Query 033797
Match_columns 111
No_of_seqs 101 out of 152
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 06:23:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033797.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033797hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10163 EnY2: Transcription f 100.0 9.3E-37 2E-41 206.3 11.7 86 22-107 1-86 (86)
2 KOG4479 Transcription factor e 100.0 3.1E-35 6.7E-40 199.5 7.8 86 24-109 4-89 (92)
3 PRK00117 recX recombination re 87.9 4 8.7E-05 29.3 7.4 48 19-67 23-70 (157)
4 PRK14135 recX recombination re 80.6 11 0.00023 29.3 7.3 73 24-100 74-147 (263)
5 KOG4479 Transcription factor e 80.5 6.1 0.00013 27.2 5.2 40 16-55 13-52 (92)
6 PF10163 EnY2: Transcription f 78.5 6.3 0.00014 26.2 4.8 31 39-69 1-31 (86)
7 PF13319 DUF4090: Protein of u 76.5 2.4 5.3E-05 28.8 2.3 33 22-54 42-74 (84)
8 TIGR02606 antidote_CC2985 puta 76.4 17 0.00037 23.3 6.2 52 27-79 13-68 (69)
9 COG2137 OraA Uncharacterized p 76.2 19 0.00041 27.3 7.3 75 22-100 35-109 (174)
10 PRK14136 recX recombination re 74.0 7.6 0.00016 32.2 5.0 57 25-81 180-251 (309)
11 PF08328 ASL_C: Adenylosuccina 73.5 7.5 0.00016 28.0 4.3 57 34-100 49-108 (115)
12 PF08766 DEK_C: DEK C terminal 72.7 13 0.00029 22.4 4.8 51 55-106 3-53 (54)
13 PF07350 DUF1479: Protein of u 72.4 17 0.00037 31.3 6.9 78 25-109 8-102 (416)
14 cd08818 CARD_MDA5_1 Caspase ac 72.4 11 0.00023 26.0 4.7 40 19-58 31-73 (88)
15 PRK14137 recX recombination re 70.2 11 0.00024 28.9 4.9 59 24-82 57-128 (195)
16 PF08542 Rep_fac_C: Replicatio 69.5 26 0.00057 22.3 8.7 61 39-105 7-68 (89)
17 COG1610 Uncharacterized conser 66.8 14 0.00031 27.6 4.7 64 32-99 79-143 (148)
18 PF06348 DUF1059: Protein of u 64.7 11 0.00024 23.4 3.3 32 73-104 20-56 (57)
19 PF05008 V-SNARE: Vesicle tran 64.5 33 0.00072 21.7 6.5 34 74-108 36-69 (79)
20 PF02631 RecX: RecX family; I 62.6 38 0.00083 23.1 6.0 26 33-58 3-28 (121)
21 PRK14134 recX recombination re 62.3 39 0.00084 27.1 6.8 41 24-65 78-118 (283)
22 PF10667 DUF2486: Protein of u 58.3 42 0.00091 27.1 6.2 59 38-107 179-237 (246)
23 PRK13738 conjugal transfer pil 56.5 18 0.00039 28.2 3.9 34 18-51 29-65 (209)
24 PF08429 PLU-1: PLU-1-like pro 56.5 41 0.00088 26.8 6.0 56 43-106 156-211 (335)
25 PF05066 HARE-HTH: HB1, ASXL, 52.6 46 0.001 20.7 4.7 46 57-103 3-53 (72)
26 PF08411 Exonuc_X-T_C: Exonucl 52.5 39 0.00085 26.9 5.3 55 54-108 214-268 (269)
27 PF03693 RHH_2: Uncharacterise 51.5 22 0.00049 23.5 3.2 61 22-84 12-77 (80)
28 PRK06995 flhF flagellar biosyn 51.3 1.3E+02 0.0029 26.2 8.7 69 35-106 170-243 (484)
29 cd05027 S-100B S-100B: S-100B 50.9 63 0.0014 21.3 5.3 50 37-87 29-82 (88)
30 PF00486 Trans_reg_C: Transcri 50.4 40 0.00087 20.5 4.1 42 65-108 18-59 (77)
31 PF14426 Imm2: Immunity protei 50.0 15 0.00033 23.6 2.1 42 51-101 11-53 (60)
32 cd07347 harmonin_N_like N-term 48.3 80 0.0017 21.0 5.6 58 40-107 8-65 (78)
33 PRK00117 recX recombination re 47.9 99 0.0021 22.0 6.7 25 58-82 78-102 (157)
34 TIGR02366 DHAK_reg probable di 47.2 36 0.00077 24.0 3.9 26 37-62 5-31 (176)
35 PF04963 Sigma54_CBD: Sigma-54 47.0 22 0.00049 26.7 3.0 21 35-55 32-52 (194)
36 cd07981 TAF12 TATA Binding Pro 46.7 37 0.00081 21.7 3.6 34 73-108 5-38 (72)
37 PRK14722 flhF flagellar biosyn 46.6 1.4E+02 0.0029 25.2 7.8 65 18-82 29-100 (374)
38 COG0735 Fur Fe2+/Zn2+ uptake r 45.3 96 0.0021 22.3 6.0 57 41-98 5-62 (145)
39 PRK09462 fur ferric uptake reg 44.5 79 0.0017 22.4 5.4 54 45-98 5-59 (148)
40 TIGR02743 TraW type-F conjugat 44.5 41 0.0009 26.1 4.1 33 18-50 31-66 (202)
41 PRK14729 miaA tRNA delta(2)-is 44.4 91 0.002 25.4 6.3 35 48-82 211-247 (300)
42 PRK11639 zinc uptake transcrip 44.1 1.1E+02 0.0024 22.5 6.2 60 38-98 7-67 (169)
43 PF08100 Dimerisation: Dimeris 43.6 38 0.00081 20.7 3.1 38 63-106 13-50 (51)
44 KOG1964 Nuclear pore complex, 43.0 90 0.002 29.1 6.6 59 34-97 309-387 (800)
45 PF05205 COMPASS-Shg1: COMPASS 42.9 1.1E+02 0.0023 21.1 5.7 24 37-60 56-79 (106)
46 PF13797 Post_transc_reg: Post 42.6 1E+02 0.0022 20.7 5.4 37 52-88 4-43 (87)
47 TIGR03499 FlhF flagellar biosy 42.5 94 0.002 24.5 6.0 49 35-83 111-161 (282)
48 cd08789 CARD_IPS-1_RIG-I Caspa 42.4 63 0.0014 21.4 4.3 40 20-59 31-70 (84)
49 PF09551 Spore_II_R: Stage II 42.1 1.3E+02 0.0029 21.9 6.2 40 25-70 31-70 (130)
50 PRK02363 DNA-directed RNA poly 41.7 1.2E+02 0.0027 21.9 6.0 42 58-102 6-47 (129)
51 cd01493 APPBP1_RUB Ubiquitin a 41.1 1.2E+02 0.0025 26.0 6.7 61 5-65 304-372 (425)
52 PF08775 ParB: ParB family; I 41.1 29 0.00064 25.0 2.7 38 71-108 25-66 (127)
53 PF10057 DUF2294: Uncharacteri 39.9 79 0.0017 21.9 4.7 41 25-66 49-89 (118)
54 TIGR03613 RutR pyrimidine util 39.5 55 0.0012 23.4 4.0 27 55-81 11-37 (202)
55 smart00513 SAP Putative DNA-bi 39.1 36 0.00078 18.7 2.3 15 92-106 21-35 (35)
56 PF07766 LETM1: LETM1-like pro 39.0 1.3E+02 0.0029 23.8 6.4 61 42-107 192-253 (268)
57 PF02777 Sod_Fe_C: Iron/mangan 37.9 61 0.0013 21.8 3.8 31 20-53 4-37 (106)
58 PF08513 LisH: LisH; InterPro 37.5 65 0.0014 16.9 4.1 25 39-63 2-26 (27)
59 PRK14828 undecaprenyl pyrophos 37.4 43 0.00092 26.8 3.3 45 33-77 116-178 (256)
60 PF08369 PCP_red: Proto-chloro 37.2 51 0.0011 19.5 2.9 26 55-80 18-43 (45)
61 PRK10668 DNA-binding transcrip 36.7 66 0.0014 23.3 4.1 19 61-79 20-38 (215)
62 PF14766 RPA_interact_N: Repli 36.6 42 0.00092 19.8 2.4 17 52-68 14-30 (42)
63 PF13625 Helicase_C_3: Helicas 36.6 70 0.0015 22.2 4.0 33 72-104 54-86 (129)
64 PF00440 TetR_N: Bacterial reg 36.1 54 0.0012 18.7 2.9 23 60-82 4-26 (47)
65 PRK14835 undecaprenyl pyrophos 35.7 58 0.0013 26.4 3.9 50 34-83 136-203 (275)
66 PF02037 SAP: SAP domain; Int 35.4 38 0.00083 18.8 2.1 14 93-106 22-35 (35)
67 PF11829 DUF3349: Protein of u 34.7 63 0.0014 22.4 3.4 45 35-83 23-69 (96)
68 PLN02848 adenylosuccinate lyas 34.6 2.2E+02 0.0048 24.5 7.4 65 27-100 377-441 (458)
69 PF06757 Ins_allergen_rp: Inse 34.1 1.2E+02 0.0025 22.4 5.1 61 19-82 115-179 (179)
70 PRK09975 DNA-binding transcrip 34.0 73 0.0016 23.0 3.9 25 38-62 14-39 (213)
71 TIGR02945 SUF_assoc FeS assemb 34.0 14 0.00031 24.4 0.1 47 50-98 49-96 (99)
72 COG1638 DctP TRAP-type C4-dica 33.3 2.5E+02 0.0054 23.0 7.3 75 19-106 250-330 (332)
73 PLN02152 indole-3-acetate beta 33.2 55 0.0012 28.0 3.5 48 36-83 403-455 (455)
74 cd00383 trans_reg_C Effector d 32.7 1.2E+02 0.0026 18.9 4.4 42 65-108 36-77 (95)
75 TIGR00511 ribulose_e2b2 ribose 32.6 2.5E+02 0.0054 22.6 7.1 54 54-108 44-97 (301)
76 PF01715 IPPT: IPP transferase 32.5 1.3E+02 0.0029 23.5 5.4 36 49-84 178-215 (253)
77 PRK02260 S-ribosylhomocysteina 32.5 1E+02 0.0022 23.3 4.4 28 49-77 123-155 (158)
78 PF06744 DUF1215: Protein of u 31.9 1.7E+02 0.0038 20.2 6.1 60 36-98 23-88 (125)
79 TIGR03181 PDH_E1_alph_x pyruva 31.7 2E+02 0.0044 23.4 6.5 26 69-98 313-338 (341)
80 TIGR02395 rpoN_sigma RNA polym 31.6 1.4E+02 0.0031 25.4 5.8 61 38-104 76-139 (429)
81 smart00862 Trans_reg_C Transcr 31.4 1.2E+02 0.0026 18.2 4.8 44 64-108 17-60 (78)
82 TIGR03384 betaine_BetI transcr 31.2 87 0.0019 21.9 3.8 27 55-81 11-37 (189)
83 PLN03229 acetyl-coenzyme A car 31.2 4.5E+02 0.0097 24.7 9.3 37 5-44 501-537 (762)
84 KOG2949 Ketopantoate hydroxyme 31.1 26 0.00056 28.7 1.2 26 49-75 111-136 (306)
85 cd08337 DED_c-FLIP_repeat1 Dea 30.6 59 0.0013 21.8 2.7 48 54-105 18-65 (80)
86 PRK15008 HTH-type transcriptio 30.4 95 0.0021 22.8 4.0 28 36-63 19-47 (212)
87 COG3609 Predicted transcriptio 30.4 1.7E+02 0.0036 19.5 5.0 25 23-48 13-37 (89)
88 PF05400 FliT: Flagellar prote 30.3 61 0.0013 20.0 2.6 18 30-47 3-20 (84)
89 TIGR03499 FlhF flagellar biosy 29.7 2.3E+02 0.0049 22.3 6.3 47 21-67 114-162 (282)
90 TIGR00763 lon ATP-dependent pr 29.6 88 0.0019 28.4 4.4 41 27-67 235-275 (775)
91 TIGR03015 pepcterm_ATPase puta 29.6 2.2E+02 0.0047 21.3 6.0 67 37-103 194-267 (269)
92 PF06649 DUF1161: Protein of u 29.4 49 0.0011 20.7 2.0 14 22-35 3-16 (52)
93 PRK11640 putative transcriptio 29.0 1E+02 0.0022 22.5 4.0 29 54-82 3-31 (191)
94 COG3433 Aryl carrier domain [S 28.2 1.6E+02 0.0035 19.7 4.4 39 46-86 22-61 (74)
95 PF05234 UAF_Rrn10: UAF comple 28.1 80 0.0017 22.9 3.2 29 56-84 4-32 (120)
96 TIGR02837 spore_II_R stage II 28.0 2.3E+02 0.0049 21.6 5.7 39 26-70 67-105 (168)
97 PF14069 SpoVIF: Stage VI spor 27.8 1.5E+02 0.0032 19.8 4.2 50 55-104 13-62 (79)
98 PF03682 UPF0158: Uncharacteri 27.7 1.7E+02 0.0037 21.6 5.0 55 19-73 83-142 (163)
99 COG3355 Predicted transcriptio 27.7 1.2E+02 0.0026 22.0 4.1 30 36-67 92-121 (126)
100 PF06504 RepC: Replication pro 27.3 55 0.0012 26.9 2.5 52 41-108 206-257 (281)
101 PRK00767 transcriptional regul 27.2 1.1E+02 0.0024 21.6 3.8 22 59-80 16-37 (197)
102 COG0020 UppS Undecaprenyl pyro 27.2 74 0.0016 25.4 3.1 37 50-86 143-179 (245)
103 COG1309 AcrR Transcriptional r 26.9 1.4E+02 0.003 19.4 4.1 27 56-82 16-42 (201)
104 PLN02555 limonoid glucosyltran 26.7 36 0.00077 29.3 1.3 36 56-91 441-476 (480)
105 PF09012 FeoC: FeoC like trans 26.4 1.5E+02 0.0032 18.3 3.9 33 61-101 5-37 (69)
106 PRK14996 TetR family transcrip 26.2 1E+02 0.0022 22.0 3.5 26 37-62 10-36 (192)
107 PLN02210 UDP-glucosyl transfer 26.1 85 0.0018 26.7 3.5 28 56-83 427-454 (456)
108 KOG1112 Ribonucleotide reducta 26.1 22 0.00048 32.2 -0.0 65 2-69 594-664 (796)
109 PF08824 Serine_rich: Serine r 26.1 1.4E+02 0.003 22.5 4.2 68 19-96 74-141 (159)
110 COG1890 RPS1A Ribosomal protei 26.0 1.1E+02 0.0024 24.3 3.8 28 56-84 137-164 (214)
111 KOG2769 Putative u4/u6 small n 25.8 1E+02 0.0022 27.5 3.9 57 29-94 181-237 (522)
112 cd01598 PurB PurB_like adenylo 25.4 2.8E+02 0.006 23.7 6.4 64 28-100 353-416 (425)
113 PF06771 Desmo_N: Viral Desmop 25.4 48 0.0011 22.7 1.5 34 73-106 10-43 (86)
114 PLN00164 glucosyltransferase; 25.3 89 0.0019 26.7 3.5 33 55-87 444-476 (480)
115 PRK05932 RNA polymerase factor 25.2 2E+02 0.0044 24.7 5.6 60 39-104 102-164 (455)
116 PF13767 DUF4168: Domain of un 25.1 1.9E+02 0.0041 18.4 6.2 56 26-81 5-67 (78)
117 PF14377 DUF4414: Domain of un 25.1 78 0.0017 21.6 2.6 29 78-106 41-69 (108)
118 cd03572 ENTH_epsin_related ENT 25.0 2E+02 0.0042 20.6 4.7 41 23-65 21-62 (122)
119 PF10249 NDUFB10: NADH-ubiquin 24.7 58 0.0013 23.8 1.9 52 28-83 54-107 (128)
120 PRK10307 putative glycosyl tra 24.5 1.3E+02 0.0029 23.9 4.2 50 29-82 352-401 (412)
121 cd08812 CARD_RIG-I_like Caspas 24.3 2E+02 0.0044 19.0 4.4 39 20-58 33-73 (88)
122 PF14689 SPOB_a: Sensor_kinase 24.1 1.1E+02 0.0023 19.0 2.9 23 30-52 32-54 (62)
123 PF06505 XylR_N: Activator of 24.0 1.4E+02 0.003 20.7 3.7 37 21-57 27-63 (103)
124 PF06799 DUF1230: Protein of u 23.8 22 0.00048 26.5 -0.4 8 49-56 102-109 (144)
125 PF03008 DUF234: Archaea bacte 23.7 2.3E+02 0.0049 18.8 4.8 40 28-68 8-47 (100)
126 PRK12469 RNA polymerase factor 23.6 2.2E+02 0.0048 24.9 5.6 66 38-105 123-191 (481)
127 COG5559 Uncharacterized conser 23.5 1.1E+02 0.0024 19.9 2.8 19 89-107 10-28 (65)
128 TIGR00763 lon ATP-dependent pr 23.4 3.7E+02 0.008 24.5 7.2 29 74-105 248-276 (775)
129 cd06460 M32_Taq Peptidase fami 23.4 2.4E+02 0.0053 23.9 5.7 48 32-83 345-392 (396)
130 COG1859 KptA RNA:NAD 2'-phosph 23.3 84 0.0018 24.8 2.7 35 46-83 52-86 (211)
131 PLN02448 UDP-glycosyltransfera 23.1 1.1E+02 0.0023 25.9 3.5 28 56-83 429-456 (459)
132 PLN02534 UDP-glycosyltransfera 23.1 1.2E+02 0.0025 26.3 3.8 30 56-85 458-487 (491)
133 COG2317 Zn-dependent carboxype 23.0 2.4E+02 0.0052 25.1 5.7 51 29-83 442-492 (497)
134 PRK08535 translation initiatio 22.9 2.7E+02 0.0058 22.5 5.7 55 53-108 48-102 (310)
135 PF08388 GIIM: Group II intron 22.8 1.3E+02 0.0029 18.6 3.2 33 56-89 3-35 (80)
136 KOG3617 WD40 and TPR repeat-co 22.7 7.5E+02 0.016 24.4 9.2 85 13-108 1072-1157(1416)
137 PF07587 PSD1: Protein of unkn 22.6 85 0.0018 24.7 2.7 29 38-68 52-80 (266)
138 COG3343 RpoE DNA-directed RNA 22.5 3E+02 0.0065 21.2 5.5 56 40-105 3-58 (175)
139 TIGR02499 HrpE_YscL_not type I 22.4 99 0.0022 21.8 2.8 24 38-61 38-61 (166)
140 PF09424 YqeY: Yqey-like prote 22.3 2.6E+02 0.0057 20.2 5.1 58 34-95 77-135 (143)
141 COG1071 AcoA Pyruvate/2-oxoglu 21.9 3.4E+02 0.0074 23.0 6.2 40 44-83 293-342 (358)
142 cd05025 S-100A1 S-100A1: S-100 21.5 2.3E+02 0.005 18.1 5.6 50 37-87 30-83 (92)
143 PF13720 Acetyltransf_11: Udp 21.4 2.5E+02 0.0054 18.4 4.8 54 48-108 23-76 (83)
144 PF14433 SUKH-3: SUKH-3 immuni 21.1 1.2E+02 0.0025 21.3 2.9 14 41-54 1-14 (142)
145 PF13026 DUF3887: Protein of u 21.0 3E+02 0.0064 19.1 5.3 35 55-91 5-39 (101)
146 PF15606 Toxin_55: Putative to 21.0 1.1E+02 0.0024 20.6 2.6 43 10-53 11-53 (77)
147 TIGR00174 miaA tRNA isopenteny 21.0 3.2E+02 0.0069 22.1 5.7 47 37-83 195-246 (287)
148 PF08973 TM1506: Domain of unk 20.8 15 0.00033 26.8 -1.8 50 57-107 76-133 (134)
149 PF01817 CM_2: Chorismate muta 20.5 70 0.0015 20.2 1.5 30 75-104 42-72 (81)
150 cd07153 Fur_like Ferric uptake 20.4 2.6E+02 0.0056 18.4 4.4 39 58-97 3-41 (116)
151 PF00298 Ribosomal_L11: Riboso 20.0 1.6E+02 0.0034 18.9 3.1 33 55-89 33-65 (69)
No 1
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=100.00 E-value=9.3e-37 Score=206.30 Aligned_cols=86 Identities=55% Similarity=1.002 Sum_probs=82.4
Q ss_pred hHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHH
Q 033797 22 TLQEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLR 101 (111)
Q Consensus 22 ~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~ 101 (111)
.|+++|+++|++||+|++|+++|++||.||||+|+||++|+++|+++|.+++||++|+++|+|+|+++||++||+||+.+
T Consensus 1 ~l~~~i~~~L~~sGe~~~L~~~L~~rL~e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~ 80 (86)
T PF10163_consen 1 QLKAQIQQRLVESGEYERLKELLRQRLIECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQR 80 (86)
T ss_dssp HHHHHHHHHHHHCTHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHcCcHHHHHHHHHHHHHHCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHh
Q 033797 102 IRAFLA 107 (111)
Q Consensus 102 Ir~fL~ 107 (111)
|++||+
T Consensus 81 Ir~~L~ 86 (86)
T PF10163_consen 81 IRAFLD 86 (86)
T ss_dssp HHHHHH
T ss_pred HHHHhC
Confidence 999995
No 2
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=100.00 E-value=3.1e-35 Score=199.52 Aligned_cols=86 Identities=48% Similarity=0.825 Sum_probs=83.0
Q ss_pred HHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHH
Q 033797 24 QEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIR 103 (111)
Q Consensus 24 k~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir 103 (111)
...++|++++||++++||++|+.||.||||.|+||.+||++|.++|.+|+|+++|+++|+|+||++|||.||+|||.+||
T Consensus 4 ~~a~~q~t~~tgdr~~lKeLL~trLvECGW~d~ik~mcrniimEkG~~n~tvdqL~AeitPkaRaLVPd~VKkEll~rir 83 (92)
T KOG4479|consen 4 PDAGYQPTLRTGDRAALKELLHTRLVECGWHDDIKEMCRNIIMEKGVDNITVDQLAAEITPKARALVPDVVKKELLLRIR 83 (92)
T ss_pred CccccchhhhcccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHhccccccHHHHHHHhCchhhhhchHHHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhh
Q 033797 104 AFLASA 109 (111)
Q Consensus 104 ~fL~~~ 109 (111)
+||.+-
T Consensus 84 t~L~~~ 89 (92)
T KOG4479|consen 84 TALDKH 89 (92)
T ss_pred HHHHHH
Confidence 999874
No 3
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=87.87 E-value=4 Score=29.27 Aligned_cols=48 Identities=19% Similarity=0.368 Sum_probs=37.2
Q ss_pred chhhHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHH
Q 033797 19 KEPTLQEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKK 67 (111)
Q Consensus 19 ~~~~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~ 67 (111)
.-+.-...|.++|..-|--+.+-+..-.+|.++||.|+- ..|...++.
T Consensus 23 ~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~-~~a~~~~~~ 70 (157)
T PRK00117 23 RREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDE-RFAESFVRS 70 (157)
T ss_pred cchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 334556678888888888888888888899999999996 666666544
No 4
>PRK14135 recX recombination regulator RecX; Provisional
Probab=80.59 E-value=11 Score=29.28 Aligned_cols=73 Identities=18% Similarity=0.258 Sum_probs=46.3
Q ss_pred HHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCC-CCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 033797 24 QEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGT-NNVTVDDLVHVITPKGRASIPDSIKTELLL 100 (111)
Q Consensus 24 k~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~-~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~ 100 (111)
...|.++|...|--+.+-+..-.+|.+.||.|+ ...|+..++..-. ..-+...|..++..++ ||.++-.+.+.
T Consensus 74 ~~el~~kL~~kg~~~~~Ie~vl~~l~~~~~ldD-~~~a~~~~~~~~~~~~~g~~~I~~kL~~kG---i~~~~Ie~~l~ 147 (263)
T PRK14135 74 EKEVRDYLKKHEISEEIISEVIDKLKEEKYIDD-KEYAESYVRTNINTGDKGPRVIKQKLLQKG---IEDEIIEEALS 147 (263)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHcCCCCH-HHHHHHHHHHHHhccccchHHHHHHHHHcC---CCHHHHHHHHH
Confidence 377888888888877777777888999999999 6777777654310 1123444444444332 44444444443
No 5
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=80.47 E-value=6.1 Score=27.23 Aligned_cols=40 Identities=20% Similarity=0.466 Sum_probs=35.5
Q ss_pred hccchhhHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHH
Q 033797 16 DQEKEPTLQEIINIKMIESGEKEKLMELLRERLVECGWKD 55 (111)
Q Consensus 16 ~~~~~~~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~D 55 (111)
+..+-..||+-++-||+|-|=.+.|+...+.-+.|-|-..
T Consensus 13 ~tgdr~~lKeLL~trLvECGW~d~ik~mcrniimEkG~~n 52 (92)
T KOG4479|consen 13 RTGDRAALKELLHTRLVECGWHDDIKEMCRNIIMEKGVDN 52 (92)
T ss_pred hcccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHhcccc
Confidence 3457789999999999999999999999999999999643
No 6
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=78.53 E-value=6.3 Score=26.24 Aligned_cols=31 Identities=32% Similarity=0.479 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHHhC
Q 033797 39 KLMELLRERLVECGWKDEMKALCRAYIKKKG 69 (111)
Q Consensus 39 rLk~lL~~rL~EcGW~DeVr~~~re~i~~~g 69 (111)
.|++.++++|+++|=++.++++-+.-+.+.|
T Consensus 1 ~l~~~i~~~L~~sGe~~~L~~~L~~rL~e~G 31 (86)
T PF10163_consen 1 QLKAQIQQRLVESGEYERLKELLRQRLIECG 31 (86)
T ss_dssp HHHHHHHHHHHHCTHHHHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHcCcHHHHHHHHHHHHHHCC
Confidence 3789999999999999999999999998887
No 7
>PF13319 DUF4090: Protein of unknown function (DUF4090)
Probab=76.51 E-value=2.4 Score=28.83 Aligned_cols=33 Identities=24% Similarity=0.542 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHhcchHHHHHHHHHHHHHhcChH
Q 033797 22 TLQEIINIKMIESGEKEKLMELLRERLVECGWK 54 (111)
Q Consensus 22 ~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~ 54 (111)
-.+.....|.|..|-+-.=.+.|+++|++.||.
T Consensus 42 GV~~sMR~RiVr~GaKH~~q~~Lnq~L~~Ag~~ 74 (84)
T PF13319_consen 42 GVSNSMRSRIVRIGAKHFDQEELNQRLIDAGWE 74 (84)
T ss_pred hhHHHHHHHHHHhccccCCHHHHHHHHHHcCcc
Confidence 356777888899999999999999999999995
No 8
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=76.41 E-value=17 Score=23.29 Aligned_cols=52 Identities=13% Similarity=0.109 Sum_probs=31.5
Q ss_pred HHHHHHhcchHHHHHHHH----HHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHH
Q 033797 27 INIKMIESGEKEKLMELL----RERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLV 79 (111)
Q Consensus 27 I~~~LveSGe~erLk~lL----~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~ 79 (111)
.-+..|+||.|.--++.+ +.--..+.|.+.+|....+-+. .|....++++++
T Consensus 13 ~i~~~V~sG~Y~s~SEVir~aLR~le~~e~~~~~Lr~~i~~g~~-sg~~~~~~d~~~ 68 (69)
T TIGR02606 13 FIRSQVQSGRYGSASEVVRAALRLLEERETKLQALRDAIEEGEQ-SGEAGRSLDDFL 68 (69)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCCCHHHHh
Confidence 334566899986555544 4444556777777777765543 343344777764
No 9
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=76.18 E-value=19 Score=27.31 Aligned_cols=75 Identities=25% Similarity=0.390 Sum_probs=52.6
Q ss_pred hHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 033797 22 TLQEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLL 100 (111)
Q Consensus 22 ~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~ 100 (111)
.-.+.|..+|.+-|--+.+=+-+-.+|.+.||-|+-+ .+..+|+.+....-..-.|-.++.-++ |++++-.+.|.
T Consensus 35 rse~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~-fAe~~i~~r~~~g~G~~rl~qeL~qkG---i~~~~Ie~aL~ 109 (174)
T COG2137 35 RSEKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTR-FAEAYIRSRSRKGKGPARLKQELKQKG---IDDEIIEEALE 109 (174)
T ss_pred HHHHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHH-HHHHHHHHHHhcccChHHHHHHHHHcC---CCHHHHHHHHh
Confidence 3456778888888888888888899999999999975 566666655432234556666666555 66666555555
No 10
>PRK14136 recX recombination regulator RecX; Provisional
Probab=74.04 E-value=7.6 Score=32.21 Aligned_cols=57 Identities=16% Similarity=0.253 Sum_probs=40.6
Q ss_pred HHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHH---------------HHHHHHHHHhCCCCCCHHHHHHh
Q 033797 25 EIINIKMIESGEKEKLMELLRERLVECGWKDEMK---------------ALCRAYIKKKGTNNVTVDDLVHV 81 (111)
Q Consensus 25 ~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr---------------~~~re~i~~~g~~~vt~~~L~~~ 81 (111)
..|.++|..-|--+.+-+.+-.+|.+.||.|+-+ ..++.+|+++|++.-.+++.+++
T Consensus 180 ~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~~kkGp~rIrqELrQKGId~eLIEqALee 251 (309)
T PRK14136 180 AELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRASRVGSARIVSELKRHAVGDALVESVGAQ 251 (309)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhchhHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 5678888888888888888899999999998864 22345556667654444444443
No 11
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=73.52 E-value=7.5 Score=27.99 Aligned_cols=57 Identities=30% Similarity=0.447 Sum_probs=40.0
Q ss_pred cchHHHHHHHHHHHHHhcCh---HHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 033797 34 SGEKEKLMELLRERLVECGW---KDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLL 100 (111)
Q Consensus 34 SGe~erLk~lL~~rL~EcGW---~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~ 100 (111)
..+|+-|.+-++.-|.-.|- ++.+|++.| | ..+|-+++.+.|.-.. ||+++|.+|+.
T Consensus 49 ~~nWeVlaEpIQTvmRr~g~~~pYE~LK~lTR------g-~~it~~~l~~fI~~L~---ip~~~k~~L~~ 108 (115)
T PF08328_consen 49 DENWEVLAEPIQTVMRRYGIPNPYEKLKELTR------G-KKITKEDLREFIESLD---IPEEAKARLLA 108 (115)
T ss_dssp CT-GGGGHHHHHHHHHHTT-SSHHHHHHHHHT------T-S---HHHHHHHHHTSS---S-HHHHHHHHH
T ss_pred HHCHHHHHHHHHHHHHHcCCCCHHHHHHHHHc------C-CCCCHHHHHHHHHhCC---CCHHHHHHHHh
Confidence 35788899999999988886 566666664 4 3788888888887665 99999999875
No 12
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=72.72 E-value=13 Score=22.42 Aligned_cols=51 Identities=18% Similarity=0.246 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHH
Q 033797 55 DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFL 106 (111)
Q Consensus 55 DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL 106 (111)
++++...+++++..+.+++|.-++...+.-+----+. +=|..|=..|..||
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~-~~K~~I~~~I~~~l 53 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVTKKQVREQLEERFGVDLS-SRKKFIKELIDEFL 53 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--S-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcH-HHHHHHHHHHHHHh
Confidence 6788999999999999999999999988866522222 45555555666665
No 13
>PF07350 DUF1479: Protein of unknown function (DUF1479); InterPro: IPR010856 This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length. Members of this family are often known as YbiU. The function of this family is unknown.; PDB: 2CSG_A 2DBI_A 2DBN_A.
Probab=72.37 E-value=17 Score=31.25 Aligned_cols=78 Identities=15% Similarity=0.253 Sum_probs=48.3
Q ss_pred HHHHHHHH-hcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhC---CCCCCHHHHHHh---------hchh----hh
Q 033797 25 EIINIKMI-ESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKG---TNNVTVDDLVHV---------ITPK----GR 87 (111)
Q Consensus 25 ~~I~~~Lv-eSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g---~~~vt~~~L~~~---------I~P~----Ar 87 (111)
+.|.+.|+ +.|+.+.|..-....|.+ ++..+. .|.+.| +..|+|.+|.+- |.-. -|
T Consensus 8 ~~lK~~L~~~~~~~~~v~~sw~rll~~------l~~~~~-~i~~~G~~~IP~i~f~di~~~~~~~~~~~~ir~rG~~VIR 80 (416)
T PF07350_consen 8 AELKRSLIAKPGNEEAVFASWERLLEA------LEREIE-EIAAKGSSIIPEIDFADIENGGVSEEFLAEIRRRGCVVIR 80 (416)
T ss_dssp HHHHHHHHHHHS-HHHHHHHHHHHHHH------HHHHHH-HHHHCT--SS-EEEHHHHHCT---HHHHHHHHHHSEEEEC
T ss_pred HHHHHHHHhhcCCHHHHHHHHHHHHHH------HHHHHH-HHHHhCCCCCceeeHHHHhCCCCCHHHHHHHHhcCEEEEe
Confidence 56778888 778777776654444332 222222 345666 344577777655 2222 26
Q ss_pred ccCCHHHHHHHHHHHHHHHhhh
Q 033797 88 ASIPDSIKTELLLRIRAFLASA 109 (111)
Q Consensus 88 ~~VP~~VK~Ell~~Ir~fL~~~ 109 (111)
..||.+.-....+.|++|+..+
T Consensus 81 ~Vvp~~ea~~w~~e~~~Y~~~n 102 (416)
T PF07350_consen 81 GVVPREEALAWKQELKEYLKAN 102 (416)
T ss_dssp TSS-HHHHHHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHHHHHhC
Confidence 7899999999999999999874
No 14
>cd08818 CARD_MDA5_1 Caspase activation and recruitment domain found in MDA5, first repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-
Probab=72.36 E-value=11 Score=25.98 Aligned_cols=40 Identities=23% Similarity=0.233 Sum_probs=33.7
Q ss_pred chhhHHHHHHHHHHhcchHHHHHHHHHHHHH---hcChHHHHH
Q 033797 19 KEPTLQEIINIKMIESGEKEKLMELLRERLV---ECGWKDEMK 58 (111)
Q Consensus 19 ~~~~lk~~I~~~LveSGe~erLk~lL~~rL~---EcGW~DeVr 58 (111)
-++..+++|++.-...|+.+...-+|..-+. +-||..+.=
T Consensus 31 L~~e~ke~I~a~~~~~Gn~~AA~~LL~~l~~~~~~~GWf~~Fl 73 (88)
T cd08818 31 LEAEVKERIRAAAATRGNIAAAELLLSTLEKGTWDPGWFREFV 73 (88)
T ss_pred CCHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCchHHHHH
Confidence 4677899999999999999998888877666 999987653
No 15
>PRK14137 recX recombination regulator RecX; Provisional
Probab=70.21 E-value=11 Score=28.91 Aligned_cols=59 Identities=19% Similarity=0.388 Sum_probs=43.2
Q ss_pred HHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHH-------------HHHHHHHHhCCCCCCHHHHHHhh
Q 033797 24 QEIINIKMIESGEKEKLMELLRERLVECGWKDEMKA-------------LCRAYIKKKGTNNVTVDDLVHVI 82 (111)
Q Consensus 24 k~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~-------------~~re~i~~~g~~~vt~~~L~~~I 82 (111)
...|.++|...|--+..-+.+-.+|.++||.|+-+= ..+..|+.+|++.-.+++.++++
T Consensus 57 ~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~~~k~~Gp~rI~~eL~qKGI~~~lI~~al~~~ 128 (195)
T PRK14137 57 AAELRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAENSRRGVGALRVRQTLRRRGVEETLIEETLAAR 128 (195)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCchHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 456778888888888888889999999999998652 24455666777655555555544
No 16
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=69.53 E-value=26 Score=22.31 Aligned_cols=61 Identities=23% Similarity=0.276 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhc-cCCHHHHHHHHHHHHHH
Q 033797 39 KLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRA-SIPDSIKTELLLRIRAF 105 (111)
Q Consensus 39 rLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~-~VP~~VK~Ell~~Ir~f 105 (111)
.+.+.+..-+. |=.++++..+.+.+.+ | .+..+++..+...... -+|+..|.+++..+-.+
T Consensus 7 ~i~~i~~~~~~--~~~~~~~~~~~~l~~~-G---~s~~~Il~~l~~~l~~~~~~~~~k~~i~~~la~~ 68 (89)
T PF08542_consen 7 VIEEILESCLN--GDFKEARKKLYELLVE-G---YSASDILKQLHEVLVESDIPDSQKAEILKILAEI 68 (89)
T ss_dssp HHHHHHHHHHH--TCHHHHHHHHHHHHHT-T-----HHHHHHHHHHHHHTSTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh--CCHHHHHHHHHHHHHc-C---CCHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 34444444444 2345577777777765 4 7888888888888877 55899999999887654
No 17
>COG1610 Uncharacterized conserved protein [Function unknown]
Probab=66.78 E-value=14 Score=27.64 Aligned_cols=64 Identities=25% Similarity=0.378 Sum_probs=52.5
Q ss_pred HhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCC-CHHHHHHhhchhhhccCCHHHHHHHH
Q 033797 32 IESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNV-TVDDLVHVITPKGRASIPDSIKTELL 99 (111)
Q Consensus 32 veSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~v-t~~~L~~~I~P~Ar~~VP~~VK~Ell 99 (111)
.|.+|-..|..+|-++|.+ ++|+.+|.+.|.+-|.... ..-.+-..+.|+.....+-....-+.
T Consensus 79 kE~~Ei~Ii~~ylP~qLsd----~e~~~~v~~aIae~Gas~~~dMGkvM~al~~k~~GkaD~~~vs~~V 143 (148)
T COG1610 79 KERAEIAIIEEYLPQQLSE----DELRALVDAAIAEVGASSMKDMGKVMKALKPKVAGKADGGRVSKLV 143 (148)
T ss_pred HHHhHHHHHHHhCcccCCH----HHHHHHHHHHHHHHHHhhHHHHHHHHHHHhHHhcccCcHHHHHHHH
Confidence 4678899999999999997 8999999999998885443 67778889999998888876655544
No 18
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=64.71 E-value=11 Score=23.37 Aligned_cols=32 Identities=22% Similarity=0.472 Sum_probs=24.1
Q ss_pred CCHHHHHHhhchhhhcc-----CCHHHHHHHHHHHHH
Q 033797 73 VTVDDLVHVITPKGRAS-----IPDSIKTELLLRIRA 104 (111)
Q Consensus 73 vt~~~L~~~I~P~Ar~~-----VP~~VK~Ell~~Ir~ 104 (111)
-|.++|++.+.-+|+.. +|+++...|-+.|++
T Consensus 20 ~tedEll~~~~~Ha~~~Hg~~~~~~el~~~ir~~I~~ 56 (57)
T PF06348_consen 20 ETEDELLEAVVEHAREVHGMTEIPEELREKIRSAIKD 56 (57)
T ss_pred CCHHHHHHHHHHHHHHhcCCccCCHHHHHHHHHHhhc
Confidence 37788888888888765 787777777777763
No 19
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=64.53 E-value=33 Score=21.65 Aligned_cols=34 Identities=15% Similarity=0.341 Sum_probs=27.4
Q ss_pred CHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 74 TVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 74 t~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
..++++..+.=.++.+ |.+.+..+..+|+.|=.+
T Consensus 36 ea~~~l~qMe~E~~~~-p~s~r~~~~~kl~~yr~~ 69 (79)
T PF05008_consen 36 EAEELLKQMELEVRSL-PPSERNQYKSKLRSYRSE 69 (79)
T ss_dssp HHHHHHHHHHHHHCTS--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHHHH
Confidence 4678888888888866 999999999999998543
No 20
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=62.63 E-value=38 Score=23.09 Aligned_cols=26 Identities=31% Similarity=0.489 Sum_probs=14.0
Q ss_pred hcchHHHHHHHHHHHHHhcChHHHHH
Q 033797 33 ESGEKEKLMELLRERLVECGWKDEMK 58 (111)
Q Consensus 33 eSGe~erLk~lL~~rL~EcGW~DeVr 58 (111)
+.|--+..-+.+-.+|.++||.|+-+
T Consensus 3 ~kg~~~e~I~~vi~~l~~~gyidD~~ 28 (121)
T PF02631_consen 3 RKGFSEEAIEEVIDRLKELGYIDDER 28 (121)
T ss_dssp HTT--HHHHHHHHHHHHHTTSS-HHH
T ss_pred ccCCCHHHHHHHHHHHHHcCCCCHHH
Confidence 33444445555666777777777654
No 21
>PRK14134 recX recombination regulator RecX; Provisional
Probab=62.27 E-value=39 Score=27.11 Aligned_cols=41 Identities=22% Similarity=0.295 Sum_probs=32.5
Q ss_pred HHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHH
Q 033797 24 QEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYI 65 (111)
Q Consensus 24 k~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i 65 (111)
...|.++|...|--+..-+..-++|.+.||.|+- ..|+.++
T Consensus 78 e~Elr~KL~~k~~~~~~Ie~vI~~L~e~~yldD~-ryA~~yv 118 (283)
T PRK14134 78 EKQIKEKLYLKEYDEDAVNRVIRFLKEYNFIDDD-KYCDMYI 118 (283)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHCCCCCHH-HHHHHHH
Confidence 4567888998888888999999999999999984 3444444
No 22
>PF10667 DUF2486: Protein of unknown function (DUF2486); InterPro: IPR018924 This family is made up of members from various Burkholderia spp. The function is unknown.
Probab=58.32 E-value=42 Score=27.11 Aligned_cols=59 Identities=17% Similarity=0.258 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHh
Q 033797 38 EKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLA 107 (111)
Q Consensus 38 erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~ 107 (111)
+||+.-+...|. .-|++=|...||+.+.++- ..=+++|..+|. -..-.|++.-+++.++
T Consensus 179 eRl~~r~~~~l~-gegr~~IEarCR~al~~h~--~~Lv~qitreva--------~aLe~e~~~WvreAv~ 237 (246)
T PF10667_consen 179 ERLRGRVANYLT-GEGRGLIEARCRDALQEHT--AWLVGQITREVA--------LALETEMMDWVREAVD 237 (246)
T ss_pred HHHHHHHHHHHc-cccHHHHHHHHHHHHHHHH--HHHHHHHHHHHH--------HHHHHHHHHHHHHHHH
Confidence 455555555554 4799999999999998872 233444444332 2344555555555443
No 23
>PRK13738 conjugal transfer pilus assembly protein TraW; Provisional
Probab=56.54 E-value=18 Score=28.25 Aligned_cols=34 Identities=29% Similarity=0.523 Sum_probs=28.7
Q ss_pred cchhhHHHHHHHHHHh---cchHHHHHHHHHHHHHhc
Q 033797 18 EKEPTLQEIINIKMIE---SGEKEKLMELLRERLVEC 51 (111)
Q Consensus 18 ~~~~~lk~~I~~~Lve---SGe~erLk~lL~~rL~Ec 51 (111)
-.|.+|-+.|++||-. ||+++++.+..++|..+.
T Consensus 29 I~E~D~L~~I~~rL~~~e~sGel~~~~~~~~~r~~~~ 65 (209)
T PRK13738 29 VKEPDMLTVIMQRLQALEQSGEMGRKMDAFKERVIRN 65 (209)
T ss_pred ccchhHHHHHHHHHHHhHhccHHHHHHHHHHHHHHHh
Confidence 3789999999999865 899999999888877664
No 24
>PF08429 PLU-1: PLU-1-like protein; InterPro: IPR013637 This domain is found in the central region of lysine-specific demethylases, which are nuclear proteins that may have a role in DNA-binding and transcription, and are associated with malignant cancer phenotypes []. The domain is also found in various other Jumonji/ARID domain-containing proteins (see IPR013129 from INTERPRO, IPR001606 from INTERPRO). ; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process
Probab=56.50 E-value=41 Score=26.80 Aligned_cols=56 Identities=21% Similarity=0.435 Sum_probs=37.8
Q ss_pred HHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHH
Q 033797 43 LLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFL 106 (111)
Q Consensus 43 lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL 106 (111)
.|+.++..+.|.++++..+.. .+.+|++++-.-|. .|..+.| .--.+.+..+.+.|
T Consensus 156 ~L~~~l~~~~W~~~~~~~~~~------~~~~tL~~l~~Ll~-~g~~l~~-~~~~~~~~~L~~~l 211 (335)
T PF08429_consen 156 QLRRRLEQLEWLEEAREILSD------PDRLTLDELRELLD-EGERLGI-PSDEKLMAELQELL 211 (335)
T ss_pred HHHHHHHHHHHHHHHHHHhcc------ccCCcHHHHHHHHH-hhhcCCC-ccchHHHHHHHHHH
Confidence 456778888999999876632 23589988887777 8888877 33334444444444
No 25
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=52.56 E-value=46 Score=20.74 Aligned_cols=46 Identities=17% Similarity=0.348 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHhhchhhhcc----CCHHH-HHHHHHHHH
Q 033797 57 MKALCRAYIKKKGTNNVTVDDLVHVITPKGRAS----IPDSI-KTELLLRIR 103 (111)
Q Consensus 57 Vr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~----VP~~V-K~Ell~~Ir 103 (111)
+.+.|.++|++.| ...++.||+++|.-...-. -|... ...|...|+
T Consensus 3 ~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 3 FKEAAYEVLEEAG-RPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp HHHHHHHHHHHH--S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred HHHHHHHHHHhcC-CCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 4678899999998 6899999999998665443 34333 336666665
No 26
>PF08411 Exonuc_X-T_C: Exonuclease C-terminal; InterPro: IPR013620 This bacterial domain is found at the C terminus of exodeoxyribonuclease I/Exonuclease I (IPR013520 from INTERPRO), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in Escherichia coli is associated with DNA deoxyribophosphodiesterase (dRPase) []. ; GO: 0008852 exodeoxyribonuclease I activity, 0006281 DNA repair; PDB: 2QXF_A 3C94_A 3HL8_A 3C95_A 1FXX_A 3HP9_A.
Probab=52.46 E-value=39 Score=26.88 Aligned_cols=55 Identities=15% Similarity=0.221 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 54 KDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 54 ~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
..+++.+|++.|...+....|+++.+.+|.-.+...--+.-+..||..+.+|+++
T Consensus 214 ~~~W~~~~~~rL~~~~~~~~tl~~~~~~i~~L~~~~~~~~~~~~lL~~L~~Y~~~ 268 (269)
T PF08411_consen 214 QQRWQEYCQQRLTDPDGGWLTLEEYFQEIEELRAEYDDDEEKQALLEALEDYAES 268 (269)
T ss_dssp HHHHHHHHHHHS-HHH-----HHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccCCccchHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHhc
Confidence 4567778888876655456899999999998888876677899999999999864
No 27
>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown. The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins. ; PDB: 3KXE_C.
Probab=51.52 E-value=22 Score=23.47 Aligned_cols=61 Identities=18% Similarity=0.265 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHhcchHHHHHHHHHHHHHh----cChHHHHHHHHHHHHHHhC-CCCCCHHHHHHhhch
Q 033797 22 TLQEIINIKMIESGEKEKLMELLRERLVE----CGWKDEMKALCRAYIKKKG-TNNVTVDDLVHVITP 84 (111)
Q Consensus 22 ~lk~~I~~~LveSGe~erLk~lL~~rL~E----cGW~DeVr~~~re~i~~~g-~~~vt~~~L~~~I~P 84 (111)
.+.+-| +..|+||.|.-.++.++.-|.- ..+...+|....+-+ +.| ....++++++++..-
T Consensus 12 ~~~~~i-~~~V~sG~Y~s~SEvvR~aLRlle~~e~~~~~Lr~~l~~g~-~sG~~~~~~~~~~~~~~~~ 77 (80)
T PF03693_consen 12 ELEAFI-EEQVASGRYSSASEVVREALRLLEEREAKLEALREALQEGL-ESGESEPFDMDDILARARR 77 (80)
T ss_dssp HHHHHH-HHHHCTTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CT-EESS--HHHHHHHCCH
T ss_pred HHHHHH-HHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCCCCCCCHHHHHHHHHh
Confidence 333434 4567899998777777665441 122233333333222 234 234677788776543
No 28
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=51.30 E-value=1.3e+02 Score=26.24 Aligned_cols=69 Identities=19% Similarity=0.183 Sum_probs=44.8
Q ss_pred chHHHHHHHHHHHHHhcChH-----HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHH
Q 033797 35 GEKEKLMELLRERLVECGWK-----DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFL 106 (111)
Q Consensus 35 Ge~erLk~lL~~rL~EcGW~-----DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL 106 (111)
.|...++++|..++..--|. +.+.....+.|-+.|+..-..++|++.+... .-++.++.-+...|...|
T Consensus 170 ~El~~lr~~l~~~~~~l~~~~~~~~~p~~~~l~~~Ll~~dv~~~la~~l~~~l~~~---~~~~~~~~~l~~~l~~~l 243 (484)
T PRK06995 170 QELRSLRGMLEEQLASLAWGERQRRDPVRAALLKHLLAAGFSAQLVRMLVDNLPEG---DDAEAALDWVQSALAKNL 243 (484)
T ss_pred HHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHCCCCHHHHHHHHHHHHhh---hchhHHHHHHHHHHHHHH
Confidence 67888999998888876663 3445556666777888777888888887543 233444444444444433
No 29
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=50.90 E-value=63 Score=21.26 Aligned_cols=50 Identities=12% Similarity=0.226 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHhcC---h-HHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhh
Q 033797 37 KEKLMELLRERLVECG---W-KDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGR 87 (111)
Q Consensus 37 ~erLk~lL~~rL~EcG---W-~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar 87 (111)
++.|+.+|+..|-.-+ + .++|..+.++. ...|...|+|++.+.-|...|.
T Consensus 29 ~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~-D~n~dG~v~f~eF~~li~~~~~ 82 (88)
T cd05027 29 KSELKELINNELSHFLEEIKEQEVVDKVMETL-DSDGDGECDFQEFMAFVAMVTT 82 (88)
T ss_pred HHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHh-CCCCCCcCcHHHHHHHHHHHHH
Confidence 5677777776443322 3 35588888765 4455567999999888876654
No 30
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=50.42 E-value=40 Score=20.47 Aligned_cols=42 Identities=17% Similarity=0.317 Sum_probs=35.7
Q ss_pred HHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 65 IKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 65 i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
+...| ..+|.++|++.|-|..- .+++..-.-.+.++|..|..
T Consensus 18 ~~~~~-~~vs~~~l~~~~w~~~~-~~~~~~l~~~I~rLR~kL~~ 59 (77)
T PF00486_consen 18 LRNPG-RVVSREELIEALWGDEE-DVSDNSLDVHISRLRKKLED 59 (77)
T ss_dssp HHTTT-SEEEHHHHHHHHTSSSS-TTCTHHHHHHHHHHHHHHHS
T ss_pred HhCCC-CCCCHHHhCChhhhccc-ccchhhHHHHHHHHHHHHhh
Confidence 34444 56899999999999987 88899999999999999876
No 31
>PF14426 Imm2: Immunity protein Imm2
Probab=50.03 E-value=15 Score=23.62 Aligned_cols=42 Identities=24% Similarity=0.466 Sum_probs=29.6
Q ss_pred cChHHHHHH-HHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHH
Q 033797 51 CGWKDEMKA-LCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLR 101 (111)
Q Consensus 51 cGW~DeVr~-~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~ 101 (111)
-||..++-+ .|+.+|..-= .+..+++|++.| |++--.++..-
T Consensus 11 gg~~pd~v~~~h~~~I~~~l-~~~~l~~Ll~~i--------p~eEae~l~~D 53 (60)
T PF14426_consen 11 GGWHPDVVEMFHRNWIHKLL-SEIPLNNLLDDI--------PSEEAEELRHD 53 (60)
T ss_pred ccCChHHHHHHHHHHHHHHH-HhCCHHHHHhhC--------CHHHHHHHHHH
Confidence 489877766 9999997653 568899999764 55555555443
No 32
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=48.35 E-value=80 Score=21.04 Aligned_cols=58 Identities=19% Similarity=0.300 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHh
Q 033797 40 LMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLA 107 (111)
Q Consensus 40 Lk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~ 107 (111)
+.+.++.-|.+.- ++.+-..++++-. . -|+++|+..+. .+++...|..|+..||.++-
T Consensus 8 f~~q~~~LL~~~E-r~~~~~~L~~Y~~----~-~~Vd~LV~~L~----~vLdtPaK~~Ll~~iR~lIp 65 (78)
T cd07347 8 FSQQVDHLLTDAE-REQVTRALERYHQ----E-RNVDDLVRDLY----LVLDTPAKLPLLQFLRQVIP 65 (78)
T ss_pred HHHHHHHHCCHHH-HHHHHHHHHHHHh----c-CCHHHHHHHHH----HHcCcHhHHHHHHHHHHHcC
Confidence 4445555554433 5566666666543 1 28999999998 68899999999999999874
No 33
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=47.88 E-value=99 Score=21.95 Aligned_cols=25 Identities=12% Similarity=0.312 Sum_probs=12.7
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHhh
Q 033797 58 KALCRAYIKKKGTNNVTVDDLVHVI 82 (111)
Q Consensus 58 r~~~re~i~~~g~~~vt~~~L~~~I 82 (111)
+...+..|..+|++.-.+++.++++
T Consensus 78 ~~~I~~~L~~kGi~~~~I~~~l~~~ 102 (157)
T PRK00117 78 PRRIRQELRQKGVDREIIEEALAEL 102 (157)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHc
Confidence 4445555566665544444444443
No 34
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=47.18 E-value=36 Score=23.97 Aligned_cols=26 Identities=8% Similarity=0.252 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHhcChHH-HHHHHHH
Q 033797 37 KEKLMELLRERLVECGWKD-EMKALCR 62 (111)
Q Consensus 37 ~erLk~lL~~rL~EcGW~D-eVr~~~r 62 (111)
+++|.+-+-+-|.+.|+.+ -|+++|+
T Consensus 5 k~~I~~a~~~Ll~~k~~~~ITV~~I~~ 31 (176)
T TIGR02366 5 KKKIAKAFKDLMEVQAFSKISVSDIMS 31 (176)
T ss_pred HHHHHHHHHHHHHHCCCccCCHHHHHH
Confidence 4567777777777777543 3444443
No 35
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=46.96 E-value=22 Score=26.69 Aligned_cols=21 Identities=24% Similarity=0.400 Sum_probs=10.6
Q ss_pred chHHHHHHHHHHHHHhcChHH
Q 033797 35 GEKEKLMELLRERLVECGWKD 55 (111)
Q Consensus 35 Ge~erLk~lL~~rL~EcGW~D 55 (111)
+.-..|-..|-.-|.+.||..
T Consensus 32 ~~~~~ia~~lI~~LD~~GyL~ 52 (194)
T PF04963_consen 32 EEEREIAEYLIDNLDDDGYLT 52 (194)
T ss_dssp TCCHHHHHHHCCCBTTTSTCS
T ss_pred HHHHHHHHHHHHcCCCCCccC
Confidence 333445555555555555543
No 36
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=46.74 E-value=37 Score=21.70 Aligned_cols=34 Identities=18% Similarity=0.356 Sum_probs=29.4
Q ss_pred CCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 73 VTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 73 vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
-++.+|+.+|-|. ..|.+++...|..-.-+|+++
T Consensus 5 ~~l~~lv~~id~~--~~~~~da~~~l~~~~e~fv~~ 38 (72)
T cd07981 5 RKLQELLKEIDPR--EQLDPDVEELLLEIADDFVDD 38 (72)
T ss_pred HHHHHHHHhhCCC--CCcCHHHHHHHHHHHHHHHHH
Confidence 4577899999886 779999999999999999876
No 37
>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=46.62 E-value=1.4e+02 Score=25.22 Aligned_cols=65 Identities=17% Similarity=0.260 Sum_probs=45.5
Q ss_pred cchhhHHHHHHHHHHhc--chHHHHHHHHHHHHHhcChHHH-----HHHHHHHHHHHhCCCCCCHHHHHHhh
Q 033797 18 EKEPTLQEIINIKMIES--GEKEKLMELLRERLVECGWKDE-----MKALCRAYIKKKGTNNVTVDDLVHVI 82 (111)
Q Consensus 18 ~~~~~lk~~I~~~LveS--Ge~erLk~lL~~rL~EcGW~De-----Vr~~~re~i~~~g~~~vt~~~L~~~I 82 (111)
...+.++.+|++...++ .|...|+.+|.+++..--|.+. ++....+.+.+.|++..-..+|++.+
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~El~~lr~ll~~~~~~~~w~~~~~~~p~~~~l~~~L~~~g~~~~l~~~l~~~~ 100 (374)
T PRK14722 29 AVADAVKARIERIVNDTVMQELGSLRELMEEQFAGLMWNERQRRNPVHGALTKYLFAAGFSAQLVRMIVDNL 100 (374)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcchhccCcHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 34556666666655544 7889999999999998889443 45556666777887665666666655
No 38
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=45.29 E-value=96 Score=22.29 Aligned_cols=57 Identities=16% Similarity=0.245 Sum_probs=43.0
Q ss_pred HHHHHHHHHhcChH-HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 033797 41 MELLRERLVECGWK-DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTEL 98 (111)
Q Consensus 41 k~lL~~rL~EcGW~-DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~El 98 (111)
...+..+|.+-|++ ..=|...-++|.+.+ +.+|.++|+..+....-.+=|..|++-|
T Consensus 5 ~~~~~~~lk~~glr~T~qR~~vl~~L~~~~-~~~sAeei~~~l~~~~p~islaTVYr~L 62 (145)
T COG0735 5 LEDAIERLKEAGLRLTPQRLAVLELLLEAD-GHLSAEELYEELREEGPGISLATVYRTL 62 (145)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHHHHhcC-CCCCHHHHHHHHHHhCCCCCHhHHHHHH
Confidence 34566788888884 666666777777665 4599999999999877777788887755
No 39
>PRK09462 fur ferric uptake regulator; Provisional
Probab=44.52 E-value=79 Score=22.37 Aligned_cols=54 Identities=15% Similarity=0.168 Sum_probs=37.2
Q ss_pred HHHHHhcChH-HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 033797 45 RERLVECGWK-DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTEL 98 (111)
Q Consensus 45 ~~rL~EcGW~-DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~El 98 (111)
.+.|.+.|.+ ..-|...-++|.+.....+|.++|++.+..+.-.+=+..|++-|
T Consensus 5 ~~~l~~~glr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L 59 (148)
T PRK09462 5 NTALKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVL 59 (148)
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHH
Confidence 3445666764 66777788888765335899999999998776544455665543
No 40
>TIGR02743 TraW type-F conjugative transfer system protein TraW. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm.
Probab=44.49 E-value=41 Score=26.07 Aligned_cols=33 Identities=27% Similarity=0.527 Sum_probs=27.0
Q ss_pred cchhhHHHHHHHHHH---hcchHHHHHHHHHHHHHh
Q 033797 18 EKEPTLQEIINIKMI---ESGEKEKLMELLRERLVE 50 (111)
Q Consensus 18 ~~~~~lk~~I~~~Lv---eSGe~erLk~lL~~rL~E 50 (111)
-.|.++=+.|++||- .||+++++.+.+++|-.+
T Consensus 31 I~E~D~L~~I~~rl~~~e~sGel~~~~~~~~~r~~~ 66 (202)
T TIGR02743 31 IAEPDMLEVIEQRLKRLEQSGELKAMQQRFQSRVLE 66 (202)
T ss_pred ccchHHHHHHHHHHHhhhhCchHHHHHHHHHHHHHH
Confidence 378999999999985 589999998887777643
No 41
>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional
Probab=44.45 E-value=91 Score=25.43 Aligned_cols=35 Identities=14% Similarity=0.315 Sum_probs=21.1
Q ss_pred HHhcChHHHHHHHHHHHHH-Hh-CCCCCCHHHHHHhh
Q 033797 48 LVECGWKDEMKALCRAYIK-KK-GTNNVTVDDLVHVI 82 (111)
Q Consensus 48 L~EcGW~DeVr~~~re~i~-~~-g~~~vt~~~L~~~I 82 (111)
..+.||.|||+.+...-.. .. ....+-|.+++..+
T Consensus 211 Ml~~GlieEv~~l~~~~~~~~~~~~~aIGYkE~~~yl 247 (300)
T PRK14729 211 MIDCGLLSEIKSLLGKGYNENTPAFKGIGYREFLLWK 247 (300)
T ss_pred HHHCCHHHHHHHHHhcCCCCCCCcceeEcHHHHHHHH
Confidence 3578999999988752110 00 12345677777766
No 42
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=44.10 E-value=1.1e+02 Score=22.48 Aligned_cols=60 Identities=8% Similarity=0.149 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHhcChH-HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 033797 38 EKLMELLRERLVECGWK-DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTEL 98 (111)
Q Consensus 38 erLk~lL~~rL~EcGW~-DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~El 98 (111)
+.+.+.+.+.|.+.|.+ ..-|...-++|.+.+ +.+|.++|++.+....-..=...|++-|
T Consensus 7 ~~~~~~~~~~L~~~GlR~T~qR~~IL~~l~~~~-~hlSa~eI~~~L~~~~~~is~aTVYRtL 67 (169)
T PRK11639 7 QELLAQAEKLCAQRNVRLTPQRLEVLRLMSLQP-GAISAYDLLDLLREAEPQAKPPTVYRAL 67 (169)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC-CCCCHHHHHHHHHhhCCCCCcchHHHHH
Confidence 44455566667788884 777777888887664 6899999999998776444444555443
No 43
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=43.56 E-value=38 Score=20.67 Aligned_cols=38 Identities=16% Similarity=0.317 Sum_probs=26.3
Q ss_pred HHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHH
Q 033797 63 AYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFL 106 (111)
Q Consensus 63 e~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL 106 (111)
++|.+.|...+|..||++.+-+ ....+-..+.||-.||
T Consensus 13 dii~~~g~~~ls~~eia~~l~~------~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 13 DIIHNAGGGPLSLSEIAARLPT------SNPSAPPMLDRIMRLL 50 (51)
T ss_dssp HHHHHHTTS-BEHHHHHHTSTC------T-TTHHHHHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHHHcCC------CCcchHHHHHHHHHHh
Confidence 4566666457899999998873 2233567888988887
No 44
>KOG1964 consensus Nuclear pore complex, rNup107 component (sc Nup84) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=43.02 E-value=90 Score=29.12 Aligned_cols=59 Identities=17% Similarity=0.348 Sum_probs=44.2
Q ss_pred cchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHh--------------------CCCCCCHHHHHHhhchhhhccCCHH
Q 033797 34 SGEKEKLMELLRERLVECGWKDEMKALCRAYIKKK--------------------GTNNVTVDDLVHVITPKGRASIPDS 93 (111)
Q Consensus 34 SGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~--------------------g~~~vt~~~L~~~I~P~Ar~~VP~~ 93 (111)
||...-+.-+ ..+||.|.|=.+.+..+..+ +..+.|.+.+++++.-.+-+.||++
T Consensus 309 SG~l~nl~~l-----~~s~Wed~vWAy~n~~v~~~ie~~l~~a~~~~tq~~p~~~~~~~lT~e~ifeEL~~~~~a~v~~e 383 (800)
T KOG1964|consen 309 SGILGNLLPL-----LKSGWEDKVWAYLNSMVQARIEAYLGAAPLNETQETPSDLFNGPLTSELIFEELRNEADARVEEE 383 (800)
T ss_pred hccccchhhH-----HhcchHHHHHHHHHHHHHHHHHHHHhhccccccCCChhhhcCCcCcHHHHHHHHHHHhhhcchhh
Confidence 5555555444 45799999999998877543 2234699999999999999999997
Q ss_pred HHHH
Q 033797 94 IKTE 97 (111)
Q Consensus 94 VK~E 97 (111)
...-
T Consensus 384 a~~~ 387 (800)
T KOG1964|consen 384 AQHP 387 (800)
T ss_pred hhch
Confidence 6554
No 45
>PF05205 COMPASS-Shg1: COMPASS (Complex proteins associated with Set1p) component shg1
Probab=42.92 E-value=1.1e+02 Score=21.10 Aligned_cols=24 Identities=17% Similarity=0.217 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHhcChHHHHHHH
Q 033797 37 KEKLMELLRERLVECGWKDEMKAL 60 (111)
Q Consensus 37 ~erLk~lL~~rL~EcGW~DeVr~~ 60 (111)
+..+..+|+..+..+|-+..+...
T Consensus 56 k~k~~alI~~~i~rs~~~~~~e~~ 79 (106)
T PF05205_consen 56 KGKARALIEGAIDRSGVYKGVERI 79 (106)
T ss_pred hHHHHHHHHHHHHHhhhhhhHHHH
Confidence 334444444444444444443333
No 46
>PF13797 Post_transc_reg: Post-transcriptional regulator
Probab=42.63 E-value=1e+02 Score=20.72 Aligned_cols=37 Identities=22% Similarity=0.366 Sum_probs=29.7
Q ss_pred ChHHHHHHHHHHHHH---HhCCCCCCHHHHHHhhchhhhc
Q 033797 52 GWKDEMKALCRAYIK---KKGTNNVTVDDLVHVITPKGRA 88 (111)
Q Consensus 52 GW~DeVr~~~re~i~---~~g~~~vt~~~L~~~I~P~Ar~ 88 (111)
.|++.|+-.|...++ .-|.++||.++|-+-++-+-..
T Consensus 4 ~~~~~v~p~l~sK~eEf~~lGY~~vt~~dlw~yl~~~~WK 43 (87)
T PF13797_consen 4 EWREQVEPALQSKAEEFHLLGYESVTEEDLWSYLTEKKWK 43 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcCcCCHHHHHHHHHHHHhc
Confidence 688899988886654 3599999999999999876544
No 47
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=42.50 E-value=94 Score=24.53 Aligned_cols=49 Identities=24% Similarity=0.292 Sum_probs=21.4
Q ss_pred chHHHHHHHHHHHHHhcChH--HHHHHHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 35 GEKEKLMELLRERLVECGWK--DEMKALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 35 Ge~erLk~lL~~rL~EcGW~--DeVr~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
.|++.|+.+|...+..-.|. +.......+.|.+.|++.--.++|++++.
T Consensus 111 ~e~~~lk~~l~~~~~~~~~~~~~~~l~~l~~~L~~~gv~~~la~~L~~~l~ 161 (282)
T TIGR03499 111 KELEALRELLERLLAGLAWLQRDPEGAKLLERLLRAGVSPELARELLEKLP 161 (282)
T ss_pred HHHHHHHHHHHHHHHhhhhcccCHHHHHHHHHHHHCCCCHHHHHHHHHHhh
Confidence 35555565555555443331 11112233344445544444444444443
No 48
>cd08789 CARD_IPS-1_RIG-I Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases. Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. MDA5 and RIG-I associate with IPS-1 through a CARD-CAR
Probab=42.41 E-value=63 Score=21.40 Aligned_cols=40 Identities=18% Similarity=0.175 Sum_probs=33.4
Q ss_pred hhhHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHH
Q 033797 20 EPTLQEIINIKMIESGEKEKLMELLRERLVECGWKDEMKA 59 (111)
Q Consensus 20 ~~~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~ 59 (111)
.++.++.|+...-..|..+....+|..-....||....-.
T Consensus 31 t~~d~e~I~a~~~~~G~~~aa~~Ll~~L~r~~~Wf~~Fl~ 70 (84)
T cd08789 31 TAEDKERIQAAENNSGNIKAAWTLLDTLVRRDNWLEPFLD 70 (84)
T ss_pred CHHHHHHHHHHHhcCChHHHHHHHHHHHhccCChHHHHHH
Confidence 4567888988877789999999999888899999877643
No 49
>PF09551 Spore_II_R: Stage II sporulation protein R (spore_II_R); InterPro: IPR014202 This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation [, ].
Probab=42.09 E-value=1.3e+02 Score=21.90 Aligned_cols=40 Identities=23% Similarity=0.390 Sum_probs=31.5
Q ss_pred HHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCC
Q 033797 25 EIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGT 70 (111)
Q Consensus 25 ~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~ 70 (111)
+.+...|-.+++.+..++.+...|. ++++.+.+.|.+.|.
T Consensus 31 ~~l~~~~~~~~~~~ea~~~i~~~~~------~Ie~~A~~~l~~~G~ 70 (130)
T PF09551_consen 31 EYLSPWLSQAKSKEEAREVIRENLP------EIEQIAEEVLAEEGY 70 (130)
T ss_pred HHHHHHhccCCCHHHHHHHHHHhHH------HHHHHHHHHHHHhCC
Confidence 3444445568889999999888875 699999999999984
No 50
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=41.74 E-value=1.2e+02 Score=21.85 Aligned_cols=42 Identities=19% Similarity=0.148 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHH
Q 033797 58 KALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRI 102 (111)
Q Consensus 58 r~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~I 102 (111)
=..|.++|+++| ..++|.+|+.+|..... ++.+-....+.++
T Consensus 6 idvAy~iL~~~~-~~m~f~dL~~ev~~~~~--~s~e~~~~~iaq~ 47 (129)
T PRK02363 6 IEVAYEILKEKK-EPMSFYDLVNEIQKYLG--KSDEEIRERIAQF 47 (129)
T ss_pred HHHHHHHHHHcC-CcccHHHHHHHHHHHhC--CCHHHHHHHHHHH
Confidence 357889998886 78999999999986654 4443333444443
No 51
>cd01493 APPBP1_RUB Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. ABPP1 contains part of the adenylation domain.
Probab=41.14 E-value=1.2e+02 Score=25.99 Aligned_cols=61 Identities=18% Similarity=0.243 Sum_probs=50.3
Q ss_pred CCCCCCCchhhhccchhhHHHHHHHHHHh--cchHHHHHHHHHHHHHhcC------hHHHHHHHHHHHH
Q 033797 5 VNRPPTPDAVEDQEKEPTLQEIINIKMIE--SGEKEKLMELLRERLVECG------WKDEMKALCRAYI 65 (111)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~lk~~I~~~Lve--SGe~erLk~lL~~rL~EcG------W~DeVr~~~re~i 65 (111)
...+|-||.-.+|......+-++|.-..+ .-+...+.+.+++.|.+.| +.++|+.-||+.-
T Consensus 304 ~g~lPl~G~lPDM~s~t~~Yi~Lq~iY~~ka~~D~~~v~~~v~~~~~~~g~~~~~I~~~~i~~FCkna~ 372 (425)
T cd01493 304 NGLLPLPGTLPDMTADTEKYIKLQNIYREKAEKDAAEVEKYVREILKSLGRSPDSISDKEIKLFCKNAA 372 (425)
T ss_pred CCCCCCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhhHH
Confidence 34689999999998888888888775553 4577788999999999988 9999999999863
No 52
>PF08775 ParB: ParB family; InterPro: IPR014884 ParB is a component of the par system which mediates accurate DNA partition during cell division. It recognises A-box and B-box DNA motifs. ParB forms an asymmetric dimer with 2 extended helix-turn-helix (HTH) motifs that bind to A-boxes. The HTH motifs emanate from a beta sheet coiled coil DNA binding module []. Both DNA binding elements are free to rotate around a flexible linker, this enables them to bind to complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site []. ; PDB: 1ZX4_A 2NTZ_B.
Probab=41.07 E-value=29 Score=25.03 Aligned_cols=38 Identities=32% Similarity=0.473 Sum_probs=28.7
Q ss_pred CCCCHHHHHHhhchhhhc----cCCHHHHHHHHHHHHHHHhh
Q 033797 71 NNVTVDDLVHVITPKGRA----SIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 71 ~~vt~~~L~~~I~P~Ar~----~VP~~VK~Ell~~Ir~fL~~ 108 (111)
+++++++++..|...-.. +-++++|..||..|+..+..
T Consensus 25 ~~~~l~~~i~~v~~~~~~~~~~~~~de~K~~Il~~ik~~~~~ 66 (127)
T PF08775_consen 25 NKVSLDELIDNVRSEIENIDDELSPDEVKKKILKLIKAELKS 66 (127)
T ss_dssp -HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHhhccccChHHHHHHHHHHHHHHHHh
Confidence 457888888888875443 44789999999999998853
No 53
>PF10057 DUF2294: Uncharacterized conserved protein (DUF2294); InterPro: IPR018745 This domain of unknown function is found in a family of hypothetical bacterial proteins with no known function. It is also found at the C terminus of proteins provisionally annotated as response regulators.
Probab=39.86 E-value=79 Score=21.92 Aligned_cols=41 Identities=22% Similarity=0.289 Sum_probs=34.5
Q ss_pred HHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHH
Q 033797 25 EIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIK 66 (111)
Q Consensus 25 ~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~ 66 (111)
+...+.|+++.+...+-...|..|.+++ .++++.+..+++.
T Consensus 49 Tp~Ek~L~~~~~g~~lv~~~R~~l~~~~-~~~l~~~ie~i~g 89 (118)
T PF10057_consen 49 TPAEKFLAETEEGRELVKQVRTSLIESL-KPELKEMIEEILG 89 (118)
T ss_pred CHHHHHHHhCcchHHHHHHHHHHHHHHH-HHHHHHHHHHHhC
Confidence 3467889999777888888999999999 9999998888763
No 54
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=39.52 E-value=55 Score=23.40 Aligned_cols=27 Identities=4% Similarity=0.192 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHh
Q 033797 55 DEMKALCRAYIKKKGTNNVTVDDLVHV 81 (111)
Q Consensus 55 DeVr~~~re~i~~~g~~~vt~~~L~~~ 81 (111)
+.|-+.+.+++.++|.+++|+.+|.++
T Consensus 11 ~~Il~aA~~lf~e~G~~~~s~~~IA~~ 37 (202)
T TIGR03613 11 KAILSAALDTFSRFGFHGTSLEQIAEL 37 (202)
T ss_pred HHHHHHHHHHHHHhCcccCCHHHHHHH
Confidence 344445555566666666666555543
No 55
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=39.14 E-value=36 Score=18.66 Aligned_cols=15 Identities=33% Similarity=0.368 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHH
Q 033797 92 DSIKTELLLRIRAFL 106 (111)
Q Consensus 92 ~~VK~Ell~~Ir~fL 106 (111)
.-.|.+|..+|.+|+
T Consensus 21 ~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 21 SGTKAELVDRLLEAL 35 (35)
T ss_pred CCCHHHHHHHHHHhC
Confidence 346888888888774
No 56
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=39.02 E-value=1.3e+02 Score=23.80 Aligned_cols=61 Identities=21% Similarity=0.261 Sum_probs=36.2
Q ss_pred HHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCH-HHHHHHHHHHHHHHh
Q 033797 42 ELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPD-SIKTELLLRIRAFLA 107 (111)
Q Consensus 42 ~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~-~VK~Ell~~Ir~fL~ 107 (111)
.+|+.||. .+...++..=+.+.++ |+++.|.+||.....-.| +-+. -...++...+..+|+
T Consensus 192 ~~lr~rL~--~~~~~l~~dD~~i~~e-Gv~~Ls~~EL~~Ac~~RG--l~~~~~s~~~lr~~L~~WL~ 253 (268)
T PF07766_consen 192 SLLRRRLR--KRLRYLKQDDRLIKRE-GVDSLSEEELQDACYERG--LRSTGLSEEELREWLKQWLQ 253 (268)
T ss_dssp HHHHHHHH--HHHHHHHHHHHHHHHH--GGGS-HHHHHHHHHHTT-----TT--HHHHHHHHHHHHH
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHh-ccccCCHHHHHHHHHHhC--CCcCCCCHHHHHHHHHHHHH
Confidence 34556665 3566677776766666 999999999998776444 4443 234566666666663
No 57
>PF02777 Sod_Fe_C: Iron/manganese superoxide dismutases, C-terminal domain Note: SCOP classifies the two domains separately.; InterPro: IPR019832 Superoxide dismutases (SODs) (1.15.1.1 from EC) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [, , ]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers. The structure of Fe/MnSODs can be divided into two domains, an alpha N-terminal domain and an alpha/beta C-terminal domain, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist []. The structure of the C-terminal domain is of the alpha/beta type, and consists of a three-stranded antiparallel beta-sheet in the order 213, along with four helices in the arrangement alpha/beta(2)/alpha/beta/alpha(2) []. This entry represents the C-terminal domain of Manganese/iron superoxide dismutase. ; GO: 0004784 superoxide dismutase activity, 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 1KKC_Y 2GOJ_B 1UES_C 1UER_C 1QNN_A 1MY6_A 1MA1_F 1P7G_Q 3EVK_D 2GPC_A ....
Probab=37.94 E-value=61 Score=21.84 Aligned_cols=31 Identities=16% Similarity=0.395 Sum_probs=25.4
Q ss_pred hhhHHHHHHHHHHhcchHHHHHHHHHHHHHh---cCh
Q 033797 20 EPTLQEIINIKMIESGEKEKLMELLRERLVE---CGW 53 (111)
Q Consensus 20 ~~~lk~~I~~~LveSGe~erLk~lL~~rL~E---cGW 53 (111)
...|.+.|+..+ |.++.+++.+...... +||
T Consensus 4 ~g~l~~~I~~~F---GS~d~fk~~f~~~a~~~~GsGW 37 (106)
T PF02777_consen 4 SGKLKKAIEEDF---GSFDNFKAEFTAAALSVFGSGW 37 (106)
T ss_dssp THHHHHHHHHHH---SSHHHHHHHHHHHHHHSSSSEE
T ss_pred CHHHHHHHHHHh---CCHHHHHHHHHHHHhcCCCCCe
Confidence 467888888876 8999999999887766 888
No 58
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=37.48 E-value=65 Score=16.89 Aligned_cols=25 Identities=36% Similarity=0.619 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHH
Q 033797 39 KLMELLRERLVECGWKDEMKALCRA 63 (111)
Q Consensus 39 rLk~lL~~rL~EcGW~DeVr~~~re 63 (111)
.|..++..=|.++|..+--+..++|
T Consensus 2 ~Ln~lI~~YL~~~Gy~~tA~~f~~E 26 (27)
T PF08513_consen 2 ELNQLIYDYLVENGYKETAKAFAKE 26 (27)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCcHHHHHHHHhc
Confidence 4666667777777777766666554
No 59
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=37.44 E-value=43 Score=26.80 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=31.8
Q ss_pred hcchHHHHHHHHHHHHHh------------------cChHHHHHHHHHHHHHHhCCCCCCHHH
Q 033797 33 ESGEKEKLMELLRERLVE------------------CGWKDEMKALCRAYIKKKGTNNVTVDD 77 (111)
Q Consensus 33 eSGe~erLk~lL~~rL~E------------------cGW~DeVr~~~re~i~~~g~~~vt~~~ 77 (111)
-.|+.+.|-+-|++.+.+ .|+++++-+.|+.++++.....++.++
T Consensus 116 ~iG~~~~lp~~~~~~~~~~e~~T~~~~~~~Lnia~~Yggr~EI~~A~~~~~~~~~~~~~~~~~ 178 (256)
T PRK14828 116 HVGSLDLLPAPSANRLKEAEEATVGNDGIKVNVAVGYGGRQEIVDAVRSLLTEHKDKGTSIDE 178 (256)
T ss_pred EECChhhCCHHHHHHHHHHHHhhcCCCCcEEEEEecCCCHHHHHHHHHHHHHHHHhCCCChhh
Confidence 357888888888777755 599999999999988653222344443
No 60
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=37.19 E-value=51 Score=19.51 Aligned_cols=26 Identities=15% Similarity=0.443 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHH
Q 033797 55 DEMKALCRAYIKKKGTNNVTVDDLVH 80 (111)
Q Consensus 55 DeVr~~~re~i~~~g~~~vt~~~L~~ 80 (111)
..+|..+-.+.+++|.+.||.+.+.+
T Consensus 18 ~~~r~~~E~~Ar~~G~~~IT~e~v~~ 43 (45)
T PF08369_consen 18 KKLRDAAEKYARERGYDEITVEVVDA 43 (45)
T ss_dssp HHHHHHHHHHHHHCT-SEE-HHHHHH
T ss_pred HHHHHHHHHHHHHcCCCeECHHHHHh
Confidence 56667777777889999999987764
No 61
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=36.66 E-value=66 Score=23.28 Aligned_cols=19 Identities=11% Similarity=0.345 Sum_probs=7.8
Q ss_pred HHHHHHHhCCCCCCHHHHH
Q 033797 61 CRAYIKKKGTNNVTVDDLV 79 (111)
Q Consensus 61 ~re~i~~~g~~~vt~~~L~ 79 (111)
+.+.+.++|.+.+|+++|.
T Consensus 20 A~~lf~e~G~~~~t~~~Ia 38 (215)
T PRK10668 20 ALRLFSQQGVSATSLADIA 38 (215)
T ss_pred HHHHHHHcCcccCCHHHHH
Confidence 3333444444444444433
No 62
>PF14766 RPA_interact_N: Replication protein A interacting N-terminal
Probab=36.64 E-value=42 Score=19.76 Aligned_cols=17 Identities=18% Similarity=0.712 Sum_probs=14.9
Q ss_pred ChHHHHHHHHHHHHHHh
Q 033797 52 GWKDEMKALCRAYIKKK 68 (111)
Q Consensus 52 GW~DeVr~~~re~i~~~ 68 (111)
-|.+.+|+-|.+-+++.
T Consensus 14 ~WKe~lR~rC~~R~r~~ 30 (42)
T PF14766_consen 14 PWKETLRERCLERVRES 30 (42)
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 59999999999998765
No 63
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=36.56 E-value=70 Score=22.17 Aligned_cols=33 Identities=9% Similarity=0.344 Sum_probs=28.3
Q ss_pred CCCHHHHHHhhchhhhccCCHHHHHHHHHHHHH
Q 033797 72 NVTVDDLVHVITPKGRASIPDSIKTELLLRIRA 104 (111)
Q Consensus 72 ~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~ 104 (111)
..+.+++++.+.-.++.-||+.|+..|.+-.+.
T Consensus 54 G~~~e~i~~~L~~~S~~~lP~~v~~~i~~w~~~ 86 (129)
T PF13625_consen 54 GLTAEEIIEFLERYSKNPLPQNVEQSIEDWARR 86 (129)
T ss_pred CCCHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence 489999999999999999999999877665544
No 64
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=36.07 E-value=54 Score=18.73 Aligned_cols=23 Identities=17% Similarity=0.299 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCCCCCHHHHHHhh
Q 033797 60 LCRAYIKKKGTNNVTVDDLVHVI 82 (111)
Q Consensus 60 ~~re~i~~~g~~~vt~~~L~~~I 82 (111)
.+.+.+.+.|.+.+|+.+|.++.
T Consensus 4 aa~~l~~~~G~~~~s~~~Ia~~~ 26 (47)
T PF00440_consen 4 AALELFAEKGYEAVSIRDIARRA 26 (47)
T ss_dssp HHHHHHHHHHTTTSSHHHHHHHH
T ss_pred HHHHHHHHhCHHhCCHHHHHHHH
Confidence 46677788899999999998765
No 65
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=35.67 E-value=58 Score=26.38 Aligned_cols=50 Identities=12% Similarity=0.228 Sum_probs=37.0
Q ss_pred cchHHHHHHHHHHHHH------------------hcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 34 SGEKEKLMELLRERLV------------------ECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 34 SGe~erLk~lL~~rL~------------------EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
.|+.+.|-+.++..+. -.|+++++-..++.+++......++.+++.+++.
T Consensus 136 iGd~~~Lp~~l~~~i~~~e~~T~~~~~~~Lnia~~Yggr~EI~~A~k~i~~~~~~g~~~~~~i~~~~~ 203 (275)
T PRK14835 136 IGRHDGFPPKVLEALEELEERTEGHEGMLLNIAVGYGGREEIVDAVKSLLLEAAATGKSPEEVAAELT 203 (275)
T ss_pred ecChhhCCHHHHHHHHHHHHHhcCCCCeEEEEEeccCCHHHHHHHHHHHHHHHHcCCCChHHhcccCC
Confidence 3888888888888775 3699999999999998764334566666644443
No 66
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=35.41 E-value=38 Score=18.76 Aligned_cols=14 Identities=36% Similarity=0.567 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHH
Q 033797 93 SIKTELLLRIRAFL 106 (111)
Q Consensus 93 ~VK~Ell~~Ir~fL 106 (111)
-.|.+|+.||.+|+
T Consensus 22 G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 22 GKKAELIERLKEHL 35 (35)
T ss_dssp SSHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhC
Confidence 34888888888775
No 67
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=34.69 E-value=63 Score=22.43 Aligned_cols=45 Identities=20% Similarity=0.381 Sum_probs=32.4
Q ss_pred chHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCC--CCCCHHHHHHhhc
Q 033797 35 GEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGT--NNVTVDDLVHVIT 83 (111)
Q Consensus 35 Ge~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~--~~vt~~~L~~~I~ 83 (111)
.+|--|-.+|+.+|-+ |+|++.+.+.+...+. +.+.+...+..|+
T Consensus 23 ~Dy~PLlALL~r~Ltd----~ev~~Va~~L~~~~~~~~~~~dI~~~I~~vt 69 (96)
T PF11829_consen 23 TDYVPLLALLRRRLTD----DEVAEVAAELAARGDPPVDRIDIGVAITRVT 69 (96)
T ss_dssp HHHHHHHHHHTTTS-H----HHHHHHHHHHHHHTSS-BSCCHHHHHHHHHC
T ss_pred CccHHHHHHhcccCCH----HHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 4677888999999987 8999999998876543 4445555555555
No 68
>PLN02848 adenylosuccinate lyase
Probab=34.63 E-value=2.2e+02 Score=24.50 Aligned_cols=65 Identities=18% Similarity=0.238 Sum_probs=40.2
Q ss_pred HHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 033797 27 INIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLL 100 (111)
Q Consensus 27 I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~ 100 (111)
+...|-.++.. +.+.+...|.+.| +.+-.+..++....+ +++-+++.+.|.-- .+|++++.+|+.
T Consensus 377 m~~nl~~~~~~--~sE~~~~~l~~~G-~~~A~e~v~~~~~~~---~~~~~~~~~~~~~~---~~~~~~~~~l~~ 441 (458)
T PLN02848 377 LAEDLDQTWEV--LAEPIQTVMRRYG-VPEPYEKLKELTRGR---AVTKESMREFIEGL---ELPEEAKDQLLK 441 (458)
T ss_pred HHHHHHccchh--HHHHHHHHHHHhC-hHHHHHHHHHHHHHc---cCCHHHHHHHHHHc---CCCHHHHHHHHh
Confidence 34444445555 6777777777777 455555555544433 46666666666542 399999988874
No 69
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=34.07 E-value=1.2e+02 Score=22.40 Aligned_cols=61 Identities=23% Similarity=0.347 Sum_probs=44.5
Q ss_pred chhhHHHHHHHHHHhcchHHHHHHHHH----HHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhh
Q 033797 19 KEPTLQEIINIKMIESGEKEKLMELLR----ERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVI 82 (111)
Q Consensus 19 ~~~~lk~~I~~~LveSGe~erLk~lL~----~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I 82 (111)
.-+.+++..++++-.|++...+-+.|+ +.+.+-=|...-=+...+.+++.| ++++.+++.|
T Consensus 115 P~~~l~aL~~~K~~~s~~F~~f~~~l~S~ef~~~~~~~~~~~~~~~~~~~L~~~G---vdv~~l~~~v 179 (179)
T PF06757_consen 115 PRDKLRALYEEKLATSPEFAEFVEALRSPEFQQLYNALWASPEFQRLLNELRENG---VDVDYLLELV 179 (179)
T ss_pred CHHHHHHHHHHHHHCCHHHHHHHHHHcCHHHHHHHHHHHcCHHHHHHHHHHHHcC---CCHHHHHHhC
Confidence 678899999999999999988877774 345555555555555556677776 6777777654
No 70
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=34.02 E-value=73 Score=22.98 Aligned_cols=25 Identities=12% Similarity=0.228 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHhcChH-HHHHHHHH
Q 033797 38 EKLMELLRERLVECGWK-DEMKALCR 62 (111)
Q Consensus 38 erLk~lL~~rL~EcGW~-DeVr~~~r 62 (111)
++|-+-..+-+.+.|+. -.|++.|+
T Consensus 14 ~~Il~aa~~lf~~~G~~~~ti~~Ia~ 39 (213)
T PRK09975 14 QELIETAIAQFALRGVSNTTLNDIAD 39 (213)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHH
Confidence 44444555555566653 34444444
No 71
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=34.01 E-value=14 Score=24.40 Aligned_cols=47 Identities=19% Similarity=0.296 Sum_probs=30.8
Q ss_pred hcChHHHHHHHHHHHHHH-hCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 033797 50 ECGWKDEMKALCRAYIKK-KGTNNVTVDDLVHVITPKGRASIPDSIKTEL 98 (111)
Q Consensus 50 EcGW~DeVr~~~re~i~~-~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~El 98 (111)
-|++.+.+++.+++.+.. .|.+++++. +..-.|-.-+++.++.|.+|
T Consensus 49 ~~~~~~~l~~~i~~al~~l~gv~~v~v~--i~~~~~~~~~~~~~~~~~~~ 96 (99)
T TIGR02945 49 NCPVAGSMPGEVENAVRAVPGVGSVTVE--LVWDPPWTPERMSEEARLEL 96 (99)
T ss_pred CCChHHHHHHHHHHHHHhCCCCceEEEE--EEeeCCCChHHCCHHHHHHc
Confidence 377888999999988876 465555433 22334555567777777665
No 72
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=33.33 E-value=2.5e+02 Score=23.00 Aligned_cols=75 Identities=17% Similarity=0.120 Sum_probs=47.6
Q ss_pred chhhHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCC------HHHHHHhhchhhhccCCH
Q 033797 19 KEPTLQEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVT------VDDLVHVITPKGRASIPD 92 (111)
Q Consensus 19 ~~~~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt------~~~L~~~I~P~Ar~~VP~ 92 (111)
-.+..++.|.+-..|++++.+= +..+..+.+.+.+++.|+.-+. |.+..+.+.+.-....|
T Consensus 250 L~~e~q~il~~aa~e~~~~~~~------------~~~~~e~~~~e~lk~~Gv~v~~~~~~~~~~~~~~~~~~~~~~~~~- 316 (332)
T COG1638 250 LPEEDQTILLEAAKEAAEEQRK------------LVEELEDELLEKLKEAGVEVVEPDAAEAFREAAKPVYDEFAKKAG- 316 (332)
T ss_pred CCHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHCCCEEecCCchHHHHHHHHHHHHHHHhhch-
Confidence 3455666666666666655432 2234445567777888854333 55667777777777776
Q ss_pred HHHHHHHHHHHHHH
Q 033797 93 SIKTELLLRIRAFL 106 (111)
Q Consensus 93 ~VK~Ell~~Ir~fL 106 (111)
.+-.+++..|++..
T Consensus 317 ~~g~~l~e~~~~~~ 330 (332)
T COG1638 317 EIGAELIEAIEAAR 330 (332)
T ss_pred hhhHHHHHHHHHhh
Confidence 67788888887754
No 73
>PLN02152 indole-3-acetate beta-glucosyltransferase
Probab=33.16 E-value=55 Score=27.99 Aligned_cols=48 Identities=17% Similarity=0.253 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHHhcC--hHHH---HHHHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 36 EKEKLMELLRERLVECG--WKDE---MKALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 36 e~erLk~lL~~rL~EcG--W~De---Vr~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
+.+.|.+.+++-|.+.| .+.. ++..+++.+.+.|....++++++++|+
T Consensus 403 ~~e~l~~av~~vm~~~~~~~r~~a~~~~~~~~~a~~~ggsS~~nl~~li~~i~ 455 (455)
T PLN02152 403 ERGEIRRCLEAVMEEKSVELRESAEKWKRLAIEAGGEGGSSDKNVEAFVKTLC 455 (455)
T ss_pred cHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHhC
Confidence 56667777777665433 3333 466677777767776678888888763
No 74
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=32.70 E-value=1.2e+02 Score=18.92 Aligned_cols=42 Identities=14% Similarity=0.238 Sum_probs=32.3
Q ss_pred HHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 65 IKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 65 i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
+...| ..+|.++|++.|-+..- .+++..-.-.+.+||..|..
T Consensus 36 ~~~~~-~~vs~~~l~~~lw~~~~-~~~~~~l~~~I~rLRkkl~~ 77 (95)
T cd00383 36 ARNPG-RVLSREQLLEAVWGDDY-DVDDRTVDVHISRLRKKLED 77 (95)
T ss_pred HhCCC-CcCCHHHHHHHhcCCCC-CCCcccHHHHHHHHHHHhcc
Confidence 34445 67899999999987654 35677788889999999865
No 75
>TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=32.58 E-value=2.5e+02 Score=22.65 Aligned_cols=54 Identities=15% Similarity=0.278 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 54 KDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 54 ~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
.+.++..+......+- ..+++...+..+.-..+..=+++.|+.++..+.+|+++
T Consensus 44 ~~~l~~~~~~L~~arP-t~v~l~nai~~~~~~i~~~~~~~~k~~l~~~~~~~~~e 97 (301)
T TIGR00511 44 RAEMREAANILISTRP-TAVSLPNAVRYVLKYMSGEDVETLRETVIERADAFINQ 97 (301)
T ss_pred HHHHHHHHHHHHHcCC-chhhHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHH
Confidence 3556666666555553 45677777777665554444578999999999999865
No 76
>PF01715 IPPT: IPP transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) [].; GO: 0005524 ATP binding, 0008033 tRNA processing; PDB: 2ZXU_A 3FOZ_A 2ZM5_B 3D3Q_A 3EXA_B 2QGN_A 3A8T_A 3EPK_B 3EPH_A 3EPJ_A ....
Probab=32.52 E-value=1.3e+02 Score=23.53 Aligned_cols=36 Identities=14% Similarity=0.280 Sum_probs=24.5
Q ss_pred HhcChHHHHHHHHHHHHHHh--CCCCCCHHHHHHhhch
Q 033797 49 VECGWKDEMKALCRAYIKKK--GTNNVTVDDLVHVITP 84 (111)
Q Consensus 49 ~EcGW~DeVr~~~re~i~~~--g~~~vt~~~L~~~I~P 84 (111)
.+.||.|||+.+........ ....+-|.++++.+.-
T Consensus 178 l~~GlleEv~~L~~~~~~~~~~~~~aIGYkE~~~~l~g 215 (253)
T PF01715_consen 178 LEQGLLEEVRALLERGLPPDLPAMQAIGYKEFIDYLEG 215 (253)
T ss_dssp HHTTHHHHHHHHHHTTGGTTSCGGGSTTHHHHHHHHTT
T ss_pred HHhHHHHHHHHHHHcCCCCcchhceeeehHHHHHhhcC
Confidence 45699999998887652211 1345678888887764
No 77
>PRK02260 S-ribosylhomocysteinase; Provisional
Probab=32.46 E-value=1e+02 Score=23.30 Aligned_cols=28 Identities=18% Similarity=0.391 Sum_probs=18.8
Q ss_pred HhcChHH-----HHHHHHHHHHHHhCCCCCCHHH
Q 033797 49 VECGWKD-----EMKALCRAYIKKKGTNNVTVDD 77 (111)
Q Consensus 49 ~EcGW~D-----eVr~~~re~i~~~g~~~vt~~~ 77 (111)
.||||+- ..|..|+.++.+ +....+++.
T Consensus 123 ~~CGny~~hsL~~Ak~~a~~~L~~-~~~~~~~~~ 155 (158)
T PRK02260 123 YQCGNYKDHSLEGAKEIARKILDQ-GISVNPNEE 155 (158)
T ss_pred hcCCChhhCCHHHHHHHHHHHHHh-hcccCchhh
Confidence 6899985 578888888864 333444443
No 78
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=31.89 E-value=1.7e+02 Score=20.16 Aligned_cols=60 Identities=18% Similarity=0.391 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHh------CCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 033797 36 EKEKLMELLRERLVECGWKDEMKALCRAYIKKK------GTNNVTVDDLVHVITPKGRASIPDSIKTEL 98 (111)
Q Consensus 36 e~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~------g~~~vt~~~L~~~I~P~Ar~~VP~~VK~El 98 (111)
-|..+..--+..|.. .|.++|-..|++.|..+ ....++++|+-+-.-|. ..+..-+++.|
T Consensus 23 ~~~~~~~~a~~~ln~-~w~~~V~~~~~~~i~gRYPF~~~s~~dv~l~Df~~fF~p~--G~ld~F~~~~L 88 (125)
T PF06744_consen 23 AWKLVLQGARSYLNK-AWQAEVYPFCRQAIAGRYPFDPDSSRDVSLADFARFFGPG--GVLDQFFNQYL 88 (125)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHhcCCCCCCCCCcccCCHHHHHHHhcCC--CcHHHHHHHHH
Confidence 344455555555554 89999999999999654 34678999999999988 55555554443
No 79
>TIGR03181 PDH_E1_alph_x pyruvate dehydrogenase E1 component, alpha subunit. Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc.
Probab=31.67 E-value=2e+02 Score=23.42 Aligned_cols=26 Identities=15% Similarity=0.332 Sum_probs=20.2
Q ss_pred CCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 033797 69 GTNNVTVDDLVHVITPKGRASIPDSIKTEL 98 (111)
Q Consensus 69 g~~~vt~~~L~~~I~P~Ar~~VP~~VK~El 98 (111)
....++.++++..|... .|+.++.+.
T Consensus 313 ~~p~P~~~~~~~~vy~~----~~~~~~~~~ 338 (341)
T TIGR03181 313 ALPPPPVDDIFDHVYAE----LPPELEEQR 338 (341)
T ss_pred hCCCCCHHHHHhhcccC----CCHHHHHHH
Confidence 45778999999999863 788887664
No 80
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=31.64 E-value=1.4e+02 Score=25.41 Aligned_cols=61 Identities=16% Similarity=0.249 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHHHH---hCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHH
Q 033797 38 EKLMELLRERLVECGWKDEMKALCRAYIKK---KGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRA 104 (111)
Q Consensus 38 erLk~lL~~rL~EcGW~DeVr~~~re~i~~---~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~ 104 (111)
.-|.+.|..+|.-..+.+..+.+|..+|.. +|.=..+++++...+- |+.+...+++..|+.
T Consensus 76 ~sL~e~L~~Ql~~~~~~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~l~------~~~~~ve~~l~~iq~ 139 (429)
T TIGR02395 76 ESLFEHLLEQLDLQLFTERDRKIALYIIDNLDEDGYLEIDLEEIADELE------VSEEEVEKVLELIQR 139 (429)
T ss_pred CCHHHHHHHHHhccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHcC------CCHHHHHHHHHHHhc
Confidence 356677777887777877888888777744 3433356777766652 566666666666654
No 81
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=31.39 E-value=1.2e+02 Score=18.16 Aligned_cols=44 Identities=16% Similarity=0.295 Sum_probs=33.2
Q ss_pred HHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 64 YIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 64 ~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
.+...| ..++.++|++.|-|..-.-++...-.-.+.++|..|..
T Consensus 17 L~~~~~-~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 17 LLRNPG-RVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred HHhCCC-CccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 334445 46899999999998643356677788899999999865
No 82
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=31.24 E-value=87 Score=21.86 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHh
Q 033797 55 DEMKALCRAYIKKKGTNNVTVDDLVHV 81 (111)
Q Consensus 55 DeVr~~~re~i~~~g~~~vt~~~L~~~ 81 (111)
+++-+.|.+.+.++|..++|+.+|.++
T Consensus 11 ~~Il~aA~~lf~~~G~~~~s~~~IA~~ 37 (189)
T TIGR03384 11 AELIDATIESIGERGSLDVTIAQIARR 37 (189)
T ss_pred HHHHHHHHHHHHhcCcccCCHHHHHHH
Confidence 445555666666667666666666544
No 83
>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional
Probab=31.24 E-value=4.5e+02 Score=24.69 Aligned_cols=37 Identities=19% Similarity=0.143 Sum_probs=25.8
Q ss_pred CCCCCCCchhhhccchhhHHHHHHHHHHhcchHHHHHHHH
Q 033797 5 VNRPPTPDAVEDQEKEPTLQEIINIKMIESGEKEKLMELL 44 (111)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~lk~~I~~~LveSGe~erLk~lL 44 (111)
.++|..|.--+ .-+.|+..||++|-+-++|-.|++.|
T Consensus 501 ~~~~~~~~L~e---K~~kLk~Efnkkl~ea~n~p~lk~Kl 537 (762)
T PLN03229 501 QDQLMHPVLME---KIEKLKDEFNKRLSRAPNYLSLKYKL 537 (762)
T ss_pred ccccccHHHHH---HHHHHHHHHHHhhhcccccHHHHHHH
Confidence 34454443322 37889999999999988888777665
No 84
>KOG2949 consensus Ketopantoate hydroxymethyltransferase [Coenzyme transport and metabolism]
Probab=31.11 E-value=26 Score=28.71 Aligned_cols=26 Identities=31% Similarity=0.615 Sum_probs=19.8
Q ss_pred HhcChHHHHHHHHHHHHHHhCCCCCCH
Q 033797 49 VECGWKDEMKALCRAYIKKKGTNNVTV 75 (111)
Q Consensus 49 ~EcGW~DeVr~~~re~i~~~g~~~vt~ 75 (111)
.|+||.|-++..++ +++..|.+.|.+
T Consensus 111 yeS~~sda~knAv~-vmk~~g~~~vK~ 136 (306)
T KOG2949|consen 111 YESSWSDAVKNAVR-VMKEGGMDAVKL 136 (306)
T ss_pred ccccHHHHHHHHHH-HHHhcCCceEEE
Confidence 68999999998876 667676665543
No 85
>cd08337 DED_c-FLIP_repeat1 Death Effector Domain, repeat 1, of cellular FLICE-Inhibitory Protein. Death Effector Domain (DED), repeat 1, similar to that found in FLICE-inhibitory protein (c-FLIP/CASH, also known as Casper/iFLICE/FLAME-1/CLARP/MRIT/usurpin). c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of the Death Inducing Signalling Complex (DISC). At low levels, c-FLIP has been shown to enhance apoptotic signaling by allosterically activating caspase-8. As a modulator of the initiator caspases, c-FLIP regulates life and death in various types of cells and tissues. All members contain two N-terminal DEDs and a C-terminal pseudo-caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association
Probab=30.57 E-value=59 Score=21.76 Aligned_cols=48 Identities=25% Similarity=0.425 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 033797 54 KDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAF 105 (111)
Q Consensus 54 ~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~f 105 (111)
.+.++=+|+..+..+.. -++.+++..+. .+++++.+.-.|++.+|+-|
T Consensus 18 ~e~L~FLC~D~ip~~~~--e~~~~l~~~L~--e~~~L~~~~L~ELLy~i~R~ 65 (80)
T cd08337 18 DELLLFLCRDAAPDCTT--AQLRDLLRALN--ERGKLTLAALAELLYRVKRF 65 (80)
T ss_pred HHHHHHHcccccccccc--hhHHHHHHHHH--HcCCCCHHHHHHHHHHHhHH
Confidence 34556678888765543 34558887765 36778888999999999875
No 86
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=30.42 E-value=95 Score=22.76 Aligned_cols=28 Identities=7% Similarity=0.340 Sum_probs=16.0
Q ss_pred hHHHHHHHHHHHHHhcChHH-HHHHHHHH
Q 033797 36 EKEKLMELLRERLVECGWKD-EMKALCRA 63 (111)
Q Consensus 36 e~erLk~lL~~rL~EcGW~D-eVr~~~re 63 (111)
.+++|-+--..-+.+-|+.. .++++|+.
T Consensus 19 ~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~ 47 (212)
T PRK15008 19 KKKAILSAALDTFSQFGFHGTRLEQIAEL 47 (212)
T ss_pred HHHHHHHHHHHHHHHhCcccCCHHHHHHH
Confidence 34555555556666667663 56655554
No 87
>COG3609 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]
Probab=30.35 E-value=1.7e+02 Score=19.47 Aligned_cols=25 Identities=36% Similarity=0.522 Sum_probs=15.1
Q ss_pred HHHHHHHHHHhcchHHHHHHHHHHHH
Q 033797 23 LQEIINIKMIESGEKEKLMELLRERL 48 (111)
Q Consensus 23 lk~~I~~~LveSGe~erLk~lL~~rL 48 (111)
+.+.| +.||++|.|.--++.++.-|
T Consensus 13 ~~~~i-~~lV~~G~y~s~SeviR~al 37 (89)
T COG3609 13 LVEFI-DELVESGRYKSRSEVIRAAL 37 (89)
T ss_pred HHHHH-HHHHHcCCCCCHHHHHHHHH
Confidence 33344 46888999966555554433
No 88
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=30.30 E-value=61 Score=20.03 Aligned_cols=18 Identities=50% Similarity=0.678 Sum_probs=13.5
Q ss_pred HHHhcchHHHHHHHHHHH
Q 033797 30 KMIESGEKEKLMELLRER 47 (111)
Q Consensus 30 ~LveSGe~erLk~lL~~r 47 (111)
.+.+.|+|+.|..++..|
T Consensus 3 ~aa~~~dWe~l~~l~~~R 20 (84)
T PF05400_consen 3 EAAEAGDWEELEELLDER 20 (84)
T ss_dssp HHHHCT-HHHHHHHHHHH
T ss_pred HHHhhCcHHHHHHHHHHH
Confidence 457899999999998554
No 89
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=29.66 E-value=2.3e+02 Score=22.32 Aligned_cols=47 Identities=17% Similarity=0.175 Sum_probs=31.7
Q ss_pred hhHHHHHHHHHHhc--chHHHHHHHHHHHHHhcChHHHHHHHHHHHHHH
Q 033797 21 PTLQEIINIKMIES--GEKEKLMELLRERLVECGWKDEMKALCRAYIKK 67 (111)
Q Consensus 21 ~~lk~~I~~~LveS--Ge~erLk~lL~~rL~EcGW~DeVr~~~re~i~~ 67 (111)
..||..|++.+-.. +...-....|..+|.+.|+-+++...+.+.+.+
T Consensus 114 ~~lk~~l~~~~~~~~~~~~~~~l~~l~~~L~~~gv~~~la~~L~~~l~~ 162 (282)
T TIGR03499 114 EALRELLERLLAGLAWLQRDPEGAKLLERLLRAGVSPELARELLEKLPE 162 (282)
T ss_pred HHHHHHHHHHHHhhhhcccCHHHHHHHHHHHHCCCCHHHHHHHHHHhhc
Confidence 34666665554321 122334467889999999999998888887764
No 90
>TIGR00763 lon ATP-dependent protease La. This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
Probab=29.57 E-value=88 Score=28.39 Aligned_cols=41 Identities=22% Similarity=0.283 Sum_probs=31.0
Q ss_pred HHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHH
Q 033797 27 INIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKK 67 (111)
Q Consensus 27 I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~ 67 (111)
|+..|=+.++.+.--+.|+++|.+.+|-+++++.+..++++
T Consensus 235 i~~eLg~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~e~~~ 275 (775)
T TIGR00763 235 IKKELGIEKDDKDELEKLKEKLEELKLPEEVKKVIEKELTK 275 (775)
T ss_pred HHHhhCCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 55555444344334488999999999999999999999875
No 91
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=29.56 E-value=2.2e+02 Score=21.26 Aligned_cols=67 Identities=16% Similarity=0.175 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHhcChHHH--HH-HHHHHHHHHhCCCCCCHHHHHHhhchhh----hccCCHHHHHHHHHHHH
Q 033797 37 KEKLMELLRERLVECGWKDE--MK-ALCRAYIKKKGTNNVTVDDLVHVITPKG----RASIPDSIKTELLLRIR 103 (111)
Q Consensus 37 ~erLk~lL~~rL~EcGW~De--Vr-~~~re~i~~~g~~~vt~~~L~~~I~P~A----r~~VP~~VK~Ell~~Ir 103 (111)
.+.+.+++..+|..+||.+. +. +.+..+.+..|-..-.+..+...+.-.| ...|..++-.+.+..|+
T Consensus 194 ~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~ 267 (269)
T TIGR03015 194 REETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEID 267 (269)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence 35566677777776665321 21 2222222223322334555555553333 45566666666665554
No 92
>PF06649 DUF1161: Protein of unknown function (DUF1161); InterPro: IPR010595 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=29.44 E-value=49 Score=20.74 Aligned_cols=14 Identities=36% Similarity=0.546 Sum_probs=6.1
Q ss_pred hHHHHHHHHHHhcc
Q 033797 22 TLQEIINIKMIESG 35 (111)
Q Consensus 22 ~lk~~I~~~LveSG 35 (111)
+||+.|.++++..|
T Consensus 3 ~lk~eI~~KI~anG 16 (52)
T PF06649_consen 3 ELKAEIEQKIIANG 16 (52)
T ss_pred HHHHHHHHHHHHcC
Confidence 34444444444433
No 93
>PRK11640 putative transcriptional regulator; Provisional
Probab=29.01 E-value=1e+02 Score=22.54 Aligned_cols=29 Identities=14% Similarity=0.330 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHhh
Q 033797 54 KDEMKALCRAYIKKKGTNNVTVDDLVHVI 82 (111)
Q Consensus 54 ~DeVr~~~re~i~~~g~~~vt~~~L~~~I 82 (111)
++.|=+.+.+.+.++|...+++++|.++.
T Consensus 3 r~~il~~A~~lf~~~Gy~~tsi~~I~~~a 31 (191)
T PRK11640 3 REDVLGEALKLLEQQGLANTTLEMLAERV 31 (191)
T ss_pred HHHHHHHHHHHHHHhCcccCCHHHHHHHh
Confidence 45666778888888898889999887765
No 94
>COG3433 Aryl carrier domain [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.19 E-value=1.6e+02 Score=19.67 Aligned_cols=39 Identities=21% Similarity=0.388 Sum_probs=30.5
Q ss_pred HHHHhcChHHHHHHHHH-HHHHHhCCCCCCHHHHHHhhchhh
Q 033797 46 ERLVECGWKDEMKALCR-AYIKKKGTNNVTVDDLVHVITPKG 86 (111)
Q Consensus 46 ~rL~EcGW~DeVr~~~r-e~i~~~g~~~vt~~~L~~~I~P~A 86 (111)
+-|+.|| -|.||.+.- +.++++|. .++|.+|.+..+=.|
T Consensus 22 eNLi~~G-LDSiR~M~L~~~wR~~G~-~i~F~~La~~PTl~a 61 (74)
T COG3433 22 ENLIDYG-LDSIRMMALLERWRKRGA-DIDFAQLAANPTLAA 61 (74)
T ss_pred hhHHHhc-hhHHHHHHHHHHHHHcCC-cccHHHHHhCccHHH
Confidence 5788888 588988775 45788884 899999998877554
No 95
>PF05234 UAF_Rrn10: UAF complex subunit Rrn10; InterPro: IPR022793 The protein Rrn10 has been identified as a component of the Upstream Activating Factor (UAF), an RNA polymerase I (pol I) specific transcription stimulatory factor [].
Probab=28.12 E-value=80 Score=22.93 Aligned_cols=29 Identities=24% Similarity=0.384 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHhhch
Q 033797 56 EMKALCRAYIKKKGTNNVTVDDLVHVITP 84 (111)
Q Consensus 56 eVr~~~re~i~~~g~~~vt~~~L~~~I~P 84 (111)
.|...|.+.|++.|...++-++++++-.+
T Consensus 4 nvyeacsdLI~~~g~~~vsaDEvL~~k~~ 32 (120)
T PF05234_consen 4 NVYEACSDLIKEFGTHVVSADEVLAEKID 32 (120)
T ss_pred cHHHHHHHHHHhcCCcccCHHHHHHHhcC
Confidence 48899999999998777999999986554
No 96
>TIGR02837 spore_II_R stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage II sporulation protein R.
Probab=28.01 E-value=2.3e+02 Score=21.65 Aligned_cols=39 Identities=23% Similarity=0.291 Sum_probs=30.2
Q ss_pred HHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCC
Q 033797 26 IINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGT 70 (111)
Q Consensus 26 ~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~ 70 (111)
.+...|-.++..+.-++.++..|. ++++.+.+.|.+.|.
T Consensus 67 ~~~~~~~~~~s~~ea~~~i~~~l~------~Ie~~a~~~l~~~G~ 105 (168)
T TIGR02837 67 EIRPWLSGLKSLEEARRVIRENLP------EIERIAESVIKAEGA 105 (168)
T ss_pred HHHHHhccCCCHHHHHHHHHHhhH------HHHHHHHHHHHHhCC
Confidence 334455677888888888888775 599999999999984
No 97
>PF14069 SpoVIF: Stage VI sporulation protein F
Probab=27.78 E-value=1.5e+02 Score=19.83 Aligned_cols=50 Identities=10% Similarity=0.200 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHH
Q 033797 55 DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRA 104 (111)
Q Consensus 55 DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~ 104 (111)
++|..+|...=...=-|.-++-+|+..|.-.|..-||++.-.+|...|.+
T Consensus 13 ~~i~kLA~sv~~adlqdE~~vR~lIk~vs~~an~~Vs~~~ed~IV~~I~~ 62 (79)
T PF14069_consen 13 EDIFKLANSVQKADLQDEKKVRQLIKQVSQIANKPVSKEQEDQIVQAIIN 62 (79)
T ss_pred HHHHHHHHhcchhhcccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHh
Confidence 55666665432221123457788888888888888998888877776653
No 98
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=27.71 E-value=1.7e+02 Score=21.63 Aligned_cols=55 Identities=16% Similarity=0.373 Sum_probs=44.9
Q ss_pred chhhHHHHHHHHHHhcchHHHHHHHHHHH-HHhcChHH----HHHHHHHHHHHHhCCCCC
Q 033797 19 KEPTLQEIINIKMIESGEKEKLMELLRER-LVECGWKD----EMKALCRAYIKKKGTNNV 73 (111)
Q Consensus 19 ~~~~lk~~I~~~LveSGe~erLk~lL~~r-L~EcGW~D----eVr~~~re~i~~~g~~~v 73 (111)
....+++.+.+-|.-.|=+-|.|+.|... -...-|++ .++..+++.++++|+.-+
T Consensus 83 ~d~~l~~~L~~ai~grgafrrFKd~L~~~~~~~e~Wy~F~~~~~r~~a~eWleen~I~~~ 142 (163)
T PF03682_consen 83 EDPDLRERLLRAIQGRGAFRRFKDILSEYPELRERWYAFREERLRERAIEWLEENGIEPV 142 (163)
T ss_pred CCHHHHHHHHHHHhCCcHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcc
Confidence 57889999999999999999999998764 33468975 788888889999987444
No 99
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=27.69 E-value=1.2e+02 Score=21.98 Aligned_cols=30 Identities=33% Similarity=0.567 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHHHhcChHHHHHHHHHHHHHH
Q 033797 36 EKEKLMELLRERLVECGWKDEMKALCRAYIKK 67 (111)
Q Consensus 36 e~erLk~lL~~rL~EcGW~DeVr~~~re~i~~ 67 (111)
+++++++.+...|.+ |++++++...++...
T Consensus 92 ~~ee~k~~i~~~l~~--w~~~~~~~i~~~~~~ 121 (126)
T COG3355 92 DPEEIKKKILKDLDE--WYDKMKQLIEEFEKK 121 (126)
T ss_pred CHHHHHHHHHHHHHH--HHHHHHHHHHHHhcc
Confidence 789999999999996 999999999887653
No 100
>PF06504 RepC: Replication protein C (RepC); InterPro: IPR010522 This family consists of several bacterial replication protein C (RepC) sequences.
Probab=27.34 E-value=55 Score=26.91 Aligned_cols=52 Identities=31% Similarity=0.498 Sum_probs=37.6
Q ss_pred HHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 41 MELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 41 k~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
..+|+++| |||.+--+ ...|.+|.|...|-|.+ .=|+.+|+ =.++||.+|.+
T Consensus 206 ArllH~rL--c~wi~pGk-----------s~~v~LDTL~~~VW~~~--a~~~~~Rk-RR~~lR~AL~E 257 (281)
T PF06504_consen 206 ARLLHQRL--CGWIDPGK-----------SRPVGLDTLCSYVWGDE--ASGSAMRK-RRQRLRKALAE 257 (281)
T ss_pred HHHHHHHH--HcCCCCCc-----------CCccchhhhhhhcCCCC--CChHHHHH-HHHHHHHHHHH
Confidence 34677777 68877443 25699999999999977 34455554 45889999976
No 101
>PRK00767 transcriptional regulator BetI; Validated
Probab=27.22 E-value=1.1e+02 Score=21.56 Aligned_cols=22 Identities=14% Similarity=0.149 Sum_probs=10.7
Q ss_pred HHHHHHHHHhCCCCCCHHHHHH
Q 033797 59 ALCRAYIKKKGTNNVTVDDLVH 80 (111)
Q Consensus 59 ~~~re~i~~~g~~~vt~~~L~~ 80 (111)
+.|.+++.++|...+|+++|.+
T Consensus 16 ~aA~~lf~~~G~~~~s~~~Ia~ 37 (197)
T PRK00767 16 DATLRAIGEVGLLDATIAQIAR 37 (197)
T ss_pred HHHHHHHHHcCcccCCHHHHHH
Confidence 3344444555555555555443
No 102
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism]
Probab=27.19 E-value=74 Score=25.36 Aligned_cols=37 Identities=14% Similarity=0.245 Sum_probs=26.8
Q ss_pred hcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhh
Q 033797 50 ECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKG 86 (111)
Q Consensus 50 EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~A 86 (111)
-.|+++++-+.||.++..--...++.+++-+++..+-
T Consensus 143 nYGGR~eI~~avr~ia~~v~~g~l~~~~I~e~~i~~~ 179 (245)
T COG0020 143 NYGGRDEIVDAVRKIAEDVAAGKLSPEDIDEELISSH 179 (245)
T ss_pred CCCCHHHHHHHHHHHHHHHHcCCCChHHcCHHHHHHh
Confidence 4699999999999999766434566666666655443
No 103
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=26.90 E-value=1.4e+02 Score=19.36 Aligned_cols=27 Identities=19% Similarity=0.276 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHhh
Q 033797 56 EMKALCRAYIKKKGTNNVTVDDLVHVI 82 (111)
Q Consensus 56 eVr~~~re~i~~~g~~~vt~~~L~~~I 82 (111)
++-..+.+.+..+|.+++|+.+|.++.
T Consensus 16 ~ii~aa~~l~~~~G~~~~t~~~Ia~~a 42 (201)
T COG1309 16 RILDAALRLFAEKGYAATTVDEIAKAA 42 (201)
T ss_pred HHHHHHHHHHHHcCcCCCCHHHHHHHh
Confidence 344445555555677777777777665
No 104
>PLN02555 limonoid glucosyltransferase
Probab=26.68 E-value=36 Score=29.33 Aligned_cols=36 Identities=14% Similarity=0.243 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCC
Q 033797 56 EMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIP 91 (111)
Q Consensus 56 eVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP 91 (111)
++++.|++.+.+.|+..-++++++++|..++.+.|.
T Consensus 441 ~l~~~a~~A~~egGSS~~~l~~~v~~i~~~~~~~~~ 476 (480)
T PLN02555 441 KWKEEAEAAVAEGGSSDRNFQEFVDKLVRKSVEIVD 476 (480)
T ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHHHhccceecc
Confidence 455667777777788888999999999988766654
No 105
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=26.44 E-value=1.5e+02 Score=18.28 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=20.7
Q ss_pred HHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHH
Q 033797 61 CRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLR 101 (111)
Q Consensus 61 ~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~ 101 (111)
.+++|+++|. +|+.+|..+.- +|.+..+.+|..
T Consensus 5 i~~~l~~~~~--~S~~eLa~~~~------~s~~~ve~mL~~ 37 (69)
T PF09012_consen 5 IRDYLRERGR--VSLAELAREFG------ISPEAVEAMLEQ 37 (69)
T ss_dssp HHHHHHHS-S--EEHHHHHHHTT--------HHHHHHHHHH
T ss_pred HHHHHHHcCC--cCHHHHHHHHC------cCHHHHHHHHHH
Confidence 5677888864 99999998875 455554444443
No 106
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=26.20 E-value=1e+02 Score=22.03 Aligned_cols=26 Identities=8% Similarity=0.258 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHhcChHH-HHHHHHH
Q 033797 37 KEKLMELLRERLVECGWKD-EMKALCR 62 (111)
Q Consensus 37 ~erLk~lL~~rL~EcGW~D-eVr~~~r 62 (111)
+++|-+--.+-+.+.|+.. .+.+.|+
T Consensus 10 R~~Il~aA~~lf~e~G~~~tSi~~Ia~ 36 (192)
T PRK14996 10 REVILQAAMRVALAEGFAAMTVRRIAS 36 (192)
T ss_pred HHHHHHHHHHHHHhcChhhccHHHHHH
Confidence 3444444555556666653 4544444
No 107
>PLN02210 UDP-glucosyl transferase
Probab=26.12 E-value=85 Score=26.68 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 56 EMKALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 56 eVr~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
++++.+++.+.+.|+...++++++++|+
T Consensus 427 ~l~~~a~~Av~~gGSS~~~l~~~v~~~~ 454 (456)
T PLN02210 427 ELKHVARLALAPGGSSARNLDLFISDIT 454 (456)
T ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHHh
Confidence 4566677777777887789999998875
No 108
>KOG1112 consensus Ribonucleotide reductase, alpha subunit [Nucleotide transport and metabolism]
Probab=26.06 E-value=22 Score=32.18 Aligned_cols=65 Identities=35% Similarity=0.410 Sum_probs=48.0
Q ss_pred CCCCCCCCCCchhhhcc-----chhhHHHHHHHHHHhcchHHHHHHHHHHHHHhcC-hHHHHHHHHHHHHHHhC
Q 033797 2 RNSVNRPPTPDAVEDQE-----KEPTLQEIINIKMIESGEKEKLMELLRERLVECG-WKDEMKALCRAYIKKKG 69 (111)
Q Consensus 2 ~~~~~~~~~~~~~~~~~-----~~~~lk~~I~~~LveSGe~erLk~lL~~rL~EcG-W~DeVr~~~re~i~~~g 69 (111)
|+|.--.|||.+.-.+. .-+-...-|-.|=+-|||.......|-.-|.|-| |.|++|+.. |..+|
T Consensus 594 RNSLl~ApMPTAsTsQIlGnNE~fEP~tsNiYsRRvlsGeFqiVN~hll~DLv~~glW~~~mKn~l---I~~nG 664 (796)
T KOG1112|consen 594 RNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFQIVNPHLLKDLVELGLWDDEMKNKL---IANNG 664 (796)
T ss_pred ccceeeccCCCcchhhhhcCccccCcccccceeeeecccceEEEcHHHHHHHHHhccCCHHHHHHH---HhcCC
Confidence 66766778887766432 2233455666677789999999999999999998 999999764 45565
No 109
>PF08824 Serine_rich: Serine rich protein interaction domain; InterPro: IPR014928 This is a serine rich protein that is found in the docking protein p130(cas) (Crk-associated substrate). The protein folds into a four helix bundle which is associated with protein-protein interactions []. ; PDB: 2L81_A 1Z23_A.
Probab=26.05 E-value=1.4e+02 Score=22.47 Aligned_cols=68 Identities=21% Similarity=0.346 Sum_probs=42.7
Q ss_pred chhhHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHH
Q 033797 19 KEPTLQEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKT 96 (111)
Q Consensus 19 ~~~~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~ 96 (111)
.+..|.+.|...|..--+--.+-....+-|.+|||-= ..+++. + .+.+.++|=.-|. .-..||+++|+
T Consensus 74 ~D~~L~~kL~~qLq~l~ds~qiL~~~~q~Ld~~~Wsl--~~La~~--k----~~~~~DdLDrfVm--vaR~vpdD~kq 141 (159)
T PF08824_consen 74 SDRNLQAKLRRQLQPLEDSYQILLQTSQALDSCNWSL--DVLARD--K----PQNKPDDLDRFVM--VARTVPDDAKQ 141 (159)
T ss_dssp TS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSH--HHHTT--------SS-TCHHHHHHHH--HHCCHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCH--HHHhcC--C----CCCCcchHHHHHH--HHHhchHHHHH
Confidence 4577777887777766666777778899999999964 344544 1 1124444433332 33689999975
No 110
>COG1890 RPS1A Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]
Probab=25.99 E-value=1.1e+02 Score=24.25 Aligned_cols=28 Identities=18% Similarity=0.465 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHhhch
Q 033797 56 EMKALCRAYIKKKGTNNVTVDDLVHVITP 84 (111)
Q Consensus 56 eVr~~~re~i~~~g~~~vt~~~L~~~I~P 84 (111)
.+|+.-.++|.+.+ ...||++++.++.+
T Consensus 137 aIRk~M~eii~~~a-~e~~f~~fv~~li~ 164 (214)
T COG1890 137 AIRKIMFEIIEEKA-SELTFEEFVQELIP 164 (214)
T ss_pred HHHHHHHHHHHHHh-ccCCHHHHHHHHhh
Confidence 46666677777776 57888888888776
No 111
>KOG2769 consensus Putative u4/u6 small nuclear ribonucleoprotein [RNA processing and modification]
Probab=25.81 E-value=1e+02 Score=27.48 Aligned_cols=57 Identities=23% Similarity=0.290 Sum_probs=40.9
Q ss_pred HHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHH
Q 033797 29 IKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSI 94 (111)
Q Consensus 29 ~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~V 94 (111)
=+|.|||.+.++.+-.+.. -|-+.+.....+.++.-| ++--..++.|.|+ +-||+.-
T Consensus 181 f~f~e~gkf~~~an~~r~~----a~le~Lq~eis~~a~k~g---I~~~~~la~~~p~--~~iP~iE 237 (522)
T KOG2769|consen 181 FLFHESGKFIKLANRHRYK----AQLERLQNEISQAARKTG---ISTATKLALIAPK--DDIPAIE 237 (522)
T ss_pred eeecccchHHHHHHHHHHH----HHHHHHHHHHHHHHHhcC---CchhhhhhhccCC--CCCchhh
Confidence 3589999999999886532 344556666666666676 3337788999998 8888743
No 112
>cd01598 PurB PurB_like adenylosuccinases (adenylsuccinate lyase, ASL). This subgroup contains EcASL, the product of the purB gene in Escherichia coli, and related proteins. It is a member of the Lyase class I family of the Lyase_I superfamily. Members of the Lyase class I family function as homotetramers to catalyze similar beta-elimination reactions in which a Calpha-N or Calpha-O bond is cleaved with the subsequent release of fumarate as one of the products. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASL catalyzes two non-sequential steps in the de novo purine biosynthesis pathway: the conversion of 5-aminoimidazole-(N-succinylocarboxamide) ribotide (SAICAR) into 5-aminoimidazole-4-carboxamide ribotide (AICAR) and; the conversion of adenylsuccinate (SAMP) into adenosine monophosphate (AMP).
Probab=25.45 E-value=2.8e+02 Score=23.68 Aligned_cols=64 Identities=20% Similarity=0.251 Sum_probs=38.7
Q ss_pred HHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 033797 28 NIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLL 100 (111)
Q Consensus 28 ~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~ 100 (111)
...|-.++. .+.+.+...|.+.||+ +-...+.+.. .| .+++.+++...|.- =.+|++++.+|+.
T Consensus 353 ~~nl~~~~~--i~sE~~~~~l~~~gr~-~Ah~~V~~~~--~~-~~~~~~~~~~~~~~---~~~~~~~~~~~~~ 416 (425)
T cd01598 353 LEDLDANWE--VLAEPIQTVMRRYGIP-NPYEKLKDLT--RG-KRIDKETLKEFIDS---LDIPEEAKAELLA 416 (425)
T ss_pred HHHHHhCcC--HHHHHHHHHHHhcChH-hHHHHHHHHh--CC-CCCCHHHHHHHHHh---CCCCHHHHHHHHh
Confidence 334444555 7788888888888993 3344443332 24 45666655555431 2488888888874
No 113
>PF06771 Desmo_N: Viral Desmoplakin N-terminus; InterPro: IPR009615 This entry represents the N terminus of viral desmoplakin. Desmoplakin is a component of mature desmosomes, which are the main adhesive junctions in epithelia and cardiac muscle. Desmoplakin is also essential for the maturation of adherens junctions []. Note that many family members are hypothetical.
Probab=25.39 E-value=48 Score=22.72 Aligned_cols=34 Identities=26% Similarity=0.412 Sum_probs=28.8
Q ss_pred CCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHH
Q 033797 73 VTVDDLVHVITPKGRASIPDSIKTELLLRIRAFL 106 (111)
Q Consensus 73 vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL 106 (111)
-||..|+..|.-+....--.+-+.+.+++||..+
T Consensus 10 ~TV~nLl~TIns~s~~~k~~~~~~d~~~rIr~II 43 (86)
T PF06771_consen 10 HTVHNLLKTINSMSQRCKTQSSTEDFLRRIRSII 43 (86)
T ss_pred HHHHHHHHHHHHHhHHhhccccchhHHHHHHHHH
Confidence 3699999999888887777788899999999876
No 114
>PLN00164 glucosyltransferase; Provisional
Probab=25.26 E-value=89 Score=26.74 Aligned_cols=33 Identities=27% Similarity=0.442 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhh
Q 033797 55 DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGR 87 (111)
Q Consensus 55 DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar 87 (111)
.++++.+++.+.+.|+..-++++++++|.+.|-
T Consensus 444 ~~~~~~~~~a~~~gGSS~~~l~~~v~~~~~~~~ 476 (480)
T PLN00164 444 AEMKAACRKAVEEGGSSYAALQRLAREIRHGAV 476 (480)
T ss_pred HHHHHHHHHHhcCCCcHHHHHHHHHHHHHhccC
Confidence 345666777777778777899999999987664
No 115
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=25.23 E-value=2e+02 Score=24.70 Aligned_cols=60 Identities=15% Similarity=0.234 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHH---hCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHH
Q 033797 39 KLMELLRERLVECGWKDEMKALCRAYIKK---KGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRA 104 (111)
Q Consensus 39 rLk~lL~~rL~EcGW~DeVr~~~re~i~~---~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~ 104 (111)
-|.+.|..+|..+.+.+..+.+|..+|.. +|.=..+++++....- ++.+.-.+++..|+.
T Consensus 102 sL~e~L~~Ql~~~~l~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~l~------~~~~~v~~~l~~lQ~ 164 (455)
T PRK05932 102 SLQDHLLEQIELTPFSETDRAIATYIIDALDDEGYLTEDLEEIAESLG------VELDEVEAVLKRIQS 164 (455)
T ss_pred CHHHHHHHHHcccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHcC------CCHHHHHHHHHHHhc
Confidence 56666777777777777777777666643 3332346666655541 455555555555544
No 116
>PF13767 DUF4168: Domain of unknown function (DUF4168)
Probab=25.10 E-value=1.9e+02 Score=18.41 Aligned_cols=56 Identities=13% Similarity=0.127 Sum_probs=33.9
Q ss_pred HHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHH-------HHHHHhCCCCCCHHHHHHh
Q 033797 26 IINIKMIESGEKEKLMELLRERLVECGWKDEMKALCR-------AYIKKKGTNNVTVDDLVHV 81 (111)
Q Consensus 26 ~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~r-------e~i~~~g~~~vt~~~L~~~ 81 (111)
.|++.-...-+-+-|+..-..+|.+|.=.++++.++. ++|.+.|.+.-.|.++...
T Consensus 5 el~~fA~A~~~ie~ir~~~~~~l~~~~~~~~~~~l~~~a~~~~~~~I~~~GLtv~~fN~I~~~ 67 (78)
T PF13767_consen 5 ELDQFARAVLEIEPIRQEYQQELQAAEDPEEIQELQEEAQEEMVEAIEENGLTVERFNEITQA 67 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4455555555666677777777777766666666555 4455566555555555544
No 117
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=25.09 E-value=78 Score=21.65 Aligned_cols=29 Identities=28% Similarity=0.296 Sum_probs=23.6
Q ss_pred HHHhhchhhhccCCHHHHHHHHHHHHHHH
Q 033797 78 LVHVITPKGRASIPDSIKTELLLRIRAFL 106 (111)
Q Consensus 78 L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL 106 (111)
--..|-|.-.+.+|++++.|++...+..-
T Consensus 41 ~~~~I~pefL~ALP~diR~EVl~qe~~~~ 69 (108)
T PF14377_consen 41 QPSQIDPEFLAALPPDIREEVLAQERRER 69 (108)
T ss_pred CccccCHHHHHhCCHHHHHHHHHHHHHHH
Confidence 34567778889999999999999887654
No 118
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=25.02 E-value=2e+02 Score=20.59 Aligned_cols=41 Identities=29% Similarity=0.271 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhc-chHHHHHHHHHHHHHhcChHHHHHHHHHHHH
Q 033797 23 LQEIINIKMIES-GEKEKLMELLRERLVECGWKDEMKALCRAYI 65 (111)
Q Consensus 23 lk~~I~~~LveS-Ge~erLk~lL~~rL~EcGW~DeVr~~~re~i 65 (111)
+.+.|.+...+| ++-..|-+.|-.||...| =-||..|-.+|
T Consensus 21 ~~~Eia~~t~~s~~~~~ei~d~L~kRL~~~~--~hVK~K~Lril 62 (122)
T cd03572 21 LYEEIAKLTRKSVGSCQELLEYLLKRLKRSS--PHVKLKVLKII 62 (122)
T ss_pred HHHHHHHHHHcCHHHHHHHHHHHHHHhcCCC--CcchHHHHHHH
Confidence 445666666666 777788888888888777 33433344444
No 119
>PF10249 NDUFB10: NADH-ubiquinone oxidoreductase subunit 10; InterPro: IPR019377 NADH-ubiquinone oxidoreductase subunit 10 of (NDUFB10) is a member of a family of conserved proteins of up to 180 residues. It is one of the 41 protein subunits within the hydrophobic fraction of the NADH:ubiquinone oxidoreductase (complex I), a multiprotein complex located in the inner mitochondrial membrane whose main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. NDUFB10 is encoded in the nucleus.
Probab=24.66 E-value=58 Score=23.76 Aligned_cols=52 Identities=17% Similarity=0.330 Sum_probs=32.6
Q ss_pred HHHHHhcchHHHHHHHHHHHHHhcChHHHHH--HHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 28 NIKMIESGEKEKLMELLRERLVECGWKDEMK--ALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 28 ~~~LveSGe~erLk~lL~~rL~EcGW~DeVr--~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
..++|. ..|-+.|++||..|-+++.+- +.|+.++..---...+|..=+.++-
T Consensus 54 RDk~VD----~EIlkILReRl~~C~~~EG~nh~qnC~~l~~qy~ea~~~y~~kYgdlg 107 (128)
T PF10249_consen 54 RDKLVD----QEILKILRERLEACYRREGVNHYQNCRKLVEQYEEAAKNYFIKYGDLG 107 (128)
T ss_pred HHHHHH----HHHHHHHHHHHHHHHHHHCcCHhhhhHHHHHHHHHHHHHHHHHHHhcC
Confidence 345663 346678999999999998764 4688877553222234444444444
No 120
>PRK10307 putative glycosyl transferase; Provisional
Probab=24.47 E-value=1.3e+02 Score=23.91 Aligned_cols=50 Identities=10% Similarity=0.211 Sum_probs=35.3
Q ss_pred HHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhh
Q 033797 29 IKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVI 82 (111)
Q Consensus 29 ~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I 82 (111)
-.+++.|+.+.|.+.|..-+..-..+.++.+.+++.+.++ -|.+.++..+
T Consensus 352 G~~~~~~d~~~la~~i~~l~~~~~~~~~~~~~a~~~~~~~----fs~~~~~~~~ 401 (412)
T PRK10307 352 GVCVEPESVEALVAAIAALARQALLRPKLGTVAREYAERT----LDKENVLRQF 401 (412)
T ss_pred cEEeCCCCHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHH----cCHHHHHHHH
Confidence 4467789999999999876666667778888888776543 5555555444
No 121
>cd08812 CARD_RIG-I_like Caspase activation and recruitment domains found in RIG-I-like DEAD box helicases. Caspase activation and recruitment domains (CARDs) found in Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. These helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I and MDA5 have been shown to recognize different sets of viruses. MDA5 and RIG-I associate with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mec
Probab=24.27 E-value=2e+02 Score=18.99 Aligned_cols=39 Identities=21% Similarity=0.155 Sum_probs=30.0
Q ss_pred hhhHHHHHHHHHHhcchHHHHHHHHHHHH--HhcChHHHHH
Q 033797 20 EPTLQEIINIKMIESGEKEKLMELLRERL--VECGWKDEMK 58 (111)
Q Consensus 20 ~~~lk~~I~~~LveSGe~erLk~lL~~rL--~EcGW~DeVr 58 (111)
.++.+++|+..=-.+|+.+....+|..-. ...||....-
T Consensus 33 ~~~~~e~I~a~~~~~g~~~aa~~Ll~~L~~~r~~~wf~~Fl 73 (88)
T cd08812 33 TDEDKEQILAEERNKGNIAAAEELLDRLERCDKPGWFQAFL 73 (88)
T ss_pred CHHHHHHHHHHHhccChHHHHHHHHHHHHHhccCCcHHHHH
Confidence 45678888886555599999999987766 6889987654
No 122
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=24.05 E-value=1.1e+02 Score=18.96 Aligned_cols=23 Identities=17% Similarity=0.276 Sum_probs=13.4
Q ss_pred HHHhcchHHHHHHHHHHHHHhcC
Q 033797 30 KMIESGEKEKLMELLRERLVECG 52 (111)
Q Consensus 30 ~LveSGe~erLk~lL~~rL~EcG 52 (111)
-|++.|++++..+.+..-..++-
T Consensus 32 gllqlg~~~~a~eYi~~~~~~~~ 54 (62)
T PF14689_consen 32 GLLQLGKYEEAKEYIKELSKDLQ 54 (62)
T ss_dssp HHHHTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHCCCHHHHHHHHHHHHHHHH
Confidence 35667777777776665544433
No 123
>PF06505 XylR_N: Activator of aromatic catabolism; InterPro: IPR010523 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to IPR004096 from INTERPRO.
Probab=23.96 E-value=1.4e+02 Score=20.74 Aligned_cols=37 Identities=19% Similarity=0.328 Sum_probs=31.8
Q ss_pred hhHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHH
Q 033797 21 PTLQEIINIKMIESGEKEKLMELLRERLVECGWKDEM 57 (111)
Q Consensus 21 ~~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeV 57 (111)
.+--..+.+-||+|=-.++=+.+|..-=..|||+|--
T Consensus 27 ~~alg~LRkELi~~lG~~~AR~iltR~Gy~~G~~DAe 63 (103)
T PF06505_consen 27 ASALGALRKELIETLGEERARGILTRMGYASGWRDAE 63 (103)
T ss_pred hhHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHH
Confidence 3344578999999999999999999999999999954
No 124
>PF06799 DUF1230: Protein of unknown function (DUF1230); InterPro: IPR009631 This family represents Ycf36, which is found in plants, encoded in the genomes of algal chloroplasts and in cyanobacteria. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=23.84 E-value=22 Score=26.45 Aligned_cols=8 Identities=50% Similarity=1.016 Sum_probs=6.6
Q ss_pred HhcChHHH
Q 033797 49 VECGWKDE 56 (111)
Q Consensus 49 ~EcGW~De 56 (111)
.|+||+|-
T Consensus 102 EESGWYDG 109 (144)
T PF06799_consen 102 EESGWYDG 109 (144)
T ss_pred cccCccCC
Confidence 58999993
No 125
>PF03008 DUF234: Archaea bacterial proteins of unknown function; InterPro: IPR004256 This represents a C-terminal domain of unknown function, usually fused to a prokaryotic putative DEXX-box ATPase domain (IPR011579 from INTERPRO) [].
Probab=23.69 E-value=2.3e+02 Score=18.77 Aligned_cols=40 Identities=25% Similarity=0.483 Sum_probs=29.5
Q ss_pred HHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHh
Q 033797 28 NIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKK 68 (111)
Q Consensus 28 ~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~ 68 (111)
+.-+++.|..+.+-+.+...|.. =.-.-...+|++.+...
T Consensus 8 ~~s~ie~g~~~~~~~~i~~~l~~-y~g~~fE~i~r~~l~~~ 47 (100)
T PF03008_consen 8 NRSLIERGRGEAVYEKIKPELNQ-YMGFAFEEICREYLRRL 47 (100)
T ss_pred cHHHHHCCCHHHHHHHHHHHHHH-HhhHHHHHHHHHHHHHh
Confidence 45678999988888888888843 23445678888888765
No 126
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=23.59 E-value=2.2e+02 Score=24.89 Aligned_cols=66 Identities=15% Similarity=0.196 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHHHH---hCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 033797 38 EKLMELLRERLVECGWKDEMKALCRAYIKK---KGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAF 105 (111)
Q Consensus 38 erLk~lL~~rL~EcGW~DeVr~~~re~i~~---~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~f 105 (111)
+-|.+.|..+|.-+.+-+..+..|..+|.. +|.=..++++|.+.+.+.. -|+.+.-..++..|+.|
T Consensus 123 ~sL~~~L~~Ql~~~~~~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~~~~~l--~~~~~~ve~vL~~iQ~l 191 (481)
T PRK12469 123 PTLHEHLHDALRLYFLTERDREIARTIIDALDDDGYLRQDLSELAEAADPEL--GLSEQELEVALRLVQSL 191 (481)
T ss_pred CCHHHHHHHHHhccCCCHHHHHHHHHHHhhCCCCCCCCCCHHHHHhcccccc--CCCHHHHHHHHHHHhcC
Confidence 358888999999999999999999888754 4543468888877632111 27777777777777763
No 127
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=23.45 E-value=1.1e+02 Score=19.90 Aligned_cols=19 Identities=37% Similarity=0.583 Sum_probs=15.5
Q ss_pred cCCHHHHHHHHHHHHHHHh
Q 033797 89 SIPDSIKTELLLRIRAFLA 107 (111)
Q Consensus 89 ~VP~~VK~Ell~~Ir~fL~ 107 (111)
-+||+.|.|++.-|.-.|+
T Consensus 10 kLPDdLKrEvldY~EfLle 28 (65)
T COG5559 10 KLPDDLKREVLDYIEFLLE 28 (65)
T ss_pred HCcHHHHHHHHHHHHHHHH
Confidence 4799999999998865554
No 128
>TIGR00763 lon ATP-dependent protease La. This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
Probab=23.40 E-value=3.7e+02 Score=24.46 Aligned_cols=29 Identities=10% Similarity=0.291 Sum_probs=21.0
Q ss_pred CHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 033797 74 TVDDLVHVITPKGRASIPDSIKTELLLRIRAF 105 (111)
Q Consensus 74 t~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~f 105 (111)
.++++-++|.-.. +|+++++.+...|..+
T Consensus 248 ~~~~~~~k~~~~~---~~~~~~~~~~~e~~~~ 276 (775)
T TIGR00763 248 ELEKLKEKLEELK---LPEEVKKVIEKELTKL 276 (775)
T ss_pred HHHHHHHHHHhcC---CCHHHHHHHHHHHHHH
Confidence 4566666664333 8999999999888755
No 129
>cd06460 M32_Taq Peptidase family M32 is a subclass of metallocarboxypeptidases which are distributed mainly in bacteria and archaea, and contain a HEXXH motif that coordinates a divalent cation such as Zn2+ or Co2+, so far only observed in the active site of neutral metallopeptidases but not in carboxypeptidases. M32 includes the thermostable carboxypeptidases (E.C. 3.4.17.19) from Thermus aquaticus (TaqCP) and Pyrococcus furiosus (PfuCP), which have broad specificities toward a wide range of C-terminal substrates that include basic, aromatic, neutral and polar amino acids. These enzymes have a similar fold to the M3 peptidases such as neurolysin and the M2 angiotensin converting enzyme (ACE). Novel peptidases from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, are the first eukaryotic M32 enzymes identified so far, thus making these enzymes an attractive potential target for drug development against these o
Probab=23.40 E-value=2.4e+02 Score=23.95 Aligned_cols=48 Identities=23% Similarity=0.373 Sum_probs=36.3
Q ss_pred HhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 32 IESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 32 veSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
+++|+.+.+.+.|++.+...|=+....++.+.. -| ..+|.+..++.++
T Consensus 345 i~~g~f~~~~~wL~e~i~~~G~~~~p~eLl~~a---tG-~~l~~~~f~~yL~ 392 (396)
T cd06460 345 IERGDFSPLLEWLRENIHQHGSRYSPDELLKKA---TG-EPLNPEYFLEYLE 392 (396)
T ss_pred HhccChHHHHHHHHHHHHhccCCCCHHHHHHHH---hC-CCCChHHHHHHHH
Confidence 789999999999999999988777766665432 25 3677777776654
No 130
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=23.34 E-value=84 Score=24.80 Aligned_cols=35 Identities=34% Similarity=0.527 Sum_probs=24.7
Q ss_pred HHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 46 ERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 46 ~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
-+|-+|||.| ++.++. .+++.| .-++++-|..-|.
T Consensus 52 l~lD~~Gwa~-i~~l~~-~~~k~~-~~~~~~~l~~iV~ 86 (211)
T COG1859 52 LRLDEEGWAD-IDELLE-GLRKAG-RWLTRELLLAVVA 86 (211)
T ss_pred eeeccccchh-HHHHHH-HHHhhc-cCCCHHHHHHHHh
Confidence 4678999999 777775 455555 4678877776554
No 131
>PLN02448 UDP-glycosyltransferase family protein
Probab=23.13 E-value=1.1e+02 Score=25.86 Aligned_cols=28 Identities=29% Similarity=0.680 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 56 EMKALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 56 eVr~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
++++.+++.+.+.|+..-++++++++++
T Consensus 429 ~~~~~~~~a~~~gGss~~~l~~~v~~~~ 456 (459)
T PLN02448 429 ELQEICRGAIAKGGSSDTNLDAFIRDIS 456 (459)
T ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHHh
Confidence 4666777777777877789999998886
No 132
>PLN02534 UDP-glycosyltransferase
Probab=23.09 E-value=1.2e+02 Score=26.33 Aligned_cols=30 Identities=13% Similarity=0.354 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHhhchh
Q 033797 56 EMKALCRAYIKKKGTNNVTVDDLVHVITPK 85 (111)
Q Consensus 56 eVr~~~re~i~~~g~~~vt~~~L~~~I~P~ 85 (111)
++++.|++.+.+.|+...++++++++|..+
T Consensus 458 elk~~a~~Av~~GGSS~~nl~~fv~~i~~~ 487 (491)
T PLN02534 458 ELGVMARKAMELGGSSHINLSILIQDVLKQ 487 (491)
T ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHHHHH
Confidence 567778888888888888999999998743
No 133
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=23.04 E-value=2.4e+02 Score=25.08 Aligned_cols=51 Identities=18% Similarity=0.283 Sum_probs=37.6
Q ss_pred HHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhc
Q 033797 29 IKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVIT 83 (111)
Q Consensus 29 ~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~ 83 (111)
..++++||++.|++.|+++...-|=+-.=.++.+.. -| +.+|.+=+++.+.
T Consensus 442 d~~i~~gd~~~i~~WL~e~ih~~Gs~~~p~eLi~~a---tG-E~lnp~y~i~yL~ 492 (497)
T COG2317 442 DALIAKGDFSPIKNWLRENIHRHGSRYPPKELLKRA---TG-EALNPEYFIDYLE 492 (497)
T ss_pred HHHHHcCCcHHHHHHHHHHHHHccCcCCcHHHHHHh---hC-CcCCHHHHHHHHH
Confidence 478999999999999999999888666555555432 34 5677766666554
No 134
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=22.91 E-value=2.7e+02 Score=22.52 Aligned_cols=55 Identities=18% Similarity=0.306 Sum_probs=37.4
Q ss_pred hHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 53 WKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 53 W~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
+.+.++..+....+.+- ..+++...+..|.-.....=.++.|..++..|.+|+++
T Consensus 48 l~~~l~~~~~~L~~arP-t~v~l~nair~v~~~~~~~~~~~~k~~l~e~~~~~~~e 102 (310)
T PRK08535 48 FKAEMRAAANILISTRP-TAVSLPNAVRYVMRYYSGETVEEARESVIERAEEFIES 102 (310)
T ss_pred HHHHHHHHHHHHHHcCC-chhhHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHH
Confidence 34557777766655553 56777777777765433333478899999999999865
No 135
>PF08388 GIIM: Group II intron, maturase-specific domain; InterPro: IPR013597 This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing [].
Probab=22.83 E-value=1.3e+02 Score=18.56 Aligned_cols=33 Identities=9% Similarity=0.314 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhcc
Q 033797 56 EMKALCRAYIKKKGTNNVTVDDLVHVITPKGRAS 89 (111)
Q Consensus 56 eVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~ 89 (111)
.+++.+++++..+ ..+.+++++++++-|.-++.
T Consensus 3 ~~~~kik~~~~~~-~~~~~~~~~i~~LN~~lrGW 35 (80)
T PF08388_consen 3 RFRRKIKEITRRR-NRGKSLEELIKKLNPILRGW 35 (80)
T ss_pred HHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHH
Confidence 4566667776322 25689999999999987764
No 136
>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]
Probab=22.67 E-value=7.5e+02 Score=24.41 Aligned_cols=85 Identities=18% Similarity=0.216 Sum_probs=59.8
Q ss_pred hhhhccchhhHHHHHHHHHHhcchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCH-HHHHHhhchhhhccCC
Q 033797 13 AVEDQEKEPTLQEIINIKMIESGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTV-DDLVHVITPKGRASIP 91 (111)
Q Consensus 13 ~~~~~~~~~~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~-~~L~~~I~P~Ar~~VP 91 (111)
.|.+..+++.|-+.--.-+.+...|++--++|..-=. ...-=++|++ .|+.+ +++.+.++|.--++.|
T Consensus 1072 ~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~ar~----~~~AlqlC~~-------~nv~vtee~aE~mTp~Kd~~~~ 1140 (1416)
T KOG3617|consen 1072 KDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLARE----FSGALQLCKN-------RNVRVTEEFAELMTPTKDDMPN 1140 (1416)
T ss_pred HhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHH----HHHHHHHHhc-------CCCchhHHHHHhcCcCcCCCcc
Confidence 3445567788888888889999999988887742111 1223345543 34655 5566667777669999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 033797 92 DSIKTELLLRIRAFLAS 108 (111)
Q Consensus 92 ~~VK~Ell~~Ir~fL~~ 108 (111)
+..++++|.+|-+|+.+
T Consensus 1141 e~~R~~vLeqvae~c~q 1157 (1416)
T KOG3617|consen 1141 EQERKQVLEQVAELCLQ 1157 (1416)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 99999999999999865
No 137
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=22.62 E-value=85 Score=24.74 Aligned_cols=29 Identities=31% Similarity=0.706 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHHHHh
Q 033797 38 EKLMELLRERLVECGWKDEMKALCRAYIKKK 68 (111)
Q Consensus 38 erLk~lL~~rL~EcGW~DeVr~~~re~i~~~ 68 (111)
..|-+.|-..+++.|| ++|.+.|.|+..+
T Consensus 52 PeLLd~La~~F~~~g~--dlK~L~R~I~~S~ 80 (266)
T PF07587_consen 52 PELLDWLAAEFVEHGW--DLKHLIRLIVTSR 80 (266)
T ss_pred HHHHHHHHHHHHHcCC--CHHHHHHHHHccH
Confidence 4677889999999999 6899999988553
No 138
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=22.50 E-value=3e+02 Score=21.22 Aligned_cols=56 Identities=23% Similarity=0.329 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 033797 40 LMELLRERLVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAF 105 (111)
Q Consensus 40 Lk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~f 105 (111)
|+.+..+.+.+- .+=..|+.++..+|- ..+|++|+.+|.-.- -+ -+.++-.+|-.|
T Consensus 3 l~~~~~qe~~el----s~IevA~~ile~~~~-~~~F~dii~EI~~~~--~~---s~~ei~~~i~~F 58 (175)
T COG3343 3 LKVLMGQELSEL----SLIEVAHAILEEKKK-PFNFSDIINEIQKLL--GV---SKEEIRSRIGQF 58 (175)
T ss_pred hHHHHHHHHHHH----HHHHHHHHHHHHcCC-CccHHHHHHHHHHHh--Cc---CHHHHHHHHHHH
Confidence 455555555543 344568888888884 899999999997432 22 244555555444
No 139
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to Pfam model pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108)
Probab=22.43 E-value=99 Score=21.77 Aligned_cols=24 Identities=25% Similarity=0.266 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHH
Q 033797 38 EKLMELLRERLVECGWKDEMKALC 61 (111)
Q Consensus 38 erLk~lL~~rL~EcGW~DeVr~~~ 61 (111)
+++++.....=.+.||.+-...+.
T Consensus 38 e~~~~~g~~~G~~~g~~e~~~~~~ 61 (166)
T TIGR02499 38 EASRQLGYEQGLEQFWQEAAAQLA 61 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444555555444443
No 140
>PF09424 YqeY: Yqey-like protein; InterPro: IPR019004 Putative protein of unknown function; the authentic protein is detected in highly purified mitochondria in high-throughput studies; YOR215C is not an essential gene. ; PDB: 1NG6_A.
Probab=22.28 E-value=2.6e+02 Score=20.19 Aligned_cols=58 Identities=21% Similarity=0.292 Sum_probs=37.3
Q ss_pred cchHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHhCCCC-CCHHHHHHhhchhhhccCCHHHH
Q 033797 34 SGEKEKLMELLRERLVECGWKDEMKALCRAYIKKKGTNN-VTVDDLVHVITPKGRASIPDSIK 95 (111)
Q Consensus 34 SGe~erLk~lL~~rL~EcGW~DeVr~~~re~i~~~g~~~-vt~~~L~~~I~P~Ar~~VP~~VK 95 (111)
.-|.+.|..+|-..|-+ ++|+..+.+.|.+-|... -+.-.+...+.|+-.+-+--..-
T Consensus 77 ~~Ei~iL~~yLP~~lse----eEi~~~v~~~i~e~ga~~~k~mG~vMk~l~~~~~G~~Dgk~v 135 (143)
T PF09424_consen 77 QAEIEILEEYLPKQLSE----EEIEAIVEEAIAELGASSMKDMGKVMKALMAKLKGRADGKKV 135 (143)
T ss_dssp HHHHHHHGGGS-----H----HHHHHHHHHHHHHTT--BGGGHHHHHHHHHHHHTTTS-HHHH
T ss_pred HHHHHHHHHhCcCCCCH----HHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHcCCcccHHHH
Confidence 44556688888888886 899999999998887543 37888888888877655544333
No 141
>COG1071 AcoA Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]
Probab=21.93 E-value=3.4e+02 Score=22.95 Aligned_cols=40 Identities=23% Similarity=0.349 Sum_probs=25.1
Q ss_pred HHHHHHhcC-----hHHHHHHHHHHHHHH-----hCCCCCCHHHHHHhhc
Q 033797 44 LRERLVECG-----WKDEMKALCRAYIKK-----KGTNNVTVDDLVHVIT 83 (111)
Q Consensus 44 L~~rL~EcG-----W~DeVr~~~re~i~~-----~g~~~vt~~~L~~~I~ 83 (111)
|+..|++-| |.+++++.|++++++ .....++.+++++.|.
T Consensus 293 ~~~~L~~~g~~see~~~~i~~e~~~~V~ea~e~a~~~p~P~~~~~~~~Vy 342 (358)
T COG1071 293 LRKYLIEAGILSEEELEAIEAEAKAEVDEAVEFAEASPYPDVSELFEDVY 342 (358)
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCChhHhhhccc
Confidence 444555555 566777777777765 2334567777777766
No 142
>cd05025 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins.
Probab=21.51 E-value=2.3e+02 Score=18.08 Aligned_cols=50 Identities=18% Similarity=0.358 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHh-cCh---HHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhh
Q 033797 37 KEKLMELLRERLVE-CGW---KDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGR 87 (111)
Q Consensus 37 ~erLk~lL~~rL~E-cGW---~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar 87 (111)
.+.|+.+|+..|-. .|+ .++++.+.+.. ...+...|+|++.+.-+.+.|-
T Consensus 30 ~~El~~~l~~~lg~~~~~~~s~~~v~~i~~~~-D~d~~G~I~f~eF~~l~~~~~~ 83 (92)
T cd05025 30 KKELKDLLQTELSDFLDAQKDADAVDKIMKEL-DENGDGEVDFQEFVVLVAALTV 83 (92)
T ss_pred HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHH-CCCCCCcCcHHHHHHHHHHHHH
Confidence 45677777654432 232 34455555543 3334456999999988887764
No 143
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=21.42 E-value=2.5e+02 Score=18.38 Aligned_cols=54 Identities=13% Similarity=0.146 Sum_probs=26.4
Q ss_pred HHhcChHHHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHHhh
Q 033797 48 LVECGWKDEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTELLLRIRAFLAS 108 (111)
Q Consensus 48 L~EcGW~DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~Ell~~Ir~fL~~ 108 (111)
|.-.||.++-....+...+--=..+.++++-+++|....-. ......|-+|+.+
T Consensus 23 LrR~Gfs~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~-------~~~v~~~~~Fi~~ 76 (83)
T PF13720_consen 23 LRRRGFSKEEISALRRAYRILFRSGLTLEEALEELEEEYPD-------SPEVREIVDFIRN 76 (83)
T ss_dssp HHHTTS-HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTS-------CHHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccC-------CHHHHHHHHHHHh
Confidence 44567766555444444322111346888888887643222 2334455556543
No 144
>PF14433 SUKH-3: SUKH-3 immunity protein
Probab=21.08 E-value=1.2e+02 Score=21.32 Aligned_cols=14 Identities=36% Similarity=0.527 Sum_probs=11.5
Q ss_pred HHHHHHHHHhcChH
Q 033797 41 MELLRERLVECGWK 54 (111)
Q Consensus 41 k~lL~~rL~EcGW~ 54 (111)
|+.+.+.|...||.
T Consensus 1 ~~~v~~~L~~aGW~ 14 (142)
T PF14433_consen 1 KEKVIELLRAAGWY 14 (142)
T ss_pred CHHHHHHHHHcCCC
Confidence 35678889999999
No 145
>PF13026 DUF3887: Protein of unknown function (DUF3887)
Probab=21.05 E-value=3e+02 Score=19.11 Aligned_cols=35 Identities=14% Similarity=0.164 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCC
Q 033797 55 DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRASIP 91 (111)
Q Consensus 55 DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP 91 (111)
++|++.+.++|.-- +.-.|+.+.+....+-.+.+|
T Consensus 5 Ekv~~~Aeevi~~~--N~~dy~~v~~~~d~~mk~aL~ 39 (101)
T PF13026_consen 5 EKVKQKAEEVIDLL--NEKDYDKVHEKYDEKMKNALT 39 (101)
T ss_pred HHHHHHHHHHHHHH--hHhhHHHHHHHHhHHHHHhcC
Confidence 44555555555432 234566666666666666666
No 146
>PF15606 Toxin_55: Putative toxin 55
Probab=20.98 E-value=1.1e+02 Score=20.55 Aligned_cols=43 Identities=23% Similarity=0.407 Sum_probs=28.4
Q ss_pred CCchhhhccchhhHHHHHHHHHHhcchHHHHHHHHHHHHHhcCh
Q 033797 10 TPDAVEDQEKEPTLQEIINIKMIESGEKEKLMELLRERLVECGW 53 (111)
Q Consensus 10 ~~~~~~~~~~~~~lk~~I~~~LveSGe~erLk~lL~~rL~EcGW 53 (111)
+||-.++..--..+...+++++...|..--.=+.|. .|++||=
T Consensus 11 a~GNqaDTgI~~~v~~~~~~~~~~~GK~~drCd~Lq-elid~g~ 53 (77)
T PF15606_consen 11 APGNQADTGIVQQVYEIISDAFQSGGKAPDRCDVLQ-ELIDCGD 53 (77)
T ss_pred cCCCchhHHHHHHHHHHHHHHHhhcCCCCcHHHHHH-HHHHccC
Confidence 356556555566778888888888887655555554 3566763
No 147
>TIGR00174 miaA tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.
Probab=20.97 E-value=3.2e+02 Score=22.10 Aligned_cols=47 Identities=21% Similarity=0.362 Sum_probs=26.9
Q ss_pred HHHHHHHHHHH---HHhcChHHHHHHHHHHHHH-Hh-CCCCCCHHHHHHhhc
Q 033797 37 KEKLMELLRER---LVECGWKDEMKALCRAYIK-KK-GTNNVTVDDLVHVIT 83 (111)
Q Consensus 37 ~erLk~lL~~r---L~EcGW~DeVr~~~re~i~-~~-g~~~vt~~~L~~~I~ 83 (111)
++.|.+-+..| ..+.||.|||+.+-..... .. ....+-|.++++.+.
T Consensus 195 r~~L~~rI~~Rv~~Mi~~Gl~eEv~~l~~~~~~~~~~~~~aIGYkE~~~~l~ 246 (287)
T TIGR00174 195 REPLHQRIEQRVHDMLESGLLAEVKALYAQYDLCDLPSIQAIGYKEFLLYLE 246 (287)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHhccCCcCCchhhhccHHHHHHHHc
Confidence 44444444333 3568999999987643211 11 124467777777765
No 148
>PF08973 TM1506: Domain of unknown function (DUF1893); InterPro: IPR015067 This family consist of hypothetical bacterial proteins. ; PDB: 1VK9_A.
Probab=20.77 E-value=15 Score=26.82 Aligned_cols=50 Identities=18% Similarity=0.232 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHhhchh--------hhccCCHHHHHHHHHHHHHHHh
Q 033797 57 MKALCRAYIKKKGTNNVTVDDLVHVITPK--------GRASIPDSIKTELLLRIRAFLA 107 (111)
Q Consensus 57 Vr~~~re~i~~~g~~~vt~~~L~~~I~P~--------Ar~~VP~~VK~Ell~~Ir~fL~ 107 (111)
|.+.+.+++++.|+ .++|++++..|.-. =.....-+--.|++..|++|+.
T Consensus 76 iS~~Al~~L~~~gI-~v~y~~~Vp~I~NR~~tg~CP~E~~v~~~~d~ee~~~~i~~~~~ 133 (134)
T PF08973_consen 76 ISEPALDLLEEAGI-KVSYDELVPYIINRDGTGMCPMETLVLEVEDPEEAYELIEEFIK 133 (134)
T ss_dssp EEHHHHHHHHHTT---EEEEEEESS-B-SSSSSB-HHHHHHHT---HHHHHHHH-----
T ss_pred HhHHHHHHHHHcCC-ceeHhhhhhhhccCCCCCCCcHHHHHHccCCHHHHHHHHHhhcC
Confidence 34678889999996 78999999888733 2223333556788888888874
No 149
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=20.49 E-value=70 Score=20.21 Aligned_cols=30 Identities=3% Similarity=0.132 Sum_probs=16.7
Q ss_pred HHHHHHhhchhhh-ccCCHHHHHHHHHHHHH
Q 033797 75 VDDLVHVITPKGR-ASIPDSIKTELLLRIRA 104 (111)
Q Consensus 75 ~~~L~~~I~P~Ar-~~VP~~VK~Ell~~Ir~ 104 (111)
-.++++.+.-.|. .-+|++.-..+...|-.
T Consensus 42 E~~v~~~~~~~~~~~~l~~~~i~~if~~ii~ 72 (81)
T PF01817_consen 42 EEEVLERLRELAEEGGLDPEFIERIFRAIIE 72 (81)
T ss_dssp HHHHHHHHHHHHHHTTSEHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhHhCCCCHHHHHHHHHHHHH
Confidence 3455666666665 55565555555555543
No 150
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=20.38 E-value=2.6e+02 Score=18.40 Aligned_cols=39 Identities=8% Similarity=0.152 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHhhchhhhccCCHHHHHH
Q 033797 58 KALCRAYIKKKGTNNVTVDDLVHVITPKGRASIPDSIKTE 97 (111)
Q Consensus 58 r~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~VP~~VK~E 97 (111)
|...-+.+.+.+ ..+|.++|++.+..+.-..=+..|++-
T Consensus 3 R~~Il~~l~~~~-~~~sa~ei~~~l~~~~~~i~~~TVYR~ 41 (116)
T cd07153 3 RLAILEVLLESD-GHLTAEEIYERLRKKGPSISLATVYRT 41 (116)
T ss_pred HHHHHHHHHhCC-CCCCHHHHHHHHHhcCCCCCHHHHHHH
Confidence 344555666553 578999999999876554445555543
No 151
>PF00298 Ribosomal_L11: Ribosomal protein L11, RNA binding domain; InterPro: IPR020783 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 1VQN_I 2OTJ_I 3G6E_I 3CME_I 1YIJ_I 1YI2_I 3G4S_I 3CMA_I 3I55_I 1VQ7_I ....
Probab=20.02 E-value=1.6e+02 Score=18.91 Aligned_cols=33 Identities=12% Similarity=0.222 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHhhchhhhcc
Q 033797 55 DEMKALCRAYIKKKGTNNVTVDDLVHVITPKGRAS 89 (111)
Q Consensus 55 DeVr~~~re~i~~~g~~~vt~~~L~~~I~P~Ar~~ 89 (111)
++|.+.++... .+..+.+++..+..|.-.|+.|
T Consensus 33 ~~i~eIAk~K~--~d~~~~~l~~~~k~v~Gta~Sm 65 (69)
T PF00298_consen 33 KQIYEIAKIKQ--KDLNAKSLESAVKSVIGTARSM 65 (69)
T ss_dssp HHHHHHHHHHT--TTSSSSSHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhh--cccccCCHHHHHHHHHHHHhcC
Confidence 56666665543 3447789999999999888865
Done!