Query 042785
Match_columns 604
No_of_seqs 146 out of 264
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:26:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042785hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4652 HORMA domain [Chromati 100.0 5.8E-40 1.2E-44 335.4 18.0 222 10-248 6-236 (324)
2 PF02301 HORMA: HORMA domain; 100.0 2.4E-38 5.3E-43 304.8 13.5 190 12-214 1-208 (208)
3 KOG3285 Spindle assembly check 100.0 6E-30 1.3E-34 244.7 12.3 188 7-223 6-200 (203)
4 KOG3186 Mitotic spindle checkp 98.7 1.9E-07 4.2E-12 90.6 11.5 172 19-221 9-196 (202)
5 PF09397 Ftsk_gamma: Ftsk gamm 96.7 0.0026 5.6E-08 53.3 4.8 54 382-437 3-56 (65)
6 smart00843 Ftsk_gamma This dom 95.4 0.027 5.8E-07 47.2 4.7 53 382-436 2-54 (63)
7 PF01325 Fe_dep_repress: Iron 92.8 0.16 3.4E-06 41.6 4.1 49 385-435 7-56 (60)
8 smart00347 HTH_MARR helix_turn 92.5 0.33 7.1E-06 40.7 5.8 75 379-459 7-81 (101)
9 PF01047 MarR: MarR family; I 92.5 0.21 4.6E-06 39.2 4.4 51 382-437 3-53 (59)
10 COG1846 MarR Transcriptional r 90.9 0.43 9.4E-06 41.0 5.0 76 380-461 20-95 (126)
11 PRK03902 manganese transport t 88.6 0.46 1E-05 44.1 3.6 45 387-433 9-54 (142)
12 PF13463 HTH_27: Winged helix 87.7 1 2.2E-05 36.0 4.5 53 384-440 5-57 (68)
13 PRK11512 DNA-binding transcrip 87.5 0.98 2.1E-05 41.8 5.0 75 378-458 36-110 (144)
14 PF12802 MarR_2: MarR family; 86.5 1 2.3E-05 35.3 4.0 52 382-436 5-56 (62)
15 TIGR01889 Staph_reg_Sar staphy 86.4 1.5 3.1E-05 39.2 5.3 80 379-461 22-102 (109)
16 smart00418 HTH_ARSR helix_turn 85.7 0.89 1.9E-05 34.6 3.1 54 397-456 8-61 (66)
17 PRK03573 transcriptional regul 85.5 1.7 3.6E-05 40.1 5.4 76 378-458 27-102 (144)
18 PF13412 HTH_24: Winged helix- 85.3 1.4 3E-05 33.6 4.0 34 397-432 15-48 (48)
19 TIGR02702 SufR_cyano iron-sulf 84.1 0.85 1.8E-05 44.9 3.0 52 398-451 14-66 (203)
20 TIGR02337 HpaR homoprotocatech 83.8 2.3 5.1E-05 38.0 5.4 74 380-459 26-99 (118)
21 PRK11014 transcriptional repre 83.5 1.6 3.5E-05 40.7 4.4 64 396-462 22-85 (141)
22 smart00345 HTH_GNTR helix_turn 82.9 1.8 4E-05 33.1 3.8 37 396-434 16-53 (60)
23 PRK13777 transcriptional regul 82.1 2.6 5.7E-05 41.8 5.5 79 377-461 40-118 (185)
24 smart00419 HTH_CRP helix_turn_ 81.4 1.7 3.8E-05 32.1 3.1 34 399-434 8-41 (48)
25 PF01978 TrmB: Sugar-specific 81.3 1.6 3.5E-05 35.5 3.1 43 393-437 16-58 (68)
26 PRK11050 manganese transport r 81.2 1.7 3.6E-05 41.4 3.6 51 384-436 35-86 (152)
27 PRK09333 30S ribosomal protein 79.0 3.4 7.3E-05 40.2 4.9 67 375-445 40-121 (150)
28 cd00090 HTH_ARSR Arsenical Res 78.8 5.3 0.00011 31.0 5.2 47 385-437 10-56 (78)
29 PRK10870 transcriptional repre 78.5 4.4 9.6E-05 39.4 5.7 79 379-461 52-130 (176)
30 COG1321 TroR Mn-dependent tran 77.5 2.5 5.4E-05 40.8 3.6 51 384-436 8-59 (154)
31 TIGR02698 CopY_TcrY copper tra 77.3 5.9 0.00013 37.0 5.9 74 383-461 5-82 (130)
32 smart00420 HTH_DEOR helix_turn 77.2 2.8 6E-05 31.3 3.1 37 398-436 13-49 (53)
33 PF10033 ATG13: Autophagy-rela 76.7 70 0.0015 32.7 13.9 84 133-223 131-228 (233)
34 PF07855 DUF1649: Protein of u 76.3 25 0.00055 34.2 10.1 72 18-90 8-94 (163)
35 PF01022 HTH_5: Bacterial regu 76.0 3.7 8.1E-05 31.5 3.5 33 398-432 14-46 (47)
36 PF00392 GntR: Bacterial regul 75.2 3.4 7.4E-05 33.4 3.3 40 396-437 20-60 (64)
37 PF13601 HTH_34: Winged helix 74.5 7.1 0.00015 33.6 5.2 63 397-461 12-74 (80)
38 cd07377 WHTH_GntR Winged helix 74.3 3 6.5E-05 32.5 2.7 33 400-434 26-58 (66)
39 PRK10263 DNA translocase FtsK; 74.2 4 8.7E-05 51.0 4.9 51 383-435 1291-1341(1355)
40 PF02082 Rrf2: Transcriptional 74.1 4.4 9.5E-05 34.5 3.8 40 399-440 25-64 (83)
41 PRK14165 winged helix-turn-hel 72.8 6.4 0.00014 40.2 5.3 67 384-456 3-72 (217)
42 PF03965 Penicillinase_R: Peni 72.4 8.8 0.00019 34.6 5.6 64 384-453 5-71 (115)
43 cd00092 HTH_CRP helix_turn_hel 70.9 4.1 8.9E-05 32.2 2.8 36 398-435 24-59 (67)
44 TIGR02944 suf_reg_Xantho FeS a 70.6 9.8 0.00021 34.7 5.5 64 397-463 23-86 (130)
45 smart00346 HTH_ICLR helix_turn 68.4 4.5 9.8E-05 34.0 2.7 35 398-434 19-53 (91)
46 TIGR00738 rrf2_super rrf2 fami 64.5 10 0.00023 34.2 4.4 34 399-434 25-58 (132)
47 PF12793 SgrR_N: Sugar transpo 64.1 20 0.00044 33.1 6.2 76 387-464 5-85 (115)
48 PF09012 FeoC: FeoC like trans 62.3 6.6 0.00014 32.5 2.5 35 398-434 13-47 (69)
49 PF13730 HTH_36: Helix-turn-he 61.6 11 0.00025 29.2 3.6 32 398-431 24-55 (55)
50 TIGR03338 phnR_burk phosphonat 61.2 15 0.00032 35.7 5.1 63 396-462 31-94 (212)
51 smart00529 HTH_DTXR Helix-turn 61.2 7.4 0.00016 33.2 2.7 33 403-437 3-35 (96)
52 TIGR01884 cas_HTH CRISPR locus 60.2 11 0.00025 37.1 4.1 50 382-436 143-192 (203)
53 PF12840 HTH_20: Helix-turn-he 60.0 11 0.00023 30.3 3.2 39 396-436 21-59 (61)
54 TIGR00498 lexA SOS regulatory 59.6 14 0.0003 36.0 4.6 62 382-445 6-70 (199)
55 PF03551 PadR: Transcriptional 58.7 17 0.00036 30.3 4.3 53 404-456 18-73 (75)
56 PF04703 FaeA: FaeA-like prote 57.3 16 0.00034 30.6 3.9 49 386-442 7-55 (62)
57 smart00550 Zalpha Z-DNA-bindin 57.2 10 0.00022 31.5 2.8 35 400-436 23-57 (68)
58 PRK10225 DNA-binding transcrip 56.6 15 0.00032 37.1 4.3 64 396-463 29-108 (257)
59 PRK05638 threonine synthase; V 56.0 13 0.00028 41.1 4.1 57 398-457 383-439 (442)
60 PF07848 PaaX: PaaX-like prote 55.9 16 0.00034 31.2 3.7 40 405-450 29-68 (70)
61 TIGR01610 phage_O_Nterm phage 55.1 11 0.00025 33.1 2.9 36 397-434 45-80 (95)
62 PF03297 Ribosomal_S25: S25 ri 54.9 18 0.0004 33.3 4.2 49 384-434 44-92 (105)
63 PF08461 HTH_12: Ribonuclease 53.5 13 0.00028 31.0 2.8 41 396-436 13-53 (66)
64 PRK09464 pdhR transcriptional 53.3 20 0.00042 36.1 4.6 64 396-463 30-110 (254)
65 PRK09334 30S ribosomal protein 50.4 25 0.00055 31.4 4.2 48 384-433 26-73 (86)
66 PRK11920 rirA iron-responsive 50.2 33 0.00072 32.8 5.4 65 396-463 21-85 (153)
67 TIGR00122 birA_repr_reg BirA b 49.9 29 0.00062 28.3 4.3 43 397-443 11-53 (69)
68 COG1725 Predicted transcriptio 49.9 25 0.00054 33.4 4.4 57 401-461 37-96 (125)
69 PF13545 HTH_Crp_2: Crp-like h 48.8 31 0.00067 28.1 4.3 32 400-433 29-60 (76)
70 PF09339 HTH_IclR: IclR helix- 47.8 19 0.00042 28.0 2.8 32 400-433 19-50 (52)
71 PRK03837 transcriptional regul 47.6 28 0.00061 34.4 4.6 44 398-445 35-79 (241)
72 PRK09954 putative kinase; Prov 47.4 21 0.00046 37.7 4.0 33 398-432 16-48 (362)
73 PRK09990 DNA-binding transcrip 46.1 30 0.00065 34.7 4.6 64 396-463 27-107 (251)
74 TIGR02277 PaaX_trns_reg phenyl 45.3 22 0.00047 37.4 3.6 48 405-458 26-73 (280)
75 PTZ00095 40S ribosomal protein 43.9 38 0.00082 33.8 4.7 59 375-434 64-138 (169)
76 PF08279 HTH_11: HTH domain; 43.5 22 0.00049 27.5 2.6 30 398-429 14-43 (55)
77 TIGR02010 IscR iron-sulfur clu 42.8 33 0.00071 31.8 4.0 62 398-462 24-85 (135)
78 COG2238 RPS19A Ribosomal prote 41.9 47 0.001 32.4 4.9 61 375-435 40-115 (147)
79 smart00344 HTH_ASNC helix_turn 40.2 38 0.00082 29.5 3.8 73 384-461 5-85 (108)
80 PRK11523 DNA-binding transcrip 39.8 38 0.00083 34.1 4.3 64 396-463 28-107 (253)
81 PRK06266 transcription initiat 39.2 51 0.0011 32.6 4.9 39 398-438 35-73 (178)
82 PF09114 MotA_activ: Transcrip 38.9 39 0.00083 30.8 3.6 49 389-437 20-68 (96)
83 PF08220 HTH_DeoR: DeoR-like h 38.9 29 0.00063 27.9 2.6 36 396-433 11-46 (57)
84 PF14394 DUF4423: Domain of un 38.6 37 0.00081 33.3 3.8 50 387-436 25-76 (171)
85 PRK11414 colanic acid/biofilm 37.8 48 0.001 32.7 4.5 60 398-463 33-95 (221)
86 COG1339 Transcriptional regula 37.2 22 0.00047 36.5 2.0 39 398-438 18-56 (214)
87 COG1522 Lrp Transcriptional re 36.6 44 0.00095 30.7 3.8 41 400-442 23-67 (154)
88 TIGR02325 C_P_lyase_phnF phosp 35.0 31 0.00068 34.0 2.7 40 401-444 34-73 (238)
89 PRK12423 LexA repressor; Provi 34.5 36 0.00078 33.7 3.1 45 401-446 27-71 (202)
90 TIGR02018 his_ut_repres histid 34.2 33 0.00071 34.1 2.7 40 401-444 27-66 (230)
91 PHA00738 putative HTH transcri 34.2 39 0.00084 31.5 3.0 49 399-452 26-74 (108)
92 PRK04984 fatty acid metabolism 33.2 62 0.0013 32.1 4.5 43 398-444 29-72 (239)
93 PRK14136 recX recombination re 33.0 27 0.00058 37.8 2.0 78 375-453 153-240 (309)
94 PRK15090 DNA-binding transcrip 32.9 24 0.00053 35.8 1.6 45 399-445 28-75 (257)
95 PRK11534 DNA-binding transcrip 32.4 69 0.0015 31.5 4.7 60 398-463 29-91 (224)
96 TIGR02812 fadR_gamma fatty aci 31.8 68 0.0015 31.8 4.5 46 396-445 26-72 (235)
97 KOG3874 Uncharacterized conser 31.3 3.6E+02 0.0078 30.7 10.1 115 66-223 64-191 (504)
98 TIGR03433 padR_acidobact trans 30.6 65 0.0014 28.5 3.7 23 412-434 36-58 (100)
99 PRK00215 LexA repressor; Valid 30.5 70 0.0015 31.3 4.3 52 384-437 6-60 (205)
100 TIGR02404 trehalos_R_Bsub treh 30.1 42 0.00091 33.3 2.7 31 402-434 27-57 (233)
101 PRK10141 DNA-binding transcrip 29.4 53 0.0011 30.6 3.0 44 399-447 30-73 (117)
102 COG3177 Fic family protein [Fu 29.3 50 0.0011 35.6 3.3 47 396-444 301-347 (348)
103 PRK11402 DNA-binding transcrip 29.2 41 0.00089 33.6 2.5 43 401-447 35-77 (241)
104 COG3682 Predicted transcriptio 29.1 72 0.0016 30.3 3.9 61 384-450 8-70 (123)
105 PRK10421 DNA-binding transcrip 28.9 74 0.0016 32.1 4.3 46 396-445 22-68 (253)
106 PRK10079 phosphonate metabolis 28.2 46 0.00099 33.4 2.6 41 401-445 37-77 (241)
107 PRK14999 histidine utilization 28.0 48 0.001 33.2 2.7 33 401-435 38-70 (241)
108 COG1733 Predicted transcriptio 27.7 1.2E+02 0.0026 28.2 5.0 67 391-460 29-97 (120)
109 cd07153 Fur_like Ferric uptake 27.2 69 0.0015 28.3 3.3 45 388-434 7-54 (116)
110 COG1802 GntR Transcriptional r 27.0 81 0.0017 31.3 4.1 63 396-462 36-99 (230)
111 PF01726 LexA_DNA_bind: LexA D 26.8 57 0.0012 27.3 2.5 36 401-437 27-62 (65)
112 PRK13626 transcriptional regul 26.8 1.4E+02 0.0031 33.8 6.5 75 387-463 9-88 (552)
113 PF10007 DUF2250: Uncharacteri 26.3 88 0.0019 28.3 3.8 54 384-439 6-59 (92)
114 COG1654 BirA Biotin operon rep 26.2 76 0.0016 27.9 3.3 50 391-443 11-60 (79)
115 PF08784 RPA_C: Replication pr 26.2 61 0.0013 28.5 2.7 32 399-432 65-96 (102)
116 COG0640 ArsR Predicted transcr 25.7 1.4E+02 0.0031 23.9 4.7 53 398-456 38-90 (110)
117 PF01638 HxlR: HxlR-like helix 25.6 1.2E+02 0.0026 26.2 4.4 52 398-451 17-68 (90)
118 COG2345 Predicted transcriptio 25.3 56 0.0012 33.7 2.7 52 398-451 24-76 (218)
119 PF14947 HTH_45: Winged helix- 24.6 1.7E+02 0.0037 24.8 5.1 33 397-431 17-49 (77)
120 PRK09764 DNA-binding transcrip 24.0 63 0.0014 32.4 2.7 40 401-444 31-70 (240)
121 PRK09834 DNA-binding transcrip 23.6 51 0.0011 33.7 2.1 42 400-443 27-71 (263)
122 PRK04172 pheS phenylalanyl-tRN 23.5 71 0.0015 36.1 3.3 51 381-436 5-55 (489)
123 TIGR00373 conserved hypothetic 23.5 95 0.0021 30.1 3.7 42 386-432 18-59 (158)
124 PF01090 Ribosomal_S19e: Ribos 23.5 1.2E+02 0.0027 29.4 4.4 61 375-435 39-114 (139)
125 PF02002 TFIIE_alpha: TFIIE al 23.3 1E+02 0.0022 27.3 3.6 43 388-435 19-61 (105)
126 PRK15481 transcriptional regul 22.8 68 0.0015 34.7 2.9 43 397-443 26-69 (431)
127 TIGR00635 ruvB Holliday juncti 22.8 1.1E+02 0.0023 31.4 4.2 58 378-437 234-292 (305)
128 PRK11169 leucine-responsive tr 22.1 70 0.0015 30.6 2.5 55 384-443 16-74 (164)
129 smart00351 PAX Paired Box doma 22.0 3.1E+02 0.0067 25.3 6.7 50 380-435 18-67 (125)
130 PRK12911 bifunctional preprote 21.5 62 0.0013 41.2 2.5 41 384-428 13-53 (1403)
131 PRK06474 hypothetical protein; 21.5 80 0.0017 31.0 2.8 41 399-440 26-66 (178)
132 PRK10857 DNA-binding transcrip 21.4 1.2E+02 0.0025 29.6 3.9 63 398-463 24-86 (164)
133 smart00753 PAM PCI/PINT associ 21.4 1.9E+02 0.004 24.3 4.7 51 398-450 23-73 (88)
134 smart00088 PINT motif in prote 21.4 1.9E+02 0.004 24.3 4.7 51 398-450 23-73 (88)
135 COG4901 Ribosomal protein S25 21.4 1.5E+02 0.0033 27.7 4.3 57 381-439 41-98 (107)
136 PF05158 RNA_pol_Rpc34: RNA po 20.8 3.2E+02 0.007 29.6 7.4 124 302-443 6-143 (327)
137 PF04492 Phage_rep_O: Bacterio 20.2 1E+02 0.0022 28.0 3.0 45 395-442 50-94 (100)
No 1
>KOG4652 consensus HORMA domain [Chromatin structure and dynamics]
Probab=100.00 E-value=5.8e-40 Score=335.37 Aligned_cols=222 Identities=30% Similarity=0.468 Sum_probs=180.7
Q ss_pred hccHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCcccccchhhhHhhcCCC---------ChhHHHHHHHHhcccceEE
Q 042785 10 EITEQDSLLLTRNLLRIAIFNISYIRGLFPENYFNDKSVPALEMKIKKLMPM---------DAESRVYDALQKKYLKTLL 80 (604)
Q Consensus 10 ~ITeqQSl~lVk~LL~vAISsIlYLRGLFPEe~F~dr~v~gLsLKIKkLlp~---------d~EsgVfDALeKgYLK~Lv 80 (604)
--+++||+.||+++|++||++|+|.|||||++||++++++++.+..+.+++. +.+.|++|||.+||||++.
T Consensus 6 ~~~e~~Sl~f~~rll~~ais~Ilr~Rgi~pe~yf~~~~v~~~~l~~~~~~~~~a~~~~li~~l~kg~~dai~~k~Lk~ls 85 (324)
T KOG4652|consen 6 LENEKQSLEFMTRLLYVAISTILRERGIFPEEYFKDRYVDGNLLVMTLLRRQDAPEGRLVSWLEKGVHDAIRQKLLKKLS 85 (324)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHhcccchHHhcccccccchhhhhhhhccCCccccchHHHHHHHHHHHHHHHHHhheE
Confidence 3468999999999999999999999999999999999999944322333332 2457899999999999999
Q ss_pred EEEEecCCCceeEEEEEEEEeecCCCCceeEEEeecCCcccCcccccccccccCHHHHHHHHHHHHHHHHHHhhhcCCCC
Q 042785 81 FCVCEAVEGPMIEEYAFSFSYSDSDSQEISMNINRTGNKKKGGTFKCNTTTEITTTQMRSSACKMVRTLVQLMRTLDRMP 160 (604)
Q Consensus 81 LvIy~~~ddpVIEsYtFsFsYs~~gg~eVsm~l~stGnkk~~~t~~~~~~s~~Tl~qIRkqI~~LIRqLi~Ltq~L~pLP 160 (604)
|+|++.++.+.||+|.|+|.|.++|+..+.|+.+-+|++... ++ ........+|++.+.|||+++.+++.|+|||
T Consensus 86 lvi~~~~d~~~IE~yifsF~Y~e~g~v~~~in~~~n~~s~~~--~e---~s~l~~ddtrr~~~~lir~~~i~~q~LePLP 160 (324)
T KOG4652|consen 86 LVITESEDPEDIEVYIFSFVYDEEGSVSARINYGINGQSSKA--FE---LSQLSMDDTRRQFAKLIRKLHICTQLLEPLP 160 (324)
T ss_pred EEEecCCCCcceeEEEEEEEecCCCceeEEEecCCCCCcCch--hh---hhhhhhHHHHHHHHHHHHHHHHHHHhccCcc
Confidence 999999977788999999999999875555554433332211 11 1234566699999999999999999999999
Q ss_pred cceeEEEEEEEecCCCCCCCCCCCcccCCccCCCCCCCCCCceeEeeeecCCCeeEEEEEEEecCCccccCCcccCCccc
Q 042785 161 EERTILMKLFYYDDVTPVDYEPPFFRCCSEEEAHNPWTKNPLKMEVGNVNSKHFVLALKVKSVLDPCEDENDDMQDDEVS 240 (604)
Q Consensus 161 deR~lsmKLlYyDDvTP~DYEPPGFk~asd~e~~y~~~knp~kv~LGs~sTghH~V~LkV~Svldp~eden~~~~~~~~s 240 (604)
.+..++|+|.| +|.+|+||+||||++++ ..+|.|+.||+.++||.|+|+||++.++|+| |+++.+++.+.
T Consensus 161 ~~~~~~~rl~Y-~e~~ppDyqP~gFkd~~--~~~y~~p~~p~~~~IG~v~~~hH~~~~kv~s------d~~d~~~~~~~- 230 (324)
T KOG4652|consen 161 QGLILSMRLYY-TERVPPDYQPEGFKDST--RAFYTLPVNPEQINIGAVSTPHHKGFVKVLS------DATDSMEKAER- 230 (324)
T ss_pred chhhhhheeee-cccCCccCCCcccccCc--cceeecCCCccceeeccccCccceeEEEEec------ccchhhhhhcc-
Confidence 97777776655 56799999999999986 4789999999999999999999999999999 77777777764
Q ss_pred cCCCcccc
Q 042785 241 LGADSVQR 248 (604)
Q Consensus 241 ~~~~~~~~ 248 (604)
++..+|
T Consensus 231 --~d~~~~ 236 (324)
T KOG4652|consen 231 --TDKISD 236 (324)
T ss_pred --cccccc
Confidence 555553
No 2
>PF02301 HORMA: HORMA domain; InterPro: IPR003511 The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. Hop1 is a meiosis-specific protein, Rev7 is required for DNA damage induced mutagenesis, and MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity [, ].; GO: 0007067 mitosis; PDB: 3ABD_B 3ABE_C 4AEZ_H 2V64_A 2VFX_A 1GO4_D 2QYF_C 3GMH_B 1KLQ_A 1S2H_A ....
Probab=100.00 E-value=2.4e-38 Score=304.76 Aligned_cols=190 Identities=36% Similarity=0.649 Sum_probs=145.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCcccccchhhhHhhcCCC-C---------hhHHHHHHHHhcccceEEE
Q 042785 12 TEQDSLLLTRNLLRIAIFNISYIRGLFPENYFNDKSVPALEMKIKKLMPM-D---------AESRVYDALQKKYLKTLLF 81 (604)
Q Consensus 12 TeqQSl~lVk~LL~vAISsIlYLRGLFPEe~F~dr~v~gLsLKIKkLlp~-d---------~EsgVfDALeKgYLK~LvL 81 (604)
|++||+.+|++||.+||++|+|+|||||+++|.+++++++.+ ++|.++ . .+.+|+|||++|||++|+|
T Consensus 1 t~~qS~~~v~~~L~~~is~Ily~R~lyP~~~F~~~~~~~~~~--k~l~~~~~~~~~~l~~~i~~~v~dai~k~~L~~v~l 78 (208)
T PF02301_consen 1 TEQQSLELVKEFLEVAISQILYLRGLYPEDCFEDRRFYGLKL--KVLVPNYSSRAPQLIDYIEKGVFDAIEKGYLKKVVL 78 (208)
T ss_dssp EHHHHHHHHHHHHHHHHHHHHHHTTSS-GGGEEEEEETTEEE-------TEEE--HHHHHHHHHHHHHHHHTTSEEEEEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhccCCHHHCcEEEecCccc--cccccccCCCcHHHHHHHHhhHHHHHhhCcceEEEE
Confidence 789999999999999999999999999999999999998865 444443 1 3469999999999999999
Q ss_pred EEEec---CCCceeEEEEEEEEeecCCCCc----eeEEEeecCCcccCcccccccccccCHHHHHHHHHHHHHHHHHHhh
Q 042785 82 CVCEA---VEGPMIEEYAFSFSYSDSDSQE----ISMNINRTGNKKKGGTFKCNTTTEITTTQMRSSACKMVRTLVQLMR 154 (604)
Q Consensus 82 vIy~~---~ddpVIEsYtFsFsYs~~gg~e----Vsm~l~stGnkk~~~t~~~~~~s~~Tl~qIRkqI~~LIRqLi~Ltq 154 (604)
+||++ .++.+||+|+|+|+|...++.. ..+.+...+ ......+..+++.+++++||+|+.+++
T Consensus 79 ~I~~~d~~~~~~~lE~y~F~~~y~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~lr~l~~~~~ 148 (208)
T PF02301_consen 79 VIYDDDPPKSNEVLERYTFSFSYFPDGGPMSPEGSSISISNNT----------SEIDPITLDEVQEQLRALLRKLISSTQ 148 (208)
T ss_dssp EEE----ETTTCEEEEEEEEEEE-TTGGGTSSC--------------------HHHCSSCHHHHHHHHHHHHHHHHHHHC
T ss_pred EEEecccCCCCceeEEEEEEEEecCCCCccccccccccccccc----------ccccCCCHHHHHHHHHHHHHHHHHHhc
Confidence 99976 2345999999999998764321 111111100 011245789999999999999999999
Q ss_pred hcCCCCcceeEEEEEEEecCCCCCCCCCCCcccCCcc-CCCCCCCCCCceeEeeeecCCCe
Q 042785 155 TLDRMPEERTILMKLFYYDDVTPVDYEPPFFRCCSEE-EAHNPWTKNPLKMEVGNVNSKHF 214 (604)
Q Consensus 155 ~L~pLPdeR~lsmKLlYyDDvTP~DYEPPGFk~asd~-e~~y~~~knp~kv~LGs~sTghH 214 (604)
.|++||++++++|+|+||++ ||+||+||||.++.+. ...+.|+.+|..+.+|+|+||||
T Consensus 149 ~L~~LP~~~~~~~~l~~~~~-tp~dy~pp~f~~~~~~~~~~~~~~~~~~~~~vg~v~t~~H 208 (208)
T PF02301_consen 149 SLPPLPDERTLTFKLLYYDD-TPEDYEPPGFEAAEEATSFPLIFDEEPERVSVGSVSTGHH 208 (208)
T ss_dssp TSSS--TTSSEEEEEEEEES--ETTSCSST-TEEES--STEEESSCSEEEEEEEEEEESSE
T ss_pred cCCCccCCceEEEEEEEEeC-CCccccCCCCCCcccccccccccccceEEEEEeeeeCCCC
Confidence 99999999999999999988 9999999999998641 22345788999999999999999
No 3
>KOG3285 consensus Spindle assembly checkpoint protein [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=99.96 E-value=6e-30 Score=244.68 Aligned_cols=188 Identities=19% Similarity=0.306 Sum_probs=151.8
Q ss_pred hhhhccHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCcccccchhh------hHhhcCCCChhHHHHHHHHhcccceEE
Q 042785 7 KEAEITEQDSLLLTRNLLRIAIFNISYIRGLFPENYFNDKSVPALEM------KIKKLMPMDAESRVYDALQKKYLKTLL 80 (604)
Q Consensus 7 ~~~~ITeqQSl~lVk~LL~vAISsIlYLRGLFPEe~F~dr~v~gLsL------KIKkLlp~d~EsgVfDALeKgYLK~Lv 80 (604)
..+.||+++|+.+|.+||.+||++|||+|||||.+.|.....|||.| ++|.+++ +..+++.+||.++.|++|+
T Consensus 6 ~~~~isLkGSa~iV~EFf~y~iNSILyQRgiYPaEdF~~vkKYgLtllvs~D~elk~f~~-~ilsQ~~~WL~~~kiqklv 84 (203)
T KOG3285|consen 6 TKNCISLKGSAQIVSEFFEYGINSILYQRGIYPAEDFVRVKKYGLTLLVSHDEELKTFIR-NILSQVHEWLSKGKIQKLV 84 (203)
T ss_pred ccceeEeechHHHHHHHHHhhhhHHHHhccCCcHHHhhHHHhcCceEEEecCHHHHHHHH-HHHHHHHHHHHhCCcceEE
Confidence 45889999999999999999999999999999999999999999986 4444443 3457999999999999999
Q ss_pred EEEEecCCCceeEEEEEEEEeecCCCCceeEEEeecCCcccCcccccccccccCHHHHHHHHHHHHHHHHHHhhhcCCCC
Q 042785 81 FCVCEAVEGPMIEEYAFSFSYSDSDSQEISMNINRTGNKKKGGTFKCNTTTEITTTQMRSSACKMVRTLVQLMRTLDRMP 160 (604)
Q Consensus 81 LvIy~~~ddpVIEsYtFsFsYs~~gg~eVsm~l~stGnkk~~~t~~~~~~s~~Tl~qIRkqI~~LIRqLi~Ltq~L~pLP 160 (604)
++|.+..++|++|+|+|++...+... .+.+ -...+....++++|+++||||++.+++||.|
T Consensus 85 lvI~~~~tgEvlErWqFnie~~~~~~---------d~~n---------a~~~k~~~~iq~EIraviRQItasVtfLP~L- 145 (203)
T KOG3285|consen 85 LVITSKHTGEVLERWQFNIETENTAS---------DGQN---------ATRVKDLKRIQNEIRAVIRQITASVTFLPLL- 145 (203)
T ss_pred EEEEecccccchhheeeeeeeecccc---------Cccc---------ccchhHHHHHHHHHHHHHHHHhhheeecccc-
Confidence 99999999999999999999775321 1110 1123577899999999999999999999555
Q ss_pred cceeEEEEEEEecCCCCCCCC-CCCcccCCccCCCCCCCCCCceeEeeeecCCCeeEEEEEEEe
Q 042785 161 EERTILMKLFYYDDVTPVDYE-PPFFRCCSEEEAHNPWTKNPLKMEVGNVNSKHFVLALKVKSV 223 (604)
Q Consensus 161 deR~lsmKLlYyDDvTP~DYE-PPGFk~asd~e~~y~~~knp~kv~LGs~sTghH~V~LkV~Sv 223 (604)
++.|.+--|.|+ + .|-+ |.-|.+++ + .++.||+.+++++|+|+.|+|...|.--
T Consensus 146 e~~ctFdvLiyT-d---kD~~vP~~W~eS~---~--~~I~n~e~VqlrsFsT~~HKVdt~V~YK 200 (203)
T KOG3285|consen 146 EEICTFDVLIYT-D---KDTEVPEKWDESG---P--KLIQNPEAVQLRSFSTSIHKVDTQVSYK 200 (203)
T ss_pred cceeEEEEEEEe-C---CCccCCcchhcCC---C--eEecChhhEEEeeccccceeecceEEec
Confidence 566634445565 4 4656 55565543 4 4567999999999999999999998753
No 4
>KOG3186 consensus Mitotic spindle checkpoint protein [Cell cycle control, cell division, chromosome partitioning]
Probab=98.67 E-value=1.9e-07 Score=90.56 Aligned_cols=172 Identities=13% Similarity=0.183 Sum_probs=114.9
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCCCCCcccccchhhhHhhcCCCC---------hhHHHHHHHHhcccceEEEEEEecCCC
Q 042785 19 LTRNLLRIAIFNISYIRGLFPENYFNDKSVPALEMKIKKLMPMD---------AESRVYDALQKKYLKTLLFCVCEAVEG 89 (604)
Q Consensus 19 lVk~LL~vAISsIlYLRGLFPEe~F~dr~v~gLsLKIKkLlp~d---------~EsgVfDALeKgYLK~LvLvIy~~~dd 89 (604)
...+++.++|.||+|.|+|||.+-|..+..|+..+ .++.. ....|.+-|+++-+..+.++|++++..
T Consensus 9 ~~~e~meV~Vh~ILYvR~~YP~~iF~k~rkYN~pv----~~S~hP~Ln~Yi~~vl~s~~elL~~~~v~~v~l~i~~KE~r 84 (202)
T KOG3186|consen 9 GWSEKMEVSVHCILYVRRLYPQDIFIKARKYNTPV----WQSRHPILNEYIEEVLQSCIELLQTGSVHQVALSIINKEQR 84 (202)
T ss_pred HHHHHHHHHHHhheeecccccHHHHHHHHhcCCce----eeecCchHHHHHHHHHHHHHHHHhcCCeeEEEEEEEccccC
Confidence 45677899999999999999999999988876533 12111 124689999999999999999997766
Q ss_pred ceeEEEEEEEEeecCCCCceeEEEeecCCcccCcccccccccccCHHHHHHHHHHHHHHHHHHhhhcCCCCcc-eeEEEE
Q 042785 90 PMIEEYAFSFSYSDSDSQEISMNINRTGNKKKGGTFKCNTTTEITTTQMRSSACKMVRTLVQLMRTLDRMPEE-RTILMK 168 (604)
Q Consensus 90 pVIEsYtFsFsYs~~gg~eVsm~l~stGnkk~~~t~~~~~~s~~Tl~qIRkqI~~LIRqLi~Ltq~L~pLPde-R~lsmK 168 (604)
| +|+|.|.+.-...+. .+ ...-+...-+-.++.|-+|-..+..||.+|.+ |.++.+
T Consensus 85 ~-~E~yvf~~~s~p~~~-----------------~~-----~d~~l~~~eq~mRa~i~kis~~~n~lp~~p~G~Ctftv~ 141 (202)
T KOG3186|consen 85 E-EERYVFSTDSIPIIP-----------------DF-----LDEFLDAYEQYMRASIIKISNITNGLPLIPQGICTFTVR 141 (202)
T ss_pred h-hhheEeeccCCCcCc-----------------hh-----HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCceeEEEEE
Confidence 6 899999986443221 00 00012334445566666777788899999999 777887
Q ss_pred EEEecCCCCCCCC------CCCcccCCccCCCCCCCCCCceeEeeeecCCCeeEEEEEE
Q 042785 169 LFYYDDVTPVDYE------PPFFRCCSEEEAHNPWTKNPLKMEVGNVNSKHFVLALKVK 221 (604)
Q Consensus 169 LlYyDDvTP~DYE------PPGFk~asd~e~~y~~~knp~kv~LGs~sTghH~V~LkV~ 221 (604)
+.-.+. +|...+ |=-|..+++.+. .+ +.+.-+-+.+++.+.-++.+-|.
T Consensus 142 vht~~~-a~r~~~~~~~~~~FPw~~~~~~~~--q~-~gv~liPl~~vd~~~lkm~i~ve 196 (202)
T KOG3186|consen 142 VHTKDG-APRPKQWEEWFLPFPWARETDATR--QF-KGVILIPLRNVDIGPLKMEIWVE 196 (202)
T ss_pred EEeccc-cccCcchHHhhcCCchhhcchhhh--hc-cCcEEEeeeecccCceEEEEEEE
Confidence 777654 555433 211222222222 12 23555777888888877777663
No 5
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=96.71 E-value=0.0026 Score=53.35 Aligned_cols=54 Identities=22% Similarity=0.415 Sum_probs=46.3
Q ss_pred cchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc
Q 042785 382 LDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 382 ~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
..|-+|-+|+-+++....++++.||.+|. +.-+-+.+|||+|+++|+|-+....
T Consensus 3 ~~D~ly~~a~~~V~~~~~~S~S~lQR~~r--IGynrAariid~LE~~GiVs~~~~~ 56 (65)
T PF09397_consen 3 EEDPLYEEAVEFVIEEGKASISLLQRKFR--IGYNRAARIIDQLEEEGIVSPANGS 56 (65)
T ss_dssp TTSTTHHHHHHHHHHCTCECHHHHHHHHT----HHHHHHHHHHHHHCTSBE---TT
T ss_pred cccHHHHHHHHHHHHcCCccHHHHHHHhC--CCHHHHHHHHHHHHHCCCCCCCCCC
Confidence 45889999999999999999999999999 9999999999999999999987654
No 6
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=95.40 E-value=0.027 Score=47.19 Aligned_cols=53 Identities=23% Similarity=0.390 Sum_probs=49.1
Q ss_pred cchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 382 LDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 382 ~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
..|-+|-+|+-+++.....+++.||-+|. +--+-+.+|||+|+++|+|-+...
T Consensus 2 ~~D~ly~~a~~~V~~~~~~S~S~lQR~~~--IGynrAariid~lE~~GiV~p~~g 54 (63)
T smart00843 2 EEDELYDEAVELVIETQKASTSLLQRRLR--IGYNRAARLIDQLEEEGIVGPANG 54 (63)
T ss_pred cccHHHHHHHHHHHHhCCCChHHHHHHHh--cchhHHHHHHHHHHHCcCCCCCCC
Confidence 35889999999999999999999999999 999999999999999999988744
No 7
>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=92.82 E-value=0.16 Score=41.62 Aligned_cols=49 Identities=22% Similarity=0.392 Sum_probs=42.7
Q ss_pred hHHHHHHhhhh-ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccc
Q 042785 385 QIYMKALYYAL-SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKG 435 (604)
Q Consensus 385 ~~y~~~~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 435 (604)
-.|.||+|... .-..|+...|...|. .+..+|.+.+.||.++|||+-..
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~--vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLG--VSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHT--S-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHC--CChHHHHHHHHHHHHCCCEEecC
Confidence 46999999977 567899999999999 99999999999999999998653
No 8
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=92.53 E-value=0.33 Score=40.66 Aligned_cols=75 Identities=19% Similarity=0.315 Sum_probs=57.2
Q ss_pred CCCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHH
Q 042785 379 SPQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKK 458 (604)
Q Consensus 379 ~~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 458 (604)
.....++..+..|++. | -+++..|...++ .++.+++++|.+|++.|||+....+ -|+|.++-.+|++-..-++.
T Consensus 7 ~l~~~~~~il~~l~~~-~--~~~~~~la~~~~--~s~~~i~~~l~~L~~~g~v~~~~~~-~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 7 GLTPTQFLVLRILYEE-G--PLSVSELAKRLG--VSPSTVTRVLDRLEKKGLIRRLPSP-EDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred CCCHHHHHHHHHHHHc-C--CcCHHHHHHHHC--CCchhHHHHHHHHHHCCCeEecCCC-CCCCeEEEEECHhHHHHHHH
Confidence 3455678888888763 3 478888888887 8999999999999999999877654 46777888888775444443
Q ss_pred h
Q 042785 459 A 459 (604)
Q Consensus 459 ~ 459 (604)
+
T Consensus 81 ~ 81 (101)
T smart00347 81 L 81 (101)
T ss_pred H
Confidence 3
No 9
>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=92.47 E-value=0.21 Score=39.17 Aligned_cols=51 Identities=24% Similarity=0.393 Sum_probs=41.5
Q ss_pred cchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc
Q 042785 382 LDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 382 ~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
..++..|..||..=| +++..|...+. .+..++++++++|++.|||+...+.
T Consensus 3 ~~q~~iL~~l~~~~~---~~~~~la~~~~--~~~~~~t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 3 PSQFRILRILYENGG---ITQSELAEKLG--ISRSTVTRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp HHHHHHHHHHHHHSS---EEHHHHHHHHT--S-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHHHHcCC---CCHHHHHHHHC--CChhHHHHHHHHHHHCCCEEeccCC
Confidence 346788888876444 88889999999 8999999999999999999876543
No 10
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=90.89 E-value=0.43 Score=40.95 Aligned_cols=76 Identities=22% Similarity=0.263 Sum_probs=61.8
Q ss_pred CCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHHh
Q 042785 380 PQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKKA 459 (604)
Q Consensus 380 ~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 459 (604)
....++..+.+||..-++.. ..|...|. +..++|+.++++|++.|||+-.-+..- +|.++=.+|++--..+.++
T Consensus 20 lt~~q~~~L~~l~~~~~~~~---~~la~~l~--i~~~~vt~~l~~Le~~glv~r~~~~~D-rR~~~l~lT~~G~~~~~~~ 93 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITV---KELAERLG--LDRSTVTRLLKRLEDKGLIERLRDPED-RRAVLVRLTEKGRELLEQL 93 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcH---HHHHHHHC--CCHHHHHHHHHHHHHCCCeeecCCccc-cceeeEEECccHHHHHHHh
Confidence 56678888999998776655 88888888 999999999999999999998877665 6777777888776666665
Q ss_pred hc
Q 042785 460 LD 461 (604)
Q Consensus 460 ~~ 461 (604)
..
T Consensus 94 ~~ 95 (126)
T COG1846 94 LP 95 (126)
T ss_pred cc
Confidence 54
No 11
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=88.63 E-value=0.46 Score=44.13 Aligned_cols=45 Identities=20% Similarity=0.538 Sum_probs=41.0
Q ss_pred HHHHHhhhhc-cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc
Q 042785 387 YMKALYYALS-MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA 433 (604)
Q Consensus 387 y~~~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 433 (604)
|.+++|..+. ..++++..|...|. +++.+|+..|.+|++.|||.-
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~~l~--vs~~svs~~l~~L~~~Gli~~ 54 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAEALS--VHPSSVTKMVQKLDKDEYLIY 54 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhC--CChhHHHHHHHHHHHCCCEEE
Confidence 8999998775 47889999999999 899999999999999999983
No 12
>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=87.69 E-value=1 Score=36.02 Aligned_cols=53 Identities=26% Similarity=0.302 Sum_probs=38.2
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccccc
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLG 440 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 (604)
++..|-+|+| .....++..|...+. +++.+++++|++|++.|||+-..+..-+
T Consensus 5 q~~vL~~l~~--~~~~~t~~~l~~~~~--~~~~~vs~~i~~L~~~glv~~~~~~~d~ 57 (68)
T PF13463_consen 5 QWQVLRALAH--SDGPMTQSDLAERLG--ISKSTVSRIIKKLEEKGLVEKERDPHDK 57 (68)
T ss_dssp HHHHHHHHT----TS-BEHHHHHHHTT----HHHHHHHHHHHHHTTSEEEEEESSCT
T ss_pred HHHHHHHHHc--cCCCcCHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEecCCCCcC
Confidence 4555555551 457788899999999 9999999999999999999766554333
No 13
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=87.49 E-value=0.98 Score=41.85 Aligned_cols=75 Identities=16% Similarity=0.233 Sum_probs=58.1
Q ss_pred CCCCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHH
Q 042785 378 KSPQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAK 457 (604)
Q Consensus 378 ~~~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 457 (604)
-......+..+..|++ ..-++.+.|...+. .+..+|++++++|++.|||+-..+.. .+|+.+=.||++=..-+.
T Consensus 36 ~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~--i~~~tvsr~l~~Le~~GlI~R~~~~~-DrR~~~l~LT~~G~~~~~ 109 (144)
T PRK11512 36 LDITAAQFKVLCSIRC---AACITPVELKKVLS--VDLGALTRMLDRLVCKGWVERLPNPN-DKRGVLVKLTTSGAAICE 109 (144)
T ss_pred cCCCHHHHHHHHHHHH---cCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEeccCcc-cCCeeEeEEChhHHHHHH
Confidence 3455667888888864 35689999999999 99999999999999999999776544 566777778876554433
Q ss_pred H
Q 042785 458 K 458 (604)
Q Consensus 458 ~ 458 (604)
+
T Consensus 110 ~ 110 (144)
T PRK11512 110 Q 110 (144)
T ss_pred H
Confidence 3
No 14
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=86.47 E-value=1 Score=35.34 Aligned_cols=52 Identities=21% Similarity=0.289 Sum_probs=39.6
Q ss_pred cchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 382 LDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 382 ~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
..++..+-+|++.=+- =+++..|...|. .+..+|+++|.+|++.|||+-..+
T Consensus 5 ~~q~~vL~~l~~~~~~-~~t~~~la~~l~--~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 5 PSQFRVLMALARHPGE-ELTQSELAERLG--ISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHHHSTTS-GEEHHHHHHHHT--S-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHHHCCCC-CcCHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4456666666664332 279999999999 999999999999999999986544
No 15
>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=86.41 E-value=1.5 Score=39.21 Aligned_cols=80 Identities=18% Similarity=0.285 Sum_probs=60.5
Q ss_pred CCCcchhHHHHHHhh-hhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHH
Q 042785 379 SPQLDDQIYMKALYY-ALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAK 457 (604)
Q Consensus 379 ~~~~~~~~y~~~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 457 (604)
.....++..+..|+. ..+-.-++...|...+. .+.++|+++|++|++.|||+-..+.. -+|+++=.+|++-...+.
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~--~~~stvs~~i~~Le~kg~I~r~~~~~-D~R~~~i~lT~~G~~~~~ 98 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEIL--IKQSALVKIIKKLSKKGYLSKERSED-DERKVIISINKEQRSKIE 98 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHC--CCHHHHHHHHHHHHHCCCEeccCCcc-cCCeEEEEECHHHHHHHH
Confidence 456667877777773 12346689999999999 99999999999999999998655433 356677778888777666
Q ss_pred Hhhc
Q 042785 458 KALD 461 (604)
Q Consensus 458 ~~~~ 461 (604)
++.+
T Consensus 99 ~~~~ 102 (109)
T TIGR01889 99 SLIS 102 (109)
T ss_pred HHHH
Confidence 6543
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=85.68 E-value=0.89 Score=34.58 Aligned_cols=54 Identities=24% Similarity=0.351 Sum_probs=41.0
Q ss_pred cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHH
Q 042785 397 MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEA 456 (604)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 456 (604)
...+++..+...|. ++..+|++.|++|+++|+|+.....| +.+ -.+|..++.++
T Consensus 8 ~~~~~~~~i~~~l~--is~~~v~~~l~~L~~~g~i~~~~~~~--~~~--~~~~~~~~~~~ 61 (66)
T smart00418 8 EGELCVCELAEILG--LSQSTVSHHLKKLREAGLVESRREGK--RVY--YSLTDEKVADL 61 (66)
T ss_pred cCCccHHHHHHHHC--CCHHHHHHHHHHHHHCCCeeeeecCC--EEE--EEEchHHHHHH
Confidence 57789999999997 99999999999999999999765433 222 23566555544
No 17
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=85.49 E-value=1.7 Score=40.06 Aligned_cols=76 Identities=12% Similarity=0.131 Sum_probs=56.4
Q ss_pred CCCCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHH
Q 042785 378 KSPQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAK 457 (604)
Q Consensus 378 ~~~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 457 (604)
-.....++..+.+|++.= ...+...|...+. .+..+|++++++|++.|||+...+.. .+|+.|=.||++=..-+.
T Consensus 27 ~glt~~q~~vL~~l~~~~--~~~t~~eLa~~l~--~~~~tvt~~v~~Le~~GlV~r~~~~~-DrR~~~l~LT~~G~~~~~ 101 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLP--PEQSQIQLAKAIG--IEQPSLVRTLDQLEEKGLISRQTCAS-DRRAKRIKLTEKAEPLIS 101 (144)
T ss_pred cCCCHHHHHHHHHHHHcC--CCCCHHHHHHHhC--CChhhHHHHHHHHHHCCCEeeecCCC-CcCeeeeEEChHHHHHHH
Confidence 345666888888887632 2467889999998 99999999999999999999765432 467777778876544333
Q ss_pred H
Q 042785 458 K 458 (604)
Q Consensus 458 ~ 458 (604)
+
T Consensus 102 ~ 102 (144)
T PRK03573 102 E 102 (144)
T ss_pred H
Confidence 3
No 18
>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=85.33 E-value=1.4 Score=33.60 Aligned_cols=34 Identities=29% Similarity=0.453 Sum_probs=29.5
Q ss_pred cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccc
Q 042785 397 MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVE 432 (604)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 432 (604)
-..+|...|..++. .+..+|++.+.+|+++|||+
T Consensus 15 ~~~~t~~ela~~~~--is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 15 NPRITQKELAEKLG--ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp CTTS-HHHHHHHHT--S-HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCHHHHHHHhC--CCHHHHHHHHHHHHHCcCcC
Confidence 45689999999999 99999999999999999986
No 19
>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=84.13 E-value=0.85 Score=44.94 Aligned_cols=52 Identities=23% Similarity=0.381 Sum_probs=41.5
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc-cccceeeehhhhHH
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR-RLGKRVIHSTLTKK 451 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 451 (604)
.-+|+..|...|. ++.++|++.+++|+++|||+....+ ..|++.++-.||++
T Consensus 14 ~~~t~~eLA~~lg--is~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~ 66 (203)
T TIGR02702 14 GQATAAALAEALA--ISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ 66 (203)
T ss_pred CCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc
Confidence 4489999999997 9999999999999999999876432 24676666566654
No 20
>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=83.76 E-value=2.3 Score=37.96 Aligned_cols=74 Identities=12% Similarity=0.121 Sum_probs=53.9
Q ss_pred CCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHHh
Q 042785 380 PQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKKA 459 (604)
Q Consensus 380 ~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 459 (604)
....++..+.+|++. .-+++..|...+. +++.+|++++++|+++|||+...+.. .+|..+-.||++-..-+.++
T Consensus 26 lt~~q~~iL~~l~~~---~~~t~~ela~~~~--~~~~tvs~~l~~Le~~GlI~r~~~~~-D~R~~~v~LT~~G~~~~~~~ 99 (118)
T TIGR02337 26 LTEQQWRILRILAEQ---GSMEFTQLANQAC--ILRPSLTGILARLERDGLVTRLKASN-DQRRVYISLTPKGQALYASL 99 (118)
T ss_pred CCHHHHHHHHHHHHc---CCcCHHHHHHHhC--CCchhHHHHHHHHHHCCCEEeccCCC-CCCeeEEEECHhHHHHHHHh
Confidence 456678888887653 3467788888887 88889999999999999999765433 45556666777655444443
No 21
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=83.52 E-value=1.6 Score=40.67 Aligned_cols=64 Identities=17% Similarity=0.313 Sum_probs=54.5
Q ss_pred ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHHhhcc
Q 042785 396 SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKKALDI 462 (604)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 (604)
|-..+++..|...+. +|.+.|||++.+|.++|||+....+.-|=++.. ...+-.|.+|..+++.
T Consensus 22 ~g~~~s~~~ia~~~~--is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~-~~~~itl~dI~~aiE~ 85 (141)
T PRK11014 22 EGRMTSISEVTEVYG--VSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK-PASTIRIGDVVRELEP 85 (141)
T ss_pred CCCccCHHHHHHHHC--cCHHHHHHHHHHHHhCCEEEEecCCCCCeeecC-CHHHCCHHHHHHHHcC
Confidence 335789999999999 999999999999999999999998888877765 4556778888888873
No 22
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=82.91 E-value=1.8 Score=33.06 Aligned_cols=37 Identities=22% Similarity=0.404 Sum_probs=32.1
Q ss_pred cccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 396 SMNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 396 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
|-..+ ++..|...+. ++..+|++.+.+|+++|+|+..
T Consensus 16 ~~~~l~s~~~la~~~~--vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 16 PGDKLPSERELAAQLG--VSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred CCCcCcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEe
Confidence 44556 8899999998 9999999999999999999754
No 23
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=82.06 E-value=2.6 Score=41.83 Aligned_cols=79 Identities=16% Similarity=0.130 Sum_probs=57.8
Q ss_pred CCCCCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHH
Q 042785 377 DKSPQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEA 456 (604)
Q Consensus 377 ~~~~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 456 (604)
.-......+..+.+||+. .-+|...|...+. .++++|++++++|++.|||+-..+.. -||+..=.||++=..-+
T Consensus 40 ~~gLt~~q~~iL~~L~~~---~~itq~eLa~~l~--l~~sTvtr~l~rLE~kGlI~R~~~~~-DrR~~~I~LTekG~~l~ 113 (185)
T PRK13777 40 PYDLNINEHHILWIAYHL---KGASISEIAKFGV--MHVSTAFNFSKKLEERGYLTFSKKED-DKRNTYIELTEKGEELL 113 (185)
T ss_pred HCCCCHHHHHHHHHHHhC---CCcCHHHHHHHHC--CCHhhHHHHHHHHHHCCCEEecCCCC-CCCeeEEEECHHHHHHH
Confidence 345677788888888874 3567888887766 78899999999999999999654432 46677777787765555
Q ss_pred HHhhc
Q 042785 457 KKALD 461 (604)
Q Consensus 457 ~~~~~ 461 (604)
.++..
T Consensus 114 ~~l~~ 118 (185)
T PRK13777 114 LETME 118 (185)
T ss_pred HHHHH
Confidence 55443
No 24
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=81.45 E-value=1.7 Score=32.14 Aligned_cols=34 Identities=18% Similarity=0.360 Sum_probs=29.8
Q ss_pred eehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 399 YVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
.++...|..++. .+..+|+++|.+|+++|+|+..
T Consensus 8 ~~s~~~la~~l~--~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLG--LTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEe
Confidence 367788888888 8999999999999999999854
No 25
>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=81.31 E-value=1.6 Score=35.53 Aligned_cols=43 Identities=23% Similarity=0.319 Sum_probs=38.1
Q ss_pred hhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc
Q 042785 393 YALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 393 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
+.|...-.|+..|...++ ++.++|++.+.+|++.|+|+....+
T Consensus 16 ~Ll~~~~~t~~eIa~~l~--i~~~~v~~~L~~L~~~GlV~~~~~~ 58 (68)
T PF01978_consen 16 ALLKNGPATAEEIAEELG--ISRSTVYRALKSLEEKGLVEREEGR 58 (68)
T ss_dssp HHHHHCHEEHHHHHHHHT--SSHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred HHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEEEcCc
Confidence 444668899999999999 9999999999999999999988744
No 26
>PRK11050 manganese transport regulator MntR; Provisional
Probab=81.23 E-value=1.7 Score=41.39 Aligned_cols=51 Identities=20% Similarity=0.353 Sum_probs=41.8
Q ss_pred hhHHHHHHhhhhc-cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 384 DQIYMKALYYALS-MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 384 ~~~y~~~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
.--|++.|+.++. ..-+++..|...|. +++++|++++.+|++.|||.....
T Consensus 35 ~e~~l~~I~~~l~~~~~~t~~eLA~~l~--is~stVsr~l~~Le~~GlI~r~~~ 86 (152)
T PRK11050 35 IEDYVELIADLIAEVGEARQVDIAARLG--VSQPTVAKMLKRLARDGLVEMRPY 86 (152)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEecC
Confidence 3446677776664 46789999999998 999999999999999999986543
No 27
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=79.01 E-value=3.4 Score=40.24 Aligned_cols=67 Identities=22% Similarity=0.364 Sum_probs=50.4
Q ss_pred ccCCCCCcchhHHHHHH---hhhhccceehhhhhhhhhhh------------hhhHHHHHHHHHHHHHhccccccccccc
Q 042785 375 LCDKSPQLDDQIYMKAL---YYALSMNYVTIAKLQKKLDK------------EANQSTVRKLIDKMIREGYVEAKGSRRL 439 (604)
Q Consensus 375 ~~~~~~~~~~~~y~~~~---~~~l~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 (604)
-...++++.|+.|..|. .|+---.-|.|..|+..+.| .+|-+.+|+++.+|++.|||+...
T Consensus 40 ~kE~~P~~~DW~Y~R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~---- 115 (150)
T PRK09333 40 HKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK---- 115 (150)
T ss_pred cccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC----
Confidence 45678888999998872 23222235788999988888 467788999999999999999654
Q ss_pred cceeee
Q 042785 440 GKRVIH 445 (604)
Q Consensus 440 ~~~~~~ 445 (604)
|-|+|-
T Consensus 116 ~GR~lT 121 (150)
T PRK09333 116 KGRVIT 121 (150)
T ss_pred CCCEeC
Confidence 555554
No 28
>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=78.75 E-value=5.3 Score=31.00 Aligned_cols=47 Identities=26% Similarity=0.405 Sum_probs=37.3
Q ss_pred hHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc
Q 042785 385 QIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 385 ~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
...+.+|++. | ++...+...|. ++..++++.+++|++.|+|....+.
T Consensus 10 ~~il~~l~~~-~---~~~~ei~~~~~--i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 10 LRILRLLLEG-P---LTVSELAERLG--LSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHHHC-C---cCHHHHHHHHC--cCHhHHHHHHHHHHHCCCeEEEEec
Confidence 4445555552 2 88888888886 8999999999999999999986655
No 29
>PRK10870 transcriptional repressor MprA; Provisional
Probab=78.46 E-value=4.4 Score=39.36 Aligned_cols=79 Identities=16% Similarity=0.221 Sum_probs=57.7
Q ss_pred CCCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHH
Q 042785 379 SPQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKK 458 (604)
Q Consensus 379 ~~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 458 (604)
.....++..+..||. .+...++...|...+. .+..+|+.++++|++.|||+-..+..= +|+.+-.||++=..-+.+
T Consensus 52 gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~--l~~~tvsr~v~rLe~kGlV~R~~~~~D-rR~~~v~LT~~G~~~~~~ 127 (176)
T PRK10870 52 GINETLFMALITLES-QENHSIQPSELSCALG--SSRTNATRIADELEKRGWIERRESDND-RRCLHLQLTEKGHEFLRE 127 (176)
T ss_pred CCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEecCCCCC-CCeeEEEECHHHHHHHHH
Confidence 345568888888874 3345678889999998 999999999999999999997655433 455555677765555555
Q ss_pred hhc
Q 042785 459 ALD 461 (604)
Q Consensus 459 ~~~ 461 (604)
+..
T Consensus 128 i~~ 130 (176)
T PRK10870 128 VLP 130 (176)
T ss_pred HHH
Confidence 443
No 30
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=77.45 E-value=2.5 Score=40.79 Aligned_cols=51 Identities=18% Similarity=0.429 Sum_probs=44.2
Q ss_pred hhHHHHHHhhhhc-cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 384 DQIYMKALYYALS-MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 384 ~~~y~~~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
.--|++++|-.+. -.++.+..|...|. ++..+|++.+.||.+.|||+-...
T Consensus 8 ~edYL~~Iy~l~~~~~~~~~~diA~~L~--Vsp~sVt~ml~rL~~~GlV~~~~y 59 (154)
T COG1321 8 EEDYLETIYELLEEKGFARTKDIAERLK--VSPPSVTEMLKRLERLGLVEYEPY 59 (154)
T ss_pred HHHHHHHHHHHHhccCcccHHHHHHHhC--CCcHHHHHHHHHHHHCCCeEEecC
Confidence 4469999997764 66899999999999 999999999999999999987443
No 31
>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=77.28 E-value=5.9 Score=36.98 Aligned_cols=74 Identities=15% Similarity=0.305 Sum_probs=53.5
Q ss_pred chhHHHHHHhhhhccceehhhhhhhhhhh--hhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHH--HHH
Q 042785 383 DDQIYMKALYYALSMNYVTIAKLQKKLDK--EANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLME--AKK 458 (604)
Q Consensus 383 ~~~~y~~~~~~~l~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~ 458 (604)
.++--|+.|+..=| +++..++..|.. ..+.++|+.+|.+|++.|||+.....| ..+.+..+++..+.+ ++.
T Consensus 5 ~E~~VM~vlW~~~~---~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr--~~~Y~p~vs~ee~~~~~~~~ 79 (130)
T TIGR02698 5 AEWEVMRVVWTLGE---TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGR--KFIYTALVSEDEAVENAAQE 79 (130)
T ss_pred HHHHHHHHHHcCCC---CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCCC--cEEEEecCCHHHHHHHHHHH
Confidence 45667889887433 588887777753 368999999999999999998764444 347777777777643 455
Q ss_pred hhc
Q 042785 459 ALD 461 (604)
Q Consensus 459 ~~~ 461 (604)
+++
T Consensus 80 ~~~ 82 (130)
T TIGR02698 80 LFS 82 (130)
T ss_pred HHH
Confidence 543
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=77.22 E-value=2.8 Score=31.25 Aligned_cols=37 Identities=19% Similarity=0.364 Sum_probs=32.7
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
..+++..|...|+ .+..+|++.|+.|.+.|+|+....
T Consensus 13 ~~~s~~~l~~~l~--~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 13 GKVSVEELAELLG--VSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred CCcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEeec
Confidence 4689999999997 899999999999999999986543
No 33
>PF10033 ATG13: Autophagy-related protein 13; InterPro: IPR018731 Members of this family of phosphoproteins are involved in cytoplasm to vacuole transport (Cvt), and more specifically in Cvt vesicle formation. They are probably involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage [, , ].
Probab=76.72 E-value=70 Score=32.71 Aligned_cols=84 Identities=17% Similarity=0.154 Sum_probs=48.7
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhhcC------CC------CcceeEEEEEEEecCCCCCCCCCC-CcccCCccCCCCCCCC
Q 042785 133 ITTTQMRSSACKMVRTLVQLMRTLD------RM------PEERTILMKLFYYDDVTPVDYEPP-FFRCCSEEEAHNPWTK 199 (604)
Q Consensus 133 ~Tl~qIRkqI~~LIRqLi~Ltq~L~------pL------PdeR~lsmKLlYyDDvTP~DYEPP-GFk~asd~e~~y~~~k 199 (604)
..+..+=++.+-|+|.|+++++.|| .| +..-.+..|++ |..-|...... ||. .+...-..
T Consensus 131 ~~l~~vYK~~ivLfRSLys~~RlLPA~kl~~~l~~~~~~~~~l~i~~Ri~--~g~~~~~~~g~~~ls-----~p~~~~~~ 203 (233)
T PF10033_consen 131 PELPTVYKRSIVLFRSLYSLTRLLPAYKLFRRLAKSSSSSSSLSIGYRIS--DGSPPILSKGRIGLS-----KPIIPSES 203 (233)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhChHHHHHHHhhhccCCCCcceeEEEEe--cCCcccccCCccccc-----ccccCCCC
Confidence 3566788899999999999999885 23 22333344443 22111111111 221 12111111
Q ss_pred -CCceeEeeeecCCCeeEEEEEEEe
Q 042785 200 -NPLKMEVGNVNSKHFVLALKVKSV 223 (604)
Q Consensus 200 -np~kv~LGs~sTghH~V~LkV~Sv 223 (604)
......+|.+.|.+=.+.+.|.-.
T Consensus 204 ~~~~~~~f~pv~Tp~G~L~isV~YR 228 (233)
T PF10033_consen 204 NHMEQYSFGPVETPLGSLCISVSYR 228 (233)
T ss_pred CceeEEEECCcccCCccEEEEEEec
Confidence 334689999999998888888754
No 34
>PF07855 DUF1649: Protein of unknown function (DUF1649); InterPro: IPR012445 This family represents Autophagy-related protein 101.
Probab=76.28 E-value=25 Score=34.18 Aligned_cols=72 Identities=15% Similarity=0.167 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCCCCCCcccccchhhhHhhcCCCChh-------HHHHHHHHhcccc--------eEEEE
Q 042785 18 LLTRNLLRIAIFNISYIRGLFPENYFNDKSVPALEMKIKKLMPMDAE-------SRVYDALQKKYLK--------TLLFC 82 (604)
Q Consensus 18 ~lVk~LL~vAISsIlYLRGLFPEe~F~dr~v~gLsLKIKkLlp~d~E-------sgVfDALeKgYLK--------~LvLv 82 (604)
..|++.++.-+..|+|.| .|+.=...+..+.-+++..-+......+ .+..+||.+.--+ .+.|.
T Consensus 8 ~~v~evv~~ilHTIlFhR-~~G~v~p~dv~~e~ldiTy~~~~~~el~~~Id~ki~~f~~~l~~~~~~~~~~~~~gqI~l~ 86 (163)
T PF07855_consen 8 SQVREVVKAILHTILFHR-AFGTVRPKDVTCEFLDITYPRCNDPELESLIDEKINQFIRQLEKHPSKSSNGLGRGQISLQ 86 (163)
T ss_pred HHHHHHHHHHHHHHHhhh-ccCcccccccccceecceeeccCcHHHHHHHHHHHHHHHHHHHhCcCccCCCcceEEEEEE
Confidence 457888999999999999 4454444433333333211111000011 3577888887766 78888
Q ss_pred EEecCCCc
Q 042785 83 VCEAVEGP 90 (604)
Q Consensus 83 Iy~~~ddp 90 (604)
+|......
T Consensus 87 F~ekr~kk 94 (163)
T PF07855_consen 87 FYEKRRKK 94 (163)
T ss_pred EEeecccc
Confidence 88876554
No 35
>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=76.03 E-value=3.7 Score=31.49 Aligned_cols=33 Identities=33% Similarity=0.478 Sum_probs=30.5
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVE 432 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 432 (604)
...+++.|...|+ .++.+|+.-+.+|.+.|||+
T Consensus 14 ~~~~~~el~~~l~--~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELG--LSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHT--S-HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhcc--ccchHHHHHHHHHHHCcCee
Confidence 7789999999999 99999999999999999996
No 36
>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=75.25 E-value=3.4 Score=33.39 Aligned_cols=40 Identities=20% Similarity=0.402 Sum_probs=33.5
Q ss_pred cccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc
Q 042785 396 SMNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 396 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
|-+.+ +...|..+++ ++.++||+.+..|..+|+|+...++
T Consensus 20 ~g~~lps~~~la~~~~--vsr~tvr~al~~L~~~g~i~~~~~~ 60 (64)
T PF00392_consen 20 PGDRLPSERELAERYG--VSRTTVREALRRLEAEGLIERRPGR 60 (64)
T ss_dssp TTSBE--HHHHHHHHT--S-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred CCCEeCCHHHHHHHhc--cCCcHHHHHHHHHHHCCcEEEECCc
Confidence 44677 9999999999 9999999999999999999876554
No 37
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=74.53 E-value=7.1 Score=33.60 Aligned_cols=63 Identities=19% Similarity=0.226 Sum_probs=47.5
Q ss_pred cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHHhhc
Q 042785 397 MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKKALD 461 (604)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 461 (604)
-+-++...|+..|. ++...+++.+.+|+.+|||+-.-..--+++...-.+|++=..+.++.++
T Consensus 12 ~~~~~f~~L~~~l~--lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~ 74 (80)
T PF13601_consen 12 NEEATFSELKEELG--LTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVA 74 (80)
T ss_dssp HSEEEHHHHHHHTT----HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhC--cCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHH
Confidence 46677888999998 9999999999999999999988766556678888899987777766554
No 38
>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=74.31 E-value=3 Score=32.49 Aligned_cols=33 Identities=27% Similarity=0.456 Sum_probs=29.4
Q ss_pred ehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 400 VTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
.++..|...+. ++..+|++.|.+|++.|||+..
T Consensus 26 ~~~~~la~~~~--is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 26 PSERELAEELG--VSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEec
Confidence 35888999997 8999999999999999999854
No 39
>PRK10263 DNA translocase FtsK; Provisional
Probab=74.24 E-value=4 Score=51.04 Aligned_cols=51 Identities=18% Similarity=0.383 Sum_probs=47.6
Q ss_pred chhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccc
Q 042785 383 DDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKG 435 (604)
Q Consensus 383 ~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 435 (604)
.|-+|-+|+-+++...-++++.||.+|. +--+-+.+|||+|+++|+|-+..
T Consensus 1291 ~D~l~~~a~~~v~~~~~~S~S~lQR~~~--iGynRAariid~lE~~Giv~p~~ 1341 (1355)
T PRK10263 1291 LDPLFDQAVQFVTEKRKASISGVQRQFR--IGYNRAARIIEQMEAQGIVSEQG 1341 (1355)
T ss_pred ccHHHHHHHHHHHhcCccCHHHHHHHhh--cChHHHHHHHHHHHHCCcCCCCC
Confidence 4889999999999999999999999999 88899999999999999998753
No 40
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=74.07 E-value=4.4 Score=34.49 Aligned_cols=40 Identities=25% Similarity=0.453 Sum_probs=33.4
Q ss_pred eehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccccc
Q 042785 399 YVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLG 440 (604)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 (604)
.+++..|...+. ++...++|++.+|++.|||+....+.-|
T Consensus 25 ~~s~~eiA~~~~--i~~~~l~kil~~L~~~Gli~s~~G~~GG 64 (83)
T PF02082_consen 25 PVSSKEIAERLG--ISPSYLRKILQKLKKAGLIESSRGRGGG 64 (83)
T ss_dssp -BEHHHHHHHHT--S-HHHHHHHHHHHHHTTSEEEETSTTSE
T ss_pred CCCHHHHHHHHC--cCHHHHHHHHHHHhhCCeeEecCCCCCc
Confidence 399999999999 9999999999999999999877544333
No 41
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=72.82 E-value=6.4 Score=40.20 Aligned_cols=67 Identities=19% Similarity=0.257 Sum_probs=47.8
Q ss_pred hhHHHHHHhhhhcc---ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHH
Q 042785 384 DQIYMKALYYALSM---NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEA 456 (604)
Q Consensus 384 ~~~y~~~~~~~l~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 456 (604)
++-|+|.|...--. ..+|...|...|. +++.+|++++.+|++.|||+....+| |. .=.+|++-..-+
T Consensus 3 ~~~~Lk~iallg~l~~~~~IS~~eLA~~L~--iS~~Tvsr~Lk~LEe~GlI~R~~~~r-~~---~v~LTekG~~ll 72 (217)
T PRK14165 3 DIEALKKLALLGAVNNTVKISSSEFANHTG--TSSKTAARILKQLEDEGYITRTIVPR-GQ---LITITEKGLDVL 72 (217)
T ss_pred hhHHHHHHHHHhccCCCCCcCHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEEEEcCC-ce---EEEECHHHHHHH
Confidence 56677776542211 2478999999998 99999999999999999999877654 22 233555544333
No 42
>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=72.38 E-value=8.8 Score=34.55 Aligned_cols=64 Identities=19% Similarity=0.407 Sum_probs=46.7
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhh--hhHHHHHHHHHHHHHhccccccccccccce-eeehhhhHHHH
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKE--ANQSTVRKLIDKMIREGYVEAKGSRRLGKR-VIHSTLTKKKL 453 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 453 (604)
++--|+.|+-.=| +|+..++..|..+ .+.++|..++.+|++.|||+.... |+. +...-++...+
T Consensus 5 E~~IM~~lW~~~~---~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~---gr~~~Y~p~is~~e~ 71 (115)
T PF03965_consen 5 ELEIMEILWESGE---ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI---GRAYVYSPLISREEY 71 (115)
T ss_dssp HHHHHHHHHHHSS---EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE---TTCEEEEESSSHHHH
T ss_pred HHHHHHHHHhCCC---CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec---CCceEEEeCCcHHHH
Confidence 4567888886544 8999999988865 789999999999999999998643 544 44445555544
No 43
>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=70.89 E-value=4.1 Score=32.19 Aligned_cols=36 Identities=19% Similarity=0.346 Sum_probs=32.0
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKG 435 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 435 (604)
..++...|...+. .+..+|+++|.+|+++|+|+..+
T Consensus 24 ~~~s~~ela~~~g--~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLG--LTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEecC
Confidence 3478889999998 89999999999999999998765
No 44
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=70.59 E-value=9.8 Score=34.70 Aligned_cols=64 Identities=17% Similarity=0.196 Sum_probs=45.6
Q ss_pred cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHHhhccc
Q 042785 397 MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKKALDID 463 (604)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 463 (604)
-..+++..|..++. +++.+|++++.+|++.|||+....+.-|-+... ...+-.+.++-++++.+
T Consensus 23 ~~~~s~~eia~~l~--is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~-~~~~it~~~v~~~l~~~ 86 (130)
T TIGR02944 23 SQPYSAAEIAEQTG--LNAPTVSKILKQLSLAGIVTSKRGVEGGYTLAR-APRDITVADIVKAVEGP 86 (130)
T ss_pred CCCccHHHHHHHHC--cCHHHHHHHHHHHHHCCcEEecCCCCCChhhcC-CccccCHHHHHHHHcCC
Confidence 35789999999999 999999999999999999986422222333322 22233467777777653
No 45
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=68.41 E-value=4.5 Score=33.99 Aligned_cols=35 Identities=31% Similarity=0.548 Sum_probs=31.9
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
..+++..|...+. ++..+|++++..|++.|||+..
T Consensus 19 ~~~t~~~ia~~l~--i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 19 GGLTLAELAERLG--LSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred CCcCHHHHHHHhC--CCHHHHHHHHHHHHHCCCeeec
Confidence 3689999999997 9999999999999999999864
No 46
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=64.51 E-value=10 Score=34.23 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=32.0
Q ss_pred eehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 399 YVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
.+++..|...+. ++...|++++.+|++.|||...
T Consensus 25 ~~s~~eia~~~~--i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 25 PVSVKEIAERQG--ISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred cCcHHHHHHHHC--cCHHHHHHHHHHHHHCCcEEec
Confidence 899999999999 9999999999999999999864
No 47
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=64.12 E-value=20 Score=33.07 Aligned_cols=76 Identities=21% Similarity=0.252 Sum_probs=58.2
Q ss_pred HHHHHhhhhc--cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccce---eeehhhhHHHHHHHHHhhc
Q 042785 387 YMKALYYALS--MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKR---VIHSTLTKKKLMEAKKALD 461 (604)
Q Consensus 387 y~~~~~~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 461 (604)
|+.-||...+ ..-||+..|...|. -+.--|+.||.||.++|.|.=...+=-|++ .++.+..+-.+..+++.|+
T Consensus 5 ~y~~L~~~~~~~~~~vtl~elA~~l~--cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~~~~~~~~~~~~~~l~ 82 (115)
T PF12793_consen 5 QYQRLWQHYGGQPVEVTLDELAELLF--CSRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLKSPEELLEQQAEELLE 82 (115)
T ss_pred HHHHHHHHcCCCCcceeHHHHHHHhC--CCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEeeCHHHHHHHHHHHHHH
Confidence 4445555444 33479999999999 888999999999999999998777766665 6677777777777777777
Q ss_pred ccc
Q 042785 462 IDF 464 (604)
Q Consensus 462 ~~~ 464 (604)
...
T Consensus 83 ~g~ 85 (115)
T PF12793_consen 83 QGK 85 (115)
T ss_pred cCC
Confidence 643
No 48
>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=62.32 E-value=6.6 Score=32.46 Aligned_cols=35 Identities=23% Similarity=0.592 Sum_probs=29.2
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
.-+++.-|...|+ ++..+|+-+++.|++.|||+.-
T Consensus 13 ~~~S~~eLa~~~~--~s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 13 GRVSLAELAREFG--ISPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp -SEEHHHHHHHTT----HHHHHHHHHHHHCCTSCEEE
T ss_pred CCcCHHHHHHHHC--cCHHHHHHHHHHHHHCCcEEEe
Confidence 4578899999999 9999999999999999999854
No 49
>PF13730 HTH_36: Helix-turn-helix domain
Probab=61.65 E-value=11 Score=29.15 Aligned_cols=32 Identities=22% Similarity=0.429 Sum_probs=28.1
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYV 431 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (604)
-|-+...|...+. .+..+|++.|.++++.|||
T Consensus 24 ~~pS~~~la~~~g--~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 24 CFPSQETLAKDLG--VSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCcCHHHHHHHHC--cCHHHHHHHHHHHHHCcCC
Confidence 4457888888887 8899999999999999996
No 50
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. 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 Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=61.22 E-value=15 Score=35.72 Aligned_cols=63 Identities=19% Similarity=0.298 Sum_probs=47.6
Q ss_pred ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhH-HHHHHHHHhhcc
Q 042785 396 SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTK-KKLMEAKKALDI 462 (604)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 462 (604)
|=+.++-..|...|. +|.+.||.-+-+|+.+|||+...++ |-.|..-...+ +.+.|++.+|+.
T Consensus 31 pG~~L~e~~La~~lg--VSRtpVReAL~~L~~eGlv~~~~~~--G~~V~~~~~~~~~ei~~~R~~lE~ 94 (212)
T TIGR03338 31 PGAKLNESDIAARLG--VSRGPVREAFRALEEAGLVRNEKNR--GVFVREISLAEADEIYELRAVLDE 94 (212)
T ss_pred CCCEecHHHHHHHhC--CChHHHHHHHHHHHHCCCEEEecCC--CeEEecCCHHHHHHHHHHHHHHHH
Confidence 445567778999998 9999999999999999999976544 87787644332 345666666665
No 51
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=61.16 E-value=7.4 Score=33.19 Aligned_cols=33 Identities=24% Similarity=0.526 Sum_probs=28.3
Q ss_pred hhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc
Q 042785 403 AKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 403 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
..|...|. +++++|++++++|++.|||....++
T Consensus 3 ~ela~~l~--is~stvs~~l~~L~~~glI~r~~~~ 35 (96)
T smart00529 3 SEIAERLN--VSPPTVTQMLKKLEKDGLVEYEPYR 35 (96)
T ss_pred HHHHHHhC--CChHHHHHHHHHHHHCCCEEEcCCC
Confidence 45666776 8999999999999999999998764
No 52
>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=60.17 E-value=11 Score=37.08 Aligned_cols=50 Identities=22% Similarity=0.350 Sum_probs=39.6
Q ss_pred cchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 382 LDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 382 ~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
..++..++.|.+ ...+++..|...|. .++.+|++.+.+|++.|||+-.+.
T Consensus 143 ~~~~~IL~~l~~---~g~~s~~eia~~l~--is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 143 REELKVLEVLKA---EGEKSVKNIAKKLG--KSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHHHHHH---cCCcCHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEEEcC
Confidence 334555555543 24689999999997 999999999999999999998763
No 53
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=60.03 E-value=11 Score=30.30 Aligned_cols=39 Identities=28% Similarity=0.382 Sum_probs=32.9
Q ss_pred ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 396 SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
.-.-.|++.|...|+ +++++++.-+.+|++.|+|+....
T Consensus 21 ~~~~~t~~ela~~l~--~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 21 SNGPMTVSELAEELG--ISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HCSTBEHHHHHHHHT--S-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred cCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCeEEecc
Confidence 446678999999998 999999999999999999986543
No 54
>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=59.63 E-value=14 Score=35.99 Aligned_cols=62 Identities=16% Similarity=0.331 Sum_probs=46.0
Q ss_pred cchhHHHHHHhhhh-ccce-ehhhhhhhhhhhhhh-HHHHHHHHHHHHHhccccccccccccceeee
Q 042785 382 LDDQIYMKALYYAL-SMNY-VTIAKLQKKLDKEAN-QSTVRKLIDKMIREGYVEAKGSRRLGKRVIH 445 (604)
Q Consensus 382 ~~~~~y~~~~~~~l-~~~~-~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 (604)
..|.-.++.|.+.. ...+ .++..|...|. .+ .++|+..|.+|++.|||+...++..|=++++
T Consensus 6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~--~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~~~ 70 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTGYPPSIREIARAVG--LRSPSAAEEHLKALERKGYIERDPGKPRAIRILD 70 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhC--CCChHHHHHHHHHHHHCCCEecCCCCCCeEEeCC
Confidence 34566666666431 1122 67888988888 65 9999999999999999999877755877765
No 55
>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=58.67 E-value=17 Score=30.26 Aligned_cols=53 Identities=15% Similarity=0.239 Sum_probs=35.1
Q ss_pred hhhhhhhh--hhhHHHHHHHHHHHHHhcccccccccc-ccceeeehhhhHHHHHHH
Q 042785 404 KLQKKLDK--EANQSTVRKLIDKMIREGYVEAKGSRR-LGKRVIHSTLTKKKLMEA 456 (604)
Q Consensus 404 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 456 (604)
.|...++| .++..++-.++++|+++|+|+...... -|.+--.=.+|++=..++
T Consensus 18 ~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l 73 (75)
T PF03551_consen 18 ELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREEL 73 (75)
T ss_dssp HHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHH
T ss_pred HHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHh
Confidence 34444444 588999999999999999999877662 333333444555443333
No 56
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=57.32 E-value=16 Score=30.62 Aligned_cols=49 Identities=24% Similarity=0.328 Sum_probs=34.8
Q ss_pred HHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccce
Q 042785 386 IYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKR 442 (604)
Q Consensus 386 ~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (604)
-|++.+. .-++...+-..++ ++.+.||+++.+|+++|.|+...- |.|+.
T Consensus 7 ~~i~~~~-----~p~~T~eiA~~~g--ls~~~aR~yL~~Le~eG~V~~~~~-~rG~~ 55 (62)
T PF04703_consen 7 EYIKEQN-----GPLKTREIADALG--LSIYQARYYLEKLEKEGKVERSPV-RRGKS 55 (62)
T ss_dssp HHHHHHT-----S-EEHHHHHHHHT--S-HHHHHHHHHHHHHCTSEEEES--SSSSS
T ss_pred HHHHHcC-----CCCCHHHHHHHhC--CCHHHHHHHHHHHHHCCCEEEecC-CCCcc
Confidence 3666652 3467777778888 999999999999999999975433 44554
No 57
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=57.25 E-value=10 Score=31.52 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=31.5
Q ss_pred ehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 400 VTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
+++.-|...|. ++..+|++++.+|.++|||+..+.
T Consensus 23 ~ta~eLa~~lg--l~~~~v~r~L~~L~~~G~V~~~~~ 57 (68)
T smart00550 23 STALQLAKNLG--LPKKEVNRVLYSLEKKGKVCKQGG 57 (68)
T ss_pred cCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEecCC
Confidence 78889999998 888899999999999999987654
No 58
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=56.55 E-value=15 Score=37.10 Aligned_cols=64 Identities=20% Similarity=0.307 Sum_probs=48.3
Q ss_pred cccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhh---------------HHHHHHHHHh
Q 042785 396 SMNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLT---------------KKKLMEAKKA 459 (604)
Q Consensus 396 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~ 459 (604)
|=+.+ +-..|..+|. +|.+.||..|.+|+.+|+|+...++ |-.|..-... -..+.|++.+
T Consensus 29 pG~~LpsE~eLa~~~g--VSRtpVREAL~~L~~eGlV~~~~~~--G~~V~~~~~~~~~~~~~~~~~~~~~~~ei~e~R~~ 104 (257)
T PRK10225 29 PGERLPPEREIAEMLD--VTRTVVREALIMLEIKGLVEVRRGA--GIYVLDSSGSHNTDSPDANVCNDAGPFELLQARQL 104 (257)
T ss_pred CCCcCcCHHHHHHHhC--CCHHHHHHHHHHHHHCCCEEEecCC--EEEEeCCCcccccchhhhhhhccCCHHHHHHHHHH
Confidence 33455 5678888898 9999999999999999999976654 7777654322 2467788888
Q ss_pred hccc
Q 042785 460 LDID 463 (604)
Q Consensus 460 ~~~~ 463 (604)
|+..
T Consensus 105 LE~~ 108 (257)
T PRK10225 105 LESN 108 (257)
T ss_pred HHHH
Confidence 8764
No 59
>PRK05638 threonine synthase; Validated
Probab=55.99 E-value=13 Score=41.09 Aligned_cols=57 Identities=25% Similarity=0.213 Sum_probs=42.7
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHH
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAK 457 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 457 (604)
.-.+++.|...|+..+++.++++.+.+|++.|+|+.. .+-|+|+.. .||++-...+.
T Consensus 383 ~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~--~~~g~~~~Y-~Lt~~g~~~l~ 439 (442)
T PRK05638 383 REMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEA--YRKGRRVYY-KLTEKGRRLLE 439 (442)
T ss_pred CCccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEe--ecCCCcEEE-EECcHHHHHHH
Confidence 3457888888888678999999999999999999875 234776644 46766554443
No 60
>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=55.89 E-value=16 Score=31.17 Aligned_cols=40 Identities=30% Similarity=0.591 Sum_probs=28.7
Q ss_pred hhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhH
Q 042785 405 LQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTK 450 (604)
Q Consensus 405 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 450 (604)
+-..+. ++..+||--+.+|+++|+++. .|.|.+..++ ||+
T Consensus 29 ll~~~G--v~e~avR~alsRl~~~G~L~~---~r~Gr~~~Y~-Lt~ 68 (70)
T PF07848_consen 29 LLAAFG--VSESAVRTALSRLVRRGWLES---ERRGRRSYYR-LTE 68 (70)
T ss_dssp HHCCTT----HHHHHHHHHHHHHTTSEEE---ECCCTEEEEE-E-H
T ss_pred HHHHcC--CChHHHHHHHHHHHHcCceee---eecCccceEe-eCC
Confidence 344555 899999999999999999996 4667777665 444
No 61
>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=55.07 E-value=11 Score=33.13 Aligned_cols=36 Identities=14% Similarity=0.177 Sum_probs=30.2
Q ss_pred cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 397 MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
...++...|..++. ++..+|+++|++|++.|||+..
T Consensus 45 ~~~is~~eLa~~~g--~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 45 QDRVTATVIAELTG--LSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CCccCHHHHHHHHC--cCHHHHHHHHHHHHHCCCeeee
Confidence 45667777777777 7889999999999999999844
No 62
>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=54.92 E-value=18 Score=33.28 Aligned_cols=49 Identities=24% Similarity=0.339 Sum_probs=44.2
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
.-+|-|.+-.+.-|.+||..-|..+|. ++-+-+|++|..|+..|.|+.-
T Consensus 44 ~~~~~kl~kEV~~~K~ITp~~lserlk--I~~SlAr~~Lr~L~~kG~Ik~V 92 (105)
T PF03297_consen 44 KETYDKLLKEVPKMKLITPSVLSERLK--INGSLARKALRELESKGLIKPV 92 (105)
T ss_dssp CHHHHHHHHHCTTSSCECHHHHHHHHC--CSCHHHHHHHHHHHHCCSSEEE
T ss_pred HHHHHHHHHHhccCcEeeHHHHHHhHh--hHHHHHHHHHHHHHHCCCEEEE
Confidence 557888777788899999999999999 9999999999999999999763
No 63
>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=53.50 E-value=13 Score=31.04 Aligned_cols=41 Identities=22% Similarity=0.319 Sum_probs=28.5
Q ss_pred ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 396 SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
|+..-.+++.-..-+=+++..+||..+..|+++||++..|+
T Consensus 13 P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g~ 53 (66)
T PF08461_consen 13 PLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVGR 53 (66)
T ss_pred CCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccCC
Confidence 44444444433333455778999999999999999985543
No 64
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=53.33 E-value=20 Score=36.05 Aligned_cols=64 Identities=20% Similarity=0.273 Sum_probs=47.5
Q ss_pred cccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeeh----------------hhhHHHHHHHHH
Q 042785 396 SMNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHS----------------TLTKKKLMEAKK 458 (604)
Q Consensus 396 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~ 458 (604)
|=+.+ +-..|..+|. +|.+.||..+-+|+.+|+|+...+ .|-.|... ..+-+.+.|++.
T Consensus 30 pG~~LpsE~eLa~~lg--VSRtpVREAL~~L~~eGlv~~~~~--~G~~V~~~~~~~~~~~~~~~~~~~~~~~~ei~e~R~ 105 (254)
T PRK09464 30 PGEKLPPERELAKQFD--VSRPSLREAIQRLEAKGLLLRRQG--GGTFVQSSLWQSFSDPLVELLSDHPESQFDLLETRH 105 (254)
T ss_pred CCCcCCCHHHHHHHhC--CCHHHHHHHHHHHHHCCCEEEecC--ceeEEecCccchhhhHHHHHhccCCchHHHHHHHHH
Confidence 44555 6778889998 999999999999999999997654 47677652 112246677887
Q ss_pred hhccc
Q 042785 459 ALDID 463 (604)
Q Consensus 459 ~~~~~ 463 (604)
+|+..
T Consensus 106 ~lE~~ 110 (254)
T PRK09464 106 ALEGI 110 (254)
T ss_pred hhHHH
Confidence 77754
No 65
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=50.40 E-value=25 Score=31.41 Aligned_cols=48 Identities=15% Similarity=0.185 Sum_probs=41.2
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA 433 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 433 (604)
.-+|=|.+--+--|.|||.+-|..+|- ++-+-+|++|..++..|.|+.
T Consensus 26 k~t~dkl~kEV~~~K~ITps~lserlk--I~~SlAr~~Lr~L~~kG~Ik~ 73 (86)
T PRK09334 26 EELLKRVAKEVKKEKIVTPYTLASKYG--IKISVAKKVLRELEKRGVLVL 73 (86)
T ss_pred HHHHHHHHHHhccCcEEcHHHHHHHhc--chHHHHHHHHHHHHHCCCEEE
Confidence 345656555666799999999999999 999999999999999999964
No 66
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=50.19 E-value=33 Score=32.84 Aligned_cols=65 Identities=14% Similarity=0.235 Sum_probs=52.1
Q ss_pred ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHHhhccc
Q 042785 396 SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKKALDID 463 (604)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 463 (604)
+-..+++..|...+. ++..-++|++.+|++.|||+..-.++=|-+.... -.+=.|.+|=++++-+
T Consensus 21 ~~~~~s~~eIA~~~~--is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~-p~eItl~dIi~aveg~ 85 (153)
T PRK11920 21 DGKLSRIPEIARAYG--VSELFLFKILQPLVEAGLVETVRGRNGGVRLGRP-AADISLFDVVRVTEDS 85 (153)
T ss_pred CCCcCcHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCC-HHHCcHHHHHHHHcCC
Confidence 446789999999998 9999999999999999999998887767666654 2455667777777653
No 67
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=49.94 E-value=29 Score=28.35 Aligned_cols=43 Identities=23% Similarity=0.160 Sum_probs=35.2
Q ss_pred cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccccccee
Q 042785 397 MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRV 443 (604)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 (604)
-.+.++..|...|. ++..+|++-|.+|.++|+.--.. +.|-++
T Consensus 11 ~~~~~~~eLa~~l~--vS~~tv~~~l~~L~~~g~~i~~~--~~g~~l 53 (69)
T TIGR00122 11 DNPFSGEKLGEALG--MSRTAVNKHIQTLREWGVDVLTV--GKGYRL 53 (69)
T ss_pred cCCcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCeEEec--CCceEe
Confidence 36788999999998 99999999999999999954333 456665
No 68
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=49.92 E-value=25 Score=33.36 Aligned_cols=57 Identities=33% Similarity=0.446 Sum_probs=43.1
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceee---ehhhhHHHHHHHHHhhc
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVI---HSTLTKKKLMEAKKALD 461 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~ 461 (604)
|+-.|-..|. +|-++|+|--..|+++|||+.. |+.|.=|= +..+.++|...+++.|+
T Consensus 37 SvRelA~~~~--VNpnTv~raY~eLE~eG~i~t~--rg~G~fV~~~~~~~~~~~~~~~~~~~l~ 96 (125)
T COG1725 37 SVRELAKDLG--VNPNTVQRAYQELEREGIVETK--RGKGTFVTEDAKEILDQLKRELAEEELE 96 (125)
T ss_pred cHHHHHHHhC--CCHHHHHHHHHHHHHCCCEEEe--cCeeEEEcCCchhhHHHHHHHHHHHHHH
Confidence 6677778888 9999999999999999999865 44454443 22566777777777666
No 69
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=48.82 E-value=31 Score=28.07 Aligned_cols=32 Identities=22% Similarity=0.480 Sum_probs=27.5
Q ss_pred ehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc
Q 042785 400 VTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA 433 (604)
Q Consensus 400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 433 (604)
+|-.-|...+. .+..+|.+++.+|.++|+|+-
T Consensus 29 lt~~~iA~~~g--~sr~tv~r~l~~l~~~g~I~~ 60 (76)
T PF13545_consen 29 LTQEEIADMLG--VSRETVSRILKRLKDEGIIEV 60 (76)
T ss_dssp SSHHHHHHHHT--SCHHHHHHHHHHHHHTTSEEE
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEE
Confidence 56667777777 888999999999999999994
No 70
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=47.83 E-value=19 Score=28.00 Aligned_cols=32 Identities=34% Similarity=0.705 Sum_probs=28.8
Q ss_pred ehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc
Q 042785 400 VTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA 433 (604)
Q Consensus 400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 433 (604)
++++.|...++ .+.++|..++..|++.|||+-
T Consensus 19 ~t~~eia~~~g--l~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 19 LTLSEIARALG--LPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp EEHHHHHHHHT--S-HHHHHHHHHHHHHTTSEEE
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHHHCcCeec
Confidence 58899999999 999999999999999999974
No 71
>PRK03837 transcriptional regulator NanR; Provisional
Probab=47.60 E-value=28 Score=34.44 Aligned_cols=44 Identities=18% Similarity=0.280 Sum_probs=36.7
Q ss_pred cee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeee
Q 042785 398 NYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIH 445 (604)
Q Consensus 398 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 (604)
+.+ +...|..+|. +|.++||..+-.++.+|+|+-.-+ .|-.|..
T Consensus 35 ~~Lp~E~~Lae~~g--VSRt~VREAL~~L~~eGlv~~~~~--~G~~V~~ 79 (241)
T PRK03837 35 DQLPSERELMAFFG--VGRPAVREALQALKRKGLVQISHG--ERARVSR 79 (241)
T ss_pred CCCCCHHHHHHHhC--CCHHHHHHHHHHHHHCCCEEEecC--CceeEec
Confidence 445 6788899999 999999999999999999998643 3777765
No 72
>PRK09954 putative kinase; Provisional
Probab=47.40 E-value=21 Score=37.70 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=31.3
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVE 432 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 432 (604)
.+++...|...|. .+.++|++.|.+|+++|||+
T Consensus 16 ~~~s~~~la~~l~--~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 16 PLIQQNEIADILQ--ISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred CCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCcC
Confidence 4899999999999 99999999999999999995
No 73
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=46.14 E-value=30 Score=34.70 Aligned_cols=64 Identities=22% Similarity=0.257 Sum_probs=49.1
Q ss_pred cccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhh----------------hHHHHHHHHH
Q 042785 396 SMNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTL----------------TKKKLMEAKK 458 (604)
Q Consensus 396 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~~ 458 (604)
|=+.+ +-..|...|. +|.+.||.-|-+|+.+|+|+...++ |-.|.-... +-+.+.|++.
T Consensus 27 pG~~LPsE~eLa~~~g--VSRtpVREAL~~L~~eGlV~~~~~~--G~~V~~~~~~~~~~~~~~~~~~~~~~~~ei~e~R~ 102 (251)
T PRK09990 27 VGQALPSERRLCEKLG--FSRSALREGLTVLRGRGIIETAQGR--GSFVARLNRVQDASPLMHLFSSQPRTLYDLLEVRA 102 (251)
T ss_pred CCCcCcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEeCCC--eeEEecCCcccccchHHHHHccCccHHHHHHHHHH
Confidence 33555 6677888888 9999999999999999999987654 777765433 3456778888
Q ss_pred hhccc
Q 042785 459 ALDID 463 (604)
Q Consensus 459 ~~~~~ 463 (604)
+|+..
T Consensus 103 ~lE~~ 107 (251)
T PRK09990 103 LLEGE 107 (251)
T ss_pred cCHHH
Confidence 88764
No 74
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator 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.
Probab=45.32 E-value=22 Score=37.43 Aligned_cols=48 Identities=23% Similarity=0.427 Sum_probs=36.8
Q ss_pred hhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHH
Q 042785 405 LQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKK 458 (604)
Q Consensus 405 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 458 (604)
+-+.+. ++..+||.++.+|+++|+|+.. |-|+|..+ .||++-....++
T Consensus 26 l~~~~g--i~~~~vr~al~RL~~~G~l~~~---~~grr~~Y-~LT~~g~~~l~~ 73 (280)
T TIGR02277 26 FLAGLG--INERLVRTAVSRLVAQGWLQSE---RKGRRSFY-SLTDKGRRRFAA 73 (280)
T ss_pred HHHhcC--CCcchHHHHHHHHHHCCCEEee---ecCCCCEE-EECHHHHHHHHH
Confidence 334455 8999999999999999999995 33777777 688877665554
No 75
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=43.89 E-value=38 Score=33.80 Aligned_cols=59 Identities=22% Similarity=0.273 Sum_probs=42.9
Q ss_pred ccCCCCCcchhHHHHHHhhhhc----cceehhhhhhhhhhhh------------hhHHHHHHHHHHHHHhcccccc
Q 042785 375 LCDKSPQLDDQIYMKALYYALS----MNYVTIAKLQKKLDKE------------ANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 375 ~~~~~~~~~~~~y~~~~~~~l~----~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
-...++++.|+.|..| .-.|. ---|-|..|....-|- +|-+.+|+++.+|++.|||+..
T Consensus 64 ~KElaP~d~DW~YiRa-ASilRkiYlrgpvGV~~Lrk~YGg~krrG~~P~h~~~aSg~iiR~~LQqLE~~glVek~ 138 (169)
T PTZ00095 64 GRELAPQNPDWYYIRC-AAVLRALYLRPDVGYGGLRKRFSSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQG 138 (169)
T ss_pred cccCCCCCccHHHHHH-HHHHHHHHhcCCccHHHHHHHHCCCCCCCCCCCcccCCchHHHHHHHHHHHHCCCEEec
Confidence 4567788899999987 22222 2245677777665553 6678999999999999999954
No 76
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=43.50 E-value=22 Score=27.49 Aligned_cols=30 Identities=23% Similarity=0.377 Sum_probs=27.5
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREG 429 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 429 (604)
.++|+..|..+|. +|..+|++-|+.|...|
T Consensus 14 ~~it~~eLa~~l~--vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 14 EPITAKELAEELG--VSRRTIRRDIKELREWG 43 (55)
T ss_dssp TSBEHHHHHHHCT--S-HHHHHHHHHHHHHTT
T ss_pred CCcCHHHHHHHhC--CCHHHHHHHHHHHHHCC
Confidence 4599999999999 99999999999999999
No 77
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=42.77 E-value=33 Score=31.82 Aligned_cols=62 Identities=18% Similarity=0.221 Sum_probs=44.2
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHHhhcc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKKALDI 462 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 (604)
..+++..|...+. ++...++|++.+|++.|||.....+ -|-=..=.+..+=.|.+|=++++-
T Consensus 24 ~~~s~~~ia~~~~--ip~~~l~kil~~L~~~glv~s~~G~-~Ggy~l~~~~~~Itl~dv~~a~eg 85 (135)
T TIGR02010 24 GPVTLADISERQG--ISLSYLEQLFAKLRKAGLVKSVRGP-GGGYQLGRPAEDISVADIIDAVDE 85 (135)
T ss_pred CcCcHHHHHHHHC--cCHHHHHHHHHHHHHCCceEEEeCC-CCCEeccCCHHHCcHHHHHHHhCC
Confidence 3689999999999 9999999999999999999864222 222223233344456666666654
No 78
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=41.87 E-value=47 Score=32.41 Aligned_cols=61 Identities=23% Similarity=0.363 Sum_probs=46.2
Q ss_pred ccCCCCCcchhHHHHH---Hhhhhccceehhhhhhhhhhhh------------hhHHHHHHHHHHHHHhccccccc
Q 042785 375 LCDKSPQLDDQIYMKA---LYYALSMNYVTIAKLQKKLDKE------------ANQSTVRKLIDKMIREGYVEAKG 435 (604)
Q Consensus 375 ~~~~~~~~~~~~y~~~---~~~~l~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~ 435 (604)
-..+.+.++|+.|+.| |.|.-=--+|.|.+|...--|- ++-+.+||++.++++.|||+-.-
T Consensus 40 ~kE~~P~~~DWwY~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~ 115 (147)
T COG2238 40 HKERPPEQEDWWYVRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP 115 (147)
T ss_pred cccCCCCCCchHHHHHHHHHHHHHhcCchhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC
Confidence 4556777899999988 2332223578899998776654 45678999999999999998765
No 79
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=40.19 E-value=38 Score=29.53 Aligned_cols=73 Identities=26% Similarity=0.403 Sum_probs=46.8
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc----cccccccee---eehhhh-HHHHHH
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK----GSRRLGKRV---IHSTLT-KKKLME 455 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~---~~~~~~-~~~~~~ 455 (604)
|.--+.+|..- .-.+...|...+. .+..+|++.|.+|++.|+|... .-+++|..+ |--.++ ..++.+
T Consensus 5 D~~il~~L~~~---~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~~~~~~~~ 79 (108)
T smart00344 5 DRKILEELQKD---ARISLAELAKKVG--LSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLESPDKLEE 79 (108)
T ss_pred HHHHHHHHHHh---CCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEECChhHHHH
Confidence 44444444432 3578889999998 9999999999999999999832 235566531 111223 244555
Q ss_pred HHHhhc
Q 042785 456 AKKALD 461 (604)
Q Consensus 456 ~~~~~~ 461 (604)
+.+.|.
T Consensus 80 v~~~l~ 85 (108)
T smart00344 80 FLEKLE 85 (108)
T ss_pred HHHHHh
Confidence 555554
No 80
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=39.85 E-value=38 Score=34.10 Aligned_cols=64 Identities=19% Similarity=0.307 Sum_probs=46.5
Q ss_pred cccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhh---------------HHHHHHHHHh
Q 042785 396 SMNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLT---------------KKKLMEAKKA 459 (604)
Q Consensus 396 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~ 459 (604)
|=+.+ +-..|..+|. +|.+.||.-+..|+.+|+|+...++ |-.|.-...- -..+.|++.+
T Consensus 28 pG~~LpsE~eLae~~g--VSRtpVREAL~~L~~eGlV~~~~~~--G~~V~~~~~~~~~~~~~~~~~~~~~~~di~e~R~~ 103 (253)
T PRK11523 28 VGDKLPAERFIADEKN--VSRTVVREAIIMLEVEGYVEVRKGS--GIHVVSNQPRHQQAADNNMEFANYGPFELLQARQL 103 (253)
T ss_pred CCCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEecCC--eeEEecCCcccccccchhhhcccCCHHHHHHHHHH
Confidence 33455 4667888898 9999999999999999999977654 7777532211 1356677887
Q ss_pred hccc
Q 042785 460 LDID 463 (604)
Q Consensus 460 ~~~~ 463 (604)
|+..
T Consensus 104 lE~~ 107 (253)
T PRK11523 104 IESN 107 (253)
T ss_pred hHHH
Confidence 7754
No 81
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.24 E-value=51 Score=32.64 Aligned_cols=39 Identities=21% Similarity=0.262 Sum_probs=34.2
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRR 438 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 (604)
..+|...|...|. ++...|||++-+|..+|+|....-|.
T Consensus 35 g~~tdeeLA~~Lg--i~~~~VRk~L~~L~e~gLv~~~r~r~ 73 (178)
T PRK06266 35 GEVTDEEIAEQTG--IKLNTVRKILYKLYDARLADYKREKD 73 (178)
T ss_pred CCcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCeEEeeeec
Confidence 5789999999998 99999999999999999999544333
No 82
>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=38.92 E-value=39 Score=30.81 Aligned_cols=49 Identities=24% Similarity=0.456 Sum_probs=39.0
Q ss_pred HHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc
Q 042785 389 KALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 389 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
..|-++-.-+++|++++...|.-+.+-+.|-.=|-.|.+.||||.+|--
T Consensus 20 ~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkglIEKSGDG 68 (96)
T PF09114_consen 20 NILIQVAKKNFITASEVREALATEMNKASVNSNIGVLIKKGLIEKSGDG 68 (96)
T ss_dssp HHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTTSEEEETTE
T ss_pred HHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcCcccccCCc
Confidence 3455666679999999999998889999999999999999999999864
No 83
>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=38.90 E-value=29 Score=27.86 Aligned_cols=36 Identities=17% Similarity=0.441 Sum_probs=32.7
Q ss_pred ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc
Q 042785 396 SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA 433 (604)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 433 (604)
.-.++++..|...|. +|..++|.=+..|++.|+|+-
T Consensus 11 ~~~~~s~~ela~~~~--VS~~TiRRDl~~L~~~g~i~r 46 (57)
T PF08220_consen 11 EKGKVSVKELAEEFG--VSEMTIRRDLNKLEKQGLIKR 46 (57)
T ss_pred HcCCEEHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEE
Confidence 347899999999998 999999999999999999863
No 84
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=38.59 E-value=37 Score=33.25 Aligned_cols=50 Identities=18% Similarity=0.274 Sum_probs=42.6
Q ss_pred HHHHHhhhhcccee--hhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 387 YMKALYYALSMNYV--TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 387 y~~~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
|.=|++..+||.-. ++..|..+|-+.++..-|++.|+.|++-|+|+..++
T Consensus 25 ~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 25 YHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 44455666776554 799999999888999999999999999999999888
No 85
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=37.78 E-value=48 Score=32.67 Aligned_cols=60 Identities=12% Similarity=0.207 Sum_probs=43.1
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhH---HHHHHHHHhhccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTK---KKLMEAKKALDID 463 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~ 463 (604)
+-++...|...|. +|-+.||.-|-.++.+|+|+...++ |-.|. .++. +.+.|++..|+..
T Consensus 33 ~~L~e~~La~~lg--VSRtpVREAL~~L~~eGLV~~~~~~--g~~v~--~~~~~~~~ei~~~R~~lE~~ 95 (221)
T PRK11414 33 ARLITKNLAEQLG--MSITPVREALLRLVSVNALSVAPAQ--AFTVP--EVSKRQLDEINRIRYELELM 95 (221)
T ss_pred CccCHHHHHHHHC--CCchhHHHHHHHHHHCCCEEecCCC--ceeec--CCCHHHHHHHHHHHHHHHHH
Confidence 3344556888888 9999999999999999999976554 55553 3333 3455667777654
No 86
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=37.16 E-value=22 Score=36.48 Aligned_cols=39 Identities=28% Similarity=0.427 Sum_probs=32.9
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRR 438 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 (604)
-++|..+|.++|+ +|+.++.+.|..|+.+|||...-+++
T Consensus 18 ~~~t~~ela~~l~--~S~qta~R~l~~le~~~~I~R~~~~~ 56 (214)
T COG1339 18 VKVTSSELAKRLG--VSSQTAARKLKELEDEGYITRTISKR 56 (214)
T ss_pred ccccHHHHHHHhC--cCcHHHHHHHHhhccCCcEEEEecCC
Confidence 5799999999999 88888888888999999998655443
No 87
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=36.62 E-value=44 Score=30.73 Aligned_cols=41 Identities=24% Similarity=0.416 Sum_probs=34.1
Q ss_pred ehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccc----cccccce
Q 042785 400 VTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKG----SRRLGKR 442 (604)
Q Consensus 400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~ 442 (604)
.+...|..+|. .+..+|+..|.+|+++|+|+.-+ .+++|..
T Consensus 23 ~~~~eia~~lg--lS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~ 67 (154)
T COG1522 23 ISNAELAERVG--LSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLD 67 (154)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCC
Confidence 67788888888 99999999999999999987643 3456776
No 88
>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=35.01 E-value=31 Score=34.03 Aligned_cols=40 Identities=25% Similarity=0.439 Sum_probs=31.3
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceee
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVI 444 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (604)
|-..|..+++ +|..+||+.|+.++++|||+.. ++.|--|.
T Consensus 34 sE~eLa~~~~--VSR~TvR~Al~~L~~eGli~r~--~G~GtfV~ 73 (238)
T TIGR02325 34 AEMQLAERFG--VNRHTVRRAIAALVERGLLRAE--QGRGTFVA 73 (238)
T ss_pred CHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEe--cCCEEEEC
Confidence 4456777777 9999999999999999999875 34455554
No 89
>PRK12423 LexA repressor; Provisional
Probab=34.53 E-value=36 Score=33.72 Aligned_cols=45 Identities=20% Similarity=0.333 Sum_probs=38.3
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeeh
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHS 446 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 446 (604)
|+..|...| |-.++++|++.+.+|++.|||+..-+++-|-+|.+.
T Consensus 27 s~~eia~~~-g~~s~~~v~~~l~~L~~~G~l~~~~~~~~~~~v~~~ 71 (202)
T PRK12423 27 SLAEIAQAF-GFASRSVARKHVQALAEAGLIEVVPNQARGIRLPGG 71 (202)
T ss_pred CHHHHHHHh-CCCChHHHHHHHHHHHHCCCEEecCCCcceeeeccc
Confidence 777787777 455899999999999999999998888888888664
No 90
>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=34.21 E-value=33 Score=34.09 Aligned_cols=40 Identities=18% Similarity=0.327 Sum_probs=31.1
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceee
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVI 444 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (604)
+-..|..++. +|..+||+.|+.++++|+|..... .|--|.
T Consensus 27 sE~eLa~~~~--VSR~TVR~Al~~L~~eGli~r~~G--~GtfV~ 66 (230)
T TIGR02018 27 SEHELVAQYG--CSRMTVNRALRELTDAGLLERRQG--VGTFVA 66 (230)
T ss_pred CHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEecC--CEEEEc
Confidence 5556777777 999999999999999999986533 354553
No 91
>PHA00738 putative HTH transcription regulator
Probab=34.15 E-value=39 Score=31.49 Aligned_cols=49 Identities=16% Similarity=0.271 Sum_probs=42.1
Q ss_pred eehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHH
Q 042785 399 YVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKK 452 (604)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 452 (604)
-.+++.|...|+ ++|.+|++-+..|.+-|+|+ .+|-|+.|+++--.+.+
T Consensus 26 ~~~V~eLae~l~--lSQptVS~HLKvLreAGLV~---srK~Gr~vyY~Ln~~~~ 74 (108)
T PHA00738 26 ILSASLISHTLL--LSYTTVLRHLKILNEQGYIE---LYKEGRTLYAKIRENSK 74 (108)
T ss_pred CccHHHHHHhhC--CCHHHHHHHHHHHHHCCceE---EEEECCEEEEEECCCcc
Confidence 378999999997 99999999999999999997 57889999988544443
No 92
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=33.20 E-value=62 Score=32.14 Aligned_cols=43 Identities=14% Similarity=0.388 Sum_probs=34.2
Q ss_pred cee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceee
Q 042785 398 NYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVI 444 (604)
Q Consensus 398 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (604)
+-+ +-..|..+|. +|.++||.-+.+|+.+|+|+...+ .|-.|-
T Consensus 29 ~~LPsE~eLae~~g--VSRt~VReAL~~L~~eGlv~~~~g--~G~~V~ 72 (239)
T PRK04984 29 SILPAERELSELIG--VTRTTLREVLQRLARDGWLTIQHG--KPTKVN 72 (239)
T ss_pred CcCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEeCC--CeeEeC
Confidence 344 5667888888 999999999999999999996544 366663
No 93
>PRK14136 recX recombination regulator RecX; Provisional
Probab=32.97 E-value=27 Score=37.76 Aligned_cols=78 Identities=27% Similarity=0.369 Sum_probs=59.8
Q ss_pred ccCCCCCcchhHHHHHHhhhhccceehhhhhhhhhhh-hhhHHHHHHHHHHHHHhcccccc---------ccccccceee
Q 042785 375 LCDKSPQLDDQIYMKALYYALSMNYVTIAKLQKKLDK-EANQSTVRKLIDKMIREGYVEAK---------GSRRLGKRVI 444 (604)
Q Consensus 375 ~~~~~~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~ 444 (604)
..-+...+.-.+|-+||++ |-..-.|...|..+|.. +.....+-.+|++|++.|||... -.++.|++.|
T Consensus 153 ~~~~~~~~~~~lk~kAL~l-LSrReRSe~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~~kkGp~rI 231 (309)
T PRK14136 153 RSRASSRPARSLKGRALGY-LSRREYSRAELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRASRVGSARI 231 (309)
T ss_pred ccccccccHHHHHHHHHHH-hhcccccHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhchhHHHH
Confidence 4444556667899999877 66677788888888863 66778999999999999998643 2345799999
Q ss_pred ehhhhHHHH
Q 042785 445 HSTLTKKKL 453 (604)
Q Consensus 445 ~~~~~~~~~ 453 (604)
-.+|-.|.+
T Consensus 232 rqELrQKGI 240 (309)
T PRK14136 232 VSELKRHAV 240 (309)
T ss_pred HHHHHHcCC
Confidence 988887765
No 94
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=32.87 E-value=24 Score=35.77 Aligned_cols=45 Identities=22% Similarity=0.369 Sum_probs=39.0
Q ss_pred eehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc---cccccccceeee
Q 042785 399 YVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA---KGSRRLGKRVIH 445 (604)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~ 445 (604)
-++++.|...|+ .+.++|..|+.-|++.|||+. .+.-+||-+++.
T Consensus 28 ~l~l~eia~~lg--l~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~~~~~ 75 (257)
T PRK15090 28 EIGITELSQRVM--MSKSTVYRFLQTMKTLGYVAQEGESEKYSLTLKLFE 75 (257)
T ss_pred CCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEEcCCCCcEEecHHHHH
Confidence 478999999999 999999999999999999974 355678988774
No 95
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=32.41 E-value=69 Score=31.54 Aligned_cols=60 Identities=13% Similarity=0.325 Sum_probs=43.8
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHH---HHHHHHHhhccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKK---KLMEAKKALDID 463 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~ 463 (604)
+-++...|..+|. +|.+.||.-+.+|+.+|+|+-..+ .|-+|.. ++.. .+.+++..|+..
T Consensus 29 ~~L~e~eLae~lg--VSRtpVREAL~~L~~eGlv~~~~~--~G~~V~~--~~~~~~~ei~~~R~~lE~~ 91 (224)
T PRK11534 29 EKLRMSLLTSRYA--LGVGPLREALSQLVAERLVTVVNQ--KGYRVAS--MSEQELLDIFDARANMEAM 91 (224)
T ss_pred CcCCHHHHHHHHC--CChHHHHHHHHHHHHCCCEEEeCC--CceEeCC--CCHHHHHHHHHHHHHHHHH
Confidence 4456677888887 999999999999999999997544 4667764 3333 455666666653
No 96
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=31.79 E-value=68 Score=31.81 Aligned_cols=46 Identities=13% Similarity=0.384 Sum_probs=37.3
Q ss_pred cccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeee
Q 042785 396 SMNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIH 445 (604)
Q Consensus 396 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 (604)
|=+.+ +-..|..+|. +|.+.||.-+-+|+.+|+|+...+| |-.|..
T Consensus 26 pG~~LpsE~~La~~lg--VSRtpVREAL~~Le~eGlV~~~~~~--G~~V~~ 72 (235)
T TIGR02812 26 PGSILPAERELSELIG--VTRTTLREVLQRLARDGWLTIQHGK--PTKVNN 72 (235)
T ss_pred CCCcCcCHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEEeCCC--ccEecC
Confidence 33455 6778889998 9999999999999999999966543 777754
No 97
>KOG3874 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.33 E-value=3.6e+02 Score=30.66 Aligned_cols=115 Identities=14% Similarity=0.199 Sum_probs=70.5
Q ss_pred HHHHHHHhccc---ceEEEEEEecC--CCc-eeEEEEEEEEeecCCCCceeEEEeecCCcccCcccccccccccCHHHHH
Q 042785 66 RVYDALQKKYL---KTLLFCVCEAV--EGP-MIEEYAFSFSYSDSDSQEISMNINRTGNKKKGGTFKCNTTTEITTTQMR 139 (604)
Q Consensus 66 gVfDALeKgYL---K~LvLvIy~~~--ddp-VIEsYtFsFsYs~~gg~eVsm~l~stGnkk~~~t~~~~~~s~~Tl~qIR 139 (604)
-.+.||.+.|. +.|.+-|.... .+- .+|.|.....-.. + .+. +...++=
T Consensus 64 e~K~altg~~p~vgl~lcvEisLkT~eGd~m~LE~W~L~~~ate--g----------------~~~-------k~~~~~Y 118 (504)
T KOG3874|consen 64 ELKSALTGSYPPVGLTLCVEISLKTPEGDLMPLEAWILSSSATE--G----------------TDD-------KSRNELY 118 (504)
T ss_pred HHHHHhccCCCccCcceEEEEEEecCCCCeeeeehheecccccc--C----------------chh-------HHHHHHH
Confidence 46777766664 24455555433 232 7899988776221 1 011 1233555
Q ss_pred HHHHHHHHHHHHHhhhcC-------CCCcceeEEEEEEEecCCCCCCCCCCCcccCCccCCCCCCCCCCceeEeeeecCC
Q 042785 140 SSACKMVRTLVQLMRTLD-------RMPEERTILMKLFYYDDVTPVDYEPPFFRCCSEEEAHNPWTKNPLKMEVGNVNSK 212 (604)
Q Consensus 140 kqI~~LIRqLi~Ltq~L~-------pLPdeR~lsmKLlYyDDvTP~DYEPPGFk~asd~e~~y~~~knp~kv~LGs~sTg 212 (604)
..+-.|+|.|+.+++.-| .-|.+..+.+|++|-++ +-. ...+--..+.||.+.|.
T Consensus 119 nrms~lLkSli~~tR~TPayrLsrkq~~~ey~I~yriyf~~~------q~s------------~lGeG~ktvkiG~l~T~ 180 (504)
T KOG3874|consen 119 NRMSTLLKSLIVSTRMTPAYRLSRKQQHLEYFIIYRIYFEND------QSS------------DLGEGKKTVKIGELVTK 180 (504)
T ss_pred HHHHHHHHHHHHHhccChhhhhhhhcCCcceEEEEEEEecCc------ccc------------ccccCceeEEeeeeeee
Confidence 667779999999998532 34567778888755321 111 12334457999999999
Q ss_pred CeeEEEEEEEe
Q 042785 213 HFVLALKVKSV 223 (604)
Q Consensus 213 hH~V~LkV~Sv 223 (604)
.-.+.+.|+-.
T Consensus 181 vG~i~ls~aYR 191 (504)
T KOG3874|consen 181 VGNISLSLAYR 191 (504)
T ss_pred eccEEEEEeee
Confidence 88888888654
No 98
>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=30.62 E-value=65 Score=28.51 Aligned_cols=23 Identities=13% Similarity=0.479 Sum_probs=20.8
Q ss_pred hhhHHHHHHHHHHHHHhcccccc
Q 042785 412 EANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 412 ~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
.+++.++..++++|+++|+|+..
T Consensus 36 ~i~~gtlY~~L~rLe~~GlI~~~ 58 (100)
T TIGR03433 36 QVEEGSLYPALHRLERRGWIAAE 58 (100)
T ss_pred ccCCCcHHHHHHHHHHCCCeEEE
Confidence 38889999999999999999973
No 99
>PRK00215 LexA repressor; Validated
Probab=30.53 E-value=70 Score=31.32 Aligned_cols=52 Identities=13% Similarity=0.233 Sum_probs=37.0
Q ss_pred hhHHHHHHhhhhc-cc-eehhhhhhhhhhhhh-hHHHHHHHHHHHHHhccccccccc
Q 042785 384 DQIYMKALYYALS-MN-YVTIAKLQKKLDKEA-NQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 384 ~~~y~~~~~~~l~-~~-~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
++.+++.|++..- -. ..++..|...+. . +.++|..++.+|++.|||+.....
T Consensus 6 q~~il~~i~~~~~~~~~~~s~~ela~~~~--~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 6 QQEILDFIRDHIEETGYPPSRREIADALG--LRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 4445555553211 11 247788888888 7 899999999999999999776544
No 100
>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=30.08 E-value=42 Score=33.31 Aligned_cols=31 Identities=26% Similarity=0.459 Sum_probs=26.1
Q ss_pred hhhhhhhhhhhhhHHHHHHHHHHHHHhcccccc
Q 042785 402 IAKLQKKLDKEANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
-..|..++. +|..+||+-|+.++++|||+..
T Consensus 27 E~eLa~~~g--VSR~TVR~Al~~L~~eGli~r~ 57 (233)
T TIGR02404 27 EHELMDQYG--ASRETVRKALNLLTEAGYIQKI 57 (233)
T ss_pred HHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEe
Confidence 345666666 9999999999999999999864
No 101
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=29.38 E-value=53 Score=30.60 Aligned_cols=44 Identities=20% Similarity=0.293 Sum_probs=37.5
Q ss_pred eehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehh
Q 042785 399 YVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHST 447 (604)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 (604)
=++++.|...|+ .+|.+|++-+..|.+-|+|.. +|-|+.++++-
T Consensus 30 ~~~v~ela~~l~--lsqstvS~HL~~L~~AGLV~~---~r~Gr~~~Y~l 73 (117)
T PRK10141 30 ELCVCDLCTALD--QSQPKISRHLALLRESGLLLD---RKQGKWVHYRL 73 (117)
T ss_pred CcCHHHHHHHHC--cCHHHHHHHHHHHHHCCceEE---EEEcCEEEEEE
Confidence 478899999997 999999999999999999975 56677777664
No 102
>COG3177 Fic family protein [Function unknown]
Probab=29.28 E-value=50 Score=35.62 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=42.7
Q ss_pred ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceee
Q 042785 396 SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVI 444 (604)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (604)
+-.|+|+.+.+..+. ++..+|++-|.+++..|+++..+.|..++.+.
T Consensus 301 ~~~~~t~~~~~~~~~--~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~~~ 347 (348)
T COG3177 301 QEGYLTAAEIEAILG--VSKATATRDLKELLELGILEEVKGRGRSKLYS 347 (348)
T ss_pred cCCCccHHHHHHHhC--ccHHHHHHHHHHHHhCCCeeecCCCCCceecc
Confidence 568999999999998 99999999999999999999999998887653
No 103
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=29.23 E-value=41 Score=33.65 Aligned_cols=43 Identities=21% Similarity=0.281 Sum_probs=33.3
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehh
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHST 447 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 (604)
+-..|..++. +|..+||+-|+.++++|||... ++.|--|.+..
T Consensus 35 sE~eLa~~~~--VSR~TvR~Al~~L~~eGli~r~--~G~GTfV~~~~ 77 (241)
T PRK11402 35 TENELCTQYN--VSRITIRKAISDLVADGVLIRW--QGKGTFVQSQK 77 (241)
T ss_pred CHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEe--cCceeEECCCc
Confidence 3456667777 8999999999999999999954 55666665543
No 104
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=29.10 E-value=72 Score=30.34 Aligned_cols=61 Identities=20% Similarity=0.359 Sum_probs=46.0
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhh--hhHHHHHHHHHHHHHhccccccccccccceeeehhhhH
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKE--ANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTK 450 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 450 (604)
+.--|++|+-. -..|+..++..|.++ .+-++|+.||.++++.|+|.. +|-|++-+++-|=+
T Consensus 8 E~eVM~ilW~~---~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~---~kdgr~~~y~pL~~ 70 (123)
T COG3682 8 EWEVMEILWSR---GPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTR---KKDGRAFRYSPLLT 70 (123)
T ss_pred HHHHHHHHHHc---CCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhh---hhcCCeeeeecccC
Confidence 34456676653 356788887777665 899999999999999999975 56777777776533
No 105
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=28.93 E-value=74 Score=32.07 Aligned_cols=46 Identities=15% Similarity=0.255 Sum_probs=37.1
Q ss_pred cccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeee
Q 042785 396 SMNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIH 445 (604)
Q Consensus 396 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 (604)
|=+.+ +-..|..+|. +|.+.||.-|..|+.+|+|+-..+ .|-.|..
T Consensus 22 pG~~LpsE~eLae~~g--VSRtpVREAL~~Le~~GlV~~~~~--~G~~V~~ 68 (253)
T PRK10421 22 AGMKLPAERQLAMQLG--VSRNSLREALAKLVSEGVLLSRRG--GGTFIRW 68 (253)
T ss_pred CCCcCCCHHHHHHHhC--CCHHHHHHHHHHHHHCCCEEEeCC--CeEEEec
Confidence 44556 5678889998 999999999999999999997644 4777754
No 106
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=28.17 E-value=46 Score=33.36 Aligned_cols=41 Identities=24% Similarity=0.563 Sum_probs=31.6
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeee
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIH 445 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 (604)
+=..|..++. +|..+||+-|+.+++||||... ++.|--|..
T Consensus 37 sE~eLa~~~~--VSR~TVR~Al~~L~~eGli~r~--~G~GtfV~~ 77 (241)
T PRK10079 37 AEQQLAARYE--VNRHTLRRAIDQLVEKGWVQRR--QGVGVLVLM 77 (241)
T ss_pred CHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEe--cCCEEEEec
Confidence 4456677777 9999999999999999999843 445656643
No 107
>PRK14999 histidine utilization repressor; Provisional
Probab=27.95 E-value=48 Score=33.22 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=27.3
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccc
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKG 435 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 435 (604)
+-..|..++. +|..+||+.|+.++++|||....
T Consensus 38 sE~eLa~~~g--VSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 38 SEAELVAQYG--FSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEec
Confidence 4456667777 99999999999999999997643
No 108
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=27.68 E-value=1.2e+02 Score=28.25 Aligned_cols=67 Identities=19% Similarity=0.205 Sum_probs=48.3
Q ss_pred HhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHH--HHHHHHHhh
Q 042785 391 LYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKK--KLMEAKKAL 460 (604)
Q Consensus 391 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 460 (604)
|||.+. .=.-...|+..+.| ++|.+.+.-+..|+++|+|+..--.--.-||--+ ||++ .|.++=..|
T Consensus 29 l~~L~~-g~~RF~eL~r~i~~-Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~-LT~~G~~L~~vl~~l 97 (120)
T COG1733 29 LRDLFD-GPKRFNELRRSIGG-ISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYR-LTEKGRDLLPVLLAL 97 (120)
T ss_pred HHHHhc-CCCcHHHHHHHccc-cCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEE-EhhhHHHHHHHHHHH
Confidence 444433 33345677777877 9999999999999999999877666555566555 7776 666666555
No 109
>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=27.24 E-value=69 Score=28.26 Aligned_cols=45 Identities=18% Similarity=0.267 Sum_probs=35.6
Q ss_pred HHHHhhhhccceehhhhhhhhhhh---hhhHHHHHHHHHHHHHhcccccc
Q 042785 388 MKALYYALSMNYVTIAKLQKKLDK---EANQSTVRKLIDKMIREGYVEAK 434 (604)
Q Consensus 388 ~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~ 434 (604)
+++|... -.++|+..|...|.. .++..||-..++.|++.|+|..-
T Consensus 7 l~~l~~~--~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 7 LEVLLES--DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREI 54 (116)
T ss_pred HHHHHhC--CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEE
Confidence 3444433 378999999999864 37999999999999999999753
No 110
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=27.00 E-value=81 Score=31.33 Aligned_cols=63 Identities=21% Similarity=0.353 Sum_probs=47.4
Q ss_pred ccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhH-HHHHHHHHhhcc
Q 042785 396 SMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTK-KKLMEAKKALDI 462 (604)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 462 (604)
|=.-++...|...|. +|-+-||..+-+++.||+|+-. .+.|-.|..-+..+ +.+-|++.+|+.
T Consensus 36 pG~~l~e~~La~~~g--vSrtPVReAL~rL~~eGlv~~~--p~rG~~V~~~~~~~~~ei~~~R~~lE~ 99 (230)
T COG1802 36 PGERLSEEELAEELG--VSRTPVREALRRLEAEGLVEIE--PNRGAFVAPLSLAEAREIFEVRELLEG 99 (230)
T ss_pred CCCCccHHHHHHHhC--CCCccHHHHHHHHHHCCCeEec--CCCCCeeCCCCHHHHHHHHHHHHHHHH
Confidence 445567777888888 9999999999999999999988 45588887665443 334556666655
No 111
>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=26.79 E-value=57 Score=27.26 Aligned_cols=36 Identities=22% Similarity=0.464 Sum_probs=27.8
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccc
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSR 437 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (604)
|+..|...|. -.|.++|...+..|++.|||+...++
T Consensus 27 t~rEIa~~~g-~~S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 27 TVREIAEALG-LKSTSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp -HHHHHHHHT-SSSHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred CHHHHHHHhC-CCChHHHHHHHHHHHHCcCccCCCCC
Confidence 6666766664 34699999999999999999865544
No 112
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=26.79 E-value=1.4e+02 Score=33.82 Aligned_cols=75 Identities=20% Similarity=0.276 Sum_probs=56.8
Q ss_pred HHHHHhhhhc--cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccce---eeehhhhHHHHHHHHHhhc
Q 042785 387 YMKALYYALS--MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKR---VIHSTLTKKKLMEAKKALD 461 (604)
Q Consensus 387 y~~~~~~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 461 (604)
|+-.||-... --.+|+..|...|- -+.--||.||.||.++|.|+=...+--||| +++.+..+-....+++.|+
T Consensus 9 ~~~~L~~~~~~~~~~~~l~~la~~l~--cs~R~~~~~l~~~~~~gwl~w~~~~GRg~~s~l~~~~~~~~~~~~~~~~~~~ 86 (552)
T PRK13626 9 QFIRLWQCCEGKSQETTLNELAELLN--CSRRHMRTLLNTMQQRGWLTWQAEAGRGKRSRLTFLYTGLALQQQRAEDLLE 86 (552)
T ss_pred HHHHHHHhcCCCcceeeHHHHHHHhc--CChhHHHHHHHHHHHCCCeeeecCCCCCCceEEEEEECHHHHHHHHHHHHHh
Confidence 4444544332 23679999999998 888899999999999999998777766665 6777777777777777776
Q ss_pred cc
Q 042785 462 ID 463 (604)
Q Consensus 462 ~~ 463 (604)
..
T Consensus 87 ~g 88 (552)
T PRK13626 87 QD 88 (552)
T ss_pred cC
Confidence 63
No 113
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=26.26 E-value=88 Score=28.26 Aligned_cols=54 Identities=17% Similarity=0.227 Sum_probs=35.1
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccc
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRL 439 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 (604)
|-.+++-|+|.-...-=..-.+...+. +...-|+.++++|++.|+|+.-.++-+
T Consensus 6 ~~l~~~IL~hl~~~~~Dy~k~ia~~l~--~~~~~v~~~l~~Le~~GLler~~g~~i 59 (92)
T PF10007_consen 6 DPLDLKILQHLKKAGPDYAKSIARRLK--IPLEEVREALEKLEEMGLLERVEGKTI 59 (92)
T ss_pred ChhHHHHHHHHHHHCCCcHHHHHHHHC--CCHHHHHHHHHHHHHCCCeEEecCccc
Confidence 445566666643332222223344454 788899999999999999998776533
No 114
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=26.21 E-value=76 Score=27.86 Aligned_cols=50 Identities=28% Similarity=0.394 Sum_probs=38.2
Q ss_pred HhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccccccee
Q 042785 391 LYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRV 443 (604)
Q Consensus 391 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 (604)
|+-.+--+|++=.+|..+|. ++.++|-|.|+++.++|| +-.+.+..|-++
T Consensus 11 ll~~~~~~~~SGe~La~~Lg--iSRtaVwK~Iq~Lr~~G~-~I~s~~~kGY~L 60 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELG--ISRTAVWKHIQQLREEGV-DIESVRGKGYLL 60 (79)
T ss_pred HHHHcCCCcccHHHHHHHHC--ccHHHHHHHHHHHHHhCC-ceEecCCCceec
Confidence 44555668999999999999 999999999999999997 223334444443
No 115
>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=26.17 E-value=61 Score=28.48 Aligned_cols=32 Identities=25% Similarity=0.403 Sum_probs=27.0
Q ss_pred eehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccc
Q 042785 399 YVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVE 432 (604)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 432 (604)
=|.+..|..+| ..+-..||+.|+.|..+|+|-
T Consensus 65 Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 65 GVHVDEIAQQL--GMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp TEEHHHHHHHS--TS-HHHHHHHHHHHHHTTSEE
T ss_pred cccHHHHHHHh--CcCHHHHHHHHHHHHhCCeEe
Confidence 47788888888 588999999999999999984
No 116
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=25.74 E-value=1.4e+02 Score=23.87 Aligned_cols=53 Identities=30% Similarity=0.406 Sum_probs=40.4
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHH
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEA 456 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 456 (604)
...+++.|...++ .++.+|..-+..+.+.|+|+. ++.|+.++-. +.+.++.++
T Consensus 38 ~~~~~~~l~~~~~--~~~~~v~~hL~~L~~~glv~~---~~~~~~~~~~-l~~~~~~~~ 90 (110)
T COG0640 38 GELTVGELAEALG--LSQSTVSHHLKVLREAGLVEL---RREGRLRLYR-LADEKVAEL 90 (110)
T ss_pred CCccHHHHHHHHC--CChhHHHHHHHHHHHCCCeEE---EecccEEEEe-cCcHHHHHH
Confidence 3566888888885 899999999999999999999 7777776655 444433333
No 117
>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=25.58 E-value=1.2e+02 Score=26.21 Aligned_cols=52 Identities=21% Similarity=0.305 Sum_probs=39.9
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHH
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKK 451 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 451 (604)
.......|+..+.| ++..+..+-+..|+++|+|+..-...-+.+|-. .||++
T Consensus 17 g~~rf~el~~~l~~-is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y-~LT~~ 68 (90)
T PF01638_consen 17 GPMRFSELQRRLPG-ISPKVLSQRLKELEEAGLVERRVYPEVPPRVEY-SLTEK 68 (90)
T ss_dssp SSEEHHHHHHHSTT-S-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEE-EE-HH
T ss_pred CCCcHHHHHHhcch-hHHHHHHHHHHHHHHcchhhcccccCCCCCCcc-CCCcC
Confidence 45566788888854 889999999999999999988777666777765 47774
No 118
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=25.28 E-value=56 Score=33.70 Aligned_cols=52 Identities=27% Similarity=0.369 Sum_probs=42.0
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccc-ccceeeehhhhHH
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRR-LGKRVIHSTLTKK 451 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 451 (604)
.=+|+..|..+|. ++..+||+-|+.++.+|+|+..-.+. -|.+--|--||++
T Consensus 24 g~~sa~elA~~Lg--is~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~ 76 (218)
T COG2345 24 GPVSADELAEELG--ISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEK 76 (218)
T ss_pred CCccHHHHHHHhC--CCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeeccc
Confidence 5678889999999 99999999999999999999883332 3666666666655
No 119
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=24.56 E-value=1.7e+02 Score=24.76 Aligned_cols=33 Identities=18% Similarity=0.284 Sum_probs=24.9
Q ss_pred cceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccc
Q 042785 397 MNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYV 431 (604)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (604)
..=.+.+.|..... .|...+.+.++.|++.|+|
T Consensus 17 ~~~~~~t~i~~~~~--L~~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 17 KGGAKKTEIMYKAN--LNYSTLKKYLKELEEKGLI 49 (77)
T ss_dssp TT-B-HHHHHTTST----HHHHHHHHHHHHHTTSE
T ss_pred cCCCCHHHHHHHhC--cCHHHHHHHHHHHHHCcCe
Confidence 34456677777776 8999999999999999999
No 120
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=24.00 E-value=63 Score=32.44 Aligned_cols=40 Identities=23% Similarity=0.345 Sum_probs=30.9
Q ss_pred hhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceee
Q 042785 401 TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVI 444 (604)
Q Consensus 401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (604)
+-..|..++. +|-.+||+.|+.++++|+|..... .|--|.
T Consensus 31 sE~eL~~~~~--VSR~TvR~Al~~L~~eGli~r~~G--~GtfV~ 70 (240)
T PRK09764 31 TESALQTEFG--VSRVTVRQALRQLVEQQILESIQG--SGTYVK 70 (240)
T ss_pred CHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEecC--ceeEEc
Confidence 4456777777 899999999999999999986533 355554
No 121
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=23.60 E-value=51 Score=33.71 Aligned_cols=42 Identities=33% Similarity=0.520 Sum_probs=35.3
Q ss_pred ehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc---ccccccccee
Q 042785 400 VTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA---KGSRRLGKRV 443 (604)
Q Consensus 400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~ 443 (604)
+++..|...|. .+.++|..|+..|++.|||+- .+.-+||-++
T Consensus 27 ls~~eia~~lg--l~kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~ 71 (263)
T PRK09834 27 ATVGLLAELTG--LHRTTVRRLLETLQEEGYVRRSASDDSFRLTLKV 71 (263)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEEecCCCcEEEcHHH
Confidence 78899999997 999999999999999999974 3445677554
No 122
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=23.54 E-value=71 Score=36.09 Aligned_cols=51 Identities=20% Similarity=0.255 Sum_probs=41.7
Q ss_pred CcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccc
Q 042785 381 QLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGS 436 (604)
Q Consensus 381 ~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (604)
...++.++++|+.. .-++...|...|. .+..+|...|++|++.|||+....
T Consensus 5 t~~e~~vL~~L~~~---~~~s~~eLA~~l~--l~~~tVt~~i~~Le~kGlV~~~~~ 55 (489)
T PRK04172 5 HPNEKKVLKALKEL---KEATLEELAEKLG--LPPEAVMRAAEWLEEKGLVKVEER 55 (489)
T ss_pred CHHHHHHHHHHHhC---CCCCHHHHHHHhC--cCHHHHHHHHHHHHhCCCEEEEee
Confidence 34578889998652 3568888888888 889999999999999999998643
No 123
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=23.48 E-value=95 Score=30.08 Aligned_cols=42 Identities=17% Similarity=0.185 Sum_probs=35.1
Q ss_pred HHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccc
Q 042785 386 IYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVE 432 (604)
Q Consensus 386 ~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 432 (604)
.=+.||. +-..+|...|...|. ++.+.|||++-+|..+|+|.
T Consensus 18 ~Vl~aL~---~~~~~tdEeLa~~Lg--i~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 18 LVLFSLG---IKGEFTDEEISLELG--IKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred HHHHHHh---ccCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCce
Confidence 3455554 236789999999997 99999999999999999995
No 124
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 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 [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=23.47 E-value=1.2e+02 Score=29.37 Aligned_cols=61 Identities=25% Similarity=0.328 Sum_probs=41.4
Q ss_pred ccCCCCCcchhHHHHH---Hhhhhccceehhhhhhhhhhh------------hhhHHHHHHHHHHHHHhccccccc
Q 042785 375 LCDKSPQLDDQIYMKA---LYYALSMNYVTIAKLQKKLDK------------EANQSTVRKLIDKMIREGYVEAKG 435 (604)
Q Consensus 375 ~~~~~~~~~~~~y~~~---~~~~l~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~ 435 (604)
-...++.+.|+.|..| |.|.-=---+.|..|....-| .+|-+.+|+++.+++.-|+|+...
T Consensus 39 ~kE~~P~~~DW~Y~RaASilRklY~~g~~GV~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~ 114 (139)
T PF01090_consen 39 HKELAPYDPDWWYIRAASILRKLYIRGPVGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDP 114 (139)
T ss_dssp S-SSTTCHHTHHHHHHHHHHHHHHHCTSB-HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEET
T ss_pred cccCCCCCCCeeeeeHHHHHHHHHHhcCcchHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecC
Confidence 5567888899999987 112111124667777755544 367889999999999999999763
No 125
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=23.31 E-value=1e+02 Score=27.30 Aligned_cols=43 Identities=30% Similarity=0.397 Sum_probs=30.0
Q ss_pred HHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccc
Q 042785 388 MKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKG 435 (604)
Q Consensus 388 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 435 (604)
|.+|.+ -..++-..|..++. .+.+.||+++-+|.++|+|.-..
T Consensus 19 l~~L~~---~~~l~de~la~~~~--l~~~~vRkiL~~L~~~~lv~~~~ 61 (105)
T PF02002_consen 19 LDALLR---KGELTDEDLAKKLG--LKPKEVRKILYKLYEDGLVSYRR 61 (105)
T ss_dssp HHHHHH---H--B-HHHHHHTT---S-HHHHHHHHHHHHHHSS-EEEE
T ss_pred HHHHHH---cCCcCHHHHHHHhC--CCHHHHHHHHHHHHHCCCeEEEE
Confidence 555552 25677888888888 89999999999999999996553
No 126
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=22.76 E-value=68 Score=34.68 Aligned_cols=43 Identities=21% Similarity=0.442 Sum_probs=34.7
Q ss_pred ccee-hhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccccccee
Q 042785 397 MNYV-TIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRV 443 (604)
Q Consensus 397 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 (604)
-+.+ ++..|..+|. +|.++|++-+++++++|||.... +.|-.|
T Consensus 26 g~~lps~r~la~~~~--vsr~tv~~a~~~L~~~g~i~~~~--~~G~~v 69 (431)
T PRK15481 26 GDSLPPVRELASELG--VNRNTVAAAYKRLVTAGLAQSQG--RNGTVI 69 (431)
T ss_pred CCcCcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEEeC--CCceEE
Confidence 3444 6788999999 99999999999999999998643 346555
No 127
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=22.76 E-value=1.1e+02 Score=31.44 Aligned_cols=58 Identities=12% Similarity=0.190 Sum_probs=46.5
Q ss_pred CCCCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHH-HHHHhccccccccc
Q 042785 378 KSPQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLID-KMIREGYVEAKGSR 437 (604)
Q Consensus 378 ~~~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 437 (604)
......|..|+.|+.-.++-.-+++..+...|. .+..+++.+++ ++++.|+|++-+.-
T Consensus 234 ~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg--~~~~~~~~~~e~~Li~~~li~~~~~g 292 (305)
T TIGR00635 234 LGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALG--EDADTIEDVYEPYLLQIGFLQRTPRG 292 (305)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhC--CCcchHHHhhhHHHHHcCCcccCCch
Confidence 345556888999998878877789999999888 77888999899 69999999744433
No 128
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=22.14 E-value=70 Score=30.62 Aligned_cols=55 Identities=13% Similarity=0.286 Sum_probs=39.6
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc-c---cccccccee
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA-K---GSRRLGKRV 443 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---~~~~~~~~~ 443 (604)
|+--+.+|-.-= =.+...|..++. .+.++|+.-|.||+++|+|+. . .-+.+|..+
T Consensus 16 D~~IL~~Lq~d~---R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI~~~~~~v~p~~lg~~~ 74 (164)
T PRK11169 16 DRNILNELQKDG---RISNVELSKRVG--LSPTPCLERVRRLERQGFIQGYTALLNPHYLDASL 74 (164)
T ss_pred HHHHHHHhccCC---CCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCeEEEEEEECHHHhCCCE
Confidence 444444444433 345578888888 999999999999999999984 2 346788764
No 129
>smart00351 PAX Paired Box domain.
Probab=22.03 E-value=3.1e+02 Score=25.35 Aligned_cols=50 Identities=14% Similarity=0.210 Sum_probs=37.9
Q ss_pred CCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccc
Q 042785 380 PQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKG 435 (604)
Q Consensus 380 ~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 435 (604)
...+...-+=+||+ .-.+...+...|. ++..+|.|+|.+-.+.|.++++.
T Consensus 18 ~s~~~R~riv~~~~----~G~s~~~iA~~~g--vs~~tV~kwi~r~~~~G~~~pk~ 67 (125)
T smart00351 18 LPDEERQRIVELAQ----NGVRPCDISRQLC--VSHGCVSKILGRYYETGSIRPGA 67 (125)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHC--cCHHHHHHHHHHHHHcCCcCCcC
Confidence 33334444455554 4457788888888 99999999999999999999974
No 130
>PRK12911 bifunctional preprotein translocase subunit SecD/SecF; Reviewed
Probab=21.54 E-value=62 Score=41.22 Aligned_cols=41 Identities=29% Similarity=0.495 Sum_probs=32.3
Q ss_pred hhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHh
Q 042785 384 DQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIRE 428 (604)
Q Consensus 384 ~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 (604)
=|.+--||||+||--.+-..-|..|+||.. ++|+|+++++.
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~ 53 (1403)
T PRK12911 13 ICVFALALYYVLPTCLYYSRPLNKKIDGRE----ARKIIERFTKQ 53 (1403)
T ss_pred hHHHHHHHHHHhhhhhhhcccccccccchH----HHHHHHHHHHH
Confidence 467888999999988777778888888754 67777777653
No 131
>PRK06474 hypothetical protein; Provisional
Probab=21.47 E-value=80 Score=31.04 Aligned_cols=41 Identities=20% Similarity=0.308 Sum_probs=34.1
Q ss_pred eehhhhhhhhhhhhhhHHHHHHHHHHHHHhcccccccccccc
Q 042785 399 YVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLG 440 (604)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 (604)
+.|++.|...|. .+++.+|..-+..|++.|+|+.-..+|.|
T Consensus 26 ~~ta~el~~~l~-~is~aTvYrhL~~L~e~GLI~~~~~~~~~ 66 (178)
T PRK06474 26 GLTPLELVKILK-DVPQATLYRHLQTMVDSGILHVVKEKKVR 66 (178)
T ss_pred CCCHHHHHHHhc-CCCHHHHHHHHHHHHHCCCEEEeeccccc
Confidence 478888888884 59999999999999999999976665543
No 132
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=21.45 E-value=1.2e+02 Score=29.64 Aligned_cols=63 Identities=16% Similarity=0.224 Sum_probs=47.1
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhHHHHHHHHHhhccc
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTKKKLMEAKKALDID 463 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 463 (604)
..|++..|...+. ++..-++|++.+|.+.|+|+....+.=| =++=-...+=.|.+|=++++.+
T Consensus 24 ~~vs~~eIA~~~~--ip~~~l~kIl~~L~~aGLv~s~rG~~GG-y~Lar~p~~Itl~dIl~aieg~ 86 (164)
T PRK10857 24 GPVPLADISERQG--ISLSYLEQLFSRLRKNGLVSSVRGPGGG-YLLGKDASSIAVGEVISAVDES 86 (164)
T ss_pred CcCcHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEeCCCCCCC-eeccCCHHHCCHHHHHHHHcCC
Confidence 4689999999999 9999999999999999999975333323 2232334555677777777754
No 133
>smart00753 PAM PCI/PINT associated module.
Probab=21.41 E-value=1.9e+02 Score=24.30 Aligned_cols=51 Identities=25% Similarity=0.330 Sum_probs=39.8
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhH
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTK 450 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 450 (604)
.=+++..|...|+ .+...|-.+|-+|..+|.|.++=+...|.=+++.....
T Consensus 23 ~~i~~~~i~~~~~--l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 23 SSISLSDLAKLLG--LSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred ceeeHHHHHHHhC--cCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 4456666777776 44446999999999999999999999998888876544
No 134
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=21.41 E-value=1.9e+02 Score=24.30 Aligned_cols=51 Identities=25% Similarity=0.330 Sum_probs=39.8
Q ss_pred ceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccceeeehhhhH
Q 042785 398 NYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKRVIHSTLTK 450 (604)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 450 (604)
.=+++..|...|+ .+...|-.+|-+|..+|.|.++=+...|.=+++.....
T Consensus 23 ~~i~~~~i~~~~~--l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 23 SSISLSDLAKLLG--LSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred ceeeHHHHHHHhC--cCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 4456666777776 44446999999999999999999999998888876544
No 135
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=21.38 E-value=1.5e+02 Score=27.68 Aligned_cols=57 Identities=23% Similarity=0.236 Sum_probs=48.8
Q ss_pred CcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc-cccccc
Q 042785 381 QLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA-KGSRRL 439 (604)
Q Consensus 381 ~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 439 (604)
-.++-+|=+.+=.+-.|.|||...|-+++- +|-+-+|+.+.-++.+|.|.. +.|||+
T Consensus 41 ~vdee~~~ki~KEV~~~r~VTpy~la~r~g--I~~SvAr~vLR~LeeeGvv~lvsknrR~ 98 (107)
T COG4901 41 TVDEELLDKIRKEVPRERVVTPYVLASRYG--INGSVARIVLRHLEEEGVVQLVSKNRRQ 98 (107)
T ss_pred hccHHHHHHHHHhcccceeecHHHHHHHhc--cchHHHHHHHHHHHhCCceeeeccCccc
Confidence 344677888888888999999999999998 999999999999999999875 456664
No 136
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=20.76 E-value=3.2e+02 Score=29.65 Aligned_cols=124 Identities=14% Similarity=0.184 Sum_probs=68.0
Q ss_pred hhHHHHHHHHHhhhcc-CCCcchhhhhhccCCChhh---------hhhccccccc---CCCcceeeccccchhhhhhhhh
Q 042785 302 EDEQQLVRVKDWINCR-HLHSVELTDVLSNFPDISV---------LVKEGLLSKG---GKDTYTINKQEKFNYEFALVKE 368 (604)
Q Consensus 302 ~~e~~~~~v~~w~~~~-~~~~~~~~dvl~~~p~i~~---------l~~~g~~~k~---~~~~~~~~~~~~~~~~~~~~~~ 368 (604)
.-.++..+|.+++..+ .-..+...+++..+|+.+. |+++|.+.-. |.-.|......+.
T Consensus 6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~~~~~l~~~~~~~~~a--------- 76 (327)
T PF05158_consen 6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLKKGGGLSYKAVSEEEA--------- 76 (327)
T ss_dssp -HHHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE-SSSEEEEE--SSS----------
T ss_pred hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEEcCCEEEEEEeCHHHH---------
Confidence 3456778888888887 6777888899999997776 8888876532 1223333322211
Q ss_pred hhcCccccCCCCCcchhHHHHHHhhhhccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccc-ccccccccee
Q 042785 369 EMDGVTLCDKSPQLDDQIYMKALYYALSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEA-KGSRRLGKRV 443 (604)
Q Consensus 369 ~~~~~~~~~~~~~~~~~~y~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 443 (604)
..-++..+++.+-+..+..+=. .=+....|..+.. ..|+.+.|++..|++.++|+. ++-+-.+|+|
T Consensus 77 ------~k~~~l~~~e~lvy~~I~~ag~-~GIw~~~i~~~t~--l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~ 143 (327)
T PF05158_consen 77 ------KKLKGLSDEERLVYQLIEEAGN-KGIWTKDIKKKTN--LHQTQLTKILKSLESKKLIKSVKSVKNPNRKV 143 (327)
T ss_dssp ----------SSSCCHHHHHHHHHHHTT-T-EEHHHHHHHCT----HHHHHHHHHHHHHTTSEEEE--SS-SS--E
T ss_pred ------hhhcCCCHHHHHHHHHHHHhCC-CCCcHHHHHHHcC--CCHHHHHHHHHHHHhCCCEEEecCcCCCCeEE
Confidence 1112233445554444433322 2344556666666 789999999999999999998 4444445544
No 137
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=20.21 E-value=1e+02 Score=28.03 Aligned_cols=45 Identities=20% Similarity=0.451 Sum_probs=38.4
Q ss_pred hccceehhhhhhhhhhhhhhHHHHHHHHHHHHHhccccccccccccce
Q 042785 395 LSMNYVTIAKLQKKLDKEANQSTVRKLIDKMIREGYVEAKGSRRLGKR 442 (604)
Q Consensus 395 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (604)
=+||.|+.+-+..+-. .+-..|.+.+..+++.|+|.-.| ++.|--
T Consensus 50 Kk~d~Is~sq~~e~tg--~~~~~V~~al~~Li~~~vI~~~g-~~~G~N 94 (100)
T PF04492_consen 50 KKMDRISNSQIAEMTG--LSRDHVSKALNELIRRGVIIRDG-KRIGVN 94 (100)
T ss_pred CccceeeHHHHHHHHC--cCHHHHHHHHHHHHHCCCEEeCC-cEEeee
Confidence 5889999999988777 88999999999999999997776 666643
Done!