Query 035517
Match_columns 161
No_of_seqs 149 out of 315
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:38:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035517.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035517hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03162 golden-2 like transcr 99.9 1.1E-25 2.4E-30 202.4 8.5 60 88-148 232-291 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.9 5.9E-25 1.3E-29 149.9 6.6 57 91-147 1-57 (57)
3 PF00249 Myb_DNA-binding: Myb- 98.6 8.1E-08 1.7E-12 61.6 5.5 48 93-144 1-48 (48)
4 cd00167 SANT 'SWI3, ADA2, N-Co 96.9 0.0041 8.8E-08 36.9 5.6 44 95-143 1-44 (45)
5 smart00717 SANT SANT SWI3, AD 96.9 0.0041 8.9E-08 37.2 5.7 44 94-143 2-46 (49)
6 smart00426 TEA TEA domain. 96.2 0.0058 1.3E-07 43.9 3.4 46 95-142 5-67 (68)
7 PF13921 Myb_DNA-bind_6: Myb-l 94.0 0.19 4.2E-06 32.7 5.4 41 96-142 1-41 (60)
8 PF01285 TEA: TEA/ATTS domain 93.3 0.059 1.3E-06 49.6 2.6 54 90-143 46-112 (431)
9 PF12776 Myb_DNA-bind_3: Myb/S 91.2 0.32 6.8E-06 34.0 3.7 51 95-145 1-63 (96)
10 KOG3841 TEF-1 and related tran 88.6 0.45 9.6E-06 44.3 3.4 58 91-148 74-146 (455)
11 KOG0457 Histone acetyltransfer 88.4 0.88 1.9E-05 42.5 5.1 48 92-145 71-119 (438)
12 PLN03212 Transcription repress 88.0 1.1 2.4E-05 39.2 5.2 50 90-143 22-71 (249)
13 PLN03212 Transcription repress 84.0 2.8 6E-05 36.7 5.7 53 81-139 66-118 (249)
14 smart00501 BRIGHT BRIGHT, ARID 83.9 1.5 3.2E-05 31.4 3.4 44 99-143 33-83 (93)
15 PLN03091 hypothetical protein; 83.3 2.3 4.9E-05 40.1 5.1 51 89-143 10-60 (459)
16 PLN03091 hypothetical protein; 80.9 5 0.00011 37.9 6.5 56 82-143 56-115 (459)
17 KOG0724 Zuotin and related mol 80.7 0.94 2E-05 38.9 1.6 57 88-150 48-104 (335)
18 COG5114 Histone acetyltransfer 68.9 6.9 0.00015 36.3 4.0 47 94-145 64-110 (432)
19 KOG0048 Transcription factor, 62.1 20 0.00043 29.9 5.3 51 83-139 52-102 (238)
20 PF13837 Myb_DNA-bind_4: Myb/S 57.0 10 0.00022 25.9 2.3 57 93-149 1-73 (90)
21 smart00351 PAX Paired Box doma 54.7 53 0.0011 24.8 6.1 45 94-146 16-60 (125)
22 cd06171 Sigma70_r4 Sigma70, re 54.1 41 0.0009 19.4 4.7 43 96-146 11-53 (55)
23 PF02954 HTH_8: Bacterial regu 45.4 60 0.0013 20.1 4.3 33 104-143 10-42 (42)
24 PF00690 Cation_ATPase_N: Cati 43.8 30 0.00065 23.1 2.9 32 118-149 5-39 (69)
25 cd08783 Death_MALT1 Death doma 41.6 50 0.0011 25.4 4.1 48 92-143 36-84 (97)
26 TIGR02894 DNA_bind_RsfA transc 39.1 24 0.00053 29.2 2.2 48 92-145 47-94 (161)
27 PF00046 Homeobox: Homeobox do 38.9 70 0.0015 20.1 4.0 54 90-146 1-54 (57)
28 PF07384 DUF1497: Protein of u 37.8 34 0.00074 23.9 2.5 20 95-114 37-56 (59)
29 PF01325 Fe_dep_repress: Iron 36.9 42 0.00091 22.6 2.8 40 102-141 7-47 (60)
30 KOG0843 Transcription factor E 36.8 60 0.0013 27.8 4.3 56 88-146 101-156 (197)
31 PRK13919 putative RNA polymera 36.3 88 0.0019 23.8 4.8 28 117-147 152-179 (186)
32 PF08671 SinI: Anti-repressor 36.1 27 0.00058 21.4 1.6 19 122-141 9-27 (30)
33 PRK11923 algU RNA polymerase s 36.0 81 0.0018 24.2 4.6 45 99-146 127-181 (193)
34 TIGR02989 Sig-70_gvs1 RNA poly 35.4 93 0.002 22.8 4.7 46 98-146 99-154 (159)
35 cd00092 HTH_CRP helix_turn_hel 33.5 1.3E+02 0.0027 19.0 5.7 43 102-147 7-53 (67)
36 PRK12541 RNA polymerase sigma 30.2 1.3E+02 0.0027 22.4 4.7 42 102-146 104-155 (161)
37 PRK09413 IS2 repressor TnpA; R 30.0 1.7E+02 0.0036 21.8 5.3 50 91-147 8-57 (121)
38 KOG0049 Transcription factor, 29.8 66 0.0014 32.6 3.9 45 89-138 356-400 (939)
39 PF13601 HTH_34: Winged helix 29.5 38 0.00083 23.9 1.7 29 114-145 12-40 (80)
40 cd00086 homeodomain Homeodomai 29.4 1.4E+02 0.0031 18.3 5.0 53 91-146 2-54 (59)
41 PF13412 HTH_24: Winged helix- 28.5 1.5E+02 0.0032 18.2 4.9 40 100-145 4-43 (48)
42 PF02201 SWIB: SWIB/MDM2 domai 28.5 50 0.0011 23.0 2.1 28 119-146 8-35 (76)
43 PF11767 SET_assoc: Histone ly 27.0 39 0.00084 23.8 1.4 25 125-149 6-30 (66)
44 COG1460 Uncharacterized protei 26.5 1.2E+02 0.0026 23.9 4.1 56 92-150 44-99 (114)
45 TIGR02937 sigma70-ECF RNA poly 26.1 1.7E+02 0.0037 20.1 4.5 26 118-146 128-153 (158)
46 PF11888 DUF3408: Protein of u 25.5 66 0.0014 24.8 2.5 43 94-146 83-125 (136)
47 PF01388 ARID: ARID/BRIGHT DNA 24.9 85 0.0018 21.8 2.8 44 99-143 37-87 (92)
48 TIGR02950 SigM_subfam RNA poly 24.8 2.1E+02 0.0045 20.8 5.0 42 102-146 97-148 (154)
49 PF08281 Sigma70_r4_2: Sigma-7 24.6 1.8E+02 0.004 18.0 4.4 26 117-145 27-52 (54)
50 PF02762 Cbl_N3: CBL proto-onc 24.4 54 0.0012 24.7 1.8 17 131-147 9-25 (86)
51 PRK12530 RNA polymerase sigma 24.2 1.5E+02 0.0033 23.0 4.4 45 99-146 123-177 (189)
52 PF08127 Propeptide_C1: Peptid 24.1 43 0.00092 21.5 1.0 35 100-141 1-35 (41)
53 TIGR02983 SigE-fam_strep RNA p 23.6 1.7E+02 0.0037 21.6 4.4 28 117-147 127-154 (162)
54 PRK00430 fis global DNA-bindin 23.5 1.9E+02 0.0041 21.3 4.5 36 103-145 59-94 (95)
55 smart00344 HTH_ASNC helix_turn 23.5 2.6E+02 0.0056 19.6 5.1 42 99-146 3-44 (108)
56 PRK01905 DNA-binding protein F 23.4 2.1E+02 0.0045 19.9 4.5 37 101-144 39-75 (77)
57 PF13384 HTH_23: Homeodomain-l 22.9 1.8E+02 0.0038 17.8 3.7 38 100-145 6-43 (50)
58 PRK09415 RNA polymerase factor 22.8 1.9E+02 0.0042 22.1 4.7 28 117-147 144-171 (179)
59 KOG1279 Chromatin remodeling f 22.6 1.6E+02 0.0034 28.4 4.8 45 91-141 251-295 (506)
60 PF14383 VARLMGL: DUF761-assoc 22.5 66 0.0014 20.6 1.6 21 114-134 10-30 (34)
61 PRK12522 RNA polymerase sigma 22.3 1.7E+02 0.0036 22.1 4.2 27 117-146 136-162 (173)
62 TIGR02985 Sig70_bacteroi1 RNA 22.1 2.2E+02 0.0047 20.5 4.6 27 117-146 130-156 (161)
63 PRK09642 RNA polymerase sigma 22.1 2.4E+02 0.0052 20.8 4.9 28 117-147 123-150 (160)
64 TIGR03879 near_KaiC_dom probab 20.9 2.5E+02 0.0055 20.2 4.6 45 92-142 11-55 (73)
65 cd02185 AroH Chorismate mutase 20.6 32 0.00068 27.1 -0.1 37 93-130 44-81 (117)
66 PRK05803 sporulation sigma fac 20.3 2.4E+02 0.0051 22.8 4.9 27 114-143 193-219 (233)
67 PF12170 DNA_pol3_tau_5: DNA p 20.2 93 0.002 24.6 2.4 33 97-135 8-41 (142)
68 PRK09640 RNA polymerase sigma 20.2 3.1E+02 0.0066 21.1 5.3 48 95-145 119-176 (188)
69 COG5118 BDP1 Transcription ini 20.1 1.8E+02 0.0039 27.9 4.6 45 89-139 361-405 (507)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.92 E-value=1.1e-25 Score=202.36 Aligned_cols=60 Identities=50% Similarity=0.804 Sum_probs=57.1
Q ss_pred cCCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhccc
Q 035517 88 RSKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSKKL 148 (161)
Q Consensus 88 r~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~kk~ 148 (161)
..||+||+||++||++||+||++|| .++|+||+||++|+|+|||++||||||||||+.+.
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 4689999999999999999999999 79999999999999999999999999999999754
No 2
>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=99.91 E-value=5.9e-25 Score=149.94 Aligned_cols=57 Identities=54% Similarity=0.862 Sum_probs=54.6
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhcc
Q 035517 91 MPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSKK 147 (161)
Q Consensus 91 k~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~kk 147 (161)
|+|++||+|||.+||+||+.||+.+.|+||.|+++|++++||+.||+|||||||++.
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k~ 57 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLKQ 57 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHccC
Confidence 589999999999999999999987999999999999999999999999999999863
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=98.64 E-value=8.1e-08 Score=61.59 Aligned_cols=48 Identities=23% Similarity=0.303 Sum_probs=42.0
Q ss_pred ceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhh
Q 035517 93 RLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYR 144 (161)
Q Consensus 93 RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR 144 (161)
|..||++.+..|++||..+|.. .|+.|...|+ .+.|..||++|.++|+
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 5689999999999999999941 5999999999 6899999999999985
No 4
>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=96.92 E-value=0.0041 Score=36.87 Aligned_cols=44 Identities=11% Similarity=0.178 Sum_probs=38.4
Q ss_pred ecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhh
Q 035517 95 RWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMY 143 (161)
Q Consensus 95 rWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKY 143 (161)
.||++.+..|+.++..+|- ..+..|...|+- .|..+|+.|.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~~--rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELPG--RTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcCC--CCHHHHHHHHHHh
Confidence 4999999999999999992 379999999864 9999999997764
No 5
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=96.91 E-value=0.0041 Score=37.23 Aligned_cols=44 Identities=11% Similarity=0.236 Sum_probs=39.1
Q ss_pred eecCHHHHHHHHHHHHHhC-CCCCCchHHHHHhcCCCCCCHHHHHHHhhhh
Q 035517 94 LRWTPDLHLSFVHAVERLG-GQEKATPKLVLQLMNVRGLSIAHVKSHLQMY 143 (161)
Q Consensus 94 lrWT~ELH~kFv~AV~~LG-G~~kAtPK~ILelM~v~gLT~~~VkSHLQKY 143 (161)
-.||++....|+.++..+| + .+..|...|+ +.|..+|+.+...+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~----~w~~Ia~~~~--~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKN----NWEKIAKELP--GRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcC----CHHHHHHHcC--CCCHHHHHHHHHHH
Confidence 4699999999999999999 4 7999999987 79999999887654
No 6
>smart00426 TEA TEA domain.
Probab=96.19 E-value=0.0058 Score=43.92 Aligned_cols=46 Identities=22% Similarity=0.420 Sum_probs=31.1
Q ss_pred ecCHHHHHHHHHHHHHhCCCCCCchH-HHH-------------HhcC-C--CCCCHHHHHHHhhh
Q 035517 95 RWTPDLHLSFVHAVERLGGQEKATPK-LVL-------------QLMN-V--RGLSIAHVKSHLQM 142 (161)
Q Consensus 95 rWT~ELH~kFv~AV~~LGG~~kAtPK-~IL-------------elM~-v--~gLT~~~VkSHLQK 142 (161)
+|.++|-..|++|+..+- . ..+-| ++. +.+- . .-.|+.||.||||.
T Consensus 5 vWp~~lE~Af~~aL~~~~-~-~g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsShIQv 67 (68)
T smart00426 5 VWSPDIEQAFQEALAIYP-P-CGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQV 67 (68)
T ss_pred cCcHHHHHHHHHHHHHcC-c-cCcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcchhee
Confidence 699999999999999874 2 22222 222 1111 1 24799999999995
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=94.05 E-value=0.19 Score=32.72 Aligned_cols=41 Identities=12% Similarity=0.250 Sum_probs=35.1
Q ss_pred cCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhh
Q 035517 96 WTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQM 142 (161)
Q Consensus 96 WT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQK 142 (161)
||++.-...+.+|..+|. .|+.|.+.|+ ..|..+|+.+...
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 999999999999999984 7999999996 6999999998888
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=93.34 E-value=0.059 Score=49.57 Aligned_cols=54 Identities=19% Similarity=0.298 Sum_probs=30.7
Q ss_pred CCCceecCHHHHHHHHHHHHHhCCCCCCchH----------HHHHhcCC---CCCCHHHHHHHhhhh
Q 035517 90 KMPRLRWTPDLHLSFVHAVERLGGQEKATPK----------LVLQLMNV---RGLSIAHVKSHLQMY 143 (161)
Q Consensus 90 Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK----------~ILelM~v---~gLT~~~VkSHLQKY 143 (161)
....-+|++++...|++|+..+--...+.-+ .|.+.+.. .-.|+.||.||||..
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 4578899999999999999977311112211 23332221 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=91.24 E-value=0.32 Score=33.99 Aligned_cols=51 Identities=14% Similarity=0.276 Sum_probs=36.1
Q ss_pred ecCHHHHHHHHHHHHHh---CCC------CCCchHHHHHhcCC---CCCCHHHHHHHhhhhhh
Q 035517 95 RWTPDLHLSFVHAVERL---GGQ------EKATPKLVLQLMNV---RGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 95 rWT~ELH~kFv~AV~~L---GG~------~kAtPK~ILelM~v---~gLT~~~VkSHLQKYR~ 145 (161)
+||++..+.||+.+-.. |.. .+..+..|++.|+- -.+|..||++|++..|.
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 12234567777763 34799999999987654
No 10
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=88.64 E-value=0.45 Score=44.33 Aligned_cols=58 Identities=26% Similarity=0.468 Sum_probs=39.0
Q ss_pred CCceecCHHHHHHHHHHHHHhC--CCCC----------CchHHHHHhcCC---CCCCHHHHHHHhhhhhhccc
Q 035517 91 MPRLRWTPDLHLSFVHAVERLG--GQEK----------ATPKLVLQLMNV---RGLSIAHVKSHLQMYRSKKL 148 (161)
Q Consensus 91 k~RlrWT~ELH~kFv~AV~~LG--G~~k----------AtPK~ILelM~v---~gLT~~~VkSHLQKYR~kk~ 148 (161)
-.--+|+++.-+.|.+|+..+- |.-| -.-..|...++. .-.||.||.||.|..-.++.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~ 146 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKL 146 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHH
Confidence 3467899999999999999763 1100 011234444443 45899999999998755443
No 11
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=88.38 E-value=0.88 Score=42.54 Aligned_cols=48 Identities=19% Similarity=0.229 Sum_probs=43.2
Q ss_pred CceecCHHHHHHHHHHHHHhC-CCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 92 PRLRWTPDLHLSFVHAVERLG-GQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 92 ~RlrWT~ELH~kFv~AV~~LG-G~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
--..||.+.-..||+|++.+| | .|..|.+.||. -|.++++.|--|+..
T Consensus 71 ~~~~WtadEEilLLea~~t~G~G----NW~dIA~hIGt--Ktkeeck~hy~k~fv 119 (438)
T KOG0457|consen 71 LDPSWTADEEILLLEAAETYGFG----NWQDIADHIGT--KTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCChHHHHHHHHHHHHhCCC----cHHHHHHHHcc--cchHHHHHHHHHHHh
Confidence 356799999999999999999 4 89999999995 899999999988765
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=88.00 E-value=1.1 Score=39.17 Aligned_cols=50 Identities=14% Similarity=0.077 Sum_probs=41.2
Q ss_pred CCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhh
Q 035517 90 KMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMY 143 (161)
Q Consensus 90 Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKY 143 (161)
...|-.||+|.-.+-+.+|..+|. ..|+.|...|+ ++.|..|++-+-..|
T Consensus 22 glKRg~WT~EEDe~L~~lV~kyG~---~nW~~IAk~~g-~gRT~KQCReRW~N~ 71 (249)
T PLN03212 22 GMKRGPWTVEEDEILVSFIKKEGE---GRWRSLPKRAG-LLRCGKSCRLRWMNY 71 (249)
T ss_pred CCcCCCCCHHHHHHHHHHHHHhCc---ccHHHHHHhhh-cCCCcchHHHHHHHh
Confidence 345778999999999999999984 47999999886 578888888776665
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=84.02 E-value=2.8 Score=36.70 Aligned_cols=53 Identities=19% Similarity=0.142 Sum_probs=44.3
Q ss_pred CceeeeecCCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHH
Q 035517 81 STVRQYVRSKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSH 139 (161)
Q Consensus 81 ~~vr~~~r~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSH 139 (161)
..+..|.++.-.+-.||.|.-..-++++..+|. .|..|...| ||.|-.+||.+
T Consensus 66 eRW~N~L~P~I~kgpWT~EED~lLlel~~~~Gn----KWs~IAk~L--pGRTDnqIKNR 118 (249)
T PLN03212 66 LRWMNYLRPSVKRGGITSDEEDLILRLHRLLGN----RWSLIAGRI--PGRTDNEIKNY 118 (249)
T ss_pred HHHHHhhchhcccCCCChHHHHHHHHHHHhccc----cHHHHHhhc--CCCCHHHHHHH
Confidence 345666777777889999999999999999984 799999977 78999999844
No 14
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=83.88 E-value=1.5 Score=31.35 Aligned_cols=44 Identities=18% Similarity=0.324 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhCCCCC----CchHHHHHhcCCCCC---CHHHHHHHhhhh
Q 035517 99 DLHLSFVHAVERLGGQEK----ATPKLVLQLMNVRGL---SIAHVKSHLQMY 143 (161)
Q Consensus 99 ELH~kFv~AV~~LGG~~k----AtPK~ILelM~v~gL---T~~~VkSHLQKY 143 (161)
+|+..|. +|..+||.+. ..|+.|++.|+++.- ...++++|-+||
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 7899897 5888999653 569999999999752 234566666665
No 15
>PLN03091 hypothetical protein; Provisional
Probab=83.26 E-value=2.3 Score=40.12 Aligned_cols=51 Identities=12% Similarity=0.161 Sum_probs=39.8
Q ss_pred CCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhh
Q 035517 89 SKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMY 143 (161)
Q Consensus 89 ~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKY 143 (161)
.+..|..||+|.-++.+.+|..+|. ..|+.|..+|+ ++.|-.|++-+-..|
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~---~nWs~IAk~~g-~gRT~KQCRERW~Ny 60 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGH---GCWSSVPKQAG-LQRCGKSCRLRWINY 60 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCc---CCHHHHhhhhc-cCcCcchHhHHHHhc
Confidence 4556778999999999999999983 47999999887 466777776554443
No 16
>PLN03091 hypothetical protein; Provisional
Probab=80.89 E-value=5 Score=37.88 Aligned_cols=56 Identities=14% Similarity=0.163 Sum_probs=46.4
Q ss_pred ceeeeecCCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHH----Hhhhh
Q 035517 82 TVRQYVRSKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKS----HLQMY 143 (161)
Q Consensus 82 ~vr~~~r~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkS----HLQKY 143 (161)
.+..|..+.-.+-.||+|.-.+.++.+..+|. .|..|...| ||.|-.+||. +|+|+
T Consensus 56 RW~NyLdP~IkKgpWT~EED~lLLeL~k~~Gn----KWskIAk~L--PGRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 56 RWINYLRPDLKRGTFSQQEENLIIELHAVLGN----RWSQIAAQL--PGRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred HHHhccCCcccCCCCCHHHHHHHHHHHHHhCc----chHHHHHhc--CCCCHHHHHHHHHHHHHHH
Confidence 34556667677889999999999999999994 899999987 7999999984 46665
No 17
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=80.71 E-value=0.94 Score=38.89 Aligned_cols=57 Identities=16% Similarity=0.028 Sum_probs=44.6
Q ss_pred cCCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhccccc
Q 035517 88 RSKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSKKLDE 150 (161)
Q Consensus 88 r~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~kk~~e 150 (161)
..+...-+||++.|.+|.+||-.. +..|..|-++.+. .+..++.+|-|+|..+....
T Consensus 48 i~~~~~~~~t~~~~~~~~~~l~~~----~~~~~~~~~~~~~--~~~v~~~~~~~~~~p~~~~~ 104 (335)
T KOG0724|consen 48 ILDDDEPRRTPDSWDKFAEALPLE----KRLEDKIEEYIGL--VFDVNIRESGQKPFPKYGKS 104 (335)
T ss_pred HHhccccccchhhhhHHHhcCccc----cccchhHHhhhhh--HHHHhhhhccCCCccccCcc
Confidence 334445569999999999988543 4589999999887 88889999999988765554
No 18
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=68.89 E-value=6.9 Score=36.26 Aligned_cols=47 Identities=17% Similarity=0.253 Sum_probs=41.4
Q ss_pred eecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 94 LRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 94 lrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
--|+.+.-..|++|.+-||- -.|..|...+|. .+.+.|++|.=||-.
T Consensus 64 e~WgadEEllli~~~~TlGl---GNW~dIadyiGs--r~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGL---GNWEDIADYIGS--RAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCC---CcHHHHHHHHhh--hhhHHHHHHHHHHHh
Confidence 46999999999999999993 289999999994 999999999888765
No 19
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=62.15 E-value=20 Score=29.90 Aligned_cols=51 Identities=20% Similarity=0.263 Sum_probs=42.6
Q ss_pred eeeeecCCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHH
Q 035517 83 VRQYVRSKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSH 139 (161)
Q Consensus 83 vr~~~r~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSH 139 (161)
.--|.++.-.|-.||+|.-..-++|-..||- .|..|+.+| ||.|-..||-|
T Consensus 52 W~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GN----rWs~IA~~L--PGRTDNeIKN~ 102 (238)
T KOG0048|consen 52 WTNYLRPDLKRGNFSDEEEDLIIKLHALLGN----RWSLIAGRL--PGRTDNEVKNH 102 (238)
T ss_pred hhcccCCCccCCCCCHHHHHHHHHHHHHHCc----HHHHHHhhC--CCcCHHHHHHH
Confidence 3456677777889999999999999999995 699998875 68999999855
No 20
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=57.03 E-value=10 Score=25.88 Aligned_cols=57 Identities=14% Similarity=0.260 Sum_probs=34.7
Q ss_pred ceecCHHHHHHHHHHHHH------hC--CCCC--CchHHHHHhcCCCC--CCHHHHHHHh----hhhhhcccc
Q 035517 93 RLRWTPDLHLSFVHAVER------LG--GQEK--ATPKLVLQLMNVRG--LSIAHVKSHL----QMYRSKKLD 149 (161)
Q Consensus 93 RlrWT~ELH~kFv~AV~~------LG--G~~k--AtPK~ILelM~v~g--LT~~~VkSHL----QKYR~kk~~ 149 (161)
|-.||++.-..|++++.. ++ +..+ ..++.|...|..-| .|..|++... ++||.-+..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~~ 73 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKDR 73 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSSS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 457999999999998877 21 2222 26788887776544 5888887654 456665443
No 21
>smart00351 PAX Paired Box domain.
Probab=54.73 E-value=53 Score=24.85 Aligned_cols=45 Identities=18% Similarity=0.157 Sum_probs=37.0
Q ss_pred eecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 94 LRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 94 lrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
--++.++-.+||.++. +| .+...|.+.++| ++.-|..-+++|+..
T Consensus 16 ~~~s~~~R~riv~~~~--~G---~s~~~iA~~~gv---s~~tV~kwi~r~~~~ 60 (125)
T smart00351 16 RPLPDEERQRIVELAQ--NG---VRPCDISRQLCV---SHGCVSKILGRYYET 60 (125)
T ss_pred CCCCHHHHHHHHHHHH--cC---CCHHHHHHHHCc---CHHHHHHHHHHHHHc
Confidence 3489999999999985 44 378899999995 888899999999863
No 22
>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=54.12 E-value=41 Score=19.43 Aligned_cols=43 Identities=12% Similarity=0.110 Sum_probs=29.0
Q ss_pred cCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 96 WTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 96 WT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
+++. .+.++.++.. .| -+++.|.+.|+ ++...|..++++.+.+
T Consensus 11 l~~~-~~~~~~~~~~-~~---~~~~~ia~~~~---~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPER-EREVILLRFG-EG---LSYEEIAEILG---ISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHH-HHHHHHHHHh-cC---CCHHHHHHHHC---cCHHHHHHHHHHHHHH
Confidence 3443 3445555442 33 48899999998 5889999998887654
No 23
>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=45.36 E-value=60 Score=20.09 Aligned_cols=33 Identities=27% Similarity=0.429 Sum_probs=25.7
Q ss_pred HHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhh
Q 035517 104 FVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMY 143 (161)
Q Consensus 104 Fv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKY 143 (161)
...|++..|| ......+.+| +++..+...|+||
T Consensus 10 i~~aL~~~~g----n~~~aA~~Lg---isr~tL~~klkk~ 42 (42)
T PF02954_consen 10 IRQALERCGG----NVSKAARLLG---ISRRTLYRKLKKY 42 (42)
T ss_dssp HHHHHHHTTT-----HHHHHHHHT---S-HHHHHHHHHHC
T ss_pred HHHHHHHhCC----CHHHHHHHHC---CCHHHHHHHHHhC
Confidence 4678889988 5678888888 5899999888887
No 24
>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=43.85 E-value=30 Score=23.07 Aligned_cols=32 Identities=28% Similarity=0.408 Sum_probs=26.4
Q ss_pred chHHHHHhcC---CCCCCHHHHHHHhhhhhhcccc
Q 035517 118 TPKLVLQLMN---VRGLSIAHVKSHLQMYRSKKLD 149 (161)
Q Consensus 118 tPK~ILelM~---v~gLT~~~VkSHLQKYR~kk~~ 149 (161)
++..|++.++ ..|||.++|..++++|=...+.
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~~~~G~N~l~ 39 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERRKKYGPNELP 39 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHHHHHSSSSTT
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHHHhccccccc
Confidence 4667888888 3899999999999999776654
No 25
>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=41.59 E-value=50 Score=25.42 Aligned_cols=48 Identities=25% Similarity=0.425 Sum_probs=39.8
Q ss_pred CceecCH-HHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhh
Q 035517 92 PRLRWTP-DLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMY 143 (161)
Q Consensus 92 ~RlrWT~-ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKY 143 (161)
+||+-++ ||+++-+..++--| ..-+.+|+.|++.|-|..+.-.-||.-
T Consensus 36 ~~fr~S~~el~~cslkvl~p~g----SPsk~LL~~~~~rg~Tv~~Ll~~L~~M 84 (97)
T cd08783 36 GRFRLSCLDLEQCSLKVLEPEG----SPSRSLLKLLGERGCTVTELSEFLQAM 84 (97)
T ss_pred CccccCHHHHHHHHHHHhcCCC----CchHHHHHHHHHcCCcHHHHHHHHHHh
Confidence 4899998 89999888887655 245678999999999999999888863
No 26
>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=39.08 E-value=24 Score=29.16 Aligned_cols=48 Identities=21% Similarity=0.319 Sum_probs=35.4
Q ss_pred CceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 92 PRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 92 ~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
=.|||..-+-..+..||+.-- ..+-.+++. ...||..+|-+-||.|..
T Consensus 47 CGFRWNs~VRkqY~~~i~~AK-kqRk~~~~~-----~~~ltl~~vI~fLq~l~~ 94 (161)
T TIGR02894 47 CGFRWNAYVRKQYEEAIELAK-KQRKELKRE-----AGSLTLQDVISFLQNLKT 94 (161)
T ss_pred hcchHHHHHHHHHHHHHHHHH-HHHhccccC-----cccCCHHHHHHHHHHHHh
Confidence 479999999999999998654 111111111 256999999999999975
No 27
>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=38.87 E-value=70 Score=20.12 Aligned_cols=54 Identities=24% Similarity=0.212 Sum_probs=33.9
Q ss_pred CCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 90 KMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 90 Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
|++|..+|++- ...|+++..... ..+...+..+...=|||..+|..=.|.-|.+
T Consensus 1 kr~r~~~t~~q-~~~L~~~f~~~~--~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 1 KRKRTRFTKEQ-LKVLEEYFQENP--YPSKEEREELAKELGLTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSSSSHHH-HHHHHHHHHHSS--SCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHH-HHHHHHHHHHhc--cccccccccccccccccccccccCHHHhHHH
Confidence 46788888654 456666666542 3344444444333368999999888876653
No 28
>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=37.82 E-value=34 Score=23.91 Aligned_cols=20 Identities=20% Similarity=0.713 Sum_probs=18.0
Q ss_pred ecCHHHHHHHHHHHHHhCCC
Q 035517 95 RWTPDLHLSFVHAVERLGGQ 114 (161)
Q Consensus 95 rWT~ELH~kFv~AV~~LGG~ 114 (161)
.+..|+|+.|-+-|+.|||.
T Consensus 37 kfnqem~aefheri~klggk 56 (59)
T PF07384_consen 37 KFNQEMQAEFHERIKKLGGK 56 (59)
T ss_pred HhhHHHHHHHHHHHHHhccc
Confidence 46789999999999999984
No 29
>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=36.94 E-value=42 Score=22.60 Aligned_cols=40 Identities=13% Similarity=0.188 Sum_probs=26.6
Q ss_pred HHHHHHHHHhC-CCCCCchHHHHHhcCCCCCCHHHHHHHhh
Q 035517 102 LSFVHAVERLG-GQEKATPKLVLQLMNVRGLSIAHVKSHLQ 141 (161)
Q Consensus 102 ~kFv~AV~~LG-G~~kAtPK~ILelM~v~gLT~~~VkSHLQ 141 (161)
..++.||..|+ +...++++.|.+.|+|.-=|...+-..|+
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 46889998886 34568899999999974334333333333
No 30
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=36.75 E-value=60 Score=27.75 Aligned_cols=56 Identities=34% Similarity=0.303 Sum_probs=47.4
Q ss_pred cCCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 88 RSKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 88 r~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
++|+.|-.+|++--.+.-+|.+.-+=+-.|.-+.+.+.++ ||-.|||--.|.-|+|
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~---LsetQVkvWFQNRRtk 156 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLS---LSETQVKVWFQNRRTK 156 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcC---CChhHhhhhhhhhhHH
Confidence 6889999999998888888888655445578889999888 7999999999998885
No 31
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.30 E-value=88 Score=23.78 Aligned_cols=28 Identities=21% Similarity=0.233 Sum_probs=22.4
Q ss_pred CchHHHHHhcCCCCCCHHHHHHHhhhhhhcc
Q 035517 117 ATPKLVLQLMNVRGLSIAHVKSHLQMYRSKK 147 (161)
Q Consensus 117 AtPK~ILelM~v~gLT~~~VkSHLQKYR~kk 147 (161)
-+++.|.+.|| +|...|+++|++-|.+.
T Consensus 152 ~s~~eIA~~lg---is~~~V~~~l~ra~~~L 179 (186)
T PRK13919 152 YTHREAAQLLG---LPLGTLKTRARRALSRL 179 (186)
T ss_pred CCHHHHHHHHC---cCHHHHHHHHHHHHHHH
Confidence 47888888888 57899999998877653
No 32
>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=36.06 E-value=27 Score=21.40 Aligned_cols=19 Identities=21% Similarity=0.399 Sum_probs=12.6
Q ss_pred HHHhcCCCCCCHHHHHHHhh
Q 035517 122 VLQLMNVRGLSIAHVKSHLQ 141 (161)
Q Consensus 122 ILelM~v~gLT~~~VkSHLQ 141 (161)
|.+.|.. |||.++|+..|+
T Consensus 9 i~eA~~~-Gls~eeir~FL~ 27 (30)
T PF08671_consen 9 IKEAKES-GLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHT-T--HHHHHHHHH
T ss_pred HHHHHHc-CCCHHHHHHHHH
Confidence 4455554 899999999886
No 33
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=36.02 E-value=81 Score=24.19 Aligned_cols=45 Identities=11% Similarity=0.209 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhCCC----------CCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 99 DLHLSFVHAVERLGGQ----------EKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 99 ELH~kFv~AV~~LGG~----------~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
+++..+..|+..|.-. +.-+++.|.+.|| +|...|++||++=|.+
T Consensus 127 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lg---is~~tv~~~l~Rar~~ 181 (193)
T PRK11923 127 EIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQ---CPVGTVRSRIFRAREA 181 (193)
T ss_pred HHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHH
Confidence 3455676777766421 2225556666666 4677788887765543
No 34
>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=35.36 E-value=93 Score=22.79 Aligned_cols=46 Identities=15% Similarity=0.167 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhCC----------CCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 98 PDLHLSFVHAVERLGG----------QEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 98 ~ELH~kFv~AV~~LGG----------~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
.+++..+..|+..|.- .+.-+.+.|.+.|| +|...|++||..=|.+
T Consensus 99 ~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~---is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 99 EDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLG---RTVNAVYKALSRLRVR 154 (159)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhC---CCHHHHHHHHHHHHHH
Confidence 3445556666666541 12336667777777 5788888887665544
No 35
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=33.48 E-value=1.3e+02 Score=19.02 Aligned_cols=43 Identities=16% Similarity=0.138 Sum_probs=27.9
Q ss_pred HHHHHHHHHhC----CCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhcc
Q 035517 102 LSFVHAVERLG----GQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSKK 147 (161)
Q Consensus 102 ~kFv~AV~~LG----G~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~kk 147 (161)
.-|+.-...+| .....+-..|.+.++ +++..|..+|++.+...
T Consensus 7 ~~l~~l~~~~~~~~~~~~~~s~~ela~~~g---~s~~tv~r~l~~L~~~g 53 (67)
T cd00092 7 SFLLNLSLRYGAGDLVQLPLTRQEIADYLG---LTRETVSRTLKELEEEG 53 (67)
T ss_pred HHHHHHHHHcCCCccccCCcCHHHHHHHHC---CCHHHHHHHHHHHHHCC
Confidence 34555455555 112344556777777 58999999999988754
No 36
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=30.24 E-value=1.3e+02 Score=22.42 Aligned_cols=42 Identities=24% Similarity=0.221 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCC----------CCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 102 LSFVHAVERLGG----------QEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 102 ~kFv~AV~~LGG----------~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
..++.|+..|.. .+.-+.+.|.+.|| +|...|++||..=|.+
T Consensus 104 ~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lg---is~~tv~~~l~Rar~~ 155 (161)
T PRK12541 104 ASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTG---LSLAKVKIELHRGRKE 155 (161)
T ss_pred HHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHH
Confidence 456666666652 13345667777777 5788899988776554
No 37
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=29.98 E-value=1.7e+02 Score=21.80 Aligned_cols=50 Identities=18% Similarity=0.102 Sum_probs=37.1
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhcc
Q 035517 91 MPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSKK 147 (161)
Q Consensus 91 k~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~kk 147 (161)
++|-+||+|+ .+.||.++- ....+...|..-++| +...|..=.++|+...
T Consensus 8 ~~rr~ys~Ef---K~~aV~~~~-~~g~sv~evA~e~gI---s~~tl~~W~r~y~~~~ 57 (121)
T PRK09413 8 EKRRRRTTQE---KIAIVQQSF-EPGMTVSLVARQHGV---AASQLFLWRKQYQEGS 57 (121)
T ss_pred CCCCCCCHHH---HHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHhhcc
Confidence 4567899998 567776553 234577888888885 8888888899998643
No 38
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=29.77 E-value=66 Score=32.64 Aligned_cols=45 Identities=24% Similarity=0.328 Sum_probs=34.1
Q ss_pred CCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHH
Q 035517 89 SKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKS 138 (161)
Q Consensus 89 ~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkS 138 (161)
+--..-+||++.-.+.+.||..+||.+-+.|.. + |||.+..|.+-
T Consensus 356 Psikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~---~--vPnRSdsQcR~ 400 (939)
T KOG0049|consen 356 PSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQ---A--VPNRSDSQCRE 400 (939)
T ss_pred ccccCCCCCCHHHHHHHHHHHHhCccchhhHHH---h--cCCccHHHHHH
Confidence 445678999999999999999999975555443 3 56777777653
No 39
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=29.46 E-value=38 Score=23.89 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=23.1
Q ss_pred CCCCchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 114 QEKATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 114 ~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
.+.++.+.|.+..+ +|..++.+||++-..
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 46789999999998 699999999998544
No 40
>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=29.43 E-value=1.4e+02 Score=18.35 Aligned_cols=53 Identities=25% Similarity=0.209 Sum_probs=37.8
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 91 MPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 91 k~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
+.|..++++- ..+|+++.... ...++..|.++...-||+..+|..-.+.-|.+
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 56677776664 35667778788777789999999988877764
No 41
>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=28.54 E-value=1.5e+02 Score=18.20 Aligned_cols=40 Identities=13% Similarity=0.100 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 100 LHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 100 LH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
-..+-+.++..-|+ ++.+.|.+.++ +|..-|..||++-..
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 35566777877654 68999999999 699999999988654
No 42
>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=28.51 E-value=50 Score=23.01 Aligned_cols=28 Identities=18% Similarity=0.195 Sum_probs=23.1
Q ss_pred hHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 119 PKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 119 PK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
...++++||...+|+.+|-++|-+|-..
T Consensus 8 s~~L~~~lg~~~~sr~~v~~~lw~YIk~ 35 (76)
T PF02201_consen 8 SPELAEFLGEDELSRSEVVKRLWQYIKE 35 (76)
T ss_dssp HHHHHHHTT-SCEEHHHHHHHHHHHHHH
T ss_pred CHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence 3567889999999999999999999653
No 43
>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=27.02 E-value=39 Score=23.77 Aligned_cols=25 Identities=24% Similarity=0.575 Sum_probs=20.0
Q ss_pred hcCCCCCCHHHHHHHhhhhhhcccc
Q 035517 125 LMNVRGLSIAHVKSHLQMYRSKKLD 149 (161)
Q Consensus 125 lM~v~gLT~~~VkSHLQKYR~kk~~ 149 (161)
.+.+.++|.+++|.+|-+|+-..+-
T Consensus 6 ~vp~~~~~v~d~K~~Lr~y~~~~I~ 30 (66)
T PF11767_consen 6 FVPVHGVTVEDFKKRLRKYRWDRIR 30 (66)
T ss_pred cCCCCCccHHHHHHHHhcCCcceEE
Confidence 3456678999999999999976543
No 44
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.51 E-value=1.2e+02 Score=23.90 Aligned_cols=56 Identities=14% Similarity=0.108 Sum_probs=43.2
Q ss_pred CceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhccccc
Q 035517 92 PRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSKKLDE 150 (161)
Q Consensus 92 ~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~kk~~e 150 (161)
.--+|.|+--+.+++-+-.+++.....--+|+++|. .|...++|=|-|+|....++
T Consensus 44 kFakldpe~a~e~veEL~~i~~~~e~~avkIadI~P---~t~~ElRsIla~e~~~~s~E 99 (114)
T COG1460 44 KFAKLDPEKARELVEELLSIVKMSEKIAVKIADIMP---RTPDELRSILAKERVMLSDE 99 (114)
T ss_pred HHhcCCHHHHHHHHHHHHhhccccHHHHHHHHHhCC---CCHHHHHHHHHHccCCCCHH
Confidence 355789999999999888887533444456788888 59999999999999876443
No 45
>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=26.09 E-value=1.7e+02 Score=20.14 Aligned_cols=26 Identities=27% Similarity=0.432 Sum_probs=18.8
Q ss_pred chHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 118 TPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 118 tPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
++..|.+.||+ |...|..++++-+.+
T Consensus 128 s~~eIA~~l~~---s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 128 SYKEIAEILGI---SVGTVKRRLKRARKK 153 (158)
T ss_pred CHHHHHHHHCC---CHHHHHHHHHHHHHH
Confidence 77788888874 777777777766544
No 46
>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=25.54 E-value=66 Score=24.82 Aligned_cols=43 Identities=19% Similarity=0.311 Sum_probs=29.6
Q ss_pred eecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 94 LRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 94 lrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
+.=..++|.+....|..+|+ .+.+--.+++ .=++-||..|+.-
T Consensus 83 vyI~~e~h~~l~~Iv~~ig~-~~~si~~yid---------NIL~~Hle~~~ee 125 (136)
T PF11888_consen 83 VYISRETHERLSRIVRVIGE-RKMSISGYID---------NILRHHLEEYREE 125 (136)
T ss_pred eEECHHHHHHHHHHHHHHCC-CCCcHHHHHH---------HHHHHHHHHHHHH
Confidence 77789999999999998885 3333333222 2256799988864
No 47
>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=24.94 E-value=85 Score=21.83 Aligned_cols=44 Identities=25% Similarity=0.343 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCC----CchHHHHHhcCCCCCCH---HHHHHHhhhh
Q 035517 99 DLHLSFVHAVERLGGQEK----ATPKLVLQLMNVRGLSI---AHVKSHLQMY 143 (161)
Q Consensus 99 ELH~kFv~AV~~LGG~~k----AtPK~ILelM~v~gLT~---~~VkSHLQKY 143 (161)
+|+..| .+|..+||.++ -.|..|.+.||++.... ..++.|-.+|
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 677777 56667888743 35889999999865322 3455555554
No 48
>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=24.79 E-value=2.1e+02 Score=20.81 Aligned_cols=42 Identities=33% Similarity=0.408 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCC----------CCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 102 LSFVHAVERLGGQ----------EKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 102 ~kFv~AV~~LGG~----------~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
..+..++..|.-. +.-+.+.|.+.|| +|...|+++|..-|.+
T Consensus 97 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lg---is~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 97 EEITHHLSRLPENYRTVLILREFKEFSYKEIAELLN---LSLAKVKSNLFRARKE 148 (154)
T ss_pred HHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHC---CCHHHHHHHHHHHHHH
Confidence 4456666666411 2235666777777 4677788887776654
No 49
>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=24.61 E-value=1.8e+02 Score=18.01 Aligned_cols=26 Identities=19% Similarity=0.266 Sum_probs=18.9
Q ss_pred CchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 117 ATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 117 AtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
-+.+.|.+.|| +|...|++||++=|.
T Consensus 27 ~s~~eIa~~l~---~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 27 MSYAEIAEILG---ISESTVKRRLRRARK 52 (54)
T ss_dssp --HHHHHHHCT---S-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHHC---cCHHHHHHHHHHHHh
Confidence 47888889887 689999999987554
No 50
>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=24.38 E-value=54 Score=24.70 Aligned_cols=17 Identities=47% Similarity=0.671 Sum_probs=13.8
Q ss_pred CCHHHHHHHhhhhhhcc
Q 035517 131 LSIAHVKSHLQMYRSKK 147 (161)
Q Consensus 131 LT~~~VkSHLQKYR~kk 147 (161)
||-++|+-.||+|+.+.
T Consensus 9 lTYdevk~~L~~~~~kp 25 (86)
T PF02762_consen 9 LTYDEVKARLQHYRDKP 25 (86)
T ss_dssp --HHHHHHHHGGGTTST
T ss_pred EeHHHHHHHHHHHhCCc
Confidence 89999999999999874
No 51
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.17 E-value=1.5e+02 Score=22.98 Aligned_cols=45 Identities=18% Similarity=0.224 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhCCC----------CCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 99 DLHLSFVHAVERLGGQ----------EKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 99 ELH~kFv~AV~~LGG~----------~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
++...+..|+.+|... +.-+-+.|.+.|| +|...|++||..=|.+
T Consensus 123 ~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lg---is~~tVk~~l~RAr~~ 177 (189)
T PRK12530 123 EFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECD---ISTSNLHVLLYRARLQ 177 (189)
T ss_pred HHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHH
Confidence 3444566777776521 1224555666666 5888899998765543
No 52
>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=24.14 E-value=43 Score=21.54 Aligned_cols=35 Identities=26% Similarity=0.193 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhh
Q 035517 100 LHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQ 141 (161)
Q Consensus 100 LH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQ 141 (161)
|-..|++-|+... ++||.= .+.++.|..+|++.|-
T Consensus 1 Lsde~I~~IN~~~----~tWkAG---~NF~~~~~~~ik~LlG 35 (41)
T PF08127_consen 1 LSDEFIDYINSKN----TTWKAG---RNFENTSIEYIKRLLG 35 (41)
T ss_dssp S-HHHHHHHHHCT-----SEEE-------SSB-HHHHHHCS-
T ss_pred CCHHHHHHHHcCC----CcccCC---CCCCCCCHHHHHHHcC
Confidence 4467899999875 366652 2246778888877664
No 53
>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=23.61 E-value=1.7e+02 Score=21.60 Aligned_cols=28 Identities=21% Similarity=0.254 Sum_probs=21.7
Q ss_pred CchHHHHHhcCCCCCCHHHHHHHhhhhhhcc
Q 035517 117 ATPKLVLQLMNVRGLSIAHVKSHLQMYRSKK 147 (161)
Q Consensus 117 AtPK~ILelM~v~gLT~~~VkSHLQKYR~kk 147 (161)
-+.+.|.+.|| ++...|++||.+=|.+.
T Consensus 127 ~s~~eIA~~lg---is~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 127 LSEAQVAEALG---ISVGTVKSRLSRALARL 154 (162)
T ss_pred CCHHHHHHHhC---CCHHHHHHHHHHHHHHH
Confidence 37778888888 57999999998766643
No 54
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=23.52 E-value=1.9e+02 Score=21.28 Aligned_cols=36 Identities=8% Similarity=0.181 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 103 SFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 103 kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
.|..|+...|| ...+..+++| +++..+...|++|.+
T Consensus 59 ~i~~aL~~~~g----n~s~AAr~LG---IsRsTL~rKLkr~gi 94 (95)
T PRK00430 59 LLDMVMQYTRG----NQTRAALMLG---INRGTLRKKLKKYGM 94 (95)
T ss_pred HHHHHHHHcCC----CHHHHHHHhC---CCHHHHHHHHHHhCC
Confidence 46788888887 5677777787 588889999988853
No 55
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=23.50 E-value=2.6e+02 Score=19.58 Aligned_cols=42 Identities=7% Similarity=0.184 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 99 DLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 99 ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
++..+.+.++.+-| .++...|.+.++ ++...|..+|++-...
T Consensus 3 ~~D~~il~~L~~~~---~~~~~~la~~l~---~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 3 EIDRKILEELQKDA---RISLAELAKKVG---LSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHHhC---CCCHHHHHHHHC---cCHHHHHHHHHHHHHC
Confidence 57788999998876 368888999987 6889999999887654
No 56
>PRK01905 DNA-binding protein Fis; Provisional
Probab=23.40 E-value=2.1e+02 Score=19.89 Aligned_cols=37 Identities=16% Similarity=0.269 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhh
Q 035517 101 HLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYR 144 (161)
Q Consensus 101 H~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR 144 (161)
...|..++...|| ......+.+| +++..+...|+||.
T Consensus 39 ~~~i~~aL~~~~g----n~s~aAr~LG---IsrstL~rklkk~g 75 (77)
T PRK01905 39 KPLLEVVMEQAGG----NQSLAAEYLG---INRNTLRKKLQQHG 75 (77)
T ss_pred HHHHHHHHHHcCC----CHHHHHHHHC---CCHHHHHHHHHHhC
Confidence 3346788888887 5667777777 58888888898884
No 57
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.87 E-value=1.8e+02 Score=17.78 Aligned_cols=38 Identities=16% Similarity=0.259 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 100 LHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 100 LH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
.....+..+.. | .+++.|.+.+|| ++..|..-+..|+.
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 489999999985 88888888888874
No 58
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=22.77 E-value=1.9e+02 Score=22.06 Aligned_cols=28 Identities=14% Similarity=0.145 Sum_probs=21.0
Q ss_pred CchHHHHHhcCCCCCCHHHHHHHhhhhhhcc
Q 035517 117 ATPKLVLQLMNVRGLSIAHVKSHLQMYRSKK 147 (161)
Q Consensus 117 AtPK~ILelM~v~gLT~~~VkSHLQKYR~kk 147 (161)
-+.+.|.+.|| ++...|++||.+-|.+.
T Consensus 144 ~s~~EIA~~l~---is~~tv~~~l~Ra~~~L 171 (179)
T PRK09415 144 LSIKEIAEVTG---VNENTVKTRLKKAKELL 171 (179)
T ss_pred CCHHHHHHHHC---CCHHHHHHHHHHHHHHH
Confidence 36667777777 58888999998877653
No 59
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=22.59 E-value=1.6e+02 Score=28.36 Aligned_cols=45 Identities=20% Similarity=0.216 Sum_probs=39.4
Q ss_pred CCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhh
Q 035517 91 MPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQ 141 (161)
Q Consensus 91 k~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQ 141 (161)
..+-.||..--...++||+.+|- .|.+|..+.+. -|+++.-.|+=
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~d----dW~kVa~hVg~--ks~eqCI~kFL 295 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGD----DWNKVADHVGT--KSQEQCILKFL 295 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcc----cHHHHHhccCC--CCHHHHHHHHH
Confidence 45778999999999999999993 89999999995 89999888753
No 60
>PF14383 VARLMGL: DUF761-associated sequence motif
Probab=22.54 E-value=66 Score=20.56 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=16.5
Q ss_pred CCCCchHHHHHhcCCCCCCHH
Q 035517 114 QEKATPKLVLQLMNVRGLSIA 134 (161)
Q Consensus 114 ~~kAtPK~ILelM~v~gLT~~ 134 (161)
....+|..|..+||++.|...
T Consensus 10 ~~~r~P~vvarLMGld~lP~~ 30 (34)
T PF14383_consen 10 PGTRAPGVVARLMGLDSLPDS 30 (34)
T ss_pred ccccChhHHHHHhccccCCcc
Confidence 456789999999999777543
No 61
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.33 E-value=1.7e+02 Score=22.11 Aligned_cols=27 Identities=22% Similarity=0.329 Sum_probs=20.5
Q ss_pred CchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 117 ATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 117 AtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
-+.+.|.+.|| ++...|++||.+=|.+
T Consensus 136 ~s~~EIA~~lg---is~~tV~~~l~Ra~~~ 162 (173)
T PRK12522 136 YSYKEMSEILN---IPIGTVKYRLNYAKKQ 162 (173)
T ss_pred CCHHHHHHHhC---CCHHHHHHHHHHHHHH
Confidence 36677888888 5789999999866554
No 62
>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=22.06 E-value=2.2e+02 Score=20.46 Aligned_cols=27 Identities=15% Similarity=0.212 Sum_probs=18.9
Q ss_pred CchHHHHHhcCCCCCCHHHHHHHhhhhhhc
Q 035517 117 ATPKLVLQLMNVRGLSIAHVKSHLQMYRSK 146 (161)
Q Consensus 117 AtPK~ILelM~v~gLT~~~VkSHLQKYR~k 146 (161)
-+++.|.+.|| +|...|+++|..=|.+
T Consensus 130 ~~~~eIA~~lg---is~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 130 KSYKEIAEELG---ISVKTVEYHISKALKE 156 (161)
T ss_pred CCHHHHHHHHC---CCHHHHHHHHHHHHHH
Confidence 36777777777 5888888887765443
No 63
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.06 E-value=2.4e+02 Score=20.82 Aligned_cols=28 Identities=11% Similarity=0.014 Sum_probs=21.0
Q ss_pred CchHHHHHhcCCCCCCHHHHHHHhhhhhhcc
Q 035517 117 ATPKLVLQLMNVRGLSIAHVKSHLQMYRSKK 147 (161)
Q Consensus 117 AtPK~ILelM~v~gLT~~~VkSHLQKYR~kk 147 (161)
-+.+.|.+.|| ++...|++||..-|.+.
T Consensus 123 ~s~~EIA~~lg---is~~tV~~~l~Rar~~L 150 (160)
T PRK09642 123 KSYQEIALQEK---IEVKTVEMKLYRARKWI 150 (160)
T ss_pred CCHHHHHHHHC---CCHHHHHHHHHHHHHHH
Confidence 36677777777 58888999998777643
No 64
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=20.94 E-value=2.5e+02 Score=20.18 Aligned_cols=45 Identities=20% Similarity=0.293 Sum_probs=30.1
Q ss_pred CceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHHhhh
Q 035517 92 PRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSHLQM 142 (161)
Q Consensus 92 ~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSHLQK 142 (161)
.|+.|=|++-+.-..-...+.| -+-+.|.+.|+ +|...|++|+-+
T Consensus 11 ~~l~~l~~~~r~af~L~R~~eG---lS~kEIAe~LG---IS~~TVk~~l~~ 55 (73)
T TIGR03879 11 ERLTWVDSLAEAAAALAREEAG---KTASEIAEELG---RTEQTVRNHLKG 55 (73)
T ss_pred HHHhcCCHHHHHHHHHHHHHcC---CCHHHHHHHHC---cCHHHHHHHHhc
Confidence 4677777664433222233344 38889999999 588899998865
No 65
>cd02185 AroH Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes, chorismate mutase may be fused to prephenate dehydratase, prephenate dehydrogenase, or 3-deoxy-D-arabino-heptulosonat-7-phosphate (DAHP) as part of a bifunctional enzyme. The AroH domain forms a homotrimer with three-fold symmetry.
Probab=20.60 E-value=32 Score=27.13 Aligned_cols=37 Identities=41% Similarity=0.572 Sum_probs=28.4
Q ss_pred ceecCHHHHHHH-HHHHHHhCCCCCCchHHHHHhcCCCC
Q 035517 93 RLRWTPDLHLSF-VHAVERLGGQEKATPKLVLQLMNVRG 130 (161)
Q Consensus 93 RlrWT~ELH~kF-v~AV~~LGG~~kAtPK~ILelM~v~g 130 (161)
-|.=|++|+..| -.|..++|| ...+|-.=.+-|.|||
T Consensus 44 ~FT~T~DL~a~FPA~aaR~~~~-~~~Vplmc~qE~~V~g 81 (117)
T cd02185 44 IFTVTPDLDAAFPAKAARELGG-WKYVPLMCAQEMDVPG 81 (117)
T ss_pred EEEeCCcccccChHHHHHhcCC-CCCcceeecCcCCCCC
Confidence 567799999999 566778875 5677777677788776
No 66
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=20.33 E-value=2.4e+02 Score=22.82 Aligned_cols=27 Identities=11% Similarity=0.076 Sum_probs=20.6
Q ss_pred CCCCchHHHHHhcCCCCCCHHHHHHHhhhh
Q 035517 114 QEKATPKLVLQLMNVRGLSIAHVKSHLQMY 143 (161)
Q Consensus 114 ~~kAtPK~ILelM~v~gLT~~~VkSHLQKY 143 (161)
.+.-+.+.|.+.|| +|...|++|+..=
T Consensus 193 ~e~~S~~EIA~~lg---is~~tV~~~~~rA 219 (233)
T PRK05803 193 GKEKTQREIAKALG---ISRSYVSRIEKRA 219 (233)
T ss_pred CCCcCHHHHHHHHC---cCHHHHHHHHHHH
Confidence 45678899999998 4788888886543
No 67
>PF12170 DNA_pol3_tau_5: DNA polymerase III tau subunit V interacting with alpha; InterPro: IPR021029 This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with PF00004 from PFAM. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme [, ]. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 2AYA_A.
Probab=20.25 E-value=93 Score=24.59 Aligned_cols=33 Identities=18% Similarity=0.310 Sum_probs=24.1
Q ss_pred CHHHHHHHHH-HHHHhCCCCCCchHHHHHhcCCCCCCHHH
Q 035517 97 TPDLHLSFVH-AVERLGGQEKATPKLVLQLMNVRGLSIAH 135 (161)
Q Consensus 97 T~ELH~kFv~-AV~~LGG~~kAtPK~ILelM~v~gLT~~~ 135 (161)
||||-.+.+. |+. - -.|-.++.-|+++||++.-
T Consensus 8 tpel~~k~~~~a~~-~-----D~W~~~i~~L~l~gl~rqL 41 (142)
T PF12170_consen 8 TPELAAKLIAEAIQ-Q-----DPWAALIEQLPLGGLVRQL 41 (142)
T ss_dssp SHHHHHHHHHHHHH-H------HHHHHHHHHT--SHHHHH
T ss_pred CHHHHHHHHHHHhc-c-----CHHHHHHHHCCCchHHHHH
Confidence 8999999866 443 2 2799999999999998754
No 68
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=20.23 E-value=3.1e+02 Score=21.08 Aligned_cols=48 Identities=6% Similarity=0.033 Sum_probs=32.7
Q ss_pred ecCHHHHHHHHHHHHHhCCC----------CCCchHHHHHhcCCCCCCHHHHHHHhhhhhh
Q 035517 95 RWTPDLHLSFVHAVERLGGQ----------EKATPKLVLQLMNVRGLSIAHVKSHLQMYRS 145 (161)
Q Consensus 95 rWT~ELH~kFv~AV~~LGG~----------~kAtPK~ILelM~v~gLT~~~VkSHLQKYR~ 145 (161)
.+.++++....++++.|... +.-+.+.|.+.|| +|...|++||..=|.
T Consensus 119 ~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lg---is~~tV~~~l~Ra~~ 176 (188)
T PRK09640 119 APKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMH---MGLSATKMRYKRALD 176 (188)
T ss_pred cccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHH
Confidence 35567777888888888632 2336667777777 477888888765443
No 69
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=20.10 E-value=1.8e+02 Score=27.86 Aligned_cols=45 Identities=22% Similarity=0.302 Sum_probs=33.8
Q ss_pred CCCCceecCHHHHHHHHHHHHHhCCCCCCchHHHHHhcCCCCCCHHHHHHH
Q 035517 89 SKMPRLRWTPDLHLSFVHAVERLGGQEKATPKLVLQLMNVRGLSIAHVKSH 139 (161)
Q Consensus 89 ~Kk~RlrWT~ELH~kFv~AV~~LGG~~kAtPK~ILelM~v~gLT~~~VkSH 139 (161)
.++.-++||...-.+|-.|+.+.|- .-..|..|. |...|.|||--
T Consensus 361 ~~~~~~~Ws~~e~ekFYKALs~wGt----dF~LIs~lf--P~R~RkqIKaK 405 (507)
T COG5118 361 KKKGALRWSKKEIEKFYKALSIWGT----DFSLISSLF--PNRERKQIKAK 405 (507)
T ss_pred CCCCCCcccHHHHHHHHHHHHHhcc----hHHHHHHhc--CchhHHHHHHH
Confidence 4567899999999999999999993 234455554 44778888743
Done!