30 t~RWva~RKAaVV~aV--~~Gl-----is~~EA~~rY~Ls~eEf~~W 69 (90)
T PF06627_consen 30 TRRWVARRKAAVVRAV--RGGL-----ISVEEACRRYGLSEEEFESW 69 (90)
T ss_dssp -S---HHHHHHHHHHH--HCTT-----S-HHHHHHCTTSSHHHHHHH
T ss_pred cccchhhHHHHHHHHH--HcCC-----CCHHHHHHHhCCCHHHHHHH
Confidence 3489999999999999 5654 23456666678898887653
No 29
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=41.29 E-value=51 Score=24.09 Aligned_cols=45 Identities=11% Similarity=0.229 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 54 DLHRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 54 ELH~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
+++..|.+|+..|.-. +.-+++.|.+.||+ |...|++|+++=|.+
T Consensus 127 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tv~~~l~Rar~~ 181 (193)
T PRK11923 127 EIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQC---PVGTVRSRIFRAREA 181 (193)
T ss_pred HHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHH
Confidence 3456677777777622 22356666677664 788888888766653
No 30
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=38.80 E-value=26 Score=20.27 Aligned_cols=19 Identities=21% Similarity=0.419 Sum_probs=12.0
Q ss_pred HHhhhCCCCCCHHHHHHhhh
Q 041956 77 VLQLMNIKGLSIAHVKSHLQ 96 (119)
Q Consensus 77 IlelM~v~gLT~~~VkSHLQ 96 (119)
|.+.|. .|+|.++|+..|+
T Consensus 9 i~eA~~-~Gls~eeir~FL~ 27 (30)
T PF08671_consen 9 IKEAKE-SGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHH-TT--HHHHHHHHH
T ss_pred HHHHHH-cCCCHHHHHHHHH
Confidence 344454 4899999999886
No 31
>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=37.63 E-value=85 Score=18.54 Aligned_cols=26 Identities=23% Similarity=0.281 Sum_probs=18.3
Q ss_pred CchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 72 ATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 72 A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
-+.+.|.+.||+ |...|+++|++=|.
T Consensus 27 ~s~~eIa~~l~~---s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 27 MSYAEIAEILGI---SESTVKRRLRRARK 52 (54)
T ss_dssp --HHHHHHHCTS----HHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCc---CHHHHHHHHHHHHh
Confidence 467888888864 89999999886543
No 32
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=37.56 E-value=77 Score=22.07 Aligned_cols=47 Identities=15% Similarity=0.194 Sum_probs=29.4
Q ss_pred CHHHHHHHHHHHHHhCC----------CCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 52 TPDLHRCFVQAVERLGG----------QERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 52 T~ELH~kFv~Av~~LGg----------~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
..+++..+..|+..|.- .+.-+.+.|.+.||+ |...|++++..=|.+
T Consensus 98 ~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~i---s~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 98 SEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGR---TVNAVYKALSRLRVR 154 (159)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCC---CHHHHHHHHHHHHHH
Confidence 34556667777777661 123356667777654 788888887665543
No 33
>cd08783 Death_MALT1 Death domain similar to that found in Mucosa-associated lymphoid tissue-lymphoma-translocation gene 1. Death domain (DD) similar to that found in Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1). Malt1, together with Bcl10 (B-cell lymphoma 10), are the integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. 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
Probab=37.14 E-value=68 Score=23.35 Aligned_cols=49 Identities=24% Similarity=0.484 Sum_probs=39.0
Q ss_pred CCceecCH-HHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhh
Q 041956 46 VPRLRWTP-DLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMY 98 (119)
Q Consensus 46 K~Rl~WT~-ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKY 98 (119)
..||+-++ |++++-+..++.-|- .-+..|+.|++.|-|..+.-.-||.-
T Consensus 35 ~~~fr~S~~el~~cslkvl~p~gS----Psk~LL~~~~~rg~Tv~~Ll~~L~~M 84 (97)
T cd08783 35 RGRFRLSCLDLEQCSLKVLEPEGS----PSRSLLKLLGERGCTVTELSEFLQAM 84 (97)
T ss_pred CCccccCHHHHHHHHHHHhcCCCC----chHHHHHHHHHcCCcHHHHHHHHHHh
Confidence 35899988 888888777776662 34668999999999999998888863
No 34
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=36.76 E-value=78 Score=22.39 Aligned_cols=43 Identities=19% Similarity=0.209 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 56 HRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 56 H~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
...++.|+..|... ++-+.+.|.+.||+ |...|++||..=|.+
T Consensus 103 ~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgi---s~~tv~~~l~Rar~~ 155 (161)
T PRK12541 103 IASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGL---SLAKVKIELHRGRKE 155 (161)
T ss_pred HHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHH
Confidence 34567777777631 33456667777764 788899988776654
No 35
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=34.99 E-value=95 Score=22.73 Aligned_cols=49 Identities=6% Similarity=0.024 Sum_probs=34.1
Q ss_pred eecCHHHHHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 49 LRWTPDLHRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 49 l~WT~ELH~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
..+.+++.....++++.|... +.-+.+.|.+.||+ |...|+++|..=+.
T Consensus 118 ~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgi---s~~tV~~~l~Ra~~ 176 (188)
T PRK09640 118 KAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHM---GLSATKMRYKRALD 176 (188)
T ss_pred ccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHH
Confidence 345677788888888888732 22366777788765 77888888765443
No 36
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=34.46 E-value=89 Score=18.14 Aligned_cols=38 Identities=13% Similarity=0.246 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 55 LHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 55 LH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
.....+..+.. | .+.+.|.+.+|+ ++..|..-+..|+.
T Consensus 6 ~R~~ii~l~~~-G----~s~~~ia~~lgv---s~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 6 RRAQIIRLLRE-G----WSIREIAKRLGV---SRSTVYRWIKRYRE 43 (50)
T ss_dssp ----HHHHHHH-T------HHHHHHHHTS----HHHHHHHHT----
T ss_pred HHHHHHHHHHC-C----CCHHHHHHHHCc---CHHHHHHHHHHccc
Confidence 34445666665 4 478999999976 78888888888874
No 37
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=33.31 E-value=60 Score=20.65 Aligned_cols=28 Identities=11% Similarity=0.201 Sum_probs=21.7
Q ss_pred HHHHHHHHHhC-CCCCCchhhHHhhhCCC
Q 041956 57 RCFVQAVERLG-GQERATPKLVLQLMNIK 84 (119)
Q Consensus 57 ~kFv~Av~~LG-g~~~A~PK~IlelM~v~ 84 (119)
..++.||..|+ +....+++.|.+.|++.
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs 35 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLGVS 35 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHTS-
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHCCC
Confidence 46889998886 23558899999999983
No 38
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=32.86 E-value=41 Score=22.23 Aligned_cols=27 Identities=19% Similarity=0.187 Sum_probs=22.5
Q ss_pred hhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 74 PKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 74 PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
....+++||...+|+.+|-+++-+|-.
T Consensus 8 s~~L~~~lg~~~~sr~~v~~~lw~YIk 34 (76)
T PF02201_consen 8 SPELAEFLGEDELSRSEVVKRLWQYIK 34 (76)
T ss_dssp HHHHHHHTT-SCEEHHHHHHHHHHHHH
T ss_pred CHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence 345778899988999999999999976
No 39
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=32.21 E-value=83 Score=28.60 Aligned_cols=44 Identities=18% Similarity=0.192 Sum_probs=38.3
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhh
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHL 95 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHL 95 (119)
..+-.||...-...++||+.+| ..|.+|..+++ ..|.++.-.|.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~----ddW~kVa~hVg--~ks~eqCI~kF 294 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYG----DDWNKVADHVG--TKSQEQCILKF 294 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhc----ccHHHHHhccC--CCCHHHHHHHH
Confidence 5677899999999999999999 36999999988 47999987774
No 40
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=31.90 E-value=35 Score=24.28 Aligned_cols=18 Identities=44% Similarity=0.538 Sum_probs=14.1
Q ss_pred CCCHHHHHHhhhhhhhcc
Q 041956 85 GLSIAHVKSHLQMYRSKK 102 (119)
Q Consensus 85 gLT~~~VkSHLQKYR~~~ 102 (119)
-||.++|+..||+|+.+.
T Consensus 8 FlTYdevk~~L~~~~~kp 25 (86)
T PF02762_consen 8 FLTYDEVKARLQHYRDKP 25 (86)
T ss_dssp T--HHHHHHHHGGGTTST
T ss_pred EEeHHHHHHHHHHHhCCc
Confidence 389999999999999863
No 41
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=31.80 E-value=93 Score=22.48 Aligned_cols=28 Identities=18% Similarity=0.218 Sum_probs=22.1
Q ss_pred CchhhHHhhhCCCCCCHHHHHHhhhhhhhcc
Q 041956 72 ATPKLVLQLMNIKGLSIAHVKSHLQMYRSKK 102 (119)
Q Consensus 72 A~PK~IlelM~v~gLT~~~VkSHLQKYR~~~ 102 (119)
-+++.|.+.||+ |...|+++|++-|.+.
T Consensus 152 ~s~~eIA~~lgi---s~~~V~~~l~ra~~~L 179 (186)
T PRK13919 152 YTHREAAQLLGL---PLGTLKTRARRALSRL 179 (186)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHHHHHHHH
Confidence 467888888875 7899999998877653
No 42
>PF09274 ParG: ParG; InterPro: IPR015354 This entry represents plasmid partition proteins; it adopts a ribbon-helix-helix fold, with a core of four alpha-helices. The proteins are an essential component of the DNA partition complex of the multi drug resistance plasmid TP228 []. ; PDB: 1P94_B.
Probab=31.48 E-value=64 Score=22.39 Aligned_cols=27 Identities=26% Similarity=0.369 Sum_probs=20.5
Q ss_pred cccCCCCceecCHHHHHHHHHHHHHhC
Q 041956 41 YVRSKVPRLRWTPDLHRCFVQAVERLG 67 (119)
Q Consensus 41 ~~~~kK~Rl~WT~ELH~kFv~Av~~LG 67 (119)
....|+-.+.-.+++|.+|=.|--.-|
T Consensus 31 s~k~Krvtv~i~EelH~r~K~~ca~~G 57 (76)
T PF09274_consen 31 SEKTKRVTVNIDEELHRRFKAACAKQG 57 (76)
T ss_dssp TTTEEEE-EEEEHHHHHHHHHHHHHHT
T ss_pred ccceEEEEEecCHHHHHHHHHHHHHcC
Confidence 334566778889999999988777778
No 43
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.11 E-value=93 Score=21.90 Aligned_cols=27 Identities=11% Similarity=0.041 Sum_probs=20.1
Q ss_pred CchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 72 ATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 72 A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
-+.+.|.+.|| ++...|++||..-|.+
T Consensus 123 ~s~~EIA~~lg---is~~tV~~~l~Rar~~ 149 (160)
T PRK09642 123 KSYQEIALQEK---IEVKTVEMKLYRARKW 149 (160)
T ss_pred CCHHHHHHHHC---CCHHHHHHHHHHHHHH
Confidence 45666777776 4888899998877764
No 44
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=31.04 E-value=1.6e+02 Score=20.75 Aligned_cols=49 Identities=16% Similarity=0.107 Sum_probs=34.8
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
++|-+||+|+ .++||.++- ....+...|..-+|| +...|..=.++|+..
T Consensus 8 ~~rr~ys~Ef---K~~aV~~~~-~~g~sv~evA~e~gI---s~~tl~~W~r~y~~~ 56 (121)
T PRK09413 8 EKRRRRTTQE---KIAIVQQSF-EPGMTVSLVARQHGV---AASQLFLWRKQYQEG 56 (121)
T ss_pred CCCCCCCHHH---HHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHhhc
Confidence 4567799998 567776653 233466677777654 888898889999864
No 45
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=30.71 E-value=33 Score=22.92 Aligned_cols=29 Identities=21% Similarity=0.243 Sum_probs=22.8
Q ss_pred CCCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 69 QERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 69 ~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
.+.++.+.|.+..+ +|..++.+||++-..
T Consensus 12 ~~~~~f~~L~~~l~---lt~g~Ls~hL~~Le~ 40 (80)
T PF13601_consen 12 NEEATFSELKEELG---LTDGNLSKHLKKLEE 40 (80)
T ss_dssp HSEEEHHHHHHHTT-----HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhC---cCHHHHHHHHHHHHH
Confidence 45688899999986 599999999998765
No 46
>PF05534 HicB: HicB family; InterPro: IPR008651 This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches [].
Probab=30.17 E-value=87 Score=19.54 Aligned_cols=24 Identities=38% Similarity=0.527 Sum_probs=20.6
Q ss_pred CCCCceecCHHHHHHHHHHHHHhC
Q 041956 44 SKVPRLRWTPDLHRCFVQAVERLG 67 (119)
Q Consensus 44 ~kK~Rl~WT~ELH~kFv~Av~~LG 67 (119)
+++=-+|-+++||++...+-..-|
T Consensus 17 sg~~~lRi~~~Lh~~l~~~A~~~g 40 (51)
T PF05534_consen 17 SGKFNLRIPPELHRALAEAAAAEG 40 (51)
T ss_pred CCceeeeCCHHHHHHHHHHHHHhC
Confidence 357788999999999998888777
No 47
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=29.36 E-value=1.2e+02 Score=17.64 Aligned_cols=53 Identities=23% Similarity=0.154 Sum_probs=37.1
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
+.|..++++- ..+++++.... .-.++..|.++...-||+..+|..-.+.-|..
T Consensus 2 ~~r~~~~~~~-~~~Le~~f~~~--~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (59)
T cd00086 2 RKRTRFTPEQ-LEELEKEFEKN--PYPSREEREELAKELGLTERQVKIWFQNRRAK 54 (59)
T ss_pred CCCCcCCHHH-HHHHHHHHHhC--CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 3455666654 55666666664 24566778788777789999999988877764
No 48
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=28.70 E-value=2e+02 Score=19.72 Aligned_cols=35 Identities=20% Similarity=0.378 Sum_probs=28.2
Q ss_pred CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhccccCC
Q 041956 70 ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSKKIDDH 106 (119)
Q Consensus 70 ~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~~~~~~ 106 (119)
.+.|...|.+.+| +=+..-|..||+-||.......
T Consensus 18 ~~pT~~~Vr~~lG--~GS~~ti~~~l~~w~~~~~~~~ 52 (120)
T PF11740_consen 18 KKPTVRAVRERLG--GGSMSTISKHLKEWREEREAQV 52 (120)
T ss_pred CCCCHHHHHHHHC--CCCHHHHHHHHHHHHHhhhccc
Confidence 5788999999998 4688889999999998644443
No 49
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=28.62 E-value=89 Score=22.43 Aligned_cols=49 Identities=18% Similarity=0.197 Sum_probs=31.2
Q ss_pred ecCHHHHHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 50 RWTPDLHRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 50 ~WT~ELH~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
.|..+.-.....|+..|... +.-+.+.|.+.||+ +...|++||..=|.+
T Consensus 104 ~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgi---s~~tV~~~l~Ra~~~ 162 (173)
T PRK12522 104 FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNI---PIGTVKYRLNYAKKQ 162 (173)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCC---CHHHHHHHHHHHHHH
Confidence 34445445555666665531 33466778888875 789999998866653
No 50
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=28.45 E-value=1.3e+02 Score=17.53 Aligned_cols=34 Identities=29% Similarity=0.419 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhh
Q 041956 58 CFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMY 98 (119)
Q Consensus 58 kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKY 98 (119)
-..+|++..||. .....+.+| +++..+.-.|+||
T Consensus 9 ~i~~aL~~~~gn----~~~aA~~Lg---isr~tL~~klkk~ 42 (42)
T PF02954_consen 9 LIRQALERCGGN----VSKAARLLG---ISRRTLYRKLKKY 42 (42)
T ss_dssp HHHHHHHHTTT-----HHHHHHHHT---S-HHHHHHHHHHC
T ss_pred HHHHHHHHhCCC----HHHHHHHHC---CCHHHHHHHHHhC
Confidence 346788888873 466777776 4888888888887
No 51
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.21 E-value=1e+02 Score=22.74 Aligned_cols=44 Identities=16% Similarity=0.175 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 54 DLHRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 54 ELH~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
++...+..|+.+|... +.-+-+.|.+.|| ++...|++||..=|.
T Consensus 123 ~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lg---is~~tVk~~l~RAr~ 176 (189)
T PRK12530 123 EFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECD---ISTSNLHVLLYRARL 176 (189)
T ss_pred HHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHH
Confidence 3445567777777621 2234555666665 488889998876554
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=28.09 E-value=1.4e+02 Score=20.71 Aligned_cols=45 Identities=11% Similarity=-0.017 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 54 DLHRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 54 ELH~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
++...+..|+.+|... +.-+.+.|.+.|| ++...|++++..=+.+
T Consensus 95 ~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~---is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 95 DVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETE---MTYYQVRWIYRQALEK 149 (154)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHH
Confidence 3445566666666521 2335555666665 4777788877665543
No 53
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=27.86 E-value=1.8e+02 Score=20.10 Aligned_cols=43 Identities=28% Similarity=0.355 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 56 HRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 56 H~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
...+..+++.|.-. +.-+.+.|.+.||+ +...|+++|..-|.+
T Consensus 96 ~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgi---s~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 96 QEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNL---SLAKVKSNLFRARKE 148 (154)
T ss_pred HHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCC---CHHHHHHHHHHHHHH
Confidence 34566777777621 22356667777764 678888887776654
No 54
>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=27.29 E-value=72 Score=21.04 Aligned_cols=44 Identities=23% Similarity=0.396 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCCCC----CchhhHHhhhCCCCCCH---HHHHHhhhhh
Q 041956 54 DLHRCFVQAVERLGGQER----ATPKLVLQLMNIKGLSI---AHVKSHLQMY 98 (119)
Q Consensus 54 ELH~kFv~Av~~LGg~~~----A~PK~IlelM~v~gLT~---~~VkSHLQKY 98 (119)
+|+.-| .+|...||.+. -.|..|.+.||++.... ..++.|=.+|
T Consensus 37 DL~~Ly-~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~ 87 (92)
T PF01388_consen 37 DLYKLY-KAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKY 87 (92)
T ss_dssp SHHHHH-HHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHH
T ss_pred cHHHHH-HHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHH
Confidence 677766 56778898743 35999999999964322 4566665555
No 55
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=27.00 E-value=1.4e+02 Score=22.98 Aligned_cols=26 Identities=15% Similarity=0.112 Sum_probs=19.6
Q ss_pred CCCCchhhHHhhhCCCCCCHHHHHHhhhh
Q 041956 69 QERATPKLVLQLMNIKGLSIAHVKSHLQM 97 (119)
Q Consensus 69 ~~~A~PK~IlelM~v~gLT~~~VkSHLQK 97 (119)
.+..+.+.|.+.||+ |...|++|+..
T Consensus 193 ~e~~S~~EIA~~lgi---s~~tV~~~~~r 218 (233)
T PRK05803 193 GKEKTQREIAKALGI---SRSYVSRIEKR 218 (233)
T ss_pred CCCcCHHHHHHHHCc---CHHHHHHHHHH
Confidence 355678889888875 78888888654
No 56
>PF08127 Propeptide_C1: Peptidase family C1 propeptide; InterPro: IPR012599 This domain is found at the N-terminal of cathepsin B and cathepsin B-like peptidases that belong to MEROPS peptidase subfamily C1A. Cathepsin B are lysosomal cysteine proteinases belonging to the papain superfamily and are unique in their ability to act as both an endo- and an exopeptidases. They are synthesized as inactive zymogens. Activation of the peptidases occurs with the removal of the propeptide [, ]. ; GO: 0004197 cysteine-type endopeptidase activity, 0050790 regulation of catalytic activity; PDB: 1MIR_A 1PBH_A 2PBH_A 3PBH_A.
Probab=26.77 E-value=48 Score=20.11 Aligned_cols=35 Identities=23% Similarity=0.169 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhh
Q 041956 55 LHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQ 96 (119)
Q Consensus 55 LH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQ 96 (119)
|-+.|++-|+...- +||+=.. +++.|..+|++.|-
T Consensus 1 Lsde~I~~IN~~~~----tWkAG~N---F~~~~~~~ik~LlG 35 (41)
T PF08127_consen 1 LSDEFIDYINSKNT----TWKAGRN---FENTSIEYIKRLLG 35 (41)
T ss_dssp S-HHHHHHHHHCT-----SEEE-------SSB-HHHHHHCS-
T ss_pred CCHHHHHHHHcCCC----cccCCCC---CCCCCHHHHHHHcC
Confidence 34678999998864 4443222 46677777776654
No 57
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=26.48 E-value=2.6e+02 Score=20.40 Aligned_cols=44 Identities=16% Similarity=0.303 Sum_probs=29.6
Q ss_pred CceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 47 PRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 47 ~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
.-+.=..++|++...-|..+|+. +.+--.+++ .=++-||..|+.
T Consensus 81 ~~vyI~~e~h~~l~~Iv~~ig~~-~~si~~yid---------NIL~~Hle~~~e 124 (136)
T PF11888_consen 81 KGVYISRETHERLSRIVRVIGER-KMSISGYID---------NILRHHLEEYRE 124 (136)
T ss_pred eeeEECHHHHHHHHHHHHHHCCC-CCcHHHHHH---------HHHHHHHHHHHH
Confidence 34888999999999999999853 233222221 125688888875
No 58
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=26.17 E-value=53 Score=21.86 Aligned_cols=28 Identities=29% Similarity=0.609 Sum_probs=21.5
Q ss_pred CCCCCCHHHHHHhhhhhhhccccCCCCc
Q 041956 82 NIKGLSIAHVKSHLQMYRSKKIDDHGQG 109 (119)
Q Consensus 82 ~v~gLT~~~VkSHLQKYR~~~~~~~g~~ 109 (119)
.+.++|.+++|.+|-+|+-..+.+...|
T Consensus 8 p~~~~~v~d~K~~Lr~y~~~~I~~d~tG 35 (66)
T PF11767_consen 8 PVHGVTVEDFKKRLRKYRWDRIRDDRTG 35 (66)
T ss_pred CCCCccHHHHHHHHhcCCcceEEecCCE
Confidence 3457899999999999998666554443
No 59
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=25.53 E-value=1.5e+02 Score=20.25 Aligned_cols=27 Identities=19% Similarity=0.226 Sum_probs=18.6
Q ss_pred CchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 72 ATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 72 A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
.+++.|.+.||+ +...|++++..=+.+
T Consensus 130 ~~~~eIA~~lgi---s~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 130 KSYKEIAEELGI---SVKTVEYHISKALKE 156 (161)
T ss_pred CCHHHHHHHHCC---CHHHHHHHHHHHHHH
Confidence 466777777764 788888887665543
No 60
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=24.68 E-value=2.1e+02 Score=18.97 Aligned_cols=43 Identities=12% Similarity=0.230 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 53 PDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 53 ~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
+++..+.+.++.+-| .++...|.+.+| ++...|..++++-...
T Consensus 2 d~~D~~il~~L~~~~---~~~~~~la~~l~---~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 2 DEIDRKILEELQKDA---RISLAELAKKVG---LSPSTVHNRVKRLEEE 44 (108)
T ss_pred CHHHHHHHHHHHHhC---CCCHHHHHHHHC---cCHHHHHHHHHHHHHC
Confidence 357788999998876 367888888886 5888999998887763
No 61
>PF14383 VARLMGL: DUF761-associated sequence motif
Probab=24.06 E-value=59 Score=19.56 Aligned_cols=21 Identities=24% Similarity=0.397 Sum_probs=16.1
Q ss_pred CCCCchhhHHhhhCCCCCCHH
Q 041956 69 QERATPKLVLQLMNIKGLSIA 89 (119)
Q Consensus 69 ~~~A~PK~IlelM~v~gLT~~ 89 (119)
....+|-.|..|||++.|-..
T Consensus 10 ~~~r~P~vvarLMGld~lP~~ 30 (34)
T PF14383_consen 10 PGTRAPGVVARLMGLDSLPDS 30 (34)
T ss_pred ccccChhHHHHHhccccCCcc
Confidence 445789999999999776543
No 62
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=22.46 E-value=1.9e+02 Score=18.96 Aligned_cols=26 Identities=31% Similarity=0.443 Sum_probs=18.4
Q ss_pred chhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 73 TPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 73 ~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
++..|.+.||+ |...|..++++-+.+
T Consensus 128 s~~eIA~~l~~---s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 128 SYKEIAEILGI---SVGTVKRRLKRARKK 153 (158)
T ss_pred CHHHHHHHHCC---CHHHHHHHHHHHHHH
Confidence 56777777765 777777777766544
No 63
>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=22.43 E-value=1.7e+02 Score=23.25 Aligned_cols=45 Identities=27% Similarity=0.228 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhcc
Q 041956 55 LHRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSKK 102 (119)
Q Consensus 55 LH~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~~ 102 (119)
+...+..|+.+|.-. +.-+-+.|.+.|| ++...|++||+.=|.+.
T Consensus 132 ~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lg---is~~tV~~~l~Rar~~L 186 (324)
T TIGR02960 132 VRLAFVAAIQYLPPRQRAVLLLRDVLGWRAAETAELLG---TSTASVNSALQRARATL 186 (324)
T ss_pred HHHHHHHHHHhCCHHHhhHhhhHHHhCCCHHHHHHHHC---CCHHHHHHHHHHHHHHH
Confidence 445577777777622 1234555666665 48889999998877643
No 64
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=22.20 E-value=1.7e+02 Score=16.87 Aligned_cols=40 Identities=15% Similarity=0.130 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 55 LHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 55 LH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
-..+-+.++..-|+ ++.+.|.+.+| +|...|..||++-..
T Consensus 4 ~~~~Il~~l~~~~~---~t~~ela~~~~---is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 4 TQRKILNYLRENPR---ITQKELAEKLG---ISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHHHHHHHCTT---S-HHHHHHHHT---S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCC---CCHHHHHHHhC---CCHHHHHHHHHHHHH
Confidence 45566777877563 68888999987 599999999987654
No 65
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=22.20 E-value=2e+02 Score=20.87 Aligned_cols=45 Identities=18% Similarity=0.152 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 54 DLHRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 54 ELH~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
+.......++..|... ++-+.+.|.+.||+ +...|++||.+-|.+
T Consensus 116 e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~i---s~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 116 AEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGV---NENTVKTRLKKAKEL 170 (179)
T ss_pred HHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHH
Confidence 3344455566655521 22356677777764 888899999887764
No 66
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=21.87 E-value=1.7e+02 Score=20.49 Aligned_cols=27 Identities=26% Similarity=0.304 Sum_probs=20.7
Q ss_pred CchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 72 ATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 72 A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
-+.+.|.+.||+ +...|++|+..=|.+
T Consensus 127 ~s~~eIA~~lgi---s~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 127 LSEAQVAEALGI---SVGTVKSRLSRALAR 153 (162)
T ss_pred CCHHHHHHHhCC---CHHHHHHHHHHHHHH
Confidence 467778888865 789999998776654
No 67
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=21.79 E-value=1.2e+02 Score=18.83 Aligned_cols=47 Identities=21% Similarity=0.294 Sum_probs=29.5
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhh
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYR 99 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR 99 (119)
+.|-+||+|+-...|..+..-| ..|.+++.--|++...+..=+.+|+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-------~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-------ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-------CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-------CceEeeecccccccccccHHHHHHh
Confidence 3567899999998888884445 2444444445678888888888887
No 68
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=21.58 E-value=1.5e+02 Score=17.92 Aligned_cols=27 Identities=30% Similarity=0.254 Sum_probs=20.3
Q ss_pred CchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 72 ATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 72 A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
-+++.|.+.|++ +..-|++|+..-+.+
T Consensus 19 ~~~~eIA~~l~i---s~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 19 MSNKEIAEELGI---SEKTVKSHRRRIMKK 45 (58)
T ss_dssp S-HHHHHHHHTS---HHHHHHHHHHHHHHH
T ss_pred CCcchhHHhcCc---chhhHHHHHHHHHHH
Confidence 579999999986 777888887766554
No 69
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.57 E-value=1.6e+02 Score=16.36 Aligned_cols=27 Identities=33% Similarity=0.309 Sum_probs=21.5
Q ss_pred CchhhHHhhhCCCCCCHHHHHHhhhhhhhc
Q 041956 72 ATPKLVLQLMNIKGLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 72 A~PK~IlelM~v~gLT~~~VkSHLQKYR~~ 101 (119)
.+.+.|.+.|++ +...|.+|++..+.+
T Consensus 19 ~s~~eia~~l~i---s~~tv~~~~~~~~~k 45 (58)
T smart00421 19 LTNKEIAERLGI---SEKTVKTHLSNIMRK 45 (58)
T ss_pred CCHHHHHHHHCC---CHHHHHHHHHHHHHH
Confidence 367889999875 889999998876654
No 70
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=21.11 E-value=1.9e+02 Score=16.83 Aligned_cols=52 Identities=21% Similarity=0.118 Sum_probs=34.3
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHHhhhhhhh
Q 041956 46 VPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKSHLQMYRS 100 (119)
Q Consensus 46 K~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~ 100 (119)
++|..+|++- ...++++.... ...++..|.++...-|||..+|..=.+.-|.
T Consensus 2 k~r~~~~~~~-~~~L~~~f~~~--~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (56)
T smart00389 2 RKRTSFTPEQ-LEELEKEFQKN--PYPSREEREELAAKLGLSERQVKVWFQNRRA 53 (56)
T ss_pred CCCCcCCHHH-HHHHHHHHHhC--CCCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence 4566676654 44556665555 2456677777777778999999876665554
No 71
>PF14075 UBN_AB: Ubinuclein conserved middle domain
Probab=21.07 E-value=1.1e+02 Score=24.58 Aligned_cols=21 Identities=14% Similarity=0.501 Sum_probs=16.6
Q ss_pred CCCCceecCHHHHHHHHHHHH
Q 041956 44 SKVPRLRWTPDLHRCFVQAVE 64 (119)
Q Consensus 44 ~kK~Rl~WT~ELH~kFv~Av~ 64 (119)
.-+.+|.||+++-..+.+-|.
T Consensus 148 ~PrKkF~Wtde~R~lL~~lv~ 168 (214)
T PF14075_consen 148 GPRKKFQWTDEIRELLCELVK 168 (214)
T ss_pred CCCcCCCCCHHHHHHHHHHHH
Confidence 447899999999888866554
No 72
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=20.89 E-value=1.8e+02 Score=26.45 Aligned_cols=43 Identities=23% Similarity=0.336 Sum_probs=32.6
Q ss_pred CCCceecCHHHHHHHHHHHHHhCCCCCCchhhHHhhhCCCCCCHHHHHH
Q 041956 45 KVPRLRWTPDLHRCFVQAVERLGGQERATPKLVLQLMNIKGLSIAHVKS 93 (119)
Q Consensus 45 kK~Rl~WT~ELH~kFv~Av~~LGg~~~A~PK~IlelM~v~gLT~~~VkS 93 (119)
++.-.+||...-.+|-.|+.+.|- + -.-|..| .|...+.||+-
T Consensus 362 ~~~~~~Ws~~e~ekFYKALs~wGt-d---F~LIs~l--fP~R~RkqIKa 404 (507)
T COG5118 362 KKGALRWSKKEIEKFYKALSIWGT-D---FSLISSL--FPNRERKQIKA 404 (507)
T ss_pred CCCCCcccHHHHHHHHHHHHHhcc-h---HHHHHHh--cCchhHHHHHH
Confidence 577899999999999999999993 2 2334444 36677777774
No 73
>KOG2983 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.65 E-value=79 Score=27.34 Aligned_cols=17 Identities=35% Similarity=0.743 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHhCCC
Q 041956 53 PDLHRCFVQAVERLGGQ 69 (119)
Q Consensus 53 ~ELH~kFv~Av~~LGg~ 69 (119)
+|||++.-+||+.|||.
T Consensus 85 ~El~qki~eaineLGga 101 (334)
T KOG2983|consen 85 PELEQKIREAINELGGA 101 (334)
T ss_pred HHHHHHHHHHHHHccce
Confidence 39999999999999985
No 74
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.22 E-value=2e+02 Score=22.82 Aligned_cols=48 Identities=19% Similarity=0.084 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHhCCC----------CCCchhhHHhhhCCCCCCHHHHHHhhhhhhhcccc
Q 041956 54 DLHRCFVQAVERLGGQ----------ERATPKLVLQLMNIKGLSIAHVKSHLQMYRSKKID 104 (119)
Q Consensus 54 ELH~kFv~Av~~LGg~----------~~A~PK~IlelM~v~gLT~~~VkSHLQKYR~~~~~ 104 (119)
++...|..+++.|.-. +.-+-+.|.+.|| +|...|+++|+.=|.+.+.
T Consensus 104 ~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg---~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 104 DLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLG---RSPAACRQLASRARKHVRA 161 (293)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHh
Confidence 3344577777777622 2235566777775 4899999999877765443
No 75
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=20.16 E-value=57 Score=29.69 Aligned_cols=17 Identities=41% Similarity=0.432 Sum_probs=15.6
Q ss_pred CCCHHHHHHhhhhhhhc
Q 041956 85 GLSIAHVKSHLQMYRSK 101 (119)
Q Consensus 85 gLT~~~VkSHLQKYR~~ 101 (119)
-||.+.|+-.||||+.+
T Consensus 262 FLTYDEVk~RLqk~~~K 278 (563)
T KOG1785|consen 262 FLTYDEVKARLQKYIKK 278 (563)
T ss_pred EeeHHHHHHHHHHHhcC
Confidence 39999999999999986
Done!