Query psy4179
Match_columns 89
No_of_seqs 117 out of 574
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 18:51:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4179.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4179hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10557 Cullin_Nedd8: Cullin 99.9 2.2E-28 4.7E-33 148.0 5.0 68 16-83 1-68 (68)
2 KOG2166|consensus 99.9 3.2E-27 6.9E-32 192.5 8.3 81 6-87 645-725 (725)
3 COG5647 Cullin, a subunit of E 99.9 4.6E-26 1E-30 184.2 8.6 85 4-89 689-773 (773)
4 KOG2167|consensus 99.9 6.9E-26 1.5E-30 180.4 7.0 82 3-89 580-661 (661)
5 KOG2284|consensus 99.9 2.1E-23 4.6E-28 163.1 7.3 87 2-89 642-728 (728)
6 KOG2285|consensus 99.7 1.7E-16 3.8E-21 125.4 6.6 82 8-89 696-777 (777)
7 PF03965 Penicillinase_R: Peni 95.6 0.015 3.2E-07 37.5 3.2 60 25-89 5-64 (115)
8 PF09012 FeoC: FeoC like trans 95.5 0.015 3.3E-07 34.4 2.8 46 27-80 4-49 (69)
9 TIGR02698 CopY_TcrY copper tra 95.0 0.04 8.8E-07 36.6 3.9 60 25-89 6-65 (130)
10 COG3682 Predicted transcriptio 94.6 0.13 2.7E-06 34.6 5.4 62 23-89 6-67 (123)
11 PF13463 HTH_27: Winged helix 92.6 0.53 1.1E-05 26.8 5.1 51 25-83 5-58 (68)
12 PF08220 HTH_DeoR: DeoR-like h 92.1 0.29 6.2E-06 28.0 3.5 47 26-80 3-49 (57)
13 PF01978 TrmB: Sugar-specific 90.3 0.15 3.3E-06 29.6 1.2 47 34-88 19-65 (68)
14 cd07153 Fur_like Ferric uptake 90.0 0.98 2.1E-05 28.5 4.8 51 27-80 5-56 (116)
15 smart00418 HTH_ARSR helix_turn 88.3 1.5 3.3E-05 23.6 4.3 45 29-82 3-47 (66)
16 PF01726 LexA_DNA_bind: LexA D 88.1 1.2 2.5E-05 26.4 3.9 56 19-81 6-62 (65)
17 PF02186 TFIIE_beta: TFIIE bet 87.7 0.98 2.1E-05 26.9 3.4 54 25-89 7-61 (65)
18 PF12802 MarR_2: MarR family; 86.8 0.35 7.6E-06 27.1 1.1 46 27-80 9-56 (62)
19 smart00550 Zalpha Z-DNA-bindin 86.2 3.2 6.9E-05 24.4 5.1 54 24-85 7-62 (68)
20 smart00344 HTH_ASNC helix_turn 85.5 2 4.4E-05 26.7 4.2 47 24-78 4-50 (108)
21 PF01047 MarR: MarR family; I 85.3 0.99 2.2E-05 25.1 2.5 46 26-79 6-51 (59)
22 TIGR02404 trehalos_R_Bsub treh 84.0 0.77 1.7E-05 32.4 1.9 36 50-86 29-64 (233)
23 PF13412 HTH_24: Winged helix- 83.0 3.2 6.9E-05 22.3 3.8 45 24-76 4-48 (48)
24 PF09756 DDRGK: DDRGK domain; 82.3 2.4 5.3E-05 30.2 3.9 58 24-89 100-157 (188)
25 TIGR02325 C_P_lyase_phnF phosp 81.6 1.1 2.4E-05 31.5 1.9 36 50-86 37-72 (238)
26 PRK10079 phosphonate metabolis 81.1 1.2 2.6E-05 31.7 2.1 36 50-86 40-75 (241)
27 PRK11402 DNA-binding transcrip 81.0 1.1 2.5E-05 31.8 1.9 36 50-86 38-73 (241)
28 smart00345 HTH_GNTR helix_turn 80.7 1.3 2.8E-05 24.1 1.7 31 50-80 25-55 (60)
29 smart00420 HTH_DEOR helix_turn 80.7 5.2 0.00011 21.0 4.1 44 28-79 5-48 (53)
30 PRK09334 30S ribosomal protein 79.9 0.93 2E-05 28.6 1.0 60 25-89 26-85 (86)
31 TIGR01889 Staph_reg_Sar staphy 78.9 1.7 3.8E-05 27.5 2.1 29 53-81 51-81 (109)
32 PRK03573 transcriptional regul 78.7 1.6 3.4E-05 28.6 1.9 30 50-79 51-80 (144)
33 smart00347 HTH_MARR helix_turn 77.3 8.7 0.00019 22.6 4.8 47 25-79 12-58 (101)
34 PRK14999 histidine utilization 77.3 1.7 3.6E-05 31.0 1.8 36 50-86 41-76 (241)
35 PF01475 FUR: Ferric uptake re 76.3 9.4 0.0002 24.2 5.0 54 25-81 10-64 (120)
36 PRK09462 fur ferric uptake reg 75.7 9.6 0.00021 25.3 5.1 52 25-79 19-72 (148)
37 COG1522 Lrp Transcriptional re 75.6 5.4 0.00012 26.0 3.8 48 23-78 8-55 (154)
38 smart00346 HTH_ICLR helix_turn 75.6 8.9 0.00019 22.7 4.5 45 28-80 10-55 (91)
39 PRK10434 srlR DNA-bindng trans 75.6 4.2 9.1E-05 29.6 3.5 47 25-79 7-53 (256)
40 PRK10906 DNA-binding transcrip 74.8 3.9 8.5E-05 29.8 3.2 47 25-79 7-53 (252)
41 COG1846 MarR Transcriptional r 74.6 2.2 4.9E-05 26.0 1.7 32 49-80 40-71 (126)
42 TIGR02018 his_ut_repres histid 74.3 2.3 5E-05 30.0 1.9 32 50-81 30-61 (230)
43 TIGR03433 padR_acidobact trans 73.8 16 0.00034 22.8 5.5 54 23-77 4-57 (100)
44 PRK11512 DNA-binding transcrip 73.5 2.7 5.9E-05 27.6 1.9 29 51-79 60-88 (144)
45 cd07377 WHTH_GntR Winged helix 73.2 2.9 6.2E-05 23.1 1.8 31 50-80 30-60 (66)
46 PRK09764 DNA-binding transcrip 72.9 2.7 5.8E-05 29.9 1.9 32 50-81 34-65 (240)
47 PF00392 GntR: Bacterial regul 72.8 2 4.4E-05 24.6 1.1 31 50-80 29-59 (64)
48 PF08784 RPA_C: Replication pr 72.6 5.5 0.00012 24.8 3.1 45 23-75 47-95 (102)
49 COG2188 PhnF Transcriptional r 72.3 2.6 5.7E-05 30.2 1.8 36 50-86 36-71 (236)
50 PF13601 HTH_34: Winged helix 71.1 7.8 0.00017 23.5 3.5 46 25-78 2-47 (80)
51 PF08766 DEK_C: DEK C terminal 70.7 14 0.0003 20.7 4.2 49 22-72 3-51 (54)
52 cd07977 TFIIE_beta_winged_heli 69.2 11 0.00024 22.8 3.9 57 23-89 9-70 (75)
53 PRK11179 DNA-binding transcrip 69.1 13 0.00029 24.8 4.6 47 23-77 9-55 (153)
54 PRK09802 DNA-binding transcrip 69.1 7.5 0.00016 28.6 3.6 48 25-80 19-66 (269)
55 COG1349 GlpR Transcriptional r 68.6 7.1 0.00015 28.5 3.4 47 26-80 8-54 (253)
56 PF13730 HTH_36: Helix-turn-he 67.9 4.1 8.9E-05 22.3 1.6 21 55-75 35-55 (55)
57 PRK11169 leucine-responsive tr 67.5 13 0.00028 25.2 4.3 47 23-77 14-60 (164)
58 PRK10870 transcriptional repre 66.2 4.8 0.0001 27.7 2.0 30 50-79 76-105 (176)
59 smart00529 HTH_DTXR Helix-turn 65.4 5 0.00011 24.2 1.8 31 50-80 4-34 (96)
60 TIGR02702 SufR_cyano iron-sulf 64.0 22 0.00047 24.8 5.0 45 26-78 4-48 (203)
61 PF09860 DUF2087: Uncharacteri 63.7 3.5 7.6E-05 24.9 0.8 26 56-85 43-68 (71)
62 cd00090 HTH_ARSR Arsenical Res 63.2 6.9 0.00015 21.5 2.0 45 28-81 12-56 (78)
63 smart00419 HTH_CRP helix_turn_ 62.8 6.1 0.00013 20.5 1.6 29 51-79 14-42 (48)
64 TIGR01610 phage_O_Nterm phage 61.7 17 0.00038 22.5 3.8 38 34-79 44-81 (95)
65 COG3355 Predicted transcriptio 61.5 8.2 0.00018 25.9 2.4 33 56-88 53-89 (126)
66 COG2865 Predicted transcriptio 61.1 22 0.00048 28.8 5.1 60 21-88 400-459 (467)
67 TIGR02337 HpaR homoprotocatech 61.0 7.3 0.00016 24.6 2.0 44 28-79 33-76 (118)
68 PF12651 RHH_3: Ribbon-helix-h 60.7 17 0.00037 19.7 3.2 31 42-72 12-42 (44)
69 PF14394 DUF4423: Domain of un 60.5 9 0.0002 26.6 2.5 25 56-80 52-76 (171)
70 PF09339 HTH_IclR: IclR helix- 59.1 6 0.00013 21.7 1.2 43 29-79 9-52 (52)
71 PRK15431 ferrous iron transpor 58.4 8.9 0.00019 23.8 2.0 31 49-79 20-50 (78)
72 COG0735 Fur Fe2+/Zn2+ uptake r 58.3 42 0.00091 22.5 5.4 55 25-82 23-78 (145)
73 PF08820 DUF1803: Domain of un 57.6 6.4 0.00014 25.2 1.3 28 50-78 33-60 (93)
74 PRK00215 LexA repressor; Valid 55.6 13 0.00029 25.7 2.7 31 55-85 33-64 (205)
75 PF03551 PadR: Transcriptional 55.0 14 0.0003 21.6 2.4 44 36-79 8-51 (75)
76 PRK14165 winged helix-turn-hel 53.4 11 0.00025 27.2 2.2 35 54-88 30-64 (217)
77 TIGR01884 cas_HTH CRISPR locus 53.3 35 0.00076 23.7 4.6 48 25-80 145-192 (203)
78 PRK09954 putative kinase; Prov 53.2 29 0.00064 25.9 4.4 43 27-77 7-49 (362)
79 PF10163 EnY2: Transcription f 52.4 53 0.0011 20.1 5.3 45 23-70 35-81 (86)
80 PF11417 Inhibitor_G39P: Loade 50.9 14 0.0003 22.3 1.9 29 36-64 41-70 (71)
81 cd00092 HTH_CRP helix_turn_hel 50.4 13 0.00028 20.6 1.7 25 55-79 35-59 (67)
82 PF08221 HTH_9: RNA polymerase 50.1 48 0.0011 19.0 4.7 53 15-75 5-57 (62)
83 PF02334 RTP: Replication term 49.7 29 0.00062 23.2 3.4 54 23-77 18-72 (122)
84 TIGR00498 lexA SOS regulatory 49.6 23 0.00049 24.4 3.1 27 55-81 35-62 (199)
85 PF06163 DUF977: Bacterial pro 49.3 53 0.0011 22.2 4.7 50 21-78 10-59 (127)
86 smart00526 H15 Domain in histo 49.1 46 0.00099 19.0 3.9 52 23-77 10-63 (66)
87 PF01638 HxlR: HxlR-like helix 48.4 52 0.0011 19.9 4.3 54 26-87 8-63 (90)
88 PF04738 Lant_dehyd_C: Lantibi 47.8 19 0.00041 28.0 2.7 36 39-78 2-38 (500)
89 PF03297 Ribosomal_S25: S25 ri 46.8 9.5 0.00021 24.8 0.8 39 50-88 64-102 (105)
90 PRK04424 fatty acid biosynthes 46.5 36 0.00079 23.6 3.8 46 26-79 10-55 (185)
91 PRK09416 lstR lineage-specific 45.9 93 0.002 21.1 6.6 69 8-78 26-96 (135)
92 PRK10411 DNA-binding transcrip 45.3 41 0.00088 24.3 4.0 45 27-79 8-52 (240)
93 PRK03902 manganese transport t 45.1 17 0.00036 23.9 1.8 44 27-78 12-55 (142)
94 PF10007 DUF2250: Uncharacteri 43.8 18 0.00039 22.9 1.7 28 54-81 30-57 (92)
95 PF11372 DUF3173: Domain of un 43.7 29 0.00064 20.4 2.5 32 36-74 2-35 (59)
96 KOG3054|consensus 43.2 62 0.0014 24.6 4.7 56 26-89 203-258 (299)
97 PF01325 Fe_dep_repress: Iron 42.9 13 0.00029 21.3 0.9 26 54-79 31-56 (60)
98 cd03527 RuBisCO_small Ribulose 42.5 23 0.0005 22.8 2.1 19 57-75 12-30 (99)
99 PF09382 RQC: RQC domain; Int 42.0 24 0.00051 21.7 2.1 24 57-80 54-77 (106)
100 PF14629 ORC4_C: Origin recogn 41.8 1.1E+02 0.0025 21.0 5.8 57 21-77 104-171 (203)
101 PF09114 MotA_activ: Transcrip 41.5 79 0.0017 20.3 4.4 23 57-79 44-66 (96)
102 TIGR03882 cyclo_dehyd_2 bacter 40.8 49 0.0011 23.2 3.7 46 25-78 32-77 (193)
103 PF10798 YmgB: Biofilm develop 40.5 64 0.0014 18.8 3.6 50 21-70 4-54 (61)
104 PF11868 DUF3388: Protein of u 40.3 14 0.00031 26.4 0.9 15 74-88 20-34 (192)
105 PF05402 PqqD: Coenzyme PQQ sy 39.7 42 0.00092 18.9 2.8 30 37-70 29-58 (68)
106 PF00538 Linker_histone: linke 39.2 80 0.0017 18.6 4.1 56 23-79 8-65 (77)
107 PRK13509 transcriptional repre 39.1 54 0.0012 23.8 3.8 46 26-79 8-53 (251)
108 PRK13777 transcriptional regul 37.3 27 0.00059 24.6 2.0 53 27-87 49-104 (185)
109 PF09681 Phage_rep_org_N: N-te 37.1 8.1 0.00017 25.6 -0.7 48 33-80 41-88 (121)
110 PF10537 WAC_Acf1_DNA_bd: ATP- 36.4 1.2E+02 0.0025 19.5 5.2 38 21-58 62-99 (102)
111 PF09170 STN1_2: CST, Suppress 36.3 34 0.00075 24.2 2.3 30 59-88 104-133 (174)
112 COG5045 Ribosomal protein S10E 36.0 21 0.00046 23.1 1.1 22 57-79 38-59 (105)
113 PF12395 DUF3658: Protein of u 35.1 87 0.0019 20.0 4.0 62 23-87 48-109 (111)
114 TIGR00738 rrf2_super rrf2 fami 34.9 35 0.00076 21.7 2.1 32 54-85 34-65 (132)
115 COG1378 Predicted transcriptio 34.5 27 0.00057 25.6 1.6 34 55-89 41-74 (247)
116 PRK02363 DNA-directed RNA poly 34.0 1.4E+02 0.0031 19.9 5.4 39 23-66 5-44 (129)
117 COG3343 RpoE DNA-directed RNA 33.7 80 0.0017 22.4 3.8 34 29-66 21-55 (175)
118 PRK12423 LexA repressor; Provi 33.6 44 0.00095 23.4 2.6 28 54-81 34-62 (202)
119 PF12358 DUF3644: Protein of u 33.5 51 0.0011 19.6 2.5 18 54-71 54-71 (77)
120 cd00073 H15 linker histone 1 a 33.3 1E+02 0.0022 18.8 3.9 56 23-79 10-65 (88)
121 TIGR01714 phage_rep_org_N phag 33.2 18 0.00038 24.0 0.4 49 32-80 38-86 (119)
122 PF01022 HTH_5: Bacterial regu 33.1 81 0.0017 16.7 3.6 42 26-76 5-46 (47)
123 PF08343 RNR_N: Ribonucleotide 33.0 31 0.00067 21.3 1.5 20 58-77 40-59 (82)
124 PF06969 HemN_C: HemN C-termin 32.6 34 0.00073 19.2 1.6 27 53-79 28-55 (66)
125 TIGR03337 phnR transcriptional 32.5 29 0.00063 24.1 1.5 31 50-80 30-60 (231)
126 TIGR03859 PQQ_PqqD coenzyme PQ 32.2 1.2E+02 0.0025 18.2 4.1 48 25-75 33-80 (81)
127 PF14947 HTH_45: Winged helix- 32.1 60 0.0013 19.2 2.7 22 56-77 30-51 (77)
128 COG3177 Fic family protein [Fu 31.5 46 0.001 25.4 2.5 35 54-88 313-347 (348)
129 PF01316 Arg_repressor: Argini 31.5 1.2E+02 0.0026 18.1 5.7 60 22-88 4-63 (70)
130 PF14261 DUF4351: Domain of un 31.0 40 0.00086 19.4 1.7 26 44-69 9-34 (59)
131 CHL00130 rbcS ribulose-1,5-bis 30.5 44 0.00095 22.9 2.0 19 58-76 15-33 (138)
132 PF13835 DUF4194: Domain of un 30.1 1.3E+02 0.0028 20.2 4.3 48 38-85 101-150 (166)
133 PLN02289 ribulose-bisphosphate 30.0 44 0.00096 23.7 2.0 19 58-76 77-95 (176)
134 PF00101 RuBisCO_small: Ribulo 29.9 56 0.0012 20.9 2.4 19 58-76 12-30 (99)
135 KOG2266|consensus 29.7 1.4E+02 0.0031 24.7 5.1 51 22-72 523-575 (594)
136 PF13404 HTH_AsnC-type: AsnC-t 29.6 96 0.0021 16.4 4.1 39 23-69 3-41 (42)
137 COG1733 Predicted transcriptio 29.5 71 0.0015 20.8 2.9 44 28-79 28-71 (120)
138 TIGR02147 Fsuc_second hypothet 29.1 48 0.001 24.8 2.2 24 57-80 151-174 (271)
139 KOG4718|consensus 29.0 1.3E+02 0.0029 22.2 4.4 54 25-80 102-157 (235)
140 COG1414 IclR Transcriptional r 28.8 56 0.0012 23.6 2.5 25 57-81 31-55 (246)
141 PF10288 DUF2392: Protein of u 28.7 89 0.0019 19.7 3.2 38 31-68 69-106 (107)
142 PF09106 SelB-wing_2: Elongati 28.5 26 0.00056 19.8 0.6 23 57-79 32-54 (59)
143 PRK11050 manganese transport r 28.5 41 0.0009 22.5 1.7 29 52-80 58-86 (152)
144 PRK11639 zinc uptake transcrip 28.3 2E+02 0.0043 19.6 5.1 53 25-80 28-81 (169)
145 PRK09834 DNA-binding transcrip 27.9 50 0.0011 23.8 2.1 41 37-86 26-66 (263)
146 COG1695 Predicted transcriptio 27.8 1.3E+02 0.0029 19.3 4.0 56 22-78 8-63 (138)
147 PF01418 HTH_6: Helix-turn-hel 27.5 65 0.0014 19.0 2.2 30 23-52 46-75 (77)
148 TIGR01201 HU_rel DNA-binding p 27.4 1.5E+02 0.0033 19.8 4.3 34 34-71 27-60 (145)
149 PF01498 HTH_Tnp_Tc3_2: Transp 27.3 63 0.0014 18.4 2.1 37 27-66 3-39 (72)
150 PF05569 Peptidase_M56: BlaR1 27.2 2E+02 0.0042 21.0 5.2 55 13-67 235-297 (299)
151 PF11313 DUF3116: Protein of u 27.1 1.7E+02 0.0036 18.4 4.1 44 38-82 21-64 (85)
152 PF07149 Pes-10: Pes-10; Inte 26.1 74 0.0016 25.1 2.8 38 29-71 12-50 (370)
153 PRK04984 fatty acid metabolism 25.9 47 0.001 23.2 1.6 31 51-81 37-67 (239)
154 PF13040 DUF3901: Protein of u 25.8 1.2E+02 0.0026 16.4 3.8 36 35-75 3-38 (40)
155 PRK15090 DNA-binding transcrip 25.4 1.5E+02 0.0034 21.1 4.3 39 35-81 26-64 (257)
156 PLN02839 nudix hydrolase 25.4 1E+02 0.0022 24.4 3.5 33 44-78 321-355 (372)
157 TIGR02944 suf_reg_Xantho FeS a 25.0 66 0.0014 20.6 2.1 26 53-78 33-58 (130)
158 TIGR01056 topB DNA topoisomera 25.0 99 0.0022 25.9 3.6 53 23-78 484-537 (660)
159 cd07064 AlkD_like_1 A new stru 24.7 1.7E+02 0.0038 20.5 4.4 59 17-80 125-183 (208)
160 PF15479 DUF4639: Domain of un 23.7 1.3E+02 0.0028 25.1 3.8 28 55-82 78-105 (576)
161 TIGR00331 hrcA heat shock gene 23.7 3.4E+02 0.0073 20.7 6.1 56 20-81 3-59 (337)
162 COG5230 Uncharacterized conser 23.3 55 0.0012 23.3 1.5 14 63-76 179-192 (194)
163 PRK08173 DNA topoisomerase III 23.3 1.2E+02 0.0026 26.3 3.8 53 23-79 490-543 (862)
164 smart00411 BHL bacterial (prok 23.1 1.7E+02 0.0037 17.2 4.1 30 38-71 1-30 (90)
165 PF14217 DUF4327: Domain of un 23.1 79 0.0017 19.1 2.0 22 58-79 3-24 (68)
166 cd00307 RuBisCO_small_like Rib 23.0 62 0.0013 20.1 1.6 16 60-75 2-17 (84)
167 PRK00441 argR arginine repress 23.0 2.3E+02 0.0051 19.1 4.6 43 24-69 5-47 (149)
168 PRK14712 conjugal transfer nic 22.9 2.3E+02 0.0049 26.7 5.6 57 22-79 185-241 (1623)
169 PF10752 DUF2533: Protein of u 22.8 2.1E+02 0.0045 18.0 5.6 38 11-50 19-56 (84)
170 KOG3344|consensus 22.7 77 0.0017 21.9 2.1 31 57-88 38-68 (150)
171 PF00216 Bac_DNA_binding: Bact 22.6 1.8E+02 0.0038 17.1 4.0 30 38-71 1-30 (90)
172 PF14557 AphA_like: Putative A 22.6 1.5E+02 0.0032 21.1 3.6 46 33-78 20-65 (175)
173 PRK02079 pyrroloquinoline quin 22.5 91 0.002 19.3 2.3 32 45-76 52-86 (88)
174 PF13062 DUF3924: Protein of u 22.3 59 0.0013 18.9 1.3 14 65-78 36-49 (62)
175 PF08696 Dna2: DNA replication 22.2 1.7E+02 0.0037 20.7 3.9 56 20-76 73-128 (209)
176 PRK10681 DNA-binding transcrip 21.8 1.9E+02 0.004 20.9 4.1 39 25-71 9-47 (252)
177 KOG2438|consensus 21.3 4.5E+02 0.0099 21.6 6.4 41 29-71 464-504 (505)
178 PRK04966 hypothetical protein; 21.3 94 0.002 18.9 2.1 19 64-83 11-29 (72)
179 PRK11032 hypothetical protein; 20.9 1.8E+02 0.0039 20.2 3.7 14 39-52 7-20 (160)
180 PRK11014 transcriptional repre 20.9 94 0.002 20.3 2.2 37 49-85 29-65 (141)
181 PRK13702 replication protein; 20.8 1.5E+02 0.0032 18.7 3.0 34 41-78 50-83 (85)
182 PRK07726 DNA topoisomerase III 20.8 1.1E+02 0.0024 25.5 3.1 52 23-78 481-534 (658)
183 smart00733 Mterf Mitochondrial 20.6 1E+02 0.0022 13.6 1.8 20 55-74 11-30 (31)
184 smart00546 CUE Domain that may 20.3 1.4E+02 0.0031 15.4 2.5 22 46-67 4-26 (43)
185 PF12047 DNMT1-RFD: Cytosine s 20.2 1.5E+02 0.0032 19.5 3.1 30 20-49 113-145 (146)
186 PF03221 HTH_Tnp_Tc5: Tc5 tran 20.1 1.7E+02 0.0036 15.9 3.4 29 42-70 7-35 (66)
No 1
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.95 E-value=2.2e-28 Score=147.96 Aligned_cols=68 Identities=54% Similarity=0.803 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCc
Q psy4179 16 IEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKD 83 (89)
Q Consensus 16 v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~ 83 (89)
|+++|...|+||||||||++|+++|++|+.+|.+.++++|.|+..+||++||+||++|||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 46899999999999999999999999999999999999999999999999999999999999998875
No 2
>KOG2166|consensus
Probab=99.94 E-value=3.2e-27 Score=192.46 Aligned_cols=81 Identities=53% Similarity=0.799 Sum_probs=78.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcce
Q psy4179 6 KLEQETTHKHIEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMY 85 (89)
Q Consensus 6 ~~e~~~t~~~v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y 85 (89)
..|++.+.+.++.||+..|+||||||||++|.+.|++|+.+|++|+++||.|++++||+|||.|||||||+|| +|+++|
T Consensus 645 ~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y 723 (725)
T KOG2166|consen 645 MDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIY 723 (725)
T ss_pred chhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcc
Confidence 3489999999999999999999999999999999999999999999999999999999999999999999999 899999
Q ss_pred ee
Q psy4179 86 HY 87 (89)
Q Consensus 86 ~Y 87 (89)
.|
T Consensus 724 ~Y 725 (725)
T KOG2166|consen 724 RY 725 (725)
T ss_pred cC
Confidence 98
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=4.6e-26 Score=184.20 Aligned_cols=85 Identities=51% Similarity=0.783 Sum_probs=81.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCc
Q psy4179 4 ELKLEQETTHKHIEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKD 83 (89)
Q Consensus 4 e~~~e~~~t~~~v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~ 83 (89)
+..+++.++++++++||.+.+|||||||||.+|+|.|++|+.+|+.++++||.|++++||++|+.|||||||+|.++| .
T Consensus 689 ~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~ 767 (773)
T COG5647 689 ECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-E 767 (773)
T ss_pred hhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-c
Confidence 445688899999999999999999999999999999999999999999999999999999999999999999999888 8
Q ss_pred ceeecC
Q psy4179 84 MYHYLA 89 (89)
Q Consensus 84 ~y~Yia 89 (89)
.|+|+|
T Consensus 768 iY~YLa 773 (773)
T COG5647 768 IYVYLA 773 (773)
T ss_pred eeeecC
Confidence 999997
No 4
>KOG2167|consensus
Probab=99.92 E-value=6.9e-26 Score=180.41 Aligned_cols=82 Identities=48% Similarity=0.731 Sum_probs=78.4
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCC
Q psy4179 3 TELKLEQETTHKHIEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHK 82 (89)
Q Consensus 3 ~e~~~e~~~t~~~v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~ 82 (89)
+|+.+|+.+|++.|.+||.+.|+||||||||++|+|+|+.|+.++.++|+ ||+.+ ++|++||.||++||++|| ++
T Consensus 580 ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n- 654 (661)
T KOG2167|consen 580 KETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN- 654 (661)
T ss_pred HHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-
Confidence 58899999999999999999999999999999999999999999999995 99888 999999999999999999 44
Q ss_pred cceeecC
Q psy4179 83 DMYHYLA 89 (89)
Q Consensus 83 ~~y~Yia 89 (89)
+.|.|+|
T Consensus 655 ~~y~yva 661 (661)
T KOG2167|consen 655 NIYNYVA 661 (661)
T ss_pred ccccccC
Confidence 8999997
No 5
>KOG2284|consensus
Probab=99.89 E-value=2.1e-23 Score=163.13 Aligned_cols=87 Identities=47% Similarity=0.744 Sum_probs=83.2
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 2 KTELKLEQETTHKHIEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 2 k~e~~~e~~~t~~~v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
.+.+++|.+.+...|.+||++.++||||||||.+|.+.|+-|+.+|++|.+.||.|++++||+|||.||++.||+|...+
T Consensus 642 ~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~ 721 (728)
T KOG2284|consen 642 NKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN 721 (728)
T ss_pred ccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999998765
Q ss_pred CcceeecC
Q psy4179 82 KDMYHYLA 89 (89)
Q Consensus 82 ~~~y~Yia 89 (89)
+.|.|+|
T Consensus 722 -dey~y~a 728 (728)
T KOG2284|consen 722 -DEYQYLA 728 (728)
T ss_pred -ccchhcC
Confidence 8999987
No 6
>KOG2285|consensus
Probab=99.66 E-value=1.7e-16 Score=125.45 Aligned_cols=82 Identities=34% Similarity=0.510 Sum_probs=77.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceee
Q psy4179 8 EQETTHKHIEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHY 87 (89)
Q Consensus 8 e~~~t~~~v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Y 87 (89)
..++-++.+.+-|....|-||++|||.+|+++..+|..+.++.|++.|.|+..+||..||||||..|++||++|-++|+|
T Consensus 696 ~~eeenesIVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiY 775 (777)
T KOG2285|consen 696 NAEEENESIVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIY 775 (777)
T ss_pred hhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceee
Confidence 34455788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q psy4179 88 LA 89 (89)
Q Consensus 88 ia 89 (89)
+|
T Consensus 776 ia 777 (777)
T KOG2285|consen 776 IA 777 (777)
T ss_pred eC
Confidence 97
No 7
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=95.61 E-value=0.015 Score=37.53 Aligned_cols=60 Identities=15% Similarity=0.232 Sum_probs=42.8
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeecC
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYLA 89 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yia 89 (89)
+..|++++=....++-.++. +.+.....+....+...+..|.+||||.|... +..|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~----~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIH----EALPEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHH----HHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHH----HHHHhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 45566666666666665555 45555567889999999999999999999864 45788864
No 8
>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=95.53 E-value=0.015 Score=34.42 Aligned_cols=46 Identities=17% Similarity=0.352 Sum_probs=35.9
Q ss_pred HHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 27 AIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 27 aIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.|-.+|+.++.++.++|-. +|..++..+..-++.|+.+|||++.+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~--------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAR--------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHH--------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 3566788888898887764 488999999999999999999999643
No 9
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=95.04 E-value=0.04 Score=36.64 Aligned_cols=60 Identities=13% Similarity=0.192 Sum_probs=43.6
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeecC
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYLA 89 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yia 89 (89)
+..|++++-....++-.++. +.+..++.+....+...+..|.+||||.|..+ +..|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~----~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDII----RILAEKKDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHH----HHHhhccCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 44567777666667655554 44554566788899999999999999999754 45788864
No 10
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=94.58 E-value=0.13 Score=34.58 Aligned_cols=62 Identities=15% Similarity=0.250 Sum_probs=50.7
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeecC
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYLA 89 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yia 89 (89)
..++.+++||=+++..+..|++.++ ...+.++.+.|+.-|-.|..||.|.|.-+ ...|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l----~~~~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEEL----PADREWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH----hhcccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence 4577889999999999988777654 44588999999999999999999999764 56677754
No 11
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=92.57 E-value=0.53 Score=26.78 Aligned_cols=51 Identities=18% Similarity=0.251 Sum_probs=33.3
Q ss_pred HHHHHHhhc-cccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc--cCCCc
Q psy4179 25 QAAIVRIMK-MRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT--ETHKD 83 (89)
Q Consensus 25 ~AaIVRiMK-~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~--~~~~~ 83 (89)
|..|...+. ....++-.+|... +..+.+.+-..|..|+++|||++. +.|..
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~--------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAER--------LGISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHH--------TT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred HHHHHHHHHccCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 455666666 6666776666543 556778888999999999999774 44443
No 12
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=92.06 E-value=0.29 Score=28.01 Aligned_cols=47 Identities=17% Similarity=0.324 Sum_probs=40.2
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
..|...++.+..++..+|.. .|.+|...++.-+..|-+.|++.|-.+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~--------~~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAE--------EFGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 45788888999999888775 488999999999999999999999654
No 13
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=90.29 E-value=0.15 Score=29.63 Aligned_cols=47 Identities=17% Similarity=0.266 Sum_probs=34.2
Q ss_pred cccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeec
Q psy4179 34 MRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYL 88 (89)
Q Consensus 34 ~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yi 88 (89)
....++-.+|... ...+.+.+-..+..|.++|+++|..+.+..|..+
T Consensus 19 ~~~~~t~~eIa~~--------l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 19 KNGPATAEEIAEE--------LGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHCHEEHHHHHHH--------HTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HcCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 5555665555443 2356788899999999999999998776666554
No 14
>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=89.97 E-value=0.98 Score=28.48 Aligned_cols=51 Identities=12% Similarity=0.190 Sum_probs=39.5
Q ss_pred HHHHhhcc-ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 27 AIVRIMKM-RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 27 aIVRiMK~-~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
+|..++.. .+.++..+|...+.+.. ..++.+.+=++++.|.+.|.|.|-..
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 45555554 56799999988876543 35788999999999999999999643
No 15
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=88.27 E-value=1.5 Score=23.65 Aligned_cols=45 Identities=13% Similarity=0.155 Sum_probs=31.0
Q ss_pred HHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCC
Q psy4179 29 VRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHK 82 (89)
Q Consensus 29 VRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~ 82 (89)
++.+. ...++..++... +..+.+.+.+.++.|.++|++....+..
T Consensus 3 l~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 3 LKLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 34444 555666654433 3467788999999999999999765433
No 16
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=88.08 E-value=1.2 Score=26.37 Aligned_cols=56 Identities=13% Similarity=0.242 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHhhccccc-cCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 19 DRKLLIQAAIVRIMKMRKT-LQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 19 dR~~~i~AaIVRiMK~~k~-l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
+|...|=..|..-+..+.- -+..|| .+.+. |. ++..+..-++.|.++|||+|+++-
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEI----a~~~g--~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREI----AEALG--LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHH----HHHHT--SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHH----HHHhC--CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 3445555555555554332 233333 34442 32 688889999999999999998764
No 17
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=87.65 E-value=0.98 Score=26.90 Aligned_cols=54 Identities=20% Similarity=0.275 Sum_probs=31.4
Q ss_pred HHHHHHhhccccc-cCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeecC
Q psy4179 25 QAAIVRIMKMRKT-LQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYLA 89 (89)
Q Consensus 25 ~AaIVRiMK~~k~-l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yia 89 (89)
=+.||.-||.+.. ++..||. +.++ +..+ +..+++|-+.+=|+-|+ +++.|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~----d~l~--~d~~----~~~~~~Lk~npKI~~d~-~~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEIL----DYLS--LDIG----KKLKQWLKNNPKIEYDP-DGNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHH----HHHT--SSS-----HHHHHHHHH-TTEEEE--TT-CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHH----HHHc--CCCC----HHHHHHHHcCCCEEEec-CCCEEEecc
Confidence 3667999998833 4555555 4554 4444 34668888888888876 457899975
No 18
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=86.81 E-value=0.35 Score=27.11 Aligned_cols=46 Identities=13% Similarity=0.223 Sum_probs=29.8
Q ss_pred HHHHhhccccc--cCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 27 AIVRIMKMRKT--LQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 27 aIVRiMK~~k~--l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.+......... ++-.+|... +..+.+.+...|..|.++||+.|..+
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~--------l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAER--------LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHH--------HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHCCCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 33444444444 555555433 44678889999999999999999654
No 19
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=86.24 E-value=3.2 Score=24.39 Aligned_cols=54 Identities=9% Similarity=0.142 Sum_probs=39.3
Q ss_pred HHHHHHHhhccccc--cCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcce
Q psy4179 24 IQAAIVRIMKMRKT--LQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMY 85 (89)
Q Consensus 24 i~AaIVRiMK~~k~--l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y 85 (89)
....|...|+.... ++-.+|..+ + -.+...+.+.+..|.+.||+.++.+.|..|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~----l----gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKN----L----GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHH----H----CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 34567788888766 776665543 2 356678999999999999999987664444
No 20
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.47 E-value=2 Score=26.66 Aligned_cols=47 Identities=13% Similarity=0.169 Sum_probs=38.9
Q ss_pred HHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 24 IQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 24 i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
++-.|++.+.....+++.+|-..+ -.+.+.+.+.+..|.++|+|.|.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l--------~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKV--------GLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeece
Confidence 466788888888889988877553 57888999999999999999863
No 21
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=85.28 E-value=0.99 Score=25.10 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=31.6
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
..+..+.-....++..+|-. .+..+.+.+-..+..|..+|||.|..
T Consensus 6 ~~iL~~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 34444455555566655443 34568889999999999999999954
No 22
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=83.97 E-value=0.77 Score=32.44 Aligned_cols=36 Identities=11% Similarity=0.351 Sum_probs=29.5
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCccee
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYH 86 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~ 86 (89)
+|..+|.++-..++++|+.|.+.|||.|-.+. .+|+
T Consensus 29 eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G~-GTfV 64 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNLLTEAGYIQKIQGK-GSIV 64 (233)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCc-eEEE
Confidence 45567999999999999999999999997653 3443
No 23
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=83.03 E-value=3.2 Score=22.27 Aligned_cols=45 Identities=16% Similarity=0.288 Sum_probs=33.8
Q ss_pred HHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhh
Q psy4179 24 IQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLE 76 (89)
Q Consensus 24 i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~ 76 (89)
.+-.|+..+.....++..+|...+ -.+.+.+...+..|.++|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 345677778888888888776553 367888999999999999984
No 24
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=82.32 E-value=2.4 Score=30.22 Aligned_cols=58 Identities=17% Similarity=0.273 Sum_probs=39.9
Q ss_pred HHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeecC
Q psy4179 24 IQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYLA 89 (89)
Q Consensus 24 i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yia 89 (89)
+-...|.-.|.+|.+...+|-. .|..++.++-..|..|...|-|.---||...|+||.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 4455678889999988777654 488889999999999999999888777888999984
No 25
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=81.58 E-value=1.1 Score=31.54 Aligned_cols=36 Identities=22% Similarity=0.454 Sum_probs=28.5
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCccee
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYH 86 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~ 86 (89)
.|..+|.++...++++|..|.+.|||.|-.+. .+|+
T Consensus 37 eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~-GtfV 72 (238)
T TIGR02325 37 QLAERFGVNRHTVRRAIAALVERGLLRAEQGR-GTFV 72 (238)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC-EEEE
Confidence 34456888899999999999999999997653 3443
No 26
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=81.11 E-value=1.2 Score=31.71 Aligned_cols=36 Identities=25% Similarity=0.537 Sum_probs=29.1
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCccee
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYH 86 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~ 86 (89)
.|...|.++...++++|+.|.+.|||.|-.+. .+|+
T Consensus 40 eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~-GtfV 75 (241)
T PRK10079 40 QLAARYEVNRHTLRRAIDQLVEKGWVQRRQGV-GVLV 75 (241)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC-EEEE
Confidence 44456889999999999999999999997754 3443
No 27
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=80.98 E-value=1.1 Score=31.76 Aligned_cols=36 Identities=17% Similarity=0.257 Sum_probs=28.4
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCccee
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYH 86 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~ 86 (89)
.|...|.++...++++|+.|.+.|||.|..+. .+|+
T Consensus 38 eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~-GTfV 73 (241)
T PRK11402 38 ELCTQYNVSRITIRKAISDLVADGVLIRWQGK-GTFV 73 (241)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecCc-eeEE
Confidence 34456788899999999999999999997653 3443
No 28
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=80.70 E-value=1.3 Score=24.12 Aligned_cols=31 Identities=6% Similarity=0.206 Sum_probs=26.0
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
++..+|..+.+.+.+.+..|.+.|+|.+.++
T Consensus 25 ~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 25 ELAAQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3445678899999999999999999988754
No 29
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=80.67 E-value=5.2 Score=20.98 Aligned_cols=44 Identities=16% Similarity=0.267 Sum_probs=31.9
Q ss_pred HHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 28 IVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 28 IVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
|...+..+..++-.+|... |..+.+.+...+..|.++|+|.+..
T Consensus 5 il~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 5 ILELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEee
Confidence 4444555555665555544 5678899999999999999998865
No 30
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=79.90 E-value=0.93 Score=28.64 Aligned_cols=60 Identities=15% Similarity=0.180 Sum_probs=44.2
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeecC
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYLA 89 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yia 89 (89)
++..-|++|.-..+.+- +...+..|+..+.+.-++.|..|-++|-|..-..+....+|.|
T Consensus 26 k~t~dkl~kEV~~~K~I-----Tps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 26 EELLKRVAKEVKKEKIV-----TPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHHHHHHHHHhccCcEE-----cHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 55556666655554331 1234566889999999999999999999988777777888875
No 31
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=78.86 E-value=1.7 Score=27.48 Aligned_cols=29 Identities=24% Similarity=0.315 Sum_probs=23.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhhhhhc--ccCC
Q psy4179 53 LRFKPRVHVIKKCIDILIEKEYLER--TETH 81 (89)
Q Consensus 53 ~~F~p~~~~iK~~IE~LIekeYl~R--~~~~ 81 (89)
..+..+.+.+-+.|..|.++|||.| +++|
T Consensus 51 ~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D 81 (109)
T TIGR01889 51 KEILIKQSALVKIIKKLSKKGYLSKERSEDD 81 (109)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEeccCCccc
Confidence 3455678889999999999999997 4444
No 32
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=78.70 E-value=1.6 Score=28.62 Aligned_cols=30 Identities=20% Similarity=0.244 Sum_probs=24.3
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.+...+-.+.+.+.+.|..|..+|||.|..
T Consensus 51 eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 51 QLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 444456677888999999999999999963
No 33
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=77.35 E-value=8.7 Score=22.64 Aligned_cols=47 Identities=19% Similarity=0.271 Sum_probs=34.6
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
+..|...+.....++..+|... +.++.+.+.+.|..|.++||+.+..
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~--------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKR--------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH--------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 4556666666666777666544 3466778899999999999998753
No 34
>PRK14999 histidine utilization repressor; Provisional
Probab=77.28 E-value=1.7 Score=30.97 Aligned_cols=36 Identities=11% Similarity=0.239 Sum_probs=28.6
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCccee
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYH 86 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~ 86 (89)
.|..+|.++-..++++|..|.+.|||.|-.+. .+|+
T Consensus 41 eLa~~~gVSR~TVR~Al~~L~~eGli~r~~Gk-GTfV 76 (241)
T PRK14999 41 ELVAQYGFSRMTINRALRELTDEGWLVRLQGV-GTFV 76 (241)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecCc-EEEE
Confidence 34446888999999999999999999997653 4443
No 35
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=76.29 E-value=9.4 Score=24.21 Aligned_cols=54 Identities=15% Similarity=0.286 Sum_probs=38.4
Q ss_pred HHHHHHhhccc-cccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 25 QAAIVRIMKMR-KTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 25 ~AaIVRiMK~~-k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
.-+|..+++.. ..++-.+|...+... ...++.+.|=++|+.|.+.|.|.+-..+
T Consensus 10 R~~Il~~l~~~~~~~ta~ei~~~l~~~---~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 10 RLAILELLKESPEHLTAEEIYDKLRKK---GPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHHHSSSEEHHHHHHHHHHT---TTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHhhhc---cCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 34555555554 578888888877632 3557899999999999999999996544
No 36
>PRK09462 fur ferric uptake regulator; Provisional
Probab=75.65 E-value=9.6 Score=25.32 Aligned_cols=52 Identities=6% Similarity=0.179 Sum_probs=40.4
Q ss_pred HHHHHHhhcc--ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 25 QAAIVRIMKM--RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 25 ~AaIVRiMK~--~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.-+|..++.. .+.++..+|...+.+.. +.++.+.|=+.++.|-+.|.|.+-.
T Consensus 19 R~~Il~~l~~~~~~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 19 RLKILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 4456666664 36899999998876544 4468899999999999999998853
No 37
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=75.65 E-value=5.4 Score=26.04 Aligned_cols=48 Identities=17% Similarity=0.196 Sum_probs=41.4
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
.++..|.+++...-.+++.+|-..+- .+.+.+..+|+.|.+.|.|+|.
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--------lS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--------LSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCceeeE
Confidence 46788999999999999988887653 6788899999999999999885
No 38
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=75.60 E-value=8.9 Score=22.73 Aligned_cols=45 Identities=16% Similarity=0.253 Sum_probs=33.4
Q ss_pred HHHhhccc-cccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 28 IVRIMKMR-KTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 28 IVRiMK~~-k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
|...+... ..++..+|...+ ..+.+.+.+.+..|.+.|||.++++
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l--------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL--------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 34444444 568887777665 3577889999999999999999753
No 39
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=75.58 E-value=4.2 Score=29.64 Aligned_cols=47 Identities=26% Similarity=0.253 Sum_probs=39.9
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
+..|...++.++.++..||.. .|.++...|++-++.|-+.|+|.|..
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~--------~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQ--------YFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 345778888899999888764 48899999999999999999999954
No 40
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=74.78 E-value=3.9 Score=29.80 Aligned_cols=47 Identities=21% Similarity=0.376 Sum_probs=40.5
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
+..|..+++.++.++-.+|.. +|.++...|.+-+..|-++|+|.|-.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~--------~l~vS~~TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVE--------HFSVSPQTIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHH--------HhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 456788889999999888775 57899999999999999999999953
No 41
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=74.63 E-value=2.2 Score=26.03 Aligned_cols=32 Identities=16% Similarity=0.276 Sum_probs=25.9
Q ss_pred HHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 49 NQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 49 ~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
..+..+...+.+.+...+..|.++||+.|..+
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 34445566889999999999999999999643
No 42
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=74.34 E-value=2.3 Score=29.97 Aligned_cols=32 Identities=13% Similarity=0.249 Sum_probs=27.3
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
.|...|.++-..++++|..|.+.|+|.|..+-
T Consensus 30 eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~ 61 (230)
T TIGR02018 30 ELVAQYGCSRMTVNRALRELTDAGLLERRQGV 61 (230)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 34456889999999999999999999997653
No 43
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=73.77 E-value=16 Score=22.78 Aligned_cols=54 Identities=6% Similarity=0.086 Sum_probs=43.6
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R 77 (89)
.++-+|.-++. .+.++=-+|...+.+.....+.++...+=..+..|-.+|||.+
T Consensus 4 ~l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 4 TLDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred hHHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 35566777776 4566777899888877766678999999999999999999998
No 44
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=73.47 E-value=2.7 Score=27.63 Aligned_cols=29 Identities=17% Similarity=0.323 Sum_probs=23.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 51 ISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 51 l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
|...+-.+.+.+-..|+.|.++|||.|.+
T Consensus 60 La~~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 60 LKKVLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 33456678888999999999999999953
No 45
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=73.23 E-value=2.9 Score=23.10 Aligned_cols=31 Identities=10% Similarity=0.186 Sum_probs=25.5
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.+..+|..+.+.+.+.+..|-+.|||.+.++
T Consensus 30 ~la~~~~is~~~v~~~l~~L~~~G~i~~~~~ 60 (66)
T cd07377 30 ELAEELGVSRTTVREALRELEAEGLVERRPG 60 (66)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 4445577889999999999999999988653
No 46
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=72.91 E-value=2.7 Score=29.94 Aligned_cols=32 Identities=16% Similarity=0.320 Sum_probs=26.7
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
.|..+|.++...++++|+.|...|||.|-.+.
T Consensus 34 eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G~ 65 (240)
T PRK09764 34 ALQTEFGVSRVTVRQALRQLVEQQILESIQGS 65 (240)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecCc
Confidence 34446888899999999999999999997653
No 47
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=72.81 E-value=2 Score=24.55 Aligned_cols=31 Identities=13% Similarity=0.279 Sum_probs=25.8
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
++..+|.++...+++++..|.+.|++.+.++
T Consensus 29 ~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 29 ELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 4445788999999999999999999998764
No 48
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=72.58 E-value=5.5 Score=24.79 Aligned_cols=45 Identities=13% Similarity=0.316 Sum_probs=28.9
Q ss_pred HHHHHHHHhhcc----ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhh
Q psy4179 23 LIQAAIVRIMKM----RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYL 75 (89)
Q Consensus 23 ~i~AaIVRiMK~----~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl 75 (89)
.++..|..++|. .--++..+|. ++| -.+...|+++|+.|++.|+|
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~----~~l----~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIA----QQL----GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHH----HHS----TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHH----HHh----CcCHHHHHHHHHHHHhCCeE
Confidence 445556666666 2224443443 444 35689999999999999976
No 49
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=72.28 E-value=2.6 Score=30.20 Aligned_cols=36 Identities=17% Similarity=0.367 Sum_probs=29.2
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCccee
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYH 86 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~ 86 (89)
.|..+|.++...++++|..|.+.|+|.|-.+. .+|+
T Consensus 36 eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~-GtfV 71 (236)
T COG2188 36 ELAEQFGVSRMTVRKALDELVEEGLIVRRQGK-GTFV 71 (236)
T ss_pred HHHHHHCCcHHHHHHHHHHHHHCCcEEEEecC-eeEE
Confidence 45567889999999999999999999997653 3443
No 50
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=71.11 E-value=7.8 Score=23.51 Aligned_cols=46 Identities=20% Similarity=0.229 Sum_probs=35.6
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
.-+|+-.+.....++|.+|-.. ...+...+.+.+..|.+.||++..
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~--------l~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEE--------LGLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHH--------TT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHH--------hCcCHHHHHHHHHHHHHCCCEEEE
Confidence 4466777777888888887754 346889999999999999999885
No 51
>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=70.73 E-value=14 Score=20.70 Aligned_cols=49 Identities=27% Similarity=0.243 Sum_probs=30.8
Q ss_pred HHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHh
Q psy4179 22 LLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEK 72 (89)
Q Consensus 22 ~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIek 72 (89)
..|.++|..||+..---+-. ...|..+|..+|..+...-|..|..+|..
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT--~k~vr~~Le~~~~~dL~~~K~~I~~~I~~ 51 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVT--KKQVREQLEERFGVDLSSRKKFIKELIDE 51 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG----HHHHHHHHHHH-SS--SHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHhHhh--HHHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 35778889999886322111 25666777777888877888888888854
No 52
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=69.22 E-value=11 Score=22.80 Aligned_cols=57 Identities=16% Similarity=0.169 Sum_probs=34.2
Q ss_pred HHHHHHHHhhcccc--ccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhh---hcccCCCcceeecC
Q psy4179 23 LIQAAIVRIMKMRK--TLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYL---ERTETHKDMYHYLA 89 (89)
Q Consensus 23 ~i~AaIVRiMK~~k--~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl---~R~~~~~~~y~Yia 89 (89)
..=|-||..||.+. -+++.|+.+++.. +... ...+++|-+..-+ +-++. .+.|.|.|
T Consensus 9 t~l~~aV~ymK~r~~~Plt~~EIl~~ls~-----~d~~----~~~~~~L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 9 TQLAKIVDYMKKRHQHPLTLDEILDYLSL-----LDIG----PKLKEWLKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhHHHHHHHHHhcCCCCccHHHHHHHHhc-----cCcc----HHHHHHHHhhhhccCceeccC-CCEEEecc
Confidence 34467899999987 5777777776642 2222 2233555544444 33333 46898875
No 53
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=69.11 E-value=13 Score=24.76 Aligned_cols=47 Identities=6% Similarity=0.064 Sum_probs=39.8
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R 77 (89)
.++-.|...+.....+++.+|-.++ -.+.+.+..+|+.|.+.|+|++
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l--------glS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF--------GVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeee
Confidence 3567788999999999998887654 3678899999999999999986
No 54
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=69.08 E-value=7.5 Score=28.59 Aligned_cols=48 Identities=15% Similarity=0.205 Sum_probs=40.4
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
+..|...++.++.++..+|... |.++...|++-|..|-+.|++.|..+
T Consensus 19 ~~~Il~~L~~~~~vtv~eLa~~--------l~VS~~TIRRDL~~Le~~G~l~r~~G 66 (269)
T PRK09802 19 REQIIQRLRQQGSVQVNDLSAL--------YGVSTVTIRNDLAFLEKQGIAVRAYG 66 (269)
T ss_pred HHHHHHHHHHcCCEeHHHHHHH--------HCCCHHHHHHHHHHHHhCCCeEEEeC
Confidence 4567888899989998887754 78999999999999999999999653
No 55
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=68.63 E-value=7.1 Score=28.46 Aligned_cols=47 Identities=19% Similarity=0.281 Sum_probs=39.6
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
-.|+.+.+.++.++-.+|.. +|.+|...|++-+..|=++|+|.|..+
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~--------~~~VS~~TIRRDL~~Le~~g~l~R~hG 54 (253)
T COG1349 8 QKILELLKEKGKVSVEELAE--------LFGVSEMTIRRDLNELEEQGLLLRVHG 54 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHH--------HhCCCHHHHHHhHHHHHHCCcEEEEeC
Confidence 35788888888888777763 599999999999999999999999543
No 56
>PF13730 HTH_36: Helix-turn-helix domain
Probab=67.94 E-value=4.1 Score=22.30 Aligned_cols=21 Identities=19% Similarity=0.275 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHHHHHHHhhhh
Q psy4179 55 FKPRVHVIKKCIDILIEKEYL 75 (89)
Q Consensus 55 F~p~~~~iK~~IE~LIekeYl 75 (89)
.-.+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 446788999999999999986
No 57
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=67.54 E-value=13 Score=25.18 Aligned_cols=47 Identities=11% Similarity=0.123 Sum_probs=40.6
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R 77 (89)
.++-.|.+++...-++++.+|-..+ -.+.+.+..+|..|.+.|.|++
T Consensus 14 ~~D~~IL~~Lq~d~R~s~~eiA~~l--------glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKDGRISNVELSKRV--------GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEE
Confidence 4788899999999999998776654 3678889999999999999986
No 58
>PRK10870 transcriptional repressor MprA; Provisional
Probab=66.24 E-value=4.8 Score=27.73 Aligned_cols=30 Identities=20% Similarity=0.294 Sum_probs=24.0
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.|...+..+.+.+-..|..|..+|||+|..
T Consensus 76 eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 76 ELSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 334455677888999999999999999954
No 59
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=65.40 E-value=5 Score=24.22 Aligned_cols=31 Identities=13% Similarity=0.162 Sum_probs=25.3
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.+...+..+.+.+-..+..|.++|||.|.++
T Consensus 4 ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 4 EIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 3444566788889999999999999999764
No 60
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=63.96 E-value=22 Score=24.83 Aligned_cols=45 Identities=9% Similarity=0.129 Sum_probs=35.7
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
-+|...++....++-.+|-.. +-.+.+.+.+.++.|.+.|+|+|.
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~--------lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEA--------LAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeEEe
Confidence 456677777777877776654 457889999999999999999986
No 61
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=63.65 E-value=3.5 Score=24.91 Aligned_cols=26 Identities=23% Similarity=0.333 Sum_probs=19.1
Q ss_pred CCCHHHHHHHHHHHHHhhhhhcccCCCcce
Q psy4179 56 KPRVHVIKKCIDILIEKEYLERTETHKDMY 85 (89)
Q Consensus 56 ~p~~~~iK~~IE~LIekeYl~R~~~~~~~y 85 (89)
-.+.+.+. -.||+-|||.|+++ .+.|
T Consensus 43 ~~D~a~LR---R~LVd~g~L~R~~d-g~~Y 68 (71)
T PF09860_consen 43 FDDYATLR---RYLVDYGLLERTRD-GSRY 68 (71)
T ss_pred cccHHHHH---HHHHHcCCeeecCC-CCee
Confidence 35777776 46899999999874 4555
No 62
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=63.19 E-value=6.9 Score=21.48 Aligned_cols=45 Identities=18% Similarity=0.248 Sum_probs=30.3
Q ss_pred HHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 28 IVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 28 IVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
|...+.... ++..++.. .+..+...+...+..|.+.|++.+..+.
T Consensus 12 il~~l~~~~-~~~~ei~~--------~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 12 ILRLLLEGP-LTVSELAE--------RLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHCC-cCHHHHHH--------HHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 333333344 66665433 2346788899999999999999986543
No 63
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=62.80 E-value=6.1 Score=20.52 Aligned_cols=29 Identities=10% Similarity=0.150 Sum_probs=23.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 51 ISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 51 l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
+...+..+.+.+.+.+..|.+.||+.++.
T Consensus 14 la~~l~~s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 14 IAELLGLTRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 33445567888999999999999998864
No 64
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=61.66 E-value=17 Score=22.49 Aligned_cols=38 Identities=8% Similarity=0.071 Sum_probs=29.1
Q ss_pred cccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 34 MRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 34 ~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
....+++.+|...+ -.+.+.+.+.|..|..+|||.|..
T Consensus 44 ~~~~is~~eLa~~~--------g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAELT--------GLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeeeec
Confidence 45667777766432 356778899999999999999875
No 65
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=61.47 E-value=8.2 Score=25.95 Aligned_cols=33 Identities=18% Similarity=0.280 Sum_probs=24.6
Q ss_pred CCCHHHHHHHHHHHHHhhhhhccc----CCCcceeec
Q psy4179 56 KPRVHVIKKCIDILIEKEYLERTE----THKDMYHYL 88 (89)
Q Consensus 56 ~p~~~~iK~~IE~LIekeYl~R~~----~~~~~y~Yi 88 (89)
.-+.+.+-+++..|++.|.+.|.. +.+-.|.|.
T Consensus 53 nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~ 89 (126)
T COG3355 53 NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYK 89 (126)
T ss_pred CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEe
Confidence 356788899999999999999952 223456664
No 66
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=61.07 E-value=22 Score=28.78 Aligned_cols=60 Identities=15% Similarity=0.182 Sum_probs=48.1
Q ss_pred HHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeec
Q psy4179 21 KLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYL 88 (89)
Q Consensus 21 ~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yi 88 (89)
...-+.+|++.++....+|-.+|-. .|-.+...+-+.|..|+.+|++.+-..+...+-|+
T Consensus 400 ~~~~~~~il~~~~en~~~T~~~L~~--------~l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v 459 (467)
T COG2865 400 LSERQEKILELIKENGKVTARELRE--------ILGISSETIRRRIANLVKRGLLKQLGSSGRGTWYV 459 (467)
T ss_pred hhHHHHHHHHHHhhccccCHHHHHH--------HhCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEe
Confidence 3444589999999999998877654 34478889999999999999999976566667776
No 67
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=61.02 E-value=7.3 Score=24.62 Aligned_cols=44 Identities=16% Similarity=0.182 Sum_probs=28.5
Q ss_pred HHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 28 IVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 28 IVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
|.........++..+|.. .+..+.+.+-..+..|.++|||.|..
T Consensus 33 iL~~l~~~~~~t~~ela~--------~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLAN--------QACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHcCCcCHHHHHH--------HhCCCchhHHHHHHHHHHCCCEEecc
Confidence 344444445555444443 33355667789999999999999954
No 68
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=60.72 E-value=17 Score=19.69 Aligned_cols=31 Identities=13% Similarity=0.250 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHHHHHh
Q psy4179 42 QLVAEVLNQISLRFKPRVHVIKKCIDILIEK 72 (89)
Q Consensus 42 ~L~~ev~~~l~~~F~p~~~~iK~~IE~LIek 72 (89)
+|....-........|-...+.++|+.++++
T Consensus 12 el~~~L~~ls~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 12 ELYEKLKELSEETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 5666666666666789999999999999864
No 69
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=60.47 E-value=9 Score=26.55 Aligned_cols=25 Identities=8% Similarity=0.234 Sum_probs=22.8
Q ss_pred CCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 56 KPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 56 ~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
..+...++.+|+.|.+-|+|+++++
T Consensus 52 ~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 52 KISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred CCCHHHHHHHHHHHHHCCCeEECCC
Confidence 4689999999999999999999875
No 70
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=59.07 E-value=6 Score=21.70 Aligned_cols=43 Identities=14% Similarity=0.295 Sum_probs=27.7
Q ss_pred HHhhccccc-cCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 29 VRIMKMRKT-LQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 29 VRiMK~~k~-l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
...+..... ++..+|...+ -.+.+.+-.-+..|.+.||++||+
T Consensus 9 L~~l~~~~~~~t~~eia~~~--------gl~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIARAL--------GLPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHCHHCTBSCEEHHHHHHHH--------TS-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHcCCCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCcCeecCc
Confidence 333333333 5666665443 134566788899999999999975
No 71
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=58.42 E-value=8.9 Score=23.78 Aligned_cols=31 Identities=19% Similarity=0.142 Sum_probs=27.3
Q ss_pred HHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 49 NQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 49 ~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.+|..+|..+.+.|..-+|.|+-+|-++|-+
T Consensus 20 ~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 20 AQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 3566679999999999999999999999976
No 72
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=58.28 E-value=42 Score=22.46 Aligned_cols=55 Identities=15% Similarity=0.192 Sum_probs=41.3
Q ss_pred HHHHHHhhcc-ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCC
Q psy4179 25 QAAIVRIMKM-RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHK 82 (89)
Q Consensus 25 ~AaIVRiMK~-~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~ 82 (89)
..+|.+++-. ...++-.+|..++...- ...+.+.+=..++.|-+.|+|.|-+...
T Consensus 23 R~~vl~~L~~~~~~~sAeei~~~l~~~~---p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 23 RLAVLELLLEADGHLSAEELYEELREEG---PGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhC---CCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 4566677664 35588888888776533 4467999999999999999999965433
No 73
>PF08820 DUF1803: Domain of unknown function (DUF1803); InterPro: IPR014924 This small protein is found in one or two copies in bacteria. The function of this is unknown.
Probab=57.64 E-value=6.4 Score=25.18 Aligned_cols=28 Identities=32% Similarity=0.535 Sum_probs=19.7
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
++++-| |....+-.-||.||.-|||.|+
T Consensus 33 ~iKk~f-~~qk~~D~fie~li~~GYI~re 60 (93)
T PF08820_consen 33 FIKKDF-PKQKRLDIFIEALIKLGYIERE 60 (93)
T ss_pred HHHHhh-ccccchhHHHHHHHHcCCeEec
Confidence 344445 3344456789999999999994
No 74
>PRK00215 LexA repressor; Validated
Probab=55.56 E-value=13 Score=25.71 Aligned_cols=31 Identities=10% Similarity=0.186 Sum_probs=23.9
Q ss_pred CCC-CHHHHHHHHHHHHHhhhhhcccCCCcce
Q psy4179 55 FKP-RVHVIKKCIDILIEKEYLERTETHKDMY 85 (89)
Q Consensus 55 F~p-~~~~iK~~IE~LIekeYl~R~~~~~~~y 85 (89)
+-. +.+.+-..+..|.++|||+|++++...+
T Consensus 33 ~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~~ 64 (205)
T PRK00215 33 LGLRSPSAVHEHLKALERKGFIRRDPGRSRAI 64 (205)
T ss_pred hCCCChHHHHHHHHHHHHCCCEEeCCCCcceE
Confidence 445 5666788999999999999987665433
No 75
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=55.04 E-value=14 Score=21.62 Aligned_cols=44 Identities=11% Similarity=0.063 Sum_probs=35.4
Q ss_pred cccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 36 KTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 36 k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
+.++=.+|...+.+.....|.++...|=..+..|-++|+|....
T Consensus 8 ~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~ 51 (75)
T PF03551_consen 8 GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRW 51 (75)
T ss_dssp S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEE
T ss_pred CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEee
Confidence 44555678888777766678999999999999999999998753
No 76
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=53.41 E-value=11 Score=27.24 Aligned_cols=35 Identities=11% Similarity=0.168 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeec
Q psy4179 54 RFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYL 88 (89)
Q Consensus 54 ~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yi 88 (89)
++..+.+.+-+.+..|-++|||.|..+....+.++
T Consensus 30 ~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L 64 (217)
T PRK14165 30 HTGTSSKTAARILKQLEDEGYITRTIVPRGQLITI 64 (217)
T ss_pred HHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence 34568889999999999999999976544444443
No 77
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=53.33 E-value=35 Score=23.73 Aligned_cols=48 Identities=10% Similarity=0.230 Sum_probs=34.7
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
+..|...+..+..++..+|... +..+.+.+-+.+..|.++||+.|..+
T Consensus 145 ~~~IL~~l~~~g~~s~~eia~~--------l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 145 ELKVLEVLKAEGEKSVKNIAKK--------LGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 3455566666566676666644 34567778899999999999999864
No 78
>PRK09954 putative kinase; Provisional
Probab=53.23 E-value=29 Score=25.93 Aligned_cols=43 Identities=14% Similarity=0.200 Sum_probs=36.3
Q ss_pred HHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy4179 27 AIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 27 aIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R 77 (89)
-|.+.++....++.++|-.. +.++.+.+.+.|..|.++||+++
T Consensus 7 ~il~~l~~~~~~s~~~la~~--------l~~s~~~v~~~i~~L~~~g~i~~ 49 (362)
T PRK09954 7 EILAILRRNPLIQQNEIADI--------LQISRSRVAAHIMDLMRKGRIKG 49 (362)
T ss_pred HHHHHHHHCCCCCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCcCC
Confidence 48889999999998887654 34889999999999999999964
No 79
>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=52.44 E-value=53 Score=20.12 Aligned_cols=45 Identities=16% Similarity=0.158 Sum_probs=32.7
Q ss_pred HHHHHHHHhhcc--ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q psy4179 23 LIQAAIVRIMKM--RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILI 70 (89)
Q Consensus 23 ~i~AaIVRiMK~--~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LI 70 (89)
.+...+-.+++. ...+++.+|+.+|........| ..+|+.+-.-|
T Consensus 35 ~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP---~~vk~ell~~I 81 (86)
T PF10163_consen 35 EVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVP---DEVKKELLQRI 81 (86)
T ss_dssp HHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS----HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCC---HHHHHHHHHHH
Confidence 456666777777 7889999999999999876543 44566665555
No 80
>PF11417 Inhibitor_G39P: Loader and inhibitor of phage G40P; InterPro: IPR024424 G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite stricture consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C-terminal is essential for helicase interaction [].; PDB: 1NO1_B.
Probab=50.90 E-value=14 Score=22.31 Aligned_cols=29 Identities=21% Similarity=0.352 Sum_probs=14.0
Q ss_pred cccCcHHHHHHHHHHhc-CCCCCCHHHHHH
Q psy4179 36 KTLQHQQLVAEVLNQIS-LRFKPRVHVIKK 64 (89)
Q Consensus 36 k~l~~~~L~~ev~~~l~-~~F~p~~~~iK~ 64 (89)
+...|......+...+. +.|+|++++|-+
T Consensus 41 ~d~~ye~v~~al~~~i~~~kfPPsiaeii~ 70 (71)
T PF11417_consen 41 KDYDYEIVMKALKKHIATNKFPPSIAEIIK 70 (71)
T ss_dssp TTS-HHHHHHHHHHHHHH-SS---GGGG--
T ss_pred HhCCHHHHHHHHHHHHHhCCCCcCHHHHhh
Confidence 34556665556655553 679999987643
No 81
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=50.41 E-value=13 Score=20.64 Aligned_cols=25 Identities=12% Similarity=0.199 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 55 FKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 55 F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
+-.+.+.+.+.+..|.+.|||.+..
T Consensus 35 ~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 35 LGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4467888999999999999999875
No 82
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 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. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=50.10 E-value=48 Score=19.03 Aligned_cols=53 Identities=21% Similarity=0.216 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhh
Q psy4179 15 HIEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYL 75 (89)
Q Consensus 15 ~v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl 75 (89)
.+.++.-..+=+.|...+-++..++..+|...+- .++..+|.++=.||..+++
T Consensus 5 ~ii~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~--------l~~~~Vk~~L~~LiQh~~v 57 (62)
T PF08221_consen 5 LIIEEHFGEIVAKVGEVLLSRGRLTLREIVRRTG--------LSPKQVKKALVVLIQHNLV 57 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHC-SEEHHHHHHHHT----------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHcChHHHHHHHHHHHcCCcCHHHHHHHhC--------CCHHHHHHHHHHHHHcCCe
Confidence 4566677788899999999999999988886552 4678899999999988765
No 83
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=49.71 E-value=29 Score=23.21 Aligned_cols=54 Identities=13% Similarity=0.352 Sum_probs=32.6
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcC-CCCCCHHHHHHHHHHHHHhhhhhc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISL-RFKPRVHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~-~F~p~~~~iK~~IE~LIekeYl~R 77 (89)
.+.--|+.+.-.++--.. +|+++..+..++ -|.|+.+.+=+++-.|++-||+.|
T Consensus 18 FlKlYiitm~e~~r~Yg~-q~Ld~lr~EFk~~Gy~P~hsEvYraLHeL~~dGilk~ 72 (122)
T PF02334_consen 18 FLKLYIITMVEQERGYGL-QLLDELRSEFKPLGYRPNHSEVYRALHELVDDGILKQ 72 (122)
T ss_dssp HHHHHHHHHHHTT-EBCT-CHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHhhhhcccchHH-HHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhhhHHHH
Confidence 345555555555553222 344555555553 489999999999999999999966
No 84
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=49.62 E-value=23 Score=24.39 Aligned_cols=27 Identities=22% Similarity=0.302 Sum_probs=22.3
Q ss_pred CCCC-HHHHHHHHHHHHHhhhhhcccCC
Q psy4179 55 FKPR-VHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 55 F~p~-~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
+-.+ .+.+-..++.|.++|||.+.++.
T Consensus 35 ~~~~s~~tv~~~l~~L~~~g~i~~~~~~ 62 (199)
T TIGR00498 35 VGLRSPSAAEEHLKALERKGYIERDPGK 62 (199)
T ss_pred hCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence 3444 78889999999999999998654
No 85
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=49.31 E-value=53 Score=22.20 Aligned_cols=50 Identities=22% Similarity=0.332 Sum_probs=40.9
Q ss_pred HHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 21 KLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 21 ~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
...|.+-||-+.+.+..++..+|...+ -.+...++.....|.+.|.|-+.
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~T--------GasR~Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAKT--------GASRNTVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHHH--------CCCHHHHHHHHHHHHHcCCeEeC
Confidence 356889999999999999999998664 35677788888888888877764
No 86
>smart00526 H15 Domain in histone families 1 and 5.
Probab=49.10 E-value=46 Score=19.01 Aligned_cols=52 Identities=21% Similarity=0.263 Sum_probs=32.2
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCC--HHHHHHHHHHHHHhhhhhc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPR--VHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~--~~~iK~~IE~LIekeYl~R 77 (89)
.|..||.. ++.++-.+.+.+...+...- ...|. ...++..+..++++|-|.+
T Consensus 10 mI~eAI~~-l~er~GsS~~aI~kyi~~~~--~~~~~~~~~~l~~~Lk~~v~~G~l~q 63 (66)
T smart00526 10 MITEAISA-LKERKGSSLQAIKKYIEANY--KVLPNNFRSLLKLALKKLVASGKLVQ 63 (66)
T ss_pred HHHHHHHH-cCCCCCCCHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHHhcCceee
Confidence 46666554 57777788777776665541 11122 3567777888887776654
No 87
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=48.43 E-value=52 Score=19.91 Aligned_cols=54 Identities=17% Similarity=0.177 Sum_probs=37.3
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC--CCcceee
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET--HKDMYHY 87 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~--~~~~y~Y 87 (89)
+.|++.+.. ..+.|++|...+ . ..+...+-+++..|.+.|.+.|... .|....|
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l----~---~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y 63 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRL----P---GISPKVLSQRLKELEEAGLVERRVYPEVPPRVEY 63 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHS----T---TS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhc----c---hhHHHHHHHHHHHHHHcchhhcccccCCCCCCcc
Confidence 345666666 788888887554 1 2578899999999999999999632 2333445
No 88
>PF04738 Lant_dehyd_C: Lantibiotic dehydratase, C terminus; InterPro: IPR006827 Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides []. They are produced by bacteria of the Firmicutes phylum, and include mutacin, subtilin, and nisin. Lantibiotic peptides contain thioether bridges termed lanthionines that are thought to be generated by dehydration of serine and threonine residues followed by addition of cysteine residues []. This family constitutes the C terminus of the enzyme proposed to catalyse the dehydration step [, ].
Probab=47.81 E-value=19 Score=27.99 Aligned_cols=36 Identities=17% Similarity=0.359 Sum_probs=28.0
Q ss_pred CcHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 39 QHQQLVAEVLNQISLRF-KPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 39 ~~~~L~~ev~~~l~~~F-~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
++.+|+.++. ..| ..+...+..-|..||++|+|..+
T Consensus 2 ~~~~l~~~L~----~~~~~~~~~~v~~~L~~Li~~~~L~~~ 38 (500)
T PF04738_consen 2 SYSELIEQLA----KEFPEAEAERVENYLRQLIEQGFLISE 38 (500)
T ss_pred hHHHHHHHHH----HhCCCCCHHHHHHHHHHHHHCCEEEec
Confidence 4556655544 455 57899999999999999999886
No 89
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 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 [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=46.81 E-value=9.5 Score=24.81 Aligned_cols=39 Identities=21% Similarity=0.233 Sum_probs=32.1
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeec
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYL 88 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yi 88 (89)
.+..||..+.+.-++.|..|-++|-|.--..++...+|.
T Consensus 64 ~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYt 102 (105)
T PF03297_consen 64 VLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYT 102 (105)
T ss_dssp HHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEE
T ss_pred HHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEe
Confidence 345678888999999999999999998876677777774
No 90
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=46.46 E-value=36 Score=23.63 Aligned_cols=46 Identities=17% Similarity=0.198 Sum_probs=36.6
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
..|...++.++.++..+|.. +|.+|...|++-+..|-+.|-+.|-.
T Consensus 10 ~~Il~~l~~~~~~~~~~La~--------~~~vS~~TiRRDl~~L~~~g~~~r~~ 55 (185)
T PRK04424 10 KALQELIEENPFITDEELAE--------KFGVSIQTIRLDRMELGIPELRERIK 55 (185)
T ss_pred HHHHHHHHHCCCEEHHHHHH--------HHCcCHHHHHHHHHHHhcchHHHHHH
Confidence 34566667777777766653 58899999999999999999998853
No 91
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=45.92 E-value=93 Score=21.10 Aligned_cols=69 Identities=13% Similarity=0.213 Sum_probs=51.2
Q ss_pred HHHHHHHHHHH--HHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 8 EQETTHKHIEE--DRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 8 e~~~t~~~v~~--dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
-.+++.+.+.+ +....+.-+|..++... +.=-+|...+.+.....|.|+...|=..+..|-+.|||...
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~l~IL~lL~~~--~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~ 96 (135)
T PRK09416 26 HQKAVREKIKQSSEKEEDILLAILQLLMNE--KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSS 96 (135)
T ss_pred hHHHHHHHHHHHhcccccHHHHHHHHHhCC--CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEe
Confidence 34455555543 33456778888888765 55558888877765557899999999999999999999874
No 92
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=45.35 E-value=41 Score=24.28 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=37.8
Q ss_pred HHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 27 AIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 27 aIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.|..+++.++.++..+|... |-++...+++-+..|-+.+.+.|..
T Consensus 8 ~Il~~l~~~~~~~~~eLa~~--------l~VS~~TiRRdL~~L~~~~~l~r~~ 52 (240)
T PRK10411 8 AIVDLLLNHTSLTTEALAEQ--------LNVSKETIRRDLNELQTQGKILRNH 52 (240)
T ss_pred HHHHHHHHcCCCcHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEec
Confidence 47888888899998888755 4588999999999999999998853
No 93
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=45.07 E-value=17 Score=23.87 Aligned_cols=44 Identities=16% Similarity=0.182 Sum_probs=30.7
Q ss_pred HHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 27 AIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 27 aIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
+|.++.......+.. .+...+.++.+.+...|..|.++|||.+.
T Consensus 12 ~I~~l~~~~~~~~~~--------ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 12 QIYLLIEEKGYARVS--------DIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHHHhcCCCcCHH--------HHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 445555555555433 33334567888899999999999999865
No 94
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=43.80 E-value=18 Score=22.94 Aligned_cols=28 Identities=29% Similarity=0.426 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 54 RFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 54 ~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
++..+...+...++.|.+.|+|+|..+.
T Consensus 30 ~l~~~~~~v~~~l~~Le~~GLler~~g~ 57 (92)
T PF10007_consen 30 RLKIPLEEVREALEKLEEMGLLERVEGK 57 (92)
T ss_pred HHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence 4567788999999999999999998653
No 95
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=43.66 E-value=29 Score=20.36 Aligned_cols=32 Identities=22% Similarity=0.491 Sum_probs=24.1
Q ss_pred cccCcHHHHHHHHHHhcCCCCCC--HHHHHHHHHHHHHhhh
Q psy4179 36 KTLQHQQLVAEVLNQISLRFKPR--VHVIKKCIDILIEKEY 74 (89)
Q Consensus 36 k~l~~~~L~~ev~~~l~~~F~p~--~~~iK~~IE~LIekeY 74 (89)
++++++||+.- -|+|. ...|+++-+.|+++||
T Consensus 2 ~tv~k~dLi~l-------Gf~~~tA~~IIrqAK~~lV~~G~ 35 (59)
T PF11372_consen 2 KTVTKKDLIEL-------GFSESTARDIIRQAKALLVQKGF 35 (59)
T ss_pred CccCHHHHHHc-------CCCHHHHHHHHHHHHHHHHHcCC
Confidence 46778888743 47764 5679999999999986
No 96
>KOG3054|consensus
Probab=43.18 E-value=62 Score=24.56 Aligned_cols=56 Identities=18% Similarity=0.274 Sum_probs=41.7
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeecC
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYLA 89 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yia 89 (89)
+-.|-..|..|.....||- +.|-....+.--.|..|+..|.|.---||...|+||.
T Consensus 203 ~eFv~YIk~nKvV~ledLa--------s~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 203 SEFVEYIKKNKVVPLEDLA--------SEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHHHhcCeeeHHHHH--------HHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 3445666666666665554 3466666666679999999999999888999999984
No 97
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=42.90 E-value=13 Score=21.32 Aligned_cols=26 Identities=19% Similarity=0.224 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 54 RFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 54 ~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
++..+++.+-..+..|-++||+.+.+
T Consensus 31 ~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 31 RLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHCCChHHHHHHHHHHHHCCCEEecC
Confidence 45678888999999999999998865
No 98
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=42.48 E-value=23 Score=22.78 Aligned_cols=19 Identities=26% Similarity=0.279 Sum_probs=17.0
Q ss_pred CCHHHHHHHHHHHHHhhhh
Q psy4179 57 PRVHVIKKCIDILIEKEYL 75 (89)
Q Consensus 57 p~~~~iK~~IE~LIekeYl 75 (89)
+|...|.+.|+.||.+||.
T Consensus 12 lt~~~i~~QI~yll~qG~~ 30 (99)
T cd03527 12 LTDEQIAKQIDYIISNGWA 30 (99)
T ss_pred CCHHHHHHHHHHHHhCCCE
Confidence 4788999999999999985
No 99
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=41.96 E-value=24 Score=21.72 Aligned_cols=24 Identities=21% Similarity=0.188 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 57 PRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 57 p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
-+...++.-|..|+..|||.-+.+
T Consensus 54 ~~~~~~~~li~~Li~~g~L~~~~~ 77 (106)
T PF09382_consen 54 MSKDDWERLIRQLILEGYLSEDNG 77 (106)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEEEC
T ss_pred CCHHHHHHHHHHHHHcCCceecCC
Confidence 478999999999999999966543
No 100
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=41.78 E-value=1.1e+02 Score=20.95 Aligned_cols=57 Identities=19% Similarity=0.118 Sum_probs=44.4
Q ss_pred HHHHHHHHHHhhcccc-ccCcHHHHHHHHHHhcCCCC----------CCHHHHHHHHHHHHHhhhhhc
Q psy4179 21 KLLIQAAIVRIMKMRK-TLQHQQLVAEVLNQISLRFK----------PRVHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 21 ~~~i~AaIVRiMK~~k-~l~~~~L~~ev~~~l~~~F~----------p~~~~iK~~IE~LIekeYl~R 77 (89)
...|=-|..|.-+.+. .++|+-+..|-.+..+.... .+.+.++++.|.|++-|.|.-
T Consensus 104 EL~LLIa~~rl~~~~~~~~NF~~vy~EY~~~~~~~~~~~~~~~~~~~~~k~v~~~a~E~L~~l~Ll~~ 171 (203)
T PF14629_consen 104 ELCLLIAAARLIKGYEETFNFEMVYDEYKKFAKSYNSSSAIVGTIKVWSKPVALKAWEHLLSLELLKP 171 (203)
T ss_pred HHHHHHHHHHHHhccCCCccHHHHHHHHHHHHHhhccccccccccccCCHHHHHHHHHHHHHCCCcee
Confidence 3455567788887777 89999888887777664333 378899999999999999976
No 101
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=41.55 E-value=79 Score=20.33 Aligned_cols=23 Identities=22% Similarity=0.366 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHHHHhhhhhccc
Q psy4179 57 PRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 57 p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.+.+.+-.+|-.||.+||++.+.
T Consensus 44 ~~~~~V~SNIGvLIKkglIEKSG 66 (96)
T PF09114_consen 44 MNKASVNSNIGVLIKKGLIEKSG 66 (96)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEET
T ss_pred hhhhHHHHhHHHHHHcCcccccC
Confidence 35677888999999999999865
No 102
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=40.85 E-value=49 Score=23.17 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=31.1
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
=+.+++.|-.. .+..+++. .+...|+ ..++...++.|.++|||.-+
T Consensus 32 ~~~L~~lLdG~--rt~~eI~~----~l~~~~p--~~~v~~~L~~L~~~G~l~~~ 77 (193)
T TIGR03882 32 YCQLAPLLDGR--RTLDEIIA----ALAGRFP--AEEVLYALDRLERRGYLVED 77 (193)
T ss_pred HHHHHHHHcCC--CCHHHHHH----HhhccCC--HHHHHHHHHHHHHCCCEecc
Confidence 35566766664 34445554 4444454 67789999999999999853
No 103
>PF10798 YmgB: Biofilm development protein YmgB/AriR; InterPro: IPR024753 YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid, which indicates that YmgB has an important function in acid-resistance []. YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole) [].; GO: 0042710 biofilm formation, 0071229 cellular response to acid; PDB: 2OXL_B.
Probab=40.54 E-value=64 Score=18.83 Aligned_cols=50 Identities=6% Similarity=0.302 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCC-CCHHHHHHHHHHHH
Q psy4179 21 KLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFK-PRVHVIKKCIDILI 70 (89)
Q Consensus 21 ~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~-p~~~~iK~~IE~LI 70 (89)
...+.+++.-+|.+.+.++...++..++..|..--. .....+++.+|..+
T Consensus 4 ~~vL~~iv~ell~~g~~vsnKaII~~LI~~LE~e~Dv~~~dvyR~~LEiVv 54 (61)
T PF10798_consen 4 SEVLGAIVRELLASGGHVSNKAIILKLIHRLESESDVVQLDVYRNALEIVV 54 (61)
T ss_dssp HHHHHHHHHHHHHTT---SHHHHHHHHHHHHHT---HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccccHHHHHHHHHHHHHHH
Confidence 346788889999999999999999999999963211 12334455555544
No 104
>PF11868 DUF3388: Protein of unknown function (DUF3388); InterPro: IPR024514 This domain is found in a family of bacterial proteins that are functionally uncharacterised. Proteins in this family are typically between 261 to 275 amino acids in length and have a N-terminal ACT domain.
Probab=40.28 E-value=14 Score=26.36 Aligned_cols=15 Identities=20% Similarity=0.758 Sum_probs=14.0
Q ss_pred hhhcccCCCcceeec
Q psy4179 74 YLERTETHKDMYHYL 88 (89)
Q Consensus 74 Yl~R~~~~~~~y~Yi 88 (89)
||+||++|+.+|.|+
T Consensus 20 yi~rd~~d~kTfrFv 34 (192)
T PF11868_consen 20 YIDRDADDKKTFRFV 34 (192)
T ss_pred ccccccCCCceeEEE
Confidence 999999999999885
No 105
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=39.71 E-value=42 Score=18.86 Aligned_cols=30 Identities=3% Similarity=0.153 Sum_probs=15.8
Q ss_pred ccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q psy4179 37 TLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILI 70 (89)
Q Consensus 37 ~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LI 70 (89)
..+-.+++..+.+ +|..++..++..+..++
T Consensus 29 ~~t~~ei~~~l~~----~y~~~~~~~~~dv~~fl 58 (68)
T PF05402_consen 29 PRTVEEIVDALAE----EYDVDPEEAEEDVEEFL 58 (68)
T ss_dssp SS-HHHHHHHHHH----HTT--HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHH----HcCCCHHHHHHHHHHHH
Confidence 4556666655544 56677766666655544
No 106
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=39.19 E-value=80 Score=18.60 Aligned_cols=56 Identities=21% Similarity=0.269 Sum_probs=39.5
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCC--CHHHHHHHHHHHHHhhhhhccc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKP--RVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p--~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.|..|| .-++.++-.+-..+...+...-.--..| -...+++.|..++++|-|.+-.
T Consensus 8 mI~eAI-~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 8 MILEAI-KALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHH-HHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHH-HHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 455554 6778888888888888777643211222 2467999999999999888754
No 107
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=39.13 E-value=54 Score=23.75 Aligned_cols=46 Identities=9% Similarity=0.156 Sum_probs=38.5
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
..|.+.++.++.++-.+|... |.++...+++-+..|-+.|.+.|-.
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~--------l~vS~~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 8 QILLELLAQLGFVTVEKVIER--------LGISPATARRDINKLDESGKLKKVR 53 (251)
T ss_pred HHHHHHHHHcCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEec
Confidence 347888888999998888755 6789999999999999999998844
No 108
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=37.29 E-value=27 Score=24.58 Aligned_cols=53 Identities=21% Similarity=0.107 Sum_probs=30.8
Q ss_pred HHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc--cCCC-cceee
Q psy4179 27 AIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT--ETHK-DMYHY 87 (89)
Q Consensus 27 aIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~--~~~~-~~y~Y 87 (89)
.|.-+.-....++-.+|.. .+..+.+.+-..|..|-++|||.|. ++|+ ..+.|
T Consensus 49 ~iL~~L~~~~~itq~eLa~--------~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~ 104 (185)
T PRK13777 49 HILWIAYHLKGASISEIAK--------FGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIE 104 (185)
T ss_pred HHHHHHHhCCCcCHHHHHH--------HHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEE
Confidence 3333444444455444443 2233455677789999999999985 4443 34444
No 109
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=37.09 E-value=8.1 Score=25.56 Aligned_cols=48 Identities=13% Similarity=0.188 Sum_probs=36.1
Q ss_pred ccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 33 KMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 33 K~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
+....+.++..+--..+.|...|.-++..|+.++..|.+-|.|+.+++
T Consensus 41 n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~ed 88 (121)
T PF09681_consen 41 NDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDED 88 (121)
T ss_pred CCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 344455555555555566666677889999999999999999999764
No 110
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=36.44 E-value=1.2e+02 Score=19.47 Aligned_cols=38 Identities=18% Similarity=0.273 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCC
Q psy4179 21 KLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPR 58 (89)
Q Consensus 21 ~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~ 58 (89)
-..+.+.|-++.-....-..++|++.|...++++|-|-
T Consensus 62 P~~l~~piL~~v~~s~~~rld~Lv~~v~~~~k~~ff~G 99 (102)
T PF10537_consen 62 PEELREPILRLVQFSTRSRLDDLVDDVYDFFKDRFFVG 99 (102)
T ss_pred CHHHHHHHHHHHHccccccHHHHHHHHHHHHHHcCcCC
Confidence 34677788888886666669999999999999999774
No 111
>PF09170 STN1_2: CST, Suppressor of cdc thirteen homolog, complex subunit STN1; InterPro: IPR015253 STN1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites [, ]. This entry represents a C-terminal uncharacterised domain ; PDB: 1WJ5_A.
Probab=36.30 E-value=34 Score=24.23 Aligned_cols=30 Identities=23% Similarity=0.397 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHhhhhhcccCCCcceeec
Q psy4179 59 VHVIKKCIDILIEKEYLERTETHKDMYHYL 88 (89)
Q Consensus 59 ~~~iK~~IE~LIekeYl~R~~~~~~~y~Yi 88 (89)
-..||.+|..|-++|++-+-.++.+.+-|+
T Consensus 104 ~~~FkeAiq~Lqe~G~Vfqk~~~~d~lY~V 133 (174)
T PF09170_consen 104 RSIFKEAIQLLQEKGIVFQKDKSQDELYYV 133 (174)
T ss_dssp HHHHHHHHHHHHHHTSEE-SS-SSS--BEE
T ss_pred HHHHHHHHHHHHHCCEEEeecCCCCceEEE
Confidence 357889999999999887765555445443
No 112
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=36.02 E-value=21 Score=23.10 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=16.9
Q ss_pred CCHHHHHHHHHHHHHhhhhhccc
Q psy4179 57 PRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 57 p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
|... +++....||++||+++..
T Consensus 38 pNL~-vika~qsl~S~GYvkt~~ 59 (105)
T COG5045 38 PNLH-VIKAMQSLISYGYVKTIH 59 (105)
T ss_pred CchH-HHHHHHHHhhcceeEEEe
Confidence 4444 566789999999999864
No 113
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=35.10 E-value=87 Score=19.97 Aligned_cols=62 Identities=23% Similarity=0.216 Sum_probs=38.7
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceee
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHY 87 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Y 87 (89)
..++.|.+-- ...-..-..++.+|+..+. ..++...+--+|..||+.|.|+=..+-.++..|
T Consensus 48 ~yD~~Il~~~-~~~~~~~arvIg~vl~~~~--~~i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQA-PDEFQKAARVIGEVLGHSD--QGIGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhcC-CccccHHHHHHHHHHHhcC--cCCChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 4566666611 1111233457777777763 337788999999999999998765443344333
No 114
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=34.90 E-value=35 Score=21.70 Aligned_cols=32 Identities=16% Similarity=0.111 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhcccCCCcce
Q psy4179 54 RFKPRVHVIKKCIDILIEKEYLERTETHKDMY 85 (89)
Q Consensus 54 ~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y 85 (89)
.+..+...+.+.+..|...|||.+..+....|
T Consensus 34 ~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy 65 (132)
T TIGR00738 34 RQGISRSYLEKILRTLRRAGLVESVRGPGGGY 65 (132)
T ss_pred HHCcCHHHHHHHHHHHHHCCcEEeccCCCCCc
Confidence 34567888999999999999998754333334
No 115
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=34.50 E-value=27 Score=25.65 Aligned_cols=34 Identities=21% Similarity=0.237 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHHHHHhhhhhcccCCCcceeecC
Q psy4179 55 FKPRVHVIKKCIDILIEKEYLERTETHKDMYHYLA 89 (89)
Q Consensus 55 F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yia 89 (89)
..|-+. +=..++.|..|||++..++.|..|..++
T Consensus 41 gvP~~k-vY~vl~sLe~kG~v~~~~g~P~~y~av~ 74 (247)
T COG1378 41 GVPRPK-VYDVLRSLEKKGLVEVIEGRPKKYRAVP 74 (247)
T ss_pred CCCchh-HHHHHHHHHHCCCEEeeCCCCceEEeCC
Confidence 344444 5668999999999999999999998763
No 116
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=33.98 E-value=1.4e+02 Score=19.86 Aligned_cols=39 Identities=26% Similarity=0.382 Sum_probs=25.7
Q ss_pred HHHHHHHHhhccc-cccCcHHHHHHHHHHhcCCCCCCHHHHHHHH
Q psy4179 23 LIQAAIVRIMKMR-KTLQHQQLVAEVLNQISLRFKPRVHVIKKCI 66 (89)
Q Consensus 23 ~i~AaIVRiMK~~-k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~I 66 (89)
.|+.| --||+.+ +.|+|.+|+.+|...+. .+...+...|
T Consensus 5 ~idvA-y~iL~~~~~~m~f~dL~~ev~~~~~----~s~e~~~~~i 44 (129)
T PRK02363 5 LIEVA-YEILKEKKEPMSFYDLVNEIQKYLG----KSDEEIRERI 44 (129)
T ss_pred HHHHH-HHHHHHcCCcccHHHHHHHHHHHhC----CCHHHHHHHH
Confidence 34445 4456554 78999999999998875 2444444444
No 117
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=33.74 E-value=80 Score=22.45 Aligned_cols=34 Identities=15% Similarity=0.292 Sum_probs=23.2
Q ss_pred HHhhccccc-cCcHHHHHHHHHHhcCCCCCCHHHHHHHH
Q psy4179 29 VRIMKMRKT-LQHQQLVAEVLNQISLRFKPRVHVIKKCI 66 (89)
Q Consensus 29 VRiMK~~k~-l~~~~L~~ev~~~l~~~F~p~~~~iK~~I 66 (89)
--||..++. ++|.+|++++...+. .+...|..+|
T Consensus 21 ~~ile~~~~~~~F~dii~EI~~~~~----~s~~ei~~~i 55 (175)
T COG3343 21 HAILEEKKKPFNFSDIINEIQKLLG----VSKEEIRSRI 55 (175)
T ss_pred HHHHHHcCCCccHHHHHHHHHHHhC----cCHHHHHHHH
Confidence 345555555 999999999988775 4455554444
No 118
>PRK12423 LexA repressor; Provisional
Probab=33.63 E-value=44 Score=23.36 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=22.7
Q ss_pred CCC-CCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 54 RFK-PRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 54 ~F~-p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
.|- .+...+.+.++.|-++|||++.++.
T Consensus 34 ~~g~~s~~~v~~~l~~L~~~G~l~~~~~~ 62 (202)
T PRK12423 34 AFGFASRSVARKHVQALAEAGLIEVVPNQ 62 (202)
T ss_pred HhCCCChHHHHHHHHHHHHCCCEEecCCC
Confidence 344 4677788999999999999998763
No 119
>PF12358 DUF3644: Protein of unknown function (DUF3644) ; InterPro: IPR022104 This domain family is found in bacteria, and is typically between 65 and 80 amino acids in length.
Probab=33.46 E-value=51 Score=19.64 Aligned_cols=18 Identities=28% Similarity=0.492 Sum_probs=16.1
Q ss_pred CCCCCHHHHHHHHHHHHH
Q psy4179 54 RFKPRVHVIKKCIDILIE 71 (89)
Q Consensus 54 ~F~p~~~~iK~~IE~LIe 71 (89)
.|.+....++.+|+.||+
T Consensus 54 ~~~~~~~~vr~NL~~Lie 71 (77)
T PF12358_consen 54 YFTNENDPVRKNLEFLIE 71 (77)
T ss_pred hccCCChHHHHHHHHHHH
Confidence 688888889999999996
No 120
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=33.34 E-value=1e+02 Score=18.75 Aligned_cols=56 Identities=16% Similarity=0.132 Sum_probs=37.9
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.|-.||. -|+.++-.+.+.+...+...-...-.--...++..|..++++|-|.+-.
T Consensus 10 MI~eAI~-~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~k 65 (88)
T cd00073 10 MVTEAIK-ALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVK 65 (88)
T ss_pred HHHHHHH-HcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeec
Confidence 4555644 6788888888888777665532110112567889999999999988754
No 121
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=33.23 E-value=18 Score=24.02 Aligned_cols=49 Identities=12% Similarity=0.148 Sum_probs=39.4
Q ss_pred hccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 32 MKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 32 MK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.+....+.+++.+--..+.|...|.-++..|+.++..|..-|-|+..++
T Consensus 38 ~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~d~ 86 (119)
T TIGR01714 38 LNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESLGLIEKKNN 86 (119)
T ss_pred hcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5666677777666666667766788889999999999999999999853
No 122
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=33.15 E-value=81 Score=16.67 Aligned_cols=42 Identities=17% Similarity=0.246 Sum_probs=29.3
Q ss_pred HHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhh
Q psy4179 26 AAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLE 76 (89)
Q Consensus 26 AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~ 76 (89)
.-|+..+.. +.++..+|... +..+.+.+..-+..|.+.|+++
T Consensus 5 ~~Il~~L~~-~~~~~~el~~~--------l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 5 LRILKLLSE-GPLTVSELAEE--------LGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHTT-SSEEHHHHHHH--------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHh-CCCchhhHHHh--------ccccchHHHHHHHHHHHCcCee
Confidence 445555555 66776666544 4467888999999999999874
No 123
>PF08343 RNR_N: Ribonucleotide reductase N-terminal; InterPro: IPR013554 This domain is found at the N terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyse the formation of deoxyribonucleotides []. It occurs together with the RNR all-alpha domain (IPR013509 from INTERPRO) and the RNR barrel domain (IPR000788 from INTERPRO). ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0006260 DNA replication, 0055114 oxidation-reduction process, 0005971 ribonucleoside-diphosphate reductase complex; PDB: 1PEM_A 2BQ1_E 1PEU_A 1PEQ_A 1PEO_A.
Probab=33.02 E-value=31 Score=21.35 Aligned_cols=20 Identities=30% Similarity=0.718 Sum_probs=14.7
Q ss_pred CHHHHHHHHHHHHHhhhhhc
Q psy4179 58 RVHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 58 ~~~~iK~~IE~LIekeYl~R 77 (89)
.-..++.+|++||+.+|...
T Consensus 40 ~F~S~~Erl~yLv~~~YYe~ 59 (82)
T PF08343_consen 40 KFNSLKERLDYLVENDYYEK 59 (82)
T ss_dssp --SSHHHHHHHHHHTTSB-H
T ss_pred ecCCHHHHHHHHHHcCcHHH
Confidence 34567899999999999764
No 124
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=32.64 E-value=34 Score=19.22 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=17.8
Q ss_pred CCCCCC-HHHHHHHHHHHHHhhhhhccc
Q psy4179 53 LRFKPR-VHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 53 ~~F~p~-~~~iK~~IE~LIekeYl~R~~ 79 (89)
.+|..+ ...+...++.|++.|++..+.
T Consensus 28 ~~~g~~~~~~~~~~l~~l~~~Gll~~~~ 55 (66)
T PF06969_consen 28 QRFGIDFAEEFQKELEELQEDGLLEIDG 55 (66)
T ss_dssp HHTT--THHH-HHHHHHHHHTTSEEE-S
T ss_pred HHHCcCHHHHHHHHHHHHHHCCCEEEeC
Confidence 345544 344588899999999998865
No 125
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=32.47 E-value=29 Score=24.10 Aligned_cols=31 Identities=16% Similarity=0.311 Sum_probs=26.4
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 50 QISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 50 ~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.|...|.++...+.+++..|.+.|+|.|..+
T Consensus 30 eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g 60 (231)
T TIGR03337 30 DLGERFNTTRVTIREALQQLEAEGLIYREDR 60 (231)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC
Confidence 4455688889999999999999999999764
No 126
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=32.19 E-value=1.2e+02 Score=18.22 Aligned_cols=48 Identities=8% Similarity=0.196 Sum_probs=27.1
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhh
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYL 75 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl 75 (89)
=+.|.+.+..++ +-.+|+..+.+.-.. -.+-..++..-++.|.++++|
T Consensus 33 g~~Iw~lldg~~--tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli 80 (81)
T TIGR03859 33 AGEILELCDGKR--SLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWL 80 (81)
T ss_pred HHHHHHHccCCC--cHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCc
Confidence 355666666544 555666555544433 223345666667777777766
No 127
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=32.11 E-value=60 Score=19.20 Aligned_cols=22 Identities=23% Similarity=0.317 Sum_probs=18.0
Q ss_pred CCCHHHHHHHHHHHHHhhhhhc
Q psy4179 56 KPRVHVIKKCIDILIEKEYLER 77 (89)
Q Consensus 56 ~p~~~~iK~~IE~LIekeYl~R 77 (89)
..+...+.+-++.|.++|+|+.
T Consensus 30 ~L~~~~~~~yL~~L~~~gLI~~ 51 (77)
T PF14947_consen 30 NLNYSTLKKYLKELEEKGLIKK 51 (77)
T ss_dssp T--HHHHHHHHHHHHHTTSEEE
T ss_pred CcCHHHHHHHHHHHHHCcCeeC
Confidence 4678889999999999999965
No 128
>COG3177 Fic family protein [Function unknown]
Probab=31.54 E-value=46 Score=25.40 Aligned_cols=35 Identities=14% Similarity=0.077 Sum_probs=29.7
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeec
Q psy4179 54 RFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYL 88 (89)
Q Consensus 54 ~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yi 88 (89)
.+..+.+.+.+.|..|.+.||+++.++.+..|.|-
T Consensus 313 ~~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~~~ 347 (348)
T COG3177 313 ILGVSKATATRDLKELLELGILEEVKGRGRSKLYS 347 (348)
T ss_pred HhCccHHHHHHHHHHHHhCCCeeecCCCCCceecc
Confidence 45678888999999999999999998877777764
No 129
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=31.51 E-value=1.2e+02 Score=18.10 Aligned_cols=60 Identities=13% Similarity=0.154 Sum_probs=38.2
Q ss_pred HHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcceeec
Q psy4179 22 LLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYHYL 88 (89)
Q Consensus 22 ~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yi 88 (89)
..-+++|-.+.+.+.--+..+|+...... -|.+|-+.|-+-|..| -+-+.++....|.|.
T Consensus 4 ~~R~~~I~~li~~~~i~sQ~eL~~~L~~~---Gi~vTQaTiSRDLkeL----~~vKv~~~~g~~~Y~ 63 (70)
T PF01316_consen 4 SKRQELIKELISEHEISSQEELVELLEEE---GIEVTQATISRDLKEL----GAVKVPDGNGKYRYV 63 (70)
T ss_dssp HHHHHHHHHHHHHS---SHHHHHHHHHHT---T-T--HHHHHHHHHHH----T-EEEECTTSSEEEE
T ss_pred HHHHHHHHHHHHHCCcCCHHHHHHHHHHc---CCCcchhHHHHHHHHc----CcEEeeCCCCCEEEE
Confidence 34578899999999999999999887654 5889998887777655 234444445667774
No 130
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=31.01 E-value=40 Score=19.45 Aligned_cols=26 Identities=23% Similarity=0.231 Sum_probs=21.0
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHH
Q psy4179 44 VAEVLNQISLRFKPRVHVIKKCIDIL 69 (89)
Q Consensus 44 ~~ev~~~l~~~F~p~~~~iK~~IE~L 69 (89)
..-+..+|..||-+-++.+...|+.|
T Consensus 9 ~~lllRlL~rrFG~lp~~~~~~I~~l 34 (59)
T PF14261_consen 9 ARLLLRLLTRRFGELPPEIQERIQQL 34 (59)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHcC
Confidence 44567788889999888888888887
No 131
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=30.54 E-value=44 Score=22.90 Aligned_cols=19 Identities=26% Similarity=0.218 Sum_probs=17.0
Q ss_pred CHHHHHHHHHHHHHhhhhh
Q psy4179 58 RVHVIKKCIDILIEKEYLE 76 (89)
Q Consensus 58 ~~~~iK~~IE~LIekeYl~ 76 (89)
|...|.+.|+++|.+|+.-
T Consensus 15 TdeqI~kQI~Y~i~~GW~p 33 (138)
T CHL00130 15 TDQQIEKQIQYAISKGWAL 33 (138)
T ss_pred CHHHHHHHHHHHHhcCCeE
Confidence 7889999999999999753
No 132
>PF13835 DUF4194: Domain of unknown function (DUF4194)
Probab=30.15 E-value=1.3e+02 Score=20.18 Aligned_cols=48 Identities=15% Similarity=0.230 Sum_probs=35.8
Q ss_pred cCcHHHHHHHHHHhc--CCCCCCHHHHHHHHHHHHHhhhhhcccCCCcce
Q psy4179 38 LQHQQLVAEVLNQIS--LRFKPRVHVIKKCIDILIEKEYLERTETHKDMY 85 (89)
Q Consensus 38 l~~~~L~~ev~~~l~--~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y 85 (89)
++..+|......... ..=.|+...++..|..|-..++|++.++|.+.|
T Consensus 101 v~~~ei~e~~~~~~~~~~d~~~~~~~~~~~l~~l~~~~ll~~~~~de~r~ 150 (166)
T PF13835_consen 101 VTREEIVEKLESFLPESRDEAPFKKRLDAALRRLKRYGLLRRLDGDEDRY 150 (166)
T ss_pred EeHHHHHHHHHHHccccccccchHHHHHHHHHHHHHCCCeeccCCCCCEE
Confidence 566777777776554 334578889999999999999999987643444
No 133
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=29.99 E-value=44 Score=23.74 Aligned_cols=19 Identities=16% Similarity=0.347 Sum_probs=16.7
Q ss_pred CHHHHHHHHHHHHHhhhhh
Q psy4179 58 RVHVIKKCIDILIEKEYLE 76 (89)
Q Consensus 58 ~~~~iK~~IE~LIekeYl~ 76 (89)
+...|.+.||+||.+|++=
T Consensus 77 tdeqI~kQVeYli~~GW~p 95 (176)
T PLN02289 77 TDEELAKEVDYLLRNKWVP 95 (176)
T ss_pred CHHHHHHHHHHHHhCCCee
Confidence 7899999999999999653
No 134
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=29.90 E-value=56 Score=20.91 Aligned_cols=19 Identities=16% Similarity=0.244 Sum_probs=15.3
Q ss_pred CHHHHHHHHHHHHHhhhhh
Q psy4179 58 RVHVIKKCIDILIEKEYLE 76 (89)
Q Consensus 58 ~~~~iK~~IE~LIekeYl~ 76 (89)
+...|.+.|+.|+.+||.=
T Consensus 12 ~~~~i~~Qv~~ll~qG~~i 30 (99)
T PF00101_consen 12 TDEEIAKQVRYLLSQGWII 30 (99)
T ss_dssp -HHHHHHHHHHHHHTT-EE
T ss_pred CHHHHHHHHHhhhhcCcee
Confidence 4788999999999999863
No 135
>KOG2266|consensus
Probab=29.75 E-value=1.4e+02 Score=24.74 Aligned_cols=51 Identities=20% Similarity=0.326 Sum_probs=34.5
Q ss_pred HHHHHHHHHhhcccc--ccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHh
Q psy4179 22 LLIQAAIVRIMKMRK--TLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEK 72 (89)
Q Consensus 22 ~~i~AaIVRiMK~~k--~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIek 72 (89)
-.|.-+|+.|+|... +.++.+++..|....---..+.-..||..|..||.+
T Consensus 523 eelk~~V~kILk~vdfntaTm~dIlKkl~~~f~~dLt~rK~~IK~~Ike~I~~ 575 (594)
T KOG2266|consen 523 EELKEVVKKILKEVDFNTATMKDILKKLYAKFPIDLTHRKDFIKDTIKELINK 575 (594)
T ss_pred HHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCcccccchHHHHHHHHHHHHH
Confidence 467788999999754 466667776665554312224467889889888864
No 136
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=29.65 E-value=96 Score=16.44 Aligned_cols=39 Identities=15% Similarity=0.229 Sum_probs=27.1
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDIL 69 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~L 69 (89)
.++-.|++.+...-..+|.+|-..+ -.+.+.+..+|..|
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l--------glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL--------GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH--------TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH--------CcCHHHHHHHHHHh
Confidence 4677899999999999998887654 25677777777665
No 137
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=29.52 E-value=71 Score=20.83 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=31.3
Q ss_pred HHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 28 IVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 28 IVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
|++-+-. ....|++|...+- ..+..++-+++..|-+.|.+.|..
T Consensus 28 Il~~L~~-g~~RF~eL~r~i~-------~Is~k~Ls~~Lk~Le~~Glv~R~~ 71 (120)
T COG1733 28 ILRDLFD-GPKRFNELRRSIG-------GISPKMLSRRLKELEEDGLVERVV 71 (120)
T ss_pred HHHHHhc-CCCcHHHHHHHcc-------ccCHHHHHHHHHHHHHCCCEEeee
Confidence 3444444 6666666654331 168899999999999999999964
No 138
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=29.12 E-value=48 Score=24.76 Aligned_cols=24 Identities=17% Similarity=0.331 Sum_probs=21.6
Q ss_pred CCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 57 PRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 57 p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.+...++.+|+.|..-|+|+++++
T Consensus 151 is~~ev~~sL~~L~~~glikk~~~ 174 (271)
T TIGR02147 151 ISAEQVKESLDLLERLGLIKKNED 174 (271)
T ss_pred CCHHHHHHHHHHHHHCCCeeECCC
Confidence 478899999999999999999864
No 139
>KOG4718|consensus
Probab=28.96 E-value=1.3e+02 Score=22.22 Aligned_cols=54 Identities=17% Similarity=0.268 Sum_probs=37.9
Q ss_pred HHHHHHhhcc-ccccCcHHHHHHHHHHhcCCCCC-CHHHHHHHHHHHHHhhhhhcccC
Q psy4179 25 QAAIVRIMKM-RKTLQHQQLVAEVLNQISLRFKP-RVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 25 ~AaIVRiMK~-~k~l~~~~L~~ev~~~l~~~F~p-~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.=||-.||++ ..-...+.-......+.+ |+| ..+.|-.-+..+++-+|+.+.++
T Consensus 102 rkalE~im~sed~~~asst~~~~~vlq~k--~k~L~ks~iE~lLqkf~q~gwf~e~eg 157 (235)
T KOG4718|consen 102 RKALEKIMSSEDCHIASSTAYNDIVLQAK--SKPLKKSRIEELLQKFIQMGWFMEVEG 157 (235)
T ss_pred HHHHHHHHhhhHhhhHHHHHHHHHHHHHh--cCCCCHHHHHHHHHHHHHhchhheecc
Confidence 3477889999 555555555555555654 443 77778888888889998888653
No 140
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=28.76 E-value=56 Score=23.61 Aligned_cols=25 Identities=16% Similarity=0.337 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 57 PRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 57 p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
.+.+.+-.-+..|.+.||+++|+++
T Consensus 31 lpksT~~RlL~tL~~~G~v~~d~~~ 55 (246)
T COG1414 31 LPKSTVHRLLQTLVELGYVEQDPED 55 (246)
T ss_pred cCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 4566678899999999999999864
No 141
>PF10288 DUF2392: Protein of unknown function (DUF2392); InterPro: IPR019407 Cytoplasmic thiouridylase is a highly conserved complex responsible for the 2-thiolation of cytosolic tRNAs []. Inactivation of this complex leads to a loss of thiolation on tRNAs, decreased viability and aberrant cell development. This entry represents the second subunit of this complex.
Probab=28.70 E-value=89 Score=19.67 Aligned_cols=38 Identities=13% Similarity=0.278 Sum_probs=31.0
Q ss_pred hhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Q psy4179 31 IMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDI 68 (89)
Q Consensus 31 iMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~ 68 (89)
..+..+.++.++|+..-+..|+.-|+-+++.|=+..+.
T Consensus 69 ~~~~~~~~SI~~L~~~fi~~Le~~ypstvsTV~RT~~K 106 (107)
T PF10288_consen 69 QSKSSKNMSINELTEDFIDNLEENYPSTVSTVVRTADK 106 (107)
T ss_pred ccccCcCCCHHHHHHHHHHHHhCcCcchHhHHHHHhhc
Confidence 45778999999999999999998898888877655443
No 142
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=28.54 E-value=26 Score=19.75 Aligned_cols=23 Identities=9% Similarity=0.147 Sum_probs=18.9
Q ss_pred CCHHHHHHHHHHHHHhhhhhccc
Q psy4179 57 PRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 57 p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
.....+...++.|+++|-|..+.
T Consensus 32 l~~k~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 32 LPPKLFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp S-HCCHHHHHHHHHHTTSEEEES
T ss_pred CCHHHHHHHHHHHHHCCCeeeEC
Confidence 36778899999999999998764
No 143
>PRK11050 manganese transport regulator MntR; Provisional
Probab=28.46 E-value=41 Score=22.51 Aligned_cols=29 Identities=14% Similarity=0.131 Sum_probs=24.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 52 SLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 52 ~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
...|..+.+.+.+.+..|.+.|||.|..+
T Consensus 58 A~~l~is~stVsr~l~~Le~~GlI~r~~~ 86 (152)
T PRK11050 58 AARLGVSQPTVAKMLKRLARDGLVEMRPY 86 (152)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 33466889999999999999999998653
No 144
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=28.31 E-value=2e+02 Score=19.61 Aligned_cols=53 Identities=13% Similarity=0.335 Sum_probs=39.9
Q ss_pred HHHHHHhhc-cccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 25 QAAIVRIMK-MRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 25 ~AaIVRiMK-~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
.-+|..+|- ....++..+|+..+.+.- ..++.+.|=..++.|.+.|.|.+-+.
T Consensus 28 R~~IL~~l~~~~~hlSa~eI~~~L~~~~---~~is~aTVYRtL~~L~e~Glv~~~~~ 81 (169)
T PRK11639 28 RLEVLRLMSLQPGAISAYDLLDLLREAE---PQAKPPTVYRALDFLLEQGFVHKVES 81 (169)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHhhC---CCCCcchHHHHHHHHHHCCCEEEEec
Confidence 345555554 456789999988876554 34678889999999999999998653
No 145
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=27.90 E-value=50 Score=23.82 Aligned_cols=41 Identities=15% Similarity=0.281 Sum_probs=29.0
Q ss_pred ccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCccee
Q psy4179 37 TLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMYH 86 (89)
Q Consensus 37 ~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y~ 86 (89)
.++..||...+ -.+.+.+-+-+..|.+.||+.|++++ ..|.
T Consensus 26 ~ls~~eia~~l--------gl~kstv~RlL~tL~~~g~v~~~~~~-~~Y~ 66 (263)
T PRK09834 26 GATVGLLAELT--------GLHRTTVRRLLETLQEEGYVRRSASD-DSFR 66 (263)
T ss_pred CCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEecCC-CcEE
Confidence 37766665543 35566678899999999999998754 3443
No 146
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=27.82 E-value=1.3e+02 Score=19.27 Aligned_cols=56 Identities=11% Similarity=0.141 Sum_probs=46.2
Q ss_pred HHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 22 LLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 22 ~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
..++.+|--++-.. .++=-+|...+-.....-|.|++..|=..+..|-+.||+.-.
T Consensus 8 g~l~~~iL~~L~~~-~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~ 63 (138)
T COG1695 8 GSLELLILSLLSEK-PSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESR 63 (138)
T ss_pred chHHHHHHHHHhcC-CchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEE
Confidence 36777888888777 666678888887777667889999999999999999999853
No 147
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=27.54 E-value=65 Score=18.99 Aligned_cols=30 Identities=17% Similarity=0.196 Sum_probs=24.4
Q ss_pred HHHHHHHHhhccccccCcHHHHHHHHHHhc
Q psy4179 23 LIQAAIVRIMKMRKTLQHQQLVAEVLNQIS 52 (89)
Q Consensus 23 ~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~ 52 (89)
.=.|+|+|.-|.-.--+|.||-..+...++
T Consensus 46 vS~sti~Rf~kkLG~~gf~efk~~l~~~~~ 75 (77)
T PF01418_consen 46 VSPSTIVRFCKKLGFSGFKEFKIALAQELS 75 (77)
T ss_dssp S-HHHHHHHHHHCTTTCHHHHHHHHHCHHH
T ss_pred CCHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Confidence 338999999999999999999888776664
No 148
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=27.44 E-value=1.5e+02 Score=19.77 Aligned_cols=34 Identities=15% Similarity=0.116 Sum_probs=26.9
Q ss_pred cccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q psy4179 34 MRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIE 71 (89)
Q Consensus 34 ~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIe 71 (89)
...+|+..+|+..+.+... .+..+++..|+.|++
T Consensus 27 ~~~~mt~~el~~~Ia~~s~----~s~~dv~~vl~~l~~ 60 (145)
T TIGR01201 27 KSGVIDFEEIAELIAEESS----LSPGDVKGIIDRLAY 60 (145)
T ss_pred eCCCcCHHHHHHHHHHHhC----CCHHHHHHHHHHHHH
Confidence 3457899999998877753 578889999988875
No 149
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=27.26 E-value=63 Score=18.45 Aligned_cols=37 Identities=14% Similarity=0.328 Sum_probs=13.3
Q ss_pred HHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHH
Q psy4179 27 AIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCI 66 (89)
Q Consensus 27 aIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~I 66 (89)
.|++..+.....+..+|..++.+. . ..++...|...+
T Consensus 3 ~I~~~v~~~p~~s~~~i~~~l~~~-~--~~vS~~TI~r~L 39 (72)
T PF01498_consen 3 RIVRMVRRNPRISAREIAQELQEA-G--ISVSKSTIRRRL 39 (72)
T ss_dssp -------------HHHHHHHT----T----S-HHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHc-c--CCcCHHHHHHHH
Confidence 478889999999999999887655 2 457777776554
No 150
>PF05569 Peptidase_M56: BlaR1 peptidase M56; InterPro: IPR008756 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M56 (clan M-). The predicted active site residues for members of this family occur in the motif HEXXH. The type example is BlaR1 peptidase from Bacillus licheniformis. Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription.
Probab=27.25 E-value=2e+02 Score=20.98 Aligned_cols=55 Identities=18% Similarity=0.236 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCC--------CCCCHHHHHHHHH
Q psy4179 13 HKHIEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLR--------FKPRVHVIKKCID 67 (89)
Q Consensus 13 ~~~v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~--------F~p~~~~iK~~IE 67 (89)
...+..+|....|++.++.|.......|.+.+-.+....... |.-+...+|++|.
T Consensus 235 ~~~~~~~~E~~cD~~vl~~l~~~~~~~Y~~~Ll~~~~~~~~~~~~~~~~~~~~~~~~lk~RI~ 297 (299)
T PF05569_consen 235 RRRIRRDRELACDEAVLRNLGKEERKAYAETLLKVAKRSQQFKRPPLASSFAFSKSQLKRRIK 297 (299)
T ss_pred HHHHHHHHHHhhhHHHHHhcCchhHHHHHHHHHHHHHhhcCCCcchhhhhccCChHHHHHHHH
Confidence 466788999999999999998888888998877776665541 1114555666664
No 151
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=27.05 E-value=1.7e+02 Score=18.37 Aligned_cols=44 Identities=14% Similarity=0.110 Sum_probs=32.9
Q ss_pred cCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCC
Q psy4179 38 LQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETHK 82 (89)
Q Consensus 38 l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~ 82 (89)
.+-.+|..+.+..- .-..+|...+--++=+|=+.|||.|+.++.
T Consensus 21 ~~i~~L~~e~~~~~-~~~~~TKNelL~~vYWLE~ngyI~R~~~~~ 64 (85)
T PF11313_consen 21 ATINHLTFEFIDFP-GAYDFTKNELLYTVYWLEENGYIFRDNNNN 64 (85)
T ss_pred ccHHHHHHHHHhcc-ccccccHHHHHHHHHHHhhcCeeEeecCCC
Confidence 44557777765443 345678889999999999999999986543
No 152
>PF07149 Pes-10: Pes-10; InterPro: IPR009819 This family consists of several Caenorhabditis elegans pes-10 and related proteins. Members of this family are typically around 400 residues in length. The function of this family is unknown.
Probab=26.09 E-value=74 Score=25.15 Aligned_cols=38 Identities=26% Similarity=0.628 Sum_probs=28.3
Q ss_pred HHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHH-HHHHHH
Q psy4179 29 VRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKC-IDILIE 71 (89)
Q Consensus 29 VRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~-IE~LIe 71 (89)
-|++|++ +++++..++++|. .+++++..+-+| +=.||.
T Consensus 12 AriI~tg----~d~~IT~ai~qL~-~~~~s~~ilDk~NlP~LI~ 50 (370)
T PF07149_consen 12 ARIIKTG----NDEMITKAINQLP-NHPVSVEILDKCNLPYLID 50 (370)
T ss_pred HHHHHhC----chHhHHHHHHhCC-CCCCcHHHHHHcCchHHHH
Confidence 5677775 4799999999995 568888777554 666665
No 153
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=25.90 E-value=47 Score=23.24 Aligned_cols=31 Identities=10% Similarity=0.135 Sum_probs=26.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 51 ISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 51 l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
|..+|-++-.-+++++..|...|+|.+.++.
T Consensus 37 Lae~~gVSRt~VReAL~~L~~eGlv~~~~g~ 67 (239)
T PRK04984 37 LSELIGVTRTTLREVLQRLARDGWLTIQHGK 67 (239)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 3345889999999999999999999987654
No 154
>PF13040 DUF3901: Protein of unknown function (DUF3901)
Probab=25.81 E-value=1.2e+02 Score=16.37 Aligned_cols=36 Identities=22% Similarity=0.135 Sum_probs=25.5
Q ss_pred ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhh
Q psy4179 35 RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYL 75 (89)
Q Consensus 35 ~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl 75 (89)
++..+|.+|+.+=-.+|-+ .+..=..||.-||+-|.
T Consensus 3 ~~~~sFeeLV~eNK~ell~-----d~~~me~Ieerie~k~~ 38 (40)
T PF13040_consen 3 RKKKSFEELVRENKQELLN-----DKEAMEKIEERIEEKHE 38 (40)
T ss_pred ccccCHHHHHHHHHHHHHc-----CHHHHHHHHHHHHHHHh
Confidence 5669999999998887742 33444577777777654
No 155
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=25.44 E-value=1.5e+02 Score=21.09 Aligned_cols=39 Identities=5% Similarity=0.168 Sum_probs=26.0
Q ss_pred ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 35 RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 35 ~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
.+.++..+|.. .+. .+.+.+-.-+..|.+.||+.|++++
T Consensus 26 ~~~l~l~eia~----~lg----l~kstv~Rll~tL~~~G~l~~~~~~ 64 (257)
T PRK15090 26 EREIGITELSQ----RVM----MSKSTVYRFLQTMKTLGYVAQEGES 64 (257)
T ss_pred CCCCCHHHHHH----HHC----cCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 34566555543 332 3345567788999999999998644
No 156
>PLN02839 nudix hydrolase
Probab=25.42 E-value=1e+02 Score=24.39 Aligned_cols=33 Identities=30% Similarity=0.477 Sum_probs=26.5
Q ss_pred HHHHHHHhcC--CCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 44 VAEVLNQISL--RFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 44 ~~ev~~~l~~--~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
+.+|.+.+.. .|+|+...+ .|+.||-.|||.-+
T Consensus 321 v~EV~~~l~~~~~fKpn~aLV--iiDFLiRhG~Itpe 355 (372)
T PLN02839 321 VAQVANVIRKTSFFKANCSLV--IIDFLFRHGFIRPE 355 (372)
T ss_pred HHHHHHHHHcCCCCCcccHHH--HHHHHHHcCCCCCC
Confidence 3667777753 499999987 78999999999865
No 157
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=25.01 E-value=66 Score=20.55 Aligned_cols=26 Identities=8% Similarity=-0.020 Sum_probs=21.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 53 LRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 53 ~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
.++..+.+.+.+.+..|.+.|+|...
T Consensus 33 ~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 33 EQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 34567888999999999999999764
No 158
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=24.99 E-value=99 Score=25.87 Aligned_cols=53 Identities=11% Similarity=0.186 Sum_probs=30.9
Q ss_pred HHHHHHHHhhcc-ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 23 LIQAAIVRIMKM-RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 23 ~i~AaIVRiMK~-~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
..+|.+++-|+. .+.+.-.+| .++...-..-..|+. --.-|+.|++++||.+.
T Consensus 484 yTeasLi~~Me~~~k~v~d~~l-~~~l~e~~GIGtpAT--rA~iI~~L~~R~Yv~~~ 537 (660)
T TIGR01056 484 YTEGTLLSAMTNPAAFVQDKGL-KKTLKETKGLGTEAT--RADIIENLFKRGFIQKK 537 (660)
T ss_pred cCHHHHHHHHHhhhhcccCHHH-HHHhhhccCCCCccc--HHHHHHHHHhCCCEEee
Confidence 346777777763 233443333 222222223455543 36678999999999875
No 159
>cd07064 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this fa
Probab=24.66 E-value=1.7e+02 Score=20.50 Aligned_cols=59 Identities=19% Similarity=0.291 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccC
Q psy4179 17 EEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTET 80 (89)
Q Consensus 17 ~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~ 80 (89)
..+..+.-.||||-.|+..+.... +++.+++..+.+ -+.-+|.++|-+++ ++|-+++++
T Consensus 125 ~s~~~W~rR~ai~~~l~~~~~~~~-~~l~~~~~~~~~---d~e~fI~KAiGW~L-Re~~k~d~~ 183 (208)
T cd07064 125 TDENFWLRRTAILHQLKYKEKTDT-DLLFEIILANLG---SKEFFIRKAIGWAL-REYSKTNPD 183 (208)
T ss_pred cCCcHHHHHHHHHHHHHHHHccCH-HHHHHHHHHhCC---ChHHHHHHHHHHHH-HHHhccCHH
Confidence 345556678899999997777554 555555555432 34778999999998 888888753
No 160
>PF15479 DUF4639: Domain of unknown function (DUF4639)
Probab=23.68 E-value=1.3e+02 Score=25.06 Aligned_cols=28 Identities=21% Similarity=0.260 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHHHHHHhhhhhcccCCC
Q psy4179 55 FKPRVHVIKKCIDILIEKEYLERTETHK 82 (89)
Q Consensus 55 F~p~~~~iK~~IE~LIekeYl~R~~~~~ 82 (89)
++-++..-+.++=.+||=.||.||++..
T Consensus 78 iPfTV~qArdamLqiiewrFLarD~GE~ 105 (576)
T PF15479_consen 78 IPFTVSQARDAMLQIIEWRFLARDEGES 105 (576)
T ss_pred cceeHHHHHHHHHHHhheeeeeccCCCC
Confidence 4457888899999999999999998765
No 161
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=23.65 E-value=3.4e+02 Score=20.72 Aligned_cols=56 Identities=14% Similarity=0.247 Sum_probs=41.4
Q ss_pred HHHH-HHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCC
Q psy4179 20 RKLL-IQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTETH 81 (89)
Q Consensus 20 R~~~-i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~ 81 (89)
|... +.|.|-...++.+.++-.+|... ..|.++.+.|+..+..|-+.|||.|-.+.
T Consensus 3 R~~~il~aIV~~~l~~~~pv~s~~l~~~------~~~~vS~aTiR~d~~~Le~~G~l~~~h~s 59 (337)
T TIGR00331 3 RQRKILKAIVEEYIKTGQPVGSKTLLEK------YNLGLSSATIRNDMADLEDLGFIEKPHTS 59 (337)
T ss_pred HHHHHHHHHHHHHHhcCCCcCHHHHHhh------cCCCCChHHHHHHHHHHHHCCCccCCCCC
Confidence 4444 44555556777788887776643 13788999999999999999999996543
No 162
>COG5230 Uncharacterized conserved protein [Function unknown]
Probab=23.32 E-value=55 Score=23.35 Aligned_cols=14 Identities=29% Similarity=0.598 Sum_probs=11.8
Q ss_pred HHHHHHHHHhhhhh
Q psy4179 63 KKCIDILIEKEYLE 76 (89)
Q Consensus 63 K~~IE~LIekeYl~ 76 (89)
+..+|.||+.||++
T Consensus 179 ~~dverLI~qGfl~ 192 (194)
T COG5230 179 KNDVERLIDQGFLR 192 (194)
T ss_pred HhHHHHHHHhhhhh
Confidence 45789999999986
No 163
>PRK08173 DNA topoisomerase III; Validated
Probab=23.30 E-value=1.2e+02 Score=26.30 Aligned_cols=53 Identities=17% Similarity=0.183 Sum_probs=32.8
Q ss_pred HHHHHHHHhhcc-ccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 23 LIQAAIVRIMKM-RKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 23 ~i~AaIVRiMK~-~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
..+|.++.-|+. .|.+.-.+|-. + +.....=|++.-=.-||.|++++||+|..
T Consensus 490 yTEatLl~aMe~~gk~v~D~el~~-~---~~~~GIGTpATRA~IIe~L~~r~Yi~~~~ 543 (862)
T PRK08173 490 YNEATLLSAMEGAGKLVEDDELRE-A---MAEKGLGTPATRAAIIEGLLGEKYLVREG 543 (862)
T ss_pred cCHHHHHHHHHhhhhccccHHHHh-h---hhcCCCCchhhHHHHHHHHHhCCcEEecC
Confidence 346777777874 33444444432 2 22234444555567799999999999864
No 164
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=23.14 E-value=1.7e+02 Score=17.21 Aligned_cols=30 Identities=13% Similarity=0.306 Sum_probs=20.2
Q ss_pred cCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q psy4179 38 LQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIE 71 (89)
Q Consensus 38 l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIe 71 (89)
|+-.||+.++.+... .+..+++..++.|.+
T Consensus 1 mtk~eli~~ia~~~~----~~~~~v~~vl~~l~~ 30 (90)
T smart00411 1 MTKSELIDAIAEKAG----LSKKDAKAAVDAFLE 30 (90)
T ss_pred CCHHHHHHHHHHHhC----CCHHHHHHHHHHHHH
Confidence 345677777766543 467888888887764
No 165
>PF14217 DUF4327: Domain of unknown function (DUF4327)
Probab=23.12 E-value=79 Score=19.10 Aligned_cols=22 Identities=18% Similarity=0.289 Sum_probs=17.1
Q ss_pred CHHHHHHHHHHHHHhhhhhccc
Q psy4179 58 RVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 58 ~~~~iK~~IE~LIekeYl~R~~ 79 (89)
+...|+...-.|+++|.+.|..
T Consensus 3 si~~iq~ear~LV~~g~v~r~q 24 (68)
T PF14217_consen 3 SIDKIQDEARSLVESGVVSRQQ 24 (68)
T ss_pred cHHHHHHHHHHHHHcCCCCccC
Confidence 4567888888888888888863
No 166
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=22.99 E-value=62 Score=20.15 Aligned_cols=16 Identities=13% Similarity=0.248 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHhhhh
Q psy4179 60 HVIKKCIDILIEKEYL 75 (89)
Q Consensus 60 ~~iK~~IE~LIekeYl 75 (89)
..|.+.|++||.+||.
T Consensus 2 ~~i~~QI~yll~qG~~ 17 (84)
T cd00307 2 EDVVEQVRQLLAQGYK 17 (84)
T ss_pred HHHHHHHHHHHHCCCE
Confidence 4578899999999985
No 167
>PRK00441 argR arginine repressor; Provisional
Probab=22.96 E-value=2.3e+02 Score=19.10 Aligned_cols=43 Identities=19% Similarity=0.280 Sum_probs=33.2
Q ss_pred HHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q psy4179 24 IQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDIL 69 (89)
Q Consensus 24 i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~L 69 (89)
=+..|.++.+.+...+..+|+....+. -|.+|.+.+.+-|..|
T Consensus 5 R~~~I~~ll~~~~~~~q~eL~~~L~~~---G~~vSqaTisRDl~~L 47 (149)
T PRK00441 5 RHAKILEIINSKEIETQEELAEELKKM---GFDVTQATVSRDIKEL 47 (149)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHhc---CCCcCHHHHHHHHHHc
Confidence 356788999999999999998765433 5889988888766544
No 168
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=22.92 E-value=2.3e+02 Score=26.74 Aligned_cols=57 Identities=16% Similarity=0.158 Sum_probs=43.1
Q ss_pred HHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhccc
Q psy4179 22 LLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERTE 79 (89)
Q Consensus 22 ~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~ 79 (89)
..+.-||-..--..-.+++.+|+..+...... ..++..+++..|+.||+.|.|-+-.
T Consensus 185 ~aV~~AI~HLsER~a~f~~~~Ll~~A~~~~~~-~~~~~~~v~~aId~~i~~g~Li~l~ 241 (1623)
T PRK14712 185 QAVTQAIAGLSERKVQFMYTDLLARTVGILPP-ENGVIERARAGIDEAISREQLIPLD 241 (1623)
T ss_pred HHHHHHHHHhhhhhhhCcHHHHHHHHHhhccc-ccccHHHHHHHHHHHHhCCCeeecc
Confidence 45666766666666678889998887775543 3458999999999999999985543
No 169
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=22.84 E-value=2.1e+02 Score=18.00 Aligned_cols=38 Identities=18% Similarity=0.334 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccccccCcHHHHHHHHHH
Q psy4179 11 TTHKHIEEDRKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQ 50 (89)
Q Consensus 11 ~t~~~v~~dR~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~ 50 (89)
..--.++..|...|++|+. .=|..+..+. |.+++|..+
T Consensus 19 k~F~~Le~~RE~aIeeav~-~c~~g~pFs~-d~IN~vT~~ 56 (84)
T PF10752_consen 19 KQFLQLEQQREAAIEEAVS-LCKQGEPFST-DKINEVTKE 56 (84)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHCCCCCcH-HHHHHHHHH
Confidence 3445688999999999943 3344444433 566666544
No 170
>KOG3344|consensus
Probab=22.70 E-value=77 Score=21.92 Aligned_cols=31 Identities=26% Similarity=0.609 Sum_probs=20.6
Q ss_pred CCHHHHHHHHHHHHHhhhhhcccCCCcceeec
Q psy4179 57 PRVHVIKKCIDILIEKEYLERTETHKDMYHYL 88 (89)
Q Consensus 57 p~~~~iK~~IE~LIekeYl~R~~~~~~~y~Yi 88 (89)
|+.. +.+...+|.++||+++.-.=...|-|+
T Consensus 38 pNL~-vikaMQSl~SrgYvkeqfaWrH~Yw~L 68 (150)
T KOG3344|consen 38 PNLH-VIKAMQSLKSRGYVKEQFAWRHFYWYL 68 (150)
T ss_pred ccHH-HHHHHHHHhhhhhHHhhhhhheeeeee
Confidence 3444 556889999999999864333444443
No 171
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=22.59 E-value=1.8e+02 Score=17.09 Aligned_cols=30 Identities=10% Similarity=0.330 Sum_probs=22.4
Q ss_pred cCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q psy4179 38 LQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIE 71 (89)
Q Consensus 38 l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIe 71 (89)
|+-.+|+..+..... .+..+++..++.|.+
T Consensus 1 Mtk~eli~~ia~~~~----~s~~~v~~vl~~~~~ 30 (90)
T PF00216_consen 1 MTKKELIKRIAEKTG----LSKKDVEAVLDALFD 30 (90)
T ss_dssp EBHHHHHHHHHHHHT----SSHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcC----CCHHHHHHHHHHHHH
Confidence 456788888887774 478888888887765
No 172
>PF14557 AphA_like: Putative AphA-like transcriptional regulator
Probab=22.59 E-value=1.5e+02 Score=21.13 Aligned_cols=46 Identities=17% Similarity=0.263 Sum_probs=40.2
Q ss_pred ccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 33 KMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 33 K~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
=.+..++|.+|...|.......+-|+...+=.+||.|-+.|.++=-
T Consensus 20 la~~p~~~~~va~~vrh~~sr~~gps~~Ll~~sie~Lr~eGlve~~ 65 (175)
T PF14557_consen 20 LARGPRRYEEVAGAVRHFASRIWGPSLDLLGTSIELLREEGLVEAV 65 (175)
T ss_pred HhcCCcCHHHHHHHHHHhccccccCchhhhhhHHHHHHhcCCcccc
Confidence 3566779999999999888888899999999999999999988754
No 173
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=22.50 E-value=91 Score=19.33 Aligned_cols=32 Identities=13% Similarity=0.340 Sum_probs=18.2
Q ss_pred HHHHHHhcCCC-CCC--HHHHHHHHHHHHHhhhhh
Q psy4179 45 AEVLNQISLRF-KPR--VHVIKKCIDILIEKEYLE 76 (89)
Q Consensus 45 ~ev~~~l~~~F-~p~--~~~iK~~IE~LIekeYl~ 76 (89)
.+++..|..+| .++ ..++..-++.|.++++|+
T Consensus 52 ~eIi~~L~~~y~~~~~~~~DV~~fl~~L~~~g~i~ 86 (88)
T PRK02079 52 AAIIAELQQQFPDVPGLDEDVLEFLEVARAKHWIE 86 (88)
T ss_pred HHHHHHHHHHccchhhHHHHHHHHHHHHHHCcCEE
Confidence 34445555566 321 356666667777777763
No 174
>PF13062 DUF3924: Protein of unknown function (DUF3924)
Probab=22.35 E-value=59 Score=18.89 Aligned_cols=14 Identities=29% Similarity=0.574 Sum_probs=11.3
Q ss_pred HHHHHHHhhhhhcc
Q psy4179 65 CIDILIEKEYLERT 78 (89)
Q Consensus 65 ~IE~LIekeYl~R~ 78 (89)
-+..||.+||++.-
T Consensus 36 lvq~liskefiq~i 49 (62)
T PF13062_consen 36 LVQSLISKEFIQAI 49 (62)
T ss_pred HHHHHHHHHHHHhc
Confidence 36789999999864
No 175
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=22.23 E-value=1.7e+02 Score=20.73 Aligned_cols=56 Identities=18% Similarity=0.253 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhh
Q psy4179 20 RKLLIQAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLE 76 (89)
Q Consensus 20 R~~~i~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~ 76 (89)
|+..|+--+.-.=-..+.|-+-.+++++.+..-.....+...+...++.+++ .|+.
T Consensus 73 RravL~er~~~~~~~s~~ml~GtIvHelfQ~~l~~~~~~~~~l~~~~~~~l~-~~~~ 128 (209)
T PF08696_consen 73 RRAVLQERFKGPGESSKPMLIGTIVHELFQKALRTNDFDLEFLEELADRILE-KYLE 128 (209)
T ss_pred cHHHHHHHhcCCCCCChhheeeeeHHHHHHHHHhccCcchHHHHHHHHHHHH-HHHH
Confidence 4444444431112223445556677777776654556678888888888887 5543
No 176
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=21.76 E-value=1.9e+02 Score=20.88 Aligned_cols=39 Identities=10% Similarity=0.130 Sum_probs=31.2
Q ss_pred HHHHHHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q psy4179 25 QAAIVRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIE 71 (89)
Q Consensus 25 ~AaIVRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIe 71 (89)
+..|...++.++.++-.+|... |.+|...|++-+..|=.
T Consensus 9 ~~~I~~~l~~~~~v~v~eLa~~--------~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 9 IGQLLQALKRSDKLHLKDAAAL--------LGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHcCCCcHHHHHHH--------hCCCHHHHHHHHHHhhc
Confidence 4567888999999998888753 77888989988887653
No 177
>KOG2438|consensus
Probab=21.34 E-value=4.5e+02 Score=21.64 Aligned_cols=41 Identities=20% Similarity=0.273 Sum_probs=33.0
Q ss_pred HHhhccccccCcHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q psy4179 29 VRIMKMRKTLQHQQLVAEVLNQISLRFKPRVHVIKKCIDILIE 71 (89)
Q Consensus 29 VRiMK~~k~l~~~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIe 71 (89)
|+-.|+.|+-+..-|+..|+..++++ .++.+|.+.++.+..
T Consensus 464 ve~~rsGk~k~~~~l~G~vmk~s~g~--a~p~~le~~l~~~L~ 504 (505)
T KOG2438|consen 464 VEQLRSGKTKSIKRLIGLVMKSSQGR--ANPKDLEKILEELLN 504 (505)
T ss_pred HHHHHcccHHHHHHHHHHHHHHhhcC--CCHHHHHHHHHHHhc
Confidence 66667778878888999999888655 778899999988764
No 178
>PRK04966 hypothetical protein; Provisional
Probab=21.32 E-value=94 Score=18.91 Aligned_cols=19 Identities=21% Similarity=0.380 Sum_probs=13.9
Q ss_pred HHHHHHHHhhhhhcccCCCc
Q psy4179 64 KCIDILIEKEYLERTETHKD 83 (89)
Q Consensus 64 ~~IE~LIekeYl~R~~~~~~ 83 (89)
..+++|| .+|+-|+..|..
T Consensus 11 eTL~nLI-eefv~ReGTdyG 29 (72)
T PRK04966 11 ETLENLI-ESFVLREGTDYG 29 (72)
T ss_pred HHHHHHH-HHHHhccCccCC
Confidence 4678888 689999766543
No 179
>PRK11032 hypothetical protein; Provisional
Probab=20.92 E-value=1.8e+02 Score=20.24 Aligned_cols=14 Identities=21% Similarity=0.354 Sum_probs=9.5
Q ss_pred CcHHHHHHHHHHhc
Q psy4179 39 QHQQLVAEVLNQIS 52 (89)
Q Consensus 39 ~~~~L~~ev~~~l~ 52 (89)
.|..|+..|.+.|+
T Consensus 7 ~Y~~ll~~v~~~l~ 20 (160)
T PRK11032 7 YYRELVASLTERLR 20 (160)
T ss_pred HHHHHHHHHHHHHH
Confidence 36677777777765
No 180
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=20.88 E-value=94 Score=20.29 Aligned_cols=37 Identities=11% Similarity=0.143 Sum_probs=28.4
Q ss_pred HHhcCCCCCCHHHHHHHHHHHHHhhhhhcccCCCcce
Q psy4179 49 NQISLRFKPRVHVIKKCIDILIEKEYLERTETHKDMY 85 (89)
Q Consensus 49 ~~l~~~F~p~~~~iK~~IE~LIekeYl~R~~~~~~~y 85 (89)
..+..+|..+...+.+.+..|-..|++.-..+-+..|
T Consensus 29 ~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~ 65 (141)
T PRK11014 29 SEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGI 65 (141)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCe
Confidence 3455568889999999999999999998766543333
No 181
>PRK13702 replication protein; Provisional
Probab=20.77 E-value=1.5e+02 Score=18.69 Aligned_cols=34 Identities=21% Similarity=0.254 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 41 QQLVAEVLNQISLRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 41 ~~L~~ev~~~l~~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
++|-...++.......-.. +-||.||++|.-.|+
T Consensus 50 n~lK~~L~elc~~~glTQA----e~IE~LIe~e~~~r~ 83 (85)
T PRK13702 50 NPLKDKLMELCEEEGLTQA----EMIERLIERELARRA 83 (85)
T ss_pred HHHHHHHHHHHHHcCCcHH----HHHHHHHHHHHHHhc
Confidence 3444444444433333222 358999999998875
No 182
>PRK07726 DNA topoisomerase III; Provisional
Probab=20.76 E-value=1.1e+02 Score=25.46 Aligned_cols=52 Identities=15% Similarity=0.229 Sum_probs=29.0
Q ss_pred HHHHHHHHhhccc-cccCcHHHHHHHHHHhc-CCCCCCHHHHHHHHHHHHHhhhhhcc
Q psy4179 23 LIQAAIVRIMKMR-KTLQHQQLVAEVLNQIS-LRFKPRVHVIKKCIDILIEKEYLERT 78 (89)
Q Consensus 23 ~i~AaIVRiMK~~-k~l~~~~L~~ev~~~l~-~~F~p~~~~iK~~IE~LIekeYl~R~ 78 (89)
..+|.++..|+.- |.+.-.+| .+.|. ....=|++.--.-|+.|++++||.+.
T Consensus 481 yTe~tLi~~Me~~~k~v~d~~~----~~~l~e~~GIGTpATra~iIe~L~~R~Yi~~~ 534 (658)
T PRK07726 481 FTEGTLLSAMENIARFVQDKEL----KKTLKETDGLGTEATRAGIIEKLFKRGYLEKK 534 (658)
T ss_pred cCHHHHHHHHHhhhhhccCHHH----HHhhcccCCCCccccHHHHHHHHHhCCCEEec
Confidence 3466666666543 33333333 12221 12333344446679999999999875
No 183
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=20.59 E-value=1e+02 Score=13.65 Aligned_cols=20 Identities=15% Similarity=0.197 Sum_probs=14.1
Q ss_pred CCCCHHHHHHHHHHHHHhhh
Q psy4179 55 FKPRVHVIKKCIDILIEKEY 74 (89)
Q Consensus 55 F~p~~~~iK~~IE~LIekeY 74 (89)
|..+...++..++.|.+-|+
T Consensus 11 l~~~~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 11 LGYSEKKLKPKVEFLKELGF 30 (31)
T ss_pred ccccHHHhhHHHHHHHHcCC
Confidence 44457788888888876553
No 184
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=20.32 E-value=1.4e+02 Score=15.43 Aligned_cols=22 Identities=27% Similarity=0.380 Sum_probs=13.8
Q ss_pred HHHHHhcCCCC-CCHHHHHHHHH
Q psy4179 46 EVLNQISLRFK-PRVHVIKKCID 67 (89)
Q Consensus 46 ev~~~l~~~F~-p~~~~iK~~IE 67 (89)
+.+.+|+..|| .+...|+.+++
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~ 26 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLE 26 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHH
Confidence 44566667786 46666666655
No 185
>PF12047 DNMT1-RFD: Cytosine specific DNA methyltransferase replication foci domain; InterPro: IPR022702 This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties []. A structure exists for the human cytosine specific DNA methyltransferase replication foci domain. ; PDB: 3AV6_A 3AV5_A 3AV4_A 3EPZ_B.
Probab=20.17 E-value=1.5e+02 Score=19.46 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHhhcccc---ccCcHHHHHHHHH
Q psy4179 20 RKLLIQAAIVRIMKMRK---TLQHQQLVAEVLN 49 (89)
Q Consensus 20 R~~~i~AaIVRiMK~~k---~l~~~~L~~ev~~ 49 (89)
|+..|--.+++.++... .+++.+|+..|..
T Consensus 113 ~~~~l~~~v~~~l~~~~~~~~~s~~d~l~~v~~ 145 (146)
T PF12047_consen 113 RKARLTVRVIHFLKKNPRASDLSYEDLLARVFR 145 (146)
T ss_dssp HHHHHHHHHHHHHHHHT---T--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCcccccCCHHHHHHHHhc
Confidence 45666677788888888 8888888888753
No 186
>PF03221 HTH_Tnp_Tc5: Tc5 transposase DNA-binding domain; InterPro: IPR006600 This entry represents a DNA-binding helix-turn-helix domain found in the pogo family of transposable elements, the centromere protein Cenp-B, and yeast PCD2. There is extensive sequence similarity between Cenp-B and transposase proteins encoded by the pogo superfamily of transposable elements, which includes the human Tigger and Jerky elements []. The HTH domain is composed of three alpha-helices, with the second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, as in other HTHs []. This conserved DNA-binding domain is found in the following proteins: Cenp-B (major centromere autoantigen B or centromere protein B), which appears to organise arrays of centromere satellite DNA into a higher order structure that then direct centromere formation and kinetochore assembly in mammalian chromosomes. The N terminus of Cenp-B contains two DNA-binding HTH domains, which bind to adjacent major grooves of DNA: a psq-type HTH domain followed by a CenpB-type HTH domain, which together bind specifically to the Cenp-B box, which occurs in alpha-satellite DNA in human centromeres []. Pogo family transposable elements includes both Tigger and Jerky elements []. Pogo contains two open reading frames flanked by inverted repeats. The N-terminal region of pogo transposase contains a Cenp-B-type HTH DNA-binding domain []. Mammalian jerky protein, involved in epileptic seizures in mice []. PDC2 (Pyruvate DeCarboxylase 2), which is a transcription factor required for the synthesis of the glycolytic enzyme pyruvate decarboxylase, required for high level expression of both the THI and the PDC genes. PDC2 may be important for a high basal level of PDC gene expression or play a positive role in the autoregulation control of PDC1 and PDC5 [, ]. ; PDB: 1HLV_A 1IUF_A.
Probab=20.14 E-value=1.7e+02 Score=15.92 Aligned_cols=29 Identities=14% Similarity=0.071 Sum_probs=18.8
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q psy4179 42 QLVAEVLNQISLRFKPRVHVIKKCIDILI 70 (89)
Q Consensus 42 ~L~~ev~~~l~~~F~p~~~~iK~~IE~LI 70 (89)
.|+.-|.......+++|..+|+..-..|-
T Consensus 7 ~L~~wi~~~~~~g~~vt~~~i~~~A~~i~ 35 (66)
T PF03221_consen 7 ALVEWIKRMRRKGFPVTREMIREKAKEIA 35 (66)
T ss_dssp HHHHHHHHHCGCT---SCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 46667777777788888888887776664
Done!