Query 020672
Match_columns 323
No_of_seqs 145 out of 1122
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:14:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020672.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020672hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0217 Uncharacterized conser 100.0 3.6E-88 7.8E-93 621.0 25.9 233 76-321 2-236 (241)
2 PRK12378 hypothetical protein; 100.0 6.2E-86 1.3E-90 611.3 27.6 232 76-322 1-234 (235)
3 PRK00110 hypothetical protein; 100.0 3.6E-85 7.9E-90 609.6 28.3 232 75-321 1-234 (245)
4 TIGR01033 DNA-binding regulato 100.0 5.1E-84 1.1E-88 599.9 28.3 235 75-322 1-237 (238)
5 PF01709 Transcrip_reg: Transc 100.0 3E-83 6.6E-88 593.7 21.5 232 78-322 1-233 (234)
6 KOG2972 Uncharacterized conser 100.0 1.6E-71 3.5E-76 510.6 21.6 254 64-322 18-273 (276)
7 PRK07562 ribonucleotide-diphos 98.8 1.3E-08 2.7E-13 112.2 7.2 70 80-149 296-371 (1220)
8 cd04888 ACT_PheB-BS C-terminal 89.0 0.97 2.1E-05 33.6 5.0 64 255-319 5-73 (76)
9 PF03927 NapD: NapD protein; 81.2 1.7 3.6E-05 34.2 3.1 60 254-318 7-69 (79)
10 PF13291 ACT_4: ACT domain; PD 77.9 4.8 0.0001 30.5 4.6 58 259-319 15-79 (80)
11 cd04878 ACT_AHAS N-terminal AC 76.5 7.5 0.00016 27.6 5.2 58 259-318 9-71 (72)
12 TIGR00119 acolac_sm acetolacta 71.7 67 0.0015 28.5 10.9 133 170-312 3-140 (157)
13 cd04877 ACT_TyrR N-terminal AC 71.3 13 0.00028 27.9 5.6 59 258-319 8-68 (74)
14 cd04876 ACT_RelA-SpoT ACT dom 69.9 16 0.00035 24.7 5.4 59 257-318 5-69 (71)
15 PRK04435 hypothetical protein; 67.6 15 0.00032 32.0 5.8 61 257-319 76-142 (147)
16 PRK10553 assembly protein for 66.7 11 0.00023 30.5 4.3 67 254-322 9-79 (87)
17 PRK11895 ilvH acetolactate syn 65.0 77 0.0017 28.2 9.9 131 170-312 4-141 (161)
18 cd04882 ACT_Bt0572_2 C-termina 63.7 31 0.00067 24.3 6.0 60 170-233 1-62 (65)
19 cd04874 ACT_Af1403 N-terminal 62.1 21 0.00045 25.3 4.9 55 260-319 10-70 (72)
20 cd04887 ACT_MalLac-Enz ACT_Mal 60.8 20 0.00043 26.3 4.7 59 257-316 6-68 (74)
21 PF02662 FlpD: Methyl-viologen 59.7 43 0.00094 28.3 7.1 94 207-312 27-123 (124)
22 PF13601 HTH_34: Winged helix 59.6 7.9 0.00017 30.2 2.4 52 260-311 27-78 (80)
23 cd04881 ACT_HSDH-Hom ACT_HSDH_ 59.0 22 0.00047 25.6 4.6 58 260-318 10-72 (79)
24 cd04879 ACT_3PGDH-like ACT_3PG 58.3 26 0.00055 24.6 4.8 56 259-319 8-69 (71)
25 PRK15385 magnesium transport p 55.6 34 0.00074 32.3 6.2 66 255-321 145-221 (225)
26 cd04879 ACT_3PGDH-like ACT_3PG 53.2 45 0.00098 23.2 5.4 57 171-227 2-58 (71)
27 COG0347 GlnK Nitrogen regulato 51.7 38 0.00083 28.7 5.3 57 254-310 3-82 (112)
28 cd04903 ACT_LSD C-terminal ACT 51.5 60 0.0013 22.7 5.8 27 171-197 2-28 (71)
29 cd04903 ACT_LSD C-terminal ACT 50.1 35 0.00077 24.0 4.4 54 260-319 9-69 (71)
30 cd04880 ACT_AAAH-PDT-like ACT 49.5 38 0.00083 25.2 4.7 52 260-314 9-69 (75)
31 PF01037 AsnC_trans_reg: AsnC 48.7 12 0.00027 27.3 1.8 24 298-321 45-69 (74)
32 cd04901 ACT_3PGDH C-terminal A 46.5 21 0.00045 25.7 2.7 56 260-319 9-67 (69)
33 PRK06737 acetolactate synthase 46.0 29 0.00062 27.3 3.5 59 259-319 11-74 (76)
34 PTZ00248 eukaryotic translatio 45.6 1.3E+02 0.0027 29.9 8.7 57 137-196 200-263 (319)
35 PRK13562 acetolactate synthase 45.2 33 0.00072 27.6 3.8 61 259-319 11-75 (84)
36 PRK11152 ilvM acetolactate syn 43.2 21 0.00046 27.9 2.4 58 258-318 11-73 (76)
37 COG2605 Predicted kinase relat 42.5 52 0.0011 32.6 5.4 52 218-277 265-317 (333)
38 PF09186 DUF1949: Domain of un 42.2 39 0.00085 23.5 3.5 47 257-306 1-49 (56)
39 PF00392 GntR: Bacterial regul 42.1 72 0.0016 23.2 5.1 50 97-148 1-50 (64)
40 PRK08178 acetolactate synthase 41.3 36 0.00078 28.0 3.6 60 260-321 18-81 (96)
41 PRK09977 putative Mg(2+) trans 41.3 36 0.00077 31.8 4.0 63 254-319 146-213 (215)
42 PRK10858 nitrogen regulatory p 41.3 58 0.0013 27.2 4.9 47 254-300 3-71 (112)
43 COG3062 NapD Uncharacterized p 40.8 57 0.0012 26.8 4.6 62 254-318 10-72 (94)
44 cd04908 ACT_Bt0572_1 N-termina 40.6 1.2E+02 0.0026 21.9 6.1 59 171-233 4-62 (66)
45 TIGR02717 AcCoA-syn-alpha acet 40.5 95 0.0021 31.7 7.3 99 205-320 265-376 (447)
46 PF13710 ACT_5: ACT domain; PD 38.6 20 0.00044 26.6 1.6 56 261-318 3-63 (63)
47 TIGR00341 conserved hypothetic 37.8 98 0.0021 30.8 6.6 57 218-278 12-68 (325)
48 PRK08577 hypothetical protein; 37.6 55 0.0012 27.7 4.3 58 261-320 67-131 (136)
49 PF14502 HTH_41: Helix-turn-he 36.1 46 0.001 24.1 3.0 44 120-168 4-47 (48)
50 PRK10665 nitrogen regulatory p 36.0 76 0.0016 26.5 4.8 24 254-277 3-26 (112)
51 PF01037 AsnC_trans_reg: AsnC 34.5 86 0.0019 22.7 4.5 21 300-320 10-30 (74)
52 TIGR00119 acolac_sm acetolacta 34.3 73 0.0016 28.2 4.7 58 259-320 10-74 (157)
53 PRK02472 murD UDP-N-acetylmura 34.3 1.1E+02 0.0024 30.5 6.6 60 122-187 280-340 (447)
54 PRK03803 murD UDP-N-acetylmura 34.0 1.3E+02 0.0028 30.2 7.1 61 122-188 278-339 (448)
55 TIGR01143 murF UDP-N-acetylmur 33.6 1.5E+02 0.0032 29.6 7.3 61 122-188 259-319 (417)
56 TIGR01087 murD UDP-N-acetylmur 32.5 1.3E+02 0.0029 29.9 6.8 61 122-188 269-330 (433)
57 cd04905 ACT_CM-PDT C-terminal 32.2 99 0.0021 23.3 4.6 53 259-314 10-71 (80)
58 PRK03806 murD UDP-N-acetylmura 31.8 1.5E+02 0.0033 29.5 7.1 61 122-188 273-334 (438)
59 PRK04663 murD UDP-N-acetylmura 31.6 1.3E+02 0.0029 30.1 6.7 61 122-188 274-335 (438)
60 PF14257 DUF4349: Domain of un 31.5 80 0.0017 29.6 4.8 62 171-232 54-118 (262)
61 PRK02705 murD UDP-N-acetylmura 31.2 1.5E+02 0.0032 29.7 6.9 61 122-188 286-347 (459)
62 PF09413 DUF2007: Domain of un 30.6 64 0.0014 23.6 3.2 54 258-311 6-67 (67)
63 PRK10773 murF UDP-N-acetylmura 30.4 1.7E+02 0.0037 29.6 7.2 61 122-188 287-348 (453)
64 PRK01390 murD UDP-N-acetylmura 30.2 1.7E+02 0.0037 29.5 7.2 59 122-186 292-351 (460)
65 TIGR01081 mpl UDP-N-acetylmura 30.0 2E+02 0.0044 28.9 7.7 60 122-188 283-343 (448)
66 PRK11895 ilvH acetolactate syn 29.9 89 0.0019 27.9 4.5 58 259-320 11-75 (161)
67 PRK14106 murD UDP-N-acetylmura 29.9 1.4E+02 0.0031 29.7 6.5 61 122-188 284-345 (450)
68 PTZ00450 macrophage migration 29.7 25 0.00054 29.4 0.9 28 112-139 67-96 (113)
69 PRK11930 putative bifunctional 29.5 1.7E+02 0.0036 32.2 7.4 61 122-188 291-352 (822)
70 PF05225 HTH_psq: helix-turn-h 29.4 54 0.0012 22.9 2.4 22 125-146 19-40 (45)
71 cd04904 ACT_AAAH ACT domain of 28.2 1.6E+02 0.0035 22.1 5.1 50 260-313 10-67 (74)
72 COG3453 Uncharacterized protei 28.0 1.5E+02 0.0032 25.8 5.2 71 218-309 15-86 (130)
73 PRK14022 UDP-N-acetylmuramoyla 27.6 2.1E+02 0.0045 29.2 7.4 59 122-188 301-360 (481)
74 cd04925 ACT_ACR_2 ACT domain-c 27.1 79 0.0017 23.8 3.2 29 170-198 2-30 (74)
75 COG3636 Predicted transcriptio 27.0 1.1E+02 0.0025 25.4 4.2 39 91-134 45-90 (100)
76 COG0745 OmpR Response regulato 26.5 1.7E+02 0.0038 27.1 6.0 26 211-238 75-100 (229)
77 TIGR00655 PurU formyltetrahydr 25.8 4.8E+02 0.01 25.1 9.1 95 165-279 40-136 (280)
78 PRK00139 murE UDP-N-acetylmura 25.7 2.5E+02 0.0054 28.4 7.5 60 122-188 283-343 (460)
79 smart00685 DM14 Repeats in fly 25.4 83 0.0018 23.7 2.9 28 84-111 16-43 (59)
80 PF13936 HTH_38: Helix-turn-he 25.3 69 0.0015 22.0 2.4 21 126-146 24-44 (44)
81 TIGR00257 IMPACT_YIGZ uncharac 25.3 2.5E+02 0.0055 25.9 6.8 69 222-306 118-189 (204)
82 PRK13210 putative L-xylulose 5 24.6 2.8E+02 0.0061 25.5 7.1 55 218-279 15-69 (284)
83 PRK01710 murD UDP-N-acetylmura 24.5 1.9E+02 0.0041 29.3 6.3 56 124-186 290-346 (458)
84 PF02016 Peptidase_S66: LD-car 24.0 98 0.0021 29.7 4.0 55 262-320 14-68 (284)
85 PF09682 Holin_LLH: Phage holi 23.6 4.1E+02 0.0089 21.7 8.0 66 82-147 28-101 (108)
86 PF05902 4_1_CTD: 4.1 protein 23.4 64 0.0014 27.5 2.2 22 112-133 77-98 (114)
87 cd04873 ACT_UUR-ACR-like ACT d 23.4 2.1E+02 0.0045 20.1 4.8 28 170-197 2-29 (70)
88 cd04902 ACT_3PGDH-xct C-termin 23.3 2.3E+02 0.0049 20.2 5.1 54 174-227 5-58 (73)
89 PF08671 SinI: Anti-repressor 23.3 1.3E+02 0.0028 19.7 3.1 23 123-145 6-28 (30)
90 PRK13209 L-xylulose 5-phosphat 23.1 3.3E+02 0.0071 25.2 7.2 54 218-279 20-74 (283)
91 COG3492 Uncharacterized protei 22.8 54 0.0012 27.0 1.6 21 298-318 15-35 (104)
92 PRK01368 murD UDP-N-acetylmura 22.7 2.4E+02 0.0052 28.8 6.7 61 122-188 280-341 (454)
93 TIGR00479 rumA 23S rRNA (uraci 22.7 76 0.0017 31.8 3.1 35 256-290 393-427 (431)
94 PHA03103 double-strand RNA-bin 22.7 1.8E+02 0.0039 26.6 5.2 43 99-149 12-54 (183)
95 PF01910 DUF77: Domain of unkn 22.6 1.9E+02 0.0041 23.2 4.8 51 264-321 19-71 (92)
96 CHL00100 ilvH acetohydroxyacid 22.5 5.8E+02 0.012 23.0 9.8 129 170-312 4-141 (174)
97 cd04909 ACT_PDH-BS C-terminal 22.4 2.9E+02 0.0063 19.7 5.5 59 171-233 4-67 (69)
98 PF14501 HATPase_c_5: GHKL dom 22.2 3.7E+02 0.008 20.9 6.4 58 138-196 13-84 (100)
99 cd04899 ACT_ACR-UUR-like_2 C-t 21.8 1.2E+02 0.0026 21.7 3.2 29 170-198 2-30 (70)
100 cd07062 Peptidase_S66_mccF_lik 21.7 1.6E+02 0.0034 28.5 4.9 56 261-320 17-72 (308)
101 PF03698 UPF0180: Uncharacteri 21.6 69 0.0015 25.5 2.0 20 261-280 7-26 (80)
102 PRK04194 hypothetical protein; 21.5 2.6E+02 0.0056 28.5 6.5 48 223-273 265-312 (392)
103 COG2605 Predicted kinase relat 21.4 3.8E+02 0.0083 26.7 7.4 98 97-212 225-328 (333)
104 PRK13168 rumA 23S rRNA m(5)U19 21.4 2E+02 0.0043 29.1 5.8 39 253-291 394-432 (443)
105 PRK11568 hypothetical protein; 21.1 3.9E+02 0.0084 24.7 7.1 70 223-308 119-191 (204)
106 TIGR01082 murC UDP-N-acetylmur 20.7 2.1E+02 0.0045 28.8 5.8 45 122-172 278-323 (448)
107 CHL00100 ilvH acetohydroxyacid 20.5 1.1E+02 0.0024 27.6 3.3 61 258-320 10-75 (174)
108 PF13740 ACT_6: ACT domain; PD 20.5 1.3E+02 0.0029 22.6 3.3 31 169-199 3-33 (76)
109 KOG0013 Uncharacterized conser 20.3 2.5E+02 0.0055 26.6 5.6 71 67-166 50-122 (231)
110 PF09536 DUF2378: Protein of u 20.2 4.7E+02 0.01 23.6 7.3 53 95-172 80-134 (178)
111 TIGR01085 murE UDP-N-acetylmur 20.1 3.9E+02 0.0084 27.0 7.6 60 122-188 291-352 (464)
No 1
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.6e-88 Score=621.03 Aligned_cols=233 Identities=40% Similarity=0.648 Sum_probs=223.1
Q ss_pred Cc-chhhHHhhhhhHhHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhccC-Cccc
Q 020672 76 MG-RRSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQEA 153 (323)
Q Consensus 76 mG-~kWsnIKh~Kaa~DakKsklfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g~-~~~~ 153 (323)
+| +||+||||+|+++|++|+|+|+||+|+|++|||.|||||++||+||.+|++||+.|||||+|||||+||+|. ++.+
T Consensus 2 aGHsKw~nIkhrK~a~Dakr~Kif~Kl~keI~vAaK~Gg~dP~~NprLr~aI~kAk~~nmPkd~IerAI~ka~G~~d~~~ 81 (241)
T COG0217 2 AGHSKWANIKHRKAAQDAKRSKIFTKLIKEITVAAKQGGPDPESNPRLRTAIEKAKAANMPKDNIERAIKKASGGKDGAN 81 (241)
T ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccCHHHHHHHHHHHHcCCCHHHHHHHHHhccCCCCccc
Confidence 34 599999999999999999999999999999999999999999999999999999999999999999999974 5579
Q ss_pred eeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEEEEeCCCCCHHHHHHHHHHCCC
Q 020672 154 FIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA 233 (323)
Q Consensus 154 ~~e~~YEg~GPgGvaiIVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI~v~~~~~d~D~lle~AIEaGA 233 (323)
|+|++|||||||||+|||||||||+|||+++||++|+|+||+||++|||+|||+|||+|.+.....++|++||.|||+||
T Consensus 82 ~~ei~YEGygP~GvaiiVe~LTDN~NRTas~vR~~F~K~GG~lg~~GSV~~mF~~kGvi~~~~~~~~ed~l~e~~ieaga 161 (241)
T COG0217 82 YEEIRYEGYGPGGVAIIVEALTDNRNRTASNVRSAFNKNGGNLGEPGSVSYMFDRKGVIVVEKNEIDEDELLEAAIEAGA 161 (241)
T ss_pred eEEEEEEeECCCceEEEEEeccCCcchhHHHHHHHHHhcCCccCCCceEEEEEeccEEEEECCCCCCHHHHHHHHHHCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999877899999999999999
Q ss_pred cccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHHHHHHHHHHccCC
Q 020672 234 EDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELD 313 (323)
Q Consensus 234 EDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~d 313 (323)
|||+.. ++.|+|+|+|++|.+|+++|+++|+++.. +++.|+|+++|++++|+.+++++|||+|||+|
T Consensus 162 eDv~~~------------~~~~~V~t~p~~~~~V~~~L~~~g~~~~~-ael~~iP~~~v~~~~e~a~k~~kLid~LEd~D 228 (241)
T COG0217 162 EDVEED------------EGSIEVYTEPEDFNKVKEALEAAGYEIES-AELTMIPQNTVELDDEDAEKLEKLIDALEDDD 228 (241)
T ss_pred hhhhcC------------CCeEEEEEChHHHHHHHHHHHHcCCceee-eeEEEecCCceecCHHHHHHHHHHHHHHhccc
Confidence 999761 24799999999999999999999999986 49999999999999999999999999999999
Q ss_pred Ccceeecc
Q 020672 314 DVDAVYTD 321 (323)
Q Consensus 314 DV~~VY~N 321 (323)
|||+||||
T Consensus 229 DVQ~Vy~N 236 (241)
T COG0217 229 DVQNVYHN 236 (241)
T ss_pred chHHHHhc
Confidence 99999999
No 2
>PRK12378 hypothetical protein; Provisional
Probab=100.00 E-value=6.2e-86 Score=611.29 Aligned_cols=232 Identities=38% Similarity=0.634 Sum_probs=220.4
Q ss_pred CcchhhHHhhhhhHhHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhccCCcccee
Q 020672 76 MGRRSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFI 155 (323)
Q Consensus 76 mG~kWsnIKh~Kaa~DakKsklfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~ 155 (323)
|||||+||||+|+++|++|+|+|+||+|+|++|||+|||||+.|++||.+|++||+.|||||+||||||||+|.++.+|+
T Consensus 1 ~g~kW~~Ikh~K~~~Da~ksk~f~kl~reI~vA~k~GG~dP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~~~~~~~ 80 (235)
T PRK12378 1 MGRAWENIKAKKAKKDGAKSKIFAKLGKEIYVAAKQGGPDPESNPALRFVIERAKKANVPKDVIERAIKKAKGGGGEDYE 80 (235)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHhccCCCCCceE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999987667899
Q ss_pred EEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEEEEeCCCCCHHHHHHHHHHCCC--
Q 020672 156 EKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA-- 233 (323)
Q Consensus 156 e~~YEg~GPgGvaiIVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI~v~~~~~d~D~lle~AIEaGA-- 233 (323)
|++|||||||||+|||||||||+|||+++||++|+|+||+||++|||.|||+|+|+|.+... ++|++||+|||+||
T Consensus 81 e~~YEgygPgGvaiiVe~lTDN~nRt~~~vr~~f~K~gg~l~~~gsv~~~Fe~kG~i~i~~~--~~d~~~e~aieaGa~~ 158 (235)
T PRK12378 81 EVRYEGFGPNGVMVIVECLTDNVNRTVANVRSAFNKNGGNLGTSGSVAFMFDHKGVFVFEGD--DEDELLEALIDADVDV 158 (235)
T ss_pred EEEEEEEcCCCcEEEEEECCCCHHHHHHHHHHHHhhcCCeECCCCceeeeeecceEEEeCCC--CHHHHHHHHHhCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999853 79999999999999
Q ss_pred cccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHHHHHHHHHHccCC
Q 020672 234 EDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELD 313 (323)
Q Consensus 234 EDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~d 313 (323)
|||.+ | ++.|+|+|+|++|.+|+++|+++||++.+ ++++|+|+++|+|++|+++++.+|+++|+++|
T Consensus 159 edv~~-----~-------~~~~~i~t~p~~~~~v~~~L~~~g~~~~~-sei~~~P~~~v~l~~e~~~~~~~li~~Led~d 225 (235)
T PRK12378 159 EDVEE-----E-------EGTITVYTDPTDFHKVKKALEAAGIEFLV-AELEMIPQNPVELSGEDLEQFEKLLDALEDDD 225 (235)
T ss_pred ccccc-----c-------CCeEEEEECHHHHHHHHHHHHHcCCCcee-eEEEEecCCCccCCHHHHHHHHHHHHHHhcCC
Confidence 66532 1 13699999999999999999999999996 59999999999999999999999999999999
Q ss_pred CcceeeccC
Q 020672 314 DVDAVYTDQ 322 (323)
Q Consensus 314 DV~~VY~N~ 322 (323)
|||+||||.
T Consensus 226 DVq~Vy~N~ 234 (235)
T PRK12378 226 DVQNVYHNV 234 (235)
T ss_pred CccceeeCC
Confidence 999999994
No 3
>PRK00110 hypothetical protein; Validated
Probab=100.00 E-value=3.6e-85 Score=609.59 Aligned_cols=232 Identities=38% Similarity=0.637 Sum_probs=220.9
Q ss_pred cCcc-hhhHHhhhhhHhHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhccC-Ccc
Q 020672 75 CMGR-RSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQE 152 (323)
Q Consensus 75 ~mG~-kWsnIKh~Kaa~DakKsklfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g~-~~~ 152 (323)
+||| ||+||||+|+++|++|+|+|+||+|+|++|||+|||||+.|++||++|++||+.|||||+||||||||+|. ++.
T Consensus 1 maGHskW~~Ikh~K~~~D~kksk~f~kl~reI~vAak~GG~DP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~~~~~ 80 (245)
T PRK00110 1 MAGHSKWANIKHRKGAQDAKRGKIFTKLIREITVAAKLGGGDPEGNPRLRLAIDKAKAANMPKDNIERAIKKGTGELDGA 80 (245)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCCCCcc
Confidence 3777 99999999999999999999999999999999999999999999999999999999999999999999986 667
Q ss_pred ceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEEEEeCCCCCHHHHHHHHHHCC
Q 020672 153 AFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAG 232 (323)
Q Consensus 153 ~~~e~~YEg~GPgGvaiIVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI~v~~~~~d~D~lle~AIEaG 232 (323)
+|++++|||||||||+|||||+|||+|||+++||++|+|+||+||++|||.|||+|+|+|.+... ++|++||.|||+|
T Consensus 81 ~~~e~~YEg~gP~GvaiiVe~lTDN~nRt~~~vR~~f~K~gG~l~~~Gsv~~~Fe~kG~i~~~~~--~~d~~~e~aieaG 158 (245)
T PRK00110 81 NYEEIRYEGYGPGGVAIIVEALTDNRNRTAAEVRHAFSKNGGNLGETGSVSYMFDRKGVIVIEPL--DEDELMEAALEAG 158 (245)
T ss_pred ceEEEEEEEEcCCCeEEEEEEecCCHHHHHHHHHHHHHhcCceeCCCcceEEEeccceEEEeCCC--CHHHHHHHHHhCC
Confidence 89999999999999999999999999999999999999999999999999999999999999743 7999999999999
Q ss_pred CcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHHHHHHHHHHccC
Q 020672 233 AEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLEL 312 (323)
Q Consensus 233 AEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~ 312 (323)
||||++. | +.|+|+|+|++|.+|+++|++.||++.+ ++++|+|+++|+|++|+++++.+|+++|+++
T Consensus 159 aeDv~~e----~--------~~~~i~~~p~~~~~v~~~L~~~g~~~~~-sei~~~P~~~v~l~~e~~~~~~~li~~Led~ 225 (245)
T PRK00110 159 AEDVETD----D--------ESFEVITAPEDFEAVRDALEAAGLEAES-AEVTMIPQNTVELDEETAEKLLKLIDALEDL 225 (245)
T ss_pred CCEeecc----C--------CeEEEEECHHHHHHHHHHHHHcCCCeee-eEEEEecCCCcccCHHHHHHHHHHHHHHhcC
Confidence 9998541 1 3599999999999999999999999986 5999999999999999999999999999999
Q ss_pred CCcceeecc
Q 020672 313 DDVDAVYTD 321 (323)
Q Consensus 313 dDV~~VY~N 321 (323)
||||+||||
T Consensus 226 dDVq~Vy~N 234 (245)
T PRK00110 226 DDVQNVYHN 234 (245)
T ss_pred CCcceEeEC
Confidence 999999999
No 4
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=100.00 E-value=5.1e-84 Score=599.94 Aligned_cols=235 Identities=36% Similarity=0.618 Sum_probs=222.4
Q ss_pred cCcc-hhhHHhhhhhHhHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhccC-Ccc
Q 020672 75 CMGR-RSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQE 152 (323)
Q Consensus 75 ~mG~-kWsnIKh~Kaa~DakKsklfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g~-~~~ 152 (323)
+||| ||+||||+|+++|++|+|+|+||+|+|++|||+|||||+.|++||++|++||+.||||++||||||||+|. ++.
T Consensus 1 maGHskw~~Ikh~K~~~D~~ksk~f~kl~r~I~vA~k~GG~DP~~N~~L~~ai~~Ak~~~~Pkd~IerAIkr~~g~~~~~ 80 (238)
T TIGR01033 1 MAGHSKWANIKHRKAAQDAKRGKIFTKLIKEIIVAAKLGGGDPESNPRLRTAIEKAKAANMPKDNIERAIKKGAGELDGS 80 (238)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCCCCcc
Confidence 3677 99999999999999999999999999999999999999999999999999999999999999999999986 567
Q ss_pred ceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEEEEeCCCCCHHHHHHHHHHCC
Q 020672 153 AFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAG 232 (323)
Q Consensus 153 ~~~e~~YEg~GPgGvaiIVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI~v~~~~~d~D~lle~AIEaG 232 (323)
+|++++|||||||||+|||||||||+|||+++||++|+|+||+||++|||.|||+|+|+|.+.....++|++||.|||+|
T Consensus 81 ~~~~~~YEg~gP~GvaiiVe~lTDN~nRt~~~ir~~f~K~gg~l~~~gsv~~~Fe~kG~i~~~~~~~~~d~~~e~aieaG 160 (238)
T TIGR01033 81 NYEEITYEGYAPGGVAIIVECLTDNKNRTASEVRSAFNKNGGSLGEPGSVSYLFSRKGVIEVPKNEVDEEDLMEAAIEAG 160 (238)
T ss_pred ceEEEEEEEEcCCceEEEEEEecCCHHhHHHHHHHHHHHcCCeeCCCCceeeeeecceEEEECCCCCCHHHHHHHHHhCC
Confidence 89999999999999999999999999999999999999999999999999999999999999855567999999999999
Q ss_pred CcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHHHHHHHHHHccC
Q 020672 233 AEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLEL 312 (323)
Q Consensus 233 AEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~ 312 (323)
||||+.. + +.|+|+|+|++|.+|+++|++.||++.+ +++.|+|+++|+|++|+++.+.+|+++|+++
T Consensus 161 Aedv~~~--------~----~~~~v~~~~~~~~~v~~~L~~~g~~i~~-sei~~~P~~~v~l~~e~~~~~~~li~~Lee~ 227 (238)
T TIGR01033 161 AEDIDVD--------D----DEFEVYTAPEELEKVKEALEAKGFPIES-AEITMIPLTTVDLDDEQAEKLLKLIDALEDD 227 (238)
T ss_pred Cceeecc--------C----CcEEEEECHHHHHHHHHHHHHcCCCcee-eEEEEecCCCcccCHHHHHHHHHHHHHHhcC
Confidence 9999531 1 1299999999999999999999999986 5999999999999999999999999999999
Q ss_pred CCcceeeccC
Q 020672 313 DDVDAVYTDQ 322 (323)
Q Consensus 313 dDV~~VY~N~ 322 (323)
||||+||||.
T Consensus 228 dDVq~Vy~N~ 237 (238)
T TIGR01033 228 DDVQEVYHNF 237 (238)
T ss_pred CCcceeeeCC
Confidence 9999999995
No 5
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=100.00 E-value=3e-83 Score=593.69 Aligned_cols=232 Identities=40% Similarity=0.651 Sum_probs=206.0
Q ss_pred chhhHHhhhhhHhHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhccC-CccceeE
Q 020672 78 RRSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQEAFIE 156 (323)
Q Consensus 78 ~kWsnIKh~Kaa~DakKsklfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g~-~~~~~~e 156 (323)
+||+||||+|+++|++|+++|+||+|+|++|||+|||||+.|++|+.+|++||+.||||++||||||||++. ++.+|++
T Consensus 1 sKW~nIkh~K~~~D~~ksk~f~kl~reI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~IerAIkk~~~~~~~~~~~~ 80 (234)
T PF01709_consen 1 SKWSNIKHKKAAQDAKKSKLFTKLSREITVAVKEGGPDPDMNPRLRSAIEKAKKANMPKDNIERAIKKASGKSDGANYEE 80 (234)
T ss_dssp -SCGGTSSSTTTTTTSHHHHHHHHHHHHHHHHHCC-S-GGGSHHHHHHHHHHHHTT--HHHHHHHHHHCCSTSST---EE
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHHHHHhCCCHHHHHHHHHhcCcCCCCcCceE
Confidence 589999999999999999999999999999999999999999999999999999999999999999999987 6778999
Q ss_pred EEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEEEEeCCCCCHHHHHHHHHHCCCccc
Q 020672 157 KVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDV 236 (323)
Q Consensus 157 ~~YEg~GPgGvaiIVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI~v~~~~~d~D~lle~AIEaGAEDV 236 (323)
++|||||||||+|||||+|||+|||+++||++|+|+||+|+++|||+|||+|+|+|.+.....++|++||+|||+|||||
T Consensus 81 ~~yEg~gP~Gvaiive~lTDN~nRt~~~ir~~~~K~gg~l~~~gsv~~~F~~kG~i~~~~~~~~~d~~~e~aIe~GaeDv 160 (234)
T PF01709_consen 81 ITYEGYGPGGVAIIVECLTDNKNRTVSDIRSIFKKNGGSLGPSGSVSFMFERKGVIEVSKKDLDEDELMEDAIEAGAEDV 160 (234)
T ss_dssp EEEEEEETTTEEEEEEEEES-HHHHHHHHHHHHHTTT-EEE-TTSSGGGEEEEEEEEEEHCCS-HHHHHHHHHHHTESEE
T ss_pred EEEEEEcCCCcEEEEEEeCCCHhHHHHHHHHHHHHcCceeCCCCcceeeeeeeEEEEEEeCCCChHHHHHHHHhCCCcEe
Confidence 99999999999999999999999999999999999999999999999999999999998777899999999999999999
Q ss_pred ccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHHHHHHHHHHccCCCcc
Q 020672 237 IEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVD 316 (323)
Q Consensus 237 ~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~dDV~ 316 (323)
++. ++.|+|+|+|++|.+|+++|++.||++.+ ++++|+|+++|+|++|+++++.+|+++|+++||||
T Consensus 161 e~~------------d~~~~~~c~p~~~~~v~~~L~~~g~~i~~-~e~~~~P~~~v~l~~e~~~~~~~lie~Lee~dDV~ 227 (234)
T PF01709_consen 161 EED------------DGEFEFICDPSDLSAVKKALEKKGYEIES-AELEYIPNNPVELSEEDAEKVEKLIEALEELDDVQ 227 (234)
T ss_dssp EEC------------TSEEEEEEEGGGHHHHHHHHHHTT---SE-EEEEEEESS-EE--HHHHHHHHHHHHHHHTSTTEE
T ss_pred eec------------CCeEEEEECHHHHHHHHHHHHHcCCCeeE-EEEEEeCCCCcccCHHHHHHHHHHHHHHhCCcCcc
Confidence 741 14699999999999999999999999996 59999999999999999999999999999999999
Q ss_pred eeeccC
Q 020672 317 AVYTDQ 322 (323)
Q Consensus 317 ~VY~N~ 322 (323)
+||||.
T Consensus 228 ~Vy~Ni 233 (234)
T PF01709_consen 228 NVYHNI 233 (234)
T ss_dssp EEEESE
T ss_pred eeeeCC
Confidence 999994
No 6
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.6e-71 Score=510.60 Aligned_cols=254 Identities=38% Similarity=0.570 Sum_probs=234.7
Q ss_pred cccccccCCcccCcc-hhhHHhhhhhHhHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHH
Q 020672 64 QVRTIRTFAPVCMGR-RSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERN 142 (323)
Q Consensus 64 ~~R~~~~~~~~~mG~-kWsnIKh~Kaa~DakKsklfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErA 142 (323)
..|++++|+..+.|| ||+||||+|++||++|+|++.||+++|.+|||.||+||.+|.+|+++++.||+.+||||+||||
T Consensus 18 ~s~sv~~s~~~~sgH~kwskIk~~Kg~nD~~rsk~~nkl~~~i~~aVk~gg~np~lN~~LAtlle~ak~~~vpkd~ien~ 97 (276)
T KOG2972|consen 18 RSRSVTTSGWIMSGHNKWSKIKHKKGANDQARSKQINKLSQGIILAVKQGGANPELNMRLATLLESAKKISVPKDGIENA 97 (276)
T ss_pred chhheecccceecccchhhhhcccccccHHHHHHHHHHHHHHHHHHHHhcCCCchhhhHHHHHHHHHHhcCCCHHHHHHH
Confidence 345667777788888 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhccCCccceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeE-EEEEeCCCCCH
Q 020672 143 IKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRAR-VVNIKFTDADK 221 (323)
Q Consensus 143 Ikra~g~~~~~~~e~~YEg~GPgGvaiIVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kG-vI~v~~~~~d~ 221 (323)
|+||+|+++..++++.||+||||||++|||++|||+||+++.||++|+|+||.+. +++.|+|++|| ||.++.+..|+
T Consensus 98 i~ras~k~~~a~e~~~ye~~gp~GV~liVealTdnknr~~~~iRs~~nk~GG~s~--~~~r~~FdkKG~Vv~V~~~~~dk 175 (276)
T KOG2972|consen 98 INRASGKEGSAVEFIEYEAMGPSGVGLIVEALTDNKNRAASSIRSIFNKHGGASA--SGVRFLFDKKGVVVNVPPEKRDK 175 (276)
T ss_pred HHHhccCCCCceEEEEEeeecCCceEEEEEeeeccHhHHHHHHHHHHHHcCCccc--ccceeEEeccceEEecChhhcch
Confidence 9999998888888899999999999999999999999999999999999998765 46899999999 77788878888
Q ss_pred HHHHHHHHHCCCcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHH
Q 020672 222 DQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMEL 301 (323)
Q Consensus 222 D~lle~AIEaGAEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~ 301 (323)
|.|...+||+||+|+..+|..|+|+||+. +.|+++|+|+++++|...|.+.||++. +++++|+|.++|+|+++++++
T Consensus 176 ~vL~ie~ie~~A~d~~~~~~~e~d~eeer--~~fkiv~e~ssl~qV~~~Lr~~G~~i~-d~~le~~P~~~vev~~~~lEk 252 (276)
T KOG2972|consen 176 DVLNIEAIEAGAEDIVAEPVLEIDEEEER--EEFKIVTEPSSLNQVAHKLRSKGFEIK-DSGLEFIPLEEVEVDVPALEK 252 (276)
T ss_pred hhhhHHHHHhcccccccCccccccccccc--ceeEEEeccchHHHHHHHhhcCCceee-ccccccccCCccccCccchHH
Confidence 88888889999999998877766555543 349999999999999999999999999 579999999999999999999
Q ss_pred HHHHHHHHccCCCcceeeccC
Q 020672 302 NKELIAKLLELDDVDAVYTDQ 322 (323)
Q Consensus 302 ~~~lid~Lee~dDV~~VY~N~ 322 (323)
+++|+++|+|+|||..||+|+
T Consensus 253 ~qkL~q~L~e~edV~~iy~ni 273 (276)
T KOG2972|consen 253 IQKLIQALYENEDVMFIYDNI 273 (276)
T ss_pred HHHHHHHHhhchhHHHHhhcc
Confidence 999999999999999999996
No 7
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=98.75 E-value=1.3e-08 Score=112.21 Aligned_cols=70 Identities=23% Similarity=0.217 Sum_probs=64.3
Q ss_pred hhHHhhhhhHhHHHHHHHHHHHHHHHHHHHHhC------CCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhccC
Q 020672 80 SSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKG------GPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK 149 (323)
Q Consensus 80 WsnIKh~Kaa~DakKsklfsKl~keI~~Avk~G------G~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g~ 149 (323)
|-+.+..|.+.+..++|+++|+.++|..|+|.| |+||+.|++|+.+|++||+.+||++.|+|+|++|.+.
T Consensus 296 ~K~~ee~Kvaalv~gski~~k~lk~I~~A~~~~~G~~~~~~DP~~NpaLk~aI~~Ak~~~vP~~~I~RvI~~A~qg 371 (1220)
T PRK07562 296 WKVKEEQKVAALVTGSKIVSKHLKAIMKACVNCEGDGDDCFDPAKNPALKREIKAAKKALVPENYIKRVIQFARQG 371 (1220)
T ss_pred hccchhhhHHhhhhcchHHHHHHHHHHHHHHhccccccccCCccccHHHHHHHHHHHhccCCHHHHHHHHHHhhcc
Confidence 334456899999999999999999999999998 7899999999999999999999999999999998754
No 8
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=89.03 E-value=0.97 Score=33.55 Aligned_cols=64 Identities=19% Similarity=0.190 Sum_probs=43.4
Q ss_pred EEEEeCcccHHHHHHHHHhCCCCeeecccceeecC----CccccCHHHHH-HHHHHHHHHccCCCcceee
Q 020672 255 YKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI----TTIEVDDEAME-LNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 255 ~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~----~~Vel~~e~~~-~~~~lid~Lee~dDV~~VY 319 (323)
++....|..+..+...|.+.|..+..- ...-.|. -.+.++-.+.+ .+.+++++|..+++|.+|+
T Consensus 5 i~~~d~~g~l~~I~~~la~~~inI~~i-~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~ 73 (76)
T cd04888 5 LLLEHRPGVLSKVLNTIAQVRGNVLTI-NQNIPIHGRANVTISIDTSTMNGDIDELLEELREIDGVEKVE 73 (76)
T ss_pred EEecCCCchHHHHHHHHHHcCCCEEEE-EeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEE
Confidence 344556778999999999999988642 1110122 12223333444 7889999999999999987
No 9
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=81.23 E-value=1.7 Score=34.17 Aligned_cols=60 Identities=15% Similarity=0.235 Sum_probs=43.4
Q ss_pred eEEEEeCcccHHHHHHHHHh-CCCCeeecccceeecC--CccccCHHHHHHHHHHHHHHccCCCccee
Q 020672 254 YYKVVSTSDNYTDITTKLRE-AGIPFETDNGSELLPI--TTIEVDDEAMELNKELIAKLLELDDVDAV 318 (323)
Q Consensus 254 ~~~v~~~p~~l~~V~~~L~~-~G~~i~~~~~i~~iP~--~~Vel~~e~~~~~~~lid~Lee~dDV~~V 318 (323)
.+.|.|.|..+..|+.+|.+ .|.+|.... +. --|.+..+......+++++|+++|.|..+
T Consensus 7 s~vV~~~p~~~~~v~~~l~~~~gvEVh~~~-----~~GKiVVtiE~~~~~~~~~~~~~i~~l~GVlsa 69 (79)
T PF03927_consen 7 SLVVHARPERLEEVAEALAAIPGVEVHAVD-----EDGKIVVTIEAESSEEEVDLIDAINALPGVLSA 69 (79)
T ss_dssp EEEEEE-CCCHHHHHHHHCCSTTEEEEEEE-----TTTEEEEEEEESSHHHHHHHHHHHCCSTTEEEE
T ss_pred EEEEEECchhHHHHHHHHHcCCCcEEEeeC-----CCCeEEEEEEeCChHHHHHHHHHHHcCCCceEE
Confidence 47899999999999999998 576664321 32 23445555556667899999999998875
No 10
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=77.86 E-value=4.8 Score=30.53 Aligned_cols=58 Identities=22% Similarity=0.279 Sum_probs=40.9
Q ss_pred eCcccHHHHHHHHHhCCCCeeecccceeec---C----CccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 259 STSDNYTDITTKLREAGIPFETDNGSELLP---I----TTIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 259 ~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP---~----~~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
-.|.-|..+...|.+.|..|.. +...+ . -.+.|.-.+.+.+..++++|+.+|+|.+|+
T Consensus 15 dr~GlL~dI~~~i~~~~~nI~~---i~~~~~~~~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 15 DRPGLLADITSVISENGVNIRS---INARTNKDDGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp --TTHHHHHHHHHHCSSSEEEE---EEEEE--ETTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred cCCCHHHHHHHHHHHCCCCeEE---EEeEEeccCCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 3577899999999999999874 23322 1 122222234567788999999999999986
No 11
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=76.49 E-value=7.5 Score=27.58 Aligned_cols=58 Identities=19% Similarity=0.205 Sum_probs=39.3
Q ss_pred eCcccHHHHHHHHHhCCCCeeecccceeecC-----CccccCHHHHHHHHHHHHHHccCCCccee
Q 020672 259 STSDNYTDITTKLREAGIPFETDNGSELLPI-----TTIEVDDEAMELNKELIAKLLELDDVDAV 318 (323)
Q Consensus 259 ~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~-----~~Vel~~e~~~~~~~lid~Lee~dDV~~V 318 (323)
-.|..+..+...|.+.|+.+... ...-.|. -.+.+.... +.+..++++|+.+++|.+|
T Consensus 9 d~~g~l~~i~~~l~~~~~~i~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 9 NEPGVLNRISGLFARRGFNIESL-TVGPTEDPGISRITIVVEGDD-DVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred CCCcHHHHHHHHHHhCCCCEEEE-EeeecCCCCeEEEEEEEECCH-HHHHHHHHHHhCCccEEEe
Confidence 34556889999999999998742 1111111 123333334 6678899999999999987
No 12
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=71.65 E-value=67 Score=28.49 Aligned_cols=133 Identities=15% Similarity=0.138 Sum_probs=74.1
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEE--EEEeCCCCCHHHHHHHHHH--CCCcccccCCCCCCC
Q 020672 170 VVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARV--VNIKFTDADKDQLLDIALD--AGAEDVIEPPVNEDD 245 (323)
Q Consensus 170 IVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGv--I~v~~~~~d~D~lle~AIE--aGAEDV~~~~~~ed~ 245 (323)
++.++.+|+...++.|-.+|++.|.++-. -.+... +..|+ +++..+. ++ +.++.... .--.||....+..+.
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~S-l~v~~t-~~~~~sriti~V~~-d~-~~i~qi~kQl~Kli~V~~V~~~~~~ 78 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIES-LTVGPT-EDPDLSRMTIVVVG-DD-KVLEQITKQLNKLVDVIKVSDLTES 78 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEE-EEEeec-CCCCEEEEEEEEEC-CH-HHHHHHHHHHhcCccEEEEEecCCC
Confidence 56789999999999999999999998731 122222 21232 3222222 32 22322222 233333322100010
Q ss_pred CcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecC-CccccCHHHHHHHHHHHHHHccC
Q 020672 246 TDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI-TTIEVDDEAMELNKELIAKLLEL 312 (323)
Q Consensus 246 ~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~-~~Vel~~e~~~~~~~lid~Lee~ 312 (323)
+-=+.+--.++|.|++++-..+.+-.+..+-.+.. +-|. -.+|++... +++..|++.|+..
T Consensus 79 ~~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~ivd-----v~~~~~~ie~tG~~-~ki~~~~~~l~~~ 140 (157)
T TIGR00119 79 AIVERELCLVKVSAPGEGRDEIIRLTNIFRGRIVD-----VSPDSYTVEVTGDS-DKIDAFLELLRPF 140 (157)
T ss_pred cceeeEEEEEEEECCccCHHHHHHHHHHhCCEEEE-----ecCCEEEEEEcCCH-HHHHHHHHHhhhc
Confidence 00012224678899999888888888877666542 2344 347776543 4456677777764
No 13
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=71.33 E-value=13 Score=27.88 Aligned_cols=59 Identities=17% Similarity=0.178 Sum_probs=41.1
Q ss_pred EeCcccHHHHHHHHHhCCCCeeecccceeecC--CccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 258 VSTSDNYTDITTKLREAGIPFETDNGSELLPI--TTIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 258 ~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~--~~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
.-.+--+..+...|.+.|+.+... +..+. -.+++.-.+.+.+..++++|..+++|..|+
T Consensus 8 ~dr~Gll~dI~~~i~~~~~nI~~~---~~~~~~~i~l~i~v~~~~~L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 8 EDRLGITQEVLDLLVEHNIDLRGI---EIDPKGRIYLNFPTIEFEKLQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred EccchHHHHHHHHHHHCCCceEEE---EEecCCeEEEEeEecCHHHHHHHHHHHhCCCCceEEE
Confidence 334556899999999999988642 22231 222233334566789999999999999987
No 14
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=69.91 E-value=16 Score=24.71 Aligned_cols=59 Identities=19% Similarity=0.190 Sum_probs=37.9
Q ss_pred EEeCcccHHHHHHHHHhCCCCeeecccceeecC------CccccCHHHHHHHHHHHHHHccCCCccee
Q 020672 257 VVSTSDNYTDITTKLREAGIPFETDNGSELLPI------TTIEVDDEAMELNKELIAKLLELDDVDAV 318 (323)
Q Consensus 257 v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~------~~Vel~~e~~~~~~~lid~Lee~dDV~~V 318 (323)
+.-.|..+..+...|.+.++.+... ...+. -.+.+.......+..+++.|..+++|..|
T Consensus 5 ~~~~~~~l~~i~~~l~~~~~~i~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~v 69 (71)
T cd04876 5 AIDRPGLLADITTVIAEEKINILSV---NTRTDDDGLATIRLTLEVRDLEHLARIMRKLRQIPGVIDV 69 (71)
T ss_pred EeccCcHHHHHHHHHHhCCCCEEEE---EeEECCCCEEEEEEEEEECCHHHHHHHHHHHhCCCCcEEE
Confidence 3445677889999999999988642 22111 12223211223467899999999999876
No 15
>PRK04435 hypothetical protein; Provisional
Probab=67.65 E-value=15 Score=31.98 Aligned_cols=61 Identities=31% Similarity=0.406 Sum_probs=43.2
Q ss_pred EEeCcccHHHHHHHHHhCCCCeeecccceeecCC-----ccccCHHHHH-HHHHHHHHHccCCCcceee
Q 020672 257 VVSTSDNYTDITTKLREAGIPFETDNGSELLPIT-----TIEVDDEAME-LNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 257 v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~-----~Vel~~e~~~-~~~~lid~Lee~dDV~~VY 319 (323)
....|..+..|.+.|.+.|.++..- . .-+|.+ .+.++-.+++ .+..|+++|+.+++|.+|.
T Consensus 76 l~Dr~GlLs~Il~~IA~~~aNIltI-~-q~i~~~g~a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~ 142 (147)
T PRK04435 76 LEDRSGTLSKVLNVIAEAGGNILTI-N-QSIPLQGRANVTISIDTSSMEGDIDELLEKLRNLDGVEKVE 142 (147)
T ss_pred EecCCCHHHHHHHHHHHcCCCeEEE-E-EEcCCCCEEEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEE
Confidence 4556778999999999999998642 1 124432 2334333443 6789999999999999985
No 16
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=66.67 E-value=11 Score=30.46 Aligned_cols=67 Identities=24% Similarity=0.274 Sum_probs=46.5
Q ss_pred eEEEEeCcccHHHHHHHHHh-CCCCeeecccceeecCCccccCHHHHHHHHHHHHHHccCCCcce---eeccC
Q 020672 254 YYKVVSTSDNYTDITTKLRE-AGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDA---VYTDQ 322 (323)
Q Consensus 254 ~~~v~~~p~~l~~V~~~L~~-~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~dDV~~---VY~N~ 322 (323)
.+.|.|.|+.+..|++.|.+ .|.+|..... =.=+--|.|..+......+.++.|+.+|.|.. |||++
T Consensus 9 SlVV~~~Pe~~~~V~~~l~~ipg~Evh~~d~--~~GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVYh~~ 79 (87)
T PRK10553 9 SLVVQAKSERISDISTQLNAFPGCEVAVSDA--PSGQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVYHQQ 79 (87)
T ss_pred EEEEEeChHHHHHHHHHHHcCCCcEEEeecC--CCCeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEEEEe
Confidence 46789999999999999998 4666542100 00123456666656666778999999999876 57653
No 17
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=65.01 E-value=77 Score=28.25 Aligned_cols=131 Identities=16% Similarity=0.145 Sum_probs=73.1
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEE----EEEeCCCCCHHHHHHHHHH--CCCcccccCCCCC
Q 020672 170 VVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARV----VNIKFTDADKDQLLDIALD--AGAEDVIEPPVNE 243 (323)
Q Consensus 170 IVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGv----I~v~~~~~d~D~lle~AIE--aGAEDV~~~~~~e 243 (323)
++.++.+|+....+.|-.+|.++|.++-. -++... +..|+ |.+.. ++ +.++..+- ..-.||....+..
T Consensus 4 ~IsV~veN~pGvL~rI~~lf~rrg~NI~S-l~v~~t-e~~~~sriti~V~~---~~-~~i~qi~kQl~KLidV~~V~~~~ 77 (161)
T PRK11895 4 TLSVLVENEPGVLSRVAGLFSRRGYNIES-LTVGPT-EDPGLSRMTIVTSG---DE-QVIEQITKQLNKLIDVLKVVDLT 77 (161)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCcEEE-EEeeec-CCCCEEEEEEEEEC---CH-HHHHHHHHHHhccccEEEEEecC
Confidence 56789999999999999999999997731 122222 21222 23333 22 22222221 2333333221001
Q ss_pred CCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecC-CccccCHHHHHHHHHHHHHHccC
Q 020672 244 DDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI-TTIEVDDEAMELNKELIAKLLEL 312 (323)
Q Consensus 244 d~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~-~~Vel~~e~~~~~~~lid~Lee~ 312 (323)
+.+-=+.+--.++|-+++..-..+.+-.+..+-.+.. .-|. -.+|++... +++..|++.|+..
T Consensus 78 ~~~~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~ivd-----v~~~~~~iE~tG~~-~ki~~~~~~l~~~ 141 (161)
T PRK11895 78 EEAHVERELALVKVRASGENRAEILRLADIFRAKIVD-----VTPESLTIEVTGDS-DKIDAFIDLLRPY 141 (161)
T ss_pred CcchhheEEEEEEEECCcccHHHHHHHHHHhCCEEEE-----ecCCEEEEEEeCCH-HHHHHHHHHhhhc
Confidence 1000012234688899998888888888877666542 2244 347776533 4456677777654
No 18
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=63.74 E-value=31 Score=24.30 Aligned_cols=60 Identities=10% Similarity=0.176 Sum_probs=40.0
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCccccCCcceeeece--eeEEEEEeCCCCCHHHHHHHHHHCCC
Q 020672 170 VVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFR--RARVVNIKFTDADKDQLLDIALDAGA 233 (323)
Q Consensus 170 IVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~--~kGvI~v~~~~~d~D~lle~AIEaGA 233 (323)
++.+..+++...++++-.+|.++|+++..-. .+... ..+.+.+..+ +.+.+++.--++|-
T Consensus 1 ~i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~--~~~~~~~~~~~v~~~ve--~~~~~~~~L~~~G~ 62 (65)
T cd04882 1 VLAVEVPDKPGGLHEILQILSEEGINIEYMY--AFVEKKGGKALLIFRTE--DIEKAIEVLQERGV 62 (65)
T ss_pred CEEEEeCCCCcHHHHHHHHHHHCCCChhheE--EEccCCCCeEEEEEEeC--CHHHHHHHHHHCCc
Confidence 3567888999999999999999999885321 11111 3455666544 36677666655663
No 19
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=62.11 E-value=21 Score=25.34 Aligned_cols=55 Identities=20% Similarity=0.151 Sum_probs=38.5
Q ss_pred CcccHHHHHHHHHhCCCCeeecccceeecC------CccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 260 TSDNYTDITTKLREAGIPFETDNGSELLPI------TTIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 260 ~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~------~~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
.|..+.++...|.+.++.+... ...|. -.+.+++. ..+..++++|++.++|..|+
T Consensus 10 ~~g~l~~i~~~l~~~~~~i~~~---~~~~~~~~~~~~~i~~~~~--~~~~~~~~~L~~~~~v~~v~ 70 (72)
T cd04874 10 KPGVLRDLTGVIAEHGGNITYT---QQFIEREGKARIYMELEGV--GDIEELVEELRSLPIVREVE 70 (72)
T ss_pred CCChHHHHHHHHHhCCCCEEEE---EEeccCCCeEEEEEEEecc--ccHHHHHHHHhCCCCeEEEE
Confidence 4567899999999999998632 11221 22444442 44567999999999999886
No 20
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=60.81 E-value=20 Score=26.29 Aligned_cols=59 Identities=20% Similarity=0.168 Sum_probs=38.8
Q ss_pred EEeCcccHHHHHHHHHhCCCCeeecccceeecCC----ccccCHHHHHHHHHHHHHHccCCCcc
Q 020672 257 VVSTSDNYTDITTKLREAGIPFETDNGSELLPIT----TIEVDDEAMELNKELIAKLLELDDVD 316 (323)
Q Consensus 257 v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~----~Vel~~e~~~~~~~lid~Lee~dDV~ 316 (323)
+.-.|..|..|...|.+.|..+... ...-.+.. .+.+.-.+.+.+..++++|+.+++|.
T Consensus 6 ~~d~~g~L~~i~~~i~~~~~nI~~v-~~~~~~~~~~~~~~~vev~~~~~l~~i~~~L~~i~gV~ 68 (74)
T cd04887 6 LPNRPGMLGRVTTAIGEAGGDIGAI-DLVEQGRDYTVRDITVDAPSEEHAETIVAAVRALPEVK 68 (74)
T ss_pred eCCCCchHHHHHHHHHHcCCcEEEE-EEEEecCCEEEEEEEEEcCCHHHHHHHHHHHhcCCCeE
Confidence 3445778999999999999998642 22222211 12233334555678999999999975
No 21
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=59.69 E-value=43 Score=28.29 Aligned_cols=94 Identities=16% Similarity=0.236 Sum_probs=51.3
Q ss_pred eeeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCCCcccccCceEE--EEeCcccHHHHHHHHHhCCCCeeecccc
Q 020672 207 RRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYK--VVSTSDNYTDITTKLREAGIPFETDNGS 284 (323)
Q Consensus 207 ~~kGvI~v~~~~~d~D~lle~AIEaGAEDV~~~~~~ed~~~ed~~~~~~~--v~~~p~~l~~V~~~L~~~G~~i~~~~~i 284 (323)
....+|.+...+.-....+..|++.||+-|.... ... ++-.|. -+-...-+..+++.|++.|++.+-- .+
T Consensus 27 ~~vriIrvpC~Grv~~~~il~Af~~GADGV~V~g----C~~---g~Ch~~~Gn~~a~~Rv~~~k~~L~~~Gi~~eRv-~~ 98 (124)
T PF02662_consen 27 PNVRIIRVPCSGRVDPEFILRAFEKGADGVLVAG----CHP---GDCHYREGNYRAEKRVERLKKLLEELGIEPERV-RL 98 (124)
T ss_pred CCeEEEEccCCCccCHHHHHHHHHcCCCEEEEeC----CCC---CCCCcchhhHHHHHHHHHHHHHHHHcCCChhHe-EE
Confidence 3456778876554445667789999999886521 000 011221 0112334667888999999885421 23
Q ss_pred eeecCCccccCHH-HHHHHHHHHHHHccC
Q 020672 285 ELLPITTIEVDDE-AMELNKELIAKLLEL 312 (323)
Q Consensus 285 ~~iP~~~Vel~~e-~~~~~~~lid~Lee~ 312 (323)
.|+... +.+ =.+.+..|.+.|+++
T Consensus 99 ~~~~~~----~~~~fa~~~~~f~~~i~~l 123 (124)
T PF02662_consen 99 YWISAP----EGKRFAEIVNEFTERIKEL 123 (124)
T ss_pred EEeCcc----cHHHHHHHHHHHHHHHHHc
Confidence 333221 112 245566677777654
No 22
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=59.63 E-value=7.9 Score=30.24 Aligned_cols=52 Identities=27% Similarity=0.195 Sum_probs=34.8
Q ss_pred CcccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHHHHHHHHHHcc
Q 020672 260 TSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLE 311 (323)
Q Consensus 260 ~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee 311 (323)
+...+.+-.+.|++.||--..-....-.|.+.+.|+++-.+.+.+.++.|++
T Consensus 27 t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~L~~ 78 (80)
T PF13601_consen 27 TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAALRE 78 (80)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHHHHH
Confidence 3556777888899999943221122335999999999988888888888865
No 23
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=58.96 E-value=22 Score=25.61 Aligned_cols=58 Identities=22% Similarity=0.194 Sum_probs=37.9
Q ss_pred CcccHHHHHHHHHhCCCCeeecccceeecC-C----ccccCHHHHHHHHHHHHHHccCCCccee
Q 020672 260 TSDNYTDITTKLREAGIPFETDNGSELLPI-T----TIEVDDEAMELNKELIAKLLELDDVDAV 318 (323)
Q Consensus 260 ~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~-~----~Vel~~e~~~~~~~lid~Lee~dDV~~V 318 (323)
.|..+..+...|.+.|+.+... .....+. . .+.+.....+.+..++++|..+++|+.+
T Consensus 10 ~~g~l~~i~~~l~~~~i~I~~~-~~~~~~~~~~~~~~i~~~~~~~~~l~~~i~~L~~~~~V~~~ 72 (79)
T cd04881 10 KPGVLAKITGILAEHGISIESV-IQKEADGGETAPVVIVTHETSEAALNAALAEIEALDAVQGV 72 (79)
T ss_pred CCcHHHHHHHHHHHcCCCeEEE-EEcccCCCCceeEEEEEccCCHHHHHHHHHHHHcCccccCC
Confidence 4557899999999999988642 1111111 1 1212233456678899999999999875
No 24
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=58.33 E-value=26 Score=24.55 Aligned_cols=56 Identities=20% Similarity=0.205 Sum_probs=38.2
Q ss_pred eCcccHHHHHHHHHhCCCCeeecccceeec------CCccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 259 STSDNYTDITTKLREAGIPFETDNGSELLP------ITTIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 259 ~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP------~~~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
-.|..+..+...|.+.|+.+... .. ..+ ...+.+++. ....++++|+++++|..|.
T Consensus 8 d~~g~l~~i~~~l~~~~~nI~~~-~~-~~~~~~~~~~~~~~v~~~---~~~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 8 DVPGVIGKVGTILGEHGINIAAM-QV-GRKEKGGIAYMVLDVDSP---VPEEVLEELKALPGIIRVR 69 (71)
T ss_pred CCCCHHHHHHHHHHhcCCCeeeE-EE-eccCCCCEEEEEEEcCCC---CCHHHHHHHHcCCCeEEEE
Confidence 34667899999999999998642 11 111 123444432 2468999999999999885
No 25
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=55.56 E-value=34 Score=32.26 Aligned_cols=66 Identities=17% Similarity=0.174 Sum_probs=42.9
Q ss_pred EEEEeCcccH----HHHHHHHHhCCCCeeecccceeec-CCcccc------CHHHHHHHHHHHHHHccCCCcceeecc
Q 020672 255 YKVVSTSDNY----TDITTKLREAGIPFETDNGSELLP-ITTIEV------DDEAMELNKELIAKLLELDDVDAVYTD 321 (323)
Q Consensus 255 ~~v~~~p~~l----~~V~~~L~~~G~~i~~~~~i~~iP-~~~Vel------~~e~~~~~~~lid~Lee~dDV~~VY~N 321 (323)
+.+.|.+++- ..+.+.|++.+|.+.+- ++.-.+ .+.+++ ...+...++++++.|...|.|+.|+.|
T Consensus 145 ~~v~~~~~~~~~vr~~L~~~l~~~~~~~~~l-~~~~~~~~~~~ei~a~l~~~~~~~~~le~iv~~L~~~pgV~~v~W~ 221 (225)
T PRK15385 145 LKVTCNKEDESAVRQWLLNIVKEAAICLQGL-GSVPAQEQGYKEIRAELVGHADYRKTRELIISRIGDNDNITAIHWS 221 (225)
T ss_pred EEEEEcCcchhHHHHHHHHHHHhCCCceEEe-EeeecCCCCeEEEEEEEEecCCchhhHHHHHHHHhCCCCeEEEEEE
Confidence 4788988764 55556667778988632 222233 234444 111234567899999999999999876
No 26
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=53.24 E-value=45 Score=23.22 Aligned_cols=57 Identities=7% Similarity=0.090 Sum_probs=34.5
Q ss_pred EEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEEEEeCCCCCHHHHHHH
Q 020672 171 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 227 (323)
Q Consensus 171 VE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI~v~~~~~d~D~lle~ 227 (323)
+.+.++|+.+..++|-.+|.++|.++..-.+........+.+.+.-++...+++++.
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~~~~~~~l~~~ 58 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDSPVPEEVLEE 58 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcCCCCCHHHHHH
Confidence 345789999999999999999999885322111111234455554433333444433
No 27
>COG0347 GlnK Nitrogen regulatory protein PII [Amino acid transport and metabolism]
Probab=51.69 E-value=38 Score=28.67 Aligned_cols=57 Identities=21% Similarity=0.310 Sum_probs=38.2
Q ss_pred eEEEEeCcccHHHHHHHHHhCCCCeeec--------------------ccceeecCCcccc--CHHHHH-HHHHHHHHHc
Q 020672 254 YYKVVSTSDNYTDITTKLREAGIPFETD--------------------NGSELLPITTIEV--DDEAME-LNKELIAKLL 310 (323)
Q Consensus 254 ~~~v~~~p~~l~~V~~~L~~~G~~i~~~--------------------~~i~~iP~~~Vel--~~e~~~-~~~~lid~Le 310 (323)
.++.+..|..|..|+++|++.|+.-..- -+.+|+|+..+++ ++|+.+ .++.+...+.
T Consensus 3 ~I~aIiRP~kl~~vkeaL~~~G~~gmTv~~V~G~G~Qkg~~e~yrg~~~~~~~lpK~~ieIvV~de~ve~vie~I~~~a~ 82 (112)
T COG0347 3 KIEAIIRPFKLDDVKEALEKAGVPGMTVTEVKGRGRQKGHTELYRGAEYEVDFLPKVKIEIVVSDEDVDEVIEAIKKAAR 82 (112)
T ss_pred EEEEEeCHHHhHHHHHHHHHcCCCceEEEeeeeecccCCccccccchhhhhhcccceEEEEEEChHHHHHHHHHHHHHHh
Confidence 4778999999999999999988752100 0235688877777 666544 3444444444
No 28
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=51.46 E-value=60 Score=22.72 Aligned_cols=27 Identities=22% Similarity=0.251 Sum_probs=23.9
Q ss_pred EEEecCChhhHHHHHHHHHhhcCcccc
Q 020672 171 VEVLTDKITRSVAAVREVVKDCGGKMA 197 (323)
Q Consensus 171 VE~lTDN~nRT~~~vR~~f~K~GG~l~ 197 (323)
+.+.++|+....++|-.+|.++|.++.
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~ 28 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIA 28 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCee
Confidence 466888999999999999999999874
No 29
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=50.13 E-value=35 Score=23.95 Aligned_cols=54 Identities=19% Similarity=0.313 Sum_probs=37.5
Q ss_pred CcccHHHHHHHHHhCCCCeeecccceeec-C------CccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 260 TSDNYTDITTKLREAGIPFETDNGSELLP-I------TTIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 260 ~p~~l~~V~~~L~~~G~~i~~~~~i~~iP-~------~~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
.|..+.++...|.+.|+.+... ...+ . -.+.+++. .+..++++|+++++|.+|.
T Consensus 9 ~~g~l~~i~~~l~~~~~~I~~~---~~~~~~~~~~~~i~i~v~~~---~~~~~i~~l~~~~~v~~v~ 69 (71)
T cd04903 9 KPGAIAKVTSVLADHEINIAFM---RVSRKEKGDQALMVIEVDQP---IDEEVIEEIKKIPNIHQVI 69 (71)
T ss_pred CCChHHHHHHHHHHcCcCeeee---EEEeccCCCeEEEEEEeCCC---CCHHHHHHHHcCCCceEEE
Confidence 3557899999999999988632 1122 1 12444443 4568999999999999885
No 30
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=49.52 E-value=38 Score=25.19 Aligned_cols=52 Identities=15% Similarity=0.210 Sum_probs=37.3
Q ss_pred CcccHHHHHHHHHhCCCCeeecccceeecCCc--------cccCHH-HHHHHHHHHHHHccCCC
Q 020672 260 TSDNYTDITTKLREAGIPFETDNGSELLPITT--------IEVDDE-AMELNKELIAKLLELDD 314 (323)
Q Consensus 260 ~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~--------Vel~~e-~~~~~~~lid~Lee~dD 314 (323)
.|..|..|.+.+++.|+.+.+ ++-+|... |+++.. +...++++++.|++.-+
T Consensus 9 ~pG~L~~vL~~f~~~~vni~~---I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~~~~ 69 (75)
T cd04880 9 KPGALAKALKVFAERGINLTK---IESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKRVTE 69 (75)
T ss_pred cCCHHHHHHHHHHHCCCCEEE---EEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhCC
Confidence 478899999999999999874 45566533 666543 34567788888887543
No 31
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=48.72 E-value=12 Score=27.30 Aligned_cols=24 Identities=29% Similarity=0.282 Sum_probs=13.9
Q ss_pred HHHHHHHHHHH-HccCCCcceeecc
Q 020672 298 AMELNKELIAK-LLELDDVDAVYTD 321 (323)
Q Consensus 298 ~~~~~~~lid~-Lee~dDV~~VY~N 321 (323)
+++.+..|+.. |..+|.|.++.+.
T Consensus 45 d~~~l~~~i~~~l~~~~gV~~~~t~ 69 (74)
T PF01037_consen 45 DMEELEEFIREKLRSIPGVRRTETS 69 (74)
T ss_dssp SHHHHHHHHHHTHHTSTTEEEEEEE
T ss_pred CHHHHHHHHHHHhhcCCCEEEEEEE
Confidence 34555556655 6666666666543
No 32
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=46.46 E-value=21 Score=25.68 Aligned_cols=56 Identities=21% Similarity=0.253 Sum_probs=37.7
Q ss_pred CcccHHHHHHHHHhCCCCeeecccce---eecCCccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 260 TSDNYTDITTKLREAGIPFETDNGSE---LLPITTIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 260 ~p~~l~~V~~~L~~~G~~i~~~~~i~---~iP~~~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
.|-.+..+...|.+.|+.+... ... -.....++++.. ....++++|..+++|.+|+
T Consensus 9 ~~g~l~~i~~~l~~~~~nI~~~-~~~~~~~~a~~~~~~~~~---~l~~li~~l~~~~~V~~v~ 67 (69)
T cd04901 9 VPGVLGQINTILAEHNINIAAQ-YLQTRGEIGYVVIDIDSE---VSEELLEALRAIPGTIRVR 67 (69)
T ss_pred CCcHHHHHHHHHHHcCCCHHHH-hccCCCCEEEEEEEcCCC---CCHHHHHHHHcCCCeEEEE
Confidence 4677899999999999887432 110 011123344443 4567999999999999986
No 33
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=46.01 E-value=29 Score=27.25 Aligned_cols=59 Identities=12% Similarity=0.016 Sum_probs=38.7
Q ss_pred eCcccHHHHHHHHHhCCCCeeeccccee--ecC-C--ccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 259 STSDNYTDITTKLREAGIPFETDNGSEL--LPI-T--TIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 259 ~~p~~l~~V~~~L~~~G~~i~~~~~i~~--iP~-~--~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
=.|.-|..+...+...||.|++- .... .|. . ++.+.. +.+.+..++..|+.+.||.+|-
T Consensus 11 n~pGVL~Ri~~lf~rRgfNI~Sl-~vg~te~~~~sriti~~~~-~~~~i~qi~kQL~KLidV~~V~ 74 (76)
T PRK06737 11 NDPSVLLRISGIFARRGYYISSL-NLNERDTSGVSEMKLTAVC-TENEATLLVSQLKKLINVLQVN 74 (76)
T ss_pred cCCCHHHHHHHHHhccCcceEEE-EecccCCCCeeEEEEEEEC-CHHHHHHHHHHHhCCcCEEEEE
Confidence 34778999999999999999742 1221 232 1 222221 2234567899999999998874
No 34
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=45.58 E-value=1.3e+02 Score=29.94 Aligned_cols=57 Identities=18% Similarity=0.252 Sum_probs=33.9
Q ss_pred HHHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCChh-------hHHHHHHHHHhhcCccc
Q 020672 137 DIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKIT-------RSVAAVREVVKDCGGKM 196 (323)
Q Consensus 137 d~IErAIkra~g~~~~~~~e~~YEg~GPgGvaiIVE~lTDN~n-------RT~~~vR~~f~K~GG~l 196 (323)
+.|.+|++.|....... ..+...-.||.-..| .+.|.++. .++..+...++|+||.+
T Consensus 200 e~IK~aL~~~~~~~~~~-~~i~i~~igaP~Y~i--~~~~~d~k~g~~~l~~a~~~i~~~i~~~gG~~ 263 (319)
T PTZ00248 200 DAVKEALIAGQEVATDE-CKITIKLIAPPQYVI--VTTCSDKDKGMEIIGAALEAIKEVIKKKGGDF 263 (319)
T ss_pred HHHHHHHHHHHhcCCCc-CcEEEEEEcCCeEEE--EEEeCCHHHHHHHHHHHHHHHHHHHHHcCCeE
Confidence 56777887775433221 234445566665544 45555655 56666777778888854
No 35
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=45.24 E-value=33 Score=27.57 Aligned_cols=61 Identities=21% Similarity=0.113 Sum_probs=40.4
Q ss_pred eCcccHHHHHHHHHhCCCCeeecc-cceeecC-C--ccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 259 STSDNYTDITTKLREAGIPFETDN-GSELLPI-T--TIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 259 ~~p~~l~~V~~~L~~~G~~i~~~~-~i~~iP~-~--~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
=.|--|..+...+...||.|++-+ +..-.|. . ++.++..+.+.++.++..|+.+.||.+|+
T Consensus 11 N~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d~~~ieqI~kQL~KlidVikV~ 75 (84)
T PRK13562 11 DQVSTLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQDDTSLHILIKKLKQQINVLTVE 75 (84)
T ss_pred CCCCHHHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCCHHHHHHHHHHHhCCccEEEEE
Confidence 347789999999999999997421 1111333 2 22232122345677889999999999998
No 36
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=43.22 E-value=21 Score=27.94 Aligned_cols=58 Identities=17% Similarity=0.079 Sum_probs=38.5
Q ss_pred EeCcccHHHHHHHHHhCCCCeeeccccee--ecC-Ccc--ccCHHHHHHHHHHHHHHccCCCccee
Q 020672 258 VSTSDNYTDITTKLREAGIPFETDNGSEL--LPI-TTI--EVDDEAMELNKELIAKLLELDDVDAV 318 (323)
Q Consensus 258 ~~~p~~l~~V~~~L~~~G~~i~~~~~i~~--iP~-~~V--el~~e~~~~~~~lid~Lee~dDV~~V 318 (323)
-=.|.-|..+..-++..||.|++- .... -|. ..+ .+++ -..++.++..|+.+.||.+|
T Consensus 11 ~n~pGVL~Ri~~lf~rRGfnI~sl-~v~~t~~~~~sriti~v~~--~~~i~ql~kQL~KL~dV~~V 73 (76)
T PRK11152 11 RFRPEVLERVLRVVRHRGFQVCSM-NMTQNTDAQNINIELTVAS--ERPIDLLSSQLNKLVDVAHV 73 (76)
T ss_pred ECCccHHHHHHHHHhcCCeeeeeE-EeeecCCCCEEEEEEEECC--CchHHHHHHHHhcCcCeEEE
Confidence 345778899999999999999742 2222 222 222 2332 23456688899999999887
No 37
>COG2605 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]
Probab=42.45 E-value=52 Score=32.59 Aligned_cols=52 Identities=13% Similarity=0.234 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHCCCcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHh-CCCC
Q 020672 218 DADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLRE-AGIP 277 (323)
Q Consensus 218 ~~d~D~lle~AIEaGAEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~-~G~~ 277 (323)
+...|.+.+.|++.||--=.-. .-++.+++-|+|+|+....|.++|+. .|+.
T Consensus 265 N~~IDriy~~A~~~GA~~gKl~--------GaG~gGFllf~~~p~k~~~l~r~l~~~~~~~ 317 (333)
T COG2605 265 NDAIDRIYELALKNGAYGGKLS--------GAGGGGFLLFFCDPSKRNELARALEKEQGFV 317 (333)
T ss_pred cHHHHHHHHHHHhcCchhceee--------ccCCccEEEEEeCccchHHHHHHHHHhcCCe
Confidence 3457899999999999754332 22456788999999999999999987 4554
No 38
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=42.21 E-value=39 Score=23.47 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=31.2
Q ss_pred EEeCcccHHHHHHHHHhCCCCeeecccceeecC--CccccCHHHHHHHHHHH
Q 020672 257 VVSTSDNYTDITTKLREAGIPFETDNGSELLPI--TTIEVDDEAMELNKELI 306 (323)
Q Consensus 257 v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~--~~Vel~~e~~~~~~~li 306 (323)
+.|+-..+..|+..|++.|+.+.. ..|--. -.+.|++++.+.+.+.+
T Consensus 1 i~~~Y~~~~~v~~~l~~~~~~i~~---~~y~~~V~~~v~v~~~~~~~f~~~l 49 (56)
T PF09186_consen 1 ISCDYSQYGKVERLLEQNGIEIVD---EDYTDDVTLTVAVPEEEVEEFKAQL 49 (56)
T ss_dssp EEE-CCCHHHHHHHHHHTTTEEEE---EEECTTEEEEEEEECCCHHHHHHHH
T ss_pred CEechhhHHHHHHHHHHCCCEEEc---ceecceEEEEEEECHHHHHHHHHHH
Confidence 357788999999999999998863 456554 34455555555444443
No 39
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=42.08 E-value=72 Score=23.20 Aligned_cols=50 Identities=22% Similarity=0.345 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhcc
Q 020672 97 LYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASE 148 (323)
Q Consensus 97 lfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g 148 (323)
++..+...|..++..|.--| +.+|-..-+-|+..+++..++.+|+++-..
T Consensus 1 l~~~i~~~l~~~I~~g~~~~--g~~lps~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 1 LYEQIYDQLRQAILSGRLPP--GDRLPSERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp HHHHHHHHHHHHHHTTSS-T--TSBE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCCC--CCEeCCHHHHHHHhccCCcHHHHHHHHHHH
Confidence 45678888999999887444 446666667789999999999999998664
No 40
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=41.35 E-value=36 Score=28.04 Aligned_cols=60 Identities=13% Similarity=0.070 Sum_probs=41.1
Q ss_pred CcccHHHHHHHHHhCCCCeeec-ccceeecC-C--ccccCHHHHHHHHHHHHHHccCCCcceeecc
Q 020672 260 TSDNYTDITTKLREAGIPFETD-NGSELLPI-T--TIEVDDEAMELNKELIAKLLELDDVDAVYTD 321 (323)
Q Consensus 260 ~p~~l~~V~~~L~~~G~~i~~~-~~i~~iP~-~--~Vel~~e~~~~~~~lid~Lee~dDV~~VY~N 321 (323)
.|--|..|..-+...||.|++- ....-.|. . ++.+.+ + +.++.++..|+.+.||.+|+..
T Consensus 18 ~pGVL~RIaglFsRRgyNIeSLtvg~te~~~iSRmtivv~~-~-~~i~Qi~kQL~KLidVikV~~l 81 (96)
T PRK08178 18 HPGVMSHVCGLFARRAFNVEGILCLPIQDGDKSRIWLLVND-D-QRLEQMISQIEKLEDVLKVRRN 81 (96)
T ss_pred CcCHHHHHHHHHhcCCcCeeeEEEeecCCCCceEEEEEEcC-c-hHHHHHHHHHhCCcCEEEEEEC
Confidence 4678899999999999999742 11111333 2 222333 2 4677899999999999999864
No 41
>PRK09977 putative Mg(2+) transport ATPase; Provisional
Probab=41.29 E-value=36 Score=31.77 Aligned_cols=63 Identities=14% Similarity=0.132 Sum_probs=42.3
Q ss_pred eEEEEeCcccHHHHHHHHHhCCCCeeecccceeecC---C--ccccCHHHHHHHHHHHHHHccCCCcceee
Q 020672 254 YYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI---T--TIEVDDEAMELNKELIAKLLELDDVDAVY 319 (323)
Q Consensus 254 ~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~---~--~Vel~~e~~~~~~~lid~Lee~dDV~~VY 319 (323)
.+.+.|.+++...+.+.|.+.++.+.+ +++.+. . .+++.-.......++++.|.++|+|+.|-
T Consensus 146 ~~~i~~~~~~~~~i~~~l~~~~i~i~~---~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~~~~V~~v~ 213 (215)
T PRK09977 146 HLQLTLVNGNVVSMLDWFKQQKIKTDL---VSLQENEDHEVVAIDITLHATTSIEDLYRLLKGIAGVKGVS 213 (215)
T ss_pred EEEEEEccccHHHHHHHHHHcCceEEE---EEEEecCCCcEEEEEEEECCCCCHHHHHHHHhcCCCceEEE
Confidence 467889999999999999999998764 233221 1 12221111123457899999999999874
No 42
>PRK10858 nitrogen regulatory protein P-II 1; Provisional
Probab=41.25 E-value=58 Score=27.19 Aligned_cols=47 Identities=23% Similarity=0.303 Sum_probs=33.6
Q ss_pred eEEEEeCcccHHHHHHHHHhCCCCeeec--------------------ccceeecCCcccc--CHHHHH
Q 020672 254 YYKVVSTSDNYTDITTKLREAGIPFETD--------------------NGSELLPITTIEV--DDEAME 300 (323)
Q Consensus 254 ~~~v~~~p~~l~~V~~~L~~~G~~i~~~--------------------~~i~~iP~~~Vel--~~e~~~ 300 (323)
.++.+..|+.+..|+++|.+.|+.-.+. ....|+|+..+++ +|++.+
T Consensus 3 ~I~AIIRp~kl~~v~~aL~~~G~~g~Tv~~V~G~G~q~g~~~~~~~~~~~~~~~pK~~ieivv~D~~v~ 71 (112)
T PRK10858 3 KIDAIIKPFKLDDVREALAEVGITGMTVTEVKGFGRQKGHTELYRGAEYMVDFLPKVKIEIVVPDDIVD 71 (112)
T ss_pred EEEEEECHHHHHHHHHHHHHCCCCeEEEEEeEecCCCCCCceeeecceeeccceeeEEEEEEEChHhHH
Confidence 3678999999999999999988762110 0134788888877 665543
No 43
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=40.82 E-value=57 Score=26.82 Aligned_cols=62 Identities=21% Similarity=0.189 Sum_probs=43.7
Q ss_pred eEEEEeCcccHHHHHHHHHhC-CCCeeecccceeecCCccccCHHHHHHHHHHHHHHccCCCccee
Q 020672 254 YYKVVSTSDNYTDITTKLREA-GIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAV 318 (323)
Q Consensus 254 ~~~v~~~p~~l~~V~~~L~~~-G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~dDV~~V 318 (323)
...|-|-|+.+.+|+.+|.+. |.+|.. ++-+ -+-.|-+..+..+.+..-++.++++|.|.+|
T Consensus 10 slVv~~~pe~l~av~~~L~~ip~~EV~~-~d~~--GKlVVVie~~~~~~l~~tie~i~nl~gVlav 72 (94)
T COG3062 10 SLVVQAKPERLSAVKTALLAIPGCEVYG-EDAE--GKLVVVIEAEDSETLLETIESIRNLPGVLAV 72 (94)
T ss_pred EEeeecCHHHHHHHHHHHhcCCCcEeec-cCCC--ceEEEEEEcCchHHHHHHHHHHhcCCceeEE
Confidence 356889999999999999884 555542 1211 1233444666677777888999999998774
No 44
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=40.61 E-value=1.2e+02 Score=21.89 Aligned_cols=59 Identities=17% Similarity=0.273 Sum_probs=40.1
Q ss_pred EEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEEEEeCCCCCHHHHHHHHHHCCC
Q 020672 171 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA 233 (323)
Q Consensus 171 VE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI~v~~~~~d~D~lle~AIEaGA 233 (323)
+.+..+|....+++|-.+|.++|.++-.-. .+.-..++++.+.. .+.+.+.+.--++|-
T Consensus 4 i~v~v~d~pG~La~v~~~l~~~~inI~~i~--~~~~~~~~~~rl~~--~~~~~~~~~L~~~G~ 62 (66)
T cd04908 4 LSVFLENKPGRLAAVTEILSEAGINIRALS--IADTSEFGILRLIV--SDPDKAKEALKEAGF 62 (66)
T ss_pred EEEEEcCCCChHHHHHHHHHHCCCCEEEEE--EEecCCCCEEEEEE--CCHHHHHHHHHHCCC
Confidence 345788999999999999999999874211 12223357777764 345676666656664
No 45
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=40.48 E-value=95 Score=31.69 Aligned_cols=99 Identities=15% Similarity=0.193 Sum_probs=62.3
Q ss_pred eceeeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCCCcccccCceEEEEeCcccHH-HHHHHHHhCCCCeeeccc
Q 020672 205 KFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYT-DITTKLREAGIPFETDNG 283 (323)
Q Consensus 205 ~F~~kGvI~v~~~~~d~D~lle~AIEaGAEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~-~V~~~L~~~G~~i~~~~~ 283 (323)
.|++.|++.+. +.|++++.+-=..-.-.-. ...+-|++..--.. -+.+.++..|+++-.-++
T Consensus 265 ~~~~~Gv~~~~----~~~el~~~~~~l~~~~~~~-------------g~rvaivs~sGG~g~l~aD~~~~~Gl~lp~ls~ 327 (447)
T TIGR02717 265 AFKQAGVIRAD----SIEELFDLARLLSNQPLPK-------------GNRVAIITNAGGPGVIATDACEENGLELAELSE 327 (447)
T ss_pred HHHHCCeEEeC----CHHHHHHHHHHHhcCCCCC-------------CCeEEEEECCchHHHHHHHHHHHcCCCcCCCCH
Confidence 58889998885 5788887765433222111 13466666665554 456777888887531100
Q ss_pred -----c-ee-----ecCCccccCH-HHHHHHHHHHHHHccCCCcceeec
Q 020672 284 -----S-EL-----LPITTIEVDD-EAMELNKELIAKLLELDDVDAVYT 320 (323)
Q Consensus 284 -----i-~~-----iP~~~Vel~~-e~~~~~~~lid~Lee~dDV~~VY~ 320 (323)
+ .+ -+.|++.+.. ..-+.+.+.++.|.++|+|..|..
T Consensus 328 ~t~~~L~~~lp~~~~~~NPlDl~~~~~~~~~~~al~~l~~dp~vd~Vlv 376 (447)
T TIGR02717 328 ATKNKLRNILPPEASIKNPVDVLGDATPERYAKALKTVAEDENVDGVVV 376 (447)
T ss_pred HHHHHHHHhCccccccCCCEecCCCCCHHHHHHHHHHHHcCCCCCEEEE
Confidence 0 11 2458888832 345678889999999999988863
No 46
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=38.62 E-value=20 Score=26.62 Aligned_cols=56 Identities=25% Similarity=0.236 Sum_probs=36.1
Q ss_pred cccHHHHHHHHHhCCCCeeeccccee--ecC-Ccc--ccCHHHHHHHHHHHHHHccCCCccee
Q 020672 261 SDNYTDITTKLREAGIPFETDNGSEL--LPI-TTI--EVDDEAMELNKELIAKLLELDDVDAV 318 (323)
Q Consensus 261 p~~l~~V~~~L~~~G~~i~~~~~i~~--iP~-~~V--el~~e~~~~~~~lid~Lee~dDV~~V 318 (323)
|.-|..+..-+...||.|++- .+.. .|. ..+ .++.++ +.+..|+..|+.+.||.+|
T Consensus 3 ~GvL~Ri~~vf~rRg~nI~sl-~v~~~~~~~~~riti~v~~~~-~~i~~l~~Ql~KlidV~~V 63 (63)
T PF13710_consen 3 PGVLNRITGVFRRRGFNIESL-SVGPTEDPGISRITIVVSGDD-REIEQLVKQLEKLIDVVKV 63 (63)
T ss_dssp TTHHHHHHHHHHTTT-EECEE-EEEE-SSTTEEEEEEEEES-C-CHHHHHHHHHHCSTTEEEE
T ss_pred cHHHHHHHHHHhcCCeEEeeE-EeeecCCCCEEEEEEEEeeCc-hhHHHHHHHHhccCCeEeC
Confidence 566888999999999999753 3333 232 223 333322 3456699999999999876
No 47
>TIGR00341 conserved hypothetical protein TIGR00341. This conserved hypothetical protein is found so far only in three archaeal genomes and in Streptomyces coelicolor. It shares a hydrophobic uncharacterized domain (see model TIGR00271) of about 180 residues with several eubacterial proteins, including the much longer protein sll1151 of Synechocystis PCC6803.
Probab=37.77 E-value=98 Score=30.78 Aligned_cols=57 Identities=7% Similarity=0.060 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHCCCcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCe
Q 020672 218 DADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPF 278 (323)
Q Consensus 218 ~~d~D~lle~AIEaGAEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i 278 (323)
....|.+.+...+.+.|++.....++ +++.+..+.|+.+.++.+.|-++|++.|+.-
T Consensus 12 ~~~~~~v~~~l~~~~~~~i~~~~~~~----~~~~~~~i~~~v~~~~~e~vld~L~~lgl~~ 68 (325)
T TIGR00341 12 KEGVVMRKEIVRGEDLEEIAIELGDK----TFIYDDRIELYVQDSDTEKIVSRLKDKLLGY 68 (325)
T ss_pred cchHHHHHHHHhccCcccceEEeccC----CCCcceEEEEEcChhhHHHHHHHHHHcCCCC
Confidence 34677877777677775443321111 1122357889999999999999999998764
No 48
>PRK08577 hypothetical protein; Provisional
Probab=37.65 E-value=55 Score=27.68 Aligned_cols=58 Identities=22% Similarity=0.259 Sum_probs=39.1
Q ss_pred cccHHHHHHHHHhCCCCeeecccceeec-------CCccccCHHHHHHHHHHHHHHccCCCcceeec
Q 020672 261 SDNYTDITTKLREAGIPFETDNGSELLP-------ITTIEVDDEAMELNKELIAKLLELDDVDAVYT 320 (323)
Q Consensus 261 p~~l~~V~~~L~~~G~~i~~~~~i~~iP-------~~~Vel~~e~~~~~~~lid~Lee~dDV~~VY~ 320 (323)
|.-|..+...|.+.|+.+... ...-.+ .-.+++++.+ ..+..++++|+.+++|..|+-
T Consensus 67 ~GvLa~I~~~l~~~~inI~~i-~~~~~~~~~~~~i~l~vev~~~~-~~l~~l~~~L~~l~~V~~V~~ 131 (136)
T PRK08577 67 PGVLAKITGLLAEHGVDILAT-ECEELKRGELAECVIIVDLSKSD-IDLEELEEELKKLEEVKEVEI 131 (136)
T ss_pred CCHHHHHHHHHHHCCCCEEEE-EEEEecCCCEEEEEEEEEeCCch-hhHHHHHHHHHcCCCEEEEEE
Confidence 446889999999999998642 222222 1224555421 345789999999999999863
No 49
>PF14502 HTH_41: Helix-turn-helix domain
Probab=36.06 E-value=46 Score=24.13 Aligned_cols=44 Identities=18% Similarity=0.259 Sum_probs=34.1
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcE
Q 020672 120 TVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVS 168 (323)
Q Consensus 120 ~~La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~GPgGva 168 (323)
-||..+-+-+.+.++..-+|++||+-=...+. +..|-.|.-|..
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~ga-----I~Le~rGh~GTf 47 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQNALKFLEENGA-----IKLESRGHLGTF 47 (48)
T ss_pred cccCCHHHHHHHhCcchhHHHHHHHHHHHCCc-----EEeeecCcCccc
Confidence 36777889999999999999999997554332 567778877764
No 50
>PRK10665 nitrogen regulatory protein P-II 2; Provisional
Probab=36.00 E-value=76 Score=26.52 Aligned_cols=24 Identities=21% Similarity=0.295 Sum_probs=21.4
Q ss_pred eEEEEeCcccHHHHHHHHHhCCCC
Q 020672 254 YYKVVSTSDNYTDITTKLREAGIP 277 (323)
Q Consensus 254 ~~~v~~~p~~l~~V~~~L~~~G~~ 277 (323)
.+..+..|+.+..|+++|.+.|+.
T Consensus 3 ~I~AIIRp~kl~~v~~AL~~~G~~ 26 (112)
T PRK10665 3 LVTVIIKPFKLEDVREALSSIGIQ 26 (112)
T ss_pred EEEEEECHHHHHHHHHHHHHCCCC
Confidence 467899999999999999998876
No 51
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=34.54 E-value=86 Score=22.67 Aligned_cols=21 Identities=24% Similarity=0.414 Sum_probs=13.0
Q ss_pred HHHHHHHHHHccCCCcceeec
Q 020672 300 ELNKELIAKLLELDDVDAVYT 320 (323)
Q Consensus 300 ~~~~~lid~Lee~dDV~~VY~ 320 (323)
+.+.++.+.|.++|+|..+|.
T Consensus 10 ~~~~~~~~~l~~~p~V~~~~~ 30 (74)
T PF01037_consen 10 DAYDEFAEALAEIPEVVECYS 30 (74)
T ss_dssp THHHHHHHHHHTSTTEEEEEE
T ss_pred chHHHHHHHHHcCCCEEEEEE
Confidence 445566666666666666664
No 52
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=34.30 E-value=73 Score=28.24 Aligned_cols=58 Identities=19% Similarity=0.198 Sum_probs=40.8
Q ss_pred eCcccHHHHHHHHHhCCCCeeecccceeecCC-------ccccCHHHHHHHHHHHHHHccCCCcceeec
Q 020672 259 STSDNYTDITTKLREAGIPFETDNGSELLPIT-------TIEVDDEAMELNKELIAKLLELDDVDAVYT 320 (323)
Q Consensus 259 ~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~-------~Vel~~e~~~~~~~lid~Lee~dDV~~VY~ 320 (323)
-.|--|..|...|...||.|.+ +.--|.. ++.++. +...+..+...|+.+.||.+|+.
T Consensus 10 n~pGvL~rI~~lf~rrg~NI~S---l~v~~t~~~~~sriti~V~~-d~~~i~qi~kQl~Kli~V~~V~~ 74 (157)
T TIGR00119 10 NEPGVLSRVAGLFTRRGFNIES---LTVGPTEDPDLSRMTIVVVG-DDKVLEQITKQLNKLVDVIKVSD 74 (157)
T ss_pred CCCcHHHHHHHHHHhCCceEEE---EEEeecCCCCEEEEEEEEEC-CHHHHHHHHHHHhcCccEEEEEe
Confidence 3477899999999999999974 2222331 123333 22456779999999999999976
No 53
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=34.29 E-value=1.1e+02 Score=30.46 Aligned_cols=60 Identities=17% Similarity=0.163 Sum_probs=42.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVRE 187 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~ 187 (323)
+..||.-|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.|+.--|..-+..-++.
T Consensus 280 a~aAia~~~~lgi~~~~i~~~L~~f~~~~------~R~e~~~~~~g~~vi~D~~a~N~~s~~~al~~ 340 (447)
T PRK02472 280 ALAAIAAAKLLGVSNEAIREVLSTFSGVK------HRLQYVGTIDGRKFYNDSKATNILATQKALSG 340 (447)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CcceEEEEECCeEEEECCCCCCHHHHHHHHHh
Confidence 46677788899999999999998655432 2555543 468889999866677766555544
No 54
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=34.02 E-value=1.3e+02 Score=30.16 Aligned_cols=61 Identities=16% Similarity=0.176 Sum_probs=44.1
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.|.---|+.-+..-++.+
T Consensus 278 alaAia~a~~lgi~~~~i~~~L~~f~g~~------~R~e~v~~~~gv~~idDs~atN~~a~~~al~~l 339 (448)
T PRK03803 278 ALAALALGEAAGLPKEAMLEVLRTFTGLP------HRCEWVREVAGVDYYNDSKGTNVGATVAAIEGL 339 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCCC------CceEEEEEeCCeEEEEcCCcCCHHHHHHHHHhh
Confidence 46778889999999999999998765432 2555444 3578788887666777777777664
No 55
>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. This family consists of the strictly bacterial MurF gene of peptidoglycan biosynthesis. This enzyme is almost always UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a few species, MurE adds lysine rather than diaminopimelate. This enzyme acts on the product from MurE activity, and so is also subfamily rather than equivalog. Staphylococcus aureus is an example of species in this MurF protein would differ.
Probab=33.63 E-value=1.5e+02 Score=29.60 Aligned_cols=61 Identities=15% Similarity=0.199 Sum_probs=43.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~GPgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|.++|+.-.+-. -+.|....+|+.+|+++.--|+.-+.+-+..+
T Consensus 259 ~laAia~~~~lGi~~~~i~~~l~~~~~~~------gR~e~~~~~~~~vidDsya~np~s~~~al~~l 319 (417)
T TIGR01143 259 ALAAAALALELGIPLEEIAEGLAELKLVK------GRFEIQTKNGLTLIDDTYNANPDSMRAALDAL 319 (417)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceeEEcCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence 45677788899999999999998765432 14443335789999998877777666666554
No 56
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase.
Probab=32.52 E-value=1.3e+02 Score=29.85 Aligned_cols=61 Identities=16% Similarity=0.219 Sum_probs=44.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.|.---|..-|..-++.+
T Consensus 269 a~aAia~a~~lgi~~~~i~~~L~~f~g~~------~R~e~v~~~~g~~~idD~~atn~~a~~~al~~~ 330 (433)
T TIGR01087 269 ILAAIALAKSLGLNLEAILEALRSFKGLP------HRLEYVGQKNGVHFYNDSKATNVHATLAALSAF 330 (433)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEEEEECCEEEEEcCCCCCHHHHHHHHHhC
Confidence 46678888999999999999998765532 2555443 3688888887767777776666654
No 57
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=32.16 E-value=99 Score=23.31 Aligned_cols=53 Identities=19% Similarity=0.239 Sum_probs=35.4
Q ss_pred eCcccHHHHHHHHHhCCCCeeecccceeecCCc--------cccCHH-HHHHHHHHHHHHccCCC
Q 020672 259 STSDNYTDITTKLREAGIPFETDNGSELLPITT--------IEVDDE-AMELNKELIAKLLELDD 314 (323)
Q Consensus 259 ~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~--------Vel~~e-~~~~~~~lid~Lee~dD 314 (323)
-.|-.|..+.+.+.+.|+.+.+ ++-.|... |+++.. +.+.+.++++.|+++.+
T Consensus 10 d~~G~L~~il~~f~~~~ini~~---i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~~~~ 71 (80)
T cd04905 10 NKPGALYDVLGVFAERGINLTK---IESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKRLTE 71 (80)
T ss_pred CCCCHHHHHHHHHHHCCcCEEE---EEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhCC
Confidence 4577889999999999999873 45555421 334322 24556778888887544
No 58
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=31.81 E-value=1.5e+02 Score=29.50 Aligned_cols=61 Identities=13% Similarity=0.183 Sum_probs=44.1
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|.++|+.-++-. -++|..+ .+|+.+|.|+.-.|+.-+..-++.+
T Consensus 273 a~aAia~a~~lgi~~~~i~~~L~~f~~~~------gR~E~v~~~~~~~~i~Ds~a~n~~a~~~al~~l 334 (438)
T PRK03806 273 ALAALALADAVGIPRASSLKALTTFTGLP------HRFQLVLEHNGVRWINDSKATNVGSTEAALNGL 334 (438)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CeEEEEEeeCCEEEEEcCCCCCHHHHHHHHHhC
Confidence 45778888999999999999998655432 2555544 3688888888777777666666554
No 59
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=31.62 E-value=1.3e+02 Score=30.13 Aligned_cols=61 Identities=15% Similarity=0.135 Sum_probs=44.3
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
..+|+.-|...++|.+.|.++|+.-++.. -++|..+ .+|+.+|-|+.--|+.-+.+-++.+
T Consensus 274 alaAia~a~~lGi~~~~i~~~L~~f~g~~------~R~e~v~~~~g~~~idDs~~tn~~s~~~Al~~~ 335 (438)
T PRK04663 274 VLVVLALLDAAGVDYRKALDALKSYTGLT------HRCQVVADNHGIKWVNDSKATNVASTLAALSGL 335 (438)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEeeeeCCcEEEeCCCcCCHHHHHHHHHhc
Confidence 45677778999999999999998765532 2444443 3688889898777777777776654
No 60
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=31.47 E-value=80 Score=29.56 Aligned_cols=62 Identities=18% Similarity=0.303 Sum_probs=44.7
Q ss_pred EEEecCChhhHHHHHHHHHhhcCccccCCcce---eeeceeeEEEEEeCCCCCHHHHHHHHHHCC
Q 020672 171 VEVLTDKITRSVAAVREVVKDCGGKMADPGSV---MFKFRRARVVNIKFTDADKDQLLDIALDAG 232 (323)
Q Consensus 171 VE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV---~f~F~~kGvI~v~~~~~d~D~lle~AIEaG 232 (323)
+...|++...+...|+.++.++||-+.....- .....+.+.+.+.-....+|++++..-+.|
T Consensus 54 l~lev~d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g 118 (262)
T PF14257_consen 54 LSLEVKDVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSELG 118 (262)
T ss_pred EEEEECCHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhccC
Confidence 56777999999999999999999977543211 233456666666655456788777766666
No 61
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=31.16 E-value=1.5e+02 Score=29.73 Aligned_cols=61 Identities=10% Similarity=0.198 Sum_probs=42.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|.++|++-.+-. -++|..+ .+|+.+|.|+---|+.-+..-++.+
T Consensus 286 alaAia~a~~lgv~~~~i~~~L~~f~~~~------gR~e~~~~~~~~~ii~Ds~a~N~~s~~~al~~l 347 (459)
T PRK02705 286 LLLAVAAARLAGLSAEAIAEALRSFPGVP------HRLERIGTINGIDFINDSKATNYDAAEVGLKAV 347 (459)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEEEeeCCcEEEEeCCCCCHHHHHHHHHhC
Confidence 45677788888999999999998755432 2455443 2578899997767776655555444
No 62
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=30.55 E-value=64 Score=23.58 Aligned_cols=54 Identities=20% Similarity=0.208 Sum_probs=30.8
Q ss_pred EeCcccHHHHHHHHHhCCCCeeec----ccc-eeecC---CccccCHHHHHHHHHHHHHHcc
Q 020672 258 VSTSDNYTDITTKLREAGIPFETD----NGS-ELLPI---TTIEVDDEAMELNKELIAKLLE 311 (323)
Q Consensus 258 ~~~p~~l~~V~~~L~~~G~~i~~~----~~i-~~iP~---~~Vel~~e~~~~~~~lid~Lee 311 (323)
..++-+..-++..|++.|++.... +.. .+.|. ..|-|.+++.++...+++.+++
T Consensus 6 ~~~~~ea~~i~~~L~~~gI~~~v~~~~~~~~~g~~g~~~~~~v~V~~~d~~~A~~il~~~~~ 67 (67)
T PF09413_consen 6 AGDPIEAELIKGLLEENGIPAFVKNEHMSGYAGEPGTGGQVEVYVPEEDYERAREILEEFEN 67 (67)
T ss_dssp E--HHHHHHHHHHHHHTT--EE--S----SS---S--SSSEEEEEEGGGHHHHHHHHHHTT-
T ss_pred cCCHHHHHHHHHHHHhCCCcEEEECCccchhhcccCccCceEEEECHHHHHHHHHHHHHhcC
Confidence 445667789999999999985321 111 12344 3455577888888888887753
No 63
>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed
Probab=30.40 E-value=1.7e+02 Score=29.61 Aligned_cols=61 Identities=11% Similarity=0.031 Sum_probs=42.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|.++|+.-++-.. ++|... ++|+.||-|+.--|+.-..+-+..+
T Consensus 287 alaAia~a~~lGi~~~~i~~~L~~~~~~~g------R~e~v~~~~g~~iIDDsYn~nP~s~~aaL~~l 348 (453)
T PRK10773 287 ALAAAALAMSVGATLDAVKAGLANLKAVPG------RLFPIQLAEGQLLLDDSYNANVGSMTAAAQVL 348 (453)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCC------ceeEEECCCCeEEEEcCCCCCHHHHHHHHHHH
Confidence 456778889999999999999987654322 334332 5778777778887777655555544
No 64
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=30.19 E-value=1.7e+02 Score=29.46 Aligned_cols=59 Identities=19% Similarity=0.229 Sum_probs=42.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVR 186 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR 186 (323)
+..|+.-|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.|+..-|+.-+.+-|+
T Consensus 292 a~aAiaa~~~lgi~~~~i~~gL~~~~~~~------gR~e~i~~~~g~~vIdDs~ahNp~s~~~aL~ 351 (460)
T PRK01390 292 AAAAYAAARALGLSPEEIAAGLASFPGLA------HRMEQVGRRGGVLFVNDSKATNADAAAKALS 351 (460)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEEeeeCCcEEEEcCCCCCHHHHHHHHH
Confidence 45667777888999999999998764432 2555444 36788888988888888776555
No 65
>TIGR01081 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase. Alternate name: murein tripeptide ligase
Probab=30.04 E-value=2e+02 Score=28.90 Aligned_cols=60 Identities=12% Similarity=0.160 Sum_probs=43.5
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..|+.-|...+++.+.|.++++...+-. -++|..+ .+|+.+|.|+ --|+.-+.+-++.+
T Consensus 283 a~~A~a~~~~lgi~~~~i~~~L~~~~~~~------~R~e~~~~~~g~~ii~D~-ahNp~s~~~~l~~l 343 (448)
T TIGR01081 283 ALMAIAAARHVGVAIEDACEALGSFVNAK------RRLELKGEANGITVYDDF-AHHPTAIEATLQGL 343 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------cceEEEEecCCeEEEEeC-CCCHHHHHHHHHHH
Confidence 45677778888999999999998655421 2555553 4688999998 77887766666555
No 66
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=29.92 E-value=89 Score=27.86 Aligned_cols=58 Identities=17% Similarity=0.196 Sum_probs=39.7
Q ss_pred eCcccHHHHHHHHHhCCCCeeecccceeecCC-------ccccCHHHHHHHHHHHHHHccCCCcceeec
Q 020672 259 STSDNYTDITTKLREAGIPFETDNGSELLPIT-------TIEVDDEAMELNKELIAKLLELDDVDAVYT 320 (323)
Q Consensus 259 ~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~-------~Vel~~e~~~~~~~lid~Lee~dDV~~VY~ 320 (323)
-.|--|..|...|...||.|.+ +...|.. .+.++. +.+.++.++..|+.+.||.+|+.
T Consensus 11 N~pGvL~rI~~lf~rrg~NI~S---l~v~~te~~~~sriti~V~~-~~~~i~qi~kQl~KLidV~~V~~ 75 (161)
T PRK11895 11 NEPGVLSRVAGLFSRRGYNIES---LTVGPTEDPGLSRMTIVTSG-DEQVIEQITKQLNKLIDVLKVVD 75 (161)
T ss_pred CCCcHHHHHHHHHHhCCCcEEE---EEeeecCCCCEEEEEEEEEC-CHHHHHHHHHHHhccccEEEEEe
Confidence 3477899999999999999974 2233331 123332 22345678889999999999875
No 67
>PRK14106 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=29.85 E-value=1.4e+02 Score=29.73 Aligned_cols=61 Identities=15% Similarity=0.171 Sum_probs=43.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|..+|+..++-. -++|... .+|+.+|+|+.--|+.-+.+-++.+
T Consensus 284 a~aAia~~~~lgi~~~~i~~~L~~~~~~~------gR~e~i~~~~~~~vi~D~~ahNP~s~~~~l~~l 345 (450)
T PRK14106 284 ALAATAAAYLLGISPDVIANTLKTFKGVE------HRIEFVAEINGVKFINDSKGTNPDAAIKALEAY 345 (450)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------cceEEEeeECCEEEEeCCCccCHHHHHHHHHhC
Confidence 56788888999999999999998755432 2444432 3567899998888887666555543
No 68
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=29.70 E-value=25 Score=29.42 Aligned_cols=28 Identities=21% Similarity=0.452 Sum_probs=20.2
Q ss_pred CCCCCCCChHHHHHHHHH--HhcCCCHHHH
Q 020672 112 GGPNPTSNTVLAAVLEKA--KELDVPKDIV 139 (323)
Q Consensus 112 GG~DP~~N~~La~aI~kA--K~~nmPKd~I 139 (323)
|+.+|+.|..|...|-+. +..++|+|.|
T Consensus 67 G~~~~~~n~~~s~~i~~~l~~~LgIp~dRi 96 (113)
T PTZ00450 67 GEYAPSKPKMMTPRITAAITKECGIPAERI 96 (113)
T ss_pred cCcCHHHHHHHHHHHHHHHHHHcCCCcccE
Confidence 667788888888887764 5667776654
No 69
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=29.48 E-value=1.7e+02 Score=32.17 Aligned_cols=61 Identities=11% Similarity=0.115 Sum_probs=45.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|.++|+.-.+-. -++|..+ .+|+.+|.|+.--|+.-+.+-++.+
T Consensus 291 alaAia~a~~lGi~~~~i~~~L~~f~~~~------gR~e~~~~~~g~~vIdDSyn~nP~s~~aaL~~l 352 (822)
T PRK11930 291 LIHCIAVLLYLGYSADQIQERMARLEPVA------MRLEVKEGINNCTLINDSYNSDLQSLDIALDFL 352 (822)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CeeEEEEcCCCcEEEECCCCCCHHHHHHHHHHH
Confidence 34567778999999999999998655432 2566655 5789999998777777777766655
No 70
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=29.37 E-value=54 Score=22.88 Aligned_cols=22 Identities=23% Similarity=0.508 Sum_probs=15.9
Q ss_pred HHHHHHhcCCCHHHHHHHHHHh
Q 020672 125 VLEKAKELDVPKDIVERNIKRA 146 (323)
Q Consensus 125 aI~kAK~~nmPKd~IErAIkra 146 (323)
.-+.|+..|||+.+|.+-++..
T Consensus 19 ~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 19 IRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp HHHHHHHHT--HHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHcCC
Confidence 4456999999999999888743
No 71
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=28.17 E-value=1.6e+02 Score=22.12 Aligned_cols=50 Identities=14% Similarity=0.164 Sum_probs=35.4
Q ss_pred CcccHHHHHHHHHhCCCCeeecccceeecCCc--------cccCHHHHHHHHHHHHHHccCC
Q 020672 260 TSDNYTDITTKLREAGIPFETDNGSELLPITT--------IEVDDEAMELNKELIAKLLELD 313 (323)
Q Consensus 260 ~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~--------Vel~~e~~~~~~~lid~Lee~d 313 (323)
.|..|..|.+.+.+.|+.+.. ++-+|... |+++.++ +.++++++.|...-
T Consensus 10 ~pG~L~~vL~~f~~~~iNlt~---IeSRP~~~~~~~y~Ffvd~~~~~-~~~~~~l~~L~~~~ 67 (74)
T cd04904 10 EVGALARALKLFEEFGVNLTH---IESRPSRRNGSEYEFFVDCEVDR-GDLDQLISSLRRVV 67 (74)
T ss_pred CCcHHHHHHHHHHHCCCcEEE---EECCCCCCCCceEEEEEEEEcCh-HHHHHHHHHHHHhc
Confidence 377889999999999999863 66677632 6665432 34677888887643
No 72
>COG3453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.04 E-value=1.5e+02 Score=25.80 Aligned_cols=71 Identities=18% Similarity=0.366 Sum_probs=45.7
Q ss_pred CCCHHHHHHHHHHCCCccccc-CCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecCCccccCH
Q 020672 218 DADKDQLLDIALDAGAEDVIE-PPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDD 296 (323)
Q Consensus 218 ~~d~D~lle~AIEaGAEDV~~-~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~ 296 (323)
..+.+++-++| ..|---|.. .| | .||+ + -..+.+++.+.+++|+.+ .|+|-+.-.+++
T Consensus 15 Qi~~~D~~~ia-a~GFksiI~nRP---D-gEe~-~---------QP~~~~i~~aa~~aGl~y------~~iPV~~~~iT~ 73 (130)
T COG3453 15 QISPADIASIA-ALGFKSIICNRP---D-GEEP-G---------QPGFAAIAAAAEAAGLTY------THIPVTGGGITE 73 (130)
T ss_pred CCCHHHHHHHH-HhccceecccCC---C-CCCC-C---------CCChHHHHHHHHhcCCce------EEeecCCCCCCH
Confidence 35667766655 566665543 22 1 1111 1 246899999999999764 478999999998
Q ss_pred HHHHHHHHHHHHH
Q 020672 297 EAMELNKELIAKL 309 (323)
Q Consensus 297 e~~~~~~~lid~L 309 (323)
++.+.+...++.+
T Consensus 74 ~dV~~f~~Al~ea 86 (130)
T COG3453 74 ADVEAFQRALDEA 86 (130)
T ss_pred HHHHHHHHHHHHh
Confidence 8876655544443
No 73
>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional
Probab=27.58 E-value=2.1e+02 Score=29.17 Aligned_cols=59 Identities=12% Similarity=0.094 Sum_probs=42.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..||.-|...++|.+.|.++|+. .+-. -+.|..+ .+|+.+|+| .--|+.-..+-+..+
T Consensus 301 alaAia~a~~lgi~~~~i~~~L~~-~~~~------gR~e~i~~~~g~~vi~D-yahNP~s~~aal~~l 360 (481)
T PRK14022 301 AMAAGLACLRLGASLEDIQKGIAQ-TPVP------GRMEVLTQSNGAKVFID-YAHNGDSLNKLIDVV 360 (481)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcc-CCCC------CCeEEEECCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 456777888899999999999986 4322 2555555 368889999 677776655555544
No 74
>cd04925 ACT_ACR_2 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.15 E-value=79 Score=23.77 Aligned_cols=29 Identities=14% Similarity=0.165 Sum_probs=26.8
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCccccC
Q 020672 170 VVEVLTDKITRSVAAVREVVKDCGGKMAD 198 (323)
Q Consensus 170 IVE~lTDN~nRT~~~vR~~f~K~GG~l~~ 198 (323)
++|+.|.++....++|-.+|..+|.++-.
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~ 30 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVE 30 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEE
Confidence 78999999999999999999999998753
No 75
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=27.00 E-value=1.1e+02 Score=25.39 Aligned_cols=39 Identities=15% Similarity=0.276 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHH-------HHHHHHhCCCCCCCChHHHHHHHHHHhcCC
Q 020672 91 DAKKAKLYSRMGKE-------VISAVKKGGPNPTSNTVLAAVLEKAKELDV 134 (323)
Q Consensus 91 DakKsklfsKl~ke-------I~~Avk~GG~DP~~N~~La~aI~kAK~~nm 134 (323)
+.+|++=.++++++ ++.|-.. ..||++.+++.-.|..|+
T Consensus 45 ~var~~GMsqvA~~aGlsRe~LYkaLS~-----~GNPtf~Til~V~kAlG~ 90 (100)
T COG3636 45 VVARSRGMSQVARKAGLSREGLYKALSP-----GGNPTFDTILAVLKALGL 90 (100)
T ss_pred HHHHhcCHHHHHHHhCccHHHHHHHhCC-----CCCCcHHHHHHHHHHcCc
Confidence 44455555666554 4445554 459999999999998886
No 76
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=26.55 E-value=1.7e+02 Score=27.05 Aligned_cols=26 Identities=23% Similarity=0.454 Sum_probs=16.0
Q ss_pred EEEEeCCCCCHHHHHHHHHHCCCccccc
Q 020672 211 VVNIKFTDADKDQLLDIALDAGAEDVIE 238 (323)
Q Consensus 211 vI~v~~~~~d~D~lle~AIEaGAEDV~~ 238 (323)
+|.++.. +.++-.-.++++||+|...
T Consensus 75 Ii~Lta~--~~~~d~v~gl~~GADDYl~ 100 (229)
T COG0745 75 IIVLTAR--DDEEDRVLGLEAGADDYLT 100 (229)
T ss_pred EEEEECC--CcHHHHHHHHhCcCCeeee
Confidence 4445433 3334455689999999754
No 77
>TIGR00655 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.
Probab=25.84 E-value=4.8e+02 Score=25.11 Aligned_cols=95 Identities=17% Similarity=0.197 Sum_probs=60.5
Q ss_pred CCcEEEEEEecCChhhHHHHHHHHHhh-cCccccCCcceeeece-eeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCC
Q 020672 165 GGVSIVVEVLTDKITRSVAAVREVVKD-CGGKMADPGSVMFKFR-RARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVN 242 (323)
Q Consensus 165 gGvaiIVE~lTDN~nRT~~~vR~~f~K-~GG~l~~~gsV~f~F~-~kGvI~v~~~~~d~D~lle~AIEaGAEDV~~~~~~ 242 (323)
|=-.|++++-.++.+.+..+++..|.. .+-.++-.-++.+.=+ .+-.|.+.+.+..+..+++ ++..|.-+.+
T Consensus 40 ~~F~mr~~v~~~~~~~~~~~l~~~l~~~~~~~~~l~i~l~~~~~~~ki~vl~Sg~g~nl~~l~~-~~~~g~l~~~----- 113 (280)
T TIGR00655 40 GRFFMRVEFQLEGFRLEESSLLAAFKSALAEKFEMTWELILADKLKRVAILVSKEDHCLGDLLW-RWYSGELDAE----- 113 (280)
T ss_pred CeEEEEEEEEeCCCCCCHHHHHHHHHHHHHHHhCCEEEEecCCCCcEEEEEEcCCChhHHHHHH-HHHcCCCCcE-----
Confidence 344567777777666788999999999 8777764333333212 2334556666777888777 5677754432
Q ss_pred CCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCee
Q 020672 243 EDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFE 279 (323)
Q Consensus 243 ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~ 279 (323)
...|+|+-.++..+ .++.|+++.
T Consensus 114 -----------i~~visn~~~~~~~---A~~~gIp~~ 136 (280)
T TIGR00655 114 -----------IALVISNHEDLRSL---VERFGIPFH 136 (280)
T ss_pred -----------EEEEEEcChhHHHH---HHHhCCCEE
Confidence 34578888777653 456787764
No 78
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=25.72 E-value=2.5e+02 Score=28.43 Aligned_cols=60 Identities=15% Similarity=0.107 Sum_probs=44.1
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
...||.-|...++|.+.|..+|+.-.+-. -++|... .+|+.+|+| .--|+.-+.+-+..+
T Consensus 283 alaAia~a~~lgi~~~~i~~~L~~~~~~~------gR~e~~~~~~~~~iI~D-yahNP~s~~aal~~l 343 (460)
T PRK00139 283 LLAALAALLALGVPLEDALAALAKLQGVP------GRMERVDAGQGPLVIVD-YAHTPDALEKVLEAL 343 (460)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CCcEEEEcCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 44577788889999999999998766432 2455554 368999999 777877776666655
No 79
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=25.37 E-value=83 Score=23.68 Aligned_cols=28 Identities=32% Similarity=0.313 Sum_probs=23.4
Q ss_pred hhhhhHhHHHHHHHHHHHHHHHHHHHHh
Q 020672 84 AGRKGAQDAKKAKLYSRMGKEVISAVKK 111 (323)
Q Consensus 84 Kh~Kaa~DakKsklfsKl~keI~~Avk~ 111 (323)
-+-|.+.|..|++.|.|++|.+..+++.
T Consensus 16 ~~AK~~gd~~kAr~~~R~~K~~~~~I~~ 43 (59)
T smart00685 16 LQAKRAGDEEKARRHLRIAKQFDDAIKA 43 (59)
T ss_pred HHHHHcCCHHHHHHHHHHHhhHHHHHHH
Confidence 4568889999999999999988777664
No 80
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=25.30 E-value=69 Score=22.02 Aligned_cols=21 Identities=38% Similarity=0.477 Sum_probs=16.1
Q ss_pred HHHHHhcCCCHHHHHHHHHHh
Q 020672 126 LEKAKELDVPKDIVERNIKRA 146 (323)
Q Consensus 126 I~kAK~~nmPKd~IErAIkra 146 (323)
-+-|+..|+++.+|-+-|||+
T Consensus 24 ~~IA~~lg~s~sTV~relkR~ 44 (44)
T PF13936_consen 24 REIAKRLGRSRSTVSRELKRN 44 (44)
T ss_dssp HHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHCcCcHHHHHHHhcC
Confidence 345899999999999999985
No 81
>TIGR00257 IMPACT_YIGZ uncharacterized protein, YigZ family. This uncharacterized protein family includes YigZ, which has been crystallized, from E. coli. YigZ is homologous to the protein product of the mouse IMPACT gene. Crystallography shows a two-domain stucture, and the C-terminal domain is suggested to bind nucleic acids. The function is unknown. Note that the ortholog from E. coli was shown fused to the pepQ gene in GenBank entry X54687. This caused occasional misidentification of this protein as pepQ; this family is found in a number of species that lack pepQ.
Probab=25.27 E-value=2.5e+02 Score=25.95 Aligned_cols=69 Identities=10% Similarity=0.029 Sum_probs=46.1
Q ss_pred HHHHHHHHH-CCCcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecC--CccccCHHH
Q 020672 222 DQLLDIALD-AGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI--TTIEVDDEA 298 (323)
Q Consensus 222 D~lle~AIE-aGAEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~--~~Vel~~e~ 298 (323)
-.....||+ ++..+... ...+.|.|+...+..|...|.+.++.+.. .+|--. -.+.++.++
T Consensus 118 ~~aa~~al~~a~~~~~~~-------------~~~~~~~~~y~~~~~v~~~l~~~~~~i~~---~~y~~~V~~~~~v~~~~ 181 (204)
T TIGR00257 118 GKSVLEALNNIQKEEKLE-------------LEILSLHCDYKQLDALERELKKFQLEIIK---SNFSNNVVLVEISGTKE 181 (204)
T ss_pred HHHHHHHHHhCCeEEEEE-------------EEEEEEEechhHHHHHHHHHHHCCCEEEe---eEecCCEEEEEEECHHH
Confidence 355566666 56655533 14689999999999999999999988763 466544 234446666
Q ss_pred HHHHHHHH
Q 020672 299 MELNKELI 306 (323)
Q Consensus 299 ~~~~~~li 306 (323)
.+.+.+.+
T Consensus 182 ~~~~~~~l 189 (204)
T TIGR00257 182 NLAFSEQL 189 (204)
T ss_pred HHHHHHHH
Confidence 55544433
No 82
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=24.62 E-value=2.8e+02 Score=25.47 Aligned_cols=55 Identities=15% Similarity=0.160 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHCCCcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCee
Q 020672 218 DADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFE 279 (323)
Q Consensus 218 ~~d~D~lle~AIEaGAEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~ 279 (323)
..+.++.++.|-++|.+-|+-... +. .......-.++.++..+++.|++.|+.+.
T Consensus 15 ~~~~~e~~~~~~~~G~~~iEl~~~--~~-----~~~~~~~~~~~~~~~~l~~~l~~~Gl~i~ 69 (284)
T PRK13210 15 HLSWEERLVFAKELGFDFVEMSVD--ES-----DERLARLDWSKEERLSLVKAIYETGVRIP 69 (284)
T ss_pred CCCHHHHHHHHHHcCCCeEEEecC--Cc-----ccccccccCCHHHHHHHHHHHHHcCCCce
Confidence 478999999999999998876321 00 00011111245678999999999999886
No 83
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=24.52 E-value=1.9e+02 Score=29.29 Aligned_cols=56 Identities=16% Similarity=0.173 Sum_probs=40.5
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHH
Q 020672 124 AVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVR 186 (323)
Q Consensus 124 ~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR 186 (323)
.|+.-|... +|.+.|.++|+.-++.. -+.|.++ .+|+-+|.|+.--|+.-+.+-|+
T Consensus 290 aA~a~a~~~-i~~~~i~~~L~~f~~~~------~R~e~~~~~~g~~~i~Dsy~~np~s~~~al~ 346 (458)
T PRK01710 290 AAFCAVNDD-VSIESMKKVATTFSGVE------HRCEFVREINGVKYYNDSIASSPTRTLAGLK 346 (458)
T ss_pred HHHHHHHhC-CCHHHHHHHHHhCCCCC------cceEEEEEECCEEEecccccCCHHHHHHHHH
Confidence 444556666 99999999998766532 2555544 58999999988889987666665
No 84
>PF02016 Peptidase_S66: LD-carboxypeptidase; InterPro: IPR003507 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature is found in the Escherichia coli microcin C7 self-immunity protein mccF and in muramoyltetrapeptide carboxypeptidase (3.4.17.13 from EC, LD-carboxypeptidase A). LD-carboxypeptidase A belongs to MEROPS peptidase family S66 (clan SS). The entry also contains uncharacterised proteins including hypothetical proteins from various bacteria archaea.; PDB: 1ZRS_A 1ZL0_B 2AUM_B 2AUN_B 3TLG_A 3TLC_A 3TLZ_B 3TLY_B 3TLE_A 3TLB_B ....
Probab=23.99 E-value=98 Score=29.65 Aligned_cols=55 Identities=11% Similarity=0.146 Sum_probs=35.3
Q ss_pred ccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHHHHHHHHHHccCCCcceeec
Q 020672 262 DNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYT 320 (323)
Q Consensus 262 ~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~dDV~~VY~ 320 (323)
+.+..-.+.|++.||++... ...+-..... ...+.++.+.|.+++.+ |+|..|+.
T Consensus 14 ~~l~~~~~~L~~~G~~v~~~-~~~~~~~~~~--ags~~~Ra~dL~~a~~d-~~i~aI~~ 68 (284)
T PF02016_consen 14 ERLERGIKRLESWGFKVVVG-PHVFKRDGYL--AGSDEERAEDLNEAFAD-PEIDAIWC 68 (284)
T ss_dssp HHHHHHHHHHHHTTEEEEE--TTTTS-BTTB--SS-HHHHHHHHHHHHHS-TTEEEEEE
T ss_pred HHHHHHHHHHHhCCCEEEEC-CcccccCCCc--CCCHHHHHHHHHHHhcC-CCCCEEEE
Confidence 46677788899999998753 3333333322 33344556778888865 88998875
No 85
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=23.63 E-value=4.1e+02 Score=21.72 Aligned_cols=66 Identities=21% Similarity=0.190 Sum_probs=40.1
Q ss_pred HHhhhhhH-hHHHHHHHHHHHHHHHHHHHHh-CCCCCCCChHHHHHHHHHHhc------CCCHHHHHHHHHHhc
Q 020672 82 KIAGRKGA-QDAKKAKLYSRMGKEVISAVKK-GGPNPTSNTVLAAVLEKAKEL------DVPKDIVERNIKRAS 147 (323)
Q Consensus 82 nIKh~Kaa-~DakKsklfsKl~keI~~Avk~-GG~DP~~N~~La~aI~kAK~~------nmPKd~IErAIkra~ 147 (323)
.++..|.+ +.-+..+++.-+++.-..||-+ ++...+..-++..|+...+.. +++.+.|+.+|..|-
T Consensus 28 ~~~~l~~k~~~e~~~~~~~~vak~Av~aveq~~~~~~~G~~K~~~A~~~v~~~L~~~gi~~t~~~i~~~IEaAV 101 (108)
T PF09682_consen 28 VIKYLKKKAGGEKLVKILEIVAKIAVNAVEQVAKEGGKGEEKKAEAVQYVKERLKKKGIKVTDEQIEGAIEAAV 101 (108)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 34444444 3334455555577766666654 333335667787777665554 788889999998763
No 86
>PF05902 4_1_CTD: 4.1 protein C-terminal domain (CTD); InterPro: IPR008379 There is a unique sequence domain at the C terminus of all known 4.1 proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24 kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates [].; GO: 0003779 actin binding, 0005198 structural molecule activity, 0005856 cytoskeleton
Probab=23.41 E-value=64 Score=27.46 Aligned_cols=22 Identities=27% Similarity=0.428 Sum_probs=19.0
Q ss_pred CCCCCCCChHHHHHHHHHHhcC
Q 020672 112 GGPNPTSNTVLAAVLEKAKELD 133 (323)
Q Consensus 112 GG~DP~~N~~La~aI~kAK~~n 133 (323)
|.+|-+....|+.||.+||.+|
T Consensus 77 GD~DIDhDqaLa~aI~eAk~q~ 98 (114)
T PF05902_consen 77 GDADIDHDQALAQAIKEAKEQH 98 (114)
T ss_pred cCCCcchHHHHHHHHHHHHHhC
Confidence 6688888999999999999765
No 87
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t
Probab=23.39 E-value=2.1e+02 Score=20.09 Aligned_cols=28 Identities=29% Similarity=0.343 Sum_probs=25.2
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCcccc
Q 020672 170 VVEVLTDKITRSVAAVREVVKDCGGKMA 197 (323)
Q Consensus 170 IVE~lTDN~nRT~~~vR~~f~K~GG~l~ 197 (323)
.+.+.++++...+++|-.+|+++|+++.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~ 29 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIH 29 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEE
Confidence 4677899999999999999999999875
No 88
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=23.35 E-value=2.3e+02 Score=20.18 Aligned_cols=54 Identities=9% Similarity=0.075 Sum_probs=32.3
Q ss_pred ecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEEEEeCCCCCHHHHHHH
Q 020672 174 LTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 227 (323)
Q Consensus 174 lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI~v~~~~~d~D~lle~ 227 (323)
...+.....++|..+|.++|.++..-..........+++.+.-+....+++++.
T Consensus 5 ~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~ 58 (73)
T cd04902 5 RNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDEPVPDEVLEE 58 (73)
T ss_pred EeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCCCCCHHHHHH
Confidence 667888899999999999999885422111112345555555433233344433
No 89
>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=23.25 E-value=1.3e+02 Score=19.68 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=17.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHH
Q 020672 123 AAVLEKAKELDVPKDIVERNIKR 145 (323)
Q Consensus 123 a~aI~kAK~~nmPKd~IErAIkr 145 (323)
-.+|..|+..|+.++-|..-++.
T Consensus 6 ~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 6 VELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHh
Confidence 46899999999999999887764
No 90
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=23.08 E-value=3.3e+02 Score=25.19 Aligned_cols=54 Identities=17% Similarity=0.089 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHCCCcccccCCCCCCCCcccccCceEE-EEeCcccHHHHHHHHHhCCCCee
Q 020672 218 DADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYK-VVSTSDNYTDITTKLREAGIPFE 279 (323)
Q Consensus 218 ~~d~D~lle~AIEaGAEDV~~~~~~ed~~~ed~~~~~~~-v~~~p~~l~~V~~~L~~~G~~i~ 279 (323)
+.+.++.+..+-++|.+-|+-... +. ..... .-..+..+..+++.|++.|+++.
T Consensus 20 ~~~~~e~~~~~~~~G~~~iEl~~~--~~------~~~~~~~~~~~~~~~~l~~~l~~~gl~i~ 74 (283)
T PRK13209 20 GECWLEKLAIAKTAGFDFVEMSVD--ES------DERLARLDWSREQRLALVNALVETGFRVN 74 (283)
T ss_pred CCCHHHHHHHHHHcCCCeEEEecC--cc------ccchhccCCCHHHHHHHHHHHHHcCCcee
Confidence 568999999999999998876321 00 00111 12257788999999999999986
No 91
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.77 E-value=54 Score=27.00 Aligned_cols=21 Identities=24% Similarity=0.349 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHccCCCccee
Q 020672 298 AMELNKELIAKLLELDDVDAV 318 (323)
Q Consensus 298 ~~~~~~~lid~Lee~dDV~~V 318 (323)
+...|..|++-|.+..|||+|
T Consensus 15 eAAaFRrLv~HL~~rsdvQNI 35 (104)
T COG3492 15 EAAAFRRLVEHLQERSDVQNI 35 (104)
T ss_pred HHHHHHHHHHHHHHhcccchh
Confidence 356889999999999999997
No 92
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=22.71 E-value=2.4e+02 Score=28.78 Aligned_cols=61 Identities=15% Similarity=0.169 Sum_probs=45.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEec-CCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGY-GGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~GP-gGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..|+.-|...++|.+.|.++|+.-++-. .++|..+- +|+.+|.|+---|+.-+..-++.+
T Consensus 280 a~aAia~~~~lgi~~~~i~~~L~~F~~~~------~Rle~v~~~~gv~~i~DS~atN~~a~~~al~~~ 341 (454)
T PRK01368 280 IAASYAVAKIIGVEPKKILESISSFQSLP------HRMQYIGSINNISFYNDSKATNAISAVQSIKAL 341 (454)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------cceEEEEEECCeEEEECCCCCCHHHHHHHHHhc
Confidence 45677778888999999999998755432 24444433 789999997777988888877766
No 93
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.
Probab=22.69 E-value=76 Score=31.85 Aligned_cols=35 Identities=14% Similarity=0.084 Sum_probs=17.9
Q ss_pred EEEeCcccHHHHHHHHHhCCCCeeecccceeecCC
Q 020672 256 KVVSTSDNYTDITTKLREAGIPFETDNGSELLPIT 290 (323)
Q Consensus 256 ~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~ 290 (323)
-|.|+|..+..-.+.|.+.||.++...-+.|.|+|
T Consensus 393 yvsc~p~tlard~~~l~~~gy~~~~~~~~DmFP~T 427 (431)
T TIGR00479 393 YVSCNPATLARDLEFLCKEGYGITWVQPVDMFPHT 427 (431)
T ss_pred EEcCCHHHHHHHHHHHHHCCeeEEEEEEeccCCCC
Confidence 34555555555555555555555433334555554
No 94
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=22.68 E-value=1.8e+02 Score=26.64 Aligned_cols=43 Identities=14% Similarity=0.268 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhccC
Q 020672 99 SRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK 149 (323)
Q Consensus 99 sKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g~ 149 (323)
..|.++|..-...|+.=| |++-||+.||+|..|.|.+-+-+..
T Consensus 12 ~~lv~~~~~~l~~~~~~~--------a~~i~~~l~~~k~~vNr~LY~l~~~ 54 (183)
T PHA03103 12 YELVKKEVKNLGLGEGIT--------AIEISRKLNIEKSEVNKQLYKLQRE 54 (183)
T ss_pred HHHHHHHHHHhccCCCcc--------HHHHHHHhCCCHHHHHHHHHHHHhc
Confidence 456777777777877654 8999999999999999999886644
No 95
>PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B.
Probab=22.62 E-value=1.9e+02 Score=23.25 Aligned_cols=51 Identities=31% Similarity=0.413 Sum_probs=33.4
Q ss_pred HHHHHHHHHhCCCCeeecccceeecC-CccccCHH-HHHHHHHHHHHHccCCCcceeecc
Q 020672 264 YTDITTKLREAGIPFETDNGSELLPI-TTIEVDDE-AMELNKELIAKLLELDDVDAVYTD 321 (323)
Q Consensus 264 l~~V~~~L~~~G~~i~~~~~i~~iP~-~~Vel~~e-~~~~~~~lid~Lee~dDV~~VY~N 321 (323)
..++-+.|++.|++++. -|. |.+|-+-+ -++.+.+..+.+.+ .++.+||++
T Consensus 19 V~~~i~~i~~sgl~y~v------~pm~T~iEGe~dev~~~i~~~~e~~~~-~G~~Rv~t~ 71 (92)
T PF01910_consen 19 VAEAIEVIKESGLKYEV------GPMGTTIEGELDEVMALIKEAHEALFE-AGAKRVVTV 71 (92)
T ss_dssp HHHHHHHHHTSSSEEEE------ETTEEEEEEEHHHHHHHHHHHHHHHHC-TTSSEEEEE
T ss_pred HHHHHHHHHHcCCceEE------cCCccEEEecHHHHHHHHHHHHHHHHH-cCCCeEEEE
Confidence 35666777777766553 265 77888743 46677777777766 457777765
No 96
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=22.54 E-value=5.8e+02 Score=23.02 Aligned_cols=129 Identities=12% Similarity=0.064 Sum_probs=72.5
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeE----EEEEeCCCCCHHHHHHH---HHH-CCCcccccCCC
Q 020672 170 VVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRAR----VVNIKFTDADKDQLLDI---ALD-AGAEDVIEPPV 241 (323)
Q Consensus 170 IVE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kG----vI~v~~~~~d~D~lle~---AIE-aGAEDV~~~~~ 241 (323)
.+.++..|+...+..|-.+|.+.|=++-. =++.- =+..| -|.++.++...+++... -+| .-++|+.+.
T Consensus 4 ~isvlv~n~PGVL~RIt~lFsrRg~NIes-Lsv~~-t~~~~~sr~TIvv~~~~~~ieqL~kQL~KLidVl~V~~~~~~-- 79 (174)
T CHL00100 4 TLSVLVEDESGVLTRIAGLFARRGFNIES-LAVGP-AEQKGISRITMVVPGDDRTIEQLTKQLYKLVNILKVQDITNI-- 79 (174)
T ss_pred EEEEEEeCcCCHHHHHHHHHHhCCCCeeE-EEeeE-cCCCCccEEEEEEECCHHHHHHHHHHHHHHhHhhEEEecCCc--
Confidence 57889999999999999999999976532 11111 01122 23344321113332221 111 334443221
Q ss_pred CCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecC-CccccCHHHHHHHHHHHHHHccC
Q 020672 242 NEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI-TTIEVDDEAMELNKELIAKLLEL 312 (323)
Q Consensus 242 ~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~-~~Vel~~e~~~~~~~lid~Lee~ 312 (323)
+ .- ..+--.++|.|++.+-..|.+-.+..+-.|.. +-|. -.+|++... +++..|++.|+..
T Consensus 80 --~-~v-~rEl~LiKv~~~~~~r~ei~~~~~~f~a~ivd-----v~~~~~~ie~tG~~-~ki~a~~~~l~~~ 141 (174)
T CHL00100 80 --P-CV-ERELMLIKINVNSQTRPEILEIAQIFRAKVVD-----LSEESLILEVTGDP-GKIVAIEQLLEKF 141 (174)
T ss_pred --c-ce-eeEEEEEEEecCCcCHHHHHHHHHHhCCEEEE-----ecCCEEEEEEcCCH-HHHHHHHHHhhhc
Confidence 0 00 12224678899998888888888877666542 2244 457786533 4456677777654
No 97
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.45 E-value=2.9e+02 Score=19.72 Aligned_cols=59 Identities=19% Similarity=0.281 Sum_probs=36.2
Q ss_pred EEEecCChhhHHHHHHHHHhhcCccccCCcceeeece---e-eEEEEEeCCC-CCHHHHHHHHHHCCC
Q 020672 171 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFR---R-ARVVNIKFTD-ADKDQLLDIALDAGA 233 (323)
Q Consensus 171 VE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~---~-kGvI~v~~~~-~d~D~lle~AIEaGA 233 (323)
+.+..+++...+..|-.+|.++|.++-.- +.+. . .+.+.+.... .+.+.+.+.--++|-
T Consensus 4 ~~v~~~d~~G~L~~l~~~l~~~~i~i~~~----~~~~~~~~~~~~~~i~v~~~~~~~~~~~~L~~~G~ 67 (69)
T cd04909 4 LYVDVPDEPGVIAEVTQILGDAGISIKNI----EILEIREGIGGILRISFKTQEDRERAKEILKEAGY 67 (69)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCceee----EeEEeecCCcEEEEEEECCHHHHHHHHHHHHHcCC
Confidence 45677888899999999999999988532 2222 1 4443333221 244555555555553
No 98
>PF14501 HATPase_c_5: GHKL domain
Probab=22.20 E-value=3.7e+02 Score=20.91 Aligned_cols=58 Identities=16% Similarity=0.301 Sum_probs=33.8
Q ss_pred HHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCChh--------------hHHHHHHHHHhhcCccc
Q 020672 138 IVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKIT--------------RSVAAVREVVKDCGGKM 196 (323)
Q Consensus 138 ~IErAIkra~g~~~~~~~e~~YEg~GPgGvaiIVE~lTDN~n--------------RT~~~vR~~f~K~GG~l 196 (323)
.||+||+-+....+..+.++.+.-.. +-+.|.|+=-+++.. ==...|+.+++|++|.+
T Consensus 13 lldNAiea~~~~~~~~~I~i~~~~~~-~~~~i~i~N~~~~~~~~~~~~~~~~~~~G~GL~~v~~i~~~y~g~~ 84 (100)
T PF14501_consen 13 LLDNAIEACKKYEDKRFISISIREEN-GFLVIIIENSCEKEIEKLESSSSKKKGHGIGLKNVKKILEKYNGSL 84 (100)
T ss_pred HHHHHHHHHHhcCCCcEEEEEEEecC-CEEEEEEEECCCCccccccccccCCCCCCcCHHHHHHHHHHCCCEE
Confidence 46777876554332556665443333 445555554443321 12568999999998865
No 99
>cd04899 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.82 E-value=1.2e+02 Score=21.72 Aligned_cols=29 Identities=21% Similarity=0.228 Sum_probs=25.8
Q ss_pred EEEEecCChhhHHHHHHHHHhhcCccccC
Q 020672 170 VVEVLTDKITRSVAAVREVVKDCGGKMAD 198 (323)
Q Consensus 170 IVE~lTDN~nRT~~~vR~~f~K~GG~l~~ 198 (323)
++.+.++++....++|-.+|.++|.++..
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~ 30 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIHS 30 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEEE
Confidence 57788999999999999999999998753
No 100
>cd07062 Peptidase_S66_mccF_like Microcin C7 self-immunity protein determines resistance to exogenous microcin C7. Microcin C7 self-immunity protein (mccF): MccF, a homolog of the LD-carboxypeptidase family, mediates resistance against exogenously added microcin C7 (MccC7), a ribosomally-encoded peptide antibiotic that contains a phosphoramidate linkage to adenosine monophosphate at its C-terminus. The plasmid-encoded mccF gene is transcribed in the opposite direction to the other five genes (mccA-E) and is required for the full expression of immunity but not for production. The catalytic triad residues (Ser, His, Glu) of LD-carboxypeptidase are also conserved in MccF, strongly suggesting that MccF shares the hydrolytic activity with LD-carboxypeptidases. Substrates of MccF have not been deduced, but could likely be microcin C7 precursors. The possible role of MccF is to defend producer cells against exogenous microcin from re-entering after having been exported. It is suggested that M
Probab=21.66 E-value=1.6e+02 Score=28.53 Aligned_cols=56 Identities=14% Similarity=0.166 Sum_probs=37.7
Q ss_pred cccHHHHHHHHHhCCCCeeecccceeecCCccccCHHHHHHHHHHHHHHccCCCcceeec
Q 020672 261 SDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYT 320 (323)
Q Consensus 261 p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~Vel~~e~~~~~~~lid~Lee~dDV~~VY~ 320 (323)
++.+....+.|++.||++... ...+.......-+ +.++...|.+++. +|+|..|+.
T Consensus 17 ~~~~~~~~~~L~~~G~~v~~~-~~~~~~~~~~ag~--~~~Ra~dL~~a~~-Dp~i~aI~~ 72 (308)
T cd07062 17 PHRLERAKKRLENLGFEVVEG-PNALKGDKYLSAS--PEERAEELMAAFA-DPSIKAIIP 72 (308)
T ss_pred HHHHHHHHHHHHhCCCEEEEe-cccccccccccCC--HHHHHHHHHHHhc-CCCCCEEEE
Confidence 355777888899999998754 4444443333333 4456677888884 678988875
No 101
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=21.60 E-value=69 Score=25.49 Aligned_cols=20 Identities=20% Similarity=0.421 Sum_probs=16.9
Q ss_pred cccHHHHHHHHHhCCCCeee
Q 020672 261 SDNYTDITTKLREAGIPFET 280 (323)
Q Consensus 261 p~~l~~V~~~L~~~G~~i~~ 280 (323)
-+.|..|+++|+++||++..
T Consensus 7 E~~Ls~v~~~L~~~GyeVv~ 26 (80)
T PF03698_consen 7 EEGLSNVKEALREKGYEVVD 26 (80)
T ss_pred cCCchHHHHHHHHCCCEEEe
Confidence 35688999999999999864
No 102
>PRK04194 hypothetical protein; Provisional
Probab=21.50 E-value=2.6e+02 Score=28.54 Aligned_cols=48 Identities=23% Similarity=0.394 Sum_probs=35.9
Q ss_pred HHHHHHHHCCCcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHh
Q 020672 223 QLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLRE 273 (323)
Q Consensus 223 ~lle~AIEaGAEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~ 273 (323)
-++|..+++||-||...|-+- ..-+..-.+.++|.|++..++.+.|-.
T Consensus 265 ~~~e~L~~~GAlDV~~tPi~M---KK~RPg~~L~vl~~~~~~~~l~~~if~ 312 (392)
T PRK04194 265 YLFERLLEAGALDVFITPITM---KKNRPGHLLTVICPPEKAEELARILFR 312 (392)
T ss_pred HHHHHHHHCCCceeeecccee---cCCCceeEEEEEeCHHHHHHHHHHHHh
Confidence 578999999999997654321 112334568999999999999999853
No 103
>COG2605 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]
Probab=21.42 E-value=3.8e+02 Score=26.73 Aligned_cols=98 Identities=14% Similarity=0.130 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHH------hcCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcEEE
Q 020672 97 LYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAK------ELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIV 170 (323)
Q Consensus 97 lfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK------~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~GPgGvaiI 170 (323)
..-.++.+...|+=.+. =+.+..+|.+.- ...++++.|+|.++.|..++.-.- ..-|=|-|| +++
T Consensus 225 ~mk~~A~~~~~al~~nd-----~~~f~~~l~~gW~~KK~ls~~ISN~~IDriy~~A~~~GA~~g---Kl~GaG~gG-Fll 295 (333)
T COG2605 225 EMKALAYEMKDALVRND-----IPEFGQILDRGWEAKKKLSSRISNDAIDRIYELALKNGAYGG---KLSGAGGGG-FLL 295 (333)
T ss_pred HHHHHHHHHHHHHHhcc-----hHHHHHHHHhHHHhhhhhccCcCcHHHHHHHHHHHhcCchhc---eeeccCCcc-EEE
Confidence 33445555555555432 356777777543 357899999999999876542111 122444344 344
Q ss_pred EEEecCChhhHHHHHHHHHhhcCccccCCcceeeeceeeEEE
Q 020672 171 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVV 212 (323)
Q Consensus 171 VE~lTDN~nRT~~~vR~~f~K~GG~l~~~gsV~f~F~~kGvI 212 (323)
+-|--.+++ +|...|.+..| .+|.|.|+..|.-
T Consensus 296 f~~~p~k~~----~l~r~l~~~~~-----~~~~~~Fd~~Gsr 328 (333)
T COG2605 296 FFCDPSKRN----ELARALEKEQG-----FVVDTSFDKEGSR 328 (333)
T ss_pred EEeCccchH----HHHHHHHHhcC-----CeEEEEecCCCeE
Confidence 445444444 44455666655 3467888888853
No 104
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=21.40 E-value=2e+02 Score=29.14 Aligned_cols=39 Identities=21% Similarity=0.203 Sum_probs=31.7
Q ss_pred ceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecCCc
Q 020672 253 RYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITT 291 (323)
Q Consensus 253 ~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~~~ 291 (323)
..+-|-|+|..|..=...|.+.||.++...-+.|.|+|+
T Consensus 394 ~ivyvSCnp~tlaRDl~~L~~~gY~l~~i~~~DmFP~T~ 432 (443)
T PRK13168 394 RIVYVSCNPATLARDAGVLVEAGYRLKRAGMLDMFPHTG 432 (443)
T ss_pred eEEEEEeChHHhhccHHHHhhCCcEEEEEEEeccCCCCC
Confidence 456789999998877778888899998665688899964
No 105
>PRK11568 hypothetical protein; Provisional
Probab=21.06 E-value=3.9e+02 Score=24.71 Aligned_cols=70 Identities=11% Similarity=0.051 Sum_probs=46.2
Q ss_pred HHHHHHHH-CCCcccccCCCCCCCCcccccCceEEEEeCcccHHHHHHHHHhCCCCeeecccceeecC--CccccCHHHH
Q 020672 223 QLLDIALD-AGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI--TTIEVDDEAM 299 (323)
Q Consensus 223 ~lle~AIE-aGAEDV~~~~~~ed~~~ed~~~~~~~v~~~p~~l~~V~~~L~~~G~~i~~~~~i~~iP~--~~Vel~~e~~ 299 (323)
.....||+ ++-.+... ...+.|.|+..++..|...|.+.++.+.. .+|--. -.+.++.++.
T Consensus 119 ~aa~~al~~a~~~~~~~-------------~~~~~i~~~y~~~~~v~~~l~~~~~~i~~---~~y~~~V~~~~~v~~~~~ 182 (204)
T PRK11568 119 GGVQQALRQLTTQRKVP-------------LTEYTLQCEYAQLAGIEALLGQFDGKIVN---SEYQAFVTLRVALPAAKV 182 (204)
T ss_pred HHHHHHHHhCCeEEEEE-------------eEEEEEEECcchHHHHHHHHHHCCCEEEc---ceecCCEEEEEEECHHHH
Confidence 45555665 56555433 24688999999999999999999988752 456433 2355566666
Q ss_pred HHHHHHHHH
Q 020672 300 ELNKELIAK 308 (323)
Q Consensus 300 ~~~~~lid~ 308 (323)
+.+...+..
T Consensus 183 ~~~~~~l~~ 191 (204)
T PRK11568 183 AEFSAKLAD 191 (204)
T ss_pred HHHHHHHHH
Confidence 655554433
No 106
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase. UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (murein tripeptide ligase) is described by TIGR01081.
Probab=20.74 E-value=2.1e+02 Score=28.79 Aligned_cols=45 Identities=22% Similarity=0.418 Sum_probs=32.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEE
Q 020672 122 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVE 172 (323)
Q Consensus 122 La~aI~kAK~~nmPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE 172 (323)
+..|+.-|...++|.+.|..+|+...+-. -++|..+ .+|+.+|.|
T Consensus 278 ~~aA~a~~~~lgi~~~~i~~~l~~f~~~~------~R~e~~~~~~gv~~i~D 323 (448)
T TIGR01082 278 ALAAIAVALELGIDFEAILRALANFQGVK------RRFEILGEFGGVLLIDD 323 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------ccceEEEEeCCeEEEEc
Confidence 45677778889999999999999776432 2444432 357888777
No 107
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=20.54 E-value=1.1e+02 Score=27.62 Aligned_cols=61 Identities=18% Similarity=0.153 Sum_probs=40.0
Q ss_pred EeCcccHHHHHHHHHhCCCCeeeccccee-----ecCCccccCHHHHHHHHHHHHHHccCCCcceeec
Q 020672 258 VSTSDNYTDITTKLREAGIPFETDNGSEL-----LPITTIEVDDEAMELNKELIAKLLELDDVDAVYT 320 (323)
Q Consensus 258 ~~~p~~l~~V~~~L~~~G~~i~~~~~i~~-----iP~~~Vel~~e~~~~~~~lid~Lee~dDV~~VY~ 320 (323)
-=.|--+..|...|...||.|++- ...- ++.-++.++..+. .++.|.+.|+.+.||.+|..
T Consensus 10 ~n~PGVL~RIt~lFsrRg~NIesL-sv~~t~~~~~sr~TIvv~~~~~-~ieqL~kQL~KLidVl~V~~ 75 (174)
T CHL00100 10 EDESGVLTRIAGLFARRGFNIESL-AVGPAEQKGISRITMVVPGDDR-TIEQLTKQLYKLVNILKVQD 75 (174)
T ss_pred eCcCCHHHHHHHHHHhCCCCeeEE-EeeEcCCCCccEEEEEEECCHH-HHHHHHHHHHHHhHhhEEEe
Confidence 335778999999999999999753 2222 1222233443222 25678888888888888765
No 108
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=20.49 E-value=1.3e+02 Score=22.61 Aligned_cols=31 Identities=29% Similarity=0.408 Sum_probs=25.1
Q ss_pred EEEEEecCChhhHHHHHHHHHhhcCccccCC
Q 020672 169 IVVEVLTDKITRSVAAVREVVKDCGGKMADP 199 (323)
Q Consensus 169 iIVE~lTDN~nRT~~~vR~~f~K~GG~l~~~ 199 (323)
+||-++-.++...++.|-.++.++||++.+.
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~ 33 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDS 33 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEEE
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEEE
Confidence 6788888899999999999999999998764
No 109
>KOG0013 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.27 E-value=2.5e+02 Score=26.56 Aligned_cols=71 Identities=18% Similarity=0.273 Sum_probs=48.5
Q ss_pred ccccCCcccCcch--hhHHhhhhhHhHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHH
Q 020672 67 TIRTFAPVCMGRR--SSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIK 144 (323)
Q Consensus 67 ~~~~~~~~~mG~k--WsnIKh~Kaa~DakKsklfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIk 144 (323)
-||-+.|.+=||| | |+-|.. ..|+-+ .|..++++|.-+-..-+|.-.|-
T Consensus 50 EFWdTapAf~GrKEIW----------DaL~aa---------~ta~e~------~d~e~Aqai~dgA~~tiP~g~l~---- 100 (231)
T KOG0013|consen 50 EFWDTAPAFGGRKEIW----------DALHAA---------VTAAEE------GDAEAAQAILDGADLTIPEGDLS---- 100 (231)
T ss_pred hhhhcccccCCcHHHH----------HHHHHH---------HHHHhc------ccHHHHHHHHhccccccCCcchH----
Confidence 3999999999986 7 333322 223332 38999999999988999965544
Q ss_pred HhccCCccceeEEEEEEEecCC
Q 020672 145 RASEKGQEAFIEKVYEVYGYGG 166 (323)
Q Consensus 145 ra~g~~~~~~~e~~YEg~GPgG 166 (323)
++-...+..|.+..|=.++|-+
T Consensus 101 ecydelg~~y~~p~ycls~p~n 122 (231)
T KOG0013|consen 101 ECYDELGGTYYEPIYCLSRPPN 122 (231)
T ss_pred HHHHhhCCeEeecceeeccCch
Confidence 3333345578888887777754
No 110
>PF09536 DUF2378: Protein of unknown function (DUF2378); InterPro: IPR011751 This family consists of a set of at least 17 paralogous proteins in Myxococcus xanthus (strain DK 1622). Members are about 200 amino acids in length. No other homologs are known; the function is unknown.
Probab=20.24 E-value=4.7e+02 Score=23.58 Aligned_cols=53 Identities=19% Similarity=0.343 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhcCCCHHHHHHHHHHhccC--CccceeEEEEEEEecCCcEEEEE
Q 020672 95 AKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK--GQEAFIEKVYEVYGYGGVSIVVE 172 (323)
Q Consensus 95 sklfsKl~keI~~Avk~GG~DP~~N~~La~aI~kAK~~nmPKd~IErAIkra~g~--~~~~~~e~~YEg~GPgGvaiIVE 172 (323)
+=.-|-++|.+...++.||| +|.+.+.... ...+|-|.+||-.||...-+.+.
T Consensus 80 gf~~T~~Gr~~~~l~~~~gP-------------------------~R~L~r~p~~~ra~~ny~e~~~~~~G~~~~rl~~~ 134 (178)
T PF09536_consen 80 GFFETLVGRALLGLARLGGP-------------------------RRLLERAPRSYRAGVNYGERRVEWLGPRSARLRMN 134 (178)
T ss_pred HHHHhHHHHHHHHHHhcCCH-------------------------HHHHHHhhHHhhhccCcceeEEEEeCCceEEEEEe
Confidence 33347888888889998887 3455555532 34679999999999988777665
No 111
>TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetase. A close homolog, scoring just below the trusted cutoff, is found (with introns) in Arabidopsis thaliana. Its role is unknown.
Probab=20.15 E-value=3.9e+02 Score=26.95 Aligned_cols=60 Identities=13% Similarity=0.112 Sum_probs=42.3
Q ss_pred HHHHHHHHHhcC-CCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCChhhHHHHHHHH
Q 020672 122 LAAVLEKAKELD-VPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 188 (323)
Q Consensus 122 La~aI~kAK~~n-mPKd~IErAIkra~g~~~~~~~e~~YEg~G-PgGvaiIVE~lTDN~nRT~~~vR~~ 188 (323)
+..|+.-|...+ +|.+.|..+|+.-.+... ++|... .+|+.+|.| ..-|+.-..+-+..+
T Consensus 291 alaAia~a~~lg~i~~e~i~~~L~~~~~~~g------R~e~~~~~~g~~vi~D-y~~NP~s~~aal~~l 352 (464)
T TIGR01085 291 LLAALATLLHLGGIDLEDIVAALEKFRGVPG------RMELVDGGQKFLVIVD-YAHTPDALEKALRTL 352 (464)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHhCCCCCC------CcEEEEcCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 345777788888 999999999987664322 333332 368899999 777777666666655
Done!