Query psy16237
Match_columns 133
No_of_seqs 112 out of 648
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 16:19:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16237.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16237hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2167|consensus 100.0 3.3E-33 7.1E-38 239.4 5.5 123 7-133 534-661 (661)
2 KOG2166|consensus 100.0 2.5E-31 5.5E-36 235.1 7.3 120 7-131 602-725 (725)
3 COG5647 Cullin, a subunit of E 100.0 4.7E-31 1E-35 229.9 8.4 126 7-133 644-773 (773)
4 PF10557 Cullin_Nedd8: Cullin 99.9 7.3E-27 1.6E-31 151.9 4.6 67 61-127 1-68 (68)
5 KOG2284|consensus 99.9 2.3E-25 4.9E-30 186.9 6.6 113 20-133 614-728 (728)
6 KOG2285|consensus 99.8 3.4E-19 7.3E-24 151.0 6.7 120 14-133 650-777 (777)
7 PF03965 Penicillinase_R: Peni 94.9 0.032 6.9E-07 38.9 3.3 59 70-133 5-64 (115)
8 PF09012 FeoC: FeoC like trans 94.4 0.044 9.6E-07 34.9 2.8 45 73-124 5-49 (69)
9 TIGR02698 CopY_TcrY copper tra 93.8 0.16 3.4E-06 36.5 5.0 59 70-133 6-65 (130)
10 COG3682 Predicted transcriptio 93.3 0.19 4.2E-06 36.2 4.7 62 68-133 6-67 (123)
11 PF13463 HTH_27: Winged helix 90.2 1 2.2E-05 27.7 4.9 51 70-127 5-58 (68)
12 PF08220 HTH_DeoR: DeoR-like h 89.3 0.57 1.2E-05 28.8 3.2 47 71-124 3-49 (57)
13 PF01978 TrmB: Sugar-specific 88.0 0.73 1.6E-05 28.8 3.2 52 73-131 13-64 (68)
14 cd07153 Fur_like Ferric uptake 86.6 1.8 3.9E-05 29.5 4.8 57 73-131 6-63 (116)
15 smart00418 HTH_ARSR helix_turn 86.2 1.8 3.9E-05 25.3 4.1 45 74-126 3-47 (66)
16 smart00344 HTH_ASNC helix_turn 82.4 2.3 5E-05 28.6 3.8 47 69-122 4-50 (108)
17 PF01726 LexA_DNA_bind: LexA D 82.3 2.9 6.3E-05 26.5 4.0 56 64-125 6-62 (65)
18 smart00550 Zalpha Z-DNA-bindin 82.1 4.7 0.0001 25.5 4.9 53 70-129 8-62 (68)
19 PF01047 MarR: MarR family; I 80.3 1.4 3.1E-05 26.4 1.9 45 72-123 7-51 (59)
20 PF12802 MarR_2: MarR family; 79.2 1.1 2.4E-05 27.0 1.2 26 99-124 31-56 (62)
21 PF09756 DDRGK: DDRGK domain; 77.9 2.5 5.5E-05 32.5 3.1 58 69-133 100-157 (188)
22 TIGR02404 trehalos_R_Bsub treh 76.8 1.9 4.1E-05 33.1 2.2 35 95-130 29-64 (233)
23 PF13412 HTH_24: Winged helix- 76.6 4.9 0.00011 23.2 3.5 44 70-120 5-48 (48)
24 PRK11402 DNA-binding transcrip 75.4 2.2 4.7E-05 33.0 2.1 34 96-130 39-73 (241)
25 PF02186 TFIIE_beta: TFIIE bet 75.2 4.9 0.00011 25.6 3.4 53 71-133 8-61 (65)
26 PRK10079 phosphonate metabolis 74.6 2.3 4.9E-05 32.9 2.1 35 95-130 40-75 (241)
27 smart00420 HTH_DEOR helix_turn 74.5 5.8 0.00013 22.5 3.4 45 73-124 5-49 (53)
28 TIGR02325 C_P_lyase_phnF phosp 73.7 2.5 5.5E-05 32.3 2.1 34 96-130 38-72 (238)
29 smart00347 HTH_MARR helix_turn 71.2 10 0.00022 24.3 4.3 48 70-124 12-59 (101)
30 PRK14999 histidine utilization 69.1 3.5 7.6E-05 31.9 2.0 31 99-130 46-76 (241)
31 smart00345 HTH_GNTR helix_turn 68.6 4.2 9.1E-05 23.8 1.9 26 99-124 30-55 (60)
32 PRK09334 30S ribosomal protein 68.1 4.7 0.0001 27.3 2.2 59 70-133 26-85 (86)
33 PRK10434 srlR DNA-bindng trans 67.9 6.4 0.00014 31.1 3.3 46 71-123 8-53 (256)
34 PRK09462 fur ferric uptake reg 67.5 15 0.00033 26.4 5.0 51 71-123 20-72 (148)
35 PF02334 RTP: Replication term 66.5 7.9 0.00017 27.7 3.1 52 69-121 19-72 (122)
36 PRK03573 transcriptional regul 66.3 4.9 0.00011 28.5 2.1 25 99-123 56-80 (144)
37 cd07977 TFIIE_beta_winged_heli 66.0 13 0.00028 24.3 3.9 56 69-133 10-70 (75)
38 smart00346 HTH_ICLR helix_turn 65.0 17 0.00036 23.3 4.4 44 74-124 11-55 (91)
39 TIGR01889 Staph_reg_Sar staphy 64.9 6 0.00013 27.0 2.3 33 99-131 53-88 (109)
40 TIGR02018 his_ut_repres histid 64.8 4.9 0.00011 30.8 2.0 34 96-130 31-65 (230)
41 PF08784 RPA_C: Replication pr 64.7 10 0.00022 25.5 3.4 45 68-119 47-95 (102)
42 PRK09764 DNA-binding transcrip 64.3 5.4 0.00012 30.8 2.2 31 99-130 39-69 (240)
43 PF09339 HTH_IclR: IclR helix- 64.0 14 0.0003 21.8 3.5 34 83-123 19-52 (52)
44 PF01475 FUR: Ferric uptake re 64.0 13 0.00027 25.6 3.8 58 72-131 12-70 (120)
45 PRK11512 DNA-binding transcrip 62.9 15 0.00032 26.1 4.1 25 99-123 64-88 (144)
46 COG2188 PhnF Transcriptional r 62.9 5.4 0.00012 31.0 2.0 34 96-130 37-71 (236)
47 TIGR03433 padR_acidobact trans 62.1 29 0.00063 23.3 5.3 52 69-121 5-57 (100)
48 PF13601 HTH_34: Winged helix 60.8 13 0.00029 24.2 3.3 45 71-122 3-47 (80)
49 cd00090 HTH_ARSR Arsenical Res 60.4 20 0.00043 21.2 3.9 36 83-125 21-56 (78)
50 PF00392 GntR: Bacterial regul 60.4 6 0.00013 24.3 1.5 29 96-124 30-59 (64)
51 COG1846 MarR Transcriptional r 59.4 7 0.00015 25.8 1.8 26 99-124 46-71 (126)
52 PF13730 HTH_36: Helix-turn-he 59.3 6.9 0.00015 23.1 1.6 21 99-119 35-55 (55)
53 TIGR02702 SufR_cyano iron-sulf 59.1 20 0.00042 27.2 4.4 44 72-122 5-48 (203)
54 PRK10906 DNA-binding transcrip 58.7 12 0.00027 29.5 3.3 46 71-123 8-53 (252)
55 COG3355 Predicted transcriptio 58.2 20 0.00044 25.9 4.1 33 100-132 53-89 (126)
56 COG1522 Lrp Transcriptional re 57.7 15 0.00033 25.9 3.5 49 68-123 8-56 (154)
57 TIGR01610 phage_O_Nterm phage 56.2 18 0.0004 24.2 3.4 38 79-123 44-81 (95)
58 cd07377 WHTH_GntR Winged helix 56.2 10 0.00022 22.5 2.0 29 96-124 31-60 (66)
59 PRK11179 DNA-binding transcrip 56.1 20 0.00043 25.9 3.9 48 68-122 9-56 (153)
60 COG1349 GlpR Transcriptional r 55.4 14 0.0003 29.2 3.1 45 72-123 9-53 (253)
61 PRK09802 DNA-binding transcrip 55.2 15 0.00033 29.3 3.4 47 71-124 20-66 (269)
62 PRK11169 leucine-responsive tr 52.5 25 0.00054 25.7 3.9 47 68-121 14-60 (164)
63 PF09860 DUF2087: Uncharacteri 52.2 15 0.00033 23.8 2.4 44 78-129 25-68 (71)
64 PRK10870 transcriptional repre 51.5 13 0.00028 27.7 2.3 26 99-124 81-106 (176)
65 smart00529 HTH_DTXR Helix-turn 51.3 13 0.00029 24.2 2.1 26 99-124 9-34 (96)
66 PRK02363 DNA-directed RNA poly 51.1 24 0.00053 25.5 3.6 40 69-112 6-46 (129)
67 PRK09954 putative kinase; Prov 51.0 23 0.00051 28.8 3.9 43 72-121 7-49 (362)
68 COG5045 Ribosomal protein S10E 50.9 13 0.00027 25.8 1.9 47 78-124 5-60 (105)
69 smart00419 HTH_CRP helix_turn_ 50.9 14 0.00029 20.7 1.9 25 99-123 18-42 (48)
70 PF12651 RHH_3: Ribbon-helix-h 49.9 22 0.00047 20.7 2.6 31 86-116 11-42 (44)
71 PF11372 DUF3173: Domain of un 49.6 19 0.00041 22.7 2.4 32 81-118 2-35 (59)
72 TIGR01884 cas_HTH CRISPR locus 49.6 36 0.00079 25.7 4.5 52 71-130 146-197 (203)
73 TIGR02337 HpaR homoprotocatech 49.2 34 0.00074 23.3 4.0 44 73-123 33-76 (118)
74 COG2865 Predicted transcriptio 48.8 36 0.00078 29.8 4.8 58 68-132 402-459 (467)
75 PF04738 Lant_dehyd_C: Lantibi 48.5 25 0.00054 29.8 3.8 39 83-123 1-39 (500)
76 KOG3054|consensus 47.7 31 0.00068 28.0 4.0 53 74-133 206-258 (299)
77 PF08766 DEK_C: DEK C terminal 46.9 47 0.001 19.9 3.9 46 67-116 3-51 (54)
78 PF03551 PadR: Transcriptional 46.8 27 0.00059 21.9 3.0 44 81-124 8-52 (75)
79 PF06163 DUF977: Bacterial pro 45.5 56 0.0012 23.7 4.7 52 66-124 10-61 (127)
80 PRK14165 winged helix-turn-hel 44.9 20 0.00042 28.1 2.4 34 99-132 31-64 (217)
81 PF14394 DUF4423: Domain of un 44.4 23 0.00051 26.5 2.7 25 100-124 52-76 (171)
82 TIGR01714 phage_rep_org_N phag 44.1 12 0.00026 26.8 1.0 48 77-124 38-86 (119)
83 PF10798 YmgB: Biofilm develop 43.9 27 0.00058 22.0 2.5 49 67-115 5-55 (61)
84 cd00092 HTH_CRP helix_turn_hel 43.2 20 0.00044 21.4 1.9 25 99-123 35-59 (67)
85 PF09681 Phage_rep_org_N: N-te 43.0 9.1 0.0002 27.3 0.3 48 77-124 40-88 (121)
86 COG0735 Fur Fe2+/Zn2+ uptake r 42.6 77 0.0017 22.9 5.2 59 71-131 24-83 (145)
87 PRK00215 LexA repressor; Valid 42.1 28 0.00061 26.1 2.9 41 82-129 23-64 (205)
88 COG3343 RpoE DNA-directed RNA 41.2 41 0.00089 25.7 3.6 36 75-113 22-58 (175)
89 PF00538 Linker_histone: linke 39.3 52 0.0011 21.0 3.5 55 68-123 8-65 (77)
90 TIGR02719 repress_PhaQ poly-be 38.3 1.6E+02 0.0034 21.5 6.6 63 57-122 13-76 (138)
91 PF03297 Ribosomal_S25: S25 ri 38.0 14 0.0003 25.9 0.5 34 99-132 69-102 (105)
92 PF14629 ORC4_C: Origin recogn 35.1 58 0.0013 24.4 3.6 55 67-121 105-171 (203)
93 TIGR00498 lexA SOS regulatory 35.1 49 0.0011 24.7 3.2 27 99-125 35-62 (199)
94 PRK03902 manganese transport t 35.1 60 0.0013 23.0 3.6 44 73-123 13-56 (142)
95 KOG4718|consensus 34.4 57 0.0012 25.9 3.5 53 71-124 103-157 (235)
96 PRK10411 DNA-binding transcrip 33.9 58 0.0013 25.4 3.6 44 73-123 9-52 (240)
97 PF01638 HxlR: HxlR-like helix 32.9 96 0.0021 20.2 4.1 53 72-131 9-63 (90)
98 PF12395 DUF3658: Protein of u 32.8 1E+02 0.0022 21.2 4.3 62 68-131 48-109 (111)
99 PF07149 Pes-10: Pes-10; Inte 32.7 42 0.00091 28.5 2.7 39 73-115 11-50 (370)
100 PF13040 DUF3901: Protein of u 32.4 77 0.0017 18.4 3.0 36 80-119 3-38 (40)
101 cd03527 RuBisCO_small Ribulose 32.0 42 0.00091 23.2 2.2 18 102-119 13-30 (99)
102 PF01498 HTH_Tnp_Tc3_2: Transp 31.8 40 0.00088 20.9 2.0 38 72-111 3-40 (72)
103 TIGR03882 cyclo_dehyd_2 bacter 31.1 82 0.0018 23.8 3.9 46 70-122 32-77 (193)
104 PRK04966 hypothetical protein; 31.1 36 0.00078 22.3 1.6 20 108-128 11-30 (72)
105 PF08820 DUF1803: Domain of un 31.1 29 0.00064 23.8 1.3 19 104-122 42-60 (93)
106 PF11417 Inhibitor_G39P: Loade 31.0 23 0.00051 22.9 0.7 28 81-108 41-70 (71)
107 PF09382 RQC: RQC domain; Int 30.8 48 0.001 22.0 2.3 24 101-124 54-77 (106)
108 PF09957 DUF2191: Uncharacteri 30.3 1.1E+02 0.0025 17.9 3.7 31 86-117 9-39 (47)
109 TIGR01056 topB DNA topoisomera 29.8 63 0.0014 29.3 3.5 53 68-123 484-538 (660)
110 COG1414 IclR Transcriptional r 29.7 96 0.0021 24.3 4.2 25 101-125 31-55 (246)
111 PRK04424 fatty acid biosynthes 29.6 55 0.0012 24.6 2.7 44 72-122 11-54 (185)
112 PRK13509 transcriptional repre 29.0 77 0.0017 24.9 3.5 45 73-124 10-54 (251)
113 PRK11639 zinc uptake transcrip 28.5 1.5E+02 0.0033 21.8 4.9 57 71-130 29-86 (169)
114 PF09114 MotA_activ: Transcrip 28.3 1.3E+02 0.0028 20.7 4.0 24 101-124 44-67 (96)
115 PRK14712 conjugal transfer nic 28.0 1.3E+02 0.0028 30.5 5.4 57 68-124 186-242 (1623)
116 PF10007 DUF2250: Uncharacteri 27.8 55 0.0012 22.3 2.2 26 99-124 31-56 (92)
117 PF05569 Peptidase_M56: BlaR1 27.5 1.1E+02 0.0023 24.3 4.2 55 58-112 235-298 (299)
118 PF15479 DUF4639: Domain of un 27.2 85 0.0018 28.0 3.7 28 99-126 78-105 (576)
119 TIGR03337 phnR transcriptional 27.0 49 0.0011 24.9 2.1 30 95-124 30-60 (231)
120 PRK13777 transcriptional regul 26.5 56 0.0012 24.9 2.2 53 73-132 50-105 (185)
121 PF08343 RNR_N: Ribonucleotide 26.4 49 0.0011 22.0 1.7 19 103-121 41-59 (82)
122 PRK12423 LexA repressor; Provi 26.1 2.4E+02 0.0051 21.3 5.7 27 99-125 35-62 (202)
123 PF01316 Arg_repressor: Argini 26.0 1.9E+02 0.004 18.6 4.4 59 68-132 5-63 (70)
124 PF13835 DUF4194: Domain of un 25.8 1.6E+02 0.0035 21.3 4.6 49 81-129 99-150 (166)
125 smart00437 TOP1Ac Bacterial DN 25.8 56 0.0012 26.0 2.3 39 81-123 208-247 (259)
126 PRK13709 conjugal transfer nic 25.6 1.6E+02 0.0034 30.2 5.6 57 68-124 318-374 (1747)
127 smart00526 H15 Domain in histo 25.4 1.5E+02 0.0032 18.1 3.8 52 68-121 10-63 (66)
128 PRK09834 DNA-binding transcrip 25.4 1.2E+02 0.0025 23.8 4.0 41 82-130 26-66 (263)
129 smart00411 BHL bacterial (prok 25.1 1.4E+02 0.0031 19.1 3.8 30 83-115 1-30 (90)
130 PF06794 UPF0270: Uncharacteri 25.0 38 0.00083 22.0 1.0 20 107-127 10-29 (70)
131 PRK07726 DNA topoisomerase III 24.9 77 0.0017 28.7 3.2 54 67-123 480-535 (658)
132 PRK15090 DNA-binding transcrip 24.5 1.4E+02 0.0029 23.2 4.2 42 80-129 26-67 (257)
133 PF00216 Bac_DNA_binding: Bact 24.4 1.3E+02 0.0028 19.1 3.5 30 83-115 1-30 (90)
134 PF07848 PaaX: PaaX-like prote 24.4 1.9E+02 0.0041 18.4 4.2 37 93-129 27-63 (70)
135 PRK00304 hypothetical protein; 24.3 50 0.0011 21.8 1.4 18 107-125 10-27 (75)
136 PRK15431 ferrous iron transpor 23.6 76 0.0016 21.1 2.2 29 95-123 21-50 (78)
137 PRK14724 DNA topoisomerase III 23.2 96 0.0021 29.7 3.5 53 67-123 508-562 (987)
138 PF09170 STN1_2: CST, Suppress 23.1 83 0.0018 24.0 2.6 30 103-132 104-133 (174)
139 TIGR01201 HU_rel DNA-binding p 22.6 1.6E+02 0.0034 21.3 3.9 34 79-115 27-60 (145)
140 TIGR02760 TraI_TIGR conjugativ 22.4 2E+02 0.0043 29.7 5.7 58 67-124 329-388 (1960)
141 PF13404 HTH_AsnC-type: AsnC-t 22.4 1.5E+02 0.0032 16.9 3.1 39 68-113 3-41 (42)
142 PF01022 HTH_5: Bacterial regu 22.0 1.6E+02 0.0034 16.7 3.2 40 73-120 7-46 (47)
143 COG3177 Fic family protein [Fu 21.8 91 0.002 25.8 2.8 34 99-132 314-347 (348)
144 PF14217 DUF4327: Domain of un 21.8 93 0.002 20.1 2.3 23 102-124 3-25 (68)
145 PF14947 HTH_45: Winged helix- 21.8 83 0.0018 20.1 2.1 23 99-121 29-51 (77)
146 PRK11569 transcriptional repre 21.7 1.6E+02 0.0034 23.2 4.1 43 79-129 40-82 (274)
147 PF01325 Fe_dep_repress: Iron 21.6 54 0.0012 20.2 1.1 26 99-124 32-57 (60)
148 KOG2266|consensus 21.6 1.7E+02 0.0036 26.2 4.4 50 67-116 523-575 (594)
149 PLN02289 ribulose-bisphosphate 21.5 81 0.0018 24.1 2.2 18 102-119 77-94 (176)
150 COG1378 Predicted transcriptio 21.4 83 0.0018 24.9 2.4 34 99-133 41-74 (247)
151 PF08461 HTH_12: Ribonuclease 21.3 1.8E+02 0.0039 18.1 3.6 49 73-123 3-52 (66)
152 PRK11032 hypothetical protein; 20.8 95 0.002 23.3 2.5 29 84-115 7-35 (160)
153 PF01454 MAGE: MAGE family; I 20.8 87 0.0019 23.3 2.3 43 79-121 117-164 (195)
154 PRK09416 lstR lineage-specific 20.6 2.9E+02 0.0062 20.2 4.9 54 67-122 42-96 (135)
155 CHL00130 rbcS ribulose-1,5-bis 20.6 90 0.0019 23.0 2.2 20 100-119 13-32 (138)
156 PF12358 DUF3644: Protein of u 20.3 93 0.002 19.9 2.1 17 99-115 55-71 (77)
157 PF06002 CST-I: Alpha-2,3-sial 20.2 33 0.00071 28.3 -0.1 68 3-77 7-81 (291)
No 1
>KOG2167|consensus
Probab=99.98 E-value=3.3e-33 Score=239.38 Aligned_cols=123 Identities=38% Similarity=0.529 Sum_probs=117.4
Q ss_pred CCCCCcceeecc-----ccCCCCCeEEEccCCCCCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccc
Q psy16237 7 MDGSCPGYIISV-----KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRK 81 (133)
Q Consensus 7 ~s~~~~~~~il~-----~~~~~~d~f~~N~~F~~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k 81 (133)
+||+|++.+.|. +++.+||.|.+|..|++|..||+|+++..+++.+|..++.++|-+||.++||||||||||+||
T Consensus 534 qsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk 613 (661)
T KOG2167|consen 534 QSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRK 613 (661)
T ss_pred HHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 799999999885 568899999999999999999999999889999999999999999999999999999999999
Q ss_pred cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 82 QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 82 ~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
+|+|+.|++++.+||+ ||+.+ ++|++||+||+||||+|| ++ +.|.|+|
T Consensus 614 ~l~h~~l~~el~~qlk-fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 614 TLSHNLLVTELFNQLK-FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred hhchhHHHHHHHHhcC-CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 9999999999999999 99999 999999999999999999 44 8999997
No 2
>KOG2166|consensus
Probab=99.97 E-value=2.5e-31 Score=235.06 Aligned_cols=120 Identities=41% Similarity=0.631 Sum_probs=110.4
Q ss_pred CCCCCcceeeccccC---CCCCeEEEccCCCCCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccc
Q psy16237 7 MDGSCPGYIISVKEL---TEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQI 83 (133)
Q Consensus 7 ~s~~~~~~~il~~~~---~~~d~f~~N~~F~~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l 83 (133)
+||+|.|+.++.++- .|++.|.+|.+|+++.+||+++.+..+ |.+.+++.+++||++.|+||||||||+||+|
T Consensus 602 ~Sl~~~K~~v~~~~~s~~~~~~~~~~N~~f~sk~~Rv~i~~~~~~----e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l 677 (725)
T KOG2166|consen 602 QSLSCLKYKILLKPMSRTSPNDEFAFNSKFTSKMRRVKIPLPPMD----ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVL 677 (725)
T ss_pred HHHHHHhHhhccCccccCCCCcEEEeeccccCcceeeccCCCCch----hHHHHHhhhhhHHHHHHHHHHHHHHHhhccc
Confidence 688888877775511 589999999999999999999976544 6678999999999999999999999999999
Q ss_pred cchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237 84 RHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSY 131 (133)
Q Consensus 84 ~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y 131 (133)
.|++|+.||++||++ |.|++.+||++||.|||||||+|| +|+++|.|
T Consensus 678 ~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 678 GHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred cHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 999999999999999 999999999999999999999999 88999998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=4.7e-31 Score=229.94 Aligned_cols=126 Identities=40% Similarity=0.649 Sum_probs=117.7
Q ss_pred CCCCCcceeeccc---cCCCCCeEEEccCCCCCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccc
Q psy16237 7 MDGSCPGYIISVK---ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQI 83 (133)
Q Consensus 7 ~s~~~~~~~il~~---~~~~~d~f~~N~~F~~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l 83 (133)
+|++|.++.++.+ .++|++.|.+|.+|++++.+|+++.+...+..++..++++++++||.+.+|||||||||++|+|
T Consensus 644 ~sl~~ak~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l 723 (773)
T COG5647 644 QSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKL 723 (773)
T ss_pred HHHHhhheeeeccccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 7899999887764 4789999999999999999999999877766667788899999999999999999999999999
Q ss_pred cchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 84 RHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 84 ~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
.|++|+.+|+.+.++ |.|++++||++||.|||||||+|.++| ..|+|+|
T Consensus 724 ~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 724 KHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred cHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999999999 999999999999999999999999888 7899997
No 4
>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=99.93 E-value=7.3e-27 Score=151.86 Aligned_cols=67 Identities=51% Similarity=0.819 Sum_probs=61.7
Q ss_pred HHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCC
Q psy16237 61 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTD 127 (133)
Q Consensus 61 v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~ 127 (133)
|+++|.+.|+||||||||++|+|+|++|+.+|.+++++ |+|+..+||++||.||++|||+||++|+|
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 47899999999999999999999999999999999998 99999999999999999999999999875
No 5
>KOG2284|consensus
Probab=99.92 E-value=2.3e-25 Score=186.86 Aligned_cols=113 Identities=45% Similarity=0.793 Sum_probs=105.8
Q ss_pred cCCCCCeEEEccCCCCCceeEEecCCC-cCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC
Q psy16237 20 ELTEDTEIRLNLGYNNKRTKLKISGAV-QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS 98 (133)
Q Consensus 20 ~~~~~d~f~~N~~F~~k~~kiki~~~~-~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~ 98 (133)
.+..+..|++|.+|++|+.|++|..+. ++..++|.+.+...|.+||++-++||||||||.||.+.|+-|+.||+.|.+.
T Consensus 614 ~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~ 693 (728)
T KOG2284|consen 614 NLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKG 693 (728)
T ss_pred ccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcc
Confidence 356778899999999999999999865 6888889999999999999999999999999999999999999999999999
Q ss_pred -CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 99 -FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 99 -F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
|.|++++||++||.||++.||+|.+.+ +.|.|+|
T Consensus 694 rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 694 RFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred cCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 999999999999999999999998776 8999997
No 6
>KOG2285|consensus
Probab=99.77 E-value=3.4e-19 Score=151.00 Aligned_cols=120 Identities=34% Similarity=0.508 Sum_probs=104.8
Q ss_pred eeeccccCCCCCeEEEccCCC-------CCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccch
Q psy16237 14 YIISVKELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHN 86 (133)
Q Consensus 14 ~~il~~~~~~~d~f~~N~~F~-------~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~ 86 (133)
....++++.+++.|.+|..|+ .++.|+++....+-..+...++.++.|-+-|....|-+|++|||.||+++..
T Consensus 650 ~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~~nA 729 (777)
T KOG2285|consen 650 TTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTYTNA 729 (777)
T ss_pred ccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence 344457788999999999996 3556777766555444444456678899999999999999999999999999
Q ss_pred HHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 87 ALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 87 eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
+|..|.++.|+. |.|+..+||++||+|||..|++||++|.|+|+|+|
T Consensus 730 qLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 730 QLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 999999999999 99999999999999999999999999999999997
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=94.90 E-value=0.032 Score=38.92 Aligned_cols=59 Identities=14% Similarity=0.254 Sum_probs=43.0
Q ss_pred HhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 70 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
+..|++++=....++-.|++.. +.. ..+..+.++.-+..|.+||||.|.... ..|+|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~~----l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g-r~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHEA----LPEERSWAYSTVQTLLNRLVEKGFLTREKIG-RAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHH----HCTTSS--HHHHHHHHHHHHHTTSEEEEEET-TCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHH----HHhccccchhHHHHHHHHHHhCCceeEeecC-CceEEEe
Confidence 4456666666666766666554 555 678999999999999999999998654 6788864
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=94.38 E-value=0.044 Score=34.93 Aligned_cols=45 Identities=24% Similarity=0.425 Sum_probs=35.9
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
|-.+|+.++.++..||-.+ |..++..+..-++.|+.+|||++.+.
T Consensus 5 i~~~l~~~~~~S~~eLa~~-------~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELARE-------FGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHH-------TT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 4567888999998887755 88999999999999999999999644
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=93.79 E-value=0.16 Score=36.51 Aligned_cols=59 Identities=19% Similarity=0.236 Sum_probs=43.2
Q ss_pred HhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 70 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
+..|++++-....++-.|++.. +.. +.+....+...+..|.+||||.|..+. ..|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~----l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~g-r~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRI----LAEKKDWSDSTIKTLLGRLVDKGCLTTEKEG-RKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHH----HhhccCCcHHHHHHHHHHHHHCCceeeecCC-CcEEEEe
Confidence 3456666655666766555544 444 667888999999999999999998554 5788865
No 10
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=93.29 E-value=0.19 Score=36.22 Aligned_cols=62 Identities=19% Similarity=0.295 Sum_probs=52.0
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
..++.+++||=+++..+-.|++.++... +.++.+.|+.-|..|..||+|.|.-++ ..|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~---~ews~sTV~TLl~RL~KKg~l~~~kdg-r~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD---REWSYSTVKTLLNRLVKKGLLTRKKDG-RAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc---ccccHHHHHHHHHHHHhccchhhhhcC-Ceeeeec
Confidence 4578889999999999988888776544 779999999999999999999998654 6788864
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=90.17 E-value=1 Score=27.70 Aligned_cols=51 Identities=22% Similarity=0.333 Sum_probs=32.5
Q ss_pred Hhhhhhhhc-ccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC--CCCCC
Q psy16237 70 QAAIVRIMK-SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT--ANSTD 127 (133)
Q Consensus 70 ~AaIVRIMK-~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~--~~d~~ 127 (133)
|..|.+.+. ....++-.+|... +..+.+.+-+.|..|+++|||+|. +.|..
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 345555566 5666666665543 557788888999999999999774 44444
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=89.29 E-value=0.57 Score=28.79 Aligned_cols=47 Identities=21% Similarity=0.399 Sum_probs=40.2
Q ss_pred hhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 71 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 71 AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
..|...++.+..++-.||.+. |..+...|++-+..|-+.++|.|..+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~-------~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEE-------FGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 356778888999998888755 88999999999999999999999654
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=88.05 E-value=0.73 Score=28.82 Aligned_cols=52 Identities=19% Similarity=0.234 Sum_probs=36.0
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 131 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y 131 (133)
+-..+-.+..++-.||... + ..+.+.+-..+..|.++|+++|....+..|..
T Consensus 13 vy~~Ll~~~~~t~~eIa~~----l---~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a 64 (68)
T PF01978_consen 13 VYLALLKNGPATAEEIAEE----L---GISRSTVYRALKSLEEKGLVEREEGRPKVYRA 64 (68)
T ss_dssp HHHHHHHHCHEEHHHHHHH----H---TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEE
T ss_pred HHHHHHHcCCCCHHHHHHH----H---CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEE
Confidence 3333335556666665544 3 37788899999999999999999876544444
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=86.59 E-value=1.8 Score=29.53 Aligned_cols=57 Identities=11% Similarity=0.223 Sum_probs=41.8
Q ss_pred hhhhhcc-cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237 73 IVRIMKS-RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 131 (133)
Q Consensus 73 IVRIMK~-~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y 131 (133)
|..+|.. .+.++-.||+..+.++. ..++.+.+=+.++.|.+.|+|.|-..+...+.|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~--~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG--PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC--CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4455544 56799999998886553 457889999999999999999996543233333
No 15
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=86.18 E-value=1.8 Score=25.34 Aligned_cols=45 Identities=13% Similarity=0.225 Sum_probs=31.1
Q ss_pred hhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCC
Q psy16237 74 VRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANST 126 (133)
Q Consensus 74 VRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~ 126 (133)
++.+. ...++..++... +..+.+.+.+.++.|.+++++.+..+..
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 33444 455665554433 3467788999999999999999876543
No 16
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=82.43 E-value=2.3 Score=28.62 Aligned_cols=47 Identities=13% Similarity=0.220 Sum_probs=39.0
Q ss_pred HHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237 69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~ 122 (133)
+|-.|++.+.....+++.+|-.. +-.+.+.+.+++..|.++|+|+|-
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~-------l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK-------VGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCeece
Confidence 45678888888888998887655 458889999999999999999963
No 17
>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=82.32 E-value=2.9 Score=26.53 Aligned_cols=56 Identities=14% Similarity=0.238 Sum_probs=33.4
Q ss_pred HhHHHHHhhhhhhhcccc-cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCC
Q psy16237 64 DRKLYLQAAIVRIMKSRK-QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS 125 (133)
Q Consensus 64 ~R~~~I~AaIVRIMK~~k-~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d 125 (133)
+|...|=.+|...+.... .-+..||.. .+. +. +...+...++.|.++|||+|+++-
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~----~~g-~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREIAE----ALG-LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHHHH----HHT-SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHH----HhC-CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 344444455555555443 233334332 232 22 578888999999999999998764
No 18
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=82.09 E-value=4.7 Score=25.53 Aligned_cols=53 Identities=11% Similarity=0.150 Sum_probs=38.3
Q ss_pred Hhhhhhhhccccc--ccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237 70 QAAIVRIMKSRKQ--IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY 129 (133)
Q Consensus 70 ~AaIVRIMK~~k~--l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y 129 (133)
+..|...|+.+.. ++-.||-.+ | -.+...+.+.+..|.++||+.++...+..|
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~----l---gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKN----L---GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH----H---CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 4456778888766 775555433 3 367778999999999999999987653433
No 19
>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=80.33 E-value=1.4 Score=26.40 Aligned_cols=45 Identities=27% Similarity=0.388 Sum_probs=30.8
Q ss_pred hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
.+..+.-....++..+|-.. +..+.+.+-+.+..|.++|||+|..
T Consensus 7 ~iL~~l~~~~~~~~~~la~~-------~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEK-------LGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHH-------HTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHcCCCCHHHHHHH-------HCCChhHHHHHHHHHHHCCCEEecc
Confidence 33444445555565554433 5578999999999999999999954
No 20
>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=79.23 E-value=1.1 Score=27.03 Aligned_cols=26 Identities=27% Similarity=0.374 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+..+.+.+-+.|..|.++|||+|..+
T Consensus 31 l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 31 LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 44778899999999999999999654
No 21
>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=77.91 E-value=2.5 Score=32.49 Aligned_cols=58 Identities=16% Similarity=0.287 Sum_probs=40.0
Q ss_pred HHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
+=...|...|.+|.+...||-.+ |.....++-.+|..|...|-|.---+|+..|+||.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~-------f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAE-------FGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHH-------H-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHHH-------cCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 33445788899999988777544 88999999999999999999988777888999984
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=76.84 E-value=1.9 Score=33.08 Aligned_cols=35 Identities=11% Similarity=0.333 Sum_probs=28.7
Q ss_pred hcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 95 QSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 95 ~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
+|.. |.++...++++|+.|++.|||.|..+- .+|+
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 3445 889999999999999999999997663 4554
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=76.62 E-value=4.9 Score=23.19 Aligned_cols=44 Identities=20% Similarity=0.393 Sum_probs=33.1
Q ss_pred HhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccc
Q psy16237 70 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVE 120 (133)
Q Consensus 70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~ 120 (133)
+-.|+..+.....++..||-.. +-.+.+.+.+.+..|.++|||+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~-------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEK-------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHH-------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH-------hCCCHHHHHHHHHHHHHCcCcC
Confidence 4456777777778888777655 3478899999999999999985
No 24
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=75.42 E-value=2.2 Score=32.99 Aligned_cols=34 Identities=18% Similarity=0.231 Sum_probs=27.7
Q ss_pred cCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 96 SKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 96 l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
|.. |.++...++++|+.|.+.|||.|..+- .+|+
T Consensus 39 La~~~~VSR~TvR~Al~~L~~eGli~r~~G~-GTfV 73 (241)
T PRK11402 39 LCTQYNVSRITIRKAISDLVADGVLIRWQGK-GTFV 73 (241)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEecCc-eeEE
Confidence 444 788899999999999999999998653 4554
No 25
>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=75.21 E-value=4.9 Score=25.64 Aligned_cols=53 Identities=19% Similarity=0.274 Sum_probs=30.8
Q ss_pred hhhhhhhcccc-cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 71 AAIVRIMKSRK-QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 71 AaIVRIMK~~k-~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
|.||..||.+. -++.+||++ .++ +... +..++.|-+.+=|+-+++ .++|.|.|
T Consensus 8 ~~~VeymK~r~~Plt~~eI~d----~l~-~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 8 AKAVEYMKKRDHPLTLEEILD----YLS-LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHH-S-B-HHHHHH----HHT-SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHhcCCCcCHHHHHH----HHc-CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 67899999982 355555554 455 4454 345677778888888765 37899975
No 26
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=74.56 E-value=2.3 Score=32.92 Aligned_cols=35 Identities=17% Similarity=0.395 Sum_probs=28.8
Q ss_pred hcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 95 QSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 95 ~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
+|.. |.++...++++|+.|++.|||.|..+- .+|+
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 3445 899999999999999999999997663 4554
No 27
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=74.51 E-value=5.8 Score=22.49 Aligned_cols=45 Identities=13% Similarity=0.279 Sum_probs=32.1
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
|.+.+..+..++-.+|... |..+.+.+.+.+..|.++++|.+..+
T Consensus 5 il~~l~~~~~~s~~~l~~~-------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 5 ILELLAQQGKVSVEELAEL-------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHcCCcCHHHHHHH-------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 3444444445555555443 56789999999999999999998654
No 28
>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=73.68 E-value=2.5 Score=32.27 Aligned_cols=34 Identities=9% Similarity=0.332 Sum_probs=27.6
Q ss_pred cCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 96 SKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 96 l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
|.. |.++...++++|+.|.+.|||.|..+- .+|+
T Consensus 38 La~~~~VSR~TvR~Al~~L~~eGli~r~~G~-GtfV 72 (238)
T TIGR02325 38 LAERFGVNRHTVRRAIAALVERGLLRAEQGR-GTFV 72 (238)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEecCC-EEEE
Confidence 444 788899999999999999999997653 4554
No 29
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=71.18 E-value=10 Score=24.30 Aligned_cols=48 Identities=19% Similarity=0.321 Sum_probs=34.3
Q ss_pred HhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 70 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+..|..++.....++-.+|... +.++.+.+.+.|..|.++|||.+..+
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~-------~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKR-------LGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH-------HCCCchhHHHHHHHHHHCCCeEecCC
Confidence 4455666666666776666543 34677788999999999999987643
No 30
>PRK14999 histidine utilization repressor; Provisional
Probab=69.10 E-value=3.5 Score=31.88 Aligned_cols=31 Identities=16% Similarity=0.339 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
|.++...++++|+.|.+.|||.|..+- .+|+
T Consensus 46 ~gVSR~TVR~Al~~L~~eGli~r~~Gk-GTfV 76 (241)
T PRK14999 46 YGFSRMTINRALRELTDEGWLVRLQGV-GTFV 76 (241)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEecCc-EEEE
Confidence 889999999999999999999997663 4554
No 31
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=68.64 E-value=4.2 Score=23.77 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
|..+...+.+.+..|.+.|+|.+..+
T Consensus 30 ~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 30 LGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 77899999999999999999998754
No 32
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=68.11 E-value=4.7 Score=27.31 Aligned_cols=59 Identities=19% Similarity=0.198 Sum_probs=42.3
Q ss_pred HhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 70 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
++..=|+||.-..+.+-- ...+.. +..+.+.-++.|..|-++|-|..-..++...+|.|
T Consensus 26 k~t~dkl~kEV~~~K~IT-----ps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 26 EELLKRVAKEVKKEKIVT-----PYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHHHHHHHHHhccCcEEc-----HHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 455566776655533211 122444 77999999999999999999988777778888875
No 33
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=67.92 E-value=6.4 Score=31.12 Aligned_cols=46 Identities=26% Similarity=0.247 Sum_probs=39.1
Q ss_pred hhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 71 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 71 AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
..|...++.++.++..||... |.++...|++-++.|-++++|.|..
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~~-------l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQY-------FDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHHH-------HCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 346777888999998888754 7799999999999999999999954
No 34
>PRK09462 fur ferric uptake regulator; Provisional
Probab=67.52 E-value=15 Score=26.38 Aligned_cols=51 Identities=10% Similarity=0.270 Sum_probs=39.6
Q ss_pred hhhhhhhcc--cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 71 AAIVRIMKS--RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 71 AaIVRIMK~--~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
-+|.+++.. .+.++..||+..+.+.. +.++.+.|=+.++.|.+.|.|.+-.
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~--~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMG--EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 345555554 36899999998876554 4568899999999999999999854
No 35
>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=66.54 E-value=7.9 Score=27.66 Aligned_cols=52 Identities=19% Similarity=0.369 Sum_probs=34.5
Q ss_pred HHhhhhhhhcccccccchHHHHHHHHhcCC--CCCCHHHHHHHHHHhhhhhcccc
Q psy16237 69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKS--FAPSISMIKKCIESLIDKNYVER 121 (133)
Q Consensus 69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~--F~p~~~~iK~~IE~LIekeYl~R 121 (133)
+.-.|+.+.-.++ .--.+|+++..+..+. |.|+.+.|=+++-.|++-|||.|
T Consensus 19 lKlYiitm~e~~r-~Yg~q~Ld~lr~EFk~~Gy~P~hsEvYraLHeL~~dGilk~ 72 (122)
T PF02334_consen 19 LKLYIITMVEQER-GYGLQLLDELRSEFKPLGYRPNHSEVYRALHELVDDGILKQ 72 (122)
T ss_dssp HHHHHHHHHHTT--EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHhhhhccc-chHHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhhhHHHH
Confidence 3444454444443 3334677787888887 99999999999999999999966
No 36
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=66.34 E-value=4.9 Score=28.49 Aligned_cols=25 Identities=12% Similarity=0.287 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
+..+.+.+-+.|+.|.++|||+|..
T Consensus 56 l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 56 IGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred hCCChhhHHHHHHHHHHCCCEeeec
Confidence 5677888899999999999999963
No 37
>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=66.03 E-value=13 Score=24.25 Aligned_cols=56 Identities=20% Similarity=0.231 Sum_probs=32.0
Q ss_pred HHhhhhhhhcccc--cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhcc---ccCCCCCCceEecC
Q psy16237 69 LQAAIVRIMKSRK--QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYV---ERTANSTDEYSYVA 133 (133)
Q Consensus 69 I~AaIVRIMK~~k--~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl---~R~~~d~~~y~Yva 133 (133)
.=|.||-.||.+- -++++|+++++-. +... ...++.|-+-.-+ +-+.. .++|.|.|
T Consensus 10 ~l~~aV~ymK~r~~~Plt~~EIl~~ls~----~d~~----~~~~~~L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 10 QLAKIVDYMKKRHQHPLTLDEILDYLSL----LDIG----PKLKEWLKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hHHHHHHHHHhcCCCCccHHHHHHHHhc----cCcc----HHHHHHHHhhhhccCceeccC-CCEEEecc
Confidence 3477899999986 5777777776532 2222 1223444433333 33333 36899875
No 38
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=64.99 E-value=17 Score=23.32 Aligned_cols=44 Identities=18% Similarity=0.311 Sum_probs=32.6
Q ss_pred hhhhccc-ccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 74 VRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 74 VRIMK~~-k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
...+... ..++-.||..++ ..+.+.+.+.+..|.+.|||.|+..
T Consensus 11 l~~l~~~~~~~t~~~ia~~l-------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 11 LRALAEEPGGLTLAELAERL-------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHhCCCCcCHHHHHHHh-------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 3344443 567777777653 4678889999999999999999754
No 39
>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=64.86 E-value=6 Score=27.02 Aligned_cols=33 Identities=18% Similarity=0.229 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHHHHhhhhhcccc--CCCCC-CceEe
Q psy16237 99 FAPSISMIKKCIESLIDKNYVER--TANST-DEYSY 131 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R--~~~d~-~~y~Y 131 (133)
+..+.+.+-+.|..|.++|||.| ++.|. ..++|
T Consensus 53 l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~ 88 (109)
T TIGR01889 53 ILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIIS 88 (109)
T ss_pred HCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEE
Confidence 45778888899999999999998 44443 44444
No 40
>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=64.78 E-value=4.9 Score=30.77 Aligned_cols=34 Identities=15% Similarity=0.290 Sum_probs=27.8
Q ss_pred cCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 96 SKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 96 l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
|.. |.++...++++|+.|.+.|+|.|..+- .+|+
T Consensus 31 La~~~~VSR~TVR~Al~~L~~eGli~r~~G~-GtfV 65 (230)
T TIGR02018 31 LVAQYGCSRMTVNRALRELTDAGLLERRQGV-GTFV 65 (230)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEecCC-EEEE
Confidence 344 889999999999999999999997663 4443
No 41
>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=64.69 E-value=10 Score=25.48 Aligned_cols=45 Identities=16% Similarity=0.282 Sum_probs=28.5
Q ss_pred HHHhhhhhhhcc----cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhcc
Q psy16237 68 YLQAAIVRIMKS----RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYV 119 (133)
Q Consensus 68 ~I~AaIVRIMK~----~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl 119 (133)
.++..|..++|. ..-++.++|. ++| ..+...|+++|+.|++.|+|
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 344445555555 2334444444 444 35789999999999999976
No 42
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=64.34 E-value=5.4 Score=30.84 Aligned_cols=31 Identities=19% Similarity=0.433 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
|.++...++++|+.|.+.|+|.|..+. .+|+
T Consensus 39 ~~VSR~TvR~Al~~L~~eGli~r~~G~-GtfV 69 (240)
T PRK09764 39 FGVSRVTVRQALRQLVEQQILESIQGS-GTYV 69 (240)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEecCc-eeEE
Confidence 788899999999999999999997663 4454
No 43
>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=64.00 E-value=14 Score=21.80 Aligned_cols=34 Identities=18% Similarity=0.409 Sum_probs=24.5
Q ss_pred ccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 83 IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 83 l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
++-.||..+ +. ...+.+-+-+..|.+.||++||+
T Consensus 19 ~t~~eia~~----~g---l~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 19 LTLSEIARA----LG---LPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp EEHHHHHHH----HT---S-HHHHHHHHHHHHHTTSEEECS
T ss_pred CCHHHHHHH----HC---cCHHHHHHHHHHHHHCcCeecCc
Confidence 566555544 32 55667788999999999999985
No 44
>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=63.97 E-value=13 Score=25.59 Aligned_cols=58 Identities=12% Similarity=0.283 Sum_probs=40.3
Q ss_pred hhhhhhcc-cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237 72 AIVRIMKS-RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 131 (133)
Q Consensus 72 aIVRIMK~-~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y 131 (133)
+|..+++. ...++-.+|...+.+.- ..++.+.|=+.|+.|.+.|.|.+-..+.....|
T Consensus 12 ~Il~~l~~~~~~~ta~ei~~~l~~~~--~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 12 AILELLKESPEHLTAEEIYDKLRKKG--PRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp HHHHHHHHHSSSEEHHHHHHHHHHTT--TT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHhhhcc--CCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 44445554 45788889998876432 567899999999999999999996544333333
No 45
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=62.95 E-value=15 Score=26.11 Aligned_cols=25 Identities=20% Similarity=0.489 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
+-.+.+.+-+.|+.|.++|||+|..
T Consensus 64 l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 64 LSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEecc
Confidence 5578888899999999999999953
No 46
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=62.92 E-value=5.4 Score=31.01 Aligned_cols=34 Identities=15% Similarity=0.373 Sum_probs=28.1
Q ss_pred cCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 96 SKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 96 l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
|.. |.++...++++|..|.+.|+|.|-.+. .+|+
T Consensus 37 La~~f~VSR~TvRkAL~~L~~eGli~r~~G~-GtfV 71 (236)
T COG2188 37 LAEQFGVSRMTVRKALDELVEEGLIVRRQGK-GTFV 71 (236)
T ss_pred HHHHHCCcHHHHHHHHHHHHHCCcEEEEecC-eeEE
Confidence 445 888999999999999999999997653 4554
No 47
>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=62.12 E-value=29 Score=23.31 Aligned_cols=52 Identities=10% Similarity=0.197 Sum_probs=42.6
Q ss_pred HHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhcccc
Q psy16237 69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVER 121 (133)
Q Consensus 69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R 121 (133)
++-+|.-++. .+.+.=-||..++.+.... +.++...+=..+..|-++|||++
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 4556666676 4567777999998887766 78899999999999999999998
No 48
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=60.84 E-value=13 Score=24.24 Aligned_cols=45 Identities=20% Similarity=0.319 Sum_probs=34.6
Q ss_pred hhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237 71 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 71 AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~ 122 (133)
-+|+-.+.....+++.+|-.. ...+...+-+.+..|.+.||+++.
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~-------l~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEE-------LGLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHH-------TT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHH-------hCcCHHHHHHHHHHHHHCCCEEEE
Confidence 345666677788888887654 348899999999999999999985
No 49
>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=60.41 E-value=20 Score=21.23 Aligned_cols=36 Identities=17% Similarity=0.279 Sum_probs=27.2
Q ss_pred ccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCC
Q psy16237 83 IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS 125 (133)
Q Consensus 83 l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d 125 (133)
++..||.. . +..+...+.+.++.|.+.++|.+..+.
T Consensus 21 ~~~~ei~~----~---~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAE----R---LGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHH----H---HCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 66655433 2 457788899999999999999986544
No 50
>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=60.36 E-value=6 Score=24.32 Aligned_cols=29 Identities=14% Similarity=0.314 Sum_probs=24.4
Q ss_pred cCC-CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 96 SKS-FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 96 l~~-F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
|.. |..+...+++++..|.+.|+|.+.+.
T Consensus 30 la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 30 LAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 444 88999999999999999999999765
No 51
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=59.43 E-value=7 Score=25.84 Aligned_cols=26 Identities=23% Similarity=0.378 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
...+.+.+-..|+.|.++||++|..+
T Consensus 46 l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 46 LGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred HCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 55889999999999999999999644
No 52
>PF13730 HTH_36: Helix-turn-helix domain
Probab=59.31 E-value=6.9 Score=23.07 Aligned_cols=21 Identities=19% Similarity=0.376 Sum_probs=18.5
Q ss_pred CCCCHHHHHHHHHHhhhhhcc
Q psy16237 99 FAPSISMIKKCIESLIDKNYV 119 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl 119 (133)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 457789999999999999997
No 53
>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=59.10 E-value=20 Score=27.17 Aligned_cols=44 Identities=18% Similarity=0.259 Sum_probs=34.6
Q ss_pred hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237 72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~ 122 (133)
.|...++....++-.+|-.. +..+...+.+.++.|.++|+|+|.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~-------lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEA-------LAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCeEEe
Confidence 45666666666777666544 458899999999999999999986
No 54
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=58.71 E-value=12 Score=29.50 Aligned_cols=46 Identities=22% Similarity=0.419 Sum_probs=39.2
Q ss_pred hhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 71 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 71 AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
..|..+++.++.++-.||.+. |..+...|++-++.|-++|+|.|-.
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~-------l~vS~~TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 8 DAIIELVKQQGYVSTEELVEH-------FSVSPQTIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred HHHHHHHHHcCCEeHHHHHHH-------hCCCHHHHHHHHHHHHHCCCEEEec
Confidence 456777899999998888753 7899999999999999999999953
No 55
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=58.17 E-value=20 Score=25.86 Aligned_cols=33 Identities=24% Similarity=0.340 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHhhhhhccccCCC----CCCceEec
Q psy16237 100 APSISMIKKCIESLIDKNYVERTAN----STDEYSYV 132 (133)
Q Consensus 100 ~p~~~~iK~~IE~LIekeYl~R~~~----d~~~y~Yv 132 (133)
.-+.+.+-+++..|++.|.++|... .+-.|.|.
T Consensus 53 nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~ 89 (126)
T COG3355 53 NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYK 89 (126)
T ss_pred CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEe
Confidence 4678888999999999999999532 23456664
No 56
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=57.65 E-value=15 Score=25.91 Aligned_cols=49 Identities=18% Similarity=0.291 Sum_probs=41.3
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
.++..|.+++...-++++.+|-..+ . .+.+.+..+|+.|.+.|.|+|..
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l----g---lS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV----G---LSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH----C---CCHHHHHHHHHHHHHCCceeeEE
Confidence 5677889999999999998887664 2 77888999999999999999853
No 57
>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=56.23 E-value=18 Score=24.21 Aligned_cols=38 Identities=13% Similarity=0.216 Sum_probs=29.4
Q ss_pred ccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 79 SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 79 ~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
....+++.||... .-.+...+-+.|..|.++|||.|..
T Consensus 44 ~~~~is~~eLa~~-------~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAEL-------TGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCeeeec
Confidence 4566777777654 2357778899999999999999875
No 58
>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=56.16 E-value=10 Score=22.51 Aligned_cols=29 Identities=17% Similarity=0.287 Sum_probs=24.3
Q ss_pred cCC-CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 96 SKS-FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 96 l~~-F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+.. |..+...+.+.+..|-+.|||.+.++
T Consensus 31 la~~~~is~~~v~~~l~~L~~~G~i~~~~~ 60 (66)
T cd07377 31 LAEELGVSRTTVREALRELEAEGLVERRPG 60 (66)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 444 67889999999999999999998653
No 59
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=56.14 E-value=20 Score=25.90 Aligned_cols=48 Identities=15% Similarity=0.178 Sum_probs=39.8
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~ 122 (133)
.+|-.|.+.+...-++++.+|-.++ -.+.+.+..+|+.|.+.|+|++.
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-------glS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-------GVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-------CcCHHHHHHHHHHHHHCCCeeeE
Confidence 3566788888888999998887553 37889999999999999999863
No 60
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=55.42 E-value=14 Score=29.22 Aligned_cols=45 Identities=18% Similarity=0.327 Sum_probs=38.4
Q ss_pred hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
.|+.+.+.++.++-.||... |.++...|++-+..|=++|+|.|..
T Consensus 9 ~Il~~l~~~g~v~v~eLa~~-------~~VS~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 9 KILELLKEKGKVSVEELAEL-------FGVSEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHcCcEEHHHHHHH-------hCCCHHHHHHhHHHHHHCCcEEEEe
Confidence 46778888888888777644 8899999999999999999999954
No 61
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=55.21 E-value=15 Score=29.27 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=39.9
Q ss_pred hhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 71 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 71 AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
..|...++.++.++-.||... |.++...|++-|+.|-+.|++.|...
T Consensus 20 ~~Il~~L~~~~~vtv~eLa~~-------l~VS~~TIRRDL~~Le~~G~l~r~~G 66 (269)
T PRK09802 20 EQIIQRLRQQGSVQVNDLSAL-------YGVSTVTIRNDLAFLEKQGIAVRAYG 66 (269)
T ss_pred HHHHHHHHHcCCEeHHHHHHH-------HCCCHHHHHHHHHHHHhCCCeEEEeC
Confidence 456788889988998888755 77999999999999999999999653
No 62
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=52.51 E-value=25 Score=25.73 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=40.3
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhcccc
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVER 121 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R 121 (133)
.+|-.|.+++...-++++.+|-.++ -.+.+.+.++|..|.+.|.|++
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 4677899999999999998776553 3788899999999999999987
No 63
>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=52.16 E-value=15 Score=23.76 Aligned_cols=44 Identities=20% Similarity=0.451 Sum_probs=27.3
Q ss_pred cccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237 78 KSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY 129 (133)
Q Consensus 78 K~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y 129 (133)
...+..+-.|+ +++ |+.|-.+...+++ .||+-+||+|+.++ +.|
T Consensus 25 ~~g~~y~E~EV-N~~---L~~~~~D~a~LRR---~LVd~g~L~R~~dg-~~Y 68 (71)
T PF09860_consen 25 EPGREYSEKEV-NEI---LKRFFDDYATLRR---YLVDYGLLERTRDG-SRY 68 (71)
T ss_pred CCCCccCHHHH-HHH---HHHHcccHHHHHH---HHHHcCCeeecCCC-Cee
Confidence 44445554443 222 3334457777774 79999999998664 556
No 64
>PRK10870 transcriptional repressor MprA; Provisional
Probab=51.48 E-value=13 Score=27.73 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+..+.+.+-+.|+.|.++|||+|..+
T Consensus 81 l~l~~~tvsr~v~rLe~kGlV~R~~~ 106 (176)
T PRK10870 81 LGSSRTNATRIADELEKRGWIERRES 106 (176)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 55778888999999999999999543
No 65
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=51.27 E-value=13 Score=24.19 Aligned_cols=26 Identities=15% Similarity=0.180 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+..+.+.+-+.+..|.++|||.|..+
T Consensus 9 l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 9 LNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred hCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 66888999999999999999999864
No 66
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=51.09 E-value=24 Score=25.45 Aligned_cols=40 Identities=20% Similarity=0.291 Sum_probs=27.1
Q ss_pred HHhhhhhhhccc-ccccchHHHHHHHHhcCCCCCCHHHHHHHHHH
Q psy16237 69 LQAAIVRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIES 112 (133)
Q Consensus 69 I~AaIVRIMK~~-k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~ 112 (133)
|+.| .-||+.+ +.|++.+|+.+|.+.+. .+...+..+|-.
T Consensus 6 idvA-y~iL~~~~~~m~f~dL~~ev~~~~~---~s~e~~~~~iaq 46 (129)
T PRK02363 6 IEVA-YEILKEKKEPMSFYDLVNEIQKYLG---KSDEEIRERIAQ 46 (129)
T ss_pred HHHH-HHHHHHcCCcccHHHHHHHHHHHhC---CCHHHHHHHHHH
Confidence 4444 4566555 78999999999998876 455555555443
No 67
>PRK09954 putative kinase; Provisional
Probab=50.96 E-value=23 Score=28.82 Aligned_cols=43 Identities=21% Similarity=0.293 Sum_probs=36.7
Q ss_pred hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhcccc
Q psy16237 72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVER 121 (133)
Q Consensus 72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R 121 (133)
-|.++++....++..+|-.. +.++.+.+.+.|..|.++||+++
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 37889999999999887654 34899999999999999999964
No 68
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=50.91 E-value=13 Score=25.78 Aligned_cols=47 Identities=26% Similarity=0.303 Sum_probs=29.1
Q ss_pred cccccccchHHHHHHHHhcCC-CC--------CCHHHHHHHHHHhhhhhccccCCC
Q psy16237 78 KSRKQIRHNALIQEVLSQSKS-FA--------PSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 78 K~~k~l~h~eL~~ev~~~l~~-F~--------p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
|..|---|+-|+++=.-.+++ |. ...-.+++...+||.+||++|.-.
T Consensus 5 k~nr~kIhq~Lf~~gv~vakkDfnl~kH~el~ipNL~vika~qsl~S~GYvkt~~~ 60 (105)
T COG5045 5 KENRYKIHQRLFQKGVAVAKKDFNLGKHRELEIPNLHVIKAMQSLISYGYVKTIHV 60 (105)
T ss_pred hHHHHHHHHHHHHhhhhHhhhhccccCCcccCCCchHHHHHHHHHhhcceeEEEee
Confidence 344444577777772223333 42 123345679999999999999643
No 69
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=50.86 E-value=14 Score=20.67 Aligned_cols=25 Identities=8% Similarity=0.267 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
+..+.+.+.+.+..|.+.|||+++.
T Consensus 18 l~~s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 18 LGLTRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 5578888999999999999999864
No 70
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=49.94 E-value=22 Score=20.69 Aligned_cols=31 Identities=16% Similarity=0.372 Sum_probs=23.1
Q ss_pred hHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhh
Q psy16237 86 NALIQEVLSQSKS-FAPSISMIKKCIESLIDK 116 (133)
Q Consensus 86 ~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIek 116 (133)
.+|+...-..... ..|-...|.++|+.|+++
T Consensus 11 ~el~~~L~~ls~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 11 KELYEKLKELSEETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 3566665544444 889999999999999874
No 71
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=49.61 E-value=19 Score=22.73 Aligned_cols=32 Identities=25% Similarity=0.488 Sum_probs=24.9
Q ss_pred ccccchHHHHHHHHhcCCCCCC--HHHHHHHHHHhhhhhc
Q psy16237 81 KQIRHNALIQEVLSQSKSFAPS--ISMIKKCIESLIDKNY 118 (133)
Q Consensus 81 k~l~h~eL~~ev~~~l~~F~p~--~~~iK~~IE~LIekeY 118 (133)
++++++||++ | .|+|. ...|+++-+.|+++||
T Consensus 2 ~tv~k~dLi~-----l-Gf~~~tA~~IIrqAK~~lV~~G~ 35 (59)
T PF11372_consen 2 KTVTKKDLIE-----L-GFSESTARDIIRQAKALLVQKGF 35 (59)
T ss_pred CccCHHHHHH-----c-CCCHHHHHHHHHHHHHHHHHcCC
Confidence 4678888874 3 38883 5679999999999986
No 72
>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=49.60 E-value=36 Score=25.68 Aligned_cols=52 Identities=15% Similarity=0.294 Sum_probs=35.9
Q ss_pred hhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 71 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 71 AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
..|...+..+..++..+|... +..+.+.+-+.+..|.++||++|... +..+.
T Consensus 146 ~~IL~~l~~~g~~s~~eia~~-------l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~ 197 (203)
T TIGR01884 146 LKVLEVLKAEGEKSVKNIAKK-------LGKSLSTISRHLRELEKKGLVEQKGR-KGKRY 197 (203)
T ss_pred HHHHHHHHHcCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEEcC-CccEE
Confidence 345555665556666666544 34677778899999999999999864 33443
No 73
>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=49.21 E-value=34 Score=23.25 Aligned_cols=44 Identities=16% Similarity=0.214 Sum_probs=29.0
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
|.........++..+|... +..+.+.+-+.|..|.++|||+|..
T Consensus 33 iL~~l~~~~~~t~~ela~~-------~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLANQ-------ACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHcCCcCHHHHHHH-------hCCCchhHHHHHHHHHHCCCEEecc
Confidence 3444445555665554433 3355556779999999999999954
No 74
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=48.77 E-value=36 Score=29.78 Aligned_cols=58 Identities=19% Similarity=0.285 Sum_probs=47.6
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV 132 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv 132 (133)
.-+.+|++.|+....++-.+|-+. |-.+...+-+.|..|+.++++++-..+...+-|+
T Consensus 402 ~~~~~il~~~~en~~~T~~~L~~~-------l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v 459 (467)
T COG2865 402 ERQEKILELIKENGKVTARELREI-------LGISSETIRRRIANLVKRGLLKQLGSSGRGTWYV 459 (467)
T ss_pred HHHHHHHHHHhhccccCHHHHHHH-------hCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEe
Confidence 334889999999999998777543 4588899999999999999999987666677776
No 75
>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=48.50 E-value=25 Score=29.76 Aligned_cols=39 Identities=13% Similarity=0.296 Sum_probs=30.8
Q ss_pred ccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 83 IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 83 l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
+++.+|+.++.+++. ..+...+..-|+.||++|+|..+-
T Consensus 1 i~~~~l~~~L~~~~~--~~~~~~v~~~L~~Li~~~~L~~~l 39 (500)
T PF04738_consen 1 ISYSELIEQLAKEFP--EAEAERVENYLRQLIEQGFLISEL 39 (500)
T ss_pred ChHHHHHHHHHHhCC--CCCHHHHHHHHHHHHHCCEEEecC
Confidence 467777776655532 579999999999999999999863
No 76
>KOG3054|consensus
Probab=47.69 E-value=31 Score=28.00 Aligned_cols=53 Identities=17% Similarity=0.305 Sum_probs=39.8
Q ss_pred hhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 74 VRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 74 VRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
|-..|..|.+...||-.+ |....++.--+|..|+..+.|.---+|+..|+||.
T Consensus 206 v~YIk~nKvV~ledLas~-------f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 206 VEYIKKNKVVPLEDLASE-------FGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHhcCeeeHHHHHHH-------hCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 445555555554444322 77877777789999999999999889999999984
No 77
>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=46.90 E-value=47 Score=19.86 Aligned_cols=46 Identities=28% Similarity=0.399 Sum_probs=26.6
Q ss_pred HHHHhhhhhhhccc--ccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhh
Q psy16237 67 LYLQAAIVRIMKSR--KQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDK 116 (133)
Q Consensus 67 ~~I~AaIVRIMK~~--k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIek 116 (133)
..|.++|..||+.. -+++-. .|.++|.. |..+...-|..|..+|..
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT~k----~vr~~Le~~~~~dL~~~K~~I~~~I~~ 51 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVTKK----QVREQLEERFGVDLSSRKKFIKELIDE 51 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG--HH----HHHHHHHHH-SS--SHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHhHhhHH----HHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 35778888888876 233333 44455555 666666777777777763
No 78
>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=46.83 E-value=27 Score=21.93 Aligned_cols=44 Identities=11% Similarity=0.156 Sum_probs=36.8
Q ss_pred ccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 81 KQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 81 k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+.++=.+|..++.+.... |.++...|=..+..|-++|+|+....
T Consensus 8 ~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~ 52 (75)
T PF03551_consen 8 GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWE 52 (75)
T ss_dssp S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEE
T ss_pred CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeee
Confidence 456667899998888777 89999999999999999999987543
No 79
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=45.46 E-value=56 Score=23.70 Aligned_cols=52 Identities=19% Similarity=0.340 Sum_probs=44.3
Q ss_pred HHHHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 66 KLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 66 ~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
...|.+-||-+-+.+.+++..||... +-.+...++.....|.+.|.|-+...
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~-------TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAK-------TGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHH-------HCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 45788999999999999999998866 45788889999999999998888653
No 80
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=44.87 E-value=20 Score=28.14 Aligned_cols=34 Identities=18% Similarity=0.265 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTANSTDEYSYV 132 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv 132 (133)
+..+.+.+-+.+..|-++|||.|..+....+.++
T Consensus 31 L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L 64 (217)
T PRK14165 31 TGTSSKTAARILKQLEDEGYITRTIVPRGQLITI 64 (217)
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence 4578889999999999999999976554555554
No 81
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=44.42 E-value=23 Score=26.46 Aligned_cols=25 Identities=12% Similarity=0.221 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 100 APSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 100 ~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
..+...++.+|+.|.+-|+|+++++
T Consensus 52 ~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 52 KISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred CCCHHHHHHHHHHHHHCCCeEECCC
Confidence 3589999999999999999999876
No 82
>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=44.06 E-value=12 Score=26.77 Aligned_cols=48 Identities=17% Similarity=0.205 Sum_probs=42.8
Q ss_pred hcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 77 MKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 77 MK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
.+....+-+++.+--..+.|+. |.-++..|+.++..|..-|-|+..++
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 6778888888888888888888 99999999999999999999999864
No 83
>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=43.87 E-value=27 Score=21.99 Aligned_cols=49 Identities=14% Similarity=0.292 Sum_probs=33.5
Q ss_pred HHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCC-CHHHHHHHHHHhhh
Q psy16237 67 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAP-SISMIKKCIESLID 115 (133)
Q Consensus 67 ~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p-~~~~iK~~IE~LIe 115 (133)
..+.+++.-+|.+.+.++...++..++..|.. -.. ....+++.+|..+.
T Consensus 5 ~vL~~iv~ell~~g~~vsnKaII~~LI~~LE~e~Dv~~~dvyR~~LEiVv~ 55 (61)
T PF10798_consen 5 EVLGAIVRELLASGGHVSNKAIILKLIHRLESESDVVQLDVYRNALEIVVG 55 (61)
T ss_dssp HHHHHHHHHHHHTT---SHHHHHHHHHHHHHT---HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHc
Confidence 46778888899999999999999999999984 222 33445666666554
No 84
>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=43.23 E-value=20 Score=21.41 Aligned_cols=25 Identities=8% Similarity=0.300 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
+-.+.+.+.+.+..|.+++||.+..
T Consensus 35 ~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 35 LGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEecC
Confidence 5578889999999999999999976
No 85
>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=43.03 E-value=9.1 Score=27.29 Aligned_cols=48 Identities=6% Similarity=0.124 Sum_probs=39.8
Q ss_pred hcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 77 MKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 77 MK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
.+....+.+++.+.-..+.|+. |.-++..|+.++..|.+-|.|+.+++
T Consensus 40 ~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~ed 88 (121)
T PF09681_consen 40 LNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDED 88 (121)
T ss_pred cCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3455667777777777788888 99999999999999999999999765
No 86
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=42.59 E-value=77 Score=22.91 Aligned_cols=59 Identities=14% Similarity=0.240 Sum_probs=42.6
Q ss_pred hhhhhhhcc-cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237 71 AAIVRIMKS-RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 131 (133)
Q Consensus 71 AaIVRIMK~-~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y 131 (133)
.+|.++|.. ...++-.+|..++.+.- ...+.+.|=+.++.|-|.|+|.|-+.......|
T Consensus 24 ~~vl~~L~~~~~~~sAeei~~~l~~~~--p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y 83 (145)
T COG0735 24 LAVLELLLEADGHLSAEELYEELREEG--PGISLATVYRTLKLLEEAGLVHRLEFEGGKTRY 83 (145)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhC--CCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEE
Confidence 455666664 35599999988876643 445789999999999999999997654333333
No 87
>PRK00215 LexA repressor; Validated
Probab=42.08 E-value=28 Score=26.12 Aligned_cols=41 Identities=12% Similarity=0.243 Sum_probs=29.0
Q ss_pred cccchHHHHHHHHhcCCCCC-CHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237 82 QIRHNALIQEVLSQSKSFAP-SISMIKKCIESLIDKNYVERTANSTDEY 129 (133)
Q Consensus 82 ~l~h~eL~~ev~~~l~~F~p-~~~~iK~~IE~LIekeYl~R~~~d~~~y 129 (133)
.++..||... +-. +.+.+-..+..|.++|||+|+.++...+
T Consensus 23 ~~s~~ela~~-------~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~~ 64 (205)
T PRK00215 23 PPSRREIADA-------LGLRSPSAVHEHLKALERKGFIRRDPGRSRAI 64 (205)
T ss_pred CCCHHHHHHH-------hCCCChHHHHHHHHHHHHCCCEEeCCCCcceE
Confidence 3455555433 445 6677788999999999999987765433
No 88
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=41.18 E-value=41 Score=25.67 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=26.4
Q ss_pred hhhccccc-ccchHHHHHHHHhcCCCCCCHHHHHHHHHHh
Q psy16237 75 RIMKSRKQ-IRHNALIQEVLSQSKSFAPSISMIKKCIESL 113 (133)
Q Consensus 75 RIMK~~k~-l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~L 113 (133)
=||..++. |++++|++++...+. .+-..|+.+|-.+
T Consensus 22 ~ile~~~~~~~F~dii~EI~~~~~---~s~~ei~~~i~~F 58 (175)
T COG3343 22 AILEEKKKPFNFSDIINEIQKLLG---VSKEEIRSRIGQF 58 (175)
T ss_pred HHHHHcCCCccHHHHHHHHHHHhC---cCHHHHHHHHHHH
Confidence 45666655 999999999988865 7777777666443
No 89
>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=39.30 E-value=52 Score=21.02 Aligned_cols=55 Identities=20% Similarity=0.285 Sum_probs=40.9
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCC-CCC--CHHHHHHHHHHhhhhhccccCC
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAP--SISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p--~~~~iK~~IE~LIekeYl~R~~ 123 (133)
.|..|| .-++.++-.+-..+...+...-.- ..| -...++++|..++++|-|.+-.
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 344453 678888889999988888775432 333 2477999999999999988854
No 90
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=38.32 E-value=1.6e+02 Score=21.48 Aligned_cols=63 Identities=13% Similarity=0.191 Sum_probs=50.5
Q ss_pred hhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccC
Q psy16237 57 TVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 57 ~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~ 122 (133)
..+.+-+-++..++.+|.-++...- +.=-+|+..+.+ . . +.++...+=..+..|-+.|||.+.
T Consensus 13 ~~~~~~ql~kg~l~~~IL~~L~~~p-~hGYeI~q~l~~-~-g~~~v~~GtLYp~L~RLE~~GlI~~~ 76 (138)
T TIGR02719 13 LAKQINGAPKNFLVPFLLLCLKDWN-LHGYKLIQMLMD-F-GFSSVDQGNVYRTLRKLEKDNLISSQ 76 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCC-CCHHHHHHHHHH-c-CCCCCCcChHHHHHHHHHHCCCEEEE
Confidence 3456677899999999999998764 555588888754 3 3 578899999999999999999973
No 91
>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=38.04 E-value=14 Score=25.90 Aligned_cols=34 Identities=15% Similarity=0.249 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTANSTDEYSYV 132 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv 132 (133)
|..+.+.-++.|..|-++|-|.--..+....+|.
T Consensus 69 lkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYt 102 (105)
T PF03297_consen 69 LKINGSLARKALRELESKGLIKPVSKHHRQRIYT 102 (105)
T ss_dssp HCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEE
T ss_pred HhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEe
Confidence 6678888899999999999998876666778874
No 92
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=35.12 E-value=58 Score=24.39 Aligned_cols=55 Identities=22% Similarity=0.236 Sum_probs=43.9
Q ss_pred HHHHhhhhhhhcccc-cccchHHHHHHHHhcCC-CCC----------CHHHHHHHHHHhhhhhcccc
Q psy16237 67 LYLQAAIVRIMKSRK-QIRHNALIQEVLSQSKS-FAP----------SISMIKKCIESLIDKNYVER 121 (133)
Q Consensus 67 ~~I~AaIVRIMK~~k-~l~h~eL~~ev~~~l~~-F~p----------~~~~iK~~IE~LIekeYl~R 121 (133)
..|=-|..|.-+.+. .+.++-++.|-.+..+. ..- +...++++.|.|++.|.|.-
T Consensus 105 L~LLIa~~rl~~~~~~~~NF~~vy~EY~~~~~~~~~~~~~~~~~~~~~k~v~~~a~E~L~~l~Ll~~ 171 (203)
T PF14629_consen 105 LCLLIAAARLIKGYEETFNFEMVYDEYKKFAKSYNSSSAIVGTIKVWSKPVALKAWEHLLSLELLKP 171 (203)
T ss_pred HHHHHHHHHHHhccCCCccHHHHHHHHHHHHHhhccccccccccccCCHHHHHHHHHHHHHCCCcee
Confidence 445566688887776 89999999888877666 333 78889999999999999987
No 93
>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=35.08 E-value=49 Score=24.67 Aligned_cols=27 Identities=22% Similarity=0.335 Sum_probs=22.3
Q ss_pred CCCC-HHHHHHHHHHhhhhhccccCCCC
Q psy16237 99 FAPS-ISMIKKCIESLIDKNYVERTANS 125 (133)
Q Consensus 99 F~p~-~~~iK~~IE~LIekeYl~R~~~d 125 (133)
+-.+ .+.+-..++.|.++|||.|.++.
T Consensus 35 ~~~~s~~tv~~~l~~L~~~g~i~~~~~~ 62 (199)
T TIGR00498 35 VGLRSPSAAEEHLKALERKGYIERDPGK 62 (199)
T ss_pred hCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence 3344 88889999999999999998654
No 94
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=35.07 E-value=60 Score=22.96 Aligned_cols=44 Identities=14% Similarity=0.215 Sum_probs=29.5
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
|.++.......+-.+|. +. +.++.+.+-..|..|.++|||.|..
T Consensus 13 I~~l~~~~~~~~~~ela----~~---l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 13 IYLLIEEKGYARVSDIA----EA---LSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHhcCCCcCHHHHH----HH---hCCChhHHHHHHHHHHHCCCEEEec
Confidence 44555555444333322 22 5578888999999999999999753
No 95
>KOG4718|consensus
Probab=34.41 E-value=57 Score=25.90 Aligned_cols=53 Identities=21% Similarity=0.326 Sum_probs=40.1
Q ss_pred hhhhhhhcc-cccccchHHHHHHHHhcCCCCC-CHHHHHHHHHHhhhhhccccCCC
Q psy16237 71 AAIVRIMKS-RKQIRHNALIQEVLSQSKSFAP-SISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 71 AaIVRIMK~-~k~l~h~eL~~ev~~~l~~F~p-~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
=+|-.||++ ..-.....-+.....+++ |+| ..+.+-.-+..+++-+|+.+.++
T Consensus 103 kalE~im~sed~~~asst~~~~~vlq~k-~k~L~ks~iE~lLqkf~q~gwf~e~eg 157 (235)
T KOG4718|consen 103 KALEKIMSSEDCHIASSTAYNDIVLQAK-SKPLKKSRIEELLQKFIQMGWFMEVEG 157 (235)
T ss_pred HHHHHHHhhhHhhhHHHHHHHHHHHHHh-cCCCCHHHHHHHHHHHHHhchhheecc
Confidence 367889999 566666666666666666 655 88888999999999999988654
No 96
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=33.86 E-value=58 Score=25.44 Aligned_cols=44 Identities=18% Similarity=0.311 Sum_probs=37.4
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
|..+++.++.++..||... |.++...|++-+..|-+++.|.|..
T Consensus 9 Il~~l~~~~~~~~~eLa~~-------l~VS~~TiRRdL~~L~~~~~l~r~~ 52 (240)
T PRK10411 9 IVDLLLNHTSLTTEALAEQ-------LNVSKETIRRDLNELQTQGKILRNH 52 (240)
T ss_pred HHHHHHHcCCCcHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEec
Confidence 6778888889998888755 5689999999999999999998853
No 97
>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=32.94 E-value=96 Score=20.21 Aligned_cols=53 Identities=19% Similarity=0.288 Sum_probs=36.5
Q ss_pred hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC--CCCceEe
Q psy16237 72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN--STDEYSY 131 (133)
Q Consensus 72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~--d~~~y~Y 131 (133)
.|++.+.. ..+.|.||...+ . ..+...+-+++..|.+.|.+.|... .+....|
T Consensus 9 ~IL~~l~~-g~~rf~el~~~l----~--~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y 63 (90)
T PF01638_consen 9 LILRALFQ-GPMRFSELQRRL----P--GISPKVLSQRLKELEEAGLVERRVYPEVPPRVEY 63 (90)
T ss_dssp HHHHHHTT-SSEEHHHHHHHS----T--TS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEE
T ss_pred HHHHHHHh-CCCcHHHHHHhc----c--hhHHHHHHHHHHHHHHcchhhcccccCCCCCCcc
Confidence 45555555 677888887553 1 3578899999999999999999633 2334455
No 98
>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=32.79 E-value=1e+02 Score=21.23 Aligned_cols=62 Identities=21% Similarity=0.235 Sum_probs=39.3
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 131 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y 131 (133)
..|+.|.+-- ...-..-..++.+|..++..+ +....+--+|+.||+.|.|+=..+-.++..|
T Consensus 48 ~yD~~Il~~~-~~~~~~~arvIg~vl~~~~~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQA-PDEFQKAARVIGEVLGHSDQG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhcC-CccccHHHHHHHHHHHhcCcC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 4555555511 111123356788888776534 7788899999999999988865544344333
No 99
>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=32.71 E-value=42 Score=28.54 Aligned_cols=39 Identities=28% Similarity=0.611 Sum_probs=29.5
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHH-HHHhhh
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKC-IESLID 115 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~-IE~LIe 115 (133)
+-|++|++ ++++++.++++|..+++++..+-+| +=.||.
T Consensus 11 LAriI~tg----~d~~IT~ai~qL~~~~~s~~ilDk~NlP~LI~ 50 (370)
T PF07149_consen 11 LARIIKTG----NDEMITKAINQLPNHPVSVEILDKCNLPYLID 50 (370)
T ss_pred HHHHHHhC----chHhHHHHHHhCCCCCCcHHHHHHcCchHHHH
Confidence 45788887 6899999999997688887776553 455554
No 100
>PF13040 DUF3901: Protein of unknown function (DUF3901)
Probab=32.39 E-value=77 Score=18.36 Aligned_cols=36 Identities=19% Similarity=0.142 Sum_probs=24.3
Q ss_pred cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhcc
Q psy16237 80 RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYV 119 (133)
Q Consensus 80 ~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl 119 (133)
++..+|.+|+.+=-.+|- +.+..=..||.-||+-|.
T Consensus 3 ~~~~sFeeLV~eNK~ell----~d~~~me~Ieerie~k~~ 38 (40)
T PF13040_consen 3 RKKKSFEELVRENKQELL----NDKEAMEKIEERIEEKHE 38 (40)
T ss_pred ccccCHHHHHHHHHHHHH----cCHHHHHHHHHHHHHHHh
Confidence 567999999998887763 333334467777776543
No 101
>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=31.98 E-value=42 Score=23.20 Aligned_cols=18 Identities=22% Similarity=0.350 Sum_probs=16.7
Q ss_pred CHHHHHHHHHHhhhhhcc
Q psy16237 102 SISMIKKCIESLIDKNYV 119 (133)
Q Consensus 102 ~~~~iK~~IE~LIekeYl 119 (133)
|...|.+.|+.||.+||.
T Consensus 13 t~~~i~~QI~yll~qG~~ 30 (99)
T cd03527 13 TDEQIAKQIDYIISNGWA 30 (99)
T ss_pred CHHHHHHHHHHHHhCCCE
Confidence 889999999999999985
No 102
>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=31.77 E-value=40 Score=20.86 Aligned_cols=38 Identities=24% Similarity=0.373 Sum_probs=14.6
Q ss_pred hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHH
Q psy16237 72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIE 111 (133)
Q Consensus 72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE 111 (133)
.|+|..+..+.++..+|..++.+. . ..++...|...+-
T Consensus 3 ~I~~~v~~~p~~s~~~i~~~l~~~-~-~~vS~~TI~r~L~ 40 (72)
T PF01498_consen 3 RIVRMVRRNPRISAREIAQELQEA-G-ISVSKSTIRRRLR 40 (72)
T ss_dssp -------------HHHHHHHT----T---S-HHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHc-c-CCcCHHHHHHHHH
Confidence 478889999999999999887666 3 7778887776653
No 103
>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=31.14 E-value=82 Score=23.84 Aligned_cols=46 Identities=11% Similarity=0.330 Sum_probs=32.8
Q ss_pred HhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237 70 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~ 122 (133)
=+.+++.|-..+ +-.||+..+... |+ ...+...++.|.++|||...
T Consensus 32 ~~~L~~lLdG~r--t~~eI~~~l~~~---~p--~~~v~~~L~~L~~~G~l~~~ 77 (193)
T TIGR03882 32 YCQLAPLLDGRR--TLDEIIAALAGR---FP--AEEVLYALDRLERRGYLVED 77 (193)
T ss_pred HHHHHHHHcCCC--CHHHHHHHhhcc---CC--HHHHHHHHHHHHHCCCEecc
Confidence 456788887744 455666554332 65 66689999999999999864
No 104
>PRK04966 hypothetical protein; Provisional
Probab=31.12 E-value=36 Score=22.29 Aligned_cols=20 Identities=30% Similarity=0.554 Sum_probs=15.4
Q ss_pred HHHHHhhhhhccccCCCCCCc
Q psy16237 108 KCIESLIDKNYVERTANSTDE 128 (133)
Q Consensus 108 ~~IE~LIekeYl~R~~~d~~~ 128 (133)
..++.||+ +|+-|+..|...
T Consensus 11 eTL~nLIe-efv~ReGTdyG~ 30 (72)
T PRK04966 11 ETLENLIE-SFVLREGTDYGE 30 (72)
T ss_pred HHHHHHHH-HHHhccCccCCc
Confidence 56788998 999998776543
No 105
>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=31.09 E-value=29 Score=23.77 Aligned_cols=19 Identities=37% Similarity=0.587 Sum_probs=15.5
Q ss_pred HHHHHHHHHhhhhhccccC
Q psy16237 104 SMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 104 ~~iK~~IE~LIekeYl~R~ 122 (133)
..+-.-||.||.-|||.|+
T Consensus 42 k~~D~fie~li~~GYI~re 60 (93)
T PF08820_consen 42 KRLDIFIEALIKLGYIERE 60 (93)
T ss_pred cchhHHHHHHHHcCCeEec
Confidence 3445689999999999993
No 106
>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=30.96 E-value=23 Score=22.91 Aligned_cols=28 Identities=25% Similarity=0.387 Sum_probs=15.5
Q ss_pred ccccchHHHHHHHHhcCC--CCCCHHHHHH
Q psy16237 81 KQIRHNALIQEVLSQSKS--FAPSISMIKK 108 (133)
Q Consensus 81 k~l~h~eL~~ev~~~l~~--F~p~~~~iK~ 108 (133)
+...|......+...+.. |||++.+|-+
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 456777777777766654 9999987643
No 107
>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=30.77 E-value=48 Score=22.02 Aligned_cols=24 Identities=21% Similarity=0.228 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHhhhhhccccCCC
Q psy16237 101 PSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 101 p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
-+...+++-|..||..+||.-+.+
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 478999999999999999966544
No 108
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=30.30 E-value=1.1e+02 Score=17.94 Aligned_cols=31 Identities=13% Similarity=0.309 Sum_probs=24.2
Q ss_pred hHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhh
Q psy16237 86 NALIQEVLSQSKSFAPSISMIKKCIESLIDKN 117 (133)
Q Consensus 86 ~eL~~ev~~~l~~F~p~~~~iK~~IE~LIeke 117 (133)
++|+.++..... +......|..+++.||.++
T Consensus 9 d~Ll~eA~~l~g-~~tk~~~V~~ALr~~i~r~ 39 (47)
T PF09957_consen 9 DELLAEAMRLTG-TKTKKEAVNEALRELIRRR 39 (47)
T ss_pred HHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHH
Confidence 478888876655 7777888899998888765
No 109
>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=29.77 E-value=63 Score=29.29 Aligned_cols=53 Identities=15% Similarity=0.390 Sum_probs=33.4
Q ss_pred HHHhhhhhhhccc-ccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 68 YLQAAIVRIMKSR-KQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 68 ~I~AaIVRIMK~~-k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
--+|.+++-|+.- |.+.-.+| .++...-.. ..|... =.-|+.|++|+||++..
T Consensus 484 yTeasLi~~Me~~~k~v~d~~l-~~~l~e~~GIGtpATr--A~iI~~L~~R~Yv~~~~ 538 (660)
T TIGR01056 484 YTEGTLLSAMTNPAAFVQDKGL-KKTLKETKGLGTEATR--ADIIENLFKRGFIQKKK 538 (660)
T ss_pred cCHHHHHHHHHhhhhcccCHHH-HHHhhhccCCCCcccH--HHHHHHHHhCCCEEeeC
Confidence 5677888888643 44444444 333333334 666433 56799999999999754
No 110
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=29.66 E-value=96 Score=24.28 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=21.3
Q ss_pred CCHHHHHHHHHHhhhhhccccCCCC
Q psy16237 101 PSISMIKKCIESLIDKNYVERTANS 125 (133)
Q Consensus 101 p~~~~iK~~IE~LIekeYl~R~~~d 125 (133)
...+.+-+-+..|++.||+++|+++
T Consensus 31 lpksT~~RlL~tL~~~G~v~~d~~~ 55 (246)
T COG1414 31 LPKSTVHRLLQTLVELGYVEQDPED 55 (246)
T ss_pred cCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 5566678899999999999999875
No 111
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=29.59 E-value=55 Score=24.59 Aligned_cols=44 Identities=23% Similarity=0.225 Sum_probs=35.4
Q ss_pred hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237 72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~ 122 (133)
.|...++.++.++-.+|... |.++...|++-+..|-+.|-+.|-
T Consensus 11 ~Il~~l~~~~~~~~~~La~~-------~~vS~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 11 ALQELIEENPFITDEELAEK-------FGVSIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHCCCEEHHHHHHH-------HCcCHHHHHHHHHHHhcchHHHHH
Confidence 34556677777877776644 889999999999999999999884
No 112
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=28.96 E-value=77 Score=24.86 Aligned_cols=45 Identities=11% Similarity=0.227 Sum_probs=37.8
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
|.+.++.++.++-.||... |.++...+++-+..|-+.|.|.|-..
T Consensus 10 Il~~l~~~~~~~~~ela~~-------l~vS~~TirRdL~~Le~~g~i~r~~g 54 (251)
T PRK13509 10 LLELLAQLGFVTVEKVIER-------LGISPATARRDINKLDESGKLKKVRN 54 (251)
T ss_pred HHHHHHHcCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 6788888889998887755 66999999999999999999988443
No 113
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=28.51 E-value=1.5e+02 Score=21.81 Aligned_cols=57 Identities=12% Similarity=0.321 Sum_probs=41.7
Q ss_pred hhhhhhhc-ccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 71 AAIVRIMK-SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 71 AaIVRIMK-~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
-+|.++|. ..+.++..+|+..+.++- ..++.+.|=+.++.|.+.|.|.+-+.+ +.|.
T Consensus 29 ~~IL~~l~~~~~hlSa~eI~~~L~~~~--~~is~aTVYRtL~~L~e~Glv~~~~~~-~~~~ 86 (169)
T PRK11639 29 LEVLRLMSLQPGAISAYDLLDLLREAE--PQAKPPTVYRALDFLLEQGFVHKVEST-NSYV 86 (169)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHhhC--CCCCcchHHHHHHHHHHCCCEEEEecC-CcEE
Confidence 34444444 356899999998876554 456788889999999999999997543 3454
No 114
>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=28.26 E-value=1.3e+02 Score=20.69 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=19.5
Q ss_pred CCHHHHHHHHHHhhhhhccccCCC
Q psy16237 101 PSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 101 p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
-+...+-.+|-.||.+||++.+.|
T Consensus 44 ~~~~~V~SNIGvLIKkglIEKSGD 67 (96)
T PF09114_consen 44 MNKASVNSNIGVLIKKGLIEKSGD 67 (96)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEETT
T ss_pred hhhhHHHHhHHHHHHcCcccccCC
Confidence 456777889999999999999754
No 115
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=27.97 E-value=1.3e+02 Score=30.53 Aligned_cols=57 Identities=12% Similarity=0.105 Sum_probs=42.2
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
.+.-||-..=-.+-.+++.+|+..+.........+..+|+..|+.||+.|.|-+-..
T Consensus 186 aV~~AI~HLsER~a~f~~~~Ll~~A~~~~~~~~~~~~~v~~aId~~i~~g~Li~l~~ 242 (1623)
T PRK14712 186 AVTQAIAGLSERKVQFMYTDLLARTVGILPPENGVIERARAGIDEAISREQLIPLDR 242 (1623)
T ss_pred HHHHHHHHhhhhhhhCcHHHHHHHHHhhcccccccHHHHHHHHHHHHhCCCeeeccc
Confidence 445555555555556889999988877665455689999999999999999865443
No 116
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=27.81 E-value=55 Score=22.29 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+..+...+...++.|.+.|+|+|..+
T Consensus 31 l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 31 LKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred HCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 45677889999999999999999875
No 117
>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=27.50 E-value=1.1e+02 Score=24.31 Aligned_cols=55 Identities=24% Similarity=0.289 Sum_probs=41.6
Q ss_pred hhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC---------CCCCHHHHHHHHHH
Q psy16237 58 VSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS---------FAPSISMIKKCIES 112 (133)
Q Consensus 58 ~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~---------F~p~~~~iK~~IE~ 112 (133)
...+..+|....|+..++.|.......|.+++-.+...... |.-+...+|+||..
T Consensus 235 ~~~~~~~~E~~cD~~vl~~l~~~~~~~Y~~~Ll~~~~~~~~~~~~~~~~~~~~~~~~lk~RI~~ 298 (299)
T PF05569_consen 235 RRRIRRDRELACDEAVLRNLGKEERKAYAETLLKVAKRSQQFKRPPLASSFAFSKSQLKRRIKM 298 (299)
T ss_pred HHHHHHHHHHhhhHHHHHhcCchhHHHHHHHHHHHHHhhcCCCcchhhhhccCChHHHHHHHHh
Confidence 45789999999999999999888888888888666655433 12256677887764
No 118
>PF15479 DUF4639: Domain of unknown function (DUF4639)
Probab=27.19 E-value=85 Score=27.98 Aligned_cols=28 Identities=11% Similarity=0.312 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCCCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTANST 126 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~d~ 126 (133)
++-++..-|.++=.+||=.||.||++..
T Consensus 78 iPfTV~qArdamLqiiewrFLarD~GE~ 105 (576)
T PF15479_consen 78 IPFTVSQARDAMLQIIEWRFLARDEGES 105 (576)
T ss_pred cceeHHHHHHHHHHHhheeeeeccCCCC
Confidence 5558888899999999999999998754
No 119
>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=27.01 E-value=49 Score=24.94 Aligned_cols=30 Identities=13% Similarity=0.256 Sum_probs=25.6
Q ss_pred hcCC-CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 95 QSKS-FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 95 ~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+|.. |.++...+++++..|.+.|+|.|...
T Consensus 30 eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g 60 (231)
T TIGR03337 30 DLGERFNTTRVTIREALQQLEAEGLIYREDR 60 (231)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC
Confidence 3444 88889999999999999999999765
No 120
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=26.54 E-value=56 Score=24.86 Aligned_cols=53 Identities=13% Similarity=0.125 Sum_probs=31.6
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC--CCC-CCceEec
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT--ANS-TDEYSYV 132 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~--~~d-~~~y~Yv 132 (133)
|.-+.-....++-.+|... ...+.+.+-..|..|-++|||.|. ++| +..++|+
T Consensus 50 iL~~L~~~~~itq~eLa~~-------l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~L 105 (185)
T PRK13777 50 ILWIAYHLKGASISEIAKF-------GVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIEL 105 (185)
T ss_pred HHHHHHhCCCcCHHHHHHH-------HCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEE
Confidence 3334444445555554432 234555577799999999999995 334 3455543
No 121
>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=26.41 E-value=49 Score=21.99 Aligned_cols=19 Identities=21% Similarity=0.613 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhhhhhcccc
Q psy16237 103 ISMIKKCIESLIDKNYVER 121 (133)
Q Consensus 103 ~~~iK~~IE~LIekeYl~R 121 (133)
-..++++|++||+.+|...
T Consensus 41 F~S~~Erl~yLv~~~YYe~ 59 (82)
T PF08343_consen 41 FNSLKERLDYLVENDYYEK 59 (82)
T ss_dssp -SSHHHHHHHHHHTTSB-H
T ss_pred cCCHHHHHHHHHHcCcHHH
Confidence 3457899999999999765
No 122
>PRK12423 LexA repressor; Provisional
Probab=26.11 E-value=2.4e+02 Score=21.25 Aligned_cols=27 Identities=26% Similarity=0.445 Sum_probs=22.6
Q ss_pred CC-CCHHHHHHHHHHhhhhhccccCCCC
Q psy16237 99 FA-PSISMIKKCIESLIDKNYVERTANS 125 (133)
Q Consensus 99 F~-p~~~~iK~~IE~LIekeYl~R~~~d 125 (133)
|- .+...+.+.++.|-++|||++.+..
T Consensus 35 ~g~~s~~~v~~~l~~L~~~G~l~~~~~~ 62 (202)
T PRK12423 35 FGFASRSVARKHVQALAEAGLIEVVPNQ 62 (202)
T ss_pred hCCCChHHHHHHHHHHHHCCCEEecCCC
Confidence 55 4778889999999999999997663
No 123
>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=26.00 E-value=1.9e+02 Score=18.56 Aligned_cols=59 Identities=15% Similarity=0.294 Sum_probs=36.9
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV 132 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv 132 (133)
.-+++|-.+.+.+.--+..||+....+. .|.+|-+.|-+-|..| +-+ |-.+....|.|.
T Consensus 5 ~R~~~I~~li~~~~i~sQ~eL~~~L~~~--Gi~vTQaTiSRDLkeL---~~v-Kv~~~~g~~~Y~ 63 (70)
T PF01316_consen 5 KRQELIKELISEHEISSQEELVELLEEE--GIEVTQATISRDLKEL---GAV-KVPDGNGKYRYV 63 (70)
T ss_dssp HHHHHHHHHHHHS---SHHHHHHHHHHT--T-T--HHHHHHHHHHH---T-E-EEECTTSSEEEE
T ss_pred HHHHHHHHHHHHCCcCCHHHHHHHHHHc--CCCcchhHHHHHHHHc---CcE-EeeCCCCCEEEE
Confidence 4567888999999999999999887654 3999988877766655 333 333334678885
No 124
>PF13835 DUF4194: Domain of unknown function (DUF4194)
Probab=25.82 E-value=1.6e+02 Score=21.34 Aligned_cols=49 Identities=14% Similarity=0.210 Sum_probs=38.3
Q ss_pred ccccchHHHHHHHHhcC--C-CCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237 81 KQIRHNALIQEVLSQSK--S-FAPSISMIKKCIESLIDKNYVERTANSTDEY 129 (133)
Q Consensus 81 k~l~h~eL~~ev~~~l~--~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y 129 (133)
-.++..||.+....... . =.|....++..|..|-..++|++.++|.+.|
T Consensus 99 ~~v~~~ei~e~~~~~~~~~~d~~~~~~~~~~~l~~l~~~~ll~~~~~de~r~ 150 (166)
T PF13835_consen 99 VVVTREEIVEKLESFLPESRDEAPFKKRLDAALRRLKRYGLLRRLDGDEDRY 150 (166)
T ss_pred EEEeHHHHHHHHHHHccccccccchHHHHHHHHHHHHHCCCeeccCCCCCEE
Confidence 34678888888777655 3 6788999999999999999999987643444
No 125
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=25.80 E-value=56 Score=25.97 Aligned_cols=39 Identities=26% Similarity=0.424 Sum_probs=25.5
Q ss_pred ccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 81 KQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 81 k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
+..+...|+..... .. ..|.. -=.-||.|++|+||++..
T Consensus 208 ~~~Te~tLl~~Me~--~GIGTpAT--ra~iIe~L~~r~Yi~~~~ 247 (259)
T smart00437 208 ARYTEASLIKLMEK--RGIGRPST--YAEIIETLLDRGYVTKEK 247 (259)
T ss_pred CCCCHHHHHHHHHH--CCCCchhh--HHHHHHHHHhCCcEEeeC
Confidence 34566666655433 23 55533 356799999999999853
No 126
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=25.59 E-value=1.6e+02 Score=30.21 Aligned_cols=57 Identities=12% Similarity=0.109 Sum_probs=41.7
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
.+.-||-..--.+-.+++.+|+..+..++........+|+..|+.+|+.|.|-+-..
T Consensus 318 av~~Ai~hLsEr~a~f~~~dL~~~Al~~~~~~~~~~~~i~~~id~~i~~g~Li~l~~ 374 (1747)
T PRK13709 318 AVTQAIAGLSDRKVQFTYTDLLARTVGILPPENGVIERARAGIDEAISREQLIPLDR 374 (1747)
T ss_pred HHHHHHHhhhhhhhcCcHHHHHHHHHHhccccCCcHHHHHHHHHHHHhcCCeecccc
Confidence 344454444445667899999999988876433337899999999999999865433
No 127
>smart00526 H15 Domain in histone families 1 and 5.
Probab=25.41 E-value=1.5e+02 Score=18.12 Aligned_cols=52 Identities=21% Similarity=0.307 Sum_probs=36.1
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCC--HHHHHHHHHHhhhhhcccc
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPS--ISMIKKCIESLIDKNYVER 121 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~--~~~iK~~IE~LIekeYl~R 121 (133)
.|..||.. ++.++-.+...+...+.+.-. ..|. ...++..+..++++|-|.+
T Consensus 10 mI~eAI~~-l~er~GsS~~aI~kyi~~~~~-~~~~~~~~~l~~~Lk~~v~~G~l~q 63 (66)
T smart00526 10 MITEAISA-LKERKGSSLQAIKKYIEANYK-VLPNNFRSLLKLALKKLVASGKLVQ 63 (66)
T ss_pred HHHHHHHH-cCCCCCCCHHHHHHHHHHhCC-CChHHHHHHHHHHHHHHHhcCceee
Confidence 45666555 688888888888877765411 2222 4678888999999887765
No 128
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=25.38 E-value=1.2e+02 Score=23.76 Aligned_cols=41 Identities=20% Similarity=0.391 Sum_probs=29.4
Q ss_pred cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237 82 QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYS 130 (133)
Q Consensus 82 ~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~ 130 (133)
.++-.||... + -.+.+.+-+-+..|.+.|||+|++++ ..|.
T Consensus 26 ~ls~~eia~~----l---gl~kstv~RlL~tL~~~g~v~~~~~~-~~Y~ 66 (263)
T PRK09834 26 GATVGLLAEL----T---GLHRTTVRRLLETLQEEGYVRRSASD-DSFR 66 (263)
T ss_pred CCCHHHHHHH----H---CcCHHHHHHHHHHHHHCCCEEEecCC-CcEE
Confidence 3666555544 3 36667778899999999999998764 3454
No 129
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.07 E-value=1.4e+02 Score=19.08 Aligned_cols=30 Identities=13% Similarity=0.314 Sum_probs=21.2
Q ss_pred ccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhh
Q psy16237 83 IRHNALIQEVLSQSKSFAPSISMIKKCIESLID 115 (133)
Q Consensus 83 l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIe 115 (133)
|+-.||+.++.+... .+..+++..++.|.+
T Consensus 1 mtk~eli~~ia~~~~---~~~~~v~~vl~~l~~ 30 (90)
T smart00411 1 MTKSELIDAIAEKAG---LSKKDAKAAVDAFLE 30 (90)
T ss_pred CCHHHHHHHHHHHhC---CCHHHHHHHHHHHHH
Confidence 455688888777655 567788888777765
No 130
>PF06794 UPF0270: Uncharacterised protein family (UPF0270); InterPro: IPR010648 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 1Y0N_A.
Probab=24.99 E-value=38 Score=21.98 Aligned_cols=20 Identities=20% Similarity=0.439 Sum_probs=10.7
Q ss_pred HHHHHHhhhhhccccCCCCCC
Q psy16237 107 KKCIESLIDKNYVERTANSTD 127 (133)
Q Consensus 107 K~~IE~LIekeYl~R~~~d~~ 127 (133)
-..++.||+ +|+-|+..|..
T Consensus 10 ~eTL~nLIe-efv~ReGTdyG 29 (70)
T PF06794_consen 10 PETLNNLIE-EFVLREGTDYG 29 (70)
T ss_dssp HHHHHHHHH-HHHH-------
T ss_pred HHHHHHHHH-HHHHccCcccC
Confidence 457888998 99999877643
No 131
>PRK07726 DNA topoisomerase III; Provisional
Probab=24.89 E-value=77 Score=28.66 Aligned_cols=54 Identities=15% Similarity=0.361 Sum_probs=31.9
Q ss_pred HHHHhhhhhhhccc-ccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 67 LYLQAAIVRIMKSR-KQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 67 ~~I~AaIVRIMK~~-k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
..-+|.++..|+.- |.+.-.+| .++...-.. ..|... =.-||.|++|+||.+..
T Consensus 480 ~yTe~tLi~~Me~~~k~v~d~~~-~~~l~e~~GIGTpATr--a~iIe~L~~R~Yi~~~~ 535 (658)
T PRK07726 480 RFTEGTLLSAMENIARFVQDKEL-KKTLKETDGLGTEATR--AGIIEKLFKRGYLEKKG 535 (658)
T ss_pred CcCHHHHHHHHHhhhhhccCHHH-HHhhcccCCCCccccH--HHHHHHHHhCCCEEecC
Confidence 34667777777653 44443333 222222234 555333 56799999999999854
No 132
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=24.54 E-value=1.4e+02 Score=23.24 Aligned_cols=42 Identities=19% Similarity=0.340 Sum_probs=28.2
Q ss_pred cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237 80 RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY 129 (133)
Q Consensus 80 ~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y 129 (133)
.+.++..||. +.+. ...+.+-+-+..|.+.||++|++++ ..|
T Consensus 26 ~~~l~l~eia----~~lg---l~kstv~Rll~tL~~~G~l~~~~~~-~~Y 67 (257)
T PRK15090 26 EREIGITELS----QRVM---MSKSTVYRFLQTMKTLGYVAQEGES-EKY 67 (257)
T ss_pred CCCCCHHHHH----HHHC---cCHHHHHHHHHHHHHCCCEEEcCCC-CcE
Confidence 3456655554 4443 4455567889999999999998654 345
No 133
>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=24.44 E-value=1.3e+02 Score=19.14 Aligned_cols=30 Identities=17% Similarity=0.365 Sum_probs=22.8
Q ss_pred ccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhh
Q psy16237 83 IRHNALIQEVLSQSKSFAPSISMIKKCIESLID 115 (133)
Q Consensus 83 l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIe 115 (133)
|+-.||+..+.+... .+..+++..|+.|.+
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 456788888887775 588888888887765
No 134
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=24.37 E-value=1.9e+02 Score=18.39 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=28.2
Q ss_pred HHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237 93 LSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY 129 (133)
Q Consensus 93 ~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y 129 (133)
+..+..|-.+...++.++-.|-.+|.|++....+..|
T Consensus 27 i~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~ 63 (70)
T PF07848_consen 27 IRLLAAFGVSESAVRTALSRLVRRGWLESERRGRRSY 63 (70)
T ss_dssp HHHHCCTT--HHHHHHHHHHHHHTTSEEEECCCTEEE
T ss_pred HHHHHHcCCChHHHHHHHHHHHHcCceeeeecCccce
Confidence 3445558899999999999999999999987665444
No 135
>PRK00304 hypothetical protein; Provisional
Probab=24.25 E-value=50 Score=21.79 Aligned_cols=18 Identities=22% Similarity=0.549 Sum_probs=14.5
Q ss_pred HHHHHHhhhhhccccCCCC
Q psy16237 107 KKCIESLIDKNYVERTANS 125 (133)
Q Consensus 107 K~~IE~LIekeYl~R~~~d 125 (133)
-..++.||+ +|+-|+..|
T Consensus 10 ~eTL~nLIe-efv~ReGTD 27 (75)
T PRK00304 10 ADTLTRLIE-DFVTRDGTD 27 (75)
T ss_pred HHHHHHHHH-HHHhccCcc
Confidence 357888998 999998765
No 136
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=23.62 E-value=76 Score=21.07 Aligned_cols=29 Identities=17% Similarity=0.177 Sum_probs=25.9
Q ss_pred hcCC-CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 95 QSKS-FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 95 ~l~~-F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
+|+. |..+.+.|.-=+|.|+-+|-++|-+
T Consensus 21 ~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 21 QISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 4555 8899999999999999999999976
No 137
>PRK14724 DNA topoisomerase III; Provisional
Probab=23.20 E-value=96 Score=29.65 Aligned_cols=53 Identities=28% Similarity=0.453 Sum_probs=34.1
Q ss_pred HHHHhhhhhhhccc-ccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 67 LYLQAAIVRIMKSR-KQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 67 ~~I~AaIVRIMK~~-k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
..-+|.++.-|..- |.+.-.+|-.. .+. .. ..|... =.-||.|++++||+|..
T Consensus 508 ryTEatLl~aME~~gk~v~d~el~~~-~~~-~GIGTpATR--A~IIe~L~~r~Yi~~~~ 562 (987)
T PRK14724 508 RYSEATLLGAMESAGKQIDDDELREA-MQE-KGLGTPATR--AAIIEGLLTEKYMLREG 562 (987)
T ss_pred CcCHHHHHHHHHhhhhcccchhhhhh-hhc-CCCCCcccH--HHHHHHHHhCCcEEecC
Confidence 35677778888743 55555555433 222 23 666333 46799999999999864
No 138
>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=23.12 E-value=83 Score=24.02 Aligned_cols=30 Identities=37% Similarity=0.455 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237 103 ISMIKKCIESLIDKNYVERTANSTDEYSYV 132 (133)
Q Consensus 103 ~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv 132 (133)
.+.||.+|..|-++|++-+-..+.+.+-||
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 356789999999999887765544444443
No 139
>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=22.58 E-value=1.6e+02 Score=21.31 Aligned_cols=34 Identities=18% Similarity=0.144 Sum_probs=26.4
Q ss_pred ccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhh
Q psy16237 79 SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLID 115 (133)
Q Consensus 79 ~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIe 115 (133)
...+|+..+|+..+.+... .+..+++..|+.|++
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 3457889999999887754 577888888888776
No 140
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=22.44 E-value=2e+02 Score=29.71 Aligned_cols=58 Identities=21% Similarity=0.147 Sum_probs=42.9
Q ss_pred HHHHhhhhhhhcccccccchHHHHHHHHhcCC--CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 67 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS--FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 67 ~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~--F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
..+..+|-..--.+-.+++.+|+..+..++.. -.++...|+..|+.||..+.|-+-+.
T Consensus 329 ~av~~Ai~~lse~~s~f~~~~L~~~a~~~l~~g~~~~~~~~i~~~id~~i~~g~Li~~~~ 388 (1960)
T TIGR02760 329 HAVEVAIAHLSQYSTQFEYEKLIEEAAKYFTAGNKIIDEIDIKKAIDELIANGQLIPLFT 388 (1960)
T ss_pred HHHHHHHHHhhheeeeccHHHHHHHHHHHhccCcCCCCHHHHHHHHHHHHhCCceecccC
Confidence 34455555555566679999999999987764 34566689999999999998866543
No 141
>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=22.41 E-value=1.5e+02 Score=16.86 Aligned_cols=39 Identities=23% Similarity=0.327 Sum_probs=27.1
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHh
Q psy16237 68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESL 113 (133)
Q Consensus 68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~L 113 (133)
.++-.|++.+...-+++|.+|-.++ -.+.+.+.++|..|
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 3677888999999999998876553 36777778787765
No 142
>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=22.03 E-value=1.6e+02 Score=16.73 Aligned_cols=40 Identities=20% Similarity=0.360 Sum_probs=27.2
Q ss_pred hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccc
Q psy16237 73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVE 120 (133)
Q Consensus 73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~ 120 (133)
|+..+.. +.++..||... +..+.+.+..-+..|.+.|+++
T Consensus 7 Il~~L~~-~~~~~~el~~~-------l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 7 ILKLLSE-GPLTVSELAEE-------LGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHTT-SSEEHHHHHHH-------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHh-CCCchhhHHHh-------ccccchHHHHHHHHHHHCcCee
Confidence 4444444 55665555544 4588889999999999999875
No 143
>COG3177 Fic family protein [Function unknown]
Probab=21.84 E-value=91 Score=25.81 Aligned_cols=34 Identities=12% Similarity=0.182 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTANSTDEYSYV 132 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv 132 (133)
...+.+.+.+.|..|.+.|||++....+..|.|-
T Consensus 314 ~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~~~ 347 (348)
T COG3177 314 LGVSKATATRDLKELLELGILEEVKGRGRSKLYS 347 (348)
T ss_pred hCccHHHHHHHHHHHHhCCCeeecCCCCCceecc
Confidence 4677888899999999999999998876777764
No 144
>PF14217 DUF4327: Domain of unknown function (DUF4327)
Probab=21.83 E-value=93 Score=20.15 Aligned_cols=23 Identities=30% Similarity=0.385 Sum_probs=18.8
Q ss_pred CHHHHHHHHHHhhhhhccccCCC
Q psy16237 102 SISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 102 ~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+...|+.....|+++|.|.|.+.
T Consensus 3 si~~iq~ear~LV~~g~v~r~qp 25 (68)
T PF14217_consen 3 SIDKIQDEARSLVESGVVSRQQP 25 (68)
T ss_pred cHHHHHHHHHHHHHcCCCCccCc
Confidence 45678889999999999999753
No 145
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=21.77 E-value=83 Score=20.06 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=18.5
Q ss_pred CCCCHHHHHHHHHHhhhhhcccc
Q psy16237 99 FAPSISMIKKCIESLIDKNYVER 121 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R 121 (133)
-..+...+++-++.|+++|+|+.
T Consensus 29 ~~L~~~~~~~yL~~L~~~gLI~~ 51 (77)
T PF14947_consen 29 ANLNYSTLKKYLKELEEKGLIKK 51 (77)
T ss_dssp ST--HHHHHHHHHHHHHTTSEEE
T ss_pred hCcCHHHHHHHHHHHHHCcCeeC
Confidence 34678889999999999999966
No 146
>PRK11569 transcriptional repressor IclR; Provisional
Probab=21.72 E-value=1.6e+02 Score=23.23 Aligned_cols=43 Identities=12% Similarity=0.239 Sum_probs=30.1
Q ss_pred ccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237 79 SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY 129 (133)
Q Consensus 79 ~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y 129 (133)
....++..||... +. ...+.+-+-+..|.+.|||+|++++ ..|
T Consensus 40 ~~~~~~lseia~~----lg---lpksTv~RlL~tL~~~G~l~~~~~~-~~Y 82 (274)
T PRK11569 40 SNGSVALTELAQQ----AG---LPNSTTHRLLTTMQQQGFVRQVGEL-GHW 82 (274)
T ss_pred CCCCcCHHHHHHH----HC---cCHHHHHHHHHHHHHCCCEEEcCCC-CeE
Confidence 4566777776654 33 4455567789999999999998664 345
No 147
>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=21.58 E-value=54 Score=20.15 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTAN 124 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~ 124 (133)
+..+++.+-+.+..|-++||+.+++.
T Consensus 32 L~vs~~tvt~ml~~L~~~GlV~~~~y 57 (60)
T PF01325_consen 32 LGVSPPTVTEMLKRLAEKGLVEYEPY 57 (60)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HCCChHHHHHHHHHHHHCCCEEecCC
Confidence 45888888999999999999998653
No 148
>KOG2266|consensus
Probab=21.56 E-value=1.7e+02 Score=26.17 Aligned_cols=50 Identities=18% Similarity=0.309 Sum_probs=37.6
Q ss_pred HHHHhhhhhhhccc--ccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhh
Q psy16237 67 LYLQAAIVRIMKSR--KQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDK 116 (133)
Q Consensus 67 ~~I~AaIVRIMK~~--k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIek 116 (133)
.+|.-+|+.|+|.. .++++.++|..|.....- ..+--.+||..|..||..
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 46778899999986 567788888777766553 344567899999888864
No 149
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=21.52 E-value=81 Score=24.10 Aligned_cols=18 Identities=17% Similarity=0.335 Sum_probs=16.1
Q ss_pred CHHHHHHHHHHhhhhhcc
Q psy16237 102 SISMIKKCIESLIDKNYV 119 (133)
Q Consensus 102 ~~~~iK~~IE~LIekeYl 119 (133)
+...|.++||+||.+|++
T Consensus 77 tdeqI~kQVeYli~~GW~ 94 (176)
T PLN02289 77 TDEELAKEVDYLLRNKWV 94 (176)
T ss_pred CHHHHHHHHHHHHhCCCe
Confidence 899999999999999854
No 150
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=21.41 E-value=83 Score=24.95 Aligned_cols=34 Identities=24% Similarity=0.272 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237 99 FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva 133 (133)
-.|-+. +=..+++|..|||++..++.|..|..++
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 444443 4468999999999999999898888764
No 151
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=21.31 E-value=1.8e+02 Score=18.12 Aligned_cols=49 Identities=12% Similarity=0.246 Sum_probs=38.0
Q ss_pred hhhhhcccc-cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237 73 IVRIMKSRK-QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 123 (133)
Q Consensus 73 IVRIMK~~k-~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~ 123 (133)
|-++++... -++..+|....... .+..+...|..++..|=+.||.+|..
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~--g~~~se~avRrrLr~me~~Glt~~~g 52 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLR--GEELSEEAVRRRLRAMERDGLTRKVG 52 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhc--ChhhhHHHHHHHHHHHHHCCCccccC
Confidence 556666664 48888888775433 38899999999999999999988754
No 152
>PRK11032 hypothetical protein; Provisional
Probab=20.78 E-value=95 Score=23.29 Aligned_cols=29 Identities=14% Similarity=0.117 Sum_probs=16.7
Q ss_pred cchHHHHHHHHhcCCCCCCHHHHHHHHHHhhh
Q psy16237 84 RHNALIQEVLSQSKSFAPSISMIKKCIESLID 115 (133)
Q Consensus 84 ~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIe 115 (133)
.|+.|+..|.+.|+. ....+++.|+.-.+
T Consensus 7 ~Y~~ll~~v~~~l~~---~~~~l~~~ve~a~~ 35 (160)
T PRK11032 7 YYRELVASLTERLRN---GERDIDALVESARK 35 (160)
T ss_pred HHHHHHHHHHHHHHh---CHHHHHHHHHHHHH
Confidence 477777777777763 22345555544433
No 153
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=20.76 E-value=87 Score=23.29 Aligned_cols=43 Identities=21% Similarity=0.200 Sum_probs=27.1
Q ss_pred ccccccchHHHHHHHHh-cCC---CCCCHHHHHHHH-HHhhhhhcccc
Q psy16237 79 SRKQIRHNALIQEVLSQ-SKS---FAPSISMIKKCI-ESLIDKNYVER 121 (133)
Q Consensus 79 ~~k~l~h~eL~~ev~~~-l~~---F~p~~~~iK~~I-E~LIekeYl~R 121 (133)
+...++.++|+...... +.. -++-..++++.| +.|+.++||.|
T Consensus 117 ~g~~i~E~~L~~~L~~lgi~~~~~~~~~g~~~~~~i~~~~vkq~YL~~ 164 (195)
T PF01454_consen 117 SGNSISEDDLWKFLRRLGIDEDEKHPILGMDIKKLILKEFVKQGYLVR 164 (195)
T ss_dssp CTT-EEHHHHHHHHHHTT--TTS-BTTTB--HHHHHHCHHHHCTSE-E
T ss_pred cCCccCHHHHHHHHHhcCCCccccCccCCCCHHHHHHHHHHHhcCHHh
Confidence 36799999999876643 110 111223788888 99999999966
No 154
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=20.62 E-value=2.9e+02 Score=20.17 Aligned_cols=54 Identities=11% Similarity=0.175 Sum_probs=43.7
Q ss_pred HHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccC
Q psy16237 67 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERT 122 (133)
Q Consensus 67 ~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~ 122 (133)
..+.-+|..++..+ +.=-+|..++.+.... |.|+...|=..+..|-+.|||...
T Consensus 42 ~~~~l~IL~lL~~~--~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~ 96 (135)
T PRK09416 42 EDILLAILQLLMNE--KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSS 96 (135)
T ss_pred ccHHHHHHHHHhCC--CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEe
Confidence 45667778877665 5556888888876555 899999999999999999999874
No 155
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=20.59 E-value=90 Score=22.95 Aligned_cols=20 Identities=25% Similarity=0.255 Sum_probs=17.4
Q ss_pred CCCHHHHHHHHHHhhhhhcc
Q psy16237 100 APSISMIKKCIESLIDKNYV 119 (133)
Q Consensus 100 ~p~~~~iK~~IE~LIekeYl 119 (133)
+.|...|.++|+.+|.+|+.
T Consensus 13 pLTdeqI~kQI~Y~i~~GW~ 32 (138)
T CHL00130 13 DLTDQQIEKQIQYAISKGWA 32 (138)
T ss_pred CCCHHHHHHHHHHHHhcCCe
Confidence 34899999999999999974
No 156
>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=20.30 E-value=93 Score=19.94 Aligned_cols=17 Identities=29% Similarity=0.466 Sum_probs=15.6
Q ss_pred CCCCHHHHHHHHHHhhh
Q psy16237 99 FAPSISMIKKCIESLID 115 (133)
Q Consensus 99 F~p~~~~iK~~IE~LIe 115 (133)
|.+....++.+|+.||+
T Consensus 55 ~~~~~~~vr~NL~~Lie 71 (77)
T PF12358_consen 55 FTNENDPVRKNLEFLIE 71 (77)
T ss_pred ccCCChHHHHHHHHHHH
Confidence 88888899999999997
No 157
>PF06002 CST-I: Alpha-2,3-sialyltransferase (CST-I); InterPro: IPR009251 This entry represents several alpha-2,3-sialyltransferase (2.4.99 from EC) proteins, most of which are found in the food-borne pathogen Campylobacter jejuni. Sialyltransferases transfer a sialic acid moiety from cytidine-5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to terminal positions of various key glycoconjugates, which play critical roles in cell recognition and adherence []. The structure of Cst-II alpha-2,3-sialyltransferase from C. jejuni consists of a 3-layer alpha/beta/alpha topology. Cst-II catalytic mechanism involves an essential histidine (general base) and two tyrosine residues (coordination of the phosphate leaving group) to carry out substrate binding and glycosyl transfer. ; PDB: 2X63_A 2X61_B 1RO7_B 2WQQ_A 2X62_B 1RO8_A 2DRJ_A 2P56_A 2P2V_A.
Probab=20.18 E-value=33 Score=28.26 Aligned_cols=68 Identities=13% Similarity=0.029 Sum_probs=35.5
Q ss_pred CCCCCCCCCcceeeccccCCCCCeEEEccCCCCCce----e---EEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhh
Q psy16237 3 TDNSMDGSCPGYIISVKELTEDTEIRLNLGYNNKRT----K---LKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVR 75 (133)
Q Consensus 3 ~~~~~s~~~~~~~il~~~~~~~d~f~~N~~F~~k~~----k---iki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVR 75 (133)
+|||.|+..--|+++ .++.|+|+.|.-|-..+. + |-.++.. -.++-.|...+.+.-.+.++..+..
T Consensus 7 ~gngps~~~~~~~~~---~~~~~~fr~n~fy~e~~~~lg~~~~~VFFn~~v----f~~Qy~T~~~Li~n~EY~~e~i~cs 79 (291)
T PF06002_consen 7 AGNGPSLKEIDYSLL---PKDFDVFRCNQFYFEDKYYLGKKVKAVFFNPCV----FFEQYYTAKQLIQNGEYEIENIYCS 79 (291)
T ss_dssp E-SSGGGGC--GGGS----SSEEEEEETTGGG-SBETT-SEECEEEE-GGG----HHHHHHHHHHHHHTTS-EECEEEE-
T ss_pred eCCCCchhhcchhhC---CCcccEEEecceecchhhhcccceeEEEechHH----HHHHHHHHHHHHhcCceeeeeeEEe
Confidence 689999999999998 667789999998754322 1 1122111 1233445555655555666554444
Q ss_pred hh
Q psy16237 76 IM 77 (133)
Q Consensus 76 IM 77 (133)
.+
T Consensus 80 ~~ 81 (291)
T PF06002_consen 80 TI 81 (291)
T ss_dssp --
T ss_pred cc
Confidence 43
Done!