Query 017157
Match_columns 376
No_of_seqs 160 out of 1127
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:06:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017157.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017157hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14134 recX recombination re 100.0 4E-31 8.6E-36 256.7 18.7 187 156-372 19-208 (283)
2 PRK00117 recX recombination re 100.0 9.6E-31 2.1E-35 231.9 17.9 149 207-373 8-156 (157)
3 COG2137 OraA Uncharacterized p 100.0 4E-30 8.7E-35 234.3 17.4 153 206-374 16-168 (174)
4 PRK14135 recX recombination re 100.0 3.7E-29 8E-34 238.3 19.1 188 156-371 15-203 (263)
5 PRK14136 recX recombination re 100.0 7.8E-29 1.7E-33 241.6 17.9 148 206-373 158-305 (309)
6 PRK14137 recX recombination re 100.0 2.6E-28 5.5E-33 226.0 17.6 146 207-373 37-182 (195)
7 PF02631 RecX: RecX family; I 99.9 1.8E-25 3.8E-30 190.6 13.4 118 234-369 1-118 (121)
8 PRK14135 recX recombination re 99.8 3E-20 6.5E-25 177.2 15.3 155 209-374 107-263 (263)
9 PRK14134 recX recombination re 99.6 3.9E-14 8.5E-19 138.1 16.7 147 224-373 124-282 (283)
10 PRK00117 recX recombination re 98.6 4.8E-07 1E-11 80.4 10.3 78 221-303 72-154 (157)
11 COG2137 OraA Uncharacterized p 98.2 9.8E-06 2.1E-10 74.6 10.2 92 212-307 73-169 (174)
12 PF02631 RecX: RecX family; I 98.2 8.1E-06 1.7E-10 69.7 8.6 86 210-301 28-118 (121)
13 PRK14137 recX recombination re 97.9 4.2E-05 9.2E-10 71.5 7.4 80 222-304 99-181 (195)
14 PRK14136 recX recombination re 97.6 0.00017 3.7E-09 71.7 7.9 76 224-303 225-303 (309)
15 TIGR02698 CopY_TcrY copper tra 82.8 25 0.00054 30.7 11.3 43 216-258 9-53 (130)
16 PF07553 Lipoprotein_Ltp: Host 80.9 4.4 9.5E-05 30.1 5.0 42 210-251 4-48 (48)
17 PF03551 PadR: Transcriptional 73.7 6.6 0.00014 30.5 4.5 42 217-258 2-48 (75)
18 TIGR03882 cyclo_dehyd_2 bacter 72.8 15 0.00033 34.1 7.5 70 213-288 32-106 (193)
19 PF03965 Penicillinase_R: Peni 70.6 44 0.00096 28.1 9.2 37 223-259 16-53 (115)
20 PF01022 HTH_5: Bacterial regu 64.5 23 0.00049 25.2 5.3 44 212-258 3-46 (47)
21 TIGR02702 SufR_cyano iron-sulf 63.0 22 0.00047 32.9 6.4 42 214-258 4-46 (203)
22 PHA01351 putative minor struct 61.9 1.2E+02 0.0027 34.3 12.4 90 211-303 579-668 (1070)
23 PF12802 MarR_2: MarR family; 61.3 23 0.0005 25.8 5.1 42 214-258 8-52 (62)
24 smart00550 Zalpha Z-DNA-bindin 60.4 29 0.00062 26.9 5.6 46 210-258 5-53 (68)
25 smart00418 HTH_ARSR helix_turn 60.0 26 0.00055 24.7 5.0 39 217-258 3-41 (66)
26 PF04695 Pex14_N: Peroxisomal 58.9 22 0.00048 31.3 5.4 46 210-255 3-51 (136)
27 PF01978 TrmB: Sugar-specific 57.4 23 0.0005 26.8 4.6 38 218-258 16-53 (68)
28 cd00090 HTH_ARSR Arsenical Res 56.5 41 0.00089 24.2 5.7 42 215-259 11-52 (78)
29 PF13463 HTH_27: Winged helix 54.9 16 0.00035 27.1 3.3 40 215-257 7-48 (68)
30 cd07153 Fur_like Ferric uptake 54.0 36 0.00078 28.1 5.6 46 214-259 4-53 (116)
31 PF13730 HTH_36: Helix-turn-he 52.1 29 0.00063 25.0 4.2 29 226-257 27-55 (55)
32 PF01475 FUR: Ferric uptake re 52.0 40 0.00087 28.3 5.7 50 210-259 7-60 (120)
33 PF12840 HTH_20: Helix-turn-he 51.7 53 0.0012 24.4 5.7 45 211-258 10-55 (61)
34 COG2345 Predicted transcriptio 51.2 96 0.0021 30.0 8.6 121 213-361 13-149 (218)
35 TIGR01926 peroxid_rel uncharac 51.1 1.4E+02 0.0029 26.5 9.2 89 213-302 65-157 (177)
36 PHA01351 putative minor struct 49.6 4.5E+02 0.0098 30.1 16.0 89 212-303 484-572 (1070)
37 PRK09416 lstR lineage-specific 49.1 40 0.00087 30.3 5.3 56 203-259 35-95 (135)
38 PF08784 RPA_C: Replication pr 49.0 19 0.00042 29.6 3.2 45 210-257 46-95 (102)
39 TIGR03433 padR_acidobact trans 48.7 24 0.00053 29.1 3.7 45 214-258 7-56 (100)
40 PF02082 Rrf2: Transcriptional 47.9 49 0.0011 26.2 5.3 31 225-258 26-56 (83)
41 PHA00435 capsid assembly prote 47.2 3.2E+02 0.0069 27.6 12.3 47 218-264 117-163 (306)
42 PF09012 FeoC: FeoC like trans 46.5 35 0.00076 26.2 4.1 34 222-258 12-45 (69)
43 COG2128 Uncharacterized conser 45.5 2.2E+02 0.0049 25.4 9.9 90 212-302 66-158 (177)
44 PRK09462 fur ferric uptake reg 45.4 60 0.0013 28.5 5.9 50 209-258 15-69 (148)
45 PF04433 SWIRM: SWIRM domain; 44.8 1.2E+02 0.0026 24.2 7.1 49 208-258 34-85 (86)
46 PF13412 HTH_24: Winged helix- 44.5 1E+02 0.0022 21.6 6.0 41 214-257 6-47 (48)
47 PF10390 ELL: RNA polymerase I 43.8 15 0.00033 36.3 2.1 56 205-260 192-248 (284)
48 COG0735 Fur Fe2+/Zn2+ uptake r 42.9 61 0.0013 28.8 5.6 62 203-264 13-78 (145)
49 COG1695 Predicted transcriptio 42.8 31 0.00067 29.7 3.6 49 212-260 10-63 (138)
50 PF01325 Fe_dep_repress: Iron 40.7 94 0.002 23.6 5.6 42 215-259 11-54 (60)
51 PF07106 TBPIP: Tat binding pr 40.5 57 0.0012 29.4 5.1 48 212-260 2-51 (169)
52 TIGR02719 repress_PhaQ poly-be 40.3 1.5E+02 0.0033 26.5 7.7 53 207-259 20-75 (138)
53 smart00345 HTH_GNTR helix_turn 39.9 57 0.0012 23.0 4.1 30 226-258 22-51 (60)
54 PF06180 CbiK: Cobalt chelatas 39.2 29 0.00064 34.1 3.2 39 218-256 33-72 (262)
55 cd07377 WHTH_GntR Winged helix 38.9 1.5E+02 0.0031 21.3 6.4 31 226-259 27-57 (66)
56 smart00346 HTH_ICLR helix_turn 38.0 1.4E+02 0.0031 23.2 6.5 39 217-258 11-51 (91)
57 PF08311 Mad3_BUB1_I: Mad3/BUB 37.7 66 0.0014 27.8 4.9 52 242-295 47-99 (126)
58 PRK11639 zinc uptake transcrip 37.6 89 0.0019 28.4 5.9 60 202-261 17-80 (169)
59 KOG0931 Predicted guanine nucl 36.7 1.4E+02 0.0029 32.4 7.7 81 223-306 189-274 (627)
60 TIGR01446 DnaD_dom DnaD and ph 36.6 1.4E+02 0.0029 22.9 6.0 42 229-271 20-61 (73)
61 PF07848 PaaX: PaaX-like prote 36.5 98 0.0021 24.5 5.3 35 225-259 21-55 (70)
62 PF08312 cwf21: cwf21 domain; 36.2 38 0.00082 24.9 2.6 26 228-253 14-39 (46)
63 PF04695 Pex14_N: Peroxisomal 36.0 99 0.0022 27.2 5.8 47 325-373 4-50 (136)
64 smart00816 Amb_V_allergen Amb 35.7 18 0.00038 26.4 0.8 20 33-52 11-30 (45)
65 PF04361 DUF494: Protein of un 34.8 90 0.002 28.4 5.4 33 226-258 22-54 (155)
66 smart00351 PAX Paired Box doma 34.5 3E+02 0.0065 23.7 10.9 74 213-290 23-108 (125)
67 PRK03430 hypothetical protein; 33.4 55 0.0012 30.1 3.8 33 227-259 23-55 (157)
68 TIGR00122 birA_repr_reg BirA b 32.1 1.4E+02 0.003 22.6 5.4 39 216-257 5-43 (69)
69 PF07223 DUF1421: Protein of u 32.0 54 0.0012 33.9 3.9 35 222-256 316-350 (358)
70 KOG4796 RNA polymerase II elon 31.9 70 0.0015 34.9 4.8 45 209-253 209-253 (604)
71 PF09106 SelB-wing_2: Elongati 31.9 30 0.00065 25.9 1.6 34 224-257 17-50 (59)
72 TIGR00738 rrf2_super rrf2 fami 31.7 1.1E+02 0.0023 25.9 5.2 32 224-258 25-56 (132)
73 PF10163 EnY2: Transcription f 29.2 68 0.0015 26.1 3.4 57 228-302 4-61 (86)
74 PF08006 DUF1700: Protein of u 28.9 2.3E+02 0.005 25.6 7.2 56 228-301 8-63 (181)
75 TIGR03544 DivI1A_domain DivIVA 28.5 34 0.00075 23.2 1.3 18 356-373 16-33 (34)
76 PF03913 Amb_V_allergen: Amb V 28.2 18 0.00038 26.3 -0.2 20 33-52 10-29 (44)
77 smart00347 HTH_MARR helix_turn 28.1 1.5E+02 0.0032 22.9 5.1 44 213-259 12-56 (101)
78 PF07261 DnaB_2: Replication i 28.1 1.1E+02 0.0024 23.3 4.2 43 229-272 20-62 (77)
79 TIGR02944 suf_reg_Xantho FeS a 27.9 1.3E+02 0.0028 25.6 5.1 38 219-259 17-57 (130)
80 cd03412 CbiK_N Anaerobic cobal 27.3 54 0.0012 28.3 2.6 35 222-256 36-70 (127)
81 smart00420 HTH_DEOR helix_turn 27.2 1.7E+02 0.0036 19.9 4.7 33 223-258 13-45 (53)
82 PF08461 HTH_12: Ribonuclease 26.9 1.5E+02 0.0032 23.0 4.8 43 216-258 3-49 (66)
83 PF13309 HTH_22: HTH domain 26.9 1.1E+02 0.0023 23.6 3.9 18 342-359 22-39 (64)
84 COG1735 Php Predicted metal-de 26.6 2E+02 0.0042 29.5 6.7 83 219-301 196-306 (316)
85 smart00777 Mad3_BUB1_I Mad3/BU 25.8 1.9E+02 0.0042 25.4 5.8 51 243-295 48-99 (125)
86 PF10152 DUF2360: Predicted co 25.8 81 0.0018 28.3 3.5 37 257-296 111-147 (148)
87 TIGR02010 IscR iron-sulfur clu 25.6 1.5E+02 0.0032 25.7 5.0 32 224-258 25-56 (135)
88 COG1654 BirA Biotin operon rep 24.8 1.9E+02 0.0042 23.5 5.2 42 213-257 8-49 (79)
89 PF01047 MarR: MarR family; I 24.5 2.3E+02 0.0051 20.3 5.3 35 221-258 14-48 (59)
90 COG1846 MarR Transcriptional r 24.1 1.6E+02 0.0035 23.3 4.8 47 210-259 21-68 (126)
91 PF00627 UBA: UBA/TS-N domain; 23.7 98 0.0021 20.9 2.9 23 348-370 4-26 (37)
92 PF13344 Hydrolase_6: Haloacid 23.5 2.1E+02 0.0045 23.6 5.4 63 218-290 34-100 (101)
93 PRK09875 putative hydrolase; P 23.2 62 0.0013 32.2 2.5 63 239-301 217-285 (292)
94 PF00325 Crp: Bacterial regula 23.0 1.8E+02 0.0039 19.8 4.0 29 226-257 4-32 (32)
95 cd00052 EH Eps15 homology doma 22.4 2.3E+02 0.005 20.3 4.9 42 225-266 16-59 (67)
96 PF03444 HrcA_DNA-bdg: Winged 22.4 1.6E+02 0.0035 24.2 4.3 35 221-258 20-54 (78)
97 PF01988 VIT1: VIT family; In 22.3 2.1E+02 0.0046 26.7 5.8 36 218-253 73-108 (213)
98 PRK03573 transcriptional regul 22.3 1.8E+02 0.004 24.8 5.0 43 213-258 33-77 (144)
99 TIGR02787 codY_Gpos GTP-sensin 21.7 6E+02 0.013 25.2 8.8 66 193-258 150-229 (251)
100 TIGR00084 ruvA Holliday juncti 20.9 6.9E+02 0.015 23.3 11.9 27 346-372 147-173 (191)
101 smart00344 HTH_ASNC helix_turn 20.4 2.6E+02 0.0057 22.6 5.4 41 215-258 7-48 (108)
102 PF08230 Cpl-7: Cpl-7 lysozyme 20.1 1.4E+02 0.003 21.9 3.0 25 342-370 16-40 (42)
No 1
>PRK14134 recX recombination regulator RecX; Provisional
Probab=99.97 E-value=4e-31 Score=256.69 Aligned_cols=187 Identities=20% Similarity=0.261 Sum_probs=154.0
Q ss_pred ccccchhhhhhcc-cccccccccccccccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHH
Q 017157 156 NILLDAAKQEFGE-EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKL 234 (376)
Q Consensus 156 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~e~~e~~~~~~~~~~~~~~~~~~~~~~~~A~~~AL~lLsrRdrS~~ELr~KL 234 (376)
||.+|+-..-..+ ++...|++.. ++|.+++.+.+ +.......+|+++||++|++|+||+.||++||
T Consensus 19 ~i~ld~~~af~v~~~~l~~~~L~k---G~eld~e~~~e----------i~~~~~~~~a~~~AL~~Ls~r~rSe~Elr~KL 85 (283)
T PRK14134 19 NVYIDEEFAFACSAELVYYHNLKK---GKVIDVNSLND----------IIKEDNYIKCKGYALKYIEKSYKTEKQIKEKL 85 (283)
T ss_pred EEEecCCeEEEecHHHHHHhCCcC---CCCcCHHHHHH----------HHHHHHHHHHHHHHHHHhccCcchHHHHHHHH
Confidence 4667764443334 5666688874 48998887764 55555688999999999999999999999999
Q ss_pred hcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCCHHHHHHHHHhhhcCCCChhHHHh
Q 017157 235 NGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGISQTDAKKAVNLVFRDGESDEDQES 314 (376)
Q Consensus 235 ~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId~eiIeeALee~~eeeeedEE~e~ 314 (376)
.++|+++++|+.||++|+++|||||.+||++|++++.+ ++||++|+++|++|||+.++|++||+++.++ +| .
T Consensus 86 ~~k~~~~~~Ie~vI~~L~e~~yldD~ryA~~yv~~~~~--~~G~~~I~~eL~qKGI~~~iIe~al~~~~~e---~e-~-- 157 (283)
T PRK14134 86 YLKEYDEDAVNRVIRFLKEYNFIDDDKYCDMYIREKIN--SYGRNKIKYTLLNKGIKENIIIEKINNIDEE---KE-K-- 157 (283)
T ss_pred HhCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH--hhhHHHHHHHHHHCCCCHHHHHHHHHhCChh---hH-H--
Confidence 99999999999999999999999999999999999875 6999999999999999999999999986321 11 2
Q ss_pred hhccchhHHHHHHHHHHHHHhhccCC--ChHHHHHHHHHHHHhCCCCHHHHHHHHHhhhh
Q 017157 315 KLGMSKHSIDRLFVQASKQWLRSQGA--PKETRKSRIIHWLQYRGFNWCVTSFILKKLES 372 (376)
Q Consensus 315 a~~Lak~~le~Ll~~AeKk~~R~~~~--~~~k~rqKlir~L~RKGFs~d~I~~vL~eie~ 372 (376)
+.+...++|++.+.... +..+.++|++++|++|||++++|..+|+++..
T Consensus 158 ---------e~a~~l~~Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~~~~ 208 (283)
T PRK14134 158 ---------KVAYKLAEKKYKILILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNELIK 208 (283)
T ss_pred ---------HHHHHHHHHhhcccccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHh
Confidence 23456667777654322 34578999999999999999999999999844
No 2
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=99.97 E-value=9.6e-31 Score=231.90 Aligned_cols=149 Identities=32% Similarity=0.481 Sum_probs=132.5
Q ss_pred HHHHHHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHH
Q 017157 207 KARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALF 286 (376)
Q Consensus 207 ~~~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLr 286 (376)
.+...|+++|+++|++|+||++||++||.++|+++++|+.||++|++.|||||.+||+.|++++.. +++|+++|+++|+
T Consensus 8 ~~~~~a~~~al~~L~~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~-~~~g~~~I~~~L~ 86 (157)
T PRK00117 8 RMYASARARALRLLARREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRAR-KGYGPRRIRQELR 86 (157)
T ss_pred cHHHHHHHHHHHHHccchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh-CCchHHHHHHHHH
Confidence 357899999999999999999999999999999999999999999999999999999999999944 8999999999999
Q ss_pred hCCCCHHHHHHHHHhhhcCCCChhHHHhhhccchhHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHhCCCCHHHHHHH
Q 017157 287 KKGISQTDAKKAVNLVFRDGESDEDQESKLGMSKHSIDRLFVQASKQWLRSQGAPKETRKSRIIHWLQYRGFNWCVTSFI 366 (376)
Q Consensus 287 qKGId~eiIeeALee~~eeeeedEE~e~a~~Lak~~le~Ll~~AeKk~~R~~~~~~~k~rqKlir~L~RKGFs~d~I~~v 366 (376)
+|||+.++|+++|+++. . |+ .+ .+..+++|++.+....+. +.++|++++|+||||++++|..+
T Consensus 87 ~kGi~~~~I~~~l~~~~--~--d~-~e-----------~a~~~~~k~~~~~~~~~~-~~k~Ki~~~L~rkGF~~~~I~~~ 149 (157)
T PRK00117 87 QKGVDREIIEEALAELD--I--DW-EE-----------LARELARKKFRRPLPDDA-KEKAKLVRFLARRGFSMDVIQRV 149 (157)
T ss_pred HcCCCHHHHHHHHHHcC--c--cH-HH-----------HHHHHHHHHcCCCCCCCH-HHHHHHHHHHHHCCCCHHHHHHH
Confidence 99999999999999874 1 22 12 345667788776655556 89999999999999999999999
Q ss_pred HHhhhhc
Q 017157 367 LKKLESQ 373 (376)
Q Consensus 367 L~eie~e 373 (376)
|++..++
T Consensus 150 l~~~~~~ 156 (157)
T PRK00117 150 LRNALDD 156 (157)
T ss_pred HHhhhcc
Confidence 9987654
No 3
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=99.97 E-value=4e-30 Score=234.29 Aligned_cols=153 Identities=32% Similarity=0.491 Sum_probs=132.2
Q ss_pred HHHHHHHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHH
Q 017157 206 AKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQAL 285 (376)
Q Consensus 206 ~~~~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeL 285 (376)
...+..++++||++|++|+||++||+.||.++|+++++|+.||.+|.++|||||.+||++|++++.+ +++||++|+|+|
T Consensus 16 ~~~~~~~~~~Al~~Ls~R~rse~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~i~~r~~-~g~G~~rl~qeL 94 (174)
T COG2137 16 SDQYAKGLNRALRLLSRRDRSEKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTRFAEAYIRSRSR-KGKGPARLKQEL 94 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHh-cccChHHHHHHH
Confidence 3358899999999999999999999999999999999999999999999999999999999999998 669999999999
Q ss_pred HhCCCCHHHHHHHHHhhhcCCCChhHHHhhhccchhHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHhCCCCHHHHHH
Q 017157 286 FKKGISQTDAKKAVNLVFRDGESDEDQESKLGMSKHSIDRLFVQASKQWLRSQGAPKETRKSRIIHWLQYRGFNWCVTSF 365 (376)
Q Consensus 286 rqKGId~eiIeeALee~~eeeeedEE~e~a~~Lak~~le~Ll~~AeKk~~R~~~~~~~k~rqKlir~L~RKGFs~d~I~~ 365 (376)
.+|||+.++|++||+..+++ +| .+.+...+.+++.+....++.+.++|++++|++|||++++|..
T Consensus 95 ~qkGi~~~~Ie~aL~~~~~~---~~------------~~~a~~~~~kk~~~~~~~~~~~~k~Ki~r~L~~rGFs~~~i~~ 159 (174)
T COG2137 95 KQKGIDDEIIEEALELIDEE---DE------------QERARKVLRKKFKRENKPPDKKEKAKIQRFLLRRGFSYEVIKE 159 (174)
T ss_pred HHcCCCHHHHHHHHhccchH---HH------------HHHHHHHHHHHhCccccCcchhHHHHHHHHHHHcCCCHHHHHH
Confidence 99999999999999865432 22 1233445566655443345678999999999999999999999
Q ss_pred HHHhhhhcC
Q 017157 366 ILKKLESQY 374 (376)
Q Consensus 366 vL~eie~e~ 374 (376)
++...+++.
T Consensus 160 ~l~~~~~~~ 168 (174)
T COG2137 160 ALNEAEEEE 168 (174)
T ss_pred HHHHhhhcc
Confidence 999987653
No 4
>PRK14135 recX recombination regulator RecX; Provisional
Probab=99.96 E-value=3.7e-29 Score=238.31 Aligned_cols=188 Identities=30% Similarity=0.361 Sum_probs=156.3
Q ss_pred ccccchhhhhhcc-cccccccccccccccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHH
Q 017157 156 NILLDAAKQEFGE-EISCEHGLFEESEVFEEPQEVAEEMKILQQKDFYLQAAKARQDAENLAVKLLATRAFTAVEMRKKL 234 (376)
Q Consensus 156 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~e~~e~~~~~~~~~~~~~~~~~~~~~~~~A~~~AL~lLsrRdrS~~ELr~KL 234 (376)
+|.+|+-..-..+ ++...+++..+ +|.+++.+.+ ........+|+++|+++|++++||..||++||
T Consensus 15 ~v~ld~~~~~~~~~~~~~~~~L~~g---~~l~~~~~~~----------i~~~~~~~~a~~~Al~~L~~r~~s~~el~~kL 81 (263)
T PRK14135 15 NIFLDEKYAFSVDEDTLVKFMLKKG---KELDEEDLEE----------IQYADQVSKGKNLALYYLSYQMRTEKEVRDYL 81 (263)
T ss_pred EEEEcCCeEEEeeHHHHHHhcCcCC---CcCCHHHHHH----------HHHHHHHHHHHHHHHHHhhhccccHHHHHHHH
Confidence 4777775554445 66666888744 8998888875 44445788999999999999999999999999
Q ss_pred hcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCCHHHHHHHHHhhhcCCCChhHHHh
Q 017157 235 NGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGISQTDAKKAVNLVFRDGESDEDQES 314 (376)
Q Consensus 235 ~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId~eiIeeALee~~eeeeedEE~e~ 314 (376)
.++|+++++|+.||++|++.|||||.+||++|++++++.+++|+++|+++|++|||+.++|++||+++.++ ++
T Consensus 82 ~~kg~~~~~Ie~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~~g~~~I~~kL~~kGi~~~~Ie~~l~~l~~~---~~---- 154 (263)
T PRK14135 82 KKHEISEEIISEVIDKLKEEKYIDDKEYAESYVRTNINTGDKGPRVIKQKLLQKGIEDEIIEEALSEYTEE---DQ---- 154 (263)
T ss_pred HHCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccccchHHHHHHHHHcCCCHHHHHHHHHhCChh---hH----
Confidence 99999999999999999999999999999999999987667999999999999999999999999986321 11
Q ss_pred hhccchhHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHhCCCCHHHHHHHHHhhh
Q 017157 315 KLGMSKHSIDRLFVQASKQWLRSQGAPKETRKSRIIHWLQYRGFNWCVTSFILKKLE 371 (376)
Q Consensus 315 a~~Lak~~le~Ll~~AeKk~~R~~~~~~~k~rqKlir~L~RKGFs~d~I~~vL~eie 371 (376)
++.+...+++++.++...+....++|++++|++|||++++|..+|++++
T Consensus 155 --------~d~a~~~~~k~~~~~~~~~~~~~k~Ki~~~L~rkGf~~~~I~~~l~~~~ 203 (263)
T PRK14135 155 --------IEVAQKLAEKLLKKYQKLPFKALKQKIIQSLLTKGFSYEVIKAALEELD 203 (263)
T ss_pred --------HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHcc
Confidence 2223344566655554456667899999999999999999999999875
No 5
>PRK14136 recX recombination regulator RecX; Provisional
Probab=99.96 E-value=7.8e-29 Score=241.60 Aligned_cols=148 Identities=18% Similarity=0.263 Sum_probs=127.0
Q ss_pred HHHHHHHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHH
Q 017157 206 AKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQAL 285 (376)
Q Consensus 206 ~~~~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeL 285 (376)
-.+...++++||+||++|+||+.||++||.++||++++|+.||++|+++|||||.+||++||+.+. ++|||++|+++|
T Consensus 158 ~~~~~~lk~kAL~lLSrReRSe~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~--~kkGp~rIrqEL 235 (309)
T PRK14136 158 SRPARSLKGRALGYLSRREYSRAELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRA--SRVGSARIVSEL 235 (309)
T ss_pred cccHHHHHHHHHHHhhcccccHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHh--hchhHHHHHHHH
Confidence 346788999999999999999999999999999999999999999999999999999999998876 469999999999
Q ss_pred HhCCCCHHHHHHHHHhhhcCCCChhHHHhhhccchhHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHhCCCCHHHHHH
Q 017157 286 FKKGISQTDAKKAVNLVFRDGESDEDQESKLGMSKHSIDRLFVQASKQWLRSQGAPKETRKSRIIHWLQYRGFNWCVTSF 365 (376)
Q Consensus 286 rqKGId~eiIeeALee~~eeeeedEE~e~a~~Lak~~le~Ll~~AeKk~~R~~~~~~~k~rqKlir~L~RKGFs~d~I~~ 365 (376)
++|||+.++|+++|+++.+ +| . +.+..+++|++.... ...+.++|+++||++|||++++|..
T Consensus 236 rQKGId~eLIEqALeeieE----DE-~-----------E~A~~L~eKK~~~~~--~d~kek~K~iRfL~rRGFS~D~I~~ 297 (309)
T PRK14136 236 KRHAVGDALVESVGAQLRE----TE-F-----------ERAQAVWRKKFGALP--QTPAERAKQARFLAARGFSSATIVK 297 (309)
T ss_pred HHcCCCHHHHHHHHHhccH----hH-H-----------HHHHHHHHHHhcccC--cCHHHHHHHHHHHHHCCCCHHHHHH
Confidence 9999999999999997621 23 2 234555667764332 2346788999999999999999999
Q ss_pred HHHhhhhc
Q 017157 366 ILKKLESQ 373 (376)
Q Consensus 366 vL~eie~e 373 (376)
+|+.+..+
T Consensus 298 vLk~~~de 305 (309)
T PRK14136 298 LLKVGDDE 305 (309)
T ss_pred HHHhchhc
Confidence 99987554
No 6
>PRK14137 recX recombination regulator RecX; Provisional
Probab=99.96 E-value=2.6e-28 Score=226.03 Aligned_cols=146 Identities=23% Similarity=0.317 Sum_probs=122.9
Q ss_pred HHHHHHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHH
Q 017157 207 KARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALF 286 (376)
Q Consensus 207 ~~~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLr 286 (376)
....+++++|+++|++|+||++||++||.++|+++++|+.||++|+++|||||.+||+.|.. . ++|||++|+++|+
T Consensus 37 e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~~---~-k~~Gp~rI~~eL~ 112 (195)
T PRK14137 37 EAREALLAYAFRALAARAMTAAELRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAENS---R-RGVGALRVRQTLR 112 (195)
T ss_pred HHHHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHH---h-cCchHHHHHHHHH
Confidence 34678999999999999999999999999999999999999999999999999999999832 3 7899999999999
Q ss_pred hCCCCHHHHHHHHHhhhcCCCChhHHHhhhccchhHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHhCCCCHHHHHHH
Q 017157 287 KKGISQTDAKKAVNLVFRDGESDEDQESKLGMSKHSIDRLFVQASKQWLRSQGAPKETRKSRIIHWLQYRGFNWCVTSFI 366 (376)
Q Consensus 287 qKGId~eiIeeALee~~eeeeedEE~e~a~~Lak~~le~Ll~~AeKk~~R~~~~~~~k~rqKlir~L~RKGFs~d~I~~v 366 (376)
+|||+.++|+++|++++.+ +| . +.+...++|++..... ..+.++|+++||++|||++++|..+
T Consensus 113 qKGI~~~lI~~al~~~d~e---de-~-----------e~a~~l~~KK~~~~~~--~~~~k~K~~~~L~rRGFs~~~I~~a 175 (195)
T PRK14137 113 RRGVEETLIEETLAARDPQ---EE-Q-----------QEARNLLERRWSSFAR--KRDPRASAYAFLARRGFSGAVIWPA 175 (195)
T ss_pred HcCCCHHHHHHHHHhcCch---hH-H-----------HHHHHHHHHhccccCc--chhHHHHHHHHHHHCCCCHHHHHHH
Confidence 9999999999999986321 12 2 2345556676654322 2356899999999999999999999
Q ss_pred HHhhhhc
Q 017157 367 LKKLESQ 373 (376)
Q Consensus 367 L~eie~e 373 (376)
|+.+..+
T Consensus 176 l~~~~~~ 182 (195)
T PRK14137 176 IREVAAL 182 (195)
T ss_pred HHHHHHh
Confidence 9987543
No 7
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=99.93 E-value=1.8e-25 Score=190.59 Aligned_cols=118 Identities=36% Similarity=0.563 Sum_probs=95.7
Q ss_pred HhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCCHHHHHHHHHhhhcCCCChhHHH
Q 017157 234 LNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGISQTDAKKAVNLVFRDGESDEDQE 313 (376)
Q Consensus 234 L~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId~eiIeeALee~~eeeeedEE~e 313 (376)
|.+||+++++|+.||++|+++|||||.+||+.|++++++.+++||++|+++|++|||+.++|+++++++ ++ .
T Consensus 1 L~~kg~~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~~~------~~-~- 72 (121)
T PF02631_consen 1 LKRKGFSEEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALEEY------DE-E- 72 (121)
T ss_dssp HHHTT--HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHTCS-------H-H-
T ss_pred CcccCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHHHh------hH-H-
Confidence 788999999999999999999999999999999999998789999999999999999999999999842 22 1
Q ss_pred hhhccchhHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHhCCCCHHHHHHHHHh
Q 017157 314 SKLGMSKHSIDRLFVQASKQWLRSQGAPKETRKSRIIHWLQYRGFNWCVTSFILKK 369 (376)
Q Consensus 314 ~a~~Lak~~le~Ll~~AeKk~~R~~~~~~~k~rqKlir~L~RKGFs~d~I~~vL~e 369 (376)
+.+.+.++|++.+....++.+.++|++++|+||||++++|..+|++
T Consensus 73 ----------e~a~~~~~kk~~~~~~~~~~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 73 ----------EEALELAEKKYRRYRKPSDRKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp ----------HHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred ----------HHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 1245667888877756677899999999999999999999999998
No 8
>PRK14135 recX recombination regulator RecX; Provisional
Probab=99.84 E-value=3e-20 Score=177.17 Aligned_cols=155 Identities=17% Similarity=0.174 Sum_probs=125.8
Q ss_pred HHHHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHH-HHHHHHHHhhhhc-CCccHHHHHHHHH
Q 017157 209 RQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDS-LYAESYSRSRWSS-ASWGPRRIKQALF 286 (376)
Q Consensus 209 ~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~-ryAesyvrsr~~~-kg~GprkIrqeLr 286 (376)
..=|..++-.++..+.+|+.+|+++|.+||+++++|+.+|+.+.+.+|+||. ++|+.+.+..... ...++++|.+.|+
T Consensus 107 ~~~a~~~~~~~~~~~~~g~~~I~~kL~~kGi~~~~Ie~~l~~l~~~~~~d~a~~~~~k~~~~~~~~~~~~~k~Ki~~~L~ 186 (263)
T PRK14135 107 KEYAESYVRTNINTGDKGPRVIKQKLLQKGIEDEIIEEALSEYTEEDQIEVAQKLAEKLLKKYQKLPFKALKQKIIQSLL 186 (263)
T ss_pred HHHHHHHHHHHHhccccchHHHHHHHHHcCCCHHHHHHHHHhCChhhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 4556777777888788999999999999999999999999999999999996 5777777655311 1246789999999
Q ss_pred hCCCCHHHHHHHHHhhhcCCCChhHHHhhhccchhHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHhCCCCHHHHHHH
Q 017157 287 KKGISQTDAKKAVNLVFRDGESDEDQESKLGMSKHSIDRLFVQASKQWLRSQGAPKETRKSRIIHWLQYRGFNWCVTSFI 366 (376)
Q Consensus 287 qKGId~eiIeeALee~~eeeeedEE~e~a~~Lak~~le~Ll~~AeKk~~R~~~~~~~k~rqKlir~L~RKGFs~d~I~~v 366 (376)
+|||+.++|..||+++..+.+++++ .+.+...++++++++...++.+.++|+++||+||||++++|..+
T Consensus 187 rkGf~~~~I~~~l~~~~~e~d~~~e-----------~e~l~~~~~k~~~k~~~~~~~k~k~K~~~~L~rrGF~~~~I~~~ 255 (263)
T PRK14135 187 TKGFSYEVIKAALEELDLEQDEEEE-----------QELLQKELEKAYRKYSKYDGYELKQKLKQALYRKGFSYDDIDSF 255 (263)
T ss_pred hCCCCHHHHHHHHHHcccCCChHHH-----------HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence 9999999999999997544332221 23455667788877766677889999999999999999999999
Q ss_pred HHhhhhcC
Q 017157 367 LKKLESQY 374 (376)
Q Consensus 367 L~eie~e~ 374 (376)
|+++++++
T Consensus 256 l~~~~~~~ 263 (263)
T PRK14135 256 LREYGIED 263 (263)
T ss_pred HHHhccCC
Confidence 99987763
No 9
>PRK14134 recX recombination regulator RecX; Provisional
Probab=99.59 E-value=3.9e-14 Score=138.09 Aligned_cols=147 Identities=16% Similarity=0.204 Sum_probs=107.5
Q ss_pred ccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcC-C------ccHHHHHHHHHhCCCCHHHHH
Q 017157 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSA-S------WGPRRIKQALFKKGISQTDAK 296 (376)
Q Consensus 224 drS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~k-g------~GprkIrqeLrqKGId~eiIe 296 (376)
.+|+..|++.|.+||+++++|+.+|+.+.. -+....|...+..++... . .-.++|.+.|.+||++.++|.
T Consensus 124 ~~G~~~I~~eL~qKGI~~~iIe~al~~~~~---e~e~e~a~~l~~Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~ 200 (283)
T PRK14134 124 SYGRNKIKYTLLNKGIKENIIIEKINNIDE---EKEKKVAYKLAEKKYKILILSEKNKFKIYKKLGPYLISRGYSSNIAE 200 (283)
T ss_pred hhhHHHHHHHHHHCCCCHHHHHHHHHhCCh---hhHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHCCCCHHHHH
Confidence 589999999999999999999999986522 233466677777665421 1 135789999999999999999
Q ss_pred HHHHhhhcCCCChhHHH---hhhccchhHHHHHHHHHHHHHhhccC--CChHHHHHHHHHHHHhCCCCHHHHHHHHHhhh
Q 017157 297 KAVNLVFRDGESDEDQE---SKLGMSKHSIDRLFVQASKQWLRSQG--APKETRKSRIIHWLQYRGFNWCVTSFILKKLE 371 (376)
Q Consensus 297 eALee~~eeeeedEE~e---~a~~Lak~~le~Ll~~AeKk~~R~~~--~~~~k~rqKlir~L~RKGFs~d~I~~vL~eie 371 (376)
.||.++..+++.+++.. .-.+..-+.++.+...|+|++.+... .+..+.++|+++||+||||+|++|+.+|+++.
T Consensus 201 ~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~kr~~~~~~~e~d~~k~~~Kl~~~L~rkGf~~e~I~~vl~~~~ 280 (283)
T PRK14134 201 WILNELIKNEALYKDNNSQNIENNIKDENIEELHNLARKRYDIIIKSEDDKNKIYRRLSNYLLRRGYSWEEVKKSLNELL 280 (283)
T ss_pred HHHHHHHhHhhhhhhccccchhhccccChHHHHHHHHHHHHhhhhcccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHh
Confidence 99999854332111100 00001112467788889999877632 33457899999999999999999999999986
Q ss_pred hc
Q 017157 372 SQ 373 (376)
Q Consensus 372 ~e 373 (376)
.+
T Consensus 281 ~~ 282 (283)
T PRK14134 281 YE 282 (283)
T ss_pred cc
Confidence 54
No 10
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=98.56 E-value=4.8e-07 Score=80.39 Aligned_cols=78 Identities=15% Similarity=0.314 Sum_probs=66.7
Q ss_pred HhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCcc-----HHHHHHHHHhCCCCHHHH
Q 017157 221 ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWG-----PRRIKQALFKKGISQTDA 295 (376)
Q Consensus 221 srRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~G-----prkIrqeLrqKGId~eiI 295 (376)
..+.+++..|+++|.+||++.++|+.+|+.+. .|+...|...+..+++ +..+ .++|.+.|.+|||+.++|
T Consensus 72 ~~~~~g~~~I~~~L~~kGi~~~~I~~~l~~~~----~d~~e~a~~~~~k~~~-~~~~~~~~~k~Ki~~~L~rkGF~~~~I 146 (157)
T PRK00117 72 ARKGYGPRRIRQELRQKGVDREIIEEALAELD----IDWEELARELARKKFR-RPLPDDAKEKAKLVRFLARRGFSMDVI 146 (157)
T ss_pred HhCCchHHHHHHHHHHcCCCHHHHHHHHHHcC----ccHHHHHHHHHHHHcC-CCCCCCHHHHHHHHHHHHHCCCCHHHH
Confidence 45789999999999999999999999999873 6777888888887765 3233 489999999999999999
Q ss_pred HHHHHhhh
Q 017157 296 KKAVNLVF 303 (376)
Q Consensus 296 eeALee~~ 303 (376)
..+|++..
T Consensus 147 ~~~l~~~~ 154 (157)
T PRK00117 147 QRVLRNAL 154 (157)
T ss_pred HHHHHhhh
Confidence 99998854
No 11
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=98.21 E-value=9.8e-06 Score=74.62 Aligned_cols=92 Identities=16% Similarity=0.197 Sum_probs=72.0
Q ss_pred HHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCC--cc---HHHHHHHHH
Q 017157 212 AENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSAS--WG---PRRIKQALF 286 (376)
Q Consensus 212 A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg--~G---prkIrqeLr 286 (376)
|..++-...... +++.-|+++|.+||+++++|+.+|+.. ...+....|...+..++.... +. +.+|.+.|.
T Consensus 73 Ae~~i~~r~~~g-~G~~rl~qeL~qkGi~~~~Ie~aL~~~---~~~~~~~~a~~~~~kk~~~~~~~~~~~~k~Ki~r~L~ 148 (174)
T COG2137 73 AEAYIRSRSRKG-KGPARLKQELKQKGIDDEIIEEALELI---DEEDEQERARKVLRKKFKRENKPPDKKEKAKIQRFLL 148 (174)
T ss_pred HHHHHHHHHhcc-cChHHHHHHHHHcCCCHHHHHHHHhcc---chHHHHHHHHHHHHHHhCccccCcchhHHHHHHHHHH
Confidence 334444444444 779999999999999999999999855 566777778888888765332 33 679999999
Q ss_pred hCCCCHHHHHHHHHhhhcCCC
Q 017157 287 KKGISQTDAKKAVNLVFRDGE 307 (376)
Q Consensus 287 qKGId~eiIeeALee~~eeee 307 (376)
.|||+.++|..+|.++.++.+
T Consensus 149 ~rGFs~~~i~~~l~~~~~~~~ 169 (174)
T COG2137 149 RRGFSYEVIKEALNEAEEEED 169 (174)
T ss_pred HcCCCHHHHHHHHHHhhhccc
Confidence 999999999999999866543
No 12
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=98.19 E-value=8.1e-06 Score=69.67 Aligned_cols=86 Identities=15% Similarity=0.222 Sum_probs=62.1
Q ss_pred HHHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcC-----CccHHHHHHH
Q 017157 210 QDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSA-----SWGPRRIKQA 284 (376)
Q Consensus 210 ~~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~k-----g~GprkIrqe 284 (376)
.=|..++-..+..+.+|+..|+++|.+||+++++|+.+|+ -++....|...++.++... ...++++.+.
T Consensus 28 ~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~------~~~~~e~a~~~~~kk~~~~~~~~~~~~~~K~~~~ 101 (121)
T PF02631_consen 28 RYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALE------EYDEEEEALELAEKKYRRYRKPSDRKRKQKLIRF 101 (121)
T ss_dssp HHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHT------CS-HHHHHHHHHHHHHHHTTTS-CHHHHHHHHHH
T ss_pred HHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHH------HhhHHHHHHHHHHHHHhcccCCCCHHHHHHHHHH
Confidence 3345566667777899999999999999999999999999 3344444666666665532 2468899999
Q ss_pred HHhCCCCHHHHHHHHHh
Q 017157 285 LFKKGISQTDAKKAVNL 301 (376)
Q Consensus 285 LrqKGId~eiIeeALee 301 (376)
|.+||++.++|..+|.+
T Consensus 102 L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 102 LMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHTT--HHHHHHHCHH
T ss_pred HHHCCCCHHHHHHHHhh
Confidence 99999999999999987
No 13
>PRK14137 recX recombination regulator RecX; Provisional
Probab=97.85 E-value=4.2e-05 Score=71.50 Aligned_cols=80 Identities=20% Similarity=0.207 Sum_probs=63.4
Q ss_pred hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhc---CCccHHHHHHHHHhCCCCHHHHHHH
Q 017157 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSS---ASWGPRRIKQALFKKGISQTDAKKA 298 (376)
Q Consensus 222 rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~---kg~GprkIrqeLrqKGId~eiIeeA 298 (376)
.+.+++..|+++|.+||+++++|+.+|+.+. ..+...-|...+..++.. ...-.+++.+.|++|||+.++|..|
T Consensus 99 ~k~~Gp~rI~~eL~qKGI~~~lI~~al~~~d---~ede~e~a~~l~~KK~~~~~~~~~~k~K~~~~L~rRGFs~~~I~~a 175 (195)
T PRK14137 99 RRGVGALRVRQTLRRRGVEETLIEETLAARD---PQEEQQEARNLLERRWSSFARKRDPRASAYAFLARRGFSGAVIWPA 175 (195)
T ss_pred hcCchHHHHHHHHHHcCCCHHHHHHHHHhcC---chhHHHHHHHHHHHhccccCcchhHHHHHHHHHHHCCCCHHHHHHH
Confidence 4678999999999999999999999998652 223456666777666542 1234688999999999999999999
Q ss_pred HHhhhc
Q 017157 299 VNLVFR 304 (376)
Q Consensus 299 Lee~~e 304 (376)
|..+..
T Consensus 176 l~~~~~ 181 (195)
T PRK14137 176 IREVAA 181 (195)
T ss_pred HHHHHH
Confidence 998644
No 14
>PRK14136 recX recombination regulator RecX; Provisional
Probab=97.61 E-value=0.00017 Score=71.66 Aligned_cols=76 Identities=12% Similarity=0.123 Sum_probs=60.1
Q ss_pred ccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcC---CccHHHHHHHHHhCCCCHHHHHHHHH
Q 017157 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSA---SWGPRRIKQALFKKGISQTDAKKAVN 300 (376)
Q Consensus 224 drS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~k---g~GprkIrqeLrqKGId~eiIeeALe 300 (376)
.+++..|+++|.+||++.++|+.+|+.+. .++...|...++.++... ..-.+++.+.|++|||+.++|..+|.
T Consensus 225 kkGp~rIrqELrQKGId~eLIEqALeeie----EDE~E~A~~L~eKK~~~~~~d~kek~K~iRfL~rRGFS~D~I~~vLk 300 (309)
T PRK14136 225 RVGSARIVSELKRHAVGDALVESVGAQLR----ETEFERAQAVWRKKFGALPQTPAERAKQARFLAARGFSSATIVKLLK 300 (309)
T ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhcc----HhHHHHHHHHHHHHhcccCcCHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 38999999999999999999999999662 244566666776665421 12357888999999999999999998
Q ss_pred hhh
Q 017157 301 LVF 303 (376)
Q Consensus 301 e~~ 303 (376)
...
T Consensus 301 ~~~ 303 (309)
T PRK14136 301 VGD 303 (309)
T ss_pred hch
Confidence 754
No 15
>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=82.78 E-value=25 Score=30.69 Aligned_cols=43 Identities=12% Similarity=0.318 Sum_probs=35.3
Q ss_pred HHHHH-HhcccCHHHHHHHHh-cCCCCHHHHHHHHHHHHHcCCcc
Q 017157 216 AVKLL-ATRAFTAVEMRKKLN-GKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 216 AL~lL-srRdrS~~ELr~KL~-~KG~sediIe~VLe~L~e~GyLD 258 (376)
.|..| .....|..+|.+.|. .+|+....|..+|.+|.+.|||.
T Consensus 9 VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~ 53 (130)
T TIGR02698 9 VMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLT 53 (130)
T ss_pred HHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCcee
Confidence 34444 455679999999995 45899999999999999999996
No 16
>PF07553 Lipoprotein_Ltp: Host cell surface-exposed lipoprotein; InterPro: IPR011434 This domain is found as 1-3 copies in a small family of proteins of unknown function.
Probab=80.94 E-value=4.4 Score=30.11 Aligned_cols=42 Identities=14% Similarity=0.200 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHhcccCHHHHHHHHhcC---CCCHHHHHHHHHHH
Q 017157 210 QDAENLAVKLLATRAFTAVEMRKKLNGK---KFPSHVIEAVITDF 251 (376)
Q Consensus 210 ~~A~~~AL~lLsrRdrS~~ELr~KL~~K---G~sediIe~VLe~L 251 (376)
+.|..+|-.|+.....|...|+..|..- ||+++.++-+|+.|
T Consensus 4 ~~Al~~Ak~Y~~~~~~Sk~~l~~QL~se~ge~Ft~e~A~YAv~~l 48 (48)
T PF07553_consen 4 KNALKKAKSYLKTMHMSKQGLYDQLTSEYGEGFTEEEAQYAVDHL 48 (48)
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHhhcccCCCHHHHHHHHHcC
Confidence 5688889999999999999999999876 99999999998754
No 17
>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=73.73 E-value=6.6 Score=30.50 Aligned_cols=42 Identities=19% Similarity=0.426 Sum_probs=37.1
Q ss_pred HHHHHhcccCHHHHHHHHhcC-----CCCHHHHHHHHHHHHHcCCcc
Q 017157 217 VKLLATRAFTAVEMRKKLNGK-----KFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 217 L~lLsrRdrS~~ELr~KL~~K-----G~sediIe~VLe~L~e~GyLD 258 (376)
|.+|..++.+..+|.+.|.+. .+++..|-.+|.+|++.|+|.
T Consensus 2 L~~L~~~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~ 48 (75)
T PF03551_consen 2 LGLLSEGPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIE 48 (75)
T ss_dssp HHHHHHS-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEE
T ss_pred hhhhccCCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEE
Confidence 678888999999999999987 377899999999999999985
No 18
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=72.80 E-value=15 Score=34.10 Aligned_cols=70 Identities=21% Similarity=0.312 Sum_probs=50.2
Q ss_pred HHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHH-----HHHHHHHHhhhhcCCccHHHHHHHHHh
Q 017157 213 ENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDS-----LYAESYSRSRWSSASWGPRRIKQALFK 287 (376)
Q Consensus 213 ~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~-----ryAesyvrsr~~~kg~GprkIrqeLrq 287 (376)
+...+.+|.- .+|..||.+.|.. +++.+.|..+|..|.+.|||-+. ..+..| +..-+..+..+.+.|++
T Consensus 32 ~~~L~~lLdG-~rt~~eI~~~l~~-~~p~~~v~~~L~~L~~~G~l~~~~~~~~~~~~~f----~~~~g~~~~~a~~~l~~ 105 (193)
T TIGR03882 32 YCQLAPLLDG-RRTLDEIIAALAG-RFPAEEVLYALDRLERRGYLVEDAPELPPAAAAF----WSGLGVDPAAALERLRQ 105 (193)
T ss_pred HHHHHHHHcC-CCCHHHHHHHhhc-cCCHHHHHHHHHHHHHCCCEeccCCCCCHHHHHH----HHHcCCCHHHHHHHHhc
Confidence 4455666665 7999999999997 89999999999999999999552 223333 22134456666666766
Q ss_pred C
Q 017157 288 K 288 (376)
Q Consensus 288 K 288 (376)
.
T Consensus 106 ~ 106 (193)
T TIGR03882 106 L 106 (193)
T ss_pred C
Confidence 3
No 19
>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=70.59 E-value=44 Score=28.06 Aligned_cols=37 Identities=11% Similarity=0.320 Sum_probs=31.4
Q ss_pred cccCHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCccH
Q 017157 223 RAFTAVEMRKKLNGK-KFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 223 RdrS~~ELr~KL~~K-G~sediIe~VLe~L~e~GyLDD 259 (376)
..-|..||.+.|.+. ++....|..+|.+|.+.|||.=
T Consensus 16 ~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~ 53 (115)
T PF03965_consen 16 GEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTR 53 (115)
T ss_dssp SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEE
T ss_pred CCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeE
Confidence 347899999999887 8999999999999999999864
No 20
>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=64.48 E-value=23 Score=25.25 Aligned_cols=44 Identities=18% Similarity=0.369 Sum_probs=38.5
Q ss_pred HHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 212 AENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 212 A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
.+-..+.+|.....+..||.+.|. ++...|..-|..|.+.|+|.
T Consensus 3 ~R~~Il~~L~~~~~~~~el~~~l~---~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSEGPLTVSELAEELG---LSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHHTTSSEEHHHHHHHHT---S-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhCCCchhhHHHhcc---ccchHHHHHHHHHHHCcCee
Confidence 356778999999999999999986 89999999999999999974
No 21
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=63.00 E-value=22 Score=32.91 Aligned_cols=42 Identities=19% Similarity=0.338 Sum_probs=35.2
Q ss_pred HHHHHHH-HhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 214 NLAVKLL-ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 214 ~~AL~lL-srRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
...|.+| .....|..+|.+.| |++...|...|..|.+.|||.
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~l---gis~~tV~~~L~~Le~~GlV~ 46 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEAL---AISPQAVRRHLKDLETEGLIE 46 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeE
Confidence 4455555 45668999999998 799999999999999999996
No 22
>PHA01351 putative minor structural protein
Probab=61.85 E-value=1.2e+02 Score=34.33 Aligned_cols=90 Identities=13% Similarity=0.073 Sum_probs=72.1
Q ss_pred HHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCC
Q 017157 211 DAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGI 290 (376)
Q Consensus 211 ~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGI 290 (376)
.-.+.-..++..--++..++..-|..-|++.+.++..+...... =+...+-.|+.+.++.=--.|+-+.++|++-|+
T Consensus 579 lQLnvyEsLakKGY~d~qq~ksElk~LGidKe~i~klin~Y~ql---~qt~~eIkYIqe~LK~f~IspkeAitELKKL~I 655 (1070)
T PHA01351 579 FQLNNIESLAKKGYLSLDEIKKQFKAIGIIKEYEDAFINFYNQE---LQISAFLTILKSQLRQFQIDPKEAETELKKLNI 655 (1070)
T ss_pred HHHHHHHHHHHhccccHHHHHHHHHhhccchhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHcccCHHHHHHHHHHcCc
Confidence 33455566777778899999999999999999999998887555 233346677888776445689999999999999
Q ss_pred CHHHHHHHHHhhh
Q 017157 291 SQTDAKKAVNLVF 303 (376)
Q Consensus 291 d~eiIeeALee~~ 303 (376)
+++++...+.+.+
T Consensus 656 SdaLAn~IV~eYf 668 (1070)
T PHA01351 656 NEYLANQIIQEEY 668 (1070)
T ss_pred hHHHHHHHHHHHh
Confidence 9999999998863
No 23
>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=61.34 E-value=23 Score=25.80 Aligned_cols=42 Identities=17% Similarity=0.395 Sum_probs=34.8
Q ss_pred HHHHHHHHhcc---cCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 214 NLAVKLLATRA---FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 214 ~~AL~lLsrRd---rS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
-.+|..|...+ .|..+|.+.|. ++...+..+|.+|++.|||.
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~---~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLG---ISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHT---S-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHC---cCHHHHHHHHHHHHHCCCEE
Confidence 45667777777 59999999886 89999999999999999984
No 24
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=60.38 E-value=29 Score=26.88 Aligned_cols=46 Identities=20% Similarity=0.395 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHhc-c--cCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 210 QDAENLAVKLLATR-A--FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 210 ~~A~~~AL~lLsrR-d--rS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
....+..|.+|..+ . .+..+|.+.| |++...|..+|..|++.|||.
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l---gl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNL---GLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 34466778888876 4 7888888876 599999999999999999984
No 25
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=60.05 E-value=26 Score=24.69 Aligned_cols=39 Identities=21% Similarity=0.409 Sum_probs=32.8
Q ss_pred HHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 217 VKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 217 L~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
+.+|.....|..+|.+.| |++...|..+|..|.+.|++.
T Consensus 3 l~~l~~~~~~~~~i~~~l---~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 3 LKLLAEGELCVCELAEIL---GLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred HHHhhcCCccHHHHHHHH---CCCHHHHHHHHHHHHHCCCee
Confidence 344556677888988888 599999999999999999996
No 26
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=58.94 E-value=22 Score=31.33 Aligned_cols=46 Identities=22% Similarity=0.159 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHh---cccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcC
Q 017157 210 QDAENLAVKLLAT---RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRG 255 (376)
Q Consensus 210 ~~A~~~AL~lLsr---RdrS~~ELr~KL~~KG~sediIe~VLe~L~e~G 255 (376)
.+..+.|.++|.. ++-+...=+..|+.||+++++|+++|.+.....
T Consensus 3 e~li~~A~~FL~~p~V~~sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 3 EDLIEQAVKFLQDPKVRNSPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHHCTTTCCCS-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHHhCCcccccCCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 3456778888875 666777888889999999999999999985544
No 27
>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=57.36 E-value=23 Score=26.81 Aligned_cols=38 Identities=21% Similarity=0.400 Sum_probs=33.5
Q ss_pred HHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 218 KLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 218 ~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
.+|.....|..+|.+.|. ++...|..+|..|.+.|+|.
T Consensus 16 ~Ll~~~~~t~~eIa~~l~---i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 16 ALLKNGPATAEEIAEELG---ISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHHHHCHEEHHHHHHHHT---SSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHcCCCCHHHHHHHHC---cCHHHHHHHHHHHHHCCCEE
Confidence 345789999999998875 99999999999999999984
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=56.50 E-value=41 Score=24.23 Aligned_cols=42 Identities=17% Similarity=0.387 Sum_probs=33.6
Q ss_pred HHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH
Q 017157 215 LAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 215 ~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD 259 (376)
..+.++.....+..+|.+.| |++...|..+|..|.+.|+|.-
T Consensus 11 ~il~~l~~~~~~~~ei~~~~---~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 11 RILRLLLEGPLTVSELAERL---GLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HHHHHHHHCCcCHHHHHHHH---CcCHhHHHHHHHHHHHCCCeEE
Confidence 34455555558888988877 7899999999999999999964
No 29
>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=54.90 E-value=16 Score=27.10 Aligned_cols=40 Identities=18% Similarity=0.464 Sum_probs=31.0
Q ss_pred HHHHHHH--hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCc
Q 017157 215 LAVKLLA--TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (376)
Q Consensus 215 ~AL~lLs--rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyL 257 (376)
.+|..|. ....+..+|.+.|. ++...|-.+|..|.+.|||
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~~---~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERLG---ISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHTT-----HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHccCCCcCHHHHHHHHC---cCHHHHHHHHHHHHHCCCE
Confidence 4566666 77778888887765 8899999999999999999
No 30
>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=54.03 E-value=36 Score=28.12 Aligned_cols=46 Identities=17% Similarity=0.264 Sum_probs=37.7
Q ss_pred HHHHHHHHh--cccCHHHHHHHHhcCC--CCHHHHHHHHHHHHHcCCccH
Q 017157 214 NLAVKLLAT--RAFTAVEMRKKLNGKK--FPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 214 ~~AL~lLsr--RdrS~~ELr~KL~~KG--~sediIe~VLe~L~e~GyLDD 259 (376)
...+.+|.. +..|..+|.+.|.+.+ ++...|-.+|+.|.+.|+|.-
T Consensus 4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 4 LAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 345566654 4589999999999874 789999999999999999874
No 31
>PF13730 HTH_36: Helix-turn-helix domain
Probab=52.10 E-value=29 Score=25.00 Aligned_cols=29 Identities=21% Similarity=0.476 Sum_probs=23.9
Q ss_pred CHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCc
Q 017157 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (376)
Q Consensus 226 S~~ELr~KL~~KG~sediIe~VLe~L~e~GyL 257 (376)
|...|.+.+ |++...|..+|..|++.|||
T Consensus 27 S~~~la~~~---g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDL---GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHH---CcCHHHHHHHHHHHHHCcCC
Confidence 445555555 89999999999999999997
No 32
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=52.01 E-value=40 Score=28.27 Aligned_cols=50 Identities=22% Similarity=0.256 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhc--ccCHHHHHHHHhcCC--CCHHHHHHHHHHHHHcCCccH
Q 017157 210 QDAENLAVKLLATR--AFTAVEMRKKLNGKK--FPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 210 ~~A~~~AL~lLsrR--drS~~ELr~KL~~KG--~sediIe~VLe~L~e~GyLDD 259 (376)
...+...+.+|... ..|..+|.+.|.++| ++...|-++|+.|.+.|+|.-
T Consensus 7 T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~ 60 (120)
T PF01475_consen 7 TPQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRK 60 (120)
T ss_dssp HHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEE
Confidence 44556666666653 689999999999875 677899999999999999864
No 33
>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=51.68 E-value=53 Score=24.41 Aligned_cols=45 Identities=18% Similarity=0.333 Sum_probs=39.1
Q ss_pred HHHHHHHHHH-HhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 211 DAENLAVKLL-ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 211 ~A~~~AL~lL-srRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
..+-..+.+| .....|..+|.+.| |++...+-.-|..|.+.|+|.
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l---~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEEL---GISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCeE
Confidence 3456778888 89999999999999 699999999999999999985
No 34
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=51.17 E-value=96 Score=29.96 Aligned_cols=121 Identities=20% Similarity=0.250 Sum_probs=79.6
Q ss_pred HHHHHHHHH-hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCC
Q 017157 213 ENLAVKLLA-TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGIS 291 (376)
Q Consensus 213 ~~~AL~lLs-rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId 291 (376)
++..+.+|. .-+.|..+|-++| |+++..|..=|+.|+..|++.=. ....|.|+-.-...|..+|.+
T Consensus 13 r~~il~lL~~~g~~sa~elA~~L---gis~~avR~HL~~Le~~Glv~~~----------~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 13 RERILELLKKSGPVSADELAEEL---GISPMAVRRHLDDLEAEGLVEVE----------RQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HHHHHHHHhccCCccHHHHHHHh---CCCHHHHHHHHHHHHhCcceeee----------eccCCCCCCceeeeecccchh
Confidence 455566666 6778999998887 59999999999999999998765 222677877777788888876
Q ss_pred H------HHHHHHHHhhhcCCCChhHHHhhhccchhHHHHHHHHHHHHHhh----c----cC-CChHHHHHHHHHHHHhC
Q 017157 292 Q------TDAKKAVNLVFRDGESDEDQESKLGMSKHSIDRLFVQASKQWLR----S----QG-APKETRKSRIIHWLQYR 356 (376)
Q Consensus 292 ~------eiIeeALee~~eeeeedEE~e~a~~Lak~~le~Ll~~AeKk~~R----~----~~-~~~~k~rqKlir~L~RK 356 (376)
. +++..+++.+.+... + + .+..+ +++++.+ + .+ .+..+.-.++...+..-
T Consensus 80 ~f~~~y~~l~~~~l~~l~~~~G--~--~--------~l~~~---l~~r~~~~~~~~~~~~~~~~~~ee~~e~Lv~l~~~~ 144 (218)
T COG2345 80 QFPKRYGELALALLDALEETGG--E--E--------ALNAF---LEKRAQAIGAQYRPAMGGDADLEEKVERLVELLSDL 144 (218)
T ss_pred hcchhhHHHHHHHHHHHHHhcc--H--H--------HHHHH---HHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhC
Confidence 3 344445555433221 1 1 11212 1222221 1 11 34567778999999999
Q ss_pred CCCHH
Q 017157 357 GFNWC 361 (376)
Q Consensus 357 GFs~d 361 (376)
||-..
T Consensus 145 gy~~e 149 (218)
T COG2345 145 GYMPE 149 (218)
T ss_pred Ccccc
Confidence 99654
No 35
>TIGR01926 peroxid_rel uncharacterized peroxidase-related enzyme. This protein family with length of about 200 amino acids. One member, from Myxococcus xanthus, is a selenoprotein, with an otherwise conserved Cys replaced by Sec. This family is drawn narrowly enough to suggest that These proteins contain a domain described by TIGR00778, with a CxxCxxxHxxxxxxxG motif. Some members of that family are known to act as peroxidases or correlate with resistance to oxidative stress.
Probab=51.15 E-value=1.4e+02 Score=26.53 Aligned_cols=89 Identities=12% Similarity=0.032 Sum_probs=55.9
Q ss_pred HHHHHHHHHhcccCHHHHH---HHHhcCCCCHHHHHHHHHHHHHcCCccH-HHHHHHHHHhhhhcCCccHHHHHHHHHhC
Q 017157 213 ENLAVKLLATRAFTAVEMR---KKLNGKKFPSHVIEAVITDFQSRGLIND-SLYAESYSRSRWSSASWGPRRIKQALFKK 288 (376)
Q Consensus 213 ~~~AL~lLsrRdrS~~ELr---~KL~~KG~sediIe~VLe~L~e~GyLDD-~ryAesyvrsr~~~kg~GprkIrqeLrqK 288 (376)
++.+.-..+.-..|.+.+- ..+...|.+++.++.+......- ..|+ .+-+..|++......+.-.....+.|++.
T Consensus 65 relv~l~vs~~ngc~yc~~~H~~~~~~~g~~~~~~~ai~~~~~~~-~~~~~e~a~l~~a~~~~~~~~~v~~~~~~~l~~~ 143 (177)
T TIGR01926 65 RELIAVVVSRANGCVYCAAVHGAALRQLSGDPDLADAVAVNFRDA-DLSPRERAMLDFAVKLTATPAKVNEADFAALRAA 143 (177)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHhcCCHHHHHHHHhCcccC-CCCHHHHHHHHHHHHHhhCcccCCHHHHHHHHHc
Confidence 3444444555555555554 45677799988888777654332 3455 55566666665543344455667889999
Q ss_pred CCCHHHHHHHHHhh
Q 017157 289 GISQTDAKKAVNLV 302 (376)
Q Consensus 289 GId~eiIeeALee~ 302 (376)
|++...|-+++.-+
T Consensus 144 g~s~~eivel~~~i 157 (177)
T TIGR01926 144 GFSDLDILDLIHSV 157 (177)
T ss_pred CCCHHHHHHHHHHH
Confidence 99998887766543
No 36
>PHA01351 putative minor structural protein
Probab=49.65 E-value=4.5e+02 Score=30.10 Aligned_cols=89 Identities=9% Similarity=0.107 Sum_probs=67.3
Q ss_pred HHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCC
Q 017157 212 AENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGIS 291 (376)
Q Consensus 212 A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId 291 (376)
.+...-.+++.-=+..+++.+-|+..||..+.++..++..-..-.++. .-.++.++++.=--+++-+..+|+.-||+
T Consensus 484 l~~~l~sl~skGi~DqkkIke~LKa~gfnks~~d~~L~~~~n~a~ies---qIK~LQ~qL~nF~IS~QD~EkELKkLg~s 560 (1070)
T PHA01351 484 LLRQLQQIVSLGIFDQKKIKEELKANKFNEQVALQILESELQFAQLQN---QLKEYQFKLNNFLISPQDLEKDLKHLGFD 560 (1070)
T ss_pred HHHHHHHHHHcccccHHHHHHHHHhcCccHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHhccCCHHHHHHHHHHcCCC
Confidence 344444566667788999999999999999999999988744433322 23455555553345899999999999999
Q ss_pred HHHHHHHHHhhh
Q 017157 292 QTDAKKAVNLVF 303 (376)
Q Consensus 292 ~eiIeeALee~~ 303 (376)
+.+|++.+.|.+
T Consensus 561 ~alIqaiI~Eyf 572 (1070)
T PHA01351 561 SAIISALIYENQ 572 (1070)
T ss_pred HHHHHHHHHHHH
Confidence 999999988754
No 37
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=49.09 E-value=40 Score=30.28 Aligned_cols=56 Identities=14% Similarity=0.164 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHhcCC-----CCHHHHHHHHHHHHHcCCccH
Q 017157 203 LQAAKARQDAENLAVKLLATRAFTAVEMRKKLNGKK-----FPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 203 ~~~~~~~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG-----~sediIe~VLe~L~e~GyLDD 259 (376)
++.........-..|.+|+.. .+-++|.+.|.+.+ .++..|-.+|.+|++.|||.-
T Consensus 35 ~~~~~~~~~~~l~IL~lL~~~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s 95 (135)
T PRK09416 35 KQSSEKEEDILLAILQLLMNE-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQS 95 (135)
T ss_pred HHHhcccccHHHHHHHHHhCC-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEE
Confidence 344344666788899999999 89999999999764 357899999999999999964
No 38
>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=48.98 E-value=19 Score=29.57 Aligned_cols=45 Identities=9% Similarity=0.237 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHh-----cccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCc
Q 017157 210 QDAENLAVKLLAT-----RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (376)
Q Consensus 210 ~~A~~~AL~lLsr-----RdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyL 257 (376)
.......+.+|.. .-.+..+|.++| +++.+.|..+|+.|...|+|
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l---~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQL---GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHS---TS-HHHHHHHHHHHHHTTSE
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHh---CcCHHHHHHHHHHHHhCCeE
Confidence 3445555666655 225678999999 89999999999999999987
No 39
>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=48.71 E-value=24 Score=29.12 Aligned_cols=45 Identities=13% Similarity=0.248 Sum_probs=39.3
Q ss_pred HHHHHHHHhcccCHHHHHHHHhcC-----CCCHHHHHHHHHHHHHcCCcc
Q 017157 214 NLAVKLLATRAFTAVEMRKKLNGK-----KFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 214 ~~AL~lLsrRdrS~~ELr~KL~~K-----G~sediIe~VLe~L~e~GyLD 258 (376)
-..|.+|+..+.+-++|.+.|.+. .+++..|-.+|.+|++.|||.
T Consensus 7 ~~iL~~L~~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~ 56 (100)
T TIGR03433 7 LLILKTLSLGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIA 56 (100)
T ss_pred HHHHHHHhcCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeE
Confidence 356788999999999999999765 477889999999999999995
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=47.85 E-value=49 Score=26.20 Aligned_cols=31 Identities=16% Similarity=0.463 Sum_probs=26.4
Q ss_pred cCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 225 rS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
.|..+|.+.+. +++..+..++..|.+.|+|.
T Consensus 26 ~s~~eiA~~~~---i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 26 VSSKEIAERLG---ISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp BEHHHHHHHHT---S-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHC---cCHHHHHHHHHHHhhCCeeE
Confidence 57888888665 99999999999999999985
No 41
>PHA00435 capsid assembly protein
Probab=47.21 E-value=3.2e+02 Score=27.64 Aligned_cols=47 Identities=15% Similarity=0.266 Sum_probs=39.2
Q ss_pred HHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHH
Q 017157 218 KLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAE 264 (376)
Q Consensus 218 ~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAe 264 (376)
.-|.-..-+-+.|.....++|++.+.|..+-+.+.+.|=|.+..|++
T Consensus 117 ~qL~e~e~gf~~mv~~Ave~Glsae~i~~i~aEY~~~g~LSeeSY~~ 163 (306)
T PHA00435 117 EQLEEHEEGFQAMVEQAVERGLSAETITRIQAEYEEEGGLSEESYAE 163 (306)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCcCHHHHHH
Confidence 33444455667888899999999999999999999999999998873
No 42
>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=46.54 E-value=35 Score=26.21 Aligned_cols=34 Identities=15% Similarity=0.402 Sum_probs=25.7
Q ss_pred hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 222 rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
+...|..+|...|. .+++.|+..|+.+...|+|.
T Consensus 12 ~~~~S~~eLa~~~~---~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 12 RGRVSLAELAREFG---ISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp S-SEEHHHHHHHTT-----HHHHHHHHHHHHCCTSCE
T ss_pred cCCcCHHHHHHHHC---cCHHHHHHHHHHHHHCCcEE
Confidence 44567777777654 99999999999999999985
No 43
>COG2128 Uncharacterized conserved protein [Function unknown]
Probab=45.52 E-value=2.2e+02 Score=25.39 Aligned_cols=90 Identities=14% Similarity=0.077 Sum_probs=66.2
Q ss_pred HHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH-HHHHHHHHHhhhhcCCcc--HHHHHHHHHhC
Q 017157 212 AENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND-SLYAESYSRSRWSSASWG--PRRIKQALFKK 288 (376)
Q Consensus 212 A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD-~ryAesyvrsr~~~kg~G--prkIrqeLrqK 288 (376)
+-.........-.||-..-+......|.+++.+..+......-+.+++ ++.+-.|+..... .+.| ..-....|+..
T Consensus 66 lv~~~~s~~ngc~~C~~~h~~~a~~~g~~~~~~~~~~~~~~~~~~~~~~e~a~L~~~~~~~~-~~~~~~~~~~~~~lr~~ 144 (177)
T COG2128 66 LVALRAARINGCAYCVAMHRKVARLLGLSADDLAALLAWRDSAAFLDPRERAALAYAAALTI-NPCGAVSDAHFAALRAA 144 (177)
T ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHcCCcHHHHHHHHhcccCCccCCHHHHHHHHHHHHHhc-CCCCCCCHHHHHHHHHc
Confidence 333344445555566666666777789999999999988877788886 8888888887765 3333 66777889999
Q ss_pred CCCHHHHHHHHHhh
Q 017157 289 GISQTDAKKAVNLV 302 (376)
Q Consensus 289 GId~eiIeeALee~ 302 (376)
|++.+.|-+++..+
T Consensus 145 g~~~~qi~el~~~i 158 (177)
T COG2128 145 GFDDEQILELVLAI 158 (177)
T ss_pred CCCHHHHHHHHHHH
Confidence 99999888876543
No 44
>PRK09462 fur ferric uptake regulator; Provisional
Probab=45.37 E-value=60 Score=28.50 Aligned_cols=50 Identities=14% Similarity=0.217 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHh---cccCHHHHHHHHhcCC--CCHHHHHHHHHHHHHcCCcc
Q 017157 209 RQDAENLAVKLLAT---RAFTAVEMRKKLNGKK--FPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 209 ~~~A~~~AL~lLsr---RdrS~~ELr~KL~~KG--~sediIe~VLe~L~e~GyLD 258 (376)
....+...+.+|.. ...|..||.++|.+.+ ++...|-++|+.|.+.|+|.
T Consensus 15 ~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~ 69 (148)
T PRK09462 15 VTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVT 69 (148)
T ss_pred CCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEE
Confidence 44556777888863 4789999999999875 67899999999999999995
No 45
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=44.84 E-value=1.2e+02 Score=24.24 Aligned_cols=49 Identities=18% Similarity=0.210 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHH--HH-hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 208 ARQDAENLAVKL--LA-TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 208 ~~~~A~~~AL~l--Ls-rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
.+-..++..+.. .. .+..|..+.+.-+. |.+...+..|.+.|...||||
T Consensus 34 ~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~--~~d~~~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 34 QYLKIRNTILAEWRKNPNKYLTKTDARKLIK--GIDVNKIRRIYDFLERWGLIN 85 (86)
T ss_dssp HHHHHHHHHHHHHHHHTTS---HHHHHHHTT--SSSHHHHHHHHHHHHHTTSSS
T ss_pred HHHHHHHHHHHHHHHCCCCcccHHHHHHHcc--ccCHHHHHHHHHHHHHcCccC
Confidence 456667776666 43 34445555544444 889999999999999999998
No 46
>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=44.53 E-value=1e+02 Score=21.61 Aligned_cols=41 Identities=20% Similarity=0.391 Sum_probs=30.9
Q ss_pred HHHHHHHHhcc-cCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCc
Q 017157 214 NLAVKLLATRA-FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (376)
Q Consensus 214 ~~AL~lLsrRd-rS~~ELr~KL~~KG~sediIe~VLe~L~e~GyL 257 (376)
...+.+|.... .|..||.+++- ++...+...|.+|.+.|||
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~---is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLG---ISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHT---S-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHcCCCCHHHHHHHhC---CCHHHHHHHHHHHHHCcCc
Confidence 34555665544 77888888775 9999999999999999997
No 47
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=43.77 E-value=15 Score=36.33 Aligned_cols=56 Identities=16% Similarity=0.242 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc-HH
Q 017157 205 AAKARQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN-DS 260 (376)
Q Consensus 205 ~~~~~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD-D~ 260 (376)
........+.+.+++|+.+.|..-||..+|.+.|+.+...+.+-.-|.+-+-+| |.
T Consensus 192 ~~v~~rplReRvIHLLALkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~l~~~~ 248 (284)
T PF10390_consen 192 SAVSKRPLRERVIHLLALKPYKKPELLLRLQKDGLSPKDKDELDSILQEVANLNKDN 248 (284)
T ss_dssp --STTS-HHHHHHHHHHHS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCCEEETTT
T ss_pred cccccccccccchhhhhcCccccHHHHHHHHhcCCChHHHHHHHHHHHHHhccCcCC
Confidence 344556678899999999999999999999999999988888888888888888 54
No 48
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=42.85 E-value=61 Score=28.78 Aligned_cols=62 Identities=13% Similarity=0.165 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhc--ccCHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCccHHHHHH
Q 017157 203 LQAAKARQDAENLAVKLLATR--AFTAVEMRKKLNGK--KFPSHVIEAVITDFQSRGLINDSLYAE 264 (376)
Q Consensus 203 ~~~~~~~~~A~~~AL~lLsrR--drS~~ELr~KL~~K--G~sediIe~VLe~L~e~GyLDD~ryAe 264 (376)
.+..+-...-+...+.+|... ..|..+|...|.+. +++...|-.+|..|.+.|+|.-..+..
T Consensus 13 k~~glr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 13 KEAGLRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred HHcCCCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 344444455567778888754 37999999999986 678899999999999999998765443
No 49
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=42.80 E-value=31 Score=29.71 Aligned_cols=49 Identities=22% Similarity=0.305 Sum_probs=42.7
Q ss_pred HHHHHHHHHHhcccCHHHHHHHHhcCC-----CCHHHHHHHHHHHHHcCCccHH
Q 017157 212 AENLAVKLLATRAFTAVEMRKKLNGKK-----FPSHVIEAVITDFQSRGLINDS 260 (376)
Q Consensus 212 A~~~AL~lLsrRdrS~~ELr~KL~~KG-----~sediIe~VLe~L~e~GyLDD~ 260 (376)
..-.++.+|+.++.+-.+|.+.+.... .++-.|..+|.+|++.|||+-.
T Consensus 10 l~~~iL~~L~~~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~ 63 (138)
T COG1695 10 LELLILSLLSEKPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESR 63 (138)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEE
Confidence 445678999999999999999998874 4678999999999999999864
No 50
>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=40.71 E-value=94 Score=23.60 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=32.7
Q ss_pred HHHHHHH--hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH
Q 017157 215 LAVKLLA--TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 215 ~AL~lLs--rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD 259 (376)
.++..|. ...-+..+|.+.|. +++..+-.+|.+|.+.||++=
T Consensus 11 ~~Iy~l~~~~~~v~~~~iA~~L~---vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 11 KAIYELSEEGGPVRTKDIAERLG---VSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp HHHHHHHHCTSSBBHHHHHHHHT---S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCCCCccHHHHHHHHC---CChHHHHHHHHHHHHCCCEEe
Confidence 4444454 45677888888886 889999999999999999964
No 51
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=40.53 E-value=57 Score=29.36 Aligned_cols=48 Identities=17% Similarity=0.370 Sum_probs=39.9
Q ss_pred HHHHHHHHHH--hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHH
Q 017157 212 AENLAVKLLA--TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDS 260 (376)
Q Consensus 212 A~~~AL~lLs--rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ 260 (376)
|....+.||- .|+||...|..-|.. +|+...|..+|+.|.+.|-|--.
T Consensus 2 Ae~~Il~y~~~qNRPys~~di~~nL~~-~~~K~~v~k~Ld~L~~~g~i~~K 51 (169)
T PF07106_consen 2 AEDAILEYMKEQNRPYSAQDIFDNLHN-KVGKTAVQKALDSLVEEGKIVEK 51 (169)
T ss_pred hHHHHHHHHHHcCCCCcHHHHHHHHHh-hccHHHHHHHHHHHHhCCCeeee
Confidence 4455666665 489999999999997 89999999999999999877543
No 52
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=40.26 E-value=1.5e+02 Score=26.52 Aligned_cols=53 Identities=8% Similarity=0.053 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHhcccCHHHHHHHHhcCC---CCHHHHHHHHHHHHHcCCccH
Q 017157 207 KARQDAENLAVKLLATRAFTAVEMRKKLNGKK---FPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 207 ~~~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG---~sediIe~VLe~L~e~GyLDD 259 (376)
+..-...-..|.+|+..+..-++|.+.|.+.| +++-.|-.+|.+|++.|||.-
T Consensus 20 l~kg~l~~~IL~~L~~~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~ 75 (138)
T TIGR02719 20 APKNFLVPFLLLCLKDWNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISS 75 (138)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEE
Confidence 44555667788999999999999999999875 467789999999999999974
No 53
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=39.92 E-value=57 Score=23.03 Aligned_cols=30 Identities=13% Similarity=0.407 Sum_probs=26.2
Q ss_pred CHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 226 S~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
|..+|.+.+ |++...|..+|..|.+.|+|.
T Consensus 22 s~~~la~~~---~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 22 SERELAAQL---GVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 677777776 699999999999999999984
No 54
>PF06180 CbiK: Cobalt chelatase (CbiK); InterPro: IPR010388 This group, typified by Salmonella typhimurium CbiK, contains anaerobic cobalt chelatases that act in the anaerobic cobalamin biosynthesis pathway [, ]. Cobalamin (vitamin B12) can be complexed with metal via ATP-dependent reactions (aerobic pathway) (e.g., in Pseudomonas denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in S. typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. This group belongs to the class of ATP-independent, single-subunit chelatases that also includes distantly related protoporphyrin IX (PPIX) ferrochelatase (HemH) (Class II chelatases) []. The structure of S. typhimurium CbiK shows that it has a remarkably similar topology to Bacillus subtilis ferrochelatase despite only weak sequence conservation []. Both enzymes contain a histidine residue identified as the metal ion ligand, but CbiK contains a second histidine in place of the glutamic acid residue identified as a general base in PPIX ferrochelatase []. Site-directed mutagenesis has confirmed a role for this histidine and a nearby glutamic acid in cobalt binding, modulating metal ion specificity as well as catalytic efficiency []. It should be noted that CysG and Met8p, which are multifunctional proteins associated with siroheme biosynthesis, include chelatase activity and can therefore be considered as the third class of chelatases []. As with the class II chelatases, they do not require ATP for activity. However, they are not structurally similar to HemH or CbiK, and it is likely that they have arisen by the acquisition of a chelatase function within a dehydrogenase catalytic framework [, ].; GO: 0016852 sirohydrochlorin cobaltochelatase activity; PDB: 1QGO_A 2XWP_A 2XVZ_A 2XVX_A 2XVY_A.
Probab=39.17 E-value=29 Score=34.09 Aligned_cols=39 Identities=26% Similarity=0.342 Sum_probs=28.9
Q ss_pred HHHHhcccCHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCC
Q 017157 218 KLLATRAFTAVEMRKKLNGK-KFPSHVIEAVITDFQSRGL 256 (376)
Q Consensus 218 ~lLsrRdrS~~ELr~KL~~K-G~sediIe~VLe~L~e~Gy 256 (376)
.+--++.+|..-++++|+++ |+.-....++|+.|.+.||
T Consensus 33 ~~~V~~AfTS~~I~~kl~~~~g~~i~~~~eaL~~L~~~G~ 72 (262)
T PF06180_consen 33 DYDVRRAFTSRIIRKKLAERDGIKIDSPEEALAKLADEGY 72 (262)
T ss_dssp TSEEEEEES-HHHHHHHHHCHT-----HHHHHHHHHHCT-
T ss_pred CCcEEEEchHHHHHHHHHhcCCCCcCCHHHHHHHHHHCCC
Confidence 35567899999999999999 8888999999999999997
No 55
>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=38.86 E-value=1.5e+02 Score=21.30 Aligned_cols=31 Identities=13% Similarity=0.421 Sum_probs=26.6
Q ss_pred CHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH
Q 017157 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 226 S~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD 259 (376)
|..+|.+.+ |++...|..+|..|.+.|||.-
T Consensus 27 ~~~~la~~~---~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 27 SERELAEEL---GVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred CHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEe
Confidence 477777776 7999999999999999999953
No 56
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=38.01 E-value=1.4e+02 Score=23.18 Aligned_cols=39 Identities=18% Similarity=0.396 Sum_probs=33.2
Q ss_pred HHHHHhc--ccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 217 VKLLATR--AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 217 L~lLsrR--drS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
+.+|+.. ..|..+|-+.| |++...|...|..|.+.|||.
T Consensus 11 l~~l~~~~~~~t~~~ia~~l---~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 11 LRALAEEPGGLTLAELAERL---GLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHhCCCCcCHHHHHHHh---CCCHHHHHHHHHHHHHCCCee
Confidence 4555553 68899999988 799999999999999999995
No 57
>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.
Probab=37.73 E-value=66 Score=27.83 Aligned_cols=52 Identities=29% Similarity=0.380 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHc-CCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCCHHHH
Q 017157 242 HVIEAVITDFQSR-GLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGISQTDA 295 (376)
Q Consensus 242 diIe~VLe~L~e~-GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId~eiI 295 (376)
...++++..+... .|-||.||.+.|+.---. ...|..|-+.|..+||.....
T Consensus 47 ~lLer~~~~f~~~~~Y~nD~RylkiWi~ya~~--~~~~~~if~~l~~~~IG~~~A 99 (126)
T PF08311_consen 47 ELLERCIRKFKDDERYKNDERYLKIWIKYADL--SSDPREIFKFLYSKGIGTKLA 99 (126)
T ss_dssp HHHHHHHHHHTTSGGGTT-HHHHHHHHHHHTT--BSHHHHHHHHHHHHTTSTTBH
T ss_pred HHHHHHHHHHhhhHhhcCCHHHHHHHHHHHHH--ccCHHHHHHHHHHcCccHHHH
Confidence 4567777777664 899999999999876543 338999999999999998654
No 58
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=37.60 E-value=89 Score=28.39 Aligned_cols=60 Identities=10% Similarity=0.102 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHh--cccCHHHHHHHHhcCC--CCHHHHHHHHHHHHHcCCccHHH
Q 017157 202 YLQAAKARQDAENLAVKLLAT--RAFTAVEMRKKLNGKK--FPSHVIEAVITDFQSRGLINDSL 261 (376)
Q Consensus 202 ~~~~~~~~~~A~~~AL~lLsr--RdrS~~ELr~KL~~KG--~sediIe~VLe~L~e~GyLDD~r 261 (376)
......-....+...+.+|.. +-.|..+|.++|.+.+ ++...|-.+|+.|.+.|+|.-..
T Consensus 17 L~~~GlR~T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 17 CAQRNVRLTPQRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred HHHcCCCCCHHHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence 333333344455677777764 4679999999999885 67889999999999999997544
No 59
>KOG0931 consensus Predicted guanine nucleotide exchange factor, contains Sec7 domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.68 E-value=1.4e+02 Score=32.40 Aligned_cols=81 Identities=15% Similarity=0.109 Sum_probs=55.6
Q ss_pred cccCHHHHHHHHhcCCCC--HHHHHHHHHHHHHcCCccHHHH-HHHHHHhhhhcCCccHHHHHHHH--HhCCCCHHHHHH
Q 017157 223 RAFTAVEMRKKLNGKKFP--SHVIEAVITDFQSRGLINDSLY-AESYSRSRWSSASWGPRRIKQAL--FKKGISQTDAKK 297 (376)
Q Consensus 223 RdrS~~ELr~KL~~KG~s--ediIe~VLe~L~e~GyLDD~ry-Aesyvrsr~~~kg~GprkIrqeL--rqKGId~eiIee 297 (376)
...+---+++.+.+-|.. ..--+.-|..|.+.|||-|.-. ...|+-. ++|.+++.|-..| ++|-+..++.+.
T Consensus 189 p~~~~Dt~~kr~YriGlnlfn~kPekGvQ~Li~rGFv~dtPvgvAhfllq---RkGLSrqMIGEflGn~~kqfnrdVLdc 265 (627)
T KOG0931|consen 189 PAFSNDTRRKRHYRIGLNLFNKKPEKGVQYLIERGFVPDTPVGVAHFLLQ---RKGLSRQMIGEFLGNRQKQFNRDVLDC 265 (627)
T ss_pred CCCcchHHHHHHhhhccchhcCCcchhhhhhhhhcccCCCchHHHHHHHh---hccchHHHHHHHhccccchhhhHHHHH
Confidence 444445555555544543 2234677889999999988422 2233323 3788999998888 679999999999
Q ss_pred HHHhhhcCC
Q 017157 298 AVNLVFRDG 306 (376)
Q Consensus 298 ALee~~eee 306 (376)
+.++++...
T Consensus 266 vvdemDfss 274 (627)
T KOG0931|consen 266 VVDEMDFSS 274 (627)
T ss_pred HHhhhcccc
Confidence 999986643
No 60
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=36.59 E-value=1.4e+02 Score=22.86 Aligned_cols=42 Identities=12% Similarity=0.117 Sum_probs=28.7
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhh
Q 017157 229 EMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRW 271 (376)
Q Consensus 229 ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~ 271 (376)
.|...+...|+++++|..++..+...|-.+ -.|++..+.++.
T Consensus 20 ~i~~~~~~~~~~~evI~~ai~~a~~~~~~~-~~Yi~~Il~~W~ 61 (73)
T TIGR01446 20 DLKYWLDEFGNSPELIKEALKEAVSNNKAN-YKYIDAILNNWK 61 (73)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHH
Confidence 344555667889999999998887765544 456666665554
No 61
>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=36.52 E-value=98 Score=24.47 Aligned_cols=35 Identities=9% Similarity=0.217 Sum_probs=29.7
Q ss_pred cCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH
Q 017157 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 225 rS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD 259 (376)
-....|.+-|..-|+++..+..+|.+|...|+|.-
T Consensus 21 i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~ 55 (70)
T PF07848_consen 21 IWVASLIRLLAAFGVSESAVRTALSRLVRRGWLES 55 (70)
T ss_dssp EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEE
T ss_pred eeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceee
Confidence 46688999999999999999999999999999853
No 62
>PF08312 cwf21: cwf21 domain; InterPro: IPR013170 The cwf21 domain is found in proteins involved in mRNA splicing. Proteins containing this domain have been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe (Fission yeast) []. In yeast, this domain binds the protein Prp8p [], a large and highly conserved U5 snRNP protein which has been proposed as a protein cofactor at the spliceosomal catalytic centre []. The cwf21 domain is found in, amongst others, the small Cwc21p protein in yeast as well as in the much larger human ortholog SRm300 (serine/arginine repetitive matrix protein). ; PDB: 2E62_A.
Probab=36.17 E-value=38 Score=24.93 Aligned_cols=26 Identities=19% Similarity=0.496 Sum_probs=20.6
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHH
Q 017157 228 VEMRKKLNGKKFPSHVIEAVITDFQS 253 (376)
Q Consensus 228 ~ELr~KL~~KG~sediIe~VLe~L~e 253 (376)
.+++.+|...|++++.|+.-++.+..
T Consensus 14 ~elrd~LEe~g~~~eeIe~kv~~~R~ 39 (46)
T PF08312_consen 14 LELRDELEEQGYSEEEIEEKVDELRK 39 (46)
T ss_dssp HHHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence 47899999999999999999988743
No 63
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=35.98 E-value=99 Score=27.22 Aligned_cols=47 Identities=19% Similarity=0.145 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhhccCCChHHHHHHHHHHHHhCCCCHHHHHHHHHhhhhc
Q 017157 325 RLFVQASKQWLRSQGAPKETRKSRIIHWLQYRGFNWCVTSFILKKLESQ 373 (376)
Q Consensus 325 ~Ll~~AeKk~~R~~~~~~~k~rqKlir~L~RKGFs~d~I~~vL~eie~e 373 (376)
.+++.|.+.+.--. .- ..-..+-+.||..||-+-++|..+|.+....
T Consensus 4 ~li~~A~~FL~~p~-V~-~sp~~~k~~FL~sKGLt~~EI~~al~~a~~~ 50 (136)
T PF04695_consen 4 DLIEQAVKFLQDPK-VR-NSPLEKKIAFLESKGLTEEEIDEALGRAGSP 50 (136)
T ss_dssp HHHHHHHHHHCTTT-CC-CS-HHHHHHHHHHCT--HHHHHHHHHHHT--
T ss_pred HHHHHHHHHhCCcc-cc-cCCHHHHHHHHHcCCCCHHHHHHHHHhcCCc
Confidence 46677767654221 10 1114566899999999999999999987544
No 64
>smart00816 Amb_V_allergen Amb V Allergen. Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphhydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens.
Probab=35.70 E-value=18 Score=26.38 Aligned_cols=20 Identities=40% Similarity=0.708 Sum_probs=17.7
Q ss_pred eeecCCCccCCcceeeecCC
Q 017157 33 SCVKGRDYSSSFPVRYVPKK 52 (376)
Q Consensus 33 ~c~~~r~~~~~~~~~y~~~~ 52 (376)
.|-+-|.|++|-|=||-|-.
T Consensus 11 ~CGekr~YCcSdpGrYCpwq 30 (45)
T smart00816 11 NCGEKRKYCCSDPGRYCPWQ 30 (45)
T ss_pred cccccCccccCCCcccCCce
Confidence 58999999999999999853
No 65
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=34.76 E-value=90 Score=28.40 Aligned_cols=33 Identities=9% Similarity=0.212 Sum_probs=28.6
Q ss_pred CHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 226 S~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
.+.+|.++|...||+.+.|.+++.+|....-+.
T Consensus 22 d~~~L~~~L~~aGF~~~eI~~Al~WL~~L~~~~ 54 (155)
T PF04361_consen 22 DQDDLTRELSAAGFEDEEINKALDWLEGLAELQ 54 (155)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcc
Confidence 378999999999999999999999997665444
No 66
>smart00351 PAX Paired Box domain.
Probab=34.50 E-value=3e+02 Score=23.66 Aligned_cols=74 Identities=11% Similarity=0.174 Sum_probs=47.7
Q ss_pred HHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHH-----------HHHHHHHHhh-hhcCCccHHH
Q 017157 213 ENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDS-----------LYAESYSRSR-WSSASWGPRR 280 (376)
Q Consensus 213 ~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~-----------ryAesyvrsr-~~~kg~Gprk 280 (376)
+.+++.+.. .-.|..+|-+.| |++...|...+.++.+.|.+... .-...++... .....++...
T Consensus 23 R~riv~~~~-~G~s~~~iA~~~---gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~e 98 (125)
T smart00351 23 RQRIVELAQ-NGVRPCDISRQL---CVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWE 98 (125)
T ss_pred HHHHHHHHH-cCCCHHHHHHHH---CcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHH
Confidence 344444443 456777776554 69999999999999998876652 0112233322 1225778888
Q ss_pred HHHHHHhCCC
Q 017157 281 IKQALFKKGI 290 (376)
Q Consensus 281 IrqeLrqKGI 290 (376)
|+..|...||
T Consensus 99 l~~~L~~~gv 108 (125)
T smart00351 99 IRDRLLSEGV 108 (125)
T ss_pred HHHHHHHcCC
Confidence 8888888777
No 67
>PRK03430 hypothetical protein; Validated
Probab=33.36 E-value=55 Score=30.06 Aligned_cols=33 Identities=9% Similarity=0.106 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH
Q 017157 227 AVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 227 ~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD 259 (376)
..+|.++|...||+.+.|..++.+|....-+.+
T Consensus 23 ~~~L~~~L~~aGF~~~eI~~AL~WLe~L~~~~~ 55 (157)
T PRK03430 23 QDKLEDDLTDAGFHREDIYNALLWLEKLADLQE 55 (157)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcc
Confidence 688999999999999999999999977754333
No 68
>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=32.07 E-value=1.4e+02 Score=22.59 Aligned_cols=39 Identities=18% Similarity=0.334 Sum_probs=33.5
Q ss_pred HHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCc
Q 017157 216 AVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (376)
Q Consensus 216 AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyL 257 (376)
.+.+|+....|..+|.+.| |++...|...|..|.+.|+.
T Consensus 5 il~~L~~~~~~~~eLa~~l---~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 5 LLALLADNPFSGEKLGEAL---GMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred HHHHHHcCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCe
Confidence 4567777788888888888 79999999999999999984
No 69
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=32.00 E-value=54 Score=33.89 Aligned_cols=35 Identities=11% Similarity=0.186 Sum_probs=31.4
Q ss_pred hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCC
Q 017157 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGL 256 (376)
Q Consensus 222 rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~Gy 256 (376)
-+.+...||.+|+...||..|.|..+|.+|+|.|-
T Consensus 316 ~~~~p~ddvidKv~~MGf~rDqV~a~v~rl~E~GQ 350 (358)
T PF07223_consen 316 GNRHPYDDVIDKVASMGFRRDQVRATVRRLTENGQ 350 (358)
T ss_pred cccCcHHHHHHHHHHcCCcHHHHHHHHHHHHhcCC
Confidence 35566789999999999999999999999999985
No 70
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=31.93 E-value=70 Score=34.90 Aligned_cols=45 Identities=18% Similarity=0.316 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHH
Q 017157 209 RQDAENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQS 253 (376)
Q Consensus 209 ~~~A~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e 253 (376)
....+.+.++||+.+.|...||..+|+.-|++++.++.+=.-|.+
T Consensus 209 ~r~ir~RviHLlalk~ykk~El~~rLk~dGl~~~e~~~i~~il~~ 253 (604)
T KOG4796|consen 209 QRPIRDRVIHLLALKAYKKPELLARLKKDGLPQEEKNKIRSILQQ 253 (604)
T ss_pred ccchHHHHHHHHHhhhcccHHHHHHHhhcCCcHHHHHHHHHHHHh
Confidence 345688999999999999999999999999999988877666655
No 71
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=31.86 E-value=30 Score=25.94 Aligned_cols=34 Identities=18% Similarity=0.450 Sum_probs=28.0
Q ss_pred ccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCc
Q 017157 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (376)
Q Consensus 224 drS~~ELr~KL~~KG~sediIe~VLe~L~e~GyL 257 (376)
-.+..||+.+|..+++++...+.+|+.+.+.|.|
T Consensus 17 G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l 50 (59)
T PF09106_consen 17 GMPKEELRSRLFKPRLPPKLFNALLEALVAEGRL 50 (59)
T ss_dssp -EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCe
Confidence 3567899999988799999999999999999976
No 72
>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=31.72 E-value=1.1e+02 Score=25.89 Aligned_cols=32 Identities=13% Similarity=0.391 Sum_probs=28.0
Q ss_pred ccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 224 drS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
..|..+|.+.|. ++...+..++..|...|||.
T Consensus 25 ~~s~~eia~~~~---i~~~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 25 PVSVKEIAERQG---ISRSYLEKILRTLRRAGLVE 56 (132)
T ss_pred cCcHHHHHHHHC---cCHHHHHHHHHHHHHCCcEE
Confidence 567788877765 99999999999999999996
No 73
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=29.24 E-value=68 Score=26.11 Aligned_cols=57 Identities=9% Similarity=0.145 Sum_probs=34.5
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHH-HHHHHHHHhhhhcCCccHHHHHHHHHhCCCCHHHHHHHHHhh
Q 017157 228 VEMRKKLNGKKFPSHVIEAVITDFQSRGLINDS-LYAESYSRSRWSSASWGPRRIKQALFKKGISQTDAKKAVNLV 302 (376)
Q Consensus 228 ~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~-ryAesyvrsr~~~kg~GprkIrqeLrqKGId~eiIeeALee~ 302 (376)
.+|.++|..-|--+..-+.+-.+|.+.||.|+- .+|+. .++++|++.-..+++++++
T Consensus 4 ~~i~~~L~~sGe~~~L~~~L~~rL~e~GW~d~vr~~~re------------------~i~~~g~~~~~~~~l~~~i 61 (86)
T PF10163_consen 4 AQIQQRLVESGEYERLKELLRQRLIECGWRDEVRQLCRE------------------IIRERGIDNLTFEDLLEEI 61 (86)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHHHTTHHHHHHHHHHH------------------HHHHH-TTTSBHHHHHHHH
T ss_pred HHHHHHHHHcCcHHHHHHHHHHHHHHCChHHHHHHHHHH------------------HHHhhCCCCCCHHHHHHHH
Confidence 355666666666666556666788888888885 33333 3334676665566665554
No 74
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=28.88 E-value=2.3e+02 Score=25.60 Aligned_cols=56 Identities=20% Similarity=0.265 Sum_probs=34.9
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCCHHHHHHHHHh
Q 017157 228 VEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGISQTDAKKAVNL 301 (376)
Q Consensus 228 ~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId~eiIeeALee 301 (376)
.+|+++|+ ++|+++++++++.+.+ |+..... .|.....|..+| |=+.+++.+.+++
T Consensus 8 ~~L~~~L~--~lp~~e~~e~l~~Y~e------------~f~d~~~-~G~sEeeii~~L---G~P~~iA~~i~~~ 63 (181)
T PF08006_consen 8 NELEKYLK--KLPEEEREEILEYYEE------------YFDDAGE-EGKSEEEIIAEL---GSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHH--cCCHHHHHHHHHHHHH------------HHHHhhh-CCCCHHHHHHHc---CCHHHHHHHHHHh
Confidence 46788886 5899999999988843 3333333 455555554433 5556666665554
No 75
>TIGR03544 DivI1A_domain DivIVA domain. This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543.
Probab=28.48 E-value=34 Score=23.18 Aligned_cols=18 Identities=17% Similarity=0.431 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHhhhhc
Q 017157 356 RGFNWCVTSFILKKLESQ 373 (376)
Q Consensus 356 KGFs~d~I~~vL~eie~e 373 (376)
+||+.+.+..+|+++..+
T Consensus 16 rGY~~~eVD~fLd~v~~~ 33 (34)
T TIGR03544 16 RGYDAAEVDAFLDRVADD 33 (34)
T ss_pred CCCCHHHHHHHHHHHHHh
Confidence 899999999999998664
No 76
>PF03913 Amb_V_allergen: Amb V Allergen; InterPro: IPR005611 Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens [].; PDB: 2BBG_A 3BBG_A 1BBG_A.
Probab=28.22 E-value=18 Score=26.27 Aligned_cols=20 Identities=40% Similarity=0.650 Sum_probs=13.0
Q ss_pred eeecCCCccCCcceeeecCC
Q 017157 33 SCVKGRDYSSSFPVRYVPKK 52 (376)
Q Consensus 33 ~c~~~r~~~~~~~~~y~~~~ 52 (376)
.|-+-|.|++|-|=||-|-.
T Consensus 10 ~CGekr~YCcSdpGrYCpwq 29 (44)
T PF03913_consen 10 ICGEKRAYCCSDPGRYCPWQ 29 (44)
T ss_dssp TTS-TTSEEE-SSSSS----
T ss_pred cccccCCeecCCCcccccce
Confidence 48899999999999999853
No 77
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=28.12 E-value=1.5e+02 Score=22.91 Aligned_cols=44 Identities=20% Similarity=0.443 Sum_probs=33.8
Q ss_pred HHHHHHHHHh-cccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH
Q 017157 213 ENLAVKLLAT-RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 213 ~~~AL~lLsr-RdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD 259 (376)
.-.++.+|.. ...+..+|.+.+ +++...|...|.+|.+.|||.-
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~~---~~s~~~i~~~l~~L~~~g~v~~ 56 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKRL---GVSPSTVTRVLDRLEKKGLIRR 56 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHH---CCCchhHHHHHHHHHHCCCeEe
Confidence 3345566654 346888888776 5889999999999999999963
No 78
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=28.06 E-value=1.1e+02 Score=23.29 Aligned_cols=43 Identities=14% Similarity=0.115 Sum_probs=29.1
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhh
Q 017157 229 EMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWS 272 (376)
Q Consensus 229 ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~ 272 (376)
.|...+...|+++++|..+|..+...|-.+ ..|+..-++++..
T Consensus 20 ~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~-~~Yi~~Il~~W~~ 62 (77)
T PF07261_consen 20 KLEKWIDDYGFSPEVVNEAIEYALENNKRS-FNYIEKILNNWKQ 62 (77)
T ss_dssp HHHHHHCCCHHHHHHHHHHHHHHHHCT--S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHHH
Confidence 344555556899999999999998766555 6666666665543
No 79
>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=27.91 E-value=1.3e+02 Score=25.56 Aligned_cols=38 Identities=13% Similarity=0.405 Sum_probs=30.3
Q ss_pred HHHhc---ccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH
Q 017157 219 LLATR---AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 219 lLsrR---drS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD 259 (376)
+|+.. ..|..+|.++|. ++...+..+|..|.+.|+|.-
T Consensus 17 ~la~~~~~~~s~~eia~~l~---is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 17 TLAQNDSQPYSAAEIAEQTG---LNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred HHHhCCCCCccHHHHHHHHC---cCHHHHHHHHHHHHHCCcEEe
Confidence 55543 257788877765 999999999999999999953
No 80
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=27.27 E-value=54 Score=28.33 Aligned_cols=35 Identities=26% Similarity=0.384 Sum_probs=31.6
Q ss_pred hcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCC
Q 017157 222 TRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGL 256 (376)
Q Consensus 222 rRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~Gy 256 (376)
+..++..-++++|.++|.....+.++|+.|.+.||
T Consensus 36 ~~afts~~i~~~l~~~~~~~p~~~eaL~~l~~~G~ 70 (127)
T cd03412 36 RWAFTSRMIRKKLKKRGIEVDTPEEALAKLAADGY 70 (127)
T ss_pred EEEecHHHHHHHHHhcCCCCCCHHHHHHHHHHCCC
Confidence 56789999999999999988899999999998886
No 81
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=27.19 E-value=1.7e+02 Score=19.94 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=28.1
Q ss_pred cccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 223 RAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 223 RdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
...+..+|.+.| +++...+...|..|.+.|+|.
T Consensus 13 ~~~s~~~l~~~l---~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 13 GKVSVEELAELL---GVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred CCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence 346778888887 789999999999999999985
No 82
>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=26.93 E-value=1.5e+02 Score=22.97 Aligned_cols=43 Identities=12% Similarity=0.275 Sum_probs=35.0
Q ss_pred HHHHHHh--cccCHHHHHHHHhcCCCC--HHHHHHHHHHHHHcCCcc
Q 017157 216 AVKLLAT--RAFTAVEMRKKLNGKKFP--SHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 216 AL~lLsr--RdrS~~ELr~KL~~KG~s--ediIe~VLe~L~e~GyLD 258 (376)
.|.+|.. .+-+..+|.+.|...|++ ++.|..-|..|.+.||+.
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~ 49 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTR 49 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcc
Confidence 4556644 457999999999988876 599999999999999665
No 83
>PF13309 HTH_22: HTH domain
Probab=26.87 E-value=1.1e+02 Score=23.59 Aligned_cols=18 Identities=22% Similarity=0.318 Sum_probs=14.6
Q ss_pred hHHHHHHHHHHHHhCCCC
Q 017157 342 KETRKSRIIHWLQYRGFN 359 (376)
Q Consensus 342 ~~k~rqKlir~L~RKGFs 359 (376)
....|..+++.|..+|+=
T Consensus 22 ~~~~k~~iV~~L~~~G~F 39 (64)
T PF13309_consen 22 SKEEKKEIVRQLYEKGIF 39 (64)
T ss_pred CHHHHHHHHHHHHHCCCc
Confidence 456788899999999973
No 84
>COG1735 Php Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]
Probab=26.56 E-value=2e+02 Score=29.46 Aligned_cols=83 Identities=17% Similarity=0.294 Sum_probs=51.6
Q ss_pred HHHhcc--cCHHHHHHHHhcCC-------------CCHHHHHHHHHHHHHcCCccHHHHH-------HH-HHHhhh-hcC
Q 017157 219 LLATRA--FTAVEMRKKLNGKK-------------FPSHVIEAVITDFQSRGLINDSLYA-------ES-YSRSRW-SSA 274 (376)
Q Consensus 219 lLsrRd--rS~~ELr~KL~~KG-------------~sediIe~VLe~L~e~GyLDD~ryA-------es-yvrsr~-~~k 274 (376)
.|+.-+ .....-.++|..+| ++++.....+.+|.+.||.|=.... .. +....+ ...
T Consensus 196 ~igH~d~n~dd~~y~~~l~~~Ga~l~fD~iG~d~y~pd~~r~~~~~~l~~~gy~d~i~ls~d~~~~~~~~~~~~~~~~~~ 275 (316)
T COG1735 196 SIGHMDPNTDDVYYQKKLADRGAFLEFDRIGKDKYYPDEDRIAPLLELVARGYADLILLSHDDICLSDDVFLKSMLKANG 275 (316)
T ss_pred eEeccCCCCChHHHHHHHHhcCceEEecccCccccCcHHHhhhhHHHHHHhhHhhheecccchhhhhhhHHHHhhhhhcC
Confidence 344443 55667778888765 4666667777888888876532111 11 111221 125
Q ss_pred Ccc----HHHHHHHHHhCCCCHHHHHHHHHh
Q 017157 275 SWG----PRRIKQALFKKGISQTDAKKAVNL 301 (376)
Q Consensus 275 g~G----prkIrqeLrqKGId~eiIeeALee 301 (376)
+|| +....-.|+++||+.+.|+..+-+
T Consensus 276 ~~g~~~I~~~fIP~Lk~~Gvde~~i~~mlvd 306 (316)
T COG1735 276 GWGYGYILNDFIPRLKRHGVDEETIDTMLVD 306 (316)
T ss_pred CcccchhhHhhHHHHHHcCCCHHHHHHHHhh
Confidence 666 456668899999999999887743
No 85
>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1. Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.
Probab=25.83 E-value=1.9e+02 Score=25.40 Aligned_cols=51 Identities=27% Similarity=0.356 Sum_probs=37.6
Q ss_pred HHHHHHHHHH-HcCCccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCCHHHH
Q 017157 243 VIEAVITDFQ-SRGLINDSLYAESYSRSRWSSASWGPRRIKQALFKKGISQTDA 295 (376)
Q Consensus 243 iIe~VLe~L~-e~GyLDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId~eiI 295 (376)
..++++..+. ...|-||.||.+.++.---. -.-|.-|-+.|..+||.....
T Consensus 48 lLerc~~~f~~~~~YknD~RyLkiWi~ya~~--~~dp~~if~~L~~~~IG~~~A 99 (125)
T smart00777 48 LLERCIRYFEDDERYKNDPRYLKIWLKYADN--CDEPRELFQFLYSKGIGTKLA 99 (125)
T ss_pred HHHHHHHHhhhhhhhcCCHHHHHHHHHHHHh--cCCHHHHHHHHHHCCcchhhH
Confidence 4556666653 34899999999987765422 234899999999999998764
No 86
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=25.83 E-value=81 Score=28.30 Aligned_cols=37 Identities=19% Similarity=0.264 Sum_probs=28.1
Q ss_pred ccHHHHHHHHHHhhhhcCCccHHHHHHHHHhCCCCHHHHH
Q 017157 257 INDSLYAESYSRSRWSSASWGPRRIKQALFKKGISQTDAK 296 (376)
Q Consensus 257 LDD~ryAesyvrsr~~~kg~GprkIrqeLrqKGId~eiIe 296 (376)
-||.+|+. |++-. . -|.-...|++++.+-|+|.++++
T Consensus 111 ~~dP~y~k-YfKMl-~-~GvP~~aVk~KM~~eGlDp~~Ld 147 (148)
T PF10152_consen 111 KDDPRYAK-YFKML-K-MGVPREAVKQKMQAEGLDPSLLD 147 (148)
T ss_pred cCCccHHH-HHHHH-H-cCCCHHHHHHHHHHcCCCHHHhc
Confidence 38999964 44322 2 46778899999999999999875
No 87
>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=25.63 E-value=1.5e+02 Score=25.68 Aligned_cols=32 Identities=13% Similarity=0.351 Sum_probs=27.3
Q ss_pred ccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 224 AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 224 drS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
..|..+|.+.+ ++|+..++.++..|.+.|+|.
T Consensus 25 ~~s~~~ia~~~---~ip~~~l~kil~~L~~~glv~ 56 (135)
T TIGR02010 25 PVTLADISERQ---GISLSYLEQLFAKLRKAGLVK 56 (135)
T ss_pred cCcHHHHHHHH---CcCHHHHHHHHHHHHHCCceE
Confidence 35777777765 499999999999999999997
No 88
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=24.78 E-value=1.9e+02 Score=23.53 Aligned_cols=42 Identities=14% Similarity=0.177 Sum_probs=33.7
Q ss_pred HHHHHHHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCc
Q 017157 213 ENLAVKLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (376)
Q Consensus 213 ~~~AL~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyL 257 (376)
....+.+++...+|-.+|.++| |++...|...|+.|++.|+-
T Consensus 8 ~~~ll~~~~~~~~SGe~La~~L---giSRtaVwK~Iq~Lr~~G~~ 49 (79)
T COG1654 8 LLLLLLLLTGNFVSGEKLAEEL---GISRTAVWKHIQQLREEGVD 49 (79)
T ss_pred HHHHHHHcCCCcccHHHHHHHH---CccHHHHHHHHHHHHHhCCc
Confidence 3445566667788888888877 59999999999999999974
No 89
>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=24.55 E-value=2.3e+02 Score=20.28 Aligned_cols=35 Identities=23% Similarity=0.470 Sum_probs=28.6
Q ss_pred HhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 221 ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 221 srRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
.....+..+|.+.+. ++...+-.++..|.+.|||.
T Consensus 14 ~~~~~~~~~la~~~~---~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 14 ENGGITQSELAEKLG---ISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HHSSEEHHHHHHHHT---S-HHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCHHHHHHHHC---CChhHHHHHHHHHHHCCCEE
Confidence 445578888888876 88999999999999999984
No 90
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=24.14 E-value=1.6e+02 Score=23.32 Aligned_cols=47 Identities=13% Similarity=0.253 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhcccCH-HHHHHHHhcCCCCHHHHHHHHHHHHHcCCccH
Q 017157 210 QDAENLAVKLLATRAFTA-VEMRKKLNGKKFPSHVIEAVITDFQSRGLIND 259 (376)
Q Consensus 210 ~~A~~~AL~lLsrRdrS~-~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD 259 (376)
....-.++..|....-.. .+|.++|. ++...+-.+|.+|.+.|||.=
T Consensus 21 t~~q~~~L~~l~~~~~~~~~~la~~l~---i~~~~vt~~l~~Le~~glv~r 68 (126)
T COG1846 21 TPPQYQVLLALYEAGGITVKELAERLG---LDRSTVTRLLKRLEDKGLIER 68 (126)
T ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHHC---CCHHHHHHHHHHHHHCCCeee
Confidence 334455666777777666 77777765 889999999999999999953
No 91
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=23.68 E-value=98 Score=20.93 Aligned_cols=23 Identities=17% Similarity=0.109 Sum_probs=14.9
Q ss_pred HHHHHHHhCCCCHHHHHHHHHhh
Q 017157 348 RIIHWLQYRGFNWCVTSFILKKL 370 (376)
Q Consensus 348 Klir~L~RKGFs~d~I~~vL~ei 370 (376)
..++.|..-||+.+.+.++|..-
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHc
Confidence 34556666688888888877653
No 92
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=23.50 E-value=2.1e+02 Score=23.55 Aligned_cols=63 Identities=19% Similarity=0.313 Sum_probs=41.8
Q ss_pred HHHHhc-ccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHhhhhcCC---ccHHHHHHHHHhCCC
Q 017157 218 KLLATR-AFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLINDSLYAESYSRSRWSSAS---WGPRRIKQALFKKGI 290 (376)
Q Consensus 218 ~lLsrR-drS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLDD~ryAesyvrsr~~~kg---~GprkIrqeLrqKGI 290 (376)
.+|+.. .+|+.++.++|...|++- .....+.-...+..|++.+...+. .|...++..|...||
T Consensus 34 ~~lTNns~~s~~~~~~~L~~~Gi~~----------~~~~i~ts~~~~~~~l~~~~~~~~v~vlG~~~l~~~l~~~G~ 100 (101)
T PF13344_consen 34 VFLTNNSSRSREEYAKKLKKLGIPV----------DEDEIITSGMAAAEYLKEHKGGKKVYVLGSDGLREELREAGF 100 (101)
T ss_dssp EEEES-SSS-HHHHHHHHHHTTTT------------GGGEEEHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHTTE
T ss_pred EEEeCCCCCCHHHHHHHHHhcCcCC----------CcCEEEChHHHHHHHHHhcCCCCEEEEEcCHHHHHHHHHcCC
Confidence 334443 378899999999999984 234556666777888887532121 288999999999886
No 93
>PRK09875 putative hydrolase; Provisional
Probab=23.23 E-value=62 Score=32.25 Aligned_cols=63 Identities=19% Similarity=0.322 Sum_probs=42.5
Q ss_pred CCHHHHHHHHHHHHHcCCccHHHHHHHHHHh-hhhc-CC----ccHHHHHHHHHhCCCCHHHHHHHHHh
Q 017157 239 FPSHVIEAVITDFQSRGLINDSLYAESYSRS-RWSS-AS----WGPRRIKQALFKKGISQTDAKKAVNL 301 (376)
Q Consensus 239 ~sediIe~VLe~L~e~GyLDD~ryAesyvrs-r~~~-kg----~GprkIrqeLrqKGId~eiIeeALee 301 (376)
++.+..-+.|..|.++||.|---.+..+.+. .+.. .+ ++...+...|+++||+.+.|+..+-+
T Consensus 217 ~pd~~r~~~i~~L~~~Gy~drilLS~D~~~~~~~~~~gg~G~~~i~~~~ip~L~~~Gvse~~I~~m~~~ 285 (292)
T PRK09875 217 YPDEKRIAMLHALRDRGLLNRVMLSMDITRRSHLKANGGYGYDYLLTTFIPQLRQSGFSQADVDVMLRE 285 (292)
T ss_pred CCHHHHHHHHHHHHhcCCCCeEEEeCCCCCcccccccCCCChhHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3556678888889999988764443333322 2211 22 33667788899999999999988753
No 94
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=22.98 E-value=1.8e+02 Score=19.84 Aligned_cols=29 Identities=17% Similarity=0.431 Sum_probs=22.1
Q ss_pred CHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCc
Q 017157 226 TAVEMRKKLNGKKFPSHVIEAVITDFQSRGLI 257 (376)
Q Consensus 226 S~~ELr~KL~~KG~sediIe~VLe~L~e~GyL 257 (376)
|.++|-..| |.+.+.+-+++.+|++.|+|
T Consensus 4 tr~diA~~l---G~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 4 TRQDIADYL---GLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp -HHHHHHHH---TS-HHHHHHHHHHHHHTTSE
T ss_pred CHHHHHHHh---CCcHHHHHHHHHHHHHcCCC
Confidence 455666655 68999999999999999986
No 95
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=22.45 E-value=2.3e+02 Score=20.28 Aligned_cols=42 Identities=17% Similarity=0.252 Sum_probs=33.2
Q ss_pred cCHHHHHHHHhcCCCCHHHHHHHHHHHHH--cCCccHHHHHHHH
Q 017157 225 FTAVEMRKKLNGKKFPSHVIEAVITDFQS--RGLINDSLYAESY 266 (376)
Q Consensus 225 rS~~ELr~KL~~KG~sediIe~VLe~L~e--~GyLDD~ryAesy 266 (376)
-+..|++.-|...|++.+.++.++..+.. .|.|+=..|...+
T Consensus 16 i~~~el~~~l~~~g~~~~~~~~i~~~~d~~~~g~i~~~ef~~~~ 59 (67)
T cd00052 16 ISGDEARPFLGKSGLPRSVLAQIWDLADTDKDGKLDKEEFAIAM 59 (67)
T ss_pred CcHHHHHHHHHHcCCCHHHHHHHHHHhcCCCCCcCCHHHHHHHH
Confidence 56788888888889999999999988854 4788877776544
No 96
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=22.44 E-value=1.6e+02 Score=24.16 Aligned_cols=35 Identities=14% Similarity=0.276 Sum_probs=30.2
Q ss_pred HhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 221 ATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 221 srRdrS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
..++-+.++|.++| +.++..|.-.|..|++.|||.
T Consensus 20 ~~~PVgSk~ia~~l---~~s~aTIRN~M~~Le~lGlve 54 (78)
T PF03444_consen 20 TGEPVGSKTIAEEL---GRSPATIRNEMADLEELGLVE 54 (78)
T ss_pred cCCCcCHHHHHHHH---CCChHHHHHHHHHHHHCCCcc
Confidence 34677888888875 678999999999999999996
No 97
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=22.29 E-value=2.1e+02 Score=26.73 Aligned_cols=36 Identities=11% Similarity=0.112 Sum_probs=29.1
Q ss_pred HHHHhcccCHHHHHHHHhcCCCCHHHHHHHHHHHHH
Q 017157 218 KLLATRAFTAVEMRKKLNGKKFPSHVIEAVITDFQS 253 (376)
Q Consensus 218 ~lLsrRdrS~~ELr~KL~~KG~sediIe~VLe~L~e 253 (376)
.+-...+.-..||.+.++++|++++.++.+.+.+.+
T Consensus 73 e~~~~pe~e~~el~~iy~~~Gl~~~~a~~i~~~l~~ 108 (213)
T PF01988_consen 73 ELENNPEEEKEELVEIYRAKGLSEEDAEEIAEELSK 108 (213)
T ss_pred HHHhChHhHHHHHHHHHHHCCCCHHHHHHHHHHHHh
Confidence 444556667778999999999999999999998865
No 98
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=22.28 E-value=1.8e+02 Score=24.85 Aligned_cols=43 Identities=9% Similarity=0.274 Sum_probs=34.1
Q ss_pred HHHHHHHHHhc-c-cCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 213 ENLAVKLLATR-A-FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 213 ~~~AL~lLsrR-d-rS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
.-.+|..|... + .|..+|.+.|. ++...|-.+|.+|++.|||-
T Consensus 33 q~~vL~~l~~~~~~~t~~eLa~~l~---~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 33 HWVTLHNIHQLPPEQSQIQLAKAIG---IEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhC---CChhhHHHHHHHHHHCCCEe
Confidence 33567777654 3 57888888775 88999999999999999994
No 99
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=21.65 E-value=6e+02 Score=25.23 Aligned_cols=66 Identities=20% Similarity=0.354 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCH-HHHHHHHhc-------------CCCCHHHHHHHHHHHHHcCCcc
Q 017157 193 MKILQQKDFYLQAAKARQDAENLAVKLLATRAFTA-VEMRKKLNG-------------KKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 193 ~~~~~~~~~~~~~~~~~~~A~~~AL~lLsrRdrS~-~ELr~KL~~-------------KG~sediIe~VLe~L~e~GyLD 258 (376)
|-|........+.+.-.+.+-+.|+.-||+.+.-. ..|-+.|.. -|++...|-+++.+|...|+|.
T Consensus 150 ~Eilr~~~~~iEee~Rkka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe 229 (251)
T TIGR02787 150 MELLRAQAEEIEEEARKKAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIE 229 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 44444444444455555666677777777652211 111111211 2577777777777777777764
No 100
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA 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=20.88 E-value=6.9e+02 Score=23.28 Aligned_cols=27 Identities=19% Similarity=0.215 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHhhhh
Q 017157 346 KSRIIHWLQYRGFNWCVTSFILKKLES 372 (376)
Q Consensus 346 rqKlir~L~RKGFs~d~I~~vL~eie~ 372 (376)
...+..+|..-||+...|..++..+..
T Consensus 147 ~~e~~~aL~~LGy~~~e~~~ai~~~~~ 173 (191)
T TIGR00084 147 RDELFEALVSLGYKPQEIQQALKKIKN 173 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhh
Confidence 467899999999999999999998853
No 101
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=20.42 E-value=2.6e+02 Score=22.56 Aligned_cols=41 Identities=17% Similarity=0.341 Sum_probs=32.6
Q ss_pred HHHHHHHhcc-cCHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcc
Q 017157 215 LAVKLLATRA-FTAVEMRKKLNGKKFPSHVIEAVITDFQSRGLIN 258 (376)
Q Consensus 215 ~AL~lLsrRd-rS~~ELr~KL~~KG~sediIe~VLe~L~e~GyLD 258 (376)
..+.+|.... .|..+|.+.| |+++..|-..|.+|.+.|+|-
T Consensus 7 ~il~~L~~~~~~~~~~la~~l---~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 7 KILEELQKDARISLAELAKKV---GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHhCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCee
Confidence 3445555543 5777888877 899999999999999999987
No 102
>PF08230 Cpl-7: Cpl-7 lysozyme C-terminal domain; InterPro: IPR013168 This domain was originally found in the C-terminal moiety of the Cp-7 lysin (lysozyme, P19385 from SWISSPROT) encoded by Bacteriophage Cp-7. It is assumed that this domain represents a cell wall binding motif although no direct evidence has been obtained so far to support this.
Probab=20.08 E-value=1.4e+02 Score=21.88 Aligned_cols=25 Identities=24% Similarity=0.377 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHhh
Q 017157 342 KETRKSRIIHWLQYRGFNWCVTSFILKKL 370 (376)
Q Consensus 342 ~~k~rqKlir~L~RKGFs~d~I~~vL~ei 370 (376)
..+++. .|-..||+|+.|+..+.++
T Consensus 16 G~eRk~----~L~~aGydY~~VQ~~VN~~ 40 (42)
T PF08230_consen 16 GEERKK----RLTAAGYDYDAVQARVNEL 40 (42)
T ss_pred cHHHHH----HHHHcCCCHHHHHHHHHHH
Confidence 344554 4567899999999988765
Done!