Query 039425
Match_columns 413
No_of_seqs 260 out of 1570
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 09:33:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039425.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039425hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 2.1E-51 4.5E-56 428.2 26.4 340 37-385 197-621 (846)
2 PF00872 Transposase_mut: Tran 99.9 3.4E-25 7.3E-30 217.9 2.2 259 2-310 74-347 (381)
3 PF10551 MULE: MULE transposas 99.9 1.7E-23 3.7E-28 165.0 8.2 90 127-219 1-93 (93)
4 COG3328 Transposase and inacti 99.6 6.8E-15 1.5E-19 142.4 16.5 237 19-310 84-326 (379)
5 smart00575 ZnF_PMZ plant mutat 98.4 1.6E-07 3.4E-12 55.8 1.8 25 348-372 1-25 (28)
6 PF06782 UPF0236: Uncharacteri 98.1 0.0003 6.4E-09 71.5 18.4 220 10-276 108-350 (470)
7 PF04434 SWIM: SWIM zinc finge 97.4 7.1E-05 1.5E-09 48.6 1.8 27 345-371 12-38 (40)
8 PF01610 DDE_Tnp_ISL3: Transpo 96.8 0.002 4.4E-08 59.9 5.3 93 124-223 2-97 (249)
9 PF13610 DDE_Tnp_IS240: DDE do 95.4 0.015 3.2E-07 49.1 3.3 81 120-205 1-81 (140)
10 PF03050 DDE_Tnp_IS66: Transpo 94.9 0.16 3.6E-06 47.7 9.4 148 19-224 3-156 (271)
11 PF13936 HTH_38: Helix-turn-he 91.5 0.13 2.7E-06 34.0 1.8 32 17-48 2-33 (44)
12 PF00665 rve: Integrase core d 89.4 2.4 5.1E-05 33.9 8.1 76 120-197 6-82 (120)
13 PF08069 Ribosomal_S13_N: Ribo 88.8 0.56 1.2E-05 33.0 3.2 37 14-50 22-59 (60)
14 PF04937 DUF659: Protein of un 88.6 4 8.6E-05 34.9 9.1 107 114-224 27-138 (153)
15 COG3316 Transposase and inacti 87.2 1.3 2.9E-05 39.7 5.4 142 19-207 8-151 (215)
16 PRK08561 rps15p 30S ribosomal 84.1 3.9 8.4E-05 34.5 6.4 38 13-50 21-59 (151)
17 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 76.3 4 8.6E-05 27.7 3.3 31 18-48 3-33 (50)
18 PF13565 HTH_32: Homeodomain-l 75.6 8.3 0.00018 28.2 5.3 44 18-62 30-76 (77)
19 PF02796 HTH_7: Helix-turn-hel 73.6 3.7 8E-05 27.0 2.6 40 18-64 4-43 (45)
20 PF14420 Clr5: Clr5 domain 71.7 15 0.00033 25.2 5.4 42 22-64 6-48 (54)
21 KOG4027 Uncharacterized conser 69.8 9.6 0.00021 32.3 4.7 36 124-159 69-107 (187)
22 PF13551 HTH_29: Winged helix- 67.8 13 0.00029 29.1 5.3 52 13-66 52-111 (112)
23 PF04218 CENP-B_N: CENP-B N-te 67.4 13 0.00027 25.5 4.3 47 17-67 4-50 (53)
24 PF06056 Terminase_5: Putative 65.4 26 0.00057 24.5 5.6 43 24-73 2-44 (58)
25 PF12554 MOZART1: Mitotic-spin 64.5 17 0.00037 24.4 4.2 31 18-48 17-47 (48)
26 PF00196 GerE: Bacterial regul 63.7 25 0.00053 24.2 5.3 44 19-70 3-46 (58)
27 PTZ00072 40S ribosomal protein 63.5 21 0.00045 29.9 5.5 50 15-64 20-73 (148)
28 KOG0400 40S ribosomal protein 60.5 9.1 0.0002 31.2 2.8 100 22-130 31-140 (151)
29 PRK13907 rnhA ribonuclease H; 59.0 95 0.0021 25.1 9.2 78 122-202 3-81 (128)
30 TIGR03147 cyt_nit_nrfF cytochr 58.9 11 0.00023 31.0 3.1 35 19-53 57-91 (126)
31 cd06171 Sigma70_r4 Sigma70, re 58.8 30 0.00066 22.4 5.1 43 19-68 10-52 (55)
32 PF10045 DUF2280: Uncharacteri 58.5 21 0.00045 28.0 4.4 41 19-60 3-43 (104)
33 smart00421 HTH_LUXR helix_turn 56.7 39 0.00085 22.3 5.4 44 18-69 2-45 (58)
34 KOG3926 F-box proteins [Amino 56.1 42 0.00091 31.3 6.6 27 334-363 284-310 (332)
35 cd00131 PAX Paired Box domain 54.9 33 0.00073 28.2 5.5 45 17-68 15-59 (128)
36 PRK14702 insertion element IS2 54.7 51 0.0011 30.8 7.4 146 22-195 11-165 (262)
37 PF08459 UvrC_HhH_N: UvrC Heli 54.1 36 0.00077 29.1 5.6 46 161-206 53-103 (155)
38 PRK10144 formate-dependent nit 53.4 15 0.00033 30.1 3.1 35 19-53 57-91 (126)
39 COG4279 Uncharacterized conser 52.9 22 0.00047 32.7 4.3 23 347-372 124-146 (266)
40 PRK09409 IS2 transposase TnpB; 52.4 60 0.0013 31.0 7.6 74 121-195 127-204 (301)
41 COG3464 Transposase and inacti 52.2 72 0.0016 31.9 8.4 72 139-218 169-240 (402)
42 PF00292 PAX: 'Paired box' dom 49.9 23 0.0005 29.0 3.7 32 18-49 16-47 (125)
43 PF13384 HTH_23: Homeodomain-l 48.9 21 0.00046 23.5 2.9 42 21-69 3-44 (50)
44 PRK00766 hypothetical protein; 48.9 1.6E+02 0.0034 26.2 9.1 90 118-207 7-127 (194)
45 PF10264 Stork_head: Winged he 48.7 53 0.0011 24.7 5.1 51 19-69 11-64 (80)
46 COG1710 Uncharacterized protei 48.7 91 0.002 25.2 6.6 61 1-69 76-136 (139)
47 PF12017 Tnp_P_element: Transp 47.4 64 0.0014 29.7 6.6 160 15-201 67-230 (236)
48 cd01110 HTH_SoxR Helix-Turn-He 47.3 1E+02 0.0022 25.8 7.3 69 17-85 36-107 (139)
49 PHA02517 putative transposase 47.0 44 0.00094 31.3 5.7 150 22-195 29-182 (277)
50 COG0735 Fur Fe2+/Zn2+ uptake r 46.0 69 0.0015 27.0 6.2 25 36-62 37-61 (145)
51 cd04769 HTH_MerR2 Helix-Turn-H 45.7 1.2E+02 0.0026 24.3 7.3 50 16-65 34-86 (116)
52 PF13082 DUF3931: Protein of u 45.6 45 0.00097 22.5 3.8 42 120-161 8-62 (66)
53 PF08281 Sigma70_r4_2: Sigma-7 41.3 70 0.0015 21.4 4.6 44 18-68 9-52 (54)
54 TIGR02047 CadR-PbrR Cd(II)/Pb( 41.1 1.8E+02 0.0039 23.7 7.8 69 16-85 35-106 (127)
55 cd00569 HTH_Hin_like Helix-tur 40.8 60 0.0013 18.6 4.0 28 18-45 4-31 (42)
56 PF12762 DDE_Tnp_IS1595: ISXO2 39.3 94 0.002 25.9 6.1 54 138-197 35-89 (151)
57 PF09278 MerR-DNA-bind: MerR, 39.1 1.3E+02 0.0028 20.9 5.9 59 25-84 4-62 (65)
58 smart00351 PAX Paired Box doma 38.4 78 0.0017 25.8 5.2 44 18-68 16-59 (125)
59 PF03918 CcmH: Cytochrome C bi 38.1 30 0.00065 29.3 2.7 34 20-53 58-91 (148)
60 PF08671 SinI: Anti-repressor 37.5 80 0.0017 18.9 3.7 27 21-47 2-28 (30)
61 PRK15320 transcriptional activ 36.3 1E+02 0.0022 27.6 5.7 45 18-70 163-207 (251)
62 PRK15411 rcsA colanic acid cap 35.7 70 0.0015 28.5 5.0 44 19-70 137-180 (207)
63 PRK09462 fur ferric uptake reg 35.0 1.3E+02 0.0028 25.2 6.2 45 18-64 13-60 (148)
64 PF06135 DUF965: Bacterial pro 34.3 95 0.0021 23.2 4.4 46 25-70 22-68 (79)
65 PRK04217 hypothetical protein; 33.7 1.4E+02 0.0031 23.9 5.8 43 17-66 40-82 (110)
66 TIGR01950 SoxR redox-sensitive 33.0 2.3E+02 0.0051 23.7 7.4 32 17-48 36-70 (142)
67 TIGR02937 sigma70-ECF RNA poly 32.8 89 0.0019 25.3 4.9 45 18-69 109-153 (158)
68 cd06170 LuxR_C_like C-terminal 32.1 1.5E+02 0.0032 19.4 5.5 43 20-70 1-43 (57)
69 cd08309 Death_IRAK Death domai 32.0 2.4E+02 0.0052 21.8 6.9 66 16-85 2-69 (95)
70 PF11829 DUF3349: Protein of u 32.0 96 0.0021 24.2 4.4 49 17-66 33-85 (96)
71 PRK03975 tfx putative transcri 31.8 1.9E+02 0.0041 24.3 6.5 61 16-85 3-63 (141)
72 PRK05473 hypothetical protein; 31.8 1.3E+02 0.0029 22.8 4.9 46 25-70 25-71 (86)
73 KOG0053 Cystathionine beta-lya 31.8 4.5E+02 0.0097 26.4 10.0 101 56-160 126-239 (409)
74 TIGR02043 ZntR Zn(II)-responsi 31.4 2.2E+02 0.0047 23.4 6.9 32 17-48 37-71 (131)
75 PRK15201 fimbriae regulatory p 30.3 1.6E+02 0.0034 26.0 5.8 46 17-70 131-176 (198)
76 PRK00118 putative DNA-binding 30.1 1.8E+02 0.0039 23.0 5.8 46 17-69 15-60 (104)
77 PF03461 TRCF: TRCF domain; I 30.1 97 0.0021 24.2 4.3 39 234-272 18-56 (101)
78 PHA02591 hypothetical protein; 30.1 73 0.0016 23.7 3.2 25 21-45 45-69 (83)
79 PF04814 HNF-1_N: Hepatocyte n 28.9 35 0.00075 29.8 1.6 31 19-49 4-34 (180)
80 PRK10840 transcriptional regul 28.7 1.3E+02 0.0027 26.6 5.5 46 17-70 148-193 (216)
81 PRK15002 redox-sensitivie tran 28.2 3E+02 0.0065 23.4 7.3 70 16-85 45-117 (154)
82 cd04784 HTH_CadR-PbrR Helix-Tu 27.0 3.4E+02 0.0074 21.9 7.9 34 16-49 35-71 (127)
83 PRK15369 two component system 26.5 2.5E+02 0.0055 23.7 7.0 45 18-70 148-192 (211)
84 PRK09483 response regulator; P 26.4 1.5E+02 0.0033 25.7 5.6 45 18-70 147-191 (217)
85 PRK07708 hypothetical protein; 26.4 4.9E+02 0.011 23.6 12.0 121 77-203 29-161 (219)
86 PRK11475 DNA-binding transcrip 26.3 1.5E+02 0.0031 26.6 5.3 45 18-70 133-177 (207)
87 smart00526 H15 Domain in histo 26.2 1.9E+02 0.0042 20.3 5.0 34 17-50 4-38 (66)
88 smart00188 IL10 Interleukin-10 26.1 3.1E+02 0.0068 22.9 6.7 42 161-210 22-67 (137)
89 cd01109 HTH_YyaN Helix-Turn-He 26.1 3.3E+02 0.0072 21.5 7.8 34 16-49 35-71 (113)
90 PF05920 Homeobox_KN: Homeobox 25.5 1.3E+02 0.0029 19.1 3.6 31 13-45 4-34 (40)
91 cd01282 HTH_MerR-like_sg3 Heli 25.3 3.4E+02 0.0075 21.4 6.9 34 16-49 34-70 (112)
92 PRK10403 transcriptional regul 24.9 2.4E+02 0.0053 24.0 6.6 58 19-85 153-210 (215)
93 cd04785 HTH_CadR-PbrR-like Hel 24.9 3.8E+02 0.0081 21.7 7.7 33 16-48 35-70 (126)
94 cd00073 H15 linker histone 1 a 24.9 1.9E+02 0.0041 21.9 5.0 35 17-51 4-39 (88)
95 PRK14667 uvrC excinuclease ABC 24.8 1.6E+02 0.0035 30.9 6.0 64 122-203 382-450 (567)
96 TIGR00721 tfx DNA-binding prot 24.5 2.5E+02 0.0054 23.5 5.9 44 19-70 6-49 (137)
97 cd01106 HTH_TipAL-Mta Helix-Tu 24.1 3.4E+02 0.0074 21.0 6.8 32 17-48 36-70 (103)
98 PRK14994 SAM-dependent 16S rib 23.7 2.5E+02 0.0054 26.7 6.6 43 20-66 242-284 (287)
99 PF01527 HTH_Tnp_1: Transposas 23.6 1.1E+02 0.0025 21.9 3.5 44 17-67 4-48 (76)
100 PF10825 DUF2752: Protein of u 23.6 33 0.00071 23.4 0.4 22 351-372 1-27 (52)
101 PF06755 DUF1219: Protein of u 23.5 1.6E+02 0.0034 23.6 4.2 26 24-49 45-70 (114)
102 PF04545 Sigma70_r4: Sigma-70, 23.4 1.5E+02 0.0031 19.5 3.7 41 18-65 3-43 (50)
103 PRK09514 zntR zinc-responsive 23.2 3.5E+02 0.0077 22.4 6.8 32 17-48 37-71 (140)
104 cd01108 HTH_CueR Helix-Turn-He 23.1 4.1E+02 0.0089 21.5 7.1 47 17-64 36-85 (127)
105 PRK12306 uvrC excinuclease ABC 22.8 2E+02 0.0043 29.9 6.1 67 122-206 387-458 (519)
106 PF04255 DUF433: Protein of un 22.7 1.9E+02 0.0042 19.7 4.2 32 26-63 22-53 (56)
107 PRK14669 uvrC excinuclease ABC 22.7 2E+02 0.0043 30.7 6.2 64 122-203 417-485 (624)
108 PF15652 Tox-SHH: HNH/Endo VII 22.6 1.3E+02 0.0028 23.6 3.5 28 22-49 69-96 (100)
109 PF03852 Vsr: DNA mismatch end 22.5 3.3E+02 0.0071 20.2 5.7 62 55-130 5-67 (75)
110 PRK00558 uvrC excinuclease ABC 22.5 1.9E+02 0.0041 30.7 6.0 67 122-206 404-475 (598)
111 PF03564 DUF1759: Protein of u 22.3 1.4E+02 0.0031 24.6 4.2 33 20-52 38-70 (145)
112 PRK14672 uvrC excinuclease ABC 22.0 2.1E+02 0.0045 30.7 6.1 67 122-205 475-545 (691)
113 PF12385 Peptidase_C70: Papain 21.9 1.9E+02 0.0041 24.8 4.7 67 106-177 95-161 (166)
114 TIGR00194 uvrC excinuclease AB 21.7 2.1E+02 0.0045 30.2 6.1 64 122-203 402-471 (574)
115 PF02171 Piwi: Piwi domain; I 21.7 4.1E+02 0.009 24.9 7.8 70 122-191 79-156 (302)
116 KOG1720 Protein tyrosine phosp 21.7 1E+02 0.0023 27.7 3.3 34 30-63 169-202 (225)
117 cd04770 HTH_HMRTR Helix-Turn-H 21.5 4.3E+02 0.0092 21.1 8.2 34 16-49 35-71 (123)
118 PRK14671 uvrC excinuclease ABC 21.5 2.1E+02 0.0046 30.4 6.1 67 122-206 436-507 (621)
119 cd06222 RnaseH RNase H (RNase 21.2 3.7E+02 0.0081 20.3 7.1 72 122-194 1-74 (130)
120 cd04783 HTH_MerR1 Helix-Turn-H 21.0 4.5E+02 0.0097 21.2 7.2 34 16-49 35-71 (126)
121 PF07162 B9-C2: Ciliary basal 20.8 1.4E+02 0.0031 25.6 4.1 36 125-160 63-101 (168)
122 cd01104 HTH_MlrA-CarA Helix-Tu 20.6 1.6E+02 0.0035 20.5 3.7 30 16-45 35-67 (68)
123 PF00538 Linker_histone: linke 20.5 1.3E+02 0.0029 22.0 3.3 33 18-50 3-36 (77)
124 PF00046 Homeobox: Homeobox do 20.4 2.8E+02 0.006 18.5 5.9 50 17-69 4-54 (57)
125 PRK09652 RNA polymerase sigma 20.1 2.2E+02 0.0048 24.0 5.2 44 18-68 127-170 (182)
126 PRK11924 RNA polymerase sigma 20.1 2.1E+02 0.0045 24.1 5.0 45 18-69 124-168 (179)
127 PF11433 DUF3198: Protein of u 20.0 2.8E+02 0.0061 18.5 4.3 25 238-262 6-30 (51)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=2.1e-51 Score=428.21 Aligned_cols=340 Identities=16% Similarity=0.243 Sum_probs=274.6
Q ss_pred ChHHHHHHHHhcCCC---CCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHh----hcCcEEEEeecCCCCceeeEEeeC
Q 039425 37 RPKDILHVLKKRNMH---NATTIRAIYNARRKYKVREQAGHSQMQLLMSKLI----EHKYIERHKSDVDTNCVEALFLAH 109 (413)
Q Consensus 37 ~~~~I~~~l~~~~~~---~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~----~~~~~~~~~~~~~~~~~~~l~~~~ 109 (413)
.++.+...+.+..++ ...+..|..|...+.|+..++ ..+++++++.+. ++|.|+|.+++|+++++++|||++
T Consensus 197 ~~r~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~r~~~~~-~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD 275 (846)
T PLN03097 197 QTRKMYAAMARQFAEYKNVVGLKNDSKSSFDKGRNLGLE-AGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVD 275 (846)
T ss_pred hhhhhHHHHHhhhhccccccccchhhcchhhHHHhhhcc-cchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEecc
Confidence 344555555444322 123445666665555554443 357788887775 689999999999999999999999
Q ss_pred hhhHHHHhhCCCEEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhccccceEEEec
Q 039425 110 PSAIESLQAFPRVLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTD 189 (413)
Q Consensus 110 ~~~~~~~~~~~~vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD 189 (413)
+.++..|..|+|||.+|+||+||+|++||..++|+|++|+++++|+||+.+|+.++|.|+|+.|++.| +++.|.+||||
T Consensus 276 ~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM-~gk~P~tIiTD 354 (846)
T PLN03097 276 AKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAM-GGQAPKVIITD 354 (846)
T ss_pred HHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHh-CCCCCceEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999 67999999999
Q ss_pred cchHHHHHHHHhCCccccccccchhHHHHHHhhcccccchhHHHHHHHhhhhhcc-CCCHHHHHHHHHHHHHhhhhhHHH
Q 039425 190 RELALMTVIQKHFPSATTFLCRWYISRNVLVNCKNLFEANEIWQTFISSWNLLIL-SASEEEFAQRLKGMETDFSKYLIA 268 (413)
Q Consensus 190 ~~~al~~Ai~~vfP~a~~~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~~~l~~-a~t~~ef~~~~~~~~~~~~~~~~~ 268 (413)
+|.||.+||.+|||++.|++|.|||.+|+.+++...+.. .+.|...|..+++ +.+++||+..|..+.++|+-. -
T Consensus 355 qd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~---~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~--~ 429 (846)
T PLN03097 355 QDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQ---HENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELK--E 429 (846)
T ss_pred CCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhh---hhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccc--c
Confidence 999999999999999999999999999999998876643 3468888888877 889999999999999998621 1
Q ss_pred HHHHHHhhhHHHHhHHHHHHhhccccccchhhhhhhhhhhhhhhhh----------------------------------
Q 039425 269 LTYIRNVWLDKYKDKFVSAWTNSVMHFRNIKASLERSLTMVQHDFK---------------------------------- 314 (413)
Q Consensus 269 ~~Y~~~~Wl~~~ke~w~~a~~~~~~~~g~~tts~~eS~~~v~~~~k---------------------------------- 314 (413)
-+|+..-| ..|++||.+|+++.+..|+.+|+++||+|...++|-
T Consensus 430 n~WL~~LY--~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~ 507 (846)
T PLN03097 430 DEWMQSLY--EDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNK 507 (846)
T ss_pred cHHHHHHH--HhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccC
Confidence 23455444 679999999999999999999999999987533210
Q ss_pred h-------hhhhhccccccHHHHHHHHHHhhhhcc---------------------------C--C--CCCCCCCceecc
Q 039425 315 L-------LIFKELRGFVATNALTMILDESRRVDS---------------------------L--G--PDVFACGCIIRH 356 (413)
Q Consensus 315 ~-------~~~~~l~g~iS~~Al~~~~~q~~~~~~---------------------------~--~--~~~~~Csc~~~~ 356 (413)
. ++-....+..|+..++++.+|+..+.. | + ....+|+|..|+
T Consensus 508 ~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE 587 (846)
T PLN03097 508 QPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFE 587 (846)
T ss_pred CcccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCee
Confidence 0 122223456677888888887765410 0 1 125799999999
Q ss_pred ccccCchHHHHHHHHHhHH-----HHhhhccccc
Q 039425 357 THGLPRAPEITEYKREEIE-----MIVKRFNDSD 385 (413)
Q Consensus 357 ~~GlPC~H~l~~~~~~~~~-----~~~~~w~~~~ 385 (413)
..||||+|+|.++....+. -|.+||++..
T Consensus 588 ~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdA 621 (846)
T PLN03097 588 YKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDA 621 (846)
T ss_pred cCccchhhHHHHHhhcCcccCchhhhhhhchhhh
Confidence 9999999999999887443 4899997433
No 2
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.90 E-value=3.4e-25 Score=217.87 Aligned_cols=259 Identities=15% Similarity=0.098 Sum_probs=203.6
Q ss_pred Cceeeeecccccc-------ccCCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCc
Q 039425 2 GSITILLHNLEGH-------SFAGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGH 74 (413)
Q Consensus 2 ~~~~~~~~~~~~h-------p~~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~ 74 (413)
|.|+|-++-.-.. |.++|.+++..+.|..|+..|+|+++|.+.|...+|+..++...|.++..++..+..
T Consensus 74 G~i~l~vPR~R~g~f~p~ll~~y~r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~--- 150 (381)
T PF00872_consen 74 GEIELRVPRDRNGSFEPQLLPKYQRREDSLEELIISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVE--- 150 (381)
T ss_pred cceeecccccccccccccccchhhhhhhhhhhhhhhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHH---
Confidence 5555555443332 345556788889999999999999999999999987455888888887776543321
Q ss_pred HHHHHHHHHHhhcCcEEEEeecCCCCceeeEEeeChhhHHHHhhC-CCEEEeeccccccCC-----CCceeeEEEeeccC
Q 039425 75 SQMQLLMSKLIEHKYIERHKSDVDTNCVEALFLAHPSAIESLQAF-PRVLIMDCTYQTNRY-----DMPLLEIAGVTSID 148 (413)
Q Consensus 75 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~~vl~iD~Ty~tn~~-----~~~l~~~~g~~~~g 148 (413)
++ . .+.+++ . ..+|++|++|-+.+. +..+++++|++.+|
T Consensus 151 ----~w----~-------~R~L~~--------------------~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG 195 (381)
T PF00872_consen 151 ----AW----R-------NRPLES--------------------EPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDG 195 (381)
T ss_pred ----HH----h-------hhcccc--------------------ccccceeeeeeecccccccccccchhhhhhhhhccc
Confidence 11 1 111111 1 246889999987653 35789999999999
Q ss_pred cEEEEEEEeecccccchHHHHHHHHHHHHhccccceEEEeccchHHHHHHHHhCCccccccccchhHHHHHHhhcccccc
Q 039425 149 LTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELALMTVIQKHFPSATTFLCRWYISRNVLVNCKNLFEA 228 (413)
Q Consensus 149 ~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al~~Ai~~vfP~a~~~lC~~Hi~kn~~~~~~~~~~~ 228 (413)
+..++|+.+..+|+.++|..+|+.|++. |...|..||+|+.+|+.+||+++||++.+|.|++|+.||+.+++.+
T Consensus 196 ~r~vLg~~~~~~Es~~~W~~~l~~L~~R--Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~---- 269 (381)
T PF00872_consen 196 RREVLGFWVGDRESAASWREFLQDLKER--GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK---- 269 (381)
T ss_pred ccceeeeecccCCccCEeeecchhhhhc--cccccceeeccccccccccccccccchhhhhheechhhhhcccccc----
Confidence 9999999999999999999999999998 8889999999999999999999999999999999999999999865
Q ss_pred hhHHHHHHHhhhhhccCCCHHHHHHHHHHHHHhhh-hhHHHHHHHHHhhhHHHHhHHHHHHhhccccc-cchhhhhhhhh
Q 039425 229 NEIWQTFISSWNLLILSASEEEFAQRLKGMETDFS-KYLIALTYIRNVWLDKYKDKFVSAWTNSVMHF-RNIKASLERSL 306 (413)
Q Consensus 229 ~~~~~~~~~~~~~l~~a~t~~ef~~~~~~~~~~~~-~~~~~~~Y~~~~Wl~~~ke~w~~a~~~~~~~~-g~~tts~~eS~ 306 (413)
..++.+..+++.+..+.+.+++.+.+++|.+.|. ++|.+.++++++|- . .| .+|.-...+. -..|||..||+
T Consensus 270 -k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~-~---~~-tf~~fP~~~~~~i~TTN~iEsl 343 (381)
T PF00872_consen 270 -KDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWD-E---LL-TFLDFPPEHRRSIRTTNAIESL 343 (381)
T ss_pred -ccchhhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccc-c---cc-ceeeecchhccccchhhhcccc
Confidence 3456788999999999999999999999999886 79999999999883 1 11 1111111111 23699999999
Q ss_pred hhhh
Q 039425 307 TMVQ 310 (413)
Q Consensus 307 ~~v~ 310 (413)
|...
T Consensus 344 n~~i 347 (381)
T PF00872_consen 344 NKEI 347 (381)
T ss_pred ccch
Confidence 9644
No 3
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.89 E-value=1.7e-23 Score=164.96 Aligned_cols=90 Identities=37% Similarity=0.594 Sum_probs=85.3
Q ss_pred ccccccCCCCceee---EEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhccccceEEEeccchHHHHHHHHhCC
Q 039425 127 CTYQTNRYDMPLLE---IAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELALMTVIQKHFP 203 (413)
Q Consensus 127 ~Ty~tn~~~~~l~~---~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al~~Ai~~vfP 203 (413)
|||+||+| ++++. ++|+|++|+.+|++|+++++|+.++|.|+|+.+++.+.. . |.+||||++.|+++||+++||
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~-~-p~~ii~D~~~~~~~Ai~~vfP 77 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQ-K-PKVIISDFDKALINAIKEVFP 77 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcccc-C-ceeeeccccHHHHHHHHHHCC
Confidence 79999999 88885 999999999999999999999999999999999999843 5 999999999999999999999
Q ss_pred ccccccccchhHHHHH
Q 039425 204 SATTFLCRWYISRNVL 219 (413)
Q Consensus 204 ~a~~~lC~~Hi~kn~~ 219 (413)
++.|++|.||+.||++
T Consensus 78 ~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 78 DARHQLCLFHILRNIK 93 (93)
T ss_pred CceEehhHHHHHHhhC
Confidence 9999999999999974
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.63 E-value=6.8e-15 Score=142.37 Aligned_cols=237 Identities=15% Similarity=0.090 Sum_probs=180.9
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHhhcCcEEEEeecCC
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLIEHKYIERHKSDVD 98 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~ 98 (413)
|-.......|..|+..|+++++|-..++.+++. .+....|..+..++..+. ..++..+.
T Consensus 84 r~~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~-~~s~~~iS~~~~~~~e~v-----------~~~~~r~l--------- 142 (379)
T COG3328 84 RRERALDLPVLSMYAKGVTTREIEALLEELYGH-KVSPSVISVVTDRLDEKV-----------KAWQNRPL--------- 142 (379)
T ss_pred hhhhhHHHHHHHHHHcCCcHHHHHHHHHHhhCc-ccCHHHhhhHHHHHHHHH-----------HHHHhccc---------
Confidence 334556688999999999999999999999744 455555555544332211 11111110
Q ss_pred CCceeeEEeeChhhHHHHhhCCCEEEeeccccccC--CCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHH
Q 039425 99 TNCVEALFLAHPSAIESLQAFPRVLIMDCTYQTNR--YDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSI 176 (413)
Q Consensus 99 ~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty~tn~--~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~ 176 (413)
.--.++++|++|.+-+ -+..++.++|++.+|+..++|+.+-.+|+ ..|.-+|..|+..
T Consensus 143 -------------------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r 202 (379)
T COG3328 143 -------------------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR 202 (379)
T ss_pred -------------------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc
Confidence 0124688999999887 44679999999999999999999999999 8899888888877
Q ss_pred HhccccceEEEeccchHHHHHHHHhCCccccccccchhHHHHHHhhcccccchhHHHHHHHhhhhhccCCCHHHHHHHHH
Q 039425 177 MEENMLASVIVTDRELALMTVIQKHFPSATTFLCRWYISRNVLVNCKNLFEANEIWQTFISSWNLLILSASEEEFAQRLK 256 (413)
Q Consensus 177 ~~~~~~p~~iitD~~~al~~Ai~~vfP~a~~~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~~~l~~a~t~~ef~~~~~ 256 (413)
|......+++|+.+++.+||.++||.+.+|.|..|+.+|+..+... .+++.+...++.+..+++.++....|.
T Consensus 203 --gl~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~-----k~~d~i~~~~~~I~~a~~~e~~~~~~~ 275 (379)
T COG3328 203 --GLSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPR-----KDQDAVLSDLRSIYIAPDAEEALLALL 275 (379)
T ss_pred --cccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhh-----hhhHHHHhhhhhhhccCCcHHHHHHHH
Confidence 6778888999999999999999999999999999999999998765 445678888888999999999999999
Q ss_pred HHHHhhh-hhHHHHHHHHHhhhHHHHhHHHHHHhhcccc---ccchhhhhhhhhhhhh
Q 039425 257 GMETDFS-KYLIALTYIRNVWLDKYKDKFVSAWTNSVMH---FRNIKASLERSLTMVQ 310 (413)
Q Consensus 257 ~~~~~~~-~~~~~~~Y~~~~Wl~~~ke~w~~a~~~~~~~---~g~~tts~~eS~~~v~ 310 (413)
.+.+.|. .+|.....+.++|.. .| . | ...|. --..+||..|++|.+.
T Consensus 276 ~~~~~w~~~yP~i~~~~~~~~~~----~~-~-F-~~fp~~~r~~i~ttN~IE~~n~~i 326 (379)
T COG3328 276 AFSELWGKRYPAILKSWRNALEE----LL-P-F-FAFPSEIRKIIYTTNAIESLNKLI 326 (379)
T ss_pred HHHHhhhhhcchHHHHHHHHHHH----hc-c-c-ccCcHHHHhHhhcchHHHHHHHHH
Confidence 9998776 688888888888742 11 0 1 11111 0135677788888644
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.38 E-value=1.6e-07 Score=55.79 Aligned_cols=25 Identities=16% Similarity=0.305 Sum_probs=22.4
Q ss_pred CCCCceeccccccCchHHHHHHHHH
Q 039425 348 FACGCIIRHTHGLPRAPEITEYKRE 372 (413)
Q Consensus 348 ~~Csc~~~~~~GlPC~H~l~~~~~~ 372 (413)
.+|+|+.|+..||||+|+|+++...
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~ 25 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHI 25 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHh
Confidence 3799999999999999999998753
No 6
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=98.06 E-value=0.0003 Score=71.50 Aligned_cols=220 Identities=13% Similarity=0.111 Sum_probs=133.8
Q ss_pred cccccccCCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHhhcCc
Q 039425 10 NLEGHSFAGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLIEHKY 89 (413)
Q Consensus 10 ~~~~hp~~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~~~~~ 89 (413)
...|=+.+.|+|++.+..|..+... +|-++..+.|....+...++...|+|..+.+....... +
T Consensus 108 e~LGl~~~~R~S~~~~~~i~~~a~~-~sYr~aa~~l~~~~~~~~iS~~tV~~~v~~~g~~~~~~------------~--- 171 (470)
T PF06782_consen 108 EKLGLKKYQRISPELKEKIVELATE-MSYRKAAEILEELLGNVSISKQTVWNIVKEAGFEEIKE------------E--- 171 (470)
T ss_pred HHhCCCcccchhHHHHHHHHHHHhh-cCHHHHHHHHhhccCCCccCHHHHHHHHHhccchhhhc------------c---
Confidence 3445567889999999999999655 99999999998887656789999999998775211100 0
Q ss_pred EEEEeecCCCCceeeEEeeChhhHHHHhhCCCEEEeeccccccC----CC--Cce-eeEEE---eec-cCcEEEEEE-Ee
Q 039425 90 IERHKSDVDTNCVEALFLAHPSAIESLQAFPRVLIMDCTYQTNR----YD--MPL-LEIAG---VTS-IDLTFSVCC-VY 157 (413)
Q Consensus 90 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty~tn~----~~--~~l-~~~~g---~~~-~g~~~~~~~-~~ 157 (413)
..+...+..|+ |-.|++|-..+ .+ ..+ ++-.| ... .++...+.- .+
T Consensus 172 ------~~~k~~~~~Ly----------------IEaDg~~v~~qg~~~~~~e~k~~~vheG~~~~~~~~~R~~L~n~~~f 229 (470)
T PF06782_consen 172 ------EKEKKKVPVLY----------------IEADGVHVKLQGKKKKKKEVKLFVVHEGWEKEKPGGKRNKLKNKRHF 229 (470)
T ss_pred ------ccccCCCCeEE----------------EecCcceecccccccccceeeEEEEEeeeeeeeccCCcceeecchhe
Confidence 00111111122 22333333211 11 111 22223 111 122222222 33
Q ss_pred ec---ccccchHHHHHHHHHHHHhcccc--ceEEEeccchHHHHHHHHhCCccccccccchhHHHHHHhhcccccchhHH
Q 039425 158 LK---LKWENNYIWALERLKSIMEENML--ASVIVTDRELALMTVIQKHFPSATTFLCRWYISRNVLVNCKNLFEANEIW 232 (413)
Q Consensus 158 ~~---~E~~~~~~~~l~~l~~~~~~~~~--p~~iitD~~~al~~Ai~~vfP~a~~~lC~~Hi~kn~~~~~~~~~~~~~~~ 232 (413)
+. ....+.|..+.+.+.+... ... -.++.+|+...+.+++. .||++.+++..||+.|.+.+.+...- +
T Consensus 230 ~~~~~~~~~~~~~~v~~~i~~~Y~-~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~---~-- 302 (470)
T PF06782_consen 230 VSGVGESAEEFWEEVLDYIYNHYD-LDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDP---E-- 302 (470)
T ss_pred ecccccchHHHHHHHHHHHHHhcC-cccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhCh---H--
Confidence 33 3445677888887777763 222 35678899988887766 99999999999999999998875421 1
Q ss_pred HHHHHhhhhhccCCCHHHHHHHHHHHHHhhh------hhHHHHHHHHHhh
Q 039425 233 QTFISSWNLLILSASEEEFAQRLKGMETDFS------KYLIALTYIRNVW 276 (413)
Q Consensus 233 ~~~~~~~~~l~~a~t~~ef~~~~~~~~~~~~------~~~~~~~Y~~~~W 276 (413)
........+...+..++...++.+..... ....+..|+.++|
T Consensus 303 --~~~~~~~al~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~ 350 (470)
T PF06782_consen 303 --LKEKIRKALKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNW 350 (470)
T ss_pred --HHHHHHHHHHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCH
Confidence 22222233345566777777777665332 2347889999999
No 7
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.44 E-value=7.1e-05 Score=48.57 Aligned_cols=27 Identities=15% Similarity=0.204 Sum_probs=24.2
Q ss_pred CCCCCCCceeccccccCchHHHHHHHH
Q 039425 345 PDVFACGCIIRHTHGLPRAPEITEYKR 371 (413)
Q Consensus 345 ~~~~~Csc~~~~~~GlPC~H~l~~~~~ 371 (413)
.....|+|..++..|.||.|++|+++.
T Consensus 12 ~~~~~CsC~~~~~~~~~CkHi~av~~~ 38 (40)
T PF04434_consen 12 IEQASCSCPYFQFRGGPCKHIVAVLLA 38 (40)
T ss_pred ccccEeeCCCccccCCcchhHHHHHHh
Confidence 457999999999999999999998864
No 8
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=96.78 E-value=0.002 Score=59.86 Aligned_cols=93 Identities=13% Similarity=-0.044 Sum_probs=66.2
Q ss_pred EeeccccccCCCCceeeEEEeec--cCcEEEEEEEeecccccchHHHHHHHH-HHHHhccccceEEEeccchHHHHHHHH
Q 039425 124 IMDCTYQTNRYDMPLLEIAGVTS--IDLTFSVCCVYLKLKWENNYIWALERL-KSIMEENMLASVIVTDRELALMTVIQK 200 (413)
Q Consensus 124 ~iD~Ty~tn~~~~~l~~~~g~~~--~g~~~~~~~~~~~~E~~~~~~~~l~~l-~~~~~~~~~p~~iitD~~~al~~Ai~~ 200 (413)
+||=+......+. |..+.+|. ++.. .+.++++-+.+++..+|..+ -.. ....+++|++|...+...|+++
T Consensus 2 giDE~~~~~g~~~--y~t~~~d~~~~~~~---il~i~~~r~~~~l~~~~~~~~~~~--~~~~v~~V~~Dm~~~y~~~~~~ 74 (249)
T PF01610_consen 2 GIDEFAFRKGHRS--YVTVVVDLDTDTGR---ILDILPGRDKETLKDFFRSLYPEE--ERKNVKVVSMDMSPPYRSAIRE 74 (249)
T ss_pred eEeeeeeecCCcc--eeEEEEECccCCce---EEEEcCCccHHHHHHHHHHhCccc--cccceEEEEcCCCccccccccc
Confidence 4555444332321 44444554 3322 23478888888887777665 333 3578899999999999999999
Q ss_pred hCCccccccccchhHHHHHHhhc
Q 039425 201 HFPSATTFLCRWYISRNVLVNCK 223 (413)
Q Consensus 201 vfP~a~~~lC~~Hi~kn~~~~~~ 223 (413)
.||+|.+..-.||+++++.+.+.
T Consensus 75 ~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 75 YFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred cccccccccccchhhhhhhhcch
Confidence 99999999999999999977544
No 9
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=95.37 E-value=0.015 Score=49.08 Aligned_cols=81 Identities=17% Similarity=-0.017 Sum_probs=64.0
Q ss_pred CCEEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhccccceEEEeccchHHHHHHH
Q 039425 120 PRVLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELALMTVIQ 199 (413)
Q Consensus 120 ~~vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al~~Ai~ 199 (413)
++.+.+|-||-+-+.. ..+....+|.+|. ++.+-+.+.-+...=..||..+.+.. ...|..|+||+..+...|++
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~--~~~p~~ivtDk~~aY~~A~~ 75 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRH--RGEPRVIVTDKLPAYPAAIK 75 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceee--ccccceeecccCCccchhhh
Confidence 4678999999765533 3556777888888 78888887777776666776666664 38999999999999999999
Q ss_pred HhCCcc
Q 039425 200 KHFPSA 205 (413)
Q Consensus 200 ~vfP~a 205 (413)
+.+|+-
T Consensus 76 ~l~~~~ 81 (140)
T PF13610_consen 76 ELNPEG 81 (140)
T ss_pred hccccc
Confidence 999874
No 10
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=94.93 E-value=0.16 Score=47.71 Aligned_cols=148 Identities=14% Similarity=0.045 Sum_probs=91.7
Q ss_pred CCCHHHHHHHHHHHh-CCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHhhcCcEEEEeecC
Q 039425 19 ILNKEKSNLLVDMSK-NNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLIEHKYIERHKSDV 97 (413)
Q Consensus 19 rlt~~~~~~i~~L~~-~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~ 97 (413)
+.++.....|.-|.- .+++-..|.+.+.+. |..++...|.|...+.... +. ...+.+.+.+..
T Consensus 3 ~~g~~~~a~i~~l~~~~~lp~~r~~~~~~~~--G~~is~~ti~~~~~~~~~~-l~--~~~~~l~~~~~~----------- 66 (271)
T PF03050_consen 3 RYGPSLLALIAYLKYVYHLPLYRIQQMLEDL--GITISRGTIANWIKRVAEA-LK--PLYEALKEELRS----------- 66 (271)
T ss_pred cCCHHHHHHHHHHHhcCCCCHHHHhhhhhcc--ceeeccchhHhHhhhhhhh-hh--hhhhhhhhhccc-----------
Confidence 445666676666555 689999999999888 4557888999988876554 21 122222333332
Q ss_pred CCCceeeEEeeChhhHHHHhhCCCEEEeeccccc-----cCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHH
Q 039425 98 DTNCVEALFLAHPSAIESLQAFPRVLIMDCTYQT-----NRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALER 172 (413)
Q Consensus 98 ~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty~t-----n~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~ 172 (413)
.+++.+|-|.-. +..+.-+.++++-+ .+.|.+.++-..+....+|..
T Consensus 67 ----------------------~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~ 118 (271)
T PF03050_consen 67 ----------------------SPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGD 118 (271)
T ss_pred ----------------------cceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcc
Confidence 334444444332 22223344444332 566666666666655444322
Q ss_pred HHHHHhccccceEEEeccchHHHHHHHHhCCccccccccchhHHHHHHhhcc
Q 039425 173 LKSIMEENMLASVIVTDRELALMTVIQKHFPSATTFLCRWYISRNVLVNCKN 224 (413)
Q Consensus 173 l~~~~~~~~~p~~iitD~~~al~~Ai~~vfP~a~~~lC~~Hi~kn~~~~~~~ 224 (413)
...+++||+-.+-.. +.++.|+.|+-|+.|.+..-...
T Consensus 119 ---------~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 119 ---------FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred ---------cceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 336999999988754 33889999999999999876554
No 11
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=91.54 E-value=0.13 Score=33.96 Aligned_cols=32 Identities=16% Similarity=0.208 Sum_probs=15.6
Q ss_pred CCCCCHHHHHHHHHHHhCCCChHHHHHHHHhc
Q 039425 17 AGILNKEKSNLLVDMSKNNVRPKDILHVLKKR 48 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~ 48 (413)
+++||++++..|..|.+.|.+.++|+..|...
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~s 33 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLGRS 33 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT--
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence 57899999999999999999999999876543
No 12
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=89.44 E-value=2.4 Score=33.91 Aligned_cols=76 Identities=12% Similarity=-0.057 Sum_probs=49.3
Q ss_pred CCEEEeeccccc-cCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhccccceEEEeccchHHHHH
Q 039425 120 PRVLIMDCTYQT-NRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELALMTV 197 (413)
Q Consensus 120 ~~vl~iD~Ty~t-n~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al~~A 197 (413)
++.+.+|.+... ...+...+.++.+|..-+. .+++.+-..++.+.+..+|....... +...|++|++|+..+..+.
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~p~~i~tD~g~~f~~~ 82 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKR-GGRPPRVIRTDNGSEFTSH 82 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHH-S-SE-SEEEEESCHHHHSH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeeccccccccccccccccccc-ccccceecccccccccccc
Confidence 468899988543 3344467778888766654 45666666656666666666555554 2233999999999998744
No 13
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=88.79 E-value=0.56 Score=32.99 Aligned_cols=37 Identities=19% Similarity=0.229 Sum_probs=27.6
Q ss_pred cccCCCCC-HHHHHHHHHHHhCCCChHHHHHHHHhcCC
Q 039425 14 HSFAGILN-KEKSNLLVDMSKNNVRPKDILHVLKKRNM 50 (413)
Q Consensus 14 hp~~rrlt-~~~~~~i~~L~~~g~~~~~I~~~l~~~~~ 50 (413)
.|..-.++ ++..+.|.+|...|++|.+|=.+|++++|
T Consensus 22 ~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~~G 59 (60)
T PF08069_consen 22 PPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQYG 59 (60)
T ss_dssp --TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHSCT
T ss_pred CCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhccC
Confidence 34555555 55678899999999999999999999984
No 14
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=88.63 E-value=4 Score=34.90 Aligned_cols=107 Identities=13% Similarity=0.059 Sum_probs=69.7
Q ss_pred HHHhhCCCEEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecc--cccchHHHHHHHHHHHHhccccceEEEeccc
Q 039425 114 ESLQAFPRVLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKL--KWENNYIWALERLKSIMEENMLASVIVTDRE 191 (413)
Q Consensus 114 ~~~~~~~~vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~--E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~ 191 (413)
+.+..++=-|..|+= +++.+.+++.++...+.|..|.-.. -.++ .+.+.+-.+|+...+-. |.....-||||..
T Consensus 27 ~~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksv-d~s~~~~~a~~l~~ll~~vIeeV-G~~nVvqVVTDn~ 102 (153)
T PF04937_consen 27 KSWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSV-DASSIIKTAEYLFELLDEVIEEV-GEENVVQVVTDNA 102 (153)
T ss_pred HHHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEE-ecccccccHHHHHHHHHHHHHHh-hhhhhhHHhccCc
Confidence 334444555666665 4455667777777777776553332 2222 34445555555555544 4566777899999
Q ss_pred hHHHHH---HHHhCCccccccccchhHHHHHHhhcc
Q 039425 192 LALMTV---IQKHFPSATTFLCRWYISRNVLVNCKN 224 (413)
Q Consensus 192 ~al~~A---i~~vfP~a~~~lC~~Hi~kn~~~~~~~ 224 (413)
..+..| +.+-+|.-....|.-|-+.-+.+.+.+
T Consensus 103 ~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 103 SNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred hhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 988877 445688888899999999888777654
No 15
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.16 E-value=1.3 Score=39.66 Aligned_cols=142 Identities=14% Similarity=0.053 Sum_probs=89.2
Q ss_pred CCCHHHHHHHHHHHhC-CCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHhhcCcEEEEeecC
Q 039425 19 ILNKEKSNLLVDMSKN-NVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLIEHKYIERHKSDV 97 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~-g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~ 97 (413)
+...+.+.....++.. |++-+.|-+.+.+.+ ......+|++..+++-... .+.+.+. .
T Consensus 8 ~f~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rg--i~v~h~Ti~rwv~k~~~~~----------~~~~~~r-----~---- 66 (215)
T COG3316 8 QFPRNIIAVAVWLYLRYGLSLRDVEEMLAERG--IEVDHETIHRWVQKYGPLL----------ARRLKRR-----K---- 66 (215)
T ss_pred hcchhhHHHHHHHHhhcchhhccHHHHHHHcC--cchhHHHHHHHHHHHhHHH----------HHHhhhh-----c----
Confidence 3344445555555655 888888888888874 4466777887777653221 1111110 0
Q ss_pred CCCceeeEEeeChhhHHHHhhCCCEEEeeccccccCCCC-ceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHH
Q 039425 98 DTNCVEALFLAHPSAIESLQAFPRVLIMDCTYQTNRYDM-PLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSI 176 (413)
Q Consensus 98 ~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty~tn~~~~-~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~ 176 (413)
+.-.+.+.+|-||-+.+.+. -|+-+ +|.+| .++.+.+...-+...=..||..+++.
T Consensus 67 -------------------~~~~~~w~vDEt~ikv~gkw~ylyrA--id~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~ 123 (215)
T COG3316 67 -------------------RKAGDSWRVDETYIKVNGKWHYLYRA--IDADG--LTLDVWLSKRRNALAAKAFLKKLLKK 123 (215)
T ss_pred -------------------cccccceeeeeeEEeeccEeeehhhh--hccCC--CeEEEEEEcccCcHHHHHHHHHHHHh
Confidence 01145788898986655443 34444 45554 45667766665555555566666665
Q ss_pred HhccccceEEEeccchHHHHHHHHhCCcccc
Q 039425 177 MEENMLASVIVTDRELALMTVIQKHFPSATT 207 (413)
Q Consensus 177 ~~~~~~p~~iitD~~~al~~Ai~~vfP~a~~ 207 (413)
...|.+|+||+......|++++-++..|
T Consensus 124 ---~g~p~v~vtDka~s~~~A~~~l~~~~eh 151 (215)
T COG3316 124 ---HGEPRVFVTDKAPSYTAALRKLGSEVEH 151 (215)
T ss_pred ---cCCCceEEecCccchHHHHHhcCcchhe
Confidence 3899999999999999999999885433
No 16
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=84.11 E-value=3.9 Score=34.46 Aligned_cols=38 Identities=18% Similarity=0.130 Sum_probs=30.5
Q ss_pred ccccCCCCCHH-HHHHHHHHHhCCCChHHHHHHHHhcCC
Q 039425 13 GHSFAGILNKE-KSNLLVDMSKNNVRPKDILHVLKKRNM 50 (413)
Q Consensus 13 ~hp~~rrlt~~-~~~~i~~L~~~g~~~~~I~~~l~~~~~ 50 (413)
..|..-.++++ ..+.|.+|...|++|++|--.|++++|
T Consensus 21 ~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~g 59 (151)
T PRK08561 21 EPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYG 59 (151)
T ss_pred CCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccC
Confidence 34544555544 578899999999999999999999995
No 17
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=76.33 E-value=4 Score=27.66 Aligned_cols=31 Identities=10% Similarity=0.131 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhc
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKR 48 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~ 48 (413)
.-||+.++..|..|.+.|++.++|...|.+.
T Consensus 3 ~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RS 33 (50)
T PF11427_consen 3 KTLTDAEQAQIDVMHQLGMSLREISRRIGRS 33 (50)
T ss_dssp ----HHHHHHHHHHHHTT--HHHHHHHHT--
T ss_pred CcCCHHHHHHHHHHHHhchhHHHHHHHhCcc
Confidence 3589999999999999999999999988765
No 18
>PF13565 HTH_32: Homeodomain-like domain
Probab=75.56 E-value=8.3 Score=28.25 Aligned_cols=44 Identities=11% Similarity=0.241 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHHHHhC--CCChHHHHHHHHhcCCCC-CcchhhHHHH
Q 039425 18 GILNKEKSNLLVDMSKN--NVRPKDILHVLKKRNMHN-ATTIRAIYNA 62 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~--g~~~~~I~~~l~~~~~~~-~~t~~di~n~ 62 (413)
++ ++++++.|..+... ..++++|...|.++++-. .++...||++
T Consensus 30 ~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 30 RK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred CC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 45 77887888888664 699999999999998533 3478888865
No 19
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=73.57 E-value=3.7 Score=26.98 Aligned_cols=40 Identities=13% Similarity=0.182 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHH
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARR 64 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~ 64 (413)
+.+++++.+.|..|++.|++..+|+..+ | ++..+||+...
T Consensus 4 ~~~~~~~~~~i~~l~~~G~si~~IA~~~-----g--vsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGMSIAEIAKQF-----G--VSRSTVYRYLN 43 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--HHHHHHHT-----T--S-HHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHH-----C--cCHHHHHHHHh
Confidence 4577888899999999999988887653 2 45667776643
No 20
>PF14420 Clr5: Clr5 domain
Probab=71.69 E-value=15 Score=25.18 Aligned_cols=42 Identities=10% Similarity=0.149 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHh-CCCChHHHHHHHHhcCCCCCcchhhHHHHHH
Q 039425 22 KEKSNLLVDMSK-NNVRPKDILHVLKKRNMHNATTIRAIYNARR 64 (413)
Q Consensus 22 ~~~~~~i~~L~~-~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~ 64 (413)
+..++.|..|+. .|.+-.+|+++|.+.+ |-..|.++..+..+
T Consensus 6 e~~K~~I~~LY~~e~~tl~~v~~~M~~~~-~F~at~rqy~~r~~ 48 (54)
T PF14420_consen 6 EPHKEEIERLYIDENKTLEEVMEIMKEEH-GFKATKRQYKRRFK 48 (54)
T ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHHHHh-CCCcCHHHHHHHHH
Confidence 457899999994 7999999999999998 55567666665444
No 21
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.78 E-value=9.6 Score=32.32 Aligned_cols=36 Identities=17% Similarity=0.226 Sum_probs=29.3
Q ss_pred Eeecccc-ccCCCCcee--eEEEeeccCcEEEEEEEeec
Q 039425 124 IMDCTYQ-TNRYDMPLL--EIAGVTSIDLTFSVCCVYLK 159 (413)
Q Consensus 124 ~iD~Ty~-tn~~~~~l~--~~~g~~~~g~~~~~~~~~~~ 159 (413)
-||.||| |+.|+.|-+ .+.|.|..|+-...||+.+.
T Consensus 69 Pievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~h 107 (187)
T KOG4027|consen 69 PIEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLH 107 (187)
T ss_pred ceEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEe
Confidence 3788997 799999954 56788999998899998764
No 22
>PF13551 HTH_29: Winged helix-turn helix
Probab=67.84 E-value=13 Score=29.10 Aligned_cols=52 Identities=12% Similarity=0.168 Sum_probs=39.4
Q ss_pred ccccCCCCCHHHHHHHHHHHhC-------CCChHHHHHHH-HhcCCCCCcchhhHHHHHHHh
Q 039425 13 GHSFAGILNKEKSNLLVDMSKN-------NVRPKDILHVL-KKRNMHNATTIRAIYNARRKY 66 (413)
Q Consensus 13 ~hp~~rrlt~~~~~~i~~L~~~-------g~~~~~I~~~l-~~~~~~~~~t~~di~n~~~~~ 66 (413)
+.|..+ |++++++.|.++... ..++..|...| .+.+ +..++...|+++.++.
T Consensus 52 g~~~~~-l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~-~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 52 GRPRKR-LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEF-GIDVSPSTIRRILKRA 111 (112)
T ss_pred CCCCCC-CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhcc-CccCCHHHHHHHHHHC
Confidence 344444 999999999988885 26789999977 6665 5567889999887753
No 23
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=67.41 E-value=13 Score=25.48 Aligned_cols=47 Identities=15% Similarity=0.114 Sum_probs=30.9
Q ss_pred CCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhh
Q 039425 17 AGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYK 67 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~ 67 (413)
.+.||-+++..|..+++.|.+.++|+.. +|=...|..+|..-+.+++
T Consensus 4 R~~LTl~eK~~iI~~~e~g~s~~~ia~~----fgv~~sTv~~I~K~k~~i~ 50 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGESKRDIARE----FGVSRSTVSTILKNKDKIL 50 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT-HHHHHHH----HT--CCHHHHHHHCHHHHC
T ss_pred CccCCHHHHHHHHHHHHcCCCHHHHHHH----hCCCHHHHHHHHHhHHHHH
Confidence 4678999999999999999987776654 4323356777776665554
No 24
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=65.38 E-value=26 Score=24.45 Aligned_cols=43 Identities=16% Similarity=0.144 Sum_probs=33.3
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcC
Q 039425 24 KSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAG 73 (413)
Q Consensus 24 ~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~ 73 (413)
.|.....|+-.|.++.+|.+.|. ++.+.|++.+++..-+...+
T Consensus 2 ~k~~A~~LY~~G~~~~eIA~~Lg-------~~~~TV~~W~~r~~W~~~~~ 44 (58)
T PF06056_consen 2 VKEQARSLYLQGWSIKEIAEELG-------VPRSTVYSWKDRYKWDELLP 44 (58)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHC-------CChHHHHHHHHhhCccccCc
Confidence 46788899999999999998763 34788999988776554433
No 25
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=64.52 E-value=17 Score=24.39 Aligned_cols=31 Identities=23% Similarity=0.459 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhc
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKR 48 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~ 48 (413)
-.|+.+......+|.++|+.|......+++.
T Consensus 17 tgLd~etL~ici~L~e~GVnPeaLA~vI~el 47 (48)
T PF12554_consen 17 TGLDRETLSICIELCENGVNPEALAAVIKEL 47 (48)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHh
Confidence 3678888899999999999999999888763
No 26
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=63.72 E-value=25 Score=24.23 Aligned_cols=44 Identities=14% Similarity=0.232 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
.||+.+.. |..+...|.++++|...+. ++.+.|++.+++++++.
T Consensus 3 ~LT~~E~~-vl~~l~~G~~~~eIA~~l~-------is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELE-VLRLLAQGMSNKEIAEELG-------ISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHH-HHHHHHTTS-HHHHHHHHT-------SHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHH-HHHHHHhcCCcchhHHhcC-------cchhhHHHHHHHHHHHh
Confidence 57777754 7777789999999999872 56777887777776664
No 27
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=63.50 E-value=21 Score=29.92 Aligned_cols=50 Identities=16% Similarity=0.115 Sum_probs=34.3
Q ss_pred ccCCCCC-HHHHHHHHHHHhCCCChHHHHHHHHhcCCCC---CcchhhHHHHHH
Q 039425 15 SFAGILN-KEKSNLLVDMSKNNVRPKDILHVLKKRNMHN---ATTIRAIYNARR 64 (413)
Q Consensus 15 p~~rrlt-~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~---~~t~~di~n~~~ 64 (413)
|..-.++ ++..+.|..|...|++|++|-..|++++|-. .+|-+.|..+..
T Consensus 20 P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~vtG~kI~rILk 73 (148)
T PTZ00072 20 PSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNVTGSKILRILK 73 (148)
T ss_pred CchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeeccchHHHHHHH
Confidence 3433444 4457889999999999999999999999421 234444544433
No 28
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=60.46 E-value=9.1 Score=31.24 Aligned_cols=100 Identities=11% Similarity=0.144 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHhCCCChHHHHHHHHhcCCCC---CcchhhHHHHHHHhhhhhhcCcHHHHHHHHH-------HhhcCcEE
Q 039425 22 KEKSNLLVDMSKNNVRPKDILHVLKKRNMHN---ATTIRAIYNARRKYKVREQAGHSQMQLLMSK-------LIEHKYIE 91 (413)
Q Consensus 22 ~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~---~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~-------l~~~~~~~ 91 (413)
++.++.|..|...|++|.||--+|++.+|-. .++-..|-++.+...... +-..++..|++. |+.+
T Consensus 31 ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~P-eiPeDLy~likkAv~iRkHLer~---- 105 (151)
T KOG0400|consen 31 DDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAP-EIPEDLYHLIKKAVAIRKHLERN---- 105 (151)
T ss_pred HHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCC-CCcHHHHHHHHHHHHHHHHHHHh----
Confidence 6679999999999999999999999988521 244555555554322111 012244444433 2211
Q ss_pred EEeecCCCCceeeEEeeChhhHHHHhhCCCEEEeecccc
Q 039425 92 RHKSDVDTNCVEALFLAHPSAIESLQAFPRVLIMDCTYQ 130 (413)
Q Consensus 92 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty~ 130 (413)
.-|.+..++ +......+-.+.++|.....+-.+++
T Consensus 106 ---RKD~d~K~R-LILveSRihRlARYYk~~~~lPp~WK 140 (151)
T KOG0400|consen 106 ---RKDKDAKFR-LILVESRIHRLARYYKTKMVLPPNWK 140 (151)
T ss_pred ---ccccccceE-EEeehHHHHHHHHHHHhcccCCCCCC
Confidence 123344553 33444555556666665555555544
No 29
>PRK13907 rnhA ribonuclease H; Provisional
Probab=58.98 E-value=95 Score=25.07 Aligned_cols=78 Identities=15% Similarity=0.014 Sum_probs=40.5
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEE-eecccccchHHHHHHHHHHHHhccccceEEEeccchHHHHHHHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCV-YLKLKWENNYIWALERLKSIMEENMLASVIVTDRELALMTVIQK 200 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~-~~~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al~~Ai~~ 200 (413)
.+.+|+.++.|....-. -++-.+..|... ..+. -..+....-|.-++..+.........+..|-||. ..+++++..
T Consensus 3 ~iy~DGa~~~~~g~~G~-G~vi~~~~~~~~-~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS-~~vi~~~~~ 79 (128)
T PRK13907 3 EVYIDGASKGNPGPSGA-GVFIKGVQPAVQ-LSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDS-QLVERAVEK 79 (128)
T ss_pred EEEEeeCCCCCCCccEE-EEEEEECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEech-HHHHHHHhH
Confidence 37899999887533211 222244444322 2221 1122233445666666666553233455666766 666777777
Q ss_pred hC
Q 039425 201 HF 202 (413)
Q Consensus 201 vf 202 (413)
.+
T Consensus 80 ~~ 81 (128)
T PRK13907 80 EY 81 (128)
T ss_pred HH
Confidence 65
No 30
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=58.91 E-value=11 Score=31.01 Aligned_cols=35 Identities=9% Similarity=0.079 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCC
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNA 53 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~ 53 (413)
.+..+.+..|.++...|.+..+|.+.+.+.||+.+
T Consensus 57 ~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~V 91 (126)
T TIGR03147 57 PIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDFV 91 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeE
Confidence 45678899999999999999999999999998753
No 31
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=58.76 E-value=30 Score=22.40 Aligned_cols=43 Identities=7% Similarity=0.077 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhh
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKV 68 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~ 68 (413)
.|++.++..+..++..|.+..+|.+.+. .+...|++...+.+.
T Consensus 10 ~l~~~~~~~~~~~~~~~~~~~~ia~~~~-------~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEGLSYEEIAEILG-------ISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHC-------cCHHHHHHHHHHHHH
Confidence 5778888888777779999999977643 566777777666543
No 32
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=58.54 E-value=21 Score=28.03 Aligned_cols=41 Identities=15% Similarity=0.154 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHH
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIY 60 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~ 60 (413)
.|+++.|.+|..-.+.--+|.++.+.+++.+ |..++..++-
T Consensus 3 ~L~~~vK~FIVQ~LAcfdTPs~v~~aVk~eF-gi~vsrQqve 43 (104)
T PF10045_consen 3 ALKKEVKAFIVQSLACFDTPSEVAEAVKEEF-GIDVSRQQVE 43 (104)
T ss_pred CccHHHHHHHHHHHHhhCCHHHHHHHHHHHh-CCccCHHHHH
Confidence 5899999999999999999999999999999 4445666553
No 33
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=56.69 E-value=39 Score=22.32 Aligned_cols=44 Identities=9% Similarity=0.151 Sum_probs=31.7
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVR 69 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~ 69 (413)
..|++.++. |..+...|.+..+|.+.+. ++...|++.+.+.+++
T Consensus 2 ~~l~~~e~~-i~~~~~~g~s~~eia~~l~-------is~~tv~~~~~~~~~k 45 (58)
T smart00421 2 ASLTPRERE-VLRLLAEGLTNKEIAERLG-------ISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCCHHHHH-HHHHHHcCCCHHHHHHHHC-------CCHHHHHHHHHHHHHH
Confidence 357888877 5566789999999987752 4667777777766544
No 34
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=56.11 E-value=42 Score=31.32 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=21.0
Q ss_pred HHHhhhhccCCCCCCCCCceeccccccCch
Q 039425 334 LDESRRVDSLGPDVFACGCIIRHTHGLPRA 363 (413)
Q Consensus 334 ~~q~~~~~~~~~~~~~Csc~~~~~~GlPC~ 363 (413)
.+||.....++ ..|.|.||...|-||.
T Consensus 284 keqyad~lhlC---rhC~~LfWks~gHPC~ 310 (332)
T KOG3926|consen 284 KEQYADTLHLC---RHCCILFWKSDGHPCT 310 (332)
T ss_pred HHHHHHHHHHH---hhceEeeecCCCCCcc
Confidence 45666555543 7899999999999995
No 35
>cd00131 PAX Paired Box domain
Probab=54.87 E-value=33 Score=28.20 Aligned_cols=45 Identities=18% Similarity=0.313 Sum_probs=35.9
Q ss_pred CCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhh
Q 039425 17 AGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKV 68 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~ 68 (413)
.+-+|.+.+..|..+.+.|+++++|...+. ++...|++++++++.
T Consensus 15 ~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~-------Vs~~tV~r~i~r~~e 59 (128)
T cd00131 15 GRPLPDSIRQRIVELAQSGIRPCDISRQLR-------VSHGCVSKILNRYYE 59 (128)
T ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHHHHHC-------cCHHHHHHHHHHHHH
Confidence 377899999999999999999999966543 566777777777654
No 36
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=54.69 E-value=51 Score=30.76 Aligned_cols=146 Identities=6% Similarity=-0.112 Sum_probs=81.9
Q ss_pred HHHHHHHHHHHh--CCCChHHHHHHHHhcCC--CC-CcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHhhcCcEEEEeec
Q 039425 22 KEKSNLLVDMSK--NNVRPKDILHVLKKRNM--HN-ATTIRAIYNARRKYKVREQAGHSQMQLLMSKLIEHKYIERHKSD 96 (413)
Q Consensus 22 ~~~~~~i~~L~~--~g~~~~~I~~~l~~~~~--~~-~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~ 96 (413)
.+....|..+.. ...-.+.|...|+++.. |. .+..+.|+++.++........ . . .. .
T Consensus 11 ~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~r------------~--~--~~--~ 72 (262)
T PRK14702 11 TDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLERK------------P--A--VP--P 72 (262)
T ss_pred HHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCccccC------------C--C--CC--C
Confidence 344555565533 45778899999988643 43 267788888777643221000 0 0 00 0
Q ss_pred CCCCceeeEEeeChhhHHHHhhCCCEEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecc-cccchHHHHHHHHHH
Q 039425 97 VDTNCVEALFLAHPSAIESLQAFPRVLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKL-KWENNYIWALERLKS 175 (413)
Q Consensus 97 ~~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~-E~~~~~~~~l~~l~~ 175 (413)
...+.... + ....-..++..|-||.....+..++..+.+|...+ .++|+.+..+ .+.+....+|+...+
T Consensus 73 ~~~~~~~~-~--------~~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~ 142 (262)
T PRK14702 73 SKRAHTGR-V--------AVKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVE 142 (262)
T ss_pred CCcCCCCc-c--------ccCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHH
Confidence 00000000 0 01122359999999865544556888888887776 6689998864 555555555554433
Q ss_pred HH-h--ccccceEEEeccchHHH
Q 039425 176 IM-E--ENMLASVIVTDRELALM 195 (413)
Q Consensus 176 ~~-~--~~~~p~~iitD~~~al~ 195 (413)
.. . ....|.+|.||+-....
T Consensus 143 ~~~~~~~~~~~~iihSD~Gsqy~ 165 (262)
T PRK14702 143 RRFGNDLPSSPVEWLTDNGSCYR 165 (262)
T ss_pred HHhcccCCCCCeEEEcCCCcccc
Confidence 32 1 12357899999876553
No 37
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=54.11 E-value=36 Score=29.13 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=32.6
Q ss_pred cccchHHHHHHHHHHHHhc-----cccceEEEeccchHHHHHHHHhCCccc
Q 039425 161 KWENNYIWALERLKSIMEE-----NMLASVIVTDRELALMTVIQKHFPSAT 206 (413)
Q Consensus 161 E~~~~~~~~l~~l~~~~~~-----~~~p~~iitD~~~al~~Ai~~vfP~a~ 206 (413)
+..+.|.-+-+.+.+.+.. ...|..|+.|+.++..+|..+++-+..
T Consensus 53 ~~~dDy~~M~Evl~RR~~~~~~~~~~lPDLilIDGG~gQl~aa~~~l~~lg 103 (155)
T PF08459_consen 53 DGGDDYAAMREVLTRRFKRLKEEKEPLPDLILIDGGKGQLNAAKEVLKELG 103 (155)
T ss_dssp STT-HHHHHHHHHHHHHCCCHHHT----SEEEESSSHHHHHHHHHHHHCTT
T ss_pred CCCcHHHHHHHHHHHHHhcccccCCCCCCEEEEcCCHHHHHHHHHHHHHcC
Confidence 4457888887878777731 257999999999999999999876543
No 38
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=53.38 E-value=15 Score=30.14 Aligned_cols=35 Identities=9% Similarity=0.036 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCC
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNA 53 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~ 53 (413)
.+..+.+..|.++...|.+..+|.+.+.+.||+.+
T Consensus 57 ~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~V 91 (126)
T PRK10144 57 PVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFV 91 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeE
Confidence 45678899999999999999999999999998753
No 39
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=52.85 E-value=22 Score=32.65 Aligned_cols=23 Identities=17% Similarity=0.132 Sum_probs=19.0
Q ss_pred CCCCCceeccccccCchHHHHHHHHH
Q 039425 347 VFACGCIIRHTHGLPRAPEITEYKRE 372 (413)
Q Consensus 347 ~~~Csc~~~~~~GlPC~H~l~~~~~~ 372 (413)
...|||.=+ -.||-|+-|+++.-
T Consensus 124 ~~dCSCPD~---anPCKHi~AvyY~l 146 (266)
T COG4279 124 STDCSCPDY---ANPCKHIAAVYYLL 146 (266)
T ss_pred ccccCCCCc---ccchHHHHHHHHHH
Confidence 578999854 57999999999863
No 40
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=52.36 E-value=60 Score=31.01 Aligned_cols=74 Identities=7% Similarity=-0.239 Sum_probs=49.9
Q ss_pred CEEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecc-cccchHHHHHHHHHHHHhc---cccceEEEeccchHHH
Q 039425 121 RVLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKL-KWENNYIWALERLKSIMEE---NMLASVIVTDRELALM 195 (413)
Q Consensus 121 ~vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~-E~~~~~~~~l~~l~~~~~~---~~~p~~iitD~~~al~ 195 (413)
.++..|-||.....+.-++..+.+|...+ .++|+.+..+ .+.+....+|+...+...+ ...|.+|.||+-....
T Consensus 127 ~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy~ 204 (301)
T PRK09409 127 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCYR 204 (301)
T ss_pred CEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCcccc
Confidence 69999999965544555777777887776 6789998875 5666655566544333211 2346789999876554
No 41
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.23 E-value=72 Score=31.92 Aligned_cols=72 Identities=14% Similarity=0.055 Sum_probs=50.1
Q ss_pred eeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhccccceEEEeccchHHHHHHHHhCCccccccccchhHHHH
Q 039425 139 LEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELALMTVIQKHFPSATTFLCRWYISRNV 218 (413)
Q Consensus 139 ~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al~~Ai~~vfP~a~~~lC~~Hi~kn~ 218 (413)
+.++.+|.+.... ..++++-+.++....|+.+ +....+.+..|...+..+++++.||+|.+..=.||+.+..
T Consensus 169 ~~~i~~D~~~~~~---i~i~~~r~~~ti~~~l~~~-----g~~~v~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~~~ 240 (402)
T COG3464 169 YQTIAVDLDTRKV---IDILEGRSVRTLRRYLRRG-----GSEQVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQYI 240 (402)
T ss_pred EEEEEEcCCCCce---eeecCCccHHHHHHHHHhC-----CCcceeEEEccccHHHHHHHHHhCCChheeeeeeeeeeeh
Confidence 3455555554222 2455666666655443332 2226889999999999999999999999999999998733
No 42
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=49.92 E-value=23 Score=29.03 Aligned_cols=32 Identities=31% Similarity=0.439 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcC
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
|-|+.+.+..|.+|...|++|.+|...|.-.+
T Consensus 16 rPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~ 47 (125)
T PF00292_consen 16 RPLPNELRQRIVELAKEGVRPCDISRQLRVSH 47 (125)
T ss_dssp SSS-HHHHHHHHHHHHTT--HHHHHHHHT--H
T ss_pred ccCcHHHHHHHHHHhhhcCCHHHHHHHHccch
Confidence 77889999999999999999999988766543
No 43
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=48.95 E-value=21 Score=23.54 Aligned_cols=42 Identities=12% Similarity=0.319 Sum_probs=22.3
Q ss_pred CHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhh
Q 039425 21 NKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVR 69 (413)
Q Consensus 21 t~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~ 69 (413)
+.+.+..+..|...|.+.++|...+. .+...|++.+++++..
T Consensus 3 ~~~~R~~ii~l~~~G~s~~~ia~~lg-------vs~~Tv~~w~kr~~~~ 44 (50)
T PF13384_consen 3 SEERRAQIIRLLREGWSIREIAKRLG-------VSRSTVYRWIKRYREE 44 (50)
T ss_dssp -------HHHHHHHT--HHHHHHHHT-------S-HHHHHHHHT-----
T ss_pred chhHHHHHHHHHHCCCCHHHHHHHHC-------cCHHHHHHHHHHcccc
Confidence 34566777888888999999988762 5678899998887654
No 44
>PRK00766 hypothetical protein; Provisional
Probab=48.93 E-value=1.6e+02 Score=26.23 Aligned_cols=90 Identities=19% Similarity=0.155 Sum_probs=46.9
Q ss_pred hCCCEEEee-ccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHH-------------------
Q 039425 118 AFPRVLIMD-CTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIM------------------- 177 (413)
Q Consensus 118 ~~~~vl~iD-~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~------------------- 177 (413)
....|+.+| +.|..+..+-..+.-+..-+++...-++|..+.-.-.+.=..+.+.++...
T Consensus 7 ~~irvlGidds~f~~~~~~~~~lvGvv~r~~~~idGv~~~~itvdG~DaT~~i~~mv~~~~~r~~i~~V~L~Git~agFN 86 (194)
T PRK00766 7 PEIRVLGIDDGTFLFKSSEKVILVGVVMRGGDWVDGVLSRWITVDGLDATEAIIEMVNSSRHKGQLRVIMLDGITYGGFN 86 (194)
T ss_pred CcceEEEEecCccccCCCCCEEEEEEEEECCeEEeeEEEEEEEECCccHHHHHHHHHHhcccccceEEEEECCEeeeeeE
Confidence 445688888 666654333334433333333333344444444433333333444433310
Q ss_pred --------hccccceEEEeccch---HHHHHHHHhCCcccc
Q 039425 178 --------EENMLASVIVTDREL---ALMTVIQKHFPSATT 207 (413)
Q Consensus 178 --------~~~~~p~~iitD~~~---al~~Ai~~vfP~a~~ 207 (413)
.....|..+++.+-+ ++.+|+++.||+...
T Consensus 87 vvD~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k~f~~~~~ 127 (194)
T PRK00766 87 VVDIEELYRETGLPVIVVMRKKPDFEAIESALKKHFSDWEE 127 (194)
T ss_pred EecHHHHHHHHCCCEEEEEecCCCHHHHHHHHHHHCCCHHH
Confidence 112456666654443 688999999998765
No 45
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=48.73 E-value=53 Score=24.66 Aligned_cols=51 Identities=14% Similarity=0.129 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHhCC--CChHHHHHHHHhcCCCCC-cchhhHHHHHHHhhhh
Q 039425 19 ILNKEKSNLLVDMSKNN--VRPKDILHVLKKRNMHNA-TTIRAIYNARRKYKVR 69 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g--~~~~~I~~~l~~~~~~~~-~t~~di~n~~~~~~~~ 69 (413)
.|.+..-..|.+|..+| ++-..|++.|.+.+|+.. ++.+.||+....+-++
T Consensus 11 PL~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~e 64 (80)
T PF10264_consen 11 PLPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKE 64 (80)
T ss_pred eHHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHc
Confidence 45677778899999875 667789999999999853 5566778776655443
No 46
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=48.72 E-value=91 Score=25.18 Aligned_cols=61 Identities=25% Similarity=0.370 Sum_probs=41.7
Q ss_pred CCceeeeeccccccccCCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhh
Q 039425 1 MGSITILLHNLEGHSFAGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVR 69 (413)
Q Consensus 1 ~~~~~~~~~~~~~hp~~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~ 69 (413)
||.=-|-+| +-|--.-|+-+......|.+|..+|.+|++|...+ | +..+++|-...++.++
T Consensus 76 ~gI~vIPvk-~KgrGrprkyd~~t~~~i~emlr~gk~preIsk~l-----G--IpirTvyY~l~k~k~~ 136 (139)
T COG1710 76 MGIKVIPVK-LKGRGRPRKYDRNTLLRIREMLRNGKTPREISKDL-----G--IPIRTVYYLLKKLKKK 136 (139)
T ss_pred CCceEeeee-ecCCCCCcccchhHHHHHHHHHHcCCCHHHHHHhh-----C--CchhhhHHHHHHHhhh
Confidence 343334444 33433446677778889999999999999997643 3 5678888777766554
No 47
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=47.39 E-value=64 Score=29.68 Aligned_cols=160 Identities=13% Similarity=0.143 Sum_probs=83.4
Q ss_pred ccCCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHhhcCcEEEEe
Q 039425 15 SFAGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLIEHKYIERHK 94 (413)
Q Consensus 15 p~~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~ 94 (413)
+..++-|.+++.....|+..| | ...++|.++ +-.+++.+.+++..+++.-+. | .+..+++.++...
T Consensus 67 ~k~~~wt~e~~~~Al~L~~~s--p-r~Y~yL~kk-~~pLPs~rTL~r~l~~v~~~p--G--i~~~il~~l~~~~------ 132 (236)
T PF12017_consen 67 GKRRRWTKEDKSFALSLYKCS--P-RAYNYLRKK-GYPLPSVRTLQRWLSKVNIDP--G--ILDFILDLLKNKS------ 132 (236)
T ss_pred CCccccCHHHHHhhheeeecC--h-HHHHHHHHc-CCCCCCHHHHHHHHHhCCCCC--C--chHHHHHHHHHcc------
Confidence 445677888888888887443 3 345666544 234578889998888765432 2 3345566655421
Q ss_pred ecCCCCceeeEEeeChhhHHHHhhCCCEEEeec----cccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHH
Q 039425 95 SDVDTNCVEALFLAHPSAIESLQAFPRVLIMDC----TYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWAL 170 (413)
Q Consensus 95 ~~~~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~----Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l 170 (413)
.++..++..+.|---.. ...+..|. .++...+ ..++.+.|+. .+..+|++|.|-..-+.+....+.
T Consensus 133 -~~~~dr~CvL~fDEm~l-------~~~~eYD~~~d~v~~~~~~-~~v~mvrGl~-~~WKQpi~~~f~t~m~~~~l~~iI 202 (236)
T PF12017_consen 133 -MSEEDRICVLSFDEMKL-------SPHLEYDPSRDEVNEPANY-VQVFMVRGLF-KSWKQPIYFDFDTSMDADILKNII 202 (236)
T ss_pred -CchhccEEEEEEeEEEc-------cceeeeccccCcccChhhh-hhHHHHHHHH-hcCCccEEEEecCcCCHHHHHHHH
Confidence 12222222222210000 01111111 1222211 1233455554 455688899985433443333333
Q ss_pred HHHHHHHhccccceEEEeccchHHHHHHHHh
Q 039425 171 ERLKSIMEENMLASVIVTDRELALMTVIQKH 201 (413)
Q Consensus 171 ~~l~~~~~~~~~p~~iitD~~~al~~Ai~~v 201 (413)
+.+. .-+-.+..+++|...+-+.+.++.
T Consensus 203 ~~l~---~~g~~VvAivsD~g~~N~~~w~~L 230 (236)
T PF12017_consen 203 EKLH---EIGYNVVAIVSDMGSNNISLWREL 230 (236)
T ss_pred HHHH---HCCCEEEEEECCCCcchHHHHHHc
Confidence 2222 225677889999999888887763
No 48
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=47.34 E-value=1e+02 Score=25.77 Aligned_cols=69 Identities=12% Similarity=0.072 Sum_probs=38.6
Q ss_pred CCCCCHHHH---HHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHh
Q 039425 17 AGILNKEKS---NLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLI 85 (413)
Q Consensus 17 ~rrlt~~~~---~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~ 85 (413)
+|+-++++. ..|..|...|++..+|.+.+.....+...+..++.......+.........++.+.+.|.
T Consensus 36 ~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~ 107 (139)
T cd01110 36 QRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALATLPEDRTPTKADWERLSRAWRDRLDERIAELQQLRDQLD 107 (139)
T ss_pred CeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566776654 447788889999999999997543232234444444433322222222234555554444
No 49
>PHA02517 putative transposase OrfB; Reviewed
Probab=46.96 E-value=44 Score=31.26 Aligned_cols=150 Identities=8% Similarity=-0.054 Sum_probs=79.1
Q ss_pred HHHHHHHHHHHh---CCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHhhcCcEEEE-eecC
Q 039425 22 KEKSNLLVDMSK---NNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLIEHKYIERH-KSDV 97 (413)
Q Consensus 22 ~~~~~~i~~L~~---~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~-~~~~ 97 (413)
++.++.|..+.. .....++|...|++. |..+..+.|+++.++......... ........ ....
T Consensus 29 ~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~--g~~vs~~tV~Rim~~~gl~~~~~~-----------k~~~~~~~~~~~~ 95 (277)
T PHA02517 29 DWLKSEILRVYDENHQVYGVRKVWRQLNRE--GIRVARCTVGRLMKELGLAGVLRG-----------KKVRTTISRKAVA 95 (277)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHHhc--CcccCHHHHHHHHHHcCCceEecC-----------CCcCCCCCCCCCC
Confidence 455777888853 257889999999877 444677888887765433110000 00000000 0000
Q ss_pred CCCceeeEEeeChhhHHHHhhCCCEEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHH
Q 039425 98 DTNCVEALFLAHPSAIESLQAFPRVLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIM 177 (413)
Q Consensus 98 ~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~ 177 (413)
..+.+..-|- ...-.+++..|-||-....+ ..+..+.+|... ..++|+.+...++.+...-+|+......
T Consensus 96 ~~n~~~r~f~--------~~~pn~~w~~D~t~~~~~~g-~~yl~~iiD~~s-r~i~~~~~~~~~~~~~~~~~l~~a~~~~ 165 (277)
T PHA02517 96 APDRVNRQFV--------ATRPNQLWVADFTYVSTWQG-WVYVAFIIDVFA-RRIVGWRVSSSMDTDFVLDALEQALWAR 165 (277)
T ss_pred CCCcccCCCC--------CCCCCCeEEeceeEEEeCCC-CEEEEEecccCC-CeeeecccCCCCChHHHHHHHHHHHHhc
Confidence 0011110000 01123689999999654434 356666666555 4567888877777665544444433332
Q ss_pred hccccceEEEeccchHHH
Q 039425 178 EENMLASVIVTDRELALM 195 (413)
Q Consensus 178 ~~~~~p~~iitD~~~al~ 195 (413)
+...+.+|.||......
T Consensus 166 -~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 166 -GRPGGLIHHSDKGSQYV 182 (277)
T ss_pred -CCCcCcEeecccccccc
Confidence 22233467799987654
No 50
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=45.97 E-value=69 Score=26.96 Aligned_cols=25 Identities=8% Similarity=0.368 Sum_probs=11.6
Q ss_pred CChHHHHHHHHhcCCCCCcchhhHHHH
Q 039425 36 VRPKDILHVLKKRNMHNATTIRAIYNA 62 (413)
Q Consensus 36 ~~~~~I~~~l~~~~~~~~~t~~di~n~ 62 (413)
++..+|...|++.+|+ +++.+|||.
T Consensus 37 ~sAeei~~~l~~~~p~--islaTVYr~ 61 (145)
T COG0735 37 LSAEELYEELREEGPG--ISLATVYRT 61 (145)
T ss_pred CCHHHHHHHHHHhCCC--CCHhHHHHH
Confidence 4555555555554433 234444443
No 51
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=45.71 E-value=1.2e+02 Score=24.31 Aligned_cols=50 Identities=2% Similarity=0.010 Sum_probs=32.8
Q ss_pred cCCCCCHHHHHH---HHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHH
Q 039425 16 FAGILNKEKSNL---LVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRK 65 (413)
Q Consensus 16 ~~rrlt~~~~~~---i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~ 65 (413)
-+|.-++.+... |..|.+.|++..+|...+.....+......++.+..+.
T Consensus 34 ~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~ 86 (116)
T cd04769 34 NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPHLQQALED 86 (116)
T ss_pred CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccCCcCcHHHHHHHHHH
Confidence 456677666554 77899999999999999987643322233444444443
No 52
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=45.55 E-value=45 Score=22.52 Aligned_cols=42 Identities=12% Similarity=0.135 Sum_probs=26.1
Q ss_pred CCEEEeeccccc-cCCCC------------ceeeEEEeeccCcEEEEEEEeeccc
Q 039425 120 PRVLIMDCTYQT-NRYDM------------PLLEIAGVTSIDLTFSVCCVYLKLK 161 (413)
Q Consensus 120 ~~vl~iD~Ty~t-n~~~~------------~l~~~~g~~~~g~~~~~~~~~~~~E 161 (413)
+.||.||+.-++ .-|.+ .-++++|.+.+|+..++...+..+|
T Consensus 8 cnvisidgkkkksdtysypklvvenktyefssfvlcgetpdgrrlvlthmistde 62 (66)
T PF13082_consen 8 CNVISIDGKKKKSDTYSYPKLVVENKTYEFSSFVLCGETPDGRRLVLTHMISTDE 62 (66)
T ss_pred ccEEEeccccccCCcccCceEEEeCceEEEEEEEEEccCCCCcEEEEEEEecchh
Confidence 456777765443 22333 3456778888888877777665554
No 53
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=41.30 E-value=70 Score=21.37 Aligned_cols=44 Identities=9% Similarity=0.116 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKV 68 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~ 68 (413)
..|++.++..+.--+-.|++..+|.+.+ | .+...|++...+.++
T Consensus 9 ~~L~~~~r~i~~l~~~~g~s~~eIa~~l-----~--~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 9 AQLPERQREIFLLRYFQGMSYAEIAEIL-----G--ISESTVKRRLRRARK 52 (54)
T ss_dssp HCS-HHHHHHHHHHHTS---HHHHHHHC-----T--S-HHHHHHHHHHHHH
T ss_pred HCCCHHHHHHHHHHHHHCcCHHHHHHHH-----C--cCHHHHHHHHHHHHh
Confidence 4688888888888888999999999876 2 456666666655543
No 54
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=41.07 E-value=1.8e+02 Score=23.69 Aligned_cols=69 Identities=9% Similarity=0.106 Sum_probs=39.4
Q ss_pred cCCCCCHHH---HHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHh
Q 039425 16 FAGILNKEK---SNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLI 85 (413)
Q Consensus 16 ~~rrlt~~~---~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~ 85 (413)
-+|.-++++ ...|..|.+.|++-.+|.+.+.....+. .+..++..............-..++.+.+.|.
T Consensus 35 gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~~~~~-~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~ 106 (127)
T TIGR02047 35 NYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPE-KSCSDVNALLDEHISHVRARIIKLQALIEQLV 106 (127)
T ss_pred CCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467777766 5567788899999999999997543222 23445444433332222222234444444443
No 55
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=40.84 E-value=60 Score=18.61 Aligned_cols=28 Identities=14% Similarity=0.030 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHH
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVL 45 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l 45 (413)
+.++++.+..|..+...|.+..+|...+
T Consensus 4 ~~~~~~~~~~i~~~~~~~~s~~~ia~~~ 31 (42)
T cd00569 4 PKLTPEQIEEARRLLAAGESVAEIARRL 31 (42)
T ss_pred CcCCHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3467778888888888999888887655
No 56
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=39.28 E-value=94 Score=25.93 Aligned_cols=54 Identities=15% Similarity=-0.062 Sum_probs=31.5
Q ss_pred eeeEEEeecc-CcEEEEEEEeecccccchHHHHHHHHHHHHhccccceEEEeccchHHHHH
Q 039425 138 LLEIAGVTSI-DLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELALMTV 197 (413)
Q Consensus 138 l~~~~g~~~~-g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al~~A 197 (413)
..++++++.. |..--+....+.+.+.++..-+++. . ...-.+|+||...+....
T Consensus 35 ~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~---~---i~~gs~i~TD~~~aY~~l 89 (151)
T PF12762_consen 35 VPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQE---H---IEPGSTIITDGWRAYNGL 89 (151)
T ss_pred cEEEEEEeecccCCceEEEEeecccccchhHHHHHH---h---hhccceeeecchhhcCcc
Confidence 4455555555 3333344445577887776554432 2 233468999999887533
No 57
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=39.10 E-value=1.3e+02 Score=20.93 Aligned_cols=59 Identities=8% Similarity=0.062 Sum_probs=32.6
Q ss_pred HHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHH
Q 039425 25 SNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKL 84 (413)
Q Consensus 25 ~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l 84 (413)
..+|..+...|+|-.+|.+.+.-.. +...+..++.......+.+...-...++.+.+.|
T Consensus 4 L~~I~~~r~lGfsL~eI~~~l~l~~-~~~~~~~~~~~~l~~~~~~i~~~i~~L~~~~~~L 62 (65)
T PF09278_consen 4 LQFIRRLRELGFSLEEIRELLELYD-QGDPPCADRRALLEEKLEEIEEQIAELQALRAQL 62 (65)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHHCC-SHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHhccC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999994332 2223445555444443333322223455544444
No 58
>smart00351 PAX Paired Box domain.
Probab=38.36 E-value=78 Score=25.83 Aligned_cols=44 Identities=25% Similarity=0.351 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKV 68 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~ 68 (413)
+.++.+++..|..++..|.+.++|...+ + ++...|++++++++.
T Consensus 16 ~~~s~~~R~riv~~~~~G~s~~~iA~~~-----g--vs~~tV~kwi~r~~~ 59 (125)
T smart00351 16 RPLPDEERQRIVELAQNGVRPCDISRQL-----C--VSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHH-----C--cCHHHHHHHHHHHHH
Confidence 5589999999999999999999885543 2 567778888777654
No 59
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=38.11 E-value=30 Score=29.34 Aligned_cols=34 Identities=9% Similarity=0.164 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCC
Q 039425 20 LNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNA 53 (413)
Q Consensus 20 lt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~ 53 (413)
+..+.+..|.++...|.+..+|.+.+.+.||..+
T Consensus 58 ~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG~~V 91 (148)
T PF03918_consen 58 IARDMRREIREMLAEGKSDEEIIDYFVERYGEFV 91 (148)
T ss_dssp HHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCcce
Confidence 3467788899999999999999999999997654
No 60
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=37.54 E-value=80 Score=18.91 Aligned_cols=27 Identities=15% Similarity=0.276 Sum_probs=19.1
Q ss_pred CHHHHHHHHHHHhCCCChHHHHHHHHh
Q 039425 21 NKEKSNLLVDMSKNNVRPKDILHVLKK 47 (413)
Q Consensus 21 t~~~~~~i~~L~~~g~~~~~I~~~l~~ 47 (413)
+++=...|....++|++..+|.++|..
T Consensus 2 D~EW~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 2 DEEWVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 344466788888899999999998864
No 61
>PRK15320 transcriptional activator SprB; Provisional
Probab=36.34 E-value=1e+02 Score=27.58 Aligned_cols=45 Identities=11% Similarity=0.056 Sum_probs=34.7
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
.+||+-+ ..|..|...|.+.++|.+.|. ++.+.|...+.++..+.
T Consensus 163 ~~LSdRE-IEVL~LLAkG~SNKEIAekL~-------LS~KTVSTYKnRLLeKL 207 (251)
T PRK15320 163 PGVTQAK-YALLILLSSGHPAIELAKKFG-------LGTKTVSIYRKKVMYRL 207 (251)
T ss_pred CCCCHHH-HHHHHHHHcCCCHHHHHHHhc-------cchhhHHHHHHHHHHHc
Confidence 5677666 467788889999999999987 56677777777776664
No 62
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=35.67 E-value=70 Score=28.55 Aligned_cols=44 Identities=9% Similarity=0.129 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
.||+-+ ..|..|...|.+.++|.+.|. ++.+.|++.++++.++.
T Consensus 137 ~LT~RE-~eVL~lla~G~snkeIA~~L~-------iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 137 SLSRTE-SSMLRMWMAGQGTIQISDQMN-------IKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCHHH-HHHHHHHHcCCCHHHHHHHcC-------CCHHHHHHHHHHHHHHh
Confidence 488877 467788889999999998775 66778888777776654
No 63
>PRK09462 fur ferric uptake regulator; Provisional
Probab=34.95 E-value=1.3e+02 Score=25.23 Aligned_cols=45 Identities=11% Similarity=0.180 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHHHHHh---CCCChHHHHHHHHhcCCCCCcchhhHHHHHH
Q 039425 18 GILNKEKSNLLVDMSK---NNVRPKDILHVLKKRNMHNATTIRAIYNARR 64 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~---~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~ 64 (413)
.|+|+.-+..+..|.. ..+++.+|.+.|++..+. +.+.+||+...
T Consensus 13 lr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~--i~~aTVYR~L~ 60 (148)
T PRK09462 13 LKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEE--IGLATVYRVLN 60 (148)
T ss_pred CCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCC--CCHHHHHHHHH
Confidence 4566666555556653 256777777777776543 44556665544
No 64
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=34.26 E-value=95 Score=23.15 Aligned_cols=46 Identities=17% Similarity=0.194 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCh-HHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 25 SNLLVDMSKNNVRP-KDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 25 ~~~i~~L~~~g~~~-~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
+..-..|.+.|..| .||.-+|-.-.|..+++.++.+|..+++-|.+
T Consensus 22 ~~Vy~AL~EKGYnPinQivGYllSGDPaYItsh~nAR~lIr~~eRDe 68 (79)
T PF06135_consen 22 KQVYAALEEKGYNPINQIVGYLLSGDPAYITSHNNARNLIRKIERDE 68 (79)
T ss_pred HHHHHHHHHcCCChHHHHHhheecCCCccccCcccHHHHHHHHhHHH
Confidence 34456777889877 57888888887887888889999888875543
No 65
>PRK04217 hypothetical protein; Provisional
Probab=33.73 E-value=1.4e+02 Score=23.89 Aligned_cols=43 Identities=7% Similarity=0.030 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHh
Q 039425 17 AGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKY 66 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~ 66 (413)
-..|++++++.+..+...|++..+|.+.+. ++...|++...+.
T Consensus 40 ~~~Lt~eereai~l~~~eGlS~~EIAk~LG-------IS~sTV~r~L~RA 82 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGLTQEEAGKRMG-------VSRGTVWRALTSA 82 (110)
T ss_pred cccCCHHHHHHHHHHHHcCCCHHHHHHHHC-------cCHHHHHHHHHHH
Confidence 467889998777777779999999988773 3455566555543
No 66
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=32.98 E-value=2.3e+02 Score=23.66 Aligned_cols=32 Identities=6% Similarity=0.022 Sum_probs=25.0
Q ss_pred CCCCCHHH---HHHHHHHHhCCCChHHHHHHHHhc
Q 039425 17 AGILNKEK---SNLLVDMSKNNVRPKDILHVLKKR 48 (413)
Q Consensus 17 ~rrlt~~~---~~~i~~L~~~g~~~~~I~~~l~~~ 48 (413)
+|+-++++ ...|..|.+.|++..+|...+...
T Consensus 36 ~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (142)
T TIGR01950 36 QRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAVL 70 (142)
T ss_pred CEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 56666665 345778888999999999999754
No 67
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=32.82 E-value=89 Score=25.29 Aligned_cols=45 Identities=13% Similarity=0.203 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVR 69 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~ 69 (413)
..|++.++..|...+-.|.+..+|.+.+. ++.+.|++.+.+.+++
T Consensus 109 ~~L~~~~~~ii~~~~~~g~s~~eIA~~l~-------~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 109 EKLPEREREVLVLRYLEGLSYKEIAEILG-------ISVGTVKRRLKRARKK 153 (158)
T ss_pred HhCCHHHHHHHhhHHhcCCCHHHHHHHHC-------CCHHHHHHHHHHHHHH
Confidence 46778887777666678999988887753 4677888888776654
No 68
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=32.12 E-value=1.5e+02 Score=19.41 Aligned_cols=43 Identities=12% Similarity=0.193 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 20 LNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 20 lt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
|++.++. +..+...|++.++|.+.+. ++.+.|++.+.+.+++.
T Consensus 1 l~~~e~~-i~~~~~~~~s~~eia~~l~-------~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 1 LTPRERE-VLRLLAEGKTNKEIADILG-------ISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CCHHHHH-HHHHHHcCCCHHHHHHHHC-------CCHHHHHHHHHHHHHHh
Confidence 4566666 4456678999999987752 46677777777766554
No 69
>cd08309 Death_IRAK Death domain of Interleukin-1 Receptor-Associated Kinases. Death Domains (DDs) found in Interleukin-1 (IL-1) Receptor-Associated Kinases (IRAK1-4) and similar proteins. IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. All four types are involved in signal transduction involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinase pathways. IRAK1 and IRAK4 are active kinases while IRAK2 and IRAK-M (also called IRAK3) are inactive. In general, IRAKs are expressed ubiquitously, except for IRAK-M which is detected only in macrophages. The insect homologs, Pelle and Tube, are important components of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in the innate immune response. Most members have an N-terminal DD followed by a kinase domain. In general, DDs are protein-protein interaction domains found in a variety of domain a
Probab=32.03 E-value=2.4e+02 Score=21.75 Aligned_cols=66 Identities=9% Similarity=-0.023 Sum_probs=49.2
Q ss_pred cCCCCCHHHHHHHHHHHhC--CCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHh
Q 039425 16 FAGILNKEKSNLLVDMSKN--NVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLI 85 (413)
Q Consensus 16 ~~rrlt~~~~~~i~~L~~~--g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~ 85 (413)
+.|.|....+..+..+.++ |-.-++++..|.+-.+..-++..+|+++....++ |.+|...+++...
T Consensus 2 ~i~~Lp~~~~~~L~~~LD~~~~~~W~~LA~~i~~~~~~~~~~~~~i~~~e~~~~~----g~SPt~~LL~~W~ 69 (95)
T cd08309 2 YIRQLPYSVLARLCKVLDPLELKGWRQLASLIPKGLGGPRYDLTDVRQIESMKQR----GRSPTRELLWDWG 69 (95)
T ss_pred cceeCCHHHHHHHHHHhCCcccCChHHHHHHhccccccCCcCHHHHHHHHHHhhc----CCChHHHHHHHHH
Confidence 3578888899999999998 8999999999987665545677788888776544 4556566665553
No 70
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=32.01 E-value=96 Score=24.18 Aligned_cols=49 Identities=14% Similarity=0.171 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHH-HHHhCC---CChHHHHHHHHhcCCCCCcchhhHHHHHHHh
Q 039425 17 AGILNKEKSNLLV-DMSKNN---VRPKDILHVLKKRNMHNATTIRAIYNARRKY 66 (413)
Q Consensus 17 ~rrlt~~~~~~i~-~L~~~g---~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~ 66 (413)
.|+||+++...|. .|...| .+.-+|-..|.+-. +...+..||.+.+.++
T Consensus 33 ~r~Ltd~ev~~Va~~L~~~~~~~~~~~dI~~~I~~vt-~~~P~~~di~RV~~~L 85 (96)
T PF11829_consen 33 RRRLTDDEVAEVAAELAARGDPPVDRIDIGVAITRVT-DELPTPEDIERVRARL 85 (96)
T ss_dssp TTTS-HHHHHHHHHHHHHHTSS-BSCCHHHHHHHHHC-SS-S-HHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH-cCCcCHHHHHHHHHHH
Confidence 5778877754443 444333 25555666665553 3345566666555544
No 71
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=31.85 E-value=1.9e+02 Score=24.32 Aligned_cols=61 Identities=10% Similarity=0.250 Sum_probs=38.1
Q ss_pred cCCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHh
Q 039425 16 FAGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLI 85 (413)
Q Consensus 16 ~~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~ 85 (413)
.-..||+.++..+ .|+..|++..+|.+.|. ++...|.+..++.++........+ ++.+.+.
T Consensus 3 ~~~~Lt~rqreVL-~lr~~GlTq~EIAe~LG-------iS~~tVs~ie~ra~kkLr~~~~tl-~~~~~l~ 63 (141)
T PRK03975 3 MESFLTERQIEVL-RLRERGLTQQEIADILG-------TSRANVSSIEKRARENIEKARETL-AFAETLN 63 (141)
T ss_pred cccCCCHHHHHHH-HHHHcCCCHHHHHHHHC-------CCHHHHHHHHHHHHHHHHHHHHHH-HHHHHcC
Confidence 3457888887765 45789999999998874 345556666555554443333333 4444443
No 72
>PRK05473 hypothetical protein; Provisional
Probab=31.84 E-value=1.3e+02 Score=22.76 Aligned_cols=46 Identities=15% Similarity=0.156 Sum_probs=35.6
Q ss_pred HHHHHHHHhCCCCh-HHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 25 SNLLVDMSKNNVRP-KDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 25 ~~~i~~L~~~g~~~-~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
+..-..|.+.|..| .||.-+|..-.|..+++.++.+|..+++-|.+
T Consensus 25 ~~Vy~AL~EKGYNPinQiVGYllSGDPaYItsh~nAR~lIrkiERDE 71 (86)
T PRK05473 25 TTVYDALEEKGYNPINQIVGYLLSGDPAYIPRHNDARNLIRKLERDE 71 (86)
T ss_pred HHHHHHHHHcCCChHHHHHhhhccCCCCccCCcccHHHHHHHHhHHH
Confidence 33445677889877 58889998888888888899999888875544
No 73
>KOG0053 consensus Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]
Probab=31.76 E-value=4.5e+02 Score=26.37 Aligned_cols=101 Identities=9% Similarity=0.025 Sum_probs=53.6
Q ss_pred hhhHHHHHHHhhhhhhcCc------HHHHHHHHHHhhcCcEEEEeecCCCCceeeEEeeChhhHHHHhhCCCEEEeeccc
Q 039425 56 IRAIYNARRKYKVREQAGH------SQMQLLMSKLIEHKYIERHKSDVDTNCVEALFLAHPSAIESLQAFPRVLIMDCTY 129 (413)
Q Consensus 56 ~~di~n~~~~~~~~~~~~~------~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty 129 (413)
+.+-+++.++... ..++. ++++.+.+.++++...+|- +...+. ..-+.=-+...++.+.++-++++|.||
T Consensus 126 Y~gT~~~l~~~~~-~~gie~~~vd~~~~~~~~~~i~~~t~~V~~-ESPsNP--ll~v~DI~~l~~la~~~g~~vvVDnTf 201 (409)
T KOG0053|consen 126 YGGTLRILRKFLP-KFGGEGDFVDVDDLKKILKAIKENTKAVFL-ESPSNP--LLKVPDIEKLARLAHKYGFLVVVDNTF 201 (409)
T ss_pred cccHHHHHHHHHH-HhCceeeeechhhHHHHHHhhccCceEEEE-ECCCCC--ccccccHHHHHHHHhhCCCEEEEeCCc
Confidence 4445555555555 33322 2455566666663333322 222222 112222356777888888999999999
Q ss_pred ccc--CCCCce-e----eEEEeeccCcEEEEEEEeecc
Q 039425 130 QTN--RYDMPL-L----EIAGVTSIDLTFSVCCVYLKL 160 (413)
Q Consensus 130 ~tn--~~~~~l-~----~~~g~~~~g~~~~~~~~~~~~ 160 (413)
.+. ..-+++ . +-.-.--.|++-++|=+++.+
T Consensus 202 ~~p~~~~pL~lGADIV~hSaTKyi~Ghsdvi~G~iv~n 239 (409)
T KOG0053|consen 202 GSPYNQDPLPLGADIVVHSATKYIGGHSDVIGGSVVLN 239 (409)
T ss_pred CcccccChhhcCCCEEEEeeeeeecCCcceeeeEEecC
Confidence 975 233444 1 222223456776676666655
No 74
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=31.38 E-value=2.2e+02 Score=23.37 Aligned_cols=32 Identities=9% Similarity=0.185 Sum_probs=24.7
Q ss_pred CCCCCHHH---HHHHHHHHhCCCChHHHHHHHHhc
Q 039425 17 AGILNKEK---SNLLVDMSKNNVRPKDILHVLKKR 48 (413)
Q Consensus 17 ~rrlt~~~---~~~i~~L~~~g~~~~~I~~~l~~~ 48 (413)
+|.-++++ ...|..|.+.|++..+|...+...
T Consensus 37 yR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~~ 71 (131)
T TIGR02043 37 YRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIK 71 (131)
T ss_pred ceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 56666655 345778889999999999999864
No 75
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=30.29 E-value=1.6e+02 Score=25.96 Aligned_cols=46 Identities=9% Similarity=0.072 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 17 AGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
.+.||+.+ ..|..|...|.+.++|.+.|. ++.++|.+.++++.++.
T Consensus 131 ~~~LSpRE-rEVLrLLAqGkTnKEIAe~L~-------IS~rTVkth~srImkKL 176 (198)
T PRK15201 131 TRHFSVTE-RHLLKLIASGYHLSETAALLS-------LSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCCCHHH-HHHHHHHHCCCCHHHHHHHhC-------CCHHHHHHHHHHHHHHh
Confidence 46688777 467778889999999998763 56777888877776654
No 76
>PRK00118 putative DNA-binding protein; Validated
Probab=30.14 E-value=1.8e+02 Score=23.00 Aligned_cols=46 Identities=11% Similarity=0.213 Sum_probs=32.3
Q ss_pred CCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhh
Q 039425 17 AGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVR 69 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~ 69 (413)
-..|++.++..+.-....|.+..+|.+.+. ++...|++...+.++.
T Consensus 15 ~~~L~ekqRevl~L~y~eg~S~~EIAe~lG-------IS~~TV~r~L~RArkk 60 (104)
T PRK00118 15 GSLLTEKQRNYMELYYLDDYSLGEIAEEFN-------VSRQAVYDNIKRTEKL 60 (104)
T ss_pred hccCCHHHHHHHHHHHHcCCCHHHHHHHHC-------cCHHHHHHHHHHHHHH
Confidence 456788888888777889999999988762 3455555555544443
No 77
>PF03461 TRCF: TRCF domain; InterPro: IPR005118 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.; GO: 0003684 damaged DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 2QSR_A 2EYQ_A.
Probab=30.07 E-value=97 Score=24.23 Aligned_cols=39 Identities=15% Similarity=0.161 Sum_probs=27.3
Q ss_pred HHHHhhhhhccCCCHHHHHHHHHHHHHhhhhhHHHHHHH
Q 039425 234 TFISSWNLLILSASEEEFAQRLKGMETDFSKYLIALTYI 272 (413)
Q Consensus 234 ~~~~~~~~l~~a~t~~ef~~~~~~~~~~~~~~~~~~~Y~ 272 (413)
+=+..++++..+.|.++.++..+++.+.|+..|+-++.+
T Consensus 18 ~Rl~~Yrrl~~~~~~~el~~l~~El~DRFG~~P~ev~~L 56 (101)
T PF03461_consen 18 ERLELYRRLASAESEEELEDLREELIDRFGPLPEEVENL 56 (101)
T ss_dssp HHHHHHHHHHC--SHHHHHHHHHHHHHHH-S--HHHHHH
T ss_pred HHHHHHHHHhhCCCHHHHHHHHHHHHHHcCCCcHHHHHH
Confidence 345677888899999999999999999999877655444
No 78
>PHA02591 hypothetical protein; Provisional
Probab=30.06 E-value=73 Score=23.69 Aligned_cols=25 Identities=8% Similarity=0.246 Sum_probs=22.0
Q ss_pred CHHHHHHHHHHHhCCCChHHHHHHH
Q 039425 21 NKEKSNLLVDMSKNNVRPKDILHVL 45 (413)
Q Consensus 21 t~~~~~~i~~L~~~g~~~~~I~~~l 45 (413)
.++..+....|.+.|++..+|.+.|
T Consensus 45 ~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 45 EDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred cchHHHHHHHHHHcCCCHHHHHHHh
Confidence 4677888999999999999999876
No 79
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=28.90 E-value=35 Score=29.82 Aligned_cols=31 Identities=23% Similarity=0.433 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcC
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
+||.+|++.+..|+.+|++..+|+..|....
T Consensus 4 ~l~~~QieLLqrL~~SG~TK~~ii~ALe~l~ 34 (180)
T PF04814_consen 4 KLTIEQIELLQRLRRSGMTKEEIIHALETLD 34 (180)
T ss_dssp HHHHHHHHHHHHHHHCT--HHHHHHHHTT--
T ss_pred cccHHHHHHHHHHHHcCCCHHHHHHHHhccC
Confidence 5788999999999999999999999999876
No 80
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=28.71 E-value=1.3e+02 Score=26.64 Aligned_cols=46 Identities=13% Similarity=0.195 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 17 AGILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
...||+-++ .|..|...|.+.++|.+.|. ++.++|.+.++++.++.
T Consensus 148 ~~~Lt~rE~-evl~~~~~G~s~~eIA~~l~-------iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 148 DKRLSPKES-EVLRLFAEGFLVTEIAKKLN-------RSIKTISSQKKSAMMKL 193 (216)
T ss_pred cccCCHHHH-HHHHHHHCCCCHHHHHHHHC-------CCHHHHHHHHHHHHHHc
Confidence 356988885 67777889999999998774 56677777777766653
No 81
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=28.16 E-value=3e+02 Score=23.43 Aligned_cols=70 Identities=4% Similarity=-0.036 Sum_probs=39.2
Q ss_pred cCCCCCHHHH---HHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHh
Q 039425 16 FAGILNKEKS---NLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLI 85 (413)
Q Consensus 16 ~~rrlt~~~~---~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~ 85 (413)
-+|+-++++. ..|..|.+.|++-.+|.+.+.....+...+..++..+......+.......++.+.+.|.
T Consensus 45 g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~~~~~~~~~~~~~~~ll~~k~~~l~~~I~~L~~~~~~L~ 117 (154)
T PRK15002 45 NQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELD 117 (154)
T ss_pred CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466666653 447788899999999999997643232233444444433322222222234555555554
No 82
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.02 E-value=3.4e+02 Score=21.94 Aligned_cols=34 Identities=9% Similarity=0.162 Sum_probs=27.1
Q ss_pred cCCCCCHHHHH---HHHHHHhCCCChHHHHHHHHhcC
Q 039425 16 FAGILNKEKSN---LLVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 16 ~~rrlt~~~~~---~i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
-+|.-++++.. .|..|.+.|++..+|...+....
T Consensus 35 gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (127)
T cd04784 35 NYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQD 71 (127)
T ss_pred CCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhh
Confidence 36777777754 68888999999999999997543
No 83
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=26.55 E-value=2.5e+02 Score=23.65 Aligned_cols=45 Identities=13% Similarity=0.258 Sum_probs=33.1
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
..||+.+++. ..|...|.+.++|.+.+ .++.+.|.+.+++++++.
T Consensus 148 ~~lt~~e~~v-l~l~~~g~~~~~Ia~~l-------~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 148 PLLTPRERQI-LKLITEGYTNRDIAEQL-------SISIKTVETHRLNMMRKL 192 (211)
T ss_pred cCCCHHHHHH-HHHHHCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHh
Confidence 4577776554 55567899999999775 257788888888877775
No 84
>PRK09483 response regulator; Provisional
Probab=26.40 E-value=1.5e+02 Score=25.67 Aligned_cols=45 Identities=11% Similarity=0.159 Sum_probs=34.7
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
..||+.+++.+ .|...|.+.++|.+.|. ++.+.|.+.+++++++.
T Consensus 147 ~~Lt~rE~~vl-~~~~~G~~~~~Ia~~l~-------is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIM-LMITKGQKVNEISEQLN-------LSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHH-HHHHCCCCHHHHHHHhC-------CCHHHHHHHHHHHHHHc
Confidence 45888887665 67789999999997762 56778888888877765
No 85
>PRK07708 hypothetical protein; Validated
Probab=26.36 E-value=4.9e+02 Score=23.56 Aligned_cols=121 Identities=7% Similarity=0.004 Sum_probs=60.8
Q ss_pred HHHHHHHHhhcCcEEEEeecCCCCceeeEEeeChhhHHHHhhCCC-----EEEeeccccccCCCCceeeEEEeeccCc-E
Q 039425 77 MQLLMSKLIEHKYIERHKSDVDTNCVEALFLAHPSAIESLQAFPR-----VLIMDCTYQTNRYDMPLLEIAGVTSIDL-T 150 (413)
Q Consensus 77 ~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~-----vl~iD~Ty~tn~~~~~l~~~~g~~~~g~-~ 150 (413)
.-.+.+.++..|...--.-.|+++ ..|..+++.++...-.+ ++++||.|..|..+.-. -++-.+..|. .
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~d~~~----~~~~~k~~~~~~~~~~~ep~~~~vY~DGs~~~n~g~aG~-GvVI~~~~g~~~ 103 (219)
T PRK07708 29 ALQLAEDFEKTGRVKELEFYDEMD----TEWSLKELKKLSKEVEEEPHEILVYFDGGFDKETKLAGL-GIVIYYKQGNKR 103 (219)
T ss_pred HHHHHHHHhhcCCceeEEEecCCC----CEeeHHHHhhhhhhhccCCCcEEEEEeeccCCCCCCcEE-EEEEEECCCCEE
Confidence 344556666666421111124433 67888888888765542 89999999766543322 2222233332 2
Q ss_pred EEEE----EEeecccccchHHHHHHHHHHHHh-cccc-ceEEEeccchHHHHHHHHhCC
Q 039425 151 FSVC----CVYLKLKWENNYIWALERLKSIME-ENML-ASVIVTDRELALMTVIQKHFP 203 (413)
Q Consensus 151 ~~~~----~~~~~~E~~~~~~~~l~~l~~~~~-~~~~-p~~iitD~~~al~~Ai~~vfP 203 (413)
+.+. +....+.+..-|.-++..+..... +... +..|.+| ...+.+++...|+
T Consensus 104 ~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D-SqlVi~qi~g~wk 161 (219)
T PRK07708 104 YRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD-SQVVLNQLAGEWP 161 (219)
T ss_pred EEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec-cHHHHHHhCCCce
Confidence 2221 111123344456666666655542 2222 3345554 4455566665553
No 86
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=26.33 E-value=1.5e+02 Score=26.60 Aligned_cols=45 Identities=11% Similarity=0.136 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
..||+-++ .|..|...|.+.++|.+.|. ++.++|.+.++++.++.
T Consensus 133 ~~LT~RE~-eVL~ll~~G~snkeIA~~L~-------iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 133 RMLSPTER-EILRFMSRGYSMPQIAEQLE-------RNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCCCHHHH-HHHHHHHCCCCHHHHHHHHC-------CCHHHHHHHHHHHHHHc
Confidence 45888885 57777778999999998863 56777877777776653
No 87
>smart00526 H15 Domain in histone families 1 and 5.
Probab=26.16 E-value=1.9e+02 Score=20.32 Aligned_cols=34 Identities=3% Similarity=0.014 Sum_probs=28.0
Q ss_pred CCCCCHHHHHHHHHHHh-CCCChHHHHHHHHhcCC
Q 039425 17 AGILNKEKSNLLVDMSK-NNVRPKDILHVLKKRNM 50 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~-~g~~~~~I~~~l~~~~~ 50 (413)
|....+...+.|..|-+ .|.+...|..+|...++
T Consensus 4 hP~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~ 38 (66)
T smart00526 4 HPPYSEMITEAISALKERKGSSLQAIKKYIEANYK 38 (66)
T ss_pred CCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence 33556678888999988 69999999999999863
No 88
>smart00188 IL10 Interleukin-10 family. Interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells.
Probab=26.13 E-value=3.1e+02 Score=22.89 Aligned_cols=42 Identities=21% Similarity=0.026 Sum_probs=23.8
Q ss_pred cccchHHHHHHHHHHHHhccccceEEEeccchHHHHHH----HHhCCccccccc
Q 039425 161 KWENNYIWALERLKSIMEENMLASVIVTDRELALMTVI----QKHFPSATTFLC 210 (413)
Q Consensus 161 E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al~~Ai----~~vfP~a~~~lC 210 (413)
++.....++++.+.+.+. . .+++.++.+-+ .+|||.|.+..|
T Consensus 22 kD~~~~vll~~~ll~~~k---~-----~~gC~~l~ell~FYLd~V~p~a~~~~~ 67 (137)
T smart00188 22 KDQLDNILLTESLLEDFK---G-----YLGCQALSEMIQFYLEEVMPQAENHGP 67 (137)
T ss_pred cchHhhHhhhHHHHHHhC---C-----CcchHHHHHHHHHHHHHHHHHHhcCCc
Confidence 333344466665555541 1 25666665554 479999976443
No 89
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.06 E-value=3.3e+02 Score=21.48 Aligned_cols=34 Identities=15% Similarity=0.108 Sum_probs=26.2
Q ss_pred cCCCCCHHHHH---HHHHHHhCCCChHHHHHHHHhcC
Q 039425 16 FAGILNKEKSN---LLVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 16 ~~rrlt~~~~~---~i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
-+|.-++++.. .|..|.+.|++..+|...+....
T Consensus 35 gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (113)
T cd01109 35 GIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRR 71 (113)
T ss_pred CCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHc
Confidence 35777776644 46788889999999999998654
No 90
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=25.54 E-value=1.3e+02 Score=19.10 Aligned_cols=31 Identities=19% Similarity=0.195 Sum_probs=17.6
Q ss_pred ccccCCCCCHHHHHHHHHHHhCCCChHHHHHHH
Q 039425 13 GHSFAGILNKEKSNLLVDMSKNNVRPKDILHVL 45 (413)
Q Consensus 13 ~hp~~rrlt~~~~~~i~~L~~~g~~~~~I~~~l 45 (413)
.|..+.--|+++|..+.... |++.+||-+-+
T Consensus 4 ~h~~nPYPs~~ek~~L~~~t--gls~~Qi~~WF 34 (40)
T PF05920_consen 4 EHLHNPYPSKEEKEELAKQT--GLSRKQISNWF 34 (40)
T ss_dssp HTTTSGS--HHHHHHHHHHH--TS-HHHHHHHH
T ss_pred HHCCCCCCCHHHHHHHHHHc--CCCHHHHHHHH
Confidence 45555556777777776554 77777766544
No 91
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.28 E-value=3.4e+02 Score=21.43 Aligned_cols=34 Identities=6% Similarity=-0.060 Sum_probs=26.0
Q ss_pred cCCCCCHHH---HHHHHHHHhCCCChHHHHHHHHhcC
Q 039425 16 FAGILNKEK---SNLLVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 16 ~~rrlt~~~---~~~i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
-+|.-++++ ...|..|.+.|++..+|.+.+....
T Consensus 34 g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~~~ 70 (112)
T cd01282 34 GYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLR 70 (112)
T ss_pred CCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 456666665 4457788889999999999988643
No 92
>PRK10403 transcriptional regulator NarP; Provisional
Probab=24.95 E-value=2.4e+02 Score=24.01 Aligned_cols=58 Identities=14% Similarity=0.133 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhhhcCcHHHHHHHHHHh
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVREQAGHSQMQLLMSKLI 85 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~ 85 (413)
.||+.+.+ |..+...|++.++|.+.|. ++.+.|++.+.+++++. +-.+..+...-.+.
T Consensus 153 ~Lt~~e~~-vl~~~~~g~s~~~ia~~l~-------~s~~tv~~~~~~i~~kl-~~~~~~~~~~~~~~ 210 (215)
T PRK10403 153 VLTERELD-VLHELAQGLSNKQIASVLN-------ISEQTVKVHIRNLLRKL-NVRSRVAATILFLQ 210 (215)
T ss_pred cCCHHHHH-HHHHHHCCCCHHHHHHHcC-------CCHHHHHHHHHHHHHHc-CCCCHHHHHHHHHH
Confidence 47877765 5556778999999988872 56788888888777664 33444444444343
No 93
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.90 E-value=3.8e+02 Score=21.72 Aligned_cols=33 Identities=6% Similarity=-0.004 Sum_probs=25.3
Q ss_pred cCCCCCHHHH---HHHHHHHhCCCChHHHHHHHHhc
Q 039425 16 FAGILNKEKS---NLLVDMSKNNVRPKDILHVLKKR 48 (413)
Q Consensus 16 ~~rrlt~~~~---~~i~~L~~~g~~~~~I~~~l~~~ 48 (413)
-+|.-++++. ..|..|...|++..+|...+...
T Consensus 35 g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04785 35 GYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALS 70 (126)
T ss_pred CccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhh
Confidence 4566676654 44778888999999999999754
No 94
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=24.90 E-value=1.9e+02 Score=21.89 Aligned_cols=35 Identities=3% Similarity=0.015 Sum_probs=28.8
Q ss_pred CCCCCHHHHHHHHHHHh-CCCChHHHHHHHHhcCCC
Q 039425 17 AGILNKEKSNLLVDMSK-NNVRPKDILHVLKKRNMH 51 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~-~g~~~~~I~~~l~~~~~~ 51 (413)
|....+...+.|..|-+ .|.|...|..+|...++.
T Consensus 4 hP~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~ 39 (88)
T cd00073 4 HPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKV 39 (88)
T ss_pred CCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCc
Confidence 44556777888888888 699999999999999854
No 95
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=24.84 E-value=1.6e+02 Score=30.92 Aligned_cols=64 Identities=16% Similarity=0.111 Sum_probs=41.7
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhc-----cccceEEEeccchHHHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEE-----NMLASVIVTDRELALMT 196 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~-----~~~p~~iitD~~~al~~ 196 (413)
|++.|+...++.|+.- .+- ..+..+.|.-+-+.+.+.+.. ...|..|+.|+-.+..+
T Consensus 382 Vvf~~G~~~k~~YR~f--~i~----------------~~~~~dD~~~m~Evl~RR~~r~~~~~~~~PDLiliDGGkgQl~ 443 (567)
T PRK14667 382 VVWEDGSMNKKEYRRY--KIK----------------TVDGIDDYASLREVLTRRARRYKEGENPMPDLWLIDGGKGQLS 443 (567)
T ss_pred EEEECCccChhhCCee--ecC----------------CCCCCCHHHHHHHHHHHHhhhccccCCCCCCEEEEeCCHHHHH
Confidence 6777777777766631 111 111235666666666655521 13699999999999999
Q ss_pred HHHHhCC
Q 039425 197 VIQKHFP 203 (413)
Q Consensus 197 Ai~~vfP 203 (413)
|+.+++-
T Consensus 444 aa~~~l~ 450 (567)
T PRK14667 444 VGIEVRD 450 (567)
T ss_pred HHHHHHH
Confidence 9999884
No 96
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=24.49 E-value=2.5e+02 Score=23.48 Aligned_cols=44 Identities=16% Similarity=0.264 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhhh
Q 039425 19 ILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVRE 70 (413)
Q Consensus 19 rlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~~ 70 (413)
-||+.++.. ..|...|++..+|.+.+. .+...|.+..++.+++.
T Consensus 6 ~Lte~qr~V-L~Lr~~GlTq~EIAe~Lg-------iS~stV~~~e~ra~kkL 49 (137)
T TIGR00721 6 FLTERQIKV-LELREKGLSQKEIAKELK-------TTRANVSAIEKRAMENI 49 (137)
T ss_pred CCCHHHHHH-HHHHHcCCCHHHHHHHHC-------cCHHHHHHHHHhHHHHH
Confidence 467667554 455789999999998875 45666666666555544
No 97
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=24.12 E-value=3.4e+02 Score=20.97 Aligned_cols=32 Identities=16% Similarity=0.189 Sum_probs=24.9
Q ss_pred CCCCCHHHHHH---HHHHHhCCCChHHHHHHHHhc
Q 039425 17 AGILNKEKSNL---LVDMSKNNVRPKDILHVLKKR 48 (413)
Q Consensus 17 ~rrlt~~~~~~---i~~L~~~g~~~~~I~~~l~~~ 48 (413)
+|.-++++... |..|...|++..+|...+...
T Consensus 36 ~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 36 YRLYTEEDLERLQQILFLKELGFSLKEIKELLKDP 70 (103)
T ss_pred ceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 56677766544 578888999999999998754
No 98
>PRK14994 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional
Probab=23.71 E-value=2.5e+02 Score=26.65 Aligned_cols=43 Identities=12% Similarity=0.108 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHh
Q 039425 20 LNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKY 66 (413)
Q Consensus 20 lt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~ 66 (413)
++++....+. +...|++++++...+.+.+ + .+.+++|+.....
T Consensus 242 ~~~~~~~~~~-~~~~~~~~k~a~~~~a~~~-~--~~k~~~Y~~~~~~ 284 (287)
T PRK14994 242 LPADALRTLA-LLQAELPLKKAAALAAEIH-G--VKKNALYKYALEQ 284 (287)
T ss_pred cchhHHHHHH-HHHcCCCHHHHHHHHHHHH-C--cCHHHHHHHHHHh
Confidence 3334333333 6667999999999999997 3 6789999876643
No 99
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=23.62 E-value=1.1e+02 Score=21.86 Aligned_cols=44 Identities=14% Similarity=0.150 Sum_probs=30.4
Q ss_pred CCCCCHHHHHHHHHHH-hCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhh
Q 039425 17 AGILNKEKSNLLVDMS-KNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYK 67 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~-~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~ 67 (413)
.++-|+++|..|..++ ..|.+..+|.... | ++...++|.+++++
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~-----g--i~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREY-----G--ISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHH-----T--S-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeeccc-----c--cccccccHHHHHHh
Confidence 4677899998888888 6787777766543 3 57899999999886
No 100
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=23.61 E-value=33 Score=23.38 Aligned_cols=22 Identities=14% Similarity=0.318 Sum_probs=15.6
Q ss_pred CceeccccccCch-----HHHHHHHHH
Q 039425 351 GCIIRHTHGLPRA-----PEITEYKRE 372 (413)
Q Consensus 351 sc~~~~~~GlPC~-----H~l~~~~~~ 372 (413)
.|.+...+|+||. +++..+++.
T Consensus 1 ~C~~~~ltG~~CPgCG~tRa~~~ll~g 27 (52)
T PF10825_consen 1 PCPFKALTGIPCPGCGMTRAFIALLHG 27 (52)
T ss_pred CCcchhhhCCCCCCCcHHHHHHHHHCC
Confidence 4889999999995 455554443
No 101
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=23.54 E-value=1.6e+02 Score=23.56 Aligned_cols=26 Identities=12% Similarity=0.340 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHhcC
Q 039425 24 KSNLLVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 24 ~~~~i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
....|.+..++|++|.+..+.|-++|
T Consensus 45 de~vI~~hidaGIs~~~AVN~LVeKY 70 (114)
T PF06755_consen 45 DETVIQEHIDAGISPADAVNFLVEKY 70 (114)
T ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45789999999999999999999876
No 102
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=23.36 E-value=1.5e+02 Score=19.48 Aligned_cols=41 Identities=7% Similarity=0.053 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHH
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRK 65 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~ 65 (413)
..|++.++..|...+-.|.+-.+|.+.+. ++...|++...+
T Consensus 3 ~~L~~~er~vi~~~y~~~~t~~eIa~~lg-------~s~~~V~~~~~~ 43 (50)
T PF04545_consen 3 DQLPPREREVIRLRYFEGLTLEEIAERLG-------ISRSTVRRILKR 43 (50)
T ss_dssp CTS-HHHHHHHHHHHTST-SHHHHHHHHT-------SCHHHHHHHHHH
T ss_pred hhCCHHHHHHHHHHhcCCCCHHHHHHHHC-------CcHHHHHHHHHH
Confidence 36899999999999989999999887763 344455554443
No 103
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=23.20 E-value=3.5e+02 Score=22.43 Aligned_cols=32 Identities=9% Similarity=0.155 Sum_probs=24.9
Q ss_pred CCCCCHHHH---HHHHHHHhCCCChHHHHHHHHhc
Q 039425 17 AGILNKEKS---NLLVDMSKNNVRPKDILHVLKKR 48 (413)
Q Consensus 17 ~rrlt~~~~---~~i~~L~~~g~~~~~I~~~l~~~ 48 (413)
+|.-++++. ..|..|.+.|++..+|...+...
T Consensus 37 yR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 71 (140)
T PRK09514 37 YRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIR 71 (140)
T ss_pred CeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 566676654 44678888999999999999754
No 104
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=23.10 E-value=4.1e+02 Score=21.52 Aligned_cols=47 Identities=6% Similarity=0.010 Sum_probs=30.1
Q ss_pred CCCCCHHHH---HHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHH
Q 039425 17 AGILNKEKS---NLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARR 64 (413)
Q Consensus 17 ~rrlt~~~~---~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~ 64 (413)
+|.-++++. ..|..|...|++-.+|...+.....+. .+..++.....
T Consensus 36 ~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~-~~~~~~~~~l~ 85 (127)
T cd01108 36 YRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPS-RASADVKALAL 85 (127)
T ss_pred ceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCC-CCHHHHHHHHH
Confidence 566666654 447788889999999999997543222 23444444433
No 105
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=22.80 E-value=2e+02 Score=29.93 Aligned_cols=67 Identities=13% Similarity=0.122 Sum_probs=43.6
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhc---c--ccceEEEeccchHHHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEE---N--MLASVIVTDRELALMT 196 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~---~--~~p~~iitD~~~al~~ 196 (413)
|++.||...++.|+-- .+-+ .+..+.|.-+-+.+.+.+.. . ..|..|+.|+-++..+
T Consensus 387 Vvf~~G~p~k~~YR~f--~Ik~----------------~~~~dDy~~m~Evl~RR~~r~~~~~~~~PDLilIDGGkgQl~ 448 (519)
T PRK12306 387 VQFRNGKPDKKNYRRF--KIKT----------------VEGIDDFASIAEVVRRRYSRLLEENSELPDLIVIDGGKGQLS 448 (519)
T ss_pred EEEeCCccChhhcCee--ecCC----------------CCCCCHHHHHHHHHHHHHhhcccccCCCCCEEEEeCCHHHHH
Confidence 6778888877777631 1111 11235666655556555521 1 3699999999999999
Q ss_pred HHHHhCCccc
Q 039425 197 VIQKHFPSAT 206 (413)
Q Consensus 197 Ai~~vfP~a~ 206 (413)
|..+++-+..
T Consensus 449 aa~~~l~elg 458 (519)
T PRK12306 449 SAFKELRKLG 458 (519)
T ss_pred HHHHHHHHcC
Confidence 9999884443
No 106
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=22.74 E-value=1.9e+02 Score=19.74 Aligned_cols=32 Identities=19% Similarity=0.188 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHH
Q 039425 26 NLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNAR 63 (413)
Q Consensus 26 ~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~ 63 (413)
..|..+.+.|.++.+|++. +|. ++..||+.+.
T Consensus 22 ~~i~~~~~~G~s~eeI~~~----yp~--Lt~~~i~aAl 53 (56)
T PF04255_consen 22 RDILDLLAAGESPEEIAED----YPS--LTLEDIRAAL 53 (56)
T ss_dssp HHHHHHHHTT--HHHHHHH----STT----HHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHH----CCC--CCHHHHHHHH
Confidence 4566666999999998765 655 6778887654
No 107
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=22.72 E-value=2e+02 Score=30.69 Aligned_cols=64 Identities=11% Similarity=0.123 Sum_probs=42.6
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhc---c--ccceEEEeccchHHHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEE---N--MLASVIVTDRELALMT 196 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~---~--~~p~~iitD~~~al~~ 196 (413)
|++.||...++.|+-- .+ -..+..+.|.-+-+.+.+.+.. . ..|..|+.|+-++..+
T Consensus 417 Vvf~~G~~~k~~YRkf--~I----------------k~~~~~DDya~M~Evl~RR~~r~~~~~~~~PDLilIDGGkgQl~ 478 (624)
T PRK14669 417 VVWEDGKMKKSDYRKF--II----------------KTVVGVDDFASMREVVTRRYSRLQEEKQPMPGLVLIDGGLGQLH 478 (624)
T ss_pred EEEECCccChhhCCee--ec----------------CCCCCCCHHHHHHHHHHHHhhccccccCCCCCEEEEeCCHHHHH
Confidence 6778888887777631 11 1111235666666666665521 1 3699999999999999
Q ss_pred HHHHhCC
Q 039425 197 VIQKHFP 203 (413)
Q Consensus 197 Ai~~vfP 203 (413)
|..+++-
T Consensus 479 aa~~vl~ 485 (624)
T PRK14669 479 AAAEALE 485 (624)
T ss_pred HHHHHHH
Confidence 9999884
No 108
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=22.64 E-value=1.3e+02 Score=23.60 Aligned_cols=28 Identities=21% Similarity=0.128 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHhCCCChHHHHHHHHhcC
Q 039425 22 KEKSNLLVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 22 ~~~~~~i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
+|......+|.++|+++......++++|
T Consensus 69 ~Ef~~~~~eM~dAGV~~~~~~~~l~~~Y 96 (100)
T PF15652_consen 69 EEFNNSYREMFDAGVSKECRKKALKAQY 96 (100)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4556667788889999999888888865
No 109
>PF03852 Vsr: DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine []. GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine []. The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology []. ; GO: 0004519 endonuclease activity, 0006298 mismatch repair; PDB: 1ODG_A 1VSR_A 1CW0_A.
Probab=22.49 E-value=3.3e+02 Score=20.19 Aligned_cols=62 Identities=8% Similarity=0.029 Sum_probs=29.0
Q ss_pred chhhHHHHHHHhhhhhhcCcHHHHHHHHHHhhcCcEEEEee-cCCCCceeeEEeeChhhHHHHhhCCCEEEeecccc
Q 039425 55 TIRAIYNARRKYKVREQAGHSQMQLLMSKLIEHKYIERHKS-DVDTNCVEALFLAHPSAIESLQAFPRVLIMDCTYQ 130 (413)
Q Consensus 55 t~~di~n~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~vl~iD~Ty~ 130 (413)
+..+-+...++++.+. -.+-..+.+.|-..|+-| ... .+-.|+..-+| ..+.-+||+||.|=
T Consensus 5 t~~~RS~~M~~ir~k~---TkpE~~lr~~L~~~G~Ry-R~~~~~lpG~PDiv~----------~~~k~aIFVdGCFW 67 (75)
T PF03852_consen 5 TPEQRSKNMSRIRSKD---TKPELALRRALHALGLRY-RLNRKDLPGKPDIVF----------PKYKIAIFVDGCFW 67 (75)
T ss_dssp -HHHHHHHHHT--SSS----HHHHHHHHHHHHTT--E-EES-TTSTT--SEEE----------GGGTEEEEEE-TTT
T ss_pred CHHHHHHHHhhccCCC---ChHHHHHHHHHHhcCCEE-EEccCcCCCCCCEEE----------CCCCEEEEEeccee
Confidence 4444444455555443 224455667777777653 322 22234443343 35566899999874
No 110
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=22.45 E-value=1.9e+02 Score=30.66 Aligned_cols=67 Identities=15% Similarity=0.145 Sum_probs=44.8
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhc-----cccceEEEeccchHHHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEE-----NMLASVIVTDRELALMT 196 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~-----~~~p~~iitD~~~al~~ 196 (413)
|++.||...++.|+.- .+- ..+..+.|.-+-+.+.+.+.. ...|..|+.|+-++..+
T Consensus 404 Vvf~~G~~~k~~YR~f--~i~----------------~~~~~dDya~m~Evl~RR~~~~~~~~~~~PDLiliDGGkgQl~ 465 (598)
T PRK00558 404 VVFEDGGPDKSEYRRY--NIK----------------GVTGGDDYAAMREVLTRRYSRLLKEFGPLPDLILIDGGKGQLN 465 (598)
T ss_pred EEEECCccChhhCCee--ecC----------------CCCCCCHHHHHHHHHHHHhhccccccCCCCCEEEEeCCHHHHH
Confidence 6777888777777631 111 112246676666666666522 24699999999999999
Q ss_pred HHHHhCCccc
Q 039425 197 VIQKHFPSAT 206 (413)
Q Consensus 197 Ai~~vfP~a~ 206 (413)
|..+++-...
T Consensus 466 ~a~~~l~~lg 475 (598)
T PRK00558 466 AAKEVLEELG 475 (598)
T ss_pred HHHHHHHHCC
Confidence 9999885443
No 111
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=22.27 E-value=1.4e+02 Score=24.63 Aligned_cols=33 Identities=15% Similarity=0.225 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCC
Q 039425 20 LNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHN 52 (413)
Q Consensus 20 lt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~ 52 (413)
|+.+.++.|..+..++-.-..+++.|.+.||..
T Consensus 38 L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~ 70 (145)
T PF03564_consen 38 LKGEAKELIRGLPLSEENYEEAWELLEERYGNP 70 (145)
T ss_pred hcchHHHHHHcccccchhhHHHHHHHHHHhCCc
Confidence 445555666666656666677777888887654
No 112
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=21.96 E-value=2.1e+02 Score=30.75 Aligned_cols=67 Identities=10% Similarity=0.172 Sum_probs=44.2
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhc----cccceEEEeccchHHHHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEE----NMLASVIVTDRELALMTV 197 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~----~~~p~~iitD~~~al~~A 197 (413)
|+|.|+-..++.|+. |.+-++ ....+.|.-+-+.+.+.+.. ...|..|+.|+-.+..+|
T Consensus 475 Vvf~~G~p~k~~YR~--f~ik~~---------------~~~~DD~asM~Evl~RR~~r~~~~~~~PDLilIDGGkgQl~a 537 (691)
T PRK14672 475 ICFKNGAPDTKNYRL--FNLRAH---------------DTRIDDFASMREAIARRYTHTPEGYTLPDLILVDGGIGHVSA 537 (691)
T ss_pred EEEECCccChhhCCe--eeccCC---------------CCCCchHHHHHHHHHHHhhcccccCCCCCEEEEeCCHHHHHH
Confidence 677788877777763 111111 01136666666666666522 247999999999999999
Q ss_pred HHHhCCcc
Q 039425 198 IQKHFPSA 205 (413)
Q Consensus 198 i~~vfP~a 205 (413)
..+++-..
T Consensus 538 a~~vl~el 545 (691)
T PRK14672 538 AQHVLDAL 545 (691)
T ss_pred HHHHHHHc
Confidence 99998443
No 113
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=21.87 E-value=1.9e+02 Score=24.82 Aligned_cols=67 Identities=7% Similarity=0.006 Sum_probs=45.7
Q ss_pred EeeChhhHHHHhhCCCEEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHH
Q 039425 106 FLAHPSAIESLQAFPRVLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIM 177 (413)
Q Consensus 106 ~~~~~~~~~~~~~~~~vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~ 177 (413)
.|.......++++|+++++-+.|= .+..-....+++|++++|..+ .+.+.|..-+-+--|+.|...+
T Consensus 95 ~~t~e~~~~LL~~yGPLwv~~~~P-~~~~~~H~~ViTGI~~dg~~i----~~~DP~~gP~~~m~l~~fn~~~ 161 (166)
T PF12385_consen 95 SYTAEGLANLLREYGPLWVAWEAP-GDSWVAHASVITGIDGDGDSI----HVHDPEQGPNLRMSLDMFNQAL 161 (166)
T ss_pred ccCHHHHHHHHHHcCCeEEEecCC-CCcceeeEEEEEeecCCCCeE----EecCcccCCCceecHHHHhhhh
Confidence 466677888999999988875443 122223788899999999654 3567776666666666665554
No 114
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=21.68 E-value=2.1e+02 Score=30.18 Aligned_cols=64 Identities=16% Similarity=0.162 Sum_probs=42.1
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHh---cc---ccceEEEeccchHHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIME---EN---MLASVIVTDRELALM 195 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~---~~---~~p~~iitD~~~al~ 195 (413)
|++.|+-+.++.|+-- .+- ..+..+.|.-+-+.+.+.+. .. ..|..|+.|+-++..
T Consensus 402 Vvf~~G~~~k~~YR~f--~i~----------------~~~~~dDya~m~Evl~RR~~r~~~~~~~~~PDLiliDGGkgQl 463 (574)
T TIGR00194 402 VVFEDGKPLKASYRRY--NIN----------------SITGGDDYAAMREVLRRRYSSIQKKNNLPLPDLILIDGGKGQL 463 (574)
T ss_pred EEEeCCccChhhCCee--ecC----------------CCCCCCHHHHHHHHHHHHHhhhccccCCCCCCEEEEeCCHHHH
Confidence 7788888888877631 111 11123556555555555542 11 479999999999999
Q ss_pred HHHHHhCC
Q 039425 196 TVIQKHFP 203 (413)
Q Consensus 196 ~Ai~~vfP 203 (413)
+|..+++-
T Consensus 464 ~aa~~~l~ 471 (574)
T TIGR00194 464 NAALEVLK 471 (574)
T ss_pred HHHHHHHH
Confidence 99999874
No 115
>PF02171 Piwi: Piwi domain; InterPro: IPR003165 This domain is found in the stem cell self-renewal protein Piwi and its relatives in Drosophila melanogaster []. It has been found in the C-terminal of a number of proteins which also contain the PAZ domain (IPR003100 from INTERPRO) in their central region, for example the Argonaute proteins. Several of these proteins have been implicated in the development and maintenance of stem cells through the RNA-mediated gene-quelling mechanisms associated with the protein DICER. ; GO: 0005515 protein binding; PDB: 4F1N_B 3LUH_B 4EI1_A 3QX8_A 3LUC_C 3LUJ_B 3LUD_B 3QX9_A 3LUG_B 3LUK_B ....
Probab=21.68 E-value=4.1e+02 Score=24.93 Aligned_cols=70 Identities=10% Similarity=0.108 Sum_probs=34.3
Q ss_pred EEEeeccccccCC-CCc-eeeEEEe-eccCcEEEEEEEeecc--cccchHHHHHHHHHHHH-h-ccc-cceEEEeccc
Q 039425 122 VLIMDCTYQTNRY-DMP-LLEIAGV-TSIDLTFSVCCVYLKL--KWENNYIWALERLKSIM-E-ENM-LASVIVTDRE 191 (413)
Q Consensus 122 vl~iD~Ty~tn~~-~~~-l~~~~g~-~~~g~~~~~~~~~~~~--E~~~~~~~~l~~l~~~~-~-~~~-~p~~iitD~~ 191 (413)
++.+|.++..... +.| +..+++. |.++..+.-.+.+... |..+.+..++....+.+ . ... .|.-||.=+|
T Consensus 79 iIGidv~h~~~~~~~~~sv~g~~~s~~~~~~~~~~~~~~~~~~~e~~~~l~~~~~~~L~~~~~~~~~~~P~~IiiyRd 156 (302)
T PF02171_consen 79 IIGIDVSHPSPGSDKNPSVVGFVASFDSDGSKYFSSVRFQDSGQEIIDNLEEIIKEALKEFKKNNGKWLPERIIIYRD 156 (302)
T ss_dssp EEEEEEEEESSTCTCSCEEEEEEEEESTTTCEEEEEEEEECTTCCCHHHHHHHHHHHHHHHHHTTTT-TTSEEEEEEE
T ss_pred EEEEEEEecCcccCCcceeeEEEEeccCccccccceeEEeccchhhhcchhhHHHHHHHHHHHHcCCCCCceEEEEEc
Confidence 7889999887776 333 3333333 4455555544444432 22233333333333322 1 233 6766665443
No 116
>KOG1720 consensus Protein tyrosine phosphatase CDC14 [Defense mechanisms]
Probab=21.66 E-value=1e+02 Score=27.69 Aligned_cols=34 Identities=6% Similarity=-0.112 Sum_probs=28.4
Q ss_pred HHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHH
Q 039425 30 DMSKNNVRPKDILHVLKKRNMHNATTIRAIYNAR 63 (413)
Q Consensus 30 ~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~ 63 (413)
-|+.-|++|.+.++.|+...||.+.+++|.+-..
T Consensus 169 lmy~~g~ta~eaI~~lR~~RpG~V~gpqQ~~l~~ 202 (225)
T KOG1720|consen 169 LMYEYGMTAGEAIAWLRICRPGAVIGPQQHKLLH 202 (225)
T ss_pred HHHHhCCCHHHHHHHHHhcCCccccCHHHHHHHH
Confidence 4555799999999999999999998888876443
No 117
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.54 E-value=4.3e+02 Score=21.13 Aligned_cols=34 Identities=9% Similarity=0.060 Sum_probs=26.7
Q ss_pred cCCCCCHHHHH---HHHHHHhCCCChHHHHHHHHhcC
Q 039425 16 FAGILNKEKSN---LLVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 16 ~~rrlt~~~~~---~i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
-+|.-++++.. .|..|.+.|++..+|...+....
T Consensus 35 gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~ 71 (123)
T cd04770 35 GYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRD 71 (123)
T ss_pred CCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhh
Confidence 46777766544 57788889999999999998754
No 118
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=21.45 E-value=2.1e+02 Score=30.45 Aligned_cols=67 Identities=15% Similarity=0.116 Sum_probs=44.6
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEEeecccccchHHHHHHHHHHHHhc-----cccceEEEeccchHHHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEE-----NMLASVIVTDRELALMT 196 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~~~E~~~~~~~~l~~l~~~~~~-----~~~p~~iitD~~~al~~ 196 (413)
|++.||-..++.|+-- .+- ..+..+.|.-+-+.+.+.+.. ...|..|+.|+-.+..+
T Consensus 436 Vvf~~G~~~k~~YR~f--~ik----------------~~~~~dDy~~m~Evl~RR~~r~~~~~~~~PDLilIDGGkgQl~ 497 (621)
T PRK14671 436 VCFVDGKPKKSDYRKF--KLR----------------SFEGSDDYAAMREVVTRRYSGSLAEELPLPDLIVIDGGKGQVN 497 (621)
T ss_pred EEEECCccChhhCCee--ecC----------------CCCCCCHHHHHHHHHHHHhhccccccCCCCCEEEEeCCHHHHH
Confidence 6777888777777631 110 111246676666666666622 13699999999999999
Q ss_pred HHHHhCCccc
Q 039425 197 VIQKHFPSAT 206 (413)
Q Consensus 197 Ai~~vfP~a~ 206 (413)
|..+++-+..
T Consensus 498 aa~~vl~~lg 507 (621)
T PRK14671 498 SAWKVLQELG 507 (621)
T ss_pred HHHHHHHHcC
Confidence 9999874433
No 119
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=21.23 E-value=3.7e+02 Score=20.33 Aligned_cols=72 Identities=13% Similarity=-0.021 Sum_probs=33.5
Q ss_pred EEEeeccccccCCCCceeeEEEeeccCcEEEEEEEee--cccccchHHHHHHHHHHHHhccccceEEEeccchHH
Q 039425 122 VLIMDCTYQTNRYDMPLLEIAGVTSIDLTFSVCCVYL--KLKWENNYIWALERLKSIMEENMLASVIVTDRELAL 194 (413)
Q Consensus 122 vl~iD~Ty~tn~~~~~l~~~~g~~~~g~~~~~~~~~~--~~E~~~~~~~~l~~l~~~~~~~~~p~~iitD~~~al 194 (413)
++++|+.+..+..+. =+-++..+..+.......... .+.....+.-++..+.........+..|.+|.....
T Consensus 1 ~~~~Dgs~~~~~~~~-g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~ 74 (130)
T cd06222 1 VIYTDGSCRGNPGPA-GAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVI 74 (130)
T ss_pred CEEecccCCCCCCce-EEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHH
Confidence 367888887653211 222333344444333333221 111122233334444443333567788899975544
No 120
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.99 E-value=4.5e+02 Score=21.20 Aligned_cols=34 Identities=9% Similarity=0.004 Sum_probs=26.6
Q ss_pred cCCCCCHHHHHH---HHHHHhCCCChHHHHHHHHhcC
Q 039425 16 FAGILNKEKSNL---LVDMSKNNVRPKDILHVLKKRN 49 (413)
Q Consensus 16 ~~rrlt~~~~~~---i~~L~~~g~~~~~I~~~l~~~~ 49 (413)
-+|.-++++... |..|.+.|++-.+|...+....
T Consensus 35 gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (126)
T cd04783 35 GYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDD 71 (126)
T ss_pred CCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence 466677765444 8889999999999999997654
No 121
>PF07162 B9-C2: Ciliary basal body-associated, B9 protein; InterPro: IPR010796 Proteins in this entry include the MSK1 protein (Q9NXB0 from SWISSPROT) and other known or predicted flagellar basal body proteome components [] or cilia-containing species. Although the function is unknown, a cilia-specific role has been suggested for the poorly characterised B9 domain [, , ]. Mutations in MSK1 have been shown to cause Meckel syndrome type 1, a severe foetal development disorder that has been reported in most populations.
Probab=20.85 E-value=1.4e+02 Score=25.64 Aligned_cols=36 Identities=17% Similarity=0.208 Sum_probs=28.3
Q ss_pred eeccccc-cCCCCce--eeEEEeeccCcEEEEEEEeecc
Q 039425 125 MDCTYQT-NRYDMPL--LEIAGVTSIDLTFSVCCVYLKL 160 (413)
Q Consensus 125 iD~Ty~t-n~~~~~l--~~~~g~~~~g~~~~~~~~~~~~ 160 (413)
+|-+|++ |.++.|- +.+.+.|..|+..+.||+.+.-
T Consensus 63 ~d~~~~~~~~~gwP~L~l~V~~~D~~gr~~~~GYG~~~l 101 (168)
T PF07162_consen 63 FDLHFKSTNPQGWPQLVLQVYSLDSWGRDRVEGYGFCHL 101 (168)
T ss_pred EEEEEEeCCCCCCceEEEEEEEEcccCCeEEeEEeEEEe
Confidence 6777764 6677774 4677899999999999998753
No 122
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=20.63 E-value=1.6e+02 Score=20.51 Aligned_cols=30 Identities=7% Similarity=0.062 Sum_probs=22.2
Q ss_pred cCCCCCHHHHHH---HHHHHhCCCChHHHHHHH
Q 039425 16 FAGILNKEKSNL---LVDMSKNNVRPKDILHVL 45 (413)
Q Consensus 16 ~~rrlt~~~~~~---i~~L~~~g~~~~~I~~~l 45 (413)
-+|..++++... |..|.+.|++..+|.+.+
T Consensus 35 ~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 35 GHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred CCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 456777766443 667788999999998765
No 123
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=20.49 E-value=1.3e+02 Score=22.02 Aligned_cols=33 Identities=6% Similarity=0.017 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHHHHHh-CCCChHHHHHHHHhcCC
Q 039425 18 GILNKEKSNLLVDMSK-NNVRPKDILHVLKKRNM 50 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~-~g~~~~~I~~~l~~~~~ 50 (413)
....+...+.|..|.+ .|.+...|..+|...++
T Consensus 3 P~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~ 36 (77)
T PF00538_consen 3 PPYSDMILEAIKALKERKGSSLQAIKKYIKAKYK 36 (77)
T ss_dssp SCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSS
T ss_pred CCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcC
Confidence 3344566778888888 79999999999999985
No 124
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=20.39 E-value=2.8e+02 Score=18.52 Aligned_cols=50 Identities=20% Similarity=0.129 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHHh-CCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhh
Q 039425 17 AGILNKEKSNLLVDMSK-NNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVR 69 (413)
Q Consensus 17 ~rrlt~~~~~~i~~L~~-~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~ 69 (413)
..++|+++...+....+ +..+..+-+..|.... | ++..+|.+.-+.-|.+
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~--l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-G--LTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-T--SSHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccccccccccccccc-c--ccccccccCHHHhHHH
Confidence 35788999898888888 4566666666777664 3 7889998887765544
No 125
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=20.12 E-value=2.2e+02 Score=24.03 Aligned_cols=44 Identities=9% Similarity=0.076 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKV 68 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~ 68 (413)
.+|++.++..+.-.+-.|++.++|...+. ++...|++...+.++
T Consensus 127 ~~L~~~~r~vl~l~~~~~~s~~eIA~~lg-------is~~tV~~~l~ra~~ 170 (182)
T PRK09652 127 ESLPEELRTAITLREIEGLSYEEIAEIMG-------CPIGTVRSRIFRARE 170 (182)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHHHC-------CCHHHHHHHHHHHHH
Confidence 45777777766666667888888877753 344555555444433
No 126
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=20.08 E-value=2.1e+02 Score=24.09 Aligned_cols=45 Identities=9% Similarity=0.157 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHhcCCCCCcchhhHHHHHHHhhhh
Q 039425 18 GILNKEKSNLLVDMSKNNVRPKDILHVLKKRNMHNATTIRAIYNARRKYKVR 69 (413)
Q Consensus 18 rrlt~~~~~~i~~L~~~g~~~~~I~~~l~~~~~~~~~t~~di~n~~~~~~~~ 69 (413)
.+|++.++..+...+..|++..+|.+.+. ++...|++...+.+..
T Consensus 124 ~~L~~~~r~i~~l~~~~~~~~~eIA~~lg-------is~~tv~~~~~ra~~~ 168 (179)
T PRK11924 124 DALPVKQREVFLLRYVEGLSYREIAEILG-------VPVGTVKSRLRRARQL 168 (179)
T ss_pred HhCCHHHHHHhhHHHHcCCCHHHHHHHHC-------CCHHHHHHHHHHHHHH
Confidence 45677776666665667888877777654 3455666665554443
No 127
>PF11433 DUF3198: Protein of unknown function (DUF3198); InterPro: IPR024504 This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.; PDB: 1X9B_A.
Probab=20.03 E-value=2.8e+02 Score=18.46 Aligned_cols=25 Identities=24% Similarity=0.258 Sum_probs=18.9
Q ss_pred hhhhhccCCCHHHHHHHHHHHHHhh
Q 039425 238 SWNLLILSASEEEFAQRLKGMETDF 262 (413)
Q Consensus 238 ~~~~l~~a~t~~ef~~~~~~~~~~~ 262 (413)
.|..++.+++...|.+.+.++....
T Consensus 6 ~Fe~~InS~SK~~Fv~nL~ELE~is 30 (51)
T PF11433_consen 6 KFESYINSESKSVFVRNLTELERIS 30 (51)
T ss_dssp HHHHHHHS--HHHHHHHHHHHHHHH
T ss_pred HHHHHhCCccHHHHHHhHHHHHHHH
Confidence 4667889999999999999987653
Done!