Query psy13880
Match_columns 256
No_of_seqs 186 out of 525
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 22:46:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13880.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13880hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1896|consensus 100.0 4.2E-41 9.1E-46 334.0 19.8 230 15-256 1114-1366(1366)
2 KOG1897|consensus 100.0 3.2E-39 6.8E-44 316.3 21.1 219 7-251 871-1094(1096)
3 KOG1898|consensus 100.0 5.7E-37 1.2E-41 301.7 17.4 210 6-253 976-1204(1205)
4 PF03178 CPSF_A: CPSF A subuni 100.0 6.6E-33 1.4E-37 252.2 20.5 154 62-222 166-321 (321)
5 COG5161 SFT1 Pre-mRNA cleavage 100.0 3.6E-28 7.8E-33 235.8 15.3 233 15-253 1068-1316(1319)
6 PF14783 BBS2_Mid: Ciliary BBS 88.7 4.1 8.8E-05 31.7 8.3 65 71-161 2-68 (111)
7 PF00325 Crp: Bacterial regula 85.3 1.7 3.7E-05 26.2 3.5 25 227-251 4-28 (32)
8 KOG1896|consensus 81.3 0.65 1.4E-05 49.1 1.0 50 5-54 781-834 (1366)
9 PF08279 HTH_11: HTH domain; 72.0 5.6 0.00012 26.0 3.3 27 226-252 16-42 (55)
10 PF13404 HTH_AsnC-type: AsnC-t 66.2 8.4 0.00018 24.4 3.0 38 213-250 5-42 (42)
11 PF08220 HTH_DeoR: DeoR-like h 65.7 9.3 0.0002 25.7 3.3 25 227-251 16-40 (57)
12 PF06971 Put_DNA-bind_N: Putat 63.8 8.9 0.00019 25.4 2.8 19 229-247 32-50 (50)
13 PF13936 HTH_38: Helix-turn-he 59.7 21 0.00045 22.6 4.0 31 216-247 12-42 (44)
14 PF13545 HTH_Crp_2: Crp-like h 56.3 18 0.0004 25.0 3.7 24 228-251 31-54 (76)
15 KOG2106|consensus 54.8 1.3E+02 0.0028 29.7 9.9 28 69-99 247-274 (626)
16 COG1654 BirA Biotin operon rep 53.5 19 0.00041 26.2 3.3 26 226-251 20-45 (79)
17 PF00400 WD40: WD domain, G-be 52.7 44 0.00096 19.4 4.6 30 67-98 10-39 (39)
18 KOG0299|consensus 52.1 74 0.0016 30.7 7.8 66 33-101 281-357 (479)
19 KOG4328|consensus 52.0 65 0.0014 31.1 7.4 92 66-175 184-275 (498)
20 smart00419 HTH_CRP helix_turn_ 51.8 26 0.00057 21.6 3.6 25 227-251 10-34 (48)
21 PF13412 HTH_24: Winged helix- 51.5 27 0.00059 22.0 3.6 37 215-251 7-43 (48)
22 PF11239 DUF3040: Protein of u 51.2 10 0.00023 27.5 1.7 26 162-187 1-26 (82)
23 PF04760 IF2_N: Translation in 48.8 24 0.00051 23.2 3.0 21 229-249 7-28 (54)
24 PF08954 DUF1900: Domain of un 48.6 68 0.0015 25.7 6.2 53 74-132 15-67 (136)
25 PF02954 HTH_8: Bacterial regu 48.5 18 0.0004 22.6 2.3 34 215-248 8-41 (42)
26 PF02978 SRP_SPB: Signal pepti 47.4 40 0.00086 25.7 4.5 28 224-251 72-99 (104)
27 PHA02955 hypothetical protein; 45.3 18 0.00039 31.3 2.5 30 214-243 68-97 (213)
28 PHA02947 S-S bond formation pa 45.1 18 0.00039 31.3 2.4 31 214-244 68-98 (215)
29 PF08280 HTH_Mga: M protein tr 44.7 32 0.0007 23.1 3.3 25 228-252 22-46 (59)
30 COG1522 Lrp Transcriptional re 44.1 23 0.0005 28.1 2.9 40 212-251 9-48 (154)
31 PF11972 HTH_13: HTH DNA bindi 43.3 55 0.0012 22.1 4.1 35 215-249 3-37 (54)
32 PF10685 KGG: Stress-induced b 43.0 23 0.00049 19.7 1.8 18 220-237 2-19 (23)
33 PF13730 HTH_36: Helix-turn-he 42.7 42 0.0009 21.7 3.5 25 227-251 27-51 (55)
34 TIGR02675 tape_meas_nterm tape 41.2 48 0.001 23.6 3.8 42 207-248 26-67 (75)
35 PHA02591 hypothetical protein; 40.6 32 0.0007 25.0 2.8 21 228-248 62-82 (83)
36 PF04539 Sigma70_r3: Sigma-70 39.9 32 0.00069 24.1 2.8 25 228-252 23-47 (78)
37 PRK13918 CRP/FNR family transc 39.5 36 0.00077 28.1 3.5 25 227-251 151-175 (202)
38 TIGR00122 birA_repr_reg BirA b 39.1 70 0.0015 21.9 4.4 38 213-251 2-39 (69)
39 cd00092 HTH_CRP helix_turn_hel 39.1 50 0.0011 21.9 3.6 26 226-251 26-51 (67)
40 smart00550 Zalpha Z-DNA-bindin 38.6 54 0.0012 22.7 3.7 37 215-251 10-48 (68)
41 smart00345 HTH_GNTR helix_turn 38.5 53 0.0012 21.0 3.6 25 227-251 22-46 (60)
42 PF14174 YycC: YycC-like prote 38.3 47 0.001 22.1 3.0 23 221-243 4-26 (53)
43 PF05920 Homeobox_KN: Homeobox 38.2 79 0.0017 19.7 4.0 27 224-250 12-38 (40)
44 PF02042 RWP-RK: RWP-RK domain 37.5 91 0.002 20.8 4.4 33 212-247 5-37 (52)
45 TIGR03697 NtcA_cyano global ni 37.3 42 0.00091 27.3 3.5 25 227-251 145-169 (193)
46 PRK15418 transcriptional regul 37.1 39 0.00084 31.0 3.5 29 223-251 27-55 (318)
47 KOG3881|consensus 35.9 89 0.0019 29.6 5.6 54 66-128 200-253 (412)
48 PRK10402 DNA-binding transcrip 34.1 51 0.0011 28.0 3.6 25 227-251 171-195 (226)
49 PF11242 DUF2774: Protein of u 33.6 49 0.0011 23.0 2.7 26 229-254 17-42 (63)
50 PF07494 Reg_prop: Two compone 33.3 64 0.0014 17.5 2.7 18 81-98 5-22 (24)
51 KOG0772|consensus 32.6 4.4E+02 0.0096 26.2 9.8 32 6-37 340-374 (641)
52 PF02001 DUF134: Protein of un 32.4 56 0.0012 25.2 3.2 44 211-254 41-86 (106)
53 smart00595 MADF subfamily of S 32.4 62 0.0013 23.1 3.4 24 228-251 30-53 (89)
54 KOG2111|consensus 32.2 4.2E+02 0.009 24.6 12.8 37 64-102 222-258 (346)
55 TIGR01610 phage_O_Nterm phage 31.8 67 0.0014 23.8 3.5 26 226-251 48-73 (95)
56 smart00420 HTH_DEOR helix_turn 31.6 91 0.002 19.3 3.7 26 226-251 15-40 (53)
57 KOG0303|consensus 31.3 3E+02 0.0065 26.4 8.3 31 74-104 268-298 (472)
58 PRK09391 fixK transcriptional 31.0 59 0.0013 27.8 3.5 25 227-251 181-205 (230)
59 PRK11179 DNA-binding transcrip 30.5 51 0.0011 26.5 2.9 41 212-252 10-50 (153)
60 PRK11753 DNA-binding transcrip 30.2 63 0.0014 26.7 3.5 26 226-251 169-194 (211)
61 KOG0283|consensus 30.2 2.4E+02 0.0051 29.0 7.9 103 39-165 370-482 (712)
62 PF00356 LacI: Bacterial regul 29.7 73 0.0016 20.5 2.9 20 228-247 2-21 (46)
63 smart00344 HTH_ASNC helix_turn 29.5 55 0.0012 24.3 2.7 39 213-251 5-43 (108)
64 PF00046 Homeobox: Homeobox do 29.4 54 0.0012 21.3 2.4 24 223-246 25-48 (57)
65 PF04405 ScdA_N: Domain of Unk 29.3 65 0.0014 21.7 2.7 24 227-250 33-56 (56)
66 PF02796 HTH_7: Helix-turn-hel 29.1 66 0.0014 20.2 2.7 22 226-247 22-43 (45)
67 KOG1332|consensus 29.0 79 0.0017 28.4 3.9 36 67-102 101-136 (299)
68 COG1356 tfx Transcriptional re 28.9 46 0.00099 26.6 2.2 27 226-252 24-54 (143)
69 PHA02662 ORF131 putative membr 28.7 41 0.0009 29.3 2.1 26 214-239 81-106 (226)
70 PF03444 HrcA_DNA-bdg: Winged 28.5 81 0.0018 22.9 3.3 35 216-250 13-48 (78)
71 PRK11161 fumarate/nitrate redu 27.1 74 0.0016 26.9 3.5 25 227-251 186-210 (235)
72 PF09124 Endonuc-dimeris: T4 r 27.1 82 0.0018 21.3 2.9 25 214-238 7-31 (54)
73 PF01325 Fe_dep_repress: Iron 26.8 1E+02 0.0022 20.9 3.4 25 227-251 24-48 (60)
74 PF14727 PHTB1_N: PTHB1 N-term 26.8 4.2E+02 0.0091 25.4 8.7 58 73-132 179-249 (418)
75 PRK09706 transcriptional repre 26.6 94 0.002 24.3 3.7 38 214-251 90-127 (135)
76 smart00421 HTH_LUXR helix_turn 26.3 1.2E+02 0.0025 18.9 3.6 24 227-250 20-43 (58)
77 KOG0296|consensus 26.1 3.2E+02 0.007 25.8 7.5 74 68-166 106-179 (399)
78 PF07751 Abi_2: Abi-like prote 26.0 1E+02 0.0022 25.0 4.0 42 214-255 139-184 (191)
79 PF08535 KorB: KorB domain; I 25.7 73 0.0016 23.3 2.7 20 227-246 5-24 (93)
80 TIGR02607 antidote_HigA addict 25.5 75 0.0016 21.9 2.7 18 227-244 20-37 (78)
81 cd07377 WHTH_GntR Winged helix 25.3 1.2E+02 0.0025 19.7 3.6 25 227-251 27-51 (66)
82 cd06171 Sigma70_r4 Sigma70, re 25.2 1.3E+02 0.0027 18.2 3.5 28 224-251 25-52 (55)
83 PF05550 Peptidase_C53: Pestiv 24.8 1.2E+02 0.0026 24.8 3.9 46 13-74 123-168 (168)
84 PF10668 Phage_terminase: Phag 24.5 75 0.0016 21.9 2.4 17 227-243 24-40 (60)
85 PF14157 YmzC: YmzC-like prote 24.4 1.3E+02 0.0027 21.0 3.4 20 84-103 31-50 (63)
86 smart00418 HTH_ARSR helix_turn 24.4 1.3E+02 0.0028 19.1 3.6 29 223-251 8-36 (66)
87 PF09669 Phage_pRha: Phage reg 24.4 1.1E+02 0.0024 22.5 3.5 23 229-251 5-27 (93)
88 PF13542 HTH_Tnp_ISL3: Helix-t 24.2 1.1E+02 0.0024 19.3 3.2 22 227-248 29-50 (52)
89 PF08222 HTH_CodY: CodY helix- 24.2 1.1E+02 0.0025 21.0 3.1 24 229-252 8-31 (61)
90 COG1342 Predicted DNA-binding 24.1 88 0.0019 23.7 2.8 29 223-251 47-75 (99)
91 KOG0272|consensus 23.6 3.2E+02 0.007 26.3 7.1 89 6-104 164-253 (459)
92 PF04703 FaeA: FaeA-like prote 23.6 1.2E+02 0.0026 20.9 3.3 25 227-251 17-41 (62)
93 PF08671 SinI: Anti-repressor 23.0 92 0.002 18.4 2.2 18 230-247 10-27 (30)
94 smart00354 HTH_LACI helix_turn 22.9 99 0.0021 21.3 2.9 20 228-247 3-22 (70)
95 PF01402 RHH_1: Ribbon-helix-h 22.3 1.8E+02 0.0038 17.3 3.6 20 229-248 15-34 (39)
96 PF02845 CUE: CUE domain; Int 22.1 2E+02 0.0044 17.6 4.5 36 215-250 7-42 (42)
97 PF09012 FeoC: FeoC like trans 22.1 1.1E+02 0.0025 20.9 3.1 23 228-250 17-39 (69)
98 PF06739 SBBP: Beta-propeller 22.1 1.3E+02 0.0027 18.4 2.9 16 84-99 16-31 (38)
99 PF04545 Sigma70_r4: Sigma-70, 21.8 1.4E+02 0.0031 18.8 3.3 24 224-247 19-42 (50)
100 PRK09802 DNA-binding transcrip 21.8 1E+02 0.0022 27.4 3.4 27 225-251 31-57 (269)
101 PF01710 HTH_Tnp_IS630: Transp 21.7 1E+02 0.0022 23.7 3.0 39 211-249 56-95 (119)
102 KOG0282|consensus 21.5 3.6E+02 0.0078 26.3 7.0 31 70-102 434-464 (503)
103 TIGR01321 TrpR trp operon repr 21.0 78 0.0017 23.8 2.1 17 227-243 57-73 (94)
104 PF01381 HTH_3: Helix-turn-hel 20.6 1.2E+02 0.0027 19.2 2.8 22 227-248 11-32 (55)
105 COG4840 Uncharacterized protei 20.5 1E+02 0.0022 21.7 2.4 45 185-237 24-68 (71)
106 PF01978 TrmB: Sugar-specific 20.5 1.6E+02 0.0034 19.9 3.5 31 221-251 18-48 (68)
107 cd06170 LuxR_C_like C-terminal 20.3 1.7E+02 0.0036 18.2 3.5 25 227-251 17-41 (57)
108 PF13543 KSR1-SAM: SAM like do 20.2 2.5E+02 0.0054 22.4 4.9 37 214-250 90-126 (129)
No 1
>KOG1896|consensus
Probab=100.00 E-value=4.2e-41 Score=334.05 Aligned_cols=230 Identities=38% Similarity=0.661 Sum_probs=195.8
Q ss_pred CCCeeEEEEEecCeEEEEEEeeCC--------------------CCceeeeeeecc-eEEEeeccccccCCCCCccceEE
Q psy13880 15 HGNRPLLLVRTQHELLIYQAFRHP--------------------KGTLKLRFKKLK-VLFVSDRSKRANEQPGLPRGVYA 73 (256)
Q Consensus 15 ~~~~~~l~~~~~~e~~iy~~~~~~--------------------~g~l~~r~~~~~-~~~~~~~~~~~~~~d~~~~~vta 73 (256)
+|.++++-..+++.-+|=.+|.+. .|...++|+.-+ .++++++ |..|+.|++
T Consensus 1114 ~GqKI~v~~l~r~~~ligVaFiD~~~yv~s~~~vknlIl~gDV~ksisfl~fqeep~rlsL~sr-------d~~~l~v~s 1186 (1366)
T KOG1896|consen 1114 QGQKIIVRKLDRDSELIGVAFIDLPLYVHSMKVVKNLILAGDVMKSISFLGFQEEPYRLSLLSR-------DFEPLNVYS 1186 (1366)
T ss_pred cCcEEEEEEeccCCcceeeEEeccceeEEehhhhhhheehhhhhhceEEEEEccCceEEEEeec-------CCchhhcee
Confidence 567887776656667777777440 444445555333 4444444 456999999
Q ss_pred EEEEEcCCeeEEEEEeCCCcEEEEeeCCCccCCCCCCeeeeeeccccCcccceEeeeecCCCCCCCCCCCCCcceE--EE
Q psy13880 74 CEFVIESSSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARSRFLT--WY 151 (256)
Q Consensus 74 ~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~~s~~g~kL~~~~~fhlG~~v~~~~~~~~~~~~~~~~~~~~~~~~l--l~ 151 (256)
+|||+++++|+|+++|+++||++|.|+|++++|++|+||+++++||+|..|++|.+.+++...+- ...++.. +|
T Consensus 1187 ~EFLVdg~~L~flvsDa~rNi~vy~Y~Pe~~eS~~G~RLv~radfhvg~~vs~m~~lp~~~~~e~----~~~~~~~~~v~ 1262 (1366)
T KOG1896|consen 1187 TEFLVDGSNLSFLVSDADRNIHVYMYAPENIESLSGQRLVRRADFHVGAHVSTMFRLPCHQNAEF----GSNSPMFYEVF 1262 (1366)
T ss_pred eeeEEcCCeeEEEEEcCCCcEEEEEeCCCCccccCcceeeeeeeeEeccceeeeEeccccccchh----ccCCchhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999986532110 0123334 49
Q ss_pred EeCCcceEEEEecChhhHHHHHHHHHHHHhcCCCCCCCCccccccccCCCccCCCCCCceeehHHHHHHhcCCHHHHHHH
Q psy13880 152 ASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRGIIDGSLVWKFLQLSLGERLEI 231 (256)
Q Consensus 152 ~T~~GsIg~l~pl~~~~~~~L~~LQ~~l~~~~~~~~Gl~~~~~R~~~~~~~~~~~~~k~~IDGDLle~Fl~L~~~~q~~i 231 (256)
||+||++|+++|++|++||||+.||++|.+.++|+|||||++||.++... ...++.|++|||+||.+|..|+.++|+++
T Consensus 1263 gtlDG~l~~~~Pl~e~~YRRL~~lQn~L~~~~~hv~GLNPr~yR~~~s~~-~~~n~~r~ilDg~ll~~f~yl~~~er~el 1341 (1366)
T KOG1896|consen 1263 GTLDGGLGHLVPLDEKTYRRLLMLQNALMDRLPHVGGLNPRAYRLLDSSL-QLSNSLRSILDGELLNRFSYLSMSEREEL 1341 (1366)
T ss_pred cccCCceeEEecCCHHHHHHHHHHHHHHHHhhhhhcCCCHHHhhhccchh-hhcCCCcccchHhHHHHhhccchhhHHHH
Confidence 99999999999999999999999999999999999999999999988776 44689999999999999999999999999
Q ss_pred HHHhCCCHHHHHHHHHHHhhhcCCC
Q psy13880 232 CKKIGSKHNDILDELYDIEALSSHF 256 (256)
Q Consensus 232 a~~lg~s~~ei~~~l~~i~~~~~~~ 256 (256)
|+++|+++.+|++||.+++.+|++|
T Consensus 1342 A~kiGt~~~eIl~DLvel~~~~s~~ 1366 (1366)
T KOG1896|consen 1342 AHKIGTTRKEILDDLVELDRLTSSL 1366 (1366)
T ss_pred HHhcCCCHHHHHHHHHHHHHHhhcC
Confidence 9999999999999999999999987
No 2
>KOG1897|consensus
Probab=100.00 E-value=3.2e-39 Score=316.33 Aligned_cols=219 Identities=19% Similarity=0.297 Sum_probs=195.6
Q ss_pred EEEEeccCCCCeeEEEEEecCeEEEEEEeeCCCCceeeeeeecceEEEeeccccccCCCCCccceEEEEEEEcCCeeEEE
Q psy13880 7 LLTVSLGLHGNRPLLLVRTQHELLIYQAFRHPKGTLKLRFKKLKVLFVSDRSKRANEQPGLPRGVYACEFVIESSSMGFM 86 (256)
Q Consensus 7 ~~~v~~g~~~~~~~l~~~~~~e~~iy~~~~~~~g~l~~r~~~~~~~~~~~~~~~~~~~d~~~~~vta~~fL~~~~~l~~l 86 (256)
+...-+...|.+++ |-+..+++.+..|+.+||.+.+++ ||+.|.|+||+++++++ +++
T Consensus 871 ~~aL~l~v~gdeI~--VgDlm~Sitll~y~~~eg~f~evA-----------------rD~~p~Wmtaveil~~d---~yl 928 (1096)
T KOG1897|consen 871 IIALDLQVKGDEIA--VGDLMRSITLLQYKGDEGNFEEVA-----------------RDYNPNWMTAVEILDDD---TYL 928 (1096)
T ss_pred eEEEEEEecCcEEE--EeeccceEEEEEEeccCCceEEee-----------------hhhCccceeeEEEecCc---eEE
Confidence 45566777788877 558888999999999999998854 47899999999999999 799
Q ss_pred EEeCCCcEEEEeeCCCccCCCCCCeeeeeeccccCcccceEeeeecCCCCCCCCCCCCCcceEEEEeCCcceEEEEecCh
Q psy13880 87 ISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARSRFLTWYASLDGALGFFLPLPE 166 (256)
Q Consensus 87 ~aD~~gNl~vl~~~p~~~~s~~g~kL~~~~~fhlG~~v~~~~~~~~~~~~~~~~~~~~~~~~ll~~T~~GsIg~l~pl~~ 166 (256)
+||++||++++++|..++++.++++|+..+.||+|+.||+|++++++..... ......+.++|||++|+||+|+.++.
T Consensus 929 gae~~gNlf~v~~d~~~~td~eR~~l~~~~~~hlGelvn~f~hg~lv~~~~~--s~~~~~~~vlfgTv~GsIG~i~sl~~ 1006 (1096)
T KOG1897|consen 929 GAENSGNLFTVRKDSDATTDEERQILEEVGKFHLGELVNKFRHGSLVMQLGD--SMIPLEPKVLFGTVNGSIGIIVSLPQ 1006 (1096)
T ss_pred eecccccEEEEEecCCCCchhhhhcccceeeEEeccceeeeeecceEeeccc--cccCCCCcEEEEEccceEEEEEecCc
Confidence 9999999999999999999999999999999999999999999998722111 11234466999999999999999999
Q ss_pred hhHHHHHHHHHHHHhcCCCCCCCCccccccccCCCccCCCCCCceeehHHHHHHhcCCHHHHHHHHHHhCCC-----HHH
Q psy13880 167 KNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRGIIDGSLVWKFLQLSLGERLEICKKIGSK-----HND 241 (256)
Q Consensus 167 ~~~~~L~~LQ~~l~~~~~~~~Gl~~~~~R~~~~~~~~~~~~~k~~IDGDLle~Fl~L~~~~q~~ia~~lg~s-----~~e 241 (256)
+.|.+|..||++|++.+|++||++|.+||+|+++.+. .|++|||||||||+|++|++++|.+|++++..+ ++|
T Consensus 1007 d~~~fL~~Lq~~irk~i~s~gglsH~~yrsf~~e~~~--~P~~gfIDGDLiEsfl~l~~~~~~~i~~~~~~~~~~~s~~e 1084 (1096)
T KOG1897|consen 1007 DWYDFLEELQRRIRKVIKSVGGLSHMDYRSFEFEKRT--SPVKGFIDGDLIESFLDLSRSKMREIVRGLEHTESLASVQE 1084 (1096)
T ss_pred chhHHHHHHHHHHHHhhcccCCcchhhHhhhhccccc--CCCcCcccchHHHhhhccCHHHHHHHHhhcccccccCCHHH
Confidence 9999999999999999999999999999999998864 799999999999999999999999999999876 999
Q ss_pred HHHHHHHHhh
Q psy13880 242 ILDELYDIEA 251 (256)
Q Consensus 242 i~~~l~~i~~ 251 (256)
|.|.+||+++
T Consensus 1085 l~k~vEel~r 1094 (1096)
T KOG1897|consen 1085 LLKIVEELTR 1094 (1096)
T ss_pred HHHHHHHHHh
Confidence 9999999975
No 3
>KOG1898|consensus
Probab=100.00 E-value=5.7e-37 Score=301.71 Aligned_cols=210 Identities=21% Similarity=0.321 Sum_probs=186.4
Q ss_pred eEEEEeccCCCCeeEEEEEecCeEEEEEEeeCCCCceeeeeeecceEEEeeccccccCCCCCccceEEEEEEEcCCeeEE
Q psy13880 6 ELLTVSLGLHGNRPLLLVRTQHELLIYQAFRHPKGTLKLRFKKLKVLFVSDRSKRANEQPGLPRGVYACEFVIESSSMGF 85 (256)
Q Consensus 6 e~~~v~~g~~~~~~~l~~~~~~e~~iy~~~~~~~g~l~~r~~~~~~~~~~~~~~~~~~~d~~~~~vta~~fL~~~~~l~~ 85 (256)
..-|.++..++.|++ |.+.+|++.|..|+.++++|.+ . ++|+.|||||++.++|++ ++
T Consensus 976 p~~Is~iqt~~~RI~--VgD~qeSV~~~~y~~~~n~l~~-----------f------adD~~pR~Vt~~~~lD~~---tv 1033 (1205)
T KOG1898|consen 976 PNRISSIQTYGARIV--VGDIQESVHFVRYRREDNQLIV-----------F------ADDPVPRHVTALELLDYD---TV 1033 (1205)
T ss_pred ceEEEEEeecceEEE--EeeccceEEEEEEecCCCeEEE-----------E------eCCCccceeeEEEEecCC---ce
Confidence 356788999999998 6699999999999886666544 3 357899999999999999 89
Q ss_pred EEEeCCCcEEEEeeCCCccCCCC------------------CCeeeeeeccccCcccceEeeeecCCCCCCCCCCCCCcc
Q psy13880 86 MISDKDKNVVLFMYQPEARESNG------------------GHRLIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARSRF 147 (256)
Q Consensus 86 l~aD~~gNl~vl~~~p~~~~s~~------------------g~kL~~~~~fhlG~~v~~~~~~~~~~~~~~~~~~~~~~~ 147 (256)
++||++||+++++.+|+.++..+ -+|.....+||+|+.++++++....|. .++
T Consensus 1034 agaDrfGNi~~vR~P~d~~e~~~edpt~~k~~~~~g~lN~~~~K~~~i~~f~v~Dvits~q~~~~i~~---------a~e 1104 (1205)
T KOG1898|consen 1034 AGADRFGNIAVVRIPPDVSEEASEDPTELKIAWEQGFLNDAPQKVQLISQFFVGDVITSLQKVSSIPG---------ARE 1104 (1205)
T ss_pred eeccccCcEEEEECCCcchhhhccCCccccceecccccccccHhhhhhhhccccCeeeeceeeeeccC---------Ccc
Confidence 99999999999999987654321 357888999999999999999887653 357
Q ss_pred eEEEEeCCcceEEEEecCh-hhHHHHHHHHHHHHhcCCCCCCCCccccccccCCCccCCCCCCceeehHHHHHHhcCCHH
Q psy13880 148 LTWYASLDGALGFFLPLPE-KNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRGIIDGSLVWKFLQLSLG 226 (256)
Q Consensus 148 ~ll~~T~~GsIg~l~pl~~-~~~~~L~~LQ~~l~~~~~~~~Gl~~~~~R~~~~~~~~~~~~~k~~IDGDLle~Fl~L~~~ 226 (256)
.++|+|+.|+||+++|+.. ++++|++.+|++|+++.|+++|+||.+||+|++ |+|.+|||||||+|+.|+..
T Consensus 1105 ~~iy~tl~GtiG~f~p~~s~~d~~Ff~~~e~~~r~e~ppl~GrDH~~yRsyy~-------Pvk~VIDGDlceqF~~L~~~ 1177 (1205)
T KOG1898|consen 1105 SLIYTTLLGTIGVFAPFLSREDVDFFQHLEMHMRKEYPPLLGRDHLEYRSYYA-------PVKKVIDGDLCEQFLRLEEN 1177 (1205)
T ss_pred eeeeeeccccceEEeecccccchHHHHHHHHhccccCCcccCcchhhhhhhcc-------chhhcccHHHHHHHhhCCHH
Confidence 8999999999999999986 699999999999999999999999999999984 89999999999999999999
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhhhc
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEALS 253 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~~~ 253 (256)
+|++||++++++++||.++|+++|+..
T Consensus 1178 ~Qe~va~el~~ti~eI~kkledir~~~ 1204 (1205)
T KOG1898|consen 1178 QQEEVAEELDRTIEEISKKLEDIRTRY 1204 (1205)
T ss_pred HHHHHHhcccCCHHHHHHHHHHHHhhc
Confidence 999999999999999999999999864
No 4
>PF03178 CPSF_A: CPSF A subunit region; InterPro: IPR004871 This family includes a region that lies towards the C terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs []. The function of the aligned region is unknown but may be involved in RNA/DNA binding.; GO: 0003676 nucleic acid binding, 0005634 nucleus; PDB: 2B5M_A 4A0K_C 4A0B_C 3I7L_A 3I8E_A 4A09_A 4A0A_A 3EI4_C 2B5L_A 3I7O_A ....
Probab=100.00 E-value=6.6e-33 Score=252.20 Aligned_cols=154 Identities=38% Similarity=0.648 Sum_probs=119.4
Q ss_pred cCCCCCccceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCCCccCCCCCC-eeeeeeccccCcccceEeeeecCCCCCCCC
Q psy13880 62 NEQPGLPRGVYACEFVIESSSMGFMISDKDKNVVLFMYQPEARESNGGH-RLIKKTDFHLGQHVNTFFKIRCKPSPISDA 140 (256)
Q Consensus 62 ~~~d~~~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~~s~~g~-kL~~~~~fhlG~~v~~~~~~~~~~~~~~~~ 140 (256)
-++|+.|+|+++++||.+++ +++++|.+||+++++++|+++++.+++ +|+..++||+|+.||+++++++.|....
T Consensus 166 va~d~~~~~v~~~~~l~d~~--~~i~~D~~gnl~~l~~~~~~~~~~~~~~~L~~~~~f~lg~~v~~~~~~~l~~~~~~-- 241 (321)
T PF03178_consen 166 VARDYQPRWVTAAEFLVDED--TIIVGDKDGNLFVLRYNPEIPNSRDGDPKLERISSFHLGDIVNSFRRGSLIPRSGS-- 241 (321)
T ss_dssp EEEESS-BEEEEEEEE-SSS--EEEEEETTSEEEEEEE-SS-SSTTTTTTBEEEEEEEE-SS-EEEEEE--SS--SSS--
T ss_pred EEecCCCccEEEEEEecCCc--EEEEEcCCCeEEEEEECCCCcccccccccceeEEEEECCCccceEEEEEeeecCCC--
Confidence 34678899999999996554 999999999999999999999999999 9999999999999999999987753111
Q ss_pred CCCCCcceEEEEeCCcceEEEEe-cChhhHHHHHHHHHHHHhcCCCCCCCCccccccccCCCccCCCCCCceeehHHHHH
Q psy13880 141 PGARSRFLTWYASLDGALGFFLP-LPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRGIIDGSLVWK 219 (256)
Q Consensus 141 ~~~~~~~~ll~~T~~GsIg~l~p-l~~~~~~~L~~LQ~~l~~~~~~~~Gl~~~~~R~~~~~~~~~~~~~k~~IDGDLle~ 219 (256)
......+.++|+|++|+||+|+| ++++.|++|+.||++|.+.++++|||||++||+++++ +. ..++|||||||||+
T Consensus 242 ~~~~~~~~i~~~T~~G~Ig~l~p~l~~~~~~~L~~lQ~~l~~~~~~~~gl~~~~~R~~~~~-~~--~~~~~~iDgdll~~ 318 (321)
T PF03178_consen 242 SESPNRPQILYGTVDGSIGVLIPFLSEEEYRFLQALQNNLRKHIPSLGGLNPRSFRSYKNP-RM--KRSKGFIDGDLLEQ 318 (321)
T ss_dssp S-TTEEEEEEEEETTS-EEEEEE-E-HHHHHHHHHHHHHHHHHS--TTS--HHHHTSEEES-EE--E--BSEEEHHHHHG
T ss_pred CcccccceEEEEecCCEEEEEEecCCHHHHHHHHHHHHHHHhhCCCCccCChHHhccccCc-cc--cCCCccCcHHHHHH
Confidence 11123578999999999999999 8999999999999999999999999999999999976 21 23899999999999
Q ss_pred Hhc
Q psy13880 220 FLQ 222 (256)
Q Consensus 220 Fl~ 222 (256)
|++
T Consensus 319 fl~ 321 (321)
T PF03178_consen 319 FLE 321 (321)
T ss_dssp GGG
T ss_pred hhC
Confidence 985
No 5
>COG5161 SFT1 Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]
Probab=99.95 E-value=3.6e-28 Score=235.81 Aligned_cols=233 Identities=21% Similarity=0.325 Sum_probs=186.1
Q ss_pred CCCeeEEEEEecCeEEEEEEeeCCCCceeeeeeecceEEEee-ccccc-----cCCCC---------CccceEEEEEEEc
Q psy13880 15 HGNRPLLLVRTQHELLIYQAFRHPKGTLKLRFKKLKVLFVSD-RSKRA-----NEQPG---------LPRGVYACEFVIE 79 (256)
Q Consensus 15 ~~~~~~l~~~~~~e~~iy~~~~~~~g~l~~r~~~~~~~~~~~-~~~~~-----~~~d~---------~~~~vta~~fL~~ 79 (256)
||++.++-...++..+|=..|.+ =+.+....+-++|.++.. ..++. ++.|| ..+.+++++||+.
T Consensus 1068 qgqKV~Vr~i~~~~~iipV~F~D-l~~ft~s~k~~~Nlll~gD~~qg~~F~gF~~ePyRm~l~s~s~~~~n~~s~efLv~ 1146 (1319)
T COG5161 1068 QGQKVMVRKIDRSSGIIPVGFYD-LHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATSTEFLVT 1146 (1319)
T ss_pred cCcEEEEEEecccCCcceeEEEe-eeeeeehhhhhhheeehhhhhcCcEEEEecCCcEEEEEecCCchhhcchhhHhhcc
Confidence 66777755555666777777755 444444455455443332 22222 44443 3467999999999
Q ss_pred CCeeEEEEEeCCCcEEEEeeCCCccCCCCCCeeeeeeccccCcccceEeeeecC-CCCCCCCCCCCCcceEEEEeCCcce
Q psy13880 80 SSSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFFKIRCK-PSPISDAPGARSRFLTWYASLDGAL 158 (256)
Q Consensus 80 ~~~l~~l~aD~~gNl~vl~~~p~~~~s~~g~kL~~~~~fhlG~~v~~~~~~~~~-~~~~~~~~~~~~~~~ll~~T~~GsI 158 (256)
+++|+|+++|++||++.+.|+|++|+|.+|+||+++++||+|...++|..++.. .++ +...+.++++++-++|++
T Consensus 1147 G~~lyf~~~Da~gnih~l~Y~P~np~S~sG~RLV~rssFtlhs~~~~m~llPrn~efG----~~~~~~f~~v~~~sdG~l 1222 (1319)
T COG5161 1147 GNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLPRNSEFG----AGFKKNFIMVYSRSDGML 1222 (1319)
T ss_pred CCeeEEEEEcCCCCEEEEecCCCCccccCcceeEeeccccccchhhhhhhccchhhhC----CCCCCceeEEEEccCCcE
Confidence 999999999999999999999999999999999999999999999999877533 222 223456889999999999
Q ss_pred EEEEecChhhHHHHHHHHHHHHhcCCCCCCCCccccccccCCCccCCCCCCceeehHHHHHHhcCCHHHHHHHHHHhCCC
Q psy13880 159 GFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRGIIDGSLVWKFLQLSLGERLEICKKIGSK 238 (256)
Q Consensus 159 g~l~pl~~~~~~~L~~LQ~~l~~~~~~~~Gl~~~~~R~~~~~~~~~~~~~k~~IDGDLle~Fl~L~~~~q~~ia~~lg~s 238 (256)
-.++|++++.|+||..+|+++...+.++|||||++||-.. +...+..+.|.+||+.+|..|-.|+.+.|+++|.++|+-
T Consensus 1223 ~~vvpisd~~YrrL~~IQ~~i~~r~~~vgGLNpr~yRL~~-d~~~~~~s~r~~ld~~ii~~F~y~~~~~r~sva~kaGr~ 1301 (1319)
T COG5161 1223 IHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYRLNS-DIHLHSLSLRSPLDLHIINLFSYFDMSTRESVASKAGRI 1301 (1319)
T ss_pred EEEeccCHHHHHHHHHHHHHHHHHHHhhcCCChhhhhhcc-CHHHhcCCcccchhhhhhhhhhhcchhhhhHHHhhcCCc
Confidence 9999999999999999999999999999999999999643 322345788999999999999999999999999999997
Q ss_pred HHHHHHHHHHHhhhc
Q psy13880 239 HNDILDELYDIEALS 253 (256)
Q Consensus 239 ~~ei~~~l~~i~~~~ 253 (256)
..-++.||.++..+.
T Consensus 1302 ~~~e~~D~i~~~~~l 1316 (1319)
T COG5161 1302 DRKEISDMIASLNLL 1316 (1319)
T ss_pred hHHHHHHHHHHHHHH
Confidence 765555777776553
No 6
>PF14783 BBS2_Mid: Ciliary BBSome complex subunit 2, middle region
Probab=88.74 E-value=4.1 Score=31.72 Aligned_cols=65 Identities=14% Similarity=0.147 Sum_probs=47.8
Q ss_pred eEEEEEEEcCC--eeEEEEEeCCCcEEEEeeCCCccCCCCCCeeeeeeccccCcccceEeeeecCCCCCCCCCCCCCcce
Q psy13880 71 VYACEFVIESS--SMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARSRFL 148 (256)
Q Consensus 71 vta~~fL~~~~--~l~~l~aD~~gNl~vl~~~p~~~~s~~g~kL~~~~~fhlG~~v~~~~~~~~~~~~~~~~~~~~~~~~ 148 (256)
|+|..+.+.++ +..++++-.+.-|++|+-+ +...++...+.|+++..+. ...
T Consensus 2 V~al~~~d~d~dg~~eLlvGs~D~~IRvf~~~------------e~~~Ei~e~~~v~~L~~~~--------------~~~ 55 (111)
T PF14783_consen 2 VTALCLFDFDGDGENELLVGSDDFEIRVFKGD------------EIVAEITETDKVTSLCSLG--------------GGR 55 (111)
T ss_pred eeEEEEEecCCCCcceEEEecCCcEEEEEeCC------------cEEEEEecccceEEEEEcC--------------CCE
Confidence 56666665433 3688999999999999853 3456677777778776432 145
Q ss_pred EEEEeCCcceEEE
Q psy13880 149 TWYASLDGALGFF 161 (256)
Q Consensus 149 ll~~T~~GsIg~l 161 (256)
..|+..+|+||+.
T Consensus 56 F~Y~l~NGTVGvY 68 (111)
T PF14783_consen 56 FAYALANGTVGVY 68 (111)
T ss_pred EEEEecCCEEEEE
Confidence 9999999999997
No 7
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=85.29 E-value=1.7 Score=26.15 Aligned_cols=25 Identities=20% Similarity=0.318 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.+++||+.+|.++|.+.+.|..++.
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 3689999999999999999888865
No 8
>KOG1896|consensus
Probab=81.34 E-value=0.65 Score=49.05 Aligned_cols=50 Identities=36% Similarity=0.558 Sum_probs=39.3
Q ss_pred eeEEEEeccCC---CCeeEEEEEecCeEEEEEEee-CCCCceeeeeeecceEEE
Q psy13880 5 QELLTVSLGLH---GNRPLLLVRTQHELLIYQAFR-HPKGTLKLRFKKLKVLFV 54 (256)
Q Consensus 5 ~e~~~v~~g~~---~~~~~l~~~~~~e~~iy~~~~-~~~g~l~~r~~~~~~~~~ 54 (256)
+++.+..||+. +.+|++.+..++|+++|.||+ +..|...++|+++|+.+.
T Consensus 781 ~q~~~~~L~~e~~~~e~~L~lv~~~~eil~Ykaf~~~~~~~~~~~f~kvp~~~~ 834 (1366)
T KOG1896|consen 781 KQLFVNPLGSEIVFKEPHLFLVVSDNEILIYKAFPQLSQGNLKVFFKKVPHNLN 834 (1366)
T ss_pred HHhhccccchhhhccCCceEEEEeCceEEEEeeccccCccchhhhhhhCCHhhc
Confidence 45566667765 677777788889999999995 568999999999997333
No 9
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=71.96 E-value=5.6 Score=26.05 Aligned_cols=27 Identities=11% Similarity=0.267 Sum_probs=22.5
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhhh
Q psy13880 226 GERLEICKKIGSKHNDILDELYDIEAL 252 (256)
Q Consensus 226 ~~q~~ia~~lg~s~~ei~~~l~~i~~~ 252 (256)
-...++|+++|+|...|.++|.+|+..
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 356899999999999999999999753
No 10
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=66.19 E-value=8.4 Score=24.38 Aligned_cols=38 Identities=11% Similarity=0.206 Sum_probs=25.5
Q ss_pred ehHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q psy13880 213 DGSLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIE 250 (256)
Q Consensus 213 DGDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~ 250 (256)
|-.+|.....=++.--.+||+++|.|...+.+.+..++
T Consensus 5 D~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 5 DRKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 33444444444555567899999999999999888764
No 11
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=65.68 E-value=9.3 Score=25.65 Aligned_cols=25 Identities=20% Similarity=0.316 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.-+++|+.+|+|...|.+||.++..
T Consensus 16 s~~ela~~~~VS~~TiRRDl~~L~~ 40 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIRRDLNKLEK 40 (57)
T ss_pred EHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3468999999999999999999865
No 12
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=63.81 E-value=8.9 Score=25.43 Aligned_cols=19 Identities=16% Similarity=0.344 Sum_probs=16.1
Q ss_pred HHHHHHhCCCHHHHHHHHH
Q psy13880 229 LEICKKIGSKHNDILDELY 247 (256)
Q Consensus 229 ~~ia~~lg~s~~ei~~~l~ 247 (256)
.++|+.+|.++.+|.|||.
T Consensus 32 ~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 32 QELAEALGITPAQVRKDLS 50 (50)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHhcccCC
Confidence 5799999999999999984
No 13
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=59.72 E-value=21 Score=22.63 Aligned_cols=31 Identities=23% Similarity=0.286 Sum_probs=20.5
Q ss_pred HHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHH
Q psy13880 216 LVWKFLQLSLGERLEICKKIGSKHNDILDELY 247 (256)
Q Consensus 216 Lle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~ 247 (256)
.|+.++... ..+.+||+.+|+++..|.+.|.
T Consensus 12 ~I~~l~~~G-~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 12 QIEALLEQG-MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHHHHCS----HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcC-CCHHHHHHHHCcCcHHHHHHHh
Confidence 466777766 4467799999999999988764
No 14
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=56.28 E-value=18 Score=24.99 Aligned_cols=24 Identities=17% Similarity=0.268 Sum_probs=21.6
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 228 RLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 228 q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
|++||+.+|+|++.+.+.|.+++.
T Consensus 31 ~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 31 QEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp HHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
Confidence 789999999999999999988865
No 15
>KOG2106|consensus
Probab=54.85 E-value=1.3e+02 Score=29.70 Aligned_cols=28 Identities=14% Similarity=0.323 Sum_probs=25.4
Q ss_pred cceEEEEEEEcCCeeEEEEEeCCCcEEEEee
Q psy13880 69 RGVYACEFVIESSSMGFMISDKDKNVVLFMY 99 (256)
Q Consensus 69 ~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~ 99 (256)
-.|+|+.|+.+++ ++.+|..|||.+...
T Consensus 247 k~Vl~v~F~engd---viTgDS~G~i~Iw~~ 274 (626)
T KOG2106|consen 247 KFVLCVTFLENGD---VITGDSGGNILIWSK 274 (626)
T ss_pred eEEEEEEEcCCCC---EEeecCCceEEEEeC
Confidence 6899999999985 888999999999876
No 16
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=53.52 E-value=19 Score=26.23 Aligned_cols=26 Identities=4% Similarity=0.220 Sum_probs=22.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 226 GERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 226 ~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.-..+||+++|.|+..|+|.|..++.
T Consensus 20 ~SGe~La~~LgiSRtaVwK~Iq~Lr~ 45 (79)
T COG1654 20 VSGEKLAEELGISRTAVWKHIQQLRE 45 (79)
T ss_pred ccHHHHHHHHCccHHHHHHHHHHHHH
Confidence 44678999999999999999999874
No 17
>PF00400 WD40: WD domain, G-beta repeat; InterPro: IPR019781 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.; PDB: 2ZKQ_a 3CFV_B 3CFS_B 1PEV_A 1NR0_A 1VYH_T 3RFH_A 3O2Z_T 3FRX_C 3U5G_g ....
Probab=52.70 E-value=44 Score=19.41 Aligned_cols=30 Identities=3% Similarity=0.083 Sum_probs=24.3
Q ss_pred CccceEEEEEEEcCCeeEEEEEeCCCcEEEEe
Q psy13880 67 LPRGVYACEFVIESSSMGFMISDKDKNVVLFM 98 (256)
Q Consensus 67 ~~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~ 98 (256)
+.-.|+++.+-.++. .++++..++.+.++.
T Consensus 10 h~~~i~~i~~~~~~~--~~~s~~~D~~i~vwd 39 (39)
T PF00400_consen 10 HSSSINSIAWSPDGN--FLASGSSDGTIRVWD 39 (39)
T ss_dssp SSSSEEEEEEETTSS--EEEEEETTSEEEEEE
T ss_pred CCCcEEEEEEecccc--cceeeCCCCEEEEEC
Confidence 355899999988866 788999999998863
No 18
>KOG0299|consensus
Probab=52.12 E-value=74 Score=30.71 Aligned_cols=66 Identities=12% Similarity=0.238 Sum_probs=45.3
Q ss_pred EEeeCCCCceeeeeeecc-eEEEeecccccc----CCC----CC--ccceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCC
Q psy13880 33 QAFRHPKGTLKLRFKKLK-VLFVSDRSKRAN----EQP----GL--PRGVYACEFVIESSSMGFMISDKDKNVVLFMYQP 101 (256)
Q Consensus 33 ~~~~~~~g~l~~r~~~~~-~~~~~~~~~~~~----~~d----~~--~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p 101 (256)
..|-++.+.+.+-+-... ..+|..||.+.. ..+ |. --.+-|+.|++++ .|+.+-++|+|.+.....
T Consensus 281 tlyGHqd~v~~IdaL~reR~vtVGgrDrT~rlwKi~eesqlifrg~~~sidcv~~In~~---HfvsGSdnG~IaLWs~~K 357 (479)
T KOG0299|consen 281 TLYGHQDGVLGIDALSRERCVTVGGRDRTVRLWKIPEESQLIFRGGEGSIDCVAFINDE---HFVSGSDNGSIALWSLLK 357 (479)
T ss_pred HHhCCccceeeechhcccceEEeccccceeEEEeccccceeeeeCCCCCeeeEEEeccc---ceeeccCCceEEEeeecc
Confidence 445566777777666444 677777777651 011 11 2257899999998 899999999999887743
No 19
>KOG4328|consensus
Probab=51.96 E-value=65 Score=31.13 Aligned_cols=92 Identities=16% Similarity=0.199 Sum_probs=58.5
Q ss_pred CCccceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCCCccCCCCCCeeeeeeccccCcccceEeeeecCCCCCCCCCCCCC
Q psy13880 66 GLPRGVYACEFVIESSSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS 145 (256)
Q Consensus 66 ~~~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~~s~~g~kL~~~~~fhlG~~v~~~~~~~~~~~~~~~~~~~~~ 145 (256)
+.++-++|++|..-++.=.++++|+.|++-+..+.-+. ++.+|-.+=+. .+..|+++. +.|. .
T Consensus 184 v~~~Rit~l~fHPt~~~~lva~GdK~G~VG~Wn~~~~~-~d~d~v~~f~~----hs~~Vs~l~---F~P~---------n 246 (498)
T KOG4328|consen 184 VTDRRITSLAFHPTENRKLVAVGDKGGQVGLWNFGTQE-KDKDGVYLFTP----HSGPVSGLK---FSPA---------N 246 (498)
T ss_pred ecccceEEEEecccCcceEEEEccCCCcEEEEecCCCC-CccCceEEecc----CCccccceE---ecCC---------C
Confidence 55677999999999886589999999999999986222 23334333211 234455543 2221 1
Q ss_pred cceEEEEeCCcceEEEEecChhhHHHHHHH
Q psy13880 146 RFLTWYASLDGALGFFLPLPEKNYRRLLML 175 (256)
Q Consensus 146 ~~~ll~~T~~GsIg~l~pl~~~~~~~L~~L 175 (256)
...++..+-||+|++. -+...+++.+..+
T Consensus 247 ~s~i~ssSyDGtiR~~-D~~~~i~e~v~s~ 275 (498)
T KOG4328|consen 247 TSQIYSSSYDGTIRLQ-DFEGNISEEVLSL 275 (498)
T ss_pred hhheeeeccCceeeee-eecchhhHHHhhc
Confidence 2458888889999863 4554556555555
No 20
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=51.81 E-value=26 Score=21.61 Aligned_cols=25 Identities=24% Similarity=0.365 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.+.++|+.+|.++..+.+.|..+..
T Consensus 10 s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 10 TRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4789999999999999888888764
No 21
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=51.50 E-value=27 Score=22.04 Aligned_cols=37 Identities=14% Similarity=0.154 Sum_probs=26.5
Q ss_pred HHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 215 SLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 215 DLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.++.....=+.-.+.++|+.+|.|...+.+.|.++..
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3454555567778999999999999888888877754
No 22
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=51.21 E-value=10 Score=27.47 Aligned_cols=26 Identities=23% Similarity=0.401 Sum_probs=22.7
Q ss_pred EecChhhHHHHHHHHHHHHhcCCCCC
Q psy13880 162 LPLPEKNYRRLLMLQNVMVTHTSHTG 187 (256)
Q Consensus 162 ~pl~~~~~~~L~~LQ~~l~~~~~~~~ 187 (256)
.|++|++-++|..||++|...-|.++
T Consensus 1 M~LSe~E~r~L~eiEr~L~~~DP~fa 26 (82)
T PF11239_consen 1 MPLSEHEQRRLEEIERQLRADDPRFA 26 (82)
T ss_pred CCCCHHHHHHHHHHHHHHHhcCcHHH
Confidence 38899999999999999999877654
No 23
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=48.78 E-value=24 Score=23.21 Aligned_cols=21 Identities=24% Similarity=0.575 Sum_probs=18.1
Q ss_pred HHHHHHhCCCHHHHHHHH-HHH
Q psy13880 229 LEICKKIGSKHNDILDEL-YDI 249 (256)
Q Consensus 229 ~~ia~~lg~s~~ei~~~l-~~i 249 (256)
.++|+++|.++.+|++.| .++
T Consensus 7 ~elAk~l~v~~~~ii~~l~~~~ 28 (54)
T PF04760_consen 7 SELAKELGVPSKEIIKKLFKEL 28 (54)
T ss_dssp THHHHHHSSSHHHHHHHH-HHH
T ss_pred HHHHHHHCcCHHHHHHHHHHhC
Confidence 479999999999999999 434
No 24
>PF08954 DUF1900: Domain of unknown function (DUF1900); InterPro: IPR015049 This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It has no known function []. ; PDB: 2B4E_A 2AQ5_A.
Probab=48.65 E-value=68 Score=25.74 Aligned_cols=53 Identities=13% Similarity=0.175 Sum_probs=33.8
Q ss_pred EEEEEcCCeeEEEEEeCCCcEEEEeeCCCccCCCCCCeeeeeeccccCcccceEeeeec
Q psy13880 74 CEFVIESSSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFFKIRC 132 (256)
Q Consensus 74 ~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~~s~~g~kL~~~~~fhlG~~v~~~~~~~~ 132 (256)
.=|.|.+..+-++++=.++||+.|++.++.| .+....+|..++..-.+..++.
T Consensus 15 ~P~yD~dt~llyl~gKGD~~ir~yEv~~~~p------~l~~l~~~~s~~~~~G~~~lPK 67 (136)
T PF08954_consen 15 MPFYDEDTNLLYLAGKGDGNIRYYEVSDESP------YLHYLSEYRSPEPQKGFAFLPK 67 (136)
T ss_dssp EEEE-TTT-EEEEEETT-S-EEEEEE-SSTT------SEEEEEEE--SS--SEEEE--G
T ss_pred EeeEcCCCCEEEEEeccCcEEEEEEEcCCCC------ceEEccccccCCCeEeeEecCc
Confidence 3456788899999999999999999976644 5888889998888777766553
No 25
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=48.47 E-value=18 Score=22.56 Aligned_cols=34 Identities=15% Similarity=0.234 Sum_probs=24.8
Q ss_pred HHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHH
Q psy13880 215 SLVWKFLQLSLGERLEICKKIGSKHNDILDELYD 248 (256)
Q Consensus 215 DLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~ 248 (256)
++|+.-+.-....+.+.|+.+|.++..+.++|..
T Consensus 8 ~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 8 QLIRQALERCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 4555555555556789999999999999998864
No 26
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=47.45 E-value=40 Score=25.74 Aligned_cols=28 Identities=14% Similarity=0.246 Sum_probs=22.2
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 224 SLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 224 ~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
..++++.||+..|++++||-+.|.....
T Consensus 72 ~~sR~~RIA~GSG~~~~eV~~ll~~f~~ 99 (104)
T PF02978_consen 72 NESRRRRIARGSGTTVQEVNELLKQFKQ 99 (104)
T ss_dssp HHHHHHHHHHHTTS-HHHHHHHHHHHHH
T ss_pred chHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 3388999999999999999888876543
No 27
>PHA02955 hypothetical protein; Provisional
Probab=45.34 E-value=18 Score=31.28 Aligned_cols=30 Identities=23% Similarity=0.261 Sum_probs=24.9
Q ss_pred hHHHHHHhcCCHHHHHHHHHHhCCCHHHHH
Q psy13880 214 GSLVWKFLQLSLGERLEICKKIGSKHNDIL 243 (256)
Q Consensus 214 GDLle~Fl~L~~~~q~~ia~~lg~s~~ei~ 243 (256)
--+.|.+..||++++.++|+++|.+.+++.
T Consensus 68 ~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~ 97 (213)
T PHA02955 68 EALIETIENFPEKEQKEIAADIGINIDDYK 97 (213)
T ss_pred HHHHHHHHhCCHHHHHHHHHHhCCChhhcc
Confidence 346678899999999999999999887633
No 28
>PHA02947 S-S bond formation pathway protein; Provisional
Probab=45.14 E-value=18 Score=31.32 Aligned_cols=31 Identities=19% Similarity=0.136 Sum_probs=25.4
Q ss_pred hHHHHHHhcCCHHHHHHHHHHhCCCHHHHHH
Q psy13880 214 GSLVWKFLQLSLGERLEICKKIGSKHNDILD 244 (256)
Q Consensus 214 GDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~ 244 (256)
--+.|.+..||++++.++|+++|.++.++.+
T Consensus 68 ~a~~Et~~~Lp~~qk~~iaa~lgId~~~~~~ 98 (215)
T PHA02947 68 KTFKEVISTLPEKERRELANEIGIDLDNDDP 98 (215)
T ss_pred HHHHHHHHhCCHHHHHHHHHHhCCChhhccc
Confidence 3466778889999999999999998866543
No 29
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=44.75 E-value=32 Score=23.11 Aligned_cols=25 Identities=16% Similarity=0.372 Sum_probs=21.2
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHhhh
Q psy13880 228 RLEICKKIGSKHNDILDELYDIEAL 252 (256)
Q Consensus 228 q~~ia~~lg~s~~ei~~~l~~i~~~ 252 (256)
-.++|+.+|.|...|.++|.+|...
T Consensus 22 ~~ela~~l~~S~rti~~~i~~L~~~ 46 (59)
T PF08280_consen 22 LKELAKKLNISERTIKNDINELNEF 46 (59)
T ss_dssp HHHHHHHCTS-HHHHHHHHHHHHTT
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3589999999999999999999754
No 30
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=44.15 E-value=23 Score=28.06 Aligned_cols=40 Identities=15% Similarity=0.273 Sum_probs=32.6
Q ss_pred eehHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 212 IDGSLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 212 IDGDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
+|-.+|+-...=.+.-+.++|+++|.|+..+.+.+..+..
T Consensus 9 ~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~ 48 (154)
T COG1522 9 IDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEE 48 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4556666666667778999999999999999998888864
No 31
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=43.30 E-value=55 Score=22.09 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=25.5
Q ss_pred HHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHH
Q psy13880 215 SLVWKFLQLSLGERLEICKKIGSKHNDILDELYDI 249 (256)
Q Consensus 215 DLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i 249 (256)
+|++-++.-|.-.-..+|+++|.|+.-..+.+.++
T Consensus 3 ~Lidll~~~P~Vsa~mva~~L~vT~~~A~~li~eL 37 (54)
T PF11972_consen 3 RLIDLLLSRPLVSAPMVAKELGVTPQAAQRLIAEL 37 (54)
T ss_pred HHHHHHHhCccccHHHHHHHhCCCHHHHHHHHHHh
Confidence 56666777777777778888888887777766665
No 32
>PF10685 KGG: Stress-induced bacterial acidophilic repeat motif; InterPro: IPR019626 This repeat contains a highly conserved, characteristic sequence motif, KGG, that is recognised by plants and lower eukaryotes. Further downstream from this motif is a Walker A, nucleotide binding motif. YciG is expressed as part of a three-gene operon, yciGFE and this operon is induced by stress and is regulated by RpoS, which controls the general stress-response in E coli. YciG was shown to be important for stationary-phase resistance to thermal stress and in particular to acid stress [].
Probab=42.97 E-value=23 Score=19.66 Aligned_cols=18 Identities=28% Similarity=0.342 Sum_probs=15.7
Q ss_pred HhcCCHHHHHHHHHHhCC
Q psy13880 220 FLQLSLGERLEICKKIGS 237 (256)
Q Consensus 220 Fl~L~~~~q~~ia~~lg~ 237 (256)
|-.++++++.+|+++-|.
T Consensus 2 Fa~~d~e~~~eig~kGG~ 19 (23)
T PF10685_consen 2 FASMDPEKAREIGRKGGQ 19 (23)
T ss_pred ccccCHHHHHHHHHhcCc
Confidence 678999999999998775
No 33
>PF13730 HTH_36: Helix-turn-helix domain
Probab=42.69 E-value=42 Score=21.73 Aligned_cols=25 Identities=12% Similarity=0.351 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.+..||+.+|.+...|.+-|.++..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3789999999999999998888864
No 34
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=41.20 E-value=48 Score=23.62 Aligned_cols=42 Identities=19% Similarity=0.303 Sum_probs=33.2
Q ss_pred CCCceeehHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHH
Q psy13880 207 PSRGIIDGSLVWKFLQLSLGERLEICKKIGSKHNDILDELYD 248 (256)
Q Consensus 207 ~~k~~IDGDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~ 248 (256)
..+|-+.|+-+.+.++=-+.....+|+.+|.+..++.+.+.+
T Consensus 26 ~~~Gkv~~ee~n~~~e~~p~~~~~lAk~~G~t~~~l~~~~~~ 67 (75)
T TIGR02675 26 LASGKLRGEEINSLLEALPGALQALAKAMGVTRGELRKMLSD 67 (75)
T ss_pred HHcCcccHHHHHHHHHHhHHHHHHHHHHhCCCHHHHHHHHHC
Confidence 356777788777777766678889999999999998877654
No 35
>PHA02591 hypothetical protein; Provisional
Probab=40.63 E-value=32 Score=25.05 Aligned_cols=21 Identities=14% Similarity=0.096 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCHHHHHHHHHH
Q psy13880 228 RLEICKKIGSKHNDILDELYD 248 (256)
Q Consensus 228 q~~ia~~lg~s~~ei~~~l~~ 248 (256)
|.+||+.+|.+.+.|.+.+.+
T Consensus 62 qeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 62 VEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHHHHHHhCCCHHHHHHHHhc
Confidence 678999999999999988763
No 36
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=39.89 E-value=32 Score=24.06 Aligned_cols=25 Identities=16% Similarity=0.205 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHhhh
Q psy13880 228 RLEICKKIGSKHNDILDELYDIEAL 252 (256)
Q Consensus 228 q~~ia~~lg~s~~ei~~~l~~i~~~ 252 (256)
-.+||+.+|.+++++.+.+...+..
T Consensus 23 ~eEiA~~lgis~~~v~~~l~~~~~~ 47 (78)
T PF04539_consen 23 DEEIAEELGISVEEVRELLQASRRP 47 (78)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHSCC
T ss_pred HHHHHHHHcccHHHHHHHHHhCCCC
Confidence 4789999999999999888765543
No 37
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=39.50 E-value=36 Score=28.08 Aligned_cols=25 Identities=12% Similarity=0.250 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.|++||+.+|++++.+.+-|.+++.
T Consensus 151 t~~~iA~~lG~tretvsR~l~~l~~ 175 (202)
T PRK13918 151 THDELAAAVGSVRETVTKVIGELSR 175 (202)
T ss_pred CHHHHHHHhCccHHHHHHHHHHHHH
Confidence 4779999999999999999988864
No 38
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=39.12 E-value=70 Score=21.86 Aligned_cols=38 Identities=5% Similarity=0.086 Sum_probs=28.2
Q ss_pred ehHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 213 DGSLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 213 DGDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
|-.+++...+=... -.++|+.+|+|...|.+.+..++.
T Consensus 2 ~~~il~~L~~~~~~-~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 2 PLRLLALLADNPFS-GEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred hHHHHHHHHcCCcC-HHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44555554443333 789999999999999999998864
No 39
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=39.06 E-value=50 Score=21.92 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=21.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 226 GERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 226 ~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
-.+.++|+.+|.+...+.+.|..+..
T Consensus 26 ~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 26 LTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34789999999999999888887764
No 40
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=38.64 E-value=54 Score=22.69 Aligned_cols=37 Identities=16% Similarity=0.281 Sum_probs=27.5
Q ss_pred HHHHHHhcCCH--HHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 215 SLVWKFLQLSL--GERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 215 DLle~Fl~L~~--~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.+|+-+..-+. -...+||+++|.+...+.+-|..|..
T Consensus 10 ~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 10 KILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34455555545 67899999999999888888877754
No 41
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=38.48 E-value=53 Score=21.01 Aligned_cols=25 Identities=20% Similarity=0.404 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
...++|+.+|+|...+.+.|..+..
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678999999999999888888764
No 42
>PF14174 YycC: YycC-like protein
Probab=38.32 E-value=47 Score=22.06 Aligned_cols=23 Identities=26% Similarity=0.486 Sum_probs=20.1
Q ss_pred hcCCHHHHHHHHHHhCCCHHHHH
Q psy13880 221 LQLSLGERLEICKKIGSKHNDIL 243 (256)
Q Consensus 221 l~L~~~~q~~ia~~lg~s~~ei~ 243 (256)
+.+|.+...++|+++|+..|+++
T Consensus 4 lqIS~eTA~kLs~~L~vPlE~lM 26 (53)
T PF14174_consen 4 LQISPETAVKLSKKLGVPLEQLM 26 (53)
T ss_pred cccCHHHHHHHHHHHCCcHHHHh
Confidence 56789999999999999988874
No 43
>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=38.21 E-value=79 Score=19.70 Aligned_cols=27 Identities=22% Similarity=0.293 Sum_probs=21.1
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHHh
Q psy13880 224 SLGERLEICKKIGSKHNDILDELYDIE 250 (256)
Q Consensus 224 ~~~~q~~ia~~lg~s~~ei~~~l~~i~ 250 (256)
+.+++.++|++.|.+..+|..=+.+.|
T Consensus 12 s~~ek~~L~~~tgls~~Qi~~WF~NaR 38 (40)
T PF05920_consen 12 SKEEKEELAKQTGLSRKQISNWFINAR 38 (40)
T ss_dssp -HHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHhH
Confidence 678888999999999999987776654
No 44
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=37.54 E-value=91 Score=20.81 Aligned_cols=33 Identities=12% Similarity=0.206 Sum_probs=25.3
Q ss_pred eehHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHH
Q psy13880 212 IDGSLVWKFLQLSLGERLEICKKIGSKHNDILDELY 247 (256)
Q Consensus 212 IDGDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~ 247 (256)
|.-+-|.+|+.||. ++.|+++|+++-.+-+...
T Consensus 5 lt~~~L~~~fhlp~---~eAA~~Lgv~~T~LKr~CR 37 (52)
T PF02042_consen 5 LTLEDLSQYFHLPI---KEAAKELGVSVTTLKRRCR 37 (52)
T ss_pred cCHHHHHHHhCCCH---HHHHHHhCCCHHHHHHHHH
Confidence 45678899999985 6789999998776655443
No 45
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=37.28 E-value=42 Score=27.31 Aligned_cols=25 Identities=28% Similarity=0.307 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.|++||+-+|++++.+.+.|.+++.
T Consensus 145 t~~~iA~~lG~tretvsR~l~~l~~ 169 (193)
T TIGR03697 145 SHQAIAEAIGSTRVTITRLLGDLRK 169 (193)
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 5899999999999999998888764
No 46
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=37.15 E-value=39 Score=30.96 Aligned_cols=29 Identities=14% Similarity=-0.003 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 223 LSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 223 L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
..--.|.+||+++|.|+..|.|.|.+-+.
T Consensus 27 ~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 27 HDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34445899999999999999999987654
No 47
>KOG3881|consensus
Probab=35.86 E-value=89 Score=29.60 Aligned_cols=54 Identities=13% Similarity=0.105 Sum_probs=38.0
Q ss_pred CCccceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCCCccCCCCCCeeeeeeccccCcccceEe
Q psy13880 66 GLPRGVYACEFVIESSSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFF 128 (256)
Q Consensus 66 ~~~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~~s~~g~kL~~~~~fhlG~~v~~~~ 128 (256)
..|.|.|++.||.....-.|+.+-..+-+++|.- .. ++ .+.++|-.++.+.++.
T Consensus 200 rVPvW~tdi~Fl~g~~~~~fat~T~~hqvR~YDt--~~-----qR--RPV~~fd~~E~~is~~ 253 (412)
T KOG3881|consen 200 RVPVWITDIRFLEGSPNYKFATITRYHQVRLYDT--RH-----QR--RPVAQFDFLENPISST 253 (412)
T ss_pred eeeeeeccceecCCCCCceEEEEecceeEEEecC--cc-----cC--cceeEeccccCcceee
Confidence 4799999999998865558999999998887653 21 11 3456666666655443
No 48
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=34.15 E-value=51 Score=28.03 Aligned_cols=25 Identities=12% Similarity=0.147 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.|++||+.+|+|++.+.+.|.+++.
T Consensus 171 t~~~lA~~lG~sretvsR~L~~L~~ 195 (226)
T PRK10402 171 KHTQAAEYLGVSYRHLLYVLAQFIQ 195 (226)
T ss_pred hHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 6899999999999999999988864
No 49
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=33.58 E-value=49 Score=22.96 Aligned_cols=26 Identities=23% Similarity=0.463 Sum_probs=21.3
Q ss_pred HHHHHHhCCCHHHHHHHHHHHhhhcC
Q psy13880 229 LEICKKIGSKHNDILDELYDIEALSS 254 (256)
Q Consensus 229 ~~ia~~lg~s~~ei~~~l~~i~~~~~ 254 (256)
.+||+++|.++.|+-+...++..|.+
T Consensus 17 veIAr~~~i~a~e~a~~w~~Ve~Ak~ 42 (63)
T PF11242_consen 17 VEIARKIGITAKEVAKAWAEVETAKE 42 (63)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 57999999999998888877776643
No 50
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=33.33 E-value=64 Score=17.52 Aligned_cols=18 Identities=17% Similarity=0.148 Sum_probs=12.6
Q ss_pred CeeEEEEEeCCCcEEEEe
Q psy13880 81 SSMGFMISDKDKNVVLFM 98 (256)
Q Consensus 81 ~~l~~l~aD~~gNl~vl~ 98 (256)
+.+.-+.-|.+|||++=.
T Consensus 5 n~I~~i~~D~~G~lWigT 22 (24)
T PF07494_consen 5 NNIYSIYEDSDGNLWIGT 22 (24)
T ss_dssp SCEEEEEE-TTSCEEEEE
T ss_pred CeEEEEEEcCCcCEEEEe
Confidence 345667789999999854
No 51
>KOG0772|consensus
Probab=32.62 E-value=4.4e+02 Score=26.20 Aligned_cols=32 Identities=19% Similarity=0.282 Sum_probs=22.1
Q ss_pred eEEEEeccCCCCeeEEEEEecC---eEEEEEEeeC
Q psy13880 6 ELLTVSLGLHGNRPLLLVRTQH---ELLIYQAFRH 37 (256)
Q Consensus 6 e~~~v~~g~~~~~~~l~~~~~~---e~~iy~~~~~ 37 (256)
-|.+--.|....||.+.|+.-. .-+...+|-|
T Consensus 340 SIQ~W~~~~~~v~p~~~vk~AH~~g~~Itsi~FS~ 374 (641)
T KOG0772|consen 340 SIQIWDKGSRTVRPVMKVKDAHLPGQDITSISFSY 374 (641)
T ss_pred ceeeeecCCcccccceEeeeccCCCCceeEEEecc
Confidence 3556666778888888877655 3566677766
No 52
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=32.38 E-value=56 Score=25.18 Aligned_cols=44 Identities=7% Similarity=0.018 Sum_probs=30.8
Q ss_pred eeehHHHHH--HhcCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhcC
Q psy13880 211 IIDGSLVWK--FLQLSLGERLEICKKIGSKHNDILDELYDIEALSS 254 (256)
Q Consensus 211 ~IDGDLle~--Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~~~~~ 254 (256)
.|.-|=+|. ..++---.|++.|+++|+|...+.+.|..-+..+|
T Consensus 41 ~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA 86 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILESARKKIA 86 (106)
T ss_pred EeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 455555554 23333445889999999999999999987766543
No 53
>smart00595 MADF subfamily of SANT domain.
Probab=32.36 E-value=62 Score=23.12 Aligned_cols=24 Identities=13% Similarity=0.212 Sum_probs=21.0
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 228 RLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 228 q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
=.+||.++|.+++++.+++..|++
T Consensus 30 W~~Ia~~l~~~~~~~~~kw~~LR~ 53 (89)
T smart00595 30 WEEIAEELGLSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 367999999999999999998875
No 54
>KOG2111|consensus
Probab=32.23 E-value=4.2e+02 Score=24.63 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=29.7
Q ss_pred CCCCccceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCCC
Q psy13880 64 QPGLPRGVYACEFVIESSSMGFMISDKDKNVVLFMYQPE 102 (256)
Q Consensus 64 ~d~~~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p~ 102 (256)
|.+.+..++|+.|-.+.. -++++.+.|-+|+|+.-+.
T Consensus 222 RG~d~A~iy~iaFSp~~s--~LavsSdKgTlHiF~l~~~ 258 (346)
T KOG2111|consen 222 RGVDRADIYCIAFSPNSS--WLAVSSDKGTLHIFSLRDT 258 (346)
T ss_pred cCCchheEEEEEeCCCcc--EEEEEcCCCeEEEEEeecC
Confidence 346778999999987775 5667888999999999653
No 55
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=31.81 E-value=67 Score=23.78 Aligned_cols=26 Identities=12% Similarity=0.143 Sum_probs=21.5
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 226 GERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 226 ~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
-.|.+||+.+|++++.+.+.|.++..
T Consensus 48 is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 48 VTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34789999999999998888887754
No 56
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=31.62 E-value=91 Score=19.25 Aligned_cols=26 Identities=19% Similarity=0.239 Sum_probs=21.7
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 226 GERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 226 ~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
-...++|+.++.++..+.+.|..+..
T Consensus 15 ~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 15 VSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45788999999999999888888754
No 57
>KOG0303|consensus
Probab=31.28 E-value=3e+02 Score=26.38 Aligned_cols=31 Identities=16% Similarity=0.247 Sum_probs=27.1
Q ss_pred EEEEEcCCeeEEEEEeCCCcEEEEeeCCCcc
Q psy13880 74 CEFVIESSSMGFMISDKDKNVVLFMYQPEAR 104 (256)
Q Consensus 74 ~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~ 104 (256)
.-|-|.|+.+-+||+-.++||+-|++.++.|
T Consensus 268 ~PFyD~dt~ivYl~GKGD~~IRYyEit~d~P 298 (472)
T KOG0303|consen 268 LPFYDPDTSIVYLCGKGDSSIRYFEITNEPP 298 (472)
T ss_pred EeeecCCCCEEEEEecCCcceEEEEecCCCc
Confidence 4567889999999999999999999987664
No 58
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=30.96 E-value=59 Score=27.78 Aligned_cols=25 Identities=16% Similarity=0.299 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.|++||+.+|++++.+.+.|.+++.
T Consensus 181 t~~~IA~~lGisretlsR~L~~L~~ 205 (230)
T PRK09391 181 SRRDIADYLGLTIETVSRALSQLQD 205 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4899999999999999998888764
No 59
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=30.52 E-value=51 Score=26.52 Aligned_cols=41 Identities=12% Similarity=0.195 Sum_probs=33.7
Q ss_pred eehHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Q psy13880 212 IDGSLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIEAL 252 (256)
Q Consensus 212 IDGDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~~~ 252 (256)
+|-.+|+....=++.-..+||+++|.|+..+.+.+..|...
T Consensus 10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56677777766677778899999999999999999888653
No 60
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=30.25 E-value=63 Score=26.70 Aligned_cols=26 Identities=23% Similarity=0.189 Sum_probs=22.2
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 226 GERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 226 ~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
-.|++||+.+|++++.+.+-|.+++.
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34789999999999999998888764
No 61
>KOG0283|consensus
Probab=30.22 E-value=2.4e+02 Score=29.01 Aligned_cols=103 Identities=17% Similarity=0.173 Sum_probs=68.2
Q ss_pred CCceeeeeeecceEEEeeccccc----cCC-C-----CCccceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCCCccCCCC
Q psy13880 39 KGTLKLRFKKLKVLFVSDRSKRA----NEQ-P-----GLPRGVYACEFVIESSSMGFMISDKDKNVVLFMYQPEARESNG 108 (256)
Q Consensus 39 ~g~l~~r~~~~~~~~~~~~~~~~----~~~-d-----~~~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~~s~~ 108 (256)
.-.|-+.|-|-+.++-.+-|++. -.+ + .++-.|||++|-.-|+. .|+.+--+|-+++-.....
T Consensus 370 ~DILDlSWSKn~fLLSSSMDKTVRLWh~~~~~CL~~F~HndfVTcVaFnPvDDr-yFiSGSLD~KvRiWsI~d~------ 442 (712)
T KOG0283|consen 370 ADILDLSWSKNNFLLSSSMDKTVRLWHPGRKECLKVFSHNDFVTCVAFNPVDDR-YFISGSLDGKVRLWSISDK------ 442 (712)
T ss_pred hhheecccccCCeeEeccccccEEeecCCCcceeeEEecCCeeEEEEecccCCC-cEeecccccceEEeecCcC------
Confidence 55677888887887778888765 111 1 45667999999955444 8999999999999876432
Q ss_pred CCeeeeeeccccCcccceEeeeecCCCCCCCCCCCCCcceEEEEeCCcceEEEEecC
Q psy13880 109 GHRLIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARSRFLTWYASLDGALGFFLPLP 165 (256)
Q Consensus 109 g~kL~~~~~fhlG~~v~~~~~~~~~~~~~~~~~~~~~~~~ll~~T~~GsIg~l~pl~ 165 (256)
+...-.+ +-+.||+++- .| .....+.||..|..-..-.-.
T Consensus 443 --~Vv~W~D--l~~lITAvcy---~P----------dGk~avIGt~~G~C~fY~t~~ 482 (712)
T KOG0283|consen 443 --KVVDWND--LRDLITAVCY---SP----------DGKGAVIGTFNGYCRFYDTEG 482 (712)
T ss_pred --eeEeehh--hhhhheeEEe---cc----------CCceEEEEEeccEEEEEEccC
Confidence 3333333 3388887663 22 124577888888776665443
No 62
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=29.73 E-value=73 Score=20.51 Aligned_cols=20 Identities=15% Similarity=0.242 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q psy13880 228 RLEICKKIGSKHNDILDELY 247 (256)
Q Consensus 228 q~~ia~~lg~s~~ei~~~l~ 247 (256)
.++||+.+|+|+..|.+-|.
T Consensus 2 i~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHh
Confidence 47899999999887777664
No 63
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=29.46 E-value=55 Score=24.28 Aligned_cols=39 Identities=15% Similarity=0.214 Sum_probs=29.0
Q ss_pred ehHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 213 DGSLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 213 DGDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
|=.++..+..-++-...++|+.+|.++..+.+.+..+..
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 334555555545556789999999999999988888754
No 64
>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=29.44 E-value=54 Score=21.31 Aligned_cols=24 Identities=25% Similarity=0.331 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q psy13880 223 LSLGERLEICKKIGSKHNDILDEL 246 (256)
Q Consensus 223 L~~~~q~~ia~~lg~s~~ei~~~l 246 (256)
.+.+++.+||.++|.+..+|..=.
T Consensus 25 p~~~~~~~la~~l~l~~~~V~~WF 48 (57)
T PF00046_consen 25 PSKEEREELAKELGLTERQVKNWF 48 (57)
T ss_dssp CHHHHHHHHHHHHTSSHHHHHHHH
T ss_pred ccccccccccccccccccccccCH
Confidence 678899999999999999886433
No 65
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=29.25 E-value=65 Score=21.73 Aligned_cols=24 Identities=25% Similarity=0.522 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIE 250 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~ 250 (256)
.-.+.+++.|.++++|++.|++++
T Consensus 33 ~L~eA~~~~~ld~~~vl~~L~~lq 56 (56)
T PF04405_consen 33 SLEEACEEKGLDPEEVLEELNALQ 56 (56)
T ss_pred hHHHHHHHcCCCHHHHHHHHHHcC
Confidence 346788999999999999998763
No 66
>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=29.14 E-value=66 Score=20.24 Aligned_cols=22 Identities=23% Similarity=0.256 Sum_probs=16.5
Q ss_pred HHHHHHHHHhCCCHHHHHHHHH
Q psy13880 226 GERLEICKKIGSKHNDILDELY 247 (256)
Q Consensus 226 ~~q~~ia~~lg~s~~ei~~~l~ 247 (256)
....+||+.+|+++..|.+.|.
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHHC
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 4578899999999999988764
No 67
>KOG1332|consensus
Probab=29.00 E-value=79 Score=28.35 Aligned_cols=36 Identities=11% Similarity=0.198 Sum_probs=32.4
Q ss_pred CccceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCCC
Q psy13880 67 LPRGVYACEFVIESSSMGFMISDKDKNVVLFMYQPE 102 (256)
Q Consensus 67 ~~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p~ 102 (256)
+...|.++.+-..+-.|.++++-.+|++.+|.|+.+
T Consensus 101 h~~SVNsV~wapheygl~LacasSDG~vsvl~~~~~ 136 (299)
T KOG1332|consen 101 HSASVNSVAWAPHEYGLLLACASSDGKVSVLTYDSS 136 (299)
T ss_pred hcccceeecccccccceEEEEeeCCCcEEEEEEcCC
Confidence 445699999999999999999999999999999865
No 68
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=28.91 E-value=46 Score=26.60 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=19.4
Q ss_pred HHHHHHHHHhCCCHHHHH----HHHHHHhhh
Q psy13880 226 GERLEICKKIGSKHNDIL----DELYDIEAL 252 (256)
Q Consensus 226 ~~q~~ia~~lg~s~~ei~----~~l~~i~~~ 252 (256)
..|++||+.+|+|...|. +.+++|..|
T Consensus 24 ~tQ~eIA~~L~TTraNvSaIEkrA~enIeka 54 (143)
T COG1356 24 LTQSEIARILKTTRANVSAIEKRALENIEKA 54 (143)
T ss_pred ccHHHHHHHHccchhhHHHHHHHHHHHHHHH
Confidence 368999999999887662 455555544
No 69
>PHA02662 ORF131 putative membrane protein; Provisional
Probab=28.66 E-value=41 Score=29.29 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=22.4
Q ss_pred hHHHHHHhcCCHHHHHHHHHHhCCCH
Q psy13880 214 GSLVWKFLQLSLGERLEICKKIGSKH 239 (256)
Q Consensus 214 GDLle~Fl~L~~~~q~~ia~~lg~s~ 239 (256)
--+.|.+..||++++.+|++++|.+.
T Consensus 81 ~Al~Et~~~Lp~~qK~~iaa~LGId~ 106 (226)
T PHA02662 81 AALAETLAELPRADRLAVAKELGVDP 106 (226)
T ss_pred HHHHHHHHhCCHHHHHHHHHHhCCCC
Confidence 45678899999999999999999754
No 70
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=28.48 E-value=81 Score=22.94 Aligned_cols=35 Identities=23% Similarity=0.330 Sum_probs=21.9
Q ss_pred HHHHHhcCCH-HHHHHHHHHhCCCHHHHHHHHHHHh
Q psy13880 216 LVWKFLQLSL-GERLEICKKIGSKHNDILDELYDIE 250 (256)
Q Consensus 216 Lle~Fl~L~~-~~q~~ia~~lg~s~~ei~~~l~~i~ 250 (256)
+|+.|..-.. -.=++||++++.++..|...+.+++
T Consensus 13 lV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le 48 (78)
T PF03444_consen 13 LVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE 48 (78)
T ss_pred HHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH
Confidence 4444444322 1236788899998888876666654
No 71
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=27.06 E-value=74 Score=26.91 Aligned_cols=25 Identities=20% Similarity=0.145 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.|++||+.+|++++.+.+-|.+++.
T Consensus 186 t~~~iA~~lG~sr~tvsR~l~~l~~ 210 (235)
T PRK11161 186 TRGDIGNYLGLTVETISRLLGRFQK 210 (235)
T ss_pred cHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 4789999999999999998888764
No 72
>PF09124 Endonuc-dimeris: T4 recombination endonuclease VII, dimerisation; InterPro: IPR015208 This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three alpha helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove []. ; PDB: 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=27.05 E-value=82 Score=21.26 Aligned_cols=25 Identities=20% Similarity=0.101 Sum_probs=21.1
Q ss_pred hHHHHHHhcCCHHHHHHHHHHhCCC
Q psy13880 214 GSLVWKFLQLSLGERLEICKKIGSK 238 (256)
Q Consensus 214 GDLle~Fl~L~~~~q~~ia~~lg~s 238 (256)
+|+...|..|+.+++...+...|..
T Consensus 7 ~D~~K~FSRl~k~eMiaem~~~G~~ 31 (54)
T PF09124_consen 7 PDKVKWFSRLTKPEMIAEMDSYGFE 31 (54)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHTT--
T ss_pred hHHHHHHHhcCHHHHHHHHHHhCCc
Confidence 7999999999999999999998853
No 73
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=26.84 E-value=1e+02 Score=20.88 Aligned_cols=25 Identities=12% Similarity=0.303 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.-.+||+.+|+++..+.+.+..+..
T Consensus 24 ~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 24 RTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp BHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cHHHHHHHHCCChHHHHHHHHHHHH
Confidence 3478999999998877766666643
No 74
>PF14727 PHTB1_N: PTHB1 N-terminus
Probab=26.77 E-value=4.2e+02 Score=25.40 Aligned_cols=58 Identities=19% Similarity=0.310 Sum_probs=42.6
Q ss_pred EEEEEEcCCeeEEEEEeCCCcEEEEeeCCCccCCC-------------CCCeeeeeeccccCcccceEeeeec
Q psy13880 73 ACEFVIESSSMGFMISDKDKNVVLFMYQPEARESN-------------GGHRLIKKTDFHLGQHVNTFFKIRC 132 (256)
Q Consensus 73 a~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~~s~-------------~g~kL~~~~~fhlG~~v~~~~~~~~ 132 (256)
...+....+ +|+.+-....|-.|+|..-+..+. +++++...=.|.+||.+..+.-+..
T Consensus 179 Pl~Y~~~tD--sfvt~sss~~l~~Yky~~La~~s~~~~~~~~~~~~~~~~k~l~~dWs~nlGE~~l~i~v~~~ 249 (418)
T PF14727_consen 179 PLCYCPRTD--SFVTASSSWTLECYKYQDLASASEASSRQSGTEQDISSGKKLNPDWSFNLGEQALDIQVVRF 249 (418)
T ss_pred CeEEeecCC--EEEEecCceeEEEecHHHhhhccccccccccccccccccccccceeEEECCceeEEEEEEEc
Confidence 344444444 789999999999999964332222 5789999999999999988876554
No 75
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.58 E-value=94 Score=24.34 Aligned_cols=38 Identities=11% Similarity=0.055 Sum_probs=31.9
Q ss_pred hHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 214 GSLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 214 GDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
-+|++.|-.||.++|+.+.+.+....+.+-+.++++-.
T Consensus 90 ~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~~~~~~~ 127 (135)
T PRK09706 90 KELLELFDALPESEQDAQLSEMRARVENFNKLFEELLK 127 (135)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999999988777777777776643
No 76
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=26.25 E-value=1.2e+02 Score=18.89 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIE 250 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~ 250 (256)
...+||+.+|.++..|.+.+..+.
T Consensus 20 s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 20 TNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999998888777654
No 77
>KOG0296|consensus
Probab=26.09 E-value=3.2e+02 Score=25.79 Aligned_cols=74 Identities=20% Similarity=0.305 Sum_probs=45.3
Q ss_pred ccceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCCCccCCCCCCeeeeeeccccCcccceEeeeecCCCCCCCCCCCCCcc
Q psy13880 68 PRGVYACEFVIESSSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARSRF 147 (256)
Q Consensus 68 ~~~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p~~~~s~~g~kL~~~~~fhlG~~v~~~~~~~~~~~~~~~~~~~~~~~ 147 (256)
.-.|||+.|--++. .++.+|.+|-+++++.... ...+.-. ..+.-+.=+...| ..+
T Consensus 106 KDSVt~~~Fshdgt--lLATGdmsG~v~v~~~stg--------~~~~~~~----~e~~dieWl~WHp----------~a~ 161 (399)
T KOG0296|consen 106 KDSVTCCSFSHDGT--LLATGDMSGKVLVFKVSTG--------GEQWKLD----QEVEDIEWLKWHP----------RAH 161 (399)
T ss_pred CCceEEEEEccCce--EEEecCCCccEEEEEcccC--------ceEEEee----cccCceEEEEecc----------ccc
Confidence 33699999987775 5667899999999987432 1122211 1222222222222 247
Q ss_pred eEEEEeCCcceEEEEecCh
Q psy13880 148 LTWYASLDGALGFFLPLPE 166 (256)
Q Consensus 148 ~ll~~T~~GsIg~l~pl~~ 166 (256)
.+++|+.+|++-+-- +++
T Consensus 162 illAG~~DGsvWmw~-ip~ 179 (399)
T KOG0296|consen 162 ILLAGSTDGSVWMWQ-IPS 179 (399)
T ss_pred EEEeecCCCcEEEEE-CCC
Confidence 789999999987754 444
No 78
>PF07751 Abi_2: Abi-like protein; InterPro: IPR011664 Bacteria have numerous mechanisms to resist bacteriophage infection. While most are based on preventing infection in the first place, the abortive infection (Abi) systems provide protection by the abortion of an existing phage infection []. Typically, these Abi systems target a crucial step of phage multiplication such as replication, transcription or translation, and lead to the death of the infected cell. These protein sequences, found in various bacterial species, are similar to those of the AbiD and AbiF proteins from Lactococcus species [, ]. The proteins are thought to have helix-turn-helix motifs, found in many DNA-binding proteins, allowing them to perform their function [].
Probab=26.02 E-value=1e+02 Score=24.97 Aligned_cols=42 Identities=19% Similarity=0.235 Sum_probs=33.1
Q ss_pred hHHHHHHhcCCHHHHHHHHHHhC-CCHH---HHHHHHHHHhhhcCC
Q psy13880 214 GSLVWKFLQLSLGERLEICKKIG-SKHN---DILDELYDIEALSSH 255 (256)
Q Consensus 214 GDLle~Fl~L~~~~q~~ia~~lg-~s~~---ei~~~l~~i~~~~~~ 255 (256)
|++..-|..|..+.+..+++.++ .+.. ..++.|.++|...||
T Consensus 139 g~~~~l~~~l~~~~~~~i~~~~~~~~~~~~~~~l~~i~~lRN~~AH 184 (191)
T PF07751_consen 139 GNLSKLYKFLKPSLKKKIAKEFFDISRKDLSNWLNSIRDLRNRIAH 184 (191)
T ss_pred cchhHHHHhcCHHHHHHHHHHhccCChhHHHHHHHHHHHHHhHhcc
Confidence 56666677799999999999998 5554 556777778888887
No 79
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=25.65 E-value=73 Score=23.34 Aligned_cols=20 Identities=25% Similarity=0.436 Sum_probs=13.3
Q ss_pred HHHHHHHHhCCCHHHHHHHH
Q psy13880 227 ERLEICKKIGSKHNDILDEL 246 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l 246 (256)
.|.+||+++|.+..-|.+.|
T Consensus 5 tq~eIA~~lGks~s~Vs~~l 24 (93)
T PF08535_consen 5 TQEEIAKRLGKSRSWVSNHL 24 (93)
T ss_dssp -HHHHHHHTT--HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 58999999998876665544
No 80
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=25.46 E-value=75 Score=21.94 Aligned_cols=18 Identities=11% Similarity=0.226 Sum_probs=8.7
Q ss_pred HHHHHHHHhCCCHHHHHH
Q psy13880 227 ERLEICKKIGSKHNDILD 244 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~ 244 (256)
.|.++|+.+|.+...|.+
T Consensus 20 t~~~lA~~~gis~~tis~ 37 (78)
T TIGR02607 20 SIRALAKALGVSRSTLSR 37 (78)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 345555555554444433
No 81
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=25.32 E-value=1.2e+02 Score=19.74 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
...++|+.+|++...+.+.|..+..
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3678999999999888888877754
No 82
>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=25.23 E-value=1.3e+02 Score=18.24 Aligned_cols=28 Identities=14% Similarity=0.039 Sum_probs=21.6
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 224 SLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 224 ~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
..-.+.+||+.+|.+...|.+.+.....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4445788999999999988887776543
No 83
>PF05550 Peptidase_C53: Pestivirus Npro endopeptidase C53; InterPro: IPR008751 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C53 (clan C-). The active site residues occur in the order E, H, C in the sequence which is unlike that in any other family. They are unique to pestiviruses. The N-terminal cysteine peptidase (Npro) encoded by the bovine viral diarrhoea virus genome is responsible for the self-cleavage that releases the N terminus of the core protein. This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core [, , , ].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=24.82 E-value=1.2e+02 Score=24.81 Aligned_cols=46 Identities=28% Similarity=0.326 Sum_probs=27.3
Q ss_pred cCCCCeeEEEEEecCeEEEEEEeeCCCCceeeeeeecceEEEeeccccccCCCCCccceEEE
Q psy13880 13 GLHGNRPLLLVRTQHELLIYQAFRHPKGTLKLRFKKLKVLFVSDRSKRANEQPGLPRGVYAC 74 (256)
Q Consensus 13 g~~~~~~~l~~~~~~e~~iy~~~~~~~g~l~~r~~~~~~~~~~~~~~~~~~~d~~~~~vta~ 74 (256)
|..|.-=+|.|-++.=+++=.|-+...-+|+-.+.+++. |+|||++
T Consensus 123 GSDgkLYHiyvC~DgCIllk~a~r~~~~vlkW~~N~Ldc----------------PLWVtSC 168 (168)
T PF05550_consen 123 GSDGKLYHIYVCIDGCILLKSASRNQPRVLKWVHNKLDC----------------PLWVTSC 168 (168)
T ss_pred CCCCCEEEEEEeccceEEeehhhcCCcceeEeeccccCC----------------cceeeeC
Confidence 556666666666666666655555545455443433333 8999874
No 84
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=24.52 E-value=75 Score=21.88 Aligned_cols=17 Identities=24% Similarity=0.395 Sum_probs=14.6
Q ss_pred HHHHHHHHhCCCHHHHH
Q psy13880 227 ERLEICKKIGSKHNDIL 243 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~ 243 (256)
+-++||+++|++...|.
T Consensus 24 ~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIR 40 (60)
T ss_pred cHHHHHHHHCCCHHHHH
Confidence 45899999999998885
No 85
>PF14157 YmzC: YmzC-like protein; PDB: 3KVP_E.
Probab=24.42 E-value=1.3e+02 Score=21.02 Aligned_cols=20 Identities=25% Similarity=0.642 Sum_probs=16.6
Q ss_pred EEEEEeCCCcEEEEeeCCCc
Q psy13880 84 GFMISDKDKNVVLFMYQPEA 103 (256)
Q Consensus 84 ~~l~aD~~gNl~vl~~~p~~ 103 (256)
+|.+-|.++-|.||+|||.-
T Consensus 31 ~Fav~~e~~~iKIfkyd~~t 50 (63)
T PF14157_consen 31 HFAVVDEDGQIKIFKYDEDT 50 (63)
T ss_dssp EEEEE-ETTEEEEEEEETTT
T ss_pred EEEEEecCCeEEEEEeCCCC
Confidence 78888999999999999853
No 86
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=24.40 E-value=1.3e+02 Score=19.07 Aligned_cols=29 Identities=10% Similarity=0.080 Sum_probs=21.8
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 223 LSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 223 L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
...-...+|++.+|.+...+.+.|..+..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44445678999999988888887777653
No 87
>PF09669 Phage_pRha: Phage regulatory protein Rha (Phage_pRha); InterPro: IPR019104 This entry represents a family of proteins which are encoded in temperate phages and bacterial prophage regions. They include the product of the late operon rha gene from lambdoid phage phi-80. The presence of this gene interferes with the infection of bacterial strains lacking the integration host factor that regulates the rha gene. Rha is thought to function as a phage regulatory protein.
Probab=24.38 E-value=1.1e+02 Score=22.47 Aligned_cols=23 Identities=22% Similarity=0.525 Sum_probs=20.7
Q ss_pred HHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 229 LEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 229 ~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.+||+..|.....|+++|+.+..
T Consensus 5 ~~IAe~~gk~H~~Vlr~I~~~~~ 27 (93)
T PF09669_consen 5 REIAEMFGKRHKNVLRDIRKLIE 27 (93)
T ss_pred HHHHHHHCccHHHHHHHHHHHHh
Confidence 58999999999999999998863
No 88
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.23 E-value=1.1e+02 Score=19.33 Aligned_cols=22 Identities=5% Similarity=0.161 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCCHHHHHHHHHH
Q psy13880 227 ERLEICKKIGSKHNDILDELYD 248 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~ 248 (256)
-+++||+..|++...|.+-+.+
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHHh
Confidence 5799999999999988877654
No 89
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=24.21 E-value=1.1e+02 Score=20.95 Aligned_cols=24 Identities=21% Similarity=0.423 Sum_probs=18.4
Q ss_pred HHHHHHhCCCHHHHHHHHHHHhhh
Q psy13880 229 LEICKKIGSKHNDILDELYDIEAL 252 (256)
Q Consensus 229 ~~ia~~lg~s~~ei~~~l~~i~~~ 252 (256)
-+||++.|.|+.-|.+.|..++.|
T Consensus 8 s~iAd~~GiTRSvIVNALRKleSa 31 (61)
T PF08222_consen 8 SKIADRVGITRSVIVNALRKLESA 31 (61)
T ss_dssp HHHHHHHT--HHHHHHHHHHHHHT
T ss_pred HHHHHHhCccHHHHHHHHHHHHhc
Confidence 479999999999999888887654
No 90
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=24.15 E-value=88 Score=23.74 Aligned_cols=29 Identities=10% Similarity=0.021 Sum_probs=23.3
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 223 LSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 223 L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
+-.=.|++.|..+|.|...+++.|..-+.
T Consensus 47 ~~~l~QeeAA~rMgISr~Tfwr~l~sAR~ 75 (99)
T COG1342 47 YEGLTQEEAALRMGISRQTFWRLLTSARK 75 (99)
T ss_pred HhhccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 34446889999999999999998876554
No 91
>KOG0272|consensus
Probab=23.60 E-value=3.2e+02 Score=26.28 Aligned_cols=89 Identities=18% Similarity=0.147 Sum_probs=61.3
Q ss_pred eEEEEeccCCCCeeEEEEEecCeEEEEEEeeCCCCceeeeeeecc-eEEEeeccccccCCCCCccceEEEEEEEcCCeeE
Q psy13880 6 ELLTVSLGLHGNRPLLLVRTQHELLIYQAFRHPKGTLKLRFKKLK-VLFVSDRSKRANEQPGLPRGVYACEFVIESSSMG 84 (256)
Q Consensus 6 e~~~v~~g~~~~~~~l~~~~~~e~~iy~~~~~~~g~l~~r~~~~~-~~~~~~~~~~~~~~d~~~~~vta~~fL~~~~~l~ 84 (256)
-+.+++.+.-+.||+..+....+..+...=-- .|..++ |..-+ +.+...+. +.-.|+|++|-..++.+.
T Consensus 164 ~~~l~~SQ~gd~rPis~~~fS~ds~~laT~sw-sG~~kv-W~~~~~~~~~~l~g--------H~~~v~~~~fhP~~~~~~ 233 (459)
T KOG0272|consen 164 SLELVCSQVGDTRPISGCSFSRDSKHLATGSW-SGLVKV-WSVPQCNLLQTLRG--------HTSRVGAAVFHPVDSDLN 233 (459)
T ss_pred hhhhhhhhccCCCcceeeEeecCCCeEEEeec-CCceeE-eecCCcceeEEEec--------cccceeeEEEccCCCccc
Confidence 45577888889999998887775544433322 555555 44222 34444443 345799999987766678
Q ss_pred EEEEeCCCcEEEEeeCCCcc
Q psy13880 85 FMISDKDKNVVLFMYQPEAR 104 (256)
Q Consensus 85 ~l~aD~~gNl~vl~~~p~~~ 104 (256)
++.+-.+|-+.++.++.+.|
T Consensus 234 lat~s~Dgtvklw~~~~e~~ 253 (459)
T KOG0272|consen 234 LATASADGTVKLWKLSQETP 253 (459)
T ss_pred eeeeccCCceeeeccCCCcc
Confidence 99999999999999987544
No 92
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=23.58 E-value=1.2e+02 Score=20.89 Aligned_cols=25 Identities=20% Similarity=0.149 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.-.+||+.+|.+..++...|..+..
T Consensus 17 ~T~eiA~~~gls~~~aR~yL~~Le~ 41 (62)
T PF04703_consen 17 KTREIADALGLSIYQARYYLEKLEK 41 (62)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3469999999999999999988764
No 93
>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=23.04 E-value=92 Score=18.36 Aligned_cols=18 Identities=22% Similarity=0.230 Sum_probs=12.8
Q ss_pred HHHHHhCCCHHHHHHHHH
Q psy13880 230 EICKKIGSKHNDILDELY 247 (256)
Q Consensus 230 ~ia~~lg~s~~ei~~~l~ 247 (256)
.-|+++|.|.+||.+-|.
T Consensus 10 ~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 10 KEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHTT--HHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHH
Confidence 348889999999988775
No 94
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=22.93 E-value=99 Score=21.31 Aligned_cols=20 Identities=10% Similarity=0.152 Sum_probs=15.8
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q psy13880 228 RLEICKKIGSKHNDILDELY 247 (256)
Q Consensus 228 q~~ia~~lg~s~~ei~~~l~ 247 (256)
+.+||+.+|++...|.+.|.
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHC
Confidence 67899999988877776654
No 95
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=22.34 E-value=1.8e+02 Score=17.28 Aligned_cols=20 Identities=20% Similarity=0.459 Sum_probs=16.3
Q ss_pred HHHHHHhCCCHHHHHHHHHH
Q psy13880 229 LEICKKIGSKHNDILDELYD 248 (256)
Q Consensus 229 ~~ia~~lg~s~~ei~~~l~~ 248 (256)
.++|++.|.|..++++.+.+
T Consensus 15 ~~~a~~~g~s~s~~ir~ai~ 34 (39)
T PF01402_consen 15 DELAKELGRSRSELIREAIR 34 (39)
T ss_dssp HHHHHHHTSSHHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 56799999999999877653
No 96
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=22.12 E-value=2e+02 Score=17.62 Aligned_cols=36 Identities=14% Similarity=0.122 Sum_probs=29.4
Q ss_pred HHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q psy13880 215 SLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIE 250 (256)
Q Consensus 215 DLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~ 250 (256)
.|.+.|-+++.+.=+.+.++-+-+++..+..|.+++
T Consensus 7 ~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~~ 42 (42)
T PF02845_consen 7 QLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEMS 42 (42)
T ss_dssp HHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred HHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 467889999999999999999989998888887653
No 97
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=22.11 E-value=1.1e+02 Score=20.92 Aligned_cols=23 Identities=13% Similarity=0.192 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHh
Q psy13880 228 RLEICKKIGSKHNDILDELYDIE 250 (256)
Q Consensus 228 q~~ia~~lg~s~~ei~~~l~~i~ 250 (256)
..+||++++++++.|...|+.+.
T Consensus 17 ~~eLa~~~~~s~~~ve~mL~~l~ 39 (69)
T PF09012_consen 17 LAELAREFGISPEAVEAMLEQLI 39 (69)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHHHHH
Confidence 46899999999999988888764
No 98
>PF06739 SBBP: Beta-propeller repeat; InterPro: IPR010620 This family is related to IPR001680 from INTERPRO and is likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller.
Probab=22.09 E-value=1.3e+02 Score=18.39 Aligned_cols=16 Identities=19% Similarity=0.241 Sum_probs=12.0
Q ss_pred EEEEEeCCCcEEEEee
Q psy13880 84 GFMISDKDKNVVLFMY 99 (256)
Q Consensus 84 ~~l~aD~~gNl~vl~~ 99 (256)
.=++.|.+||+++.-+
T Consensus 16 ~~IavD~~GNiYv~G~ 31 (38)
T PF06739_consen 16 NGIAVDSNGNIYVTGY 31 (38)
T ss_pred EEEEECCCCCEEEEEe
Confidence 4456899999988765
No 99
>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=21.84 E-value=1.4e+02 Score=18.76 Aligned_cols=24 Identities=17% Similarity=0.104 Sum_probs=17.8
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHH
Q psy13880 224 SLGERLEICKKIGSKHNDILDELY 247 (256)
Q Consensus 224 ~~~~q~~ia~~lg~s~~ei~~~l~ 247 (256)
..-...+||+.+|.|.+.|.+...
T Consensus 19 ~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp ST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHH
Confidence 334478999999999988866544
No 100
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=21.75 E-value=1e+02 Score=27.40 Aligned_cols=27 Identities=15% Similarity=0.087 Sum_probs=22.9
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 225 LGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 225 ~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
.-.-.++|+.+|+|...|.+||..|+.
T Consensus 31 ~vtv~eLa~~l~VS~~TIRRDL~~Le~ 57 (269)
T PRK09802 31 SVQVNDLSALYGVSTVTIRNDLAFLEK 57 (269)
T ss_pred CEeHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 344578999999999999999999854
No 101
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.75 E-value=1e+02 Score=23.71 Aligned_cols=39 Identities=15% Similarity=0.195 Sum_probs=32.1
Q ss_pred eeehHHHHHHhc-CCHHHHHHHHHHhCCCHHHHHHHHHHH
Q psy13880 211 IIDGSLVWKFLQ-LSLGERLEICKKIGSKHNDILDELYDI 249 (256)
Q Consensus 211 ~IDGDLle~Fl~-L~~~~q~~ia~~lg~s~~ei~~~l~~i 249 (256)
-||-|-|..+.. -|...+.|+|+.+|+++..|+.-|..+
T Consensus 56 Kid~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 56 KIDRDELKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred cccHHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 678888888755 477778899999999999999888765
No 102
>KOG0282|consensus
Probab=21.53 E-value=3.6e+02 Score=26.35 Aligned_cols=31 Identities=13% Similarity=0.222 Sum_probs=25.6
Q ss_pred ceEEEEEEEcCCeeEEEEEeCCCcEEEEeeCCC
Q psy13880 70 GVYACEFVIESSSMGFMISDKDKNVVLFMYQPE 102 (256)
Q Consensus 70 ~vta~~fL~~~~~l~~l~aD~~gNl~vl~~~p~ 102 (256)
.-+.++|-.++. +++.+|.+|+++++.+.+.
T Consensus 434 ys~~v~fSpDG~--~l~SGdsdG~v~~wdwkt~ 464 (503)
T KOG0282|consen 434 YSCQVDFSPDGR--TLCSGDSDGKVNFWDWKTT 464 (503)
T ss_pred ceeeEEEcCCCC--eEEeecCCccEEEeechhh
Confidence 456788888886 7888999999999998753
No 103
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=20.96 E-value=78 Score=23.85 Aligned_cols=17 Identities=29% Similarity=0.386 Sum_probs=11.7
Q ss_pred HHHHHHHHhCCCHHHHH
Q psy13880 227 ERLEICKKIGSKHNDIL 243 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~ 243 (256)
.|++||+++|+|...|.
T Consensus 57 tQrEIa~~lGiS~atIs 73 (94)
T TIGR01321 57 SQREIASKLGVSIATIT 73 (94)
T ss_pred CHHHHHHHhCCChhhhh
Confidence 47777888887665554
No 104
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=20.62 E-value=1.2e+02 Score=19.21 Aligned_cols=22 Identities=18% Similarity=0.228 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCCHHHHHHHHHH
Q psy13880 227 ERLEICKKIGSKHNDILDELYD 248 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~ 248 (256)
.|+++|+.+|.++..|.+-+..
T Consensus 11 s~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTT
T ss_pred CHHHHHHHhCCCcchhHHHhcC
Confidence 3689999999988877765543
No 105
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.51 E-value=1e+02 Score=21.72 Aligned_cols=45 Identities=22% Similarity=0.271 Sum_probs=32.2
Q ss_pred CCCCCCccccccccCCCccCCCCCCceeehHHHHHHhcCCHHHHHHHHHHhCC
Q psy13880 185 HTGGLNPRAFRTYKGKGYYAGNPSRGIIDGSLVWKFLQLSLGERLEICKKIGS 237 (256)
Q Consensus 185 ~~~Gl~~~~~R~~~~~~~~~~~~~k~~IDGDLle~Fl~L~~~~q~~ia~~lg~ 237 (256)
.+|=++|..|-..+.+. -..+ -|++.+=..+|++++..||.++|+
T Consensus 24 N~gvl~~e~~d~~~~ed------Ltdi--y~mvkkkenfSpsEmqaiA~eL~r 68 (71)
T COG4840 24 NVGVLDPEKYDNANYED------LTDI--YDMVKKKENFSPSEMQAIADELGR 68 (71)
T ss_pred hhhccCHHhcccccHHH------HHHH--HHHHHHhccCCHHHHHHHHHHHHH
Confidence 45778888887644221 1111 477888888999999999999984
No 106
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=20.45 E-value=1.6e+02 Score=19.93 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=24.2
Q ss_pred hcCCHHHHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 221 LQLSLGERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 221 l~L~~~~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
+.-......+||+.+|.+...+.+.|..+..
T Consensus 18 l~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 18 LKNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3445666789999999999888888877753
No 107
>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=20.33 E-value=1.7e+02 Score=18.22 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhh
Q psy13880 227 ERLEICKKIGSKHNDILDELYDIEA 251 (256)
Q Consensus 227 ~q~~ia~~lg~s~~ei~~~l~~i~~ 251 (256)
..++||+.+|.++..|.+.+..+..
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5688999999999988888776544
No 108
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=20.15 E-value=2.5e+02 Score=22.41 Aligned_cols=37 Identities=16% Similarity=0.124 Sum_probs=30.8
Q ss_pred hHHHHHHhcCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q psy13880 214 GSLVWKFLQLSLGERLEICKKIGSKHNDILDELYDIE 250 (256)
Q Consensus 214 GDLle~Fl~L~~~~q~~ia~~lg~s~~ei~~~l~~i~ 250 (256)
.--++..++|+..+-+++.++.|.+.||..+-...+.
T Consensus 90 ~~tLe~Llemsd~el~~~l~~~g~~~EE~rRL~~Al~ 126 (129)
T PF13543_consen 90 VLTLEALLEMSDEELKEILNRCGAREEECRRLCRALS 126 (129)
T ss_pred hcCHHHHHhCCHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4457889999999999999999999998877665543
Done!