Query 026745
Match_columns 234
No_of_seqs 116 out of 1053
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 12:05:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026745.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026745hhsearch_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 3.4E-76 7.4E-81 508.2 22.5 206 14-232 30-236 (241)
2 PRK00110 hypothetical protein; 100.0 6E-74 1.3E-78 502.7 24.3 215 3-232 10-234 (245)
3 PRK12378 hypothetical protein; 100.0 7.4E-74 1.6E-78 499.1 23.6 207 12-233 26-234 (235)
4 PF01709 Transcrip_reg: Transc 100.0 1.2E-73 2.6E-78 498.9 20.7 206 14-232 26-232 (234)
5 TIGR01033 DNA-binding regulato 100.0 5.6E-73 1.2E-77 495.1 24.1 209 12-233 28-237 (238)
6 KOG2972 Uncharacterized conser 100.0 1.3E-59 2.8E-64 404.7 19.0 223 6-233 50-273 (276)
7 PRK07562 ribonucleotide-diphos 98.0 5E-06 1.1E-10 86.6 5.4 49 12-60 317-371 (1220)
8 cd04888 ACT_PheB-BS C-terminal 88.4 1.2 2.5E-05 31.0 4.8 63 167-230 6-73 (76)
9 PF03927 NapD: NapD protein; 80.1 2.4 5.1E-05 31.0 3.4 60 165-229 7-69 (79)
10 cd04882 ACT_Bt0572_2 C-termina 72.4 18 0.0004 23.8 6.1 61 82-144 2-62 (65)
11 PF13291 ACT_4: ACT domain; PD 71.9 7.7 0.00017 27.4 4.2 64 166-230 9-79 (80)
12 cd04878 ACT_AHAS N-terminal AC 70.7 14 0.0003 24.5 5.2 57 171-229 10-71 (72)
13 TIGR00119 acolac_sm acetolacta 69.5 63 0.0014 26.7 10.9 134 81-223 3-140 (157)
14 cd04876 ACT_RelA-SpoT ACT dom 69.4 18 0.00039 23.0 5.4 60 169-229 6-69 (71)
15 cd04877 ACT_TyrR N-terminal AC 68.1 17 0.00036 25.4 5.2 57 171-230 10-68 (74)
16 PRK11895 ilvH acetolactate syn 66.9 73 0.0016 26.4 10.0 133 81-224 4-142 (161)
17 PRK04435 hypothetical protein; 65.0 14 0.00031 30.0 4.9 61 168-230 76-142 (147)
18 cd04879 ACT_3PGDH-like ACT_3PG 63.3 35 0.00075 22.3 5.9 26 83-108 3-28 (71)
19 PRK10553 assembly protein for 63.1 15 0.00032 27.5 4.3 65 165-232 9-78 (87)
20 PF13601 HTH_34: Winged helix 62.3 6.9 0.00015 28.5 2.3 52 171-222 27-78 (80)
21 PRK15385 magnesium transport p 62.1 26 0.00057 30.8 6.3 66 166-232 145-221 (225)
22 cd04903 ACT_LSD C-terminal ACT 61.6 43 0.00092 22.0 6.2 27 82-108 2-28 (71)
23 PF14502 HTH_41: Helix-turn-he 60.0 12 0.00025 25.1 2.9 43 32-79 5-47 (48)
24 PF02662 FlpD: Methyl-viologen 59.2 71 0.0015 25.1 7.8 92 119-223 28-123 (124)
25 cd04874 ACT_Af1403 N-terminal 59.0 28 0.00061 23.0 4.9 55 171-230 10-70 (72)
26 PF09186 DUF1949: Domain of un 57.2 19 0.00041 23.4 3.7 47 168-217 1-49 (56)
27 PRK13562 acetolactate synthase 56.3 20 0.00044 26.7 3.9 60 170-230 11-75 (84)
28 cd04881 ACT_HSDH-Hom ACT_HSDH_ 55.8 27 0.00059 23.5 4.5 58 171-229 10-72 (79)
29 COG2605 Predicted kinase relat 54.5 30 0.00065 31.9 5.5 53 129-189 265-318 (333)
30 cd04887 ACT_MalLac-Enz ACT_Mal 54.2 38 0.00083 23.1 5.0 59 168-227 6-68 (74)
31 PF01037 AsnC_trans_reg: AsnC 54.1 9.6 0.00021 26.1 1.9 24 209-232 45-69 (74)
32 PRK06737 acetolactate synthase 52.4 22 0.00048 25.9 3.6 60 170-230 11-74 (76)
33 PRK08178 acetolactate synthase 52.1 21 0.00046 27.3 3.5 60 171-232 18-81 (96)
34 PF05225 HTH_psq: helix-turn-h 51.8 16 0.00034 23.7 2.5 22 36-57 19-40 (45)
35 PRK03803 murD UDP-N-acetylmura 50.1 56 0.0012 30.8 6.9 61 33-99 278-339 (448)
36 cd04880 ACT_AAAH-PDT-like ACT 49.6 37 0.00081 23.5 4.4 52 170-224 8-68 (75)
37 TIGR01143 murF UDP-N-acetylmur 49.5 64 0.0014 30.2 7.2 61 33-99 259-319 (417)
38 PRK02472 murD UDP-N-acetylmura 49.5 44 0.00095 31.3 6.1 60 33-98 280-340 (447)
39 TIGR01087 murD UDP-N-acetylmur 48.4 57 0.0012 30.5 6.6 61 33-99 269-330 (433)
40 PRK03806 murD UDP-N-acetylmura 47.4 67 0.0015 30.1 7.0 61 33-99 273-334 (438)
41 PRK02705 murD UDP-N-acetylmura 47.3 63 0.0014 30.4 6.8 61 33-99 286-347 (459)
42 PRK11152 ilvM acetolactate syn 47.3 17 0.00037 26.4 2.3 59 170-229 12-73 (76)
43 PRK04663 murD UDP-N-acetylmura 46.9 60 0.0013 30.6 6.6 61 33-99 274-335 (438)
44 TIGR01081 mpl UDP-N-acetylmura 45.8 88 0.0019 29.5 7.6 60 33-99 283-343 (448)
45 PRK11930 putative bifunctional 45.0 74 0.0016 32.8 7.3 61 33-99 291-352 (822)
46 PRK14106 murD UDP-N-acetylmura 44.7 63 0.0014 30.3 6.3 61 33-99 284-345 (450)
47 PRK01390 murD UDP-N-acetylmura 44.7 79 0.0017 29.9 7.1 60 33-98 292-352 (460)
48 PRK10773 murF UDP-N-acetylmura 44.3 82 0.0018 29.9 7.1 61 33-99 287-348 (453)
49 cd04908 ACT_Bt0572_1 N-termina 44.3 97 0.0021 20.8 6.3 59 82-144 4-62 (66)
50 PTZ00248 eukaryotic translatio 44.3 1.4E+02 0.003 27.7 8.2 57 48-107 200-263 (319)
51 PF08671 SinI: Anti-repressor 44.0 55 0.0012 19.6 3.7 25 32-56 4-28 (30)
52 cd04901 ACT_3PGDH C-terminal A 42.1 30 0.00064 23.2 2.8 56 171-230 9-67 (69)
53 PRK14022 UDP-N-acetylmuramoyla 41.6 1E+02 0.0022 29.5 7.3 59 33-99 301-360 (481)
54 PF13710 ACT_5: ACT domain; PD 41.3 22 0.00047 24.6 2.0 56 172-229 3-63 (63)
55 PF14257 DUF4349: Domain of un 40.3 48 0.001 29.1 4.6 62 82-143 54-118 (262)
56 PRK00139 murE UDP-N-acetylmura 39.5 1.2E+02 0.0026 28.9 7.4 60 33-99 283-343 (460)
57 PF13936 HTH_38: Helix-turn-he 38.7 31 0.00067 22.0 2.3 20 38-57 25-44 (44)
58 PRK01368 murD UDP-N-acetylmura 38.6 94 0.002 29.7 6.6 61 33-99 280-341 (454)
59 PF01037 AsnC_trans_reg: AsnC 38.5 81 0.0018 21.3 4.7 21 211-231 10-30 (74)
60 TIGR00119 acolac_sm acetolacta 37.3 67 0.0014 26.5 4.6 58 170-231 10-74 (157)
61 cd04925 ACT_ACR_2 ACT domain-c 37.2 47 0.001 23.3 3.3 28 81-108 2-29 (74)
62 PRK01710 murD UDP-N-acetylmura 36.8 92 0.002 29.6 6.2 58 34-98 289-347 (458)
63 PTZ00450 macrophage migration 36.5 17 0.00037 28.3 1.0 28 23-50 67-96 (113)
64 TIGR00257 IMPACT_YIGZ uncharac 36.1 1.5E+02 0.0031 25.6 6.7 71 132-218 117-190 (204)
65 PRK10858 nitrogen regulatory p 35.9 83 0.0018 24.4 4.7 24 165-188 3-26 (112)
66 PRK09977 putative Mg(2+) trans 35.8 52 0.0011 28.7 3.9 63 165-230 146-213 (215)
67 TIGR01085 murE UDP-N-acetylmur 34.7 1.6E+02 0.0035 27.8 7.5 60 33-99 291-352 (464)
68 PRK08577 hypothetical protein; 34.2 77 0.0017 25.0 4.4 57 172-230 67-130 (136)
69 cd04905 ACT_CM-PDT C-terminal 32.5 93 0.002 21.8 4.3 53 170-225 10-71 (80)
70 cd04883 ACT_AcuB C-terminal AC 31.9 1.6E+02 0.0034 19.7 5.8 59 83-144 5-66 (72)
71 PRK11895 ilvH acetolactate syn 31.6 87 0.0019 26.0 4.4 58 170-231 11-75 (161)
72 PF02829 3H: 3H domain; Inter 31.5 2.3E+02 0.0051 21.5 6.6 88 88-188 6-97 (98)
73 TIGR00341 conserved hypothetic 31.2 2E+02 0.0043 26.7 7.1 57 129-189 12-68 (325)
74 PRK11568 hypothetical protein; 30.9 2.3E+02 0.0051 24.4 7.1 71 133-219 118-191 (204)
75 PRK02006 murD UDP-N-acetylmura 30.3 1.5E+02 0.0033 28.4 6.6 60 33-98 325-385 (498)
76 TIGR01082 murC UDP-N-acetylmur 30.1 1.1E+02 0.0025 28.8 5.6 45 33-83 278-323 (448)
77 PRK11929 putative bifunctional 29.9 1.6E+02 0.0034 30.8 7.0 61 33-99 796-857 (958)
78 PF03698 UPF0180: Uncharacteri 29.3 45 0.00097 24.6 2.1 19 173-191 8-26 (80)
79 TIGR02717 AcCoA-syn-alpha acet 29.0 2.2E+02 0.0047 27.2 7.3 99 116-231 265-376 (447)
80 cd04899 ACT_ACR-UUR-like_2 C-t 29.0 79 0.0017 21.1 3.3 28 81-108 2-29 (70)
81 cd04873 ACT_UUR-ACR-like ACT d 29.0 1.7E+02 0.0037 19.1 5.0 28 81-108 2-29 (70)
82 cd04904 ACT_AAAH ACT domain of 28.8 1.5E+02 0.0033 20.7 4.8 50 171-224 10-67 (74)
83 PF00488 MutS_V: MutS domain V 28.7 46 0.001 29.0 2.5 24 34-57 206-229 (235)
84 cd04909 ACT_PDH-BS C-terminal 27.9 1.9E+02 0.0041 19.3 5.7 27 82-108 4-30 (69)
85 PF07942 N2227: N2227-like pro 27.7 73 0.0016 28.7 3.6 68 80-149 173-240 (270)
86 PRK01438 murD UDP-N-acetylmura 27.6 1.8E+02 0.0039 27.6 6.5 61 33-99 305-366 (480)
87 smart00497 IENR1 Intron encode 27.5 43 0.00094 21.5 1.6 26 32-57 16-41 (53)
88 TIGR00479 rumA 23S rRNA (uraci 27.5 52 0.0011 31.0 2.8 34 168-201 394-427 (431)
89 PF05902 4_1_CTD: 4.1 protein 27.3 53 0.0012 25.9 2.3 23 22-44 76-98 (114)
90 KOG2121 Predicted metal-depend 27.3 27 0.00059 35.7 0.8 54 37-90 223-280 (746)
91 cd04902 ACT_3PGDH-xct C-termin 27.0 1.9E+02 0.0042 19.1 5.7 24 85-108 5-28 (73)
92 COG0347 GlnK Nitrogen regulato 27.0 72 0.0016 25.1 3.0 57 165-221 3-82 (112)
93 COG3636 Predicted transcriptio 26.3 74 0.0016 24.5 2.8 27 14-45 64-90 (100)
94 PF13740 ACT_6: ACT domain; PD 26.1 87 0.0019 22.0 3.1 30 80-109 3-32 (76)
95 COG3062 NapD Uncharacterized p 26.1 1.5E+02 0.0033 22.5 4.5 62 165-229 10-72 (94)
96 PF11588 DUF3243: Protein of u 25.9 23 0.00049 26.3 0.0 26 32-57 13-38 (81)
97 TIGR00655 PurU formyltetrahydr 25.9 4.9E+02 0.011 23.4 9.1 95 76-190 40-136 (280)
98 PF14501 HATPase_c_5: GHKL dom 25.5 2.7E+02 0.0058 20.2 6.4 59 49-108 13-85 (100)
99 COG3453 Uncharacterized protei 25.4 2E+02 0.0043 23.2 5.2 41 174-220 46-86 (130)
100 CHL00100 ilvH acetohydroxyacid 25.4 97 0.0021 26.1 3.7 60 170-231 11-75 (174)
101 cd04927 ACT_ACR-like_2 Second 25.0 87 0.0019 22.1 3.0 29 80-108 1-29 (76)
102 PRK03094 hypothetical protein; 24.8 59 0.0013 24.0 2.0 18 173-190 8-25 (80)
103 CHL00100 ilvH acetohydroxyacid 24.8 4.2E+02 0.0091 22.2 9.9 129 81-223 4-141 (174)
104 PRK00421 murC UDP-N-acetylmura 24.8 3E+02 0.0066 26.0 7.4 51 33-90 284-335 (461)
105 PF00533 BRCT: BRCA1 C Terminu 24.5 97 0.0021 20.8 3.1 28 77-107 8-35 (78)
106 COG2605 Predicted kinase relat 24.2 3.8E+02 0.0083 24.9 7.5 79 31-122 243-327 (333)
107 PRK13168 rumA 23S rRNA m(5)U19 23.4 1.8E+02 0.0039 27.6 5.6 39 164-202 394-432 (443)
108 COG3492 Uncharacterized protei 23.3 56 0.0012 24.9 1.6 21 209-229 15-35 (104)
109 PF12637 TSCPD: TSCPD domain; 22.8 77 0.0017 23.7 2.4 34 21-55 32-65 (95)
110 PRK06027 purU formyltetrahydro 22.1 5.8E+02 0.013 22.9 9.1 93 78-190 48-141 (286)
111 PF06135 DUF965: Bacterial pro 22.0 63 0.0014 23.8 1.7 33 174-207 20-53 (79)
112 PRK04308 murD UDP-N-acetylmura 21.9 2.8E+02 0.006 26.1 6.5 60 33-98 280-340 (445)
113 PRK03369 murD UDP-N-acetylmura 21.8 2.5E+02 0.0053 27.1 6.2 59 33-97 288-347 (488)
114 cd03285 ABC_MSH2_euk MutS2 hom 21.5 94 0.002 26.7 3.0 25 33-57 194-218 (222)
115 TIGR03793 TOMM_pelo TOMM prope 21.4 1.6E+02 0.0034 21.5 3.7 35 179-213 28-74 (77)
116 PF13730 HTH_36: Helix-turn-he 21.3 88 0.0019 20.2 2.2 28 22-56 21-48 (55)
117 PF08769 Spo0A_C: Sporulation 21.0 86 0.0019 24.1 2.4 23 37-59 44-66 (106)
118 PF05423 Mycobact_memb: Mycoba 21.0 1.4E+02 0.0031 24.1 3.8 20 66-85 51-70 (140)
119 PRK11929 putative bifunctional 21.0 3.2E+02 0.0069 28.6 7.3 60 33-99 312-375 (958)
120 COG2425 Uncharacterized protei 20.9 1.4E+02 0.003 28.9 4.3 60 17-79 339-413 (437)
121 PF04967 HTH_10: HTH DNA bindi 20.9 1.3E+02 0.0029 20.2 3.0 41 16-59 9-49 (53)
122 PRK00141 murD UDP-N-acetylmura 20.7 2.9E+02 0.0064 26.4 6.5 61 33-99 294-355 (473)
123 PF09413 DUF2007: Domain of un 20.3 1.3E+02 0.0027 20.4 2.9 53 169-221 6-66 (67)
124 PF00675 Peptidase_M16: Insuli 20.2 3.3E+02 0.0071 21.0 5.7 77 18-102 17-97 (149)
No 1
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.4e-76 Score=508.16 Aligned_cols=206 Identities=39% Similarity=0.632 Sum_probs=197.2
Q ss_pred hhhHHHHhhCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHhccC-CccceeEEEEEEEecCCcEEEEEEecCCchhh
Q 026745 14 KSYLRNVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQEAFIEKVYEVYGYGGVSIVVEVLTDKITRS 92 (234)
Q Consensus 14 keI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~-~~~~~~~~~yE~~gPgGvaiIVe~~TdN~nRt 92 (234)
|+|++|+|+|||||++|||||.+|++||++||||++|||||+||+|. +..+|.+++|||||||||+|||||||||+|||
T Consensus 30 keI~vAaK~Gg~dP~~NprLr~aI~kAk~~nmPkd~IerAI~ka~G~~d~~~~~ei~YEGygP~GvaiiVe~LTDN~NRT 109 (241)
T COG0217 30 KEITVAAKQGGPDPESNPRLRTAIEKAKAANMPKDNIERAIKKASGGKDGANYEEIRYEGYGPGGVAIIVEALTDNRNRT 109 (241)
T ss_pred HHHHHHHHhcCCCCccCHHHHHHHHHHHHcCCCHHHHHHHHHhccCCCCccceEEEEEEeECCCceEEEEEeccCCcchh
Confidence 99999999999999999999999999999999999999999999974 45689999999999999999999999999999
Q ss_pred HHHHHHHHhhcCccccCCcceeeecceeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCceEEEEecc
Q 026745 93 VAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTS 172 (234)
Q Consensus 93 ~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~~~~~~~~p 172 (234)
+++||++|+|+||+|+++|||+|||+|+|+|.+..+..++|++||.|||+||+||+.. ++.|+|+|+|
T Consensus 110 as~vR~~F~K~GG~lg~~GSV~~mF~~kGvi~~~~~~~~ed~l~e~~ieagaeDv~~~------------~~~~~V~t~p 177 (241)
T COG0217 110 ASNVRSAFNKNGGNLGEPGSVSYMFDRKGVIVVEKNEIDEDELLEAAIEAGAEDVEED------------EGSIEVYTEP 177 (241)
T ss_pred HHHHHHHHHhcCCccCCCceEEEEEeccEEEEECCCCCCHHHHHHHHHHCCchhhhcC------------CCeEEEEECh
Confidence 9999999999999999999999999999999998877899999999999999999751 2579999999
Q ss_pred ccHHHHHHHHHHCCCCeeecccceeecCcccccCHHHHHHHHHHHHHHccCCCcceeecc
Q 026745 173 DNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYTD 232 (234)
Q Consensus 173 ~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy~N 232 (234)
++|.+|+.+|++.|+++.. +++.|+|+++|++++++.+++++||++||++||||+||||
T Consensus 178 ~~~~~V~~~L~~~g~~~~~-ael~~iP~~~v~~~~e~a~k~~kLid~LEd~DDVQ~Vy~N 236 (241)
T COG0217 178 EDFNKVKEALEAAGYEIES-AELTMIPQNTVELDDEDAEKLEKLIDALEDDDDVQNVYHN 236 (241)
T ss_pred HHHHHHHHHHHHcCCceee-eeEEEecCCceecCHHHHHHHHHHHHHHhcccchHHHHhc
Confidence 9999999999999999986 5999999999999999999999999999999999999999
No 2
>PRK00110 hypothetical protein; Validated
Probab=100.00 E-value=6e-74 Score=502.66 Aligned_cols=215 Identities=35% Similarity=0.569 Sum_probs=199.1
Q ss_pred chhhhhhcchh---------hhhHHHHhhCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHhccC-CccceeEEEEEE
Q 026745 3 RKQSCIRGWGR---------KSYLRNVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQEAFIEKVYEV 72 (234)
Q Consensus 3 ~~~s~~~~~~~---------keI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~-~~~~~~~~~yE~ 72 (234)
|||.|.+.+.+ |+|++|||+|||||+.|++||++|++||++||||++||||||||+|. ++.+|++++|||
T Consensus 10 Ikh~K~~~D~kksk~f~kl~reI~vAak~GG~DP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~~~~~~~~e~~YEg 89 (245)
T PRK00110 10 IKHRKGAQDAKRGKIFTKLIREITVAAKLGGGDPEGNPRLRLAIDKAKAANMPKDNIERAIKKGTGELDGANYEEIRYEG 89 (245)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCCCCccceEEEEEEE
Confidence 45555555443 99999999999999999999999999999999999999999999986 556899999999
Q ss_pred EecCCcEEEEEEecCCchhhHHHHHHHHhhcCccccCCcceeeecceeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCC
Q 026745 73 YGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPV 152 (234)
Q Consensus 73 ~gPgGvaiIVe~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~ 152 (234)
||||||+|||||+|||+|||+++||++|+|+||+|+++|||.|+|+|+|+|.+... ++|++||.|||+|||||+..
T Consensus 90 ~gP~GvaiiVe~lTDN~nRt~~~vR~~f~K~gG~l~~~Gsv~~~Fe~kG~i~~~~~--~~d~~~e~aieaGaeDv~~e-- 165 (245)
T PRK00110 90 YGPGGVAIIVEALTDNRNRTAAEVRHAFSKNGGNLGETGSVSYMFDRKGVIVIEPL--DEDELMEAALEAGAEDVETD-- 165 (245)
T ss_pred EcCCCeEEEEEEecCCHHHHHHHHHHHHHhcCceeCCCcceEEEeccceEEEeCCC--CHHHHHHHHHhCCCCEeecc--
Confidence 99999999999999999999999999999999999999999999999999999743 78999999999999998531
Q ss_pred CCCCCccccCCceEEEEeccccHHHHHHHHHHCCCCeeecccceeecCcccccCHHHHHHHHHHHHHHccCCCcceeecc
Q 026745 153 NEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYTD 232 (234)
Q Consensus 153 ~ed~~~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy~N 232 (234)
+ +.|+|+|+|++|.+|+++|++.||++.. +++.|+|+++|+|++++++++.+|+++|+++||||+||||
T Consensus 166 -------~---~~~~i~~~p~~~~~v~~~L~~~g~~~~~-sei~~~P~~~v~l~~e~~~~~~~li~~Led~dDVq~Vy~N 234 (245)
T PRK00110 166 -------D---ESFEVITAPEDFEAVRDALEAAGLEAES-AEVTMIPQNTVELDEETAEKLLKLIDALEDLDDVQNVYHN 234 (245)
T ss_pred -------C---CeEEEEECHHHHHHHHHHHHHcCCCeee-eEEEEecCCCcccCHHHHHHHHHHHHHHhcCCCcceEeEC
Confidence 1 3599999999999999999999999986 5999999999999999999999999999999999999999
No 3
>PRK12378 hypothetical protein; Provisional
Probab=100.00 E-value=7.4e-74 Score=499.14 Aligned_cols=207 Identities=38% Similarity=0.594 Sum_probs=193.8
Q ss_pred hhhhhHHHHhhCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCCchh
Q 026745 12 GRKSYLRNVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITR 91 (234)
Q Consensus 12 ~~keI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGvaiIVe~~TdN~nR 91 (234)
..|+|++|||+|||||+.||+||++|++||++||||++||||||||+|.++.+|++++|||||||||+|||||||||+||
T Consensus 26 l~reI~vA~k~GG~dP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~~~~~~~e~~YEgygPgGvaiiVe~lTDN~nR 105 (235)
T PRK12378 26 LGKEIYVAAKQGGPDPESNPALRFVIERAKKANVPKDVIERAIKKAKGGGGEDYEEVRYEGFGPNGVMVIVECLTDNVNR 105 (235)
T ss_pred HHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHhccCCCCCceEEEEEEEEcCCCcEEEEEECCCCHHH
Confidence 33999999999999999999999999999999999999999999999875567999999999999999999999999999
Q ss_pred hHHHHHHHHhhcCccccCCcceeeecceeEEEEEeCCCCCHHHHHHHHHHCCC--cccccCCCCCCCCccccCCceEEEE
Q 026745 92 SVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA--EDVIEPPVNEDDTDEDRAERYYKVV 169 (234)
Q Consensus 92 t~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~~~~~~d~~~e~AIE~GA--eDv~~~~~~ed~~~ed~~~~~~~~~ 169 (234)
|+++||++|+|+||+|+++|||+|+|+|+|+|.+... ++|++||.|||+|| +||.. + ++.|+|+
T Consensus 106 t~~~vr~~f~K~gg~l~~~gsv~~~Fe~kG~i~i~~~--~~d~~~e~aieaGa~~edv~~---------~---~~~~~i~ 171 (235)
T PRK12378 106 TVANVRSAFNKNGGNLGTSGSVAFMFDHKGVFVFEGD--DEDELLEALIDADVDVEDVEE---------E---EGTITVY 171 (235)
T ss_pred HHHHHHHHHhhcCCeECCCCceeeeeecceEEEeCCC--CHHHHHHHHHhCCCCcccccc---------c---CCeEEEE
Confidence 9999999999999999999999999999999999754 79999999999988 66632 1 1369999
Q ss_pred eccccHHHHHHHHHHCCCCeeecccceeecCcccccCHHHHHHHHHHHHHHccCCCcceeeccC
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYTDQ 233 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy~N~ 233 (234)
|+|++|.+|+++|++.||++.+ +++.|+|+++|+|++++.+++.+|+++|+++||||+||||.
T Consensus 172 t~p~~~~~v~~~L~~~g~~~~~-sei~~~P~~~v~l~~e~~~~~~~li~~Led~dDVq~Vy~N~ 234 (235)
T PRK12378 172 TDPTDFHKVKKALEAAGIEFLV-AELEMIPQNPVELSGEDLEQFEKLLDALEDDDDVQNVYHNV 234 (235)
T ss_pred ECHHHHHHHHHHHHHcCCCcee-eEEEEecCCCccCCHHHHHHHHHHHHHHhcCCCccceeeCC
Confidence 9999999999999999999986 59999999999999999999999999999999999999994
No 4
>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=1.2e-73 Score=498.88 Aligned_cols=206 Identities=38% Similarity=0.636 Sum_probs=181.2
Q ss_pred hhhHHHHhhCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHhccC-CccceeEEEEEEEecCCcEEEEEEecCCchhh
Q 026745 14 KSYLRNVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQEAFIEKVYEVYGYGGVSIVVEVLTDKITRS 92 (234)
Q Consensus 14 keI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~-~~~~~~~~~yE~~gPgGvaiIVe~~TdN~nRt 92 (234)
|+|++|||+|||||+.|++||++|++||++||||++||||||||++. +..+|++++|||||||||+|||||+|||+|||
T Consensus 26 reI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~IerAIkk~~~~~~~~~~~~~~yEg~gP~Gvaiive~lTDN~nRt 105 (234)
T PF01709_consen 26 REITVAVKEGGPDPDMNPRLRSAIEKAKKANMPKDNIERAIKKASGKSDGANYEEITYEGYGPGGVAIIVECLTDNKNRT 105 (234)
T ss_dssp HHHHHHHHCC-S-GGGSHHHHHHHHHHHHTT--HHHHHHHHHHCCSTSST---EEEEEEEEETTTEEEEEEEEES-HHHH
T ss_pred HHHHHHHHcCCCCCCcCHHHHHHHHHHHHhCCCHHHHHHHHHhcCcCCCCcCceEEEEEEEcCCCcEEEEEEeCCCHhHH
Confidence 99999999999999999999999999999999999999999999987 66789999999999999999999999999999
Q ss_pred HHHHHHHHhhcCccccCCcceeeecceeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCceEEEEecc
Q 026745 93 VAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTS 172 (234)
Q Consensus 93 ~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~~~~~~~~p 172 (234)
+++||++|+|+||+|+++|||+|+|+|+|+|.+++...++|++||.|||+|||||++. ++.|+|+|+|
T Consensus 106 ~~~ir~~~~K~gg~l~~~gsv~~~F~~kG~i~~~~~~~~~d~~~e~aIe~GaeDve~~------------d~~~~~~c~p 173 (234)
T PF01709_consen 106 VSDIRSIFKKNGGSLGPSGSVSFMFERKGVIEVSKKDLDEDELMEDAIEAGAEDVEED------------DGEFEFICDP 173 (234)
T ss_dssp HHHHHHHHHTTT-EEE-TTSSGGGEEEEEEEEEEHCCS-HHHHHHHHHHHTESEEEEC------------TSEEEEEEEG
T ss_pred HHHHHHHHHHcCceeCCCCcceeeeeeeEEEEEEeCCCChHHHHHHHHhCCCcEeeec------------CCeEEEEECH
Confidence 9999999999999999999999999999999998767899999999999999999741 2469999999
Q ss_pred ccHHHHHHHHHHCCCCeeecccceeecCcccccCHHHHHHHHHHHHHHccCCCcceeecc
Q 026745 173 DNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYTD 232 (234)
Q Consensus 173 ~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy~N 232 (234)
++|.+|+++|++.||++.. ++++|+|+++|+|++++++++.+|+++|+++||||+||||
T Consensus 174 ~~~~~v~~~L~~~g~~i~~-~e~~~~P~~~v~l~~e~~~~~~~lie~Lee~dDV~~Vy~N 232 (234)
T PF01709_consen 174 SDLSAVKKALEKKGYEIES-AELEYIPNNPVELSEEDAEKVEKLIEALEELDDVQNVYHN 232 (234)
T ss_dssp GGHHHHHHHHHHTT---SE-EEEEEEESS-EE--HHHHHHHHHHHHHHHTSTTEEEEEES
T ss_pred HHHHHHHHHHHHcCCCeeE-EEEEEeCCCCcccCHHHHHHHHHHHHHHhCCcCcceeeeC
Confidence 9999999999999999986 5999999999999999999999999999999999999999
No 5
>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=5.6e-73 Score=495.11 Aligned_cols=209 Identities=35% Similarity=0.594 Sum_probs=195.7
Q ss_pred hhhhhHHHHhhCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHhccC-CccceeEEEEEEEecCCcEEEEEEecCCch
Q 026745 12 GRKSYLRNVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK-GQEAFIEKVYEVYGYGGVSIVVEVLTDKIT 90 (234)
Q Consensus 12 ~~keI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~-~~~~~~~~~yE~~gPgGvaiIVe~~TdN~n 90 (234)
..|+|++|||+|||||+.|++||++|++||++||||++||||||||+|. +..+|++++|||||||||+|||||||||+|
T Consensus 28 l~r~I~vA~k~GG~DP~~N~~L~~ai~~Ak~~~~Pkd~IerAIkr~~g~~~~~~~~~~~YEg~gP~GvaiiVe~lTDN~n 107 (238)
T TIGR01033 28 LIKEIIVAAKLGGGDPESNPRLRTAIEKAKAANMPKDNIERAIKKGAGELDGSNYEEITYEGYAPGGVAIIVECLTDNKN 107 (238)
T ss_pred HHHHHHHHHHcCCCCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCCCCccceEEEEEEEEcCCceEEEEEEecCCHH
Confidence 3399999999999999999999999999999999999999999999986 556899999999999999999999999999
Q ss_pred hhHHHHHHHHhhcCccccCCcceeeecceeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCceEEEEe
Q 026745 91 RSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVS 170 (234)
Q Consensus 91 Rt~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~~~~~~~ 170 (234)
||+++||++|+|+||+|+++|||.|+|+|+|+|.+..+..++|++||.|||+|||||+.. ++ .|+|+|
T Consensus 108 Rt~~~ir~~f~K~gg~l~~~gsv~~~Fe~kG~i~~~~~~~~~d~~~e~aieaGAedv~~~--------~~----~~~v~~ 175 (238)
T TIGR01033 108 RTASEVRSAFNKNGGSLGEPGSVSYLFSRKGVIEVPKNEVDEEDLMEAAIEAGAEDIDVD--------DD----EFEVYT 175 (238)
T ss_pred hHHHHHHHHHHHcCCeeCCCCceeeeeecceEEEECCCCCCHHHHHHHHHhCCCceeecc--------CC----cEEEEE
Confidence 999999999999999999999999999999999998554678999999999999999531 11 299999
Q ss_pred ccccHHHHHHHHHHCCCCeeecccceeecCcccccCHHHHHHHHHHHHHHccCCCcceeeccC
Q 026745 171 TSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYTDQ 233 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy~N~ 233 (234)
+|++|.+|+++|++.||++.. +++.|+|+++|+|++++.+.+.+|+++|+++||||+||||.
T Consensus 176 ~~~~~~~v~~~L~~~g~~i~~-sei~~~P~~~v~l~~e~~~~~~~li~~Lee~dDVq~Vy~N~ 237 (238)
T TIGR01033 176 APEELEKVKEALEAKGFPIES-AEITMIPLTTVDLDDEQAEKLLKLIDALEDDDDVQEVYHNF 237 (238)
T ss_pred CHHHHHHHHHHHHHcCCCcee-eEEEEecCCCcccCHHHHHHHHHHHHHHhcCCCcceeeeCC
Confidence 999999999999999999986 59999999999999999999999999999999999999994
No 6
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.3e-59 Score=404.72 Aligned_cols=223 Identities=37% Similarity=0.538 Sum_probs=199.4
Q ss_pred hhhhcchhhhhHHHHhhCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEe
Q 026745 6 SCIRGWGRKSYLRNVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVL 85 (234)
Q Consensus 6 s~~~~~~~keI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGvaiIVe~~ 85 (234)
|+...+..++|..|||.||+||.+|.+||++++.||+.+|||+.|||||+||+++++...+.+.||+||||||++|||++
T Consensus 50 sk~~nkl~~~i~~aVk~gg~np~lN~~LAtlle~ak~~~vpkd~ien~i~ras~k~~~a~e~~~ye~~gp~GV~liVeal 129 (276)
T KOG2972|consen 50 SKQINKLSQGIILAVKQGGANPELNMRLATLLESAKKISVPKDGIENAINRASGKEGSAVEFIEYEAMGPSGVGLIVEAL 129 (276)
T ss_pred HHHHHHHHHHHHHHHHhcCCCchhhhHHHHHHHHHHhcCCCHHHHHHHHHHhccCCCCceEEEEEeeecCCceEEEEEee
Confidence 44455555999999999999999999999999999999999999999999999987777777899999999999999999
Q ss_pred cCCchhhHHHHHHHHhhcCccccCCcceeeecceeE-EEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCc
Q 026745 86 TDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRAR-VVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAER 164 (234)
Q Consensus 86 TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~F~~~g-~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~ 164 (234)
|||+||+++.||++|+|+||.+. ++++|+|++|| ++.++++..+.|.+.-.+||+||+|+...|.-|.|+++++ .
T Consensus 130 Tdnknr~~~~iRs~~nk~GG~s~--~~~r~~FdkKG~Vv~V~~~~~dk~vL~ie~ie~~A~d~~~~~~~e~d~eeer--~ 205 (276)
T KOG2972|consen 130 TDNKNRAASSIRSIFNKHGGASA--SGVRFLFDKKGVVVNVPPEKRDKDVLNIEAIEAGAEDIVAEPVLEIDEEEER--E 205 (276)
T ss_pred eccHhHHHHHHHHHHHHcCCccc--ccceeEEeccceEEecChhhcchhhhhHHHHHhcccccccCccccccccccc--c
Confidence 99999999999999999998665 46788888888 7788877778778888889999999887665555544443 3
Q ss_pred eEEEEeccccHHHHHHHHHHCCCCeeecccceeecCcccccCHHHHHHHHHHHHHHccCCCcceeeccC
Q 026745 165 YYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVYTDQ 233 (234)
Q Consensus 165 ~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy~N~ 233 (234)
.|+|+|+|++|++|...|.+.||++.. ++++|+|.++|+++++.++++++|+++|.+++||..||+|.
T Consensus 206 ~fkiv~e~ssl~qV~~~Lr~~G~~i~d-~~le~~P~~~vev~~~~lEk~qkL~q~L~e~edV~~iy~ni 273 (276)
T KOG2972|consen 206 EFKIVTEPSSLNQVAHKLRSKGFEIKD-SGLEFIPLEEVEVDVPALEKIQKLIQALYENEDVMFIYDNI 273 (276)
T ss_pred eeEEEeccchHHHHHHHhhcCCceeec-cccccccCCccccCccchHHHHHHHHHHhhchhHHHHhhcc
Confidence 499999999999999999999999985 69999999999999989999999999999999999999994
No 7
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=98.05 E-value=5e-06 Score=86.59 Aligned_cols=49 Identities=22% Similarity=0.293 Sum_probs=45.1
Q ss_pred hhhhhHHHHhhC------CCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHhccC
Q 026745 12 GRKSYLRNVKKG------GPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEK 60 (234)
Q Consensus 12 ~~keI~~Avk~G------G~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~ 60 (234)
..++|..|+|.| |+||..|++|+.+|.+||+.+||++.|+|+|+++.+.
T Consensus 317 ~lk~I~~A~~~~~G~~~~~~DP~~NpaLk~aI~~Ak~~~vP~~~I~RvI~~A~qg 371 (1220)
T PRK07562 317 HLKAIMKACVNCEGDGDDCFDPAKNPALKREIKAAKKALVPENYIKRVIQFARQG 371 (1220)
T ss_pred HHHHHHHHHHhccccccccCCccccHHHHHHHHHHHhccCCHHHHHHHHHHhhcc
Confidence 338999999998 6899999999999999999999999999999998653
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=88.37 E-value=1.2 Score=31.04 Aligned_cols=63 Identities=19% Similarity=0.187 Sum_probs=42.2
Q ss_pred EEEeccccHHHHHHHHHHCCCCeeecccceeecCc----ccccCHHHHH-HHHHHHHHHccCCCcceee
Q 026745 167 KVVSTSDNYTDITTKLREAGIPFETDNGSELLPIT----TIEVDDEAME-LNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 167 ~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~----~V~l~~e~~~-~~~~li~~Lee~dDV~~Vy 230 (234)
.....|..+..+...|.+.|..+..- ...-.|.. ...+.-...+ .+.+++++|+.+++|.+|+
T Consensus 6 ~~~d~~g~l~~I~~~la~~~inI~~i-~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~ 73 (76)
T cd04888 6 LLEHRPGVLSKVLNTIAQVRGNVLTI-NQNIPIHGRANVTISIDTSTMNGDIDELLEELREIDGVEKVE 73 (76)
T ss_pred EecCCCchHHHHHHHHHHcCCCEEEE-EeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEE
Confidence 34556778999999999999987532 11001221 1223223344 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=80.11 E-value=2.4 Score=31.02 Aligned_cols=60 Identities=15% Similarity=0.223 Sum_probs=43.2
Q ss_pred eEEEEeccccHHHHHHHHHH-CCCCeeecccceeecC--cccccCHHHHHHHHHHHHHHccCCCccee
Q 026745 165 YYKVVSTSDNYTDITTKLRE-AGIPFETDNGSELLPI--TTIEVDDEAMELNKELIAKLLELDDVDAV 229 (234)
Q Consensus 165 ~~~~~~~p~~~~~v~~~L~~-~g~~i~~~~~~~~iP~--~~V~l~~e~~~~~~~li~~Lee~dDV~~V 229 (234)
.+.|.|.|..+..|+.+|.+ .|.+|... + +. --|.+..+......+++++|+.+|.|..+
T Consensus 7 s~vV~~~p~~~~~v~~~l~~~~gvEVh~~-~----~~GKiVVtiE~~~~~~~~~~~~~i~~l~GVlsa 69 (79)
T PF03927_consen 7 SLVVHARPERLEEVAEALAAIPGVEVHAV-D----EDGKIVVTIEAESSEEEVDLIDAINALPGVLSA 69 (79)
T ss_dssp EEEEEE-CCCHHHHHHHHCCSTTEEEEEE-E----TTTEEEEEEEESSHHHHHHHHHHHCCSTTEEEE
T ss_pred EEEEEECchhHHHHHHHHHcCCCcEEEee-C----CCCeEEEEEEeCChHHHHHHHHHHHcCCCceEE
Confidence 47789999999999999998 47666432 1 22 23555555556667899999999998775
No 10
>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=72.42 E-value=18 Score=23.82 Aligned_cols=61 Identities=8% Similarity=0.124 Sum_probs=39.2
Q ss_pred EEEecCCchhhHHHHHHHHhhcCccccCCcceeeecceeEEEEEeCCCCCHHHHHHHHHHCCC
Q 026745 82 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA 144 (234)
Q Consensus 82 Ve~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~~~~~~d~~~e~AIE~GA 144 (234)
+.+..+++...++.+-.+|.++|+++..-..........+.+.+..+ +.+++.+..-+.|-
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve--~~~~~~~~L~~~G~ 62 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTE--DIEKAIEVLQERGV 62 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeC--CHHHHHHHHHHCCc
Confidence 56678899999999999999999988521111111113445555543 36677776666664
No 11
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=71.87 E-value=7.7 Score=27.45 Aligned_cols=64 Identities=20% Similarity=0.262 Sum_probs=41.7
Q ss_pred EEEEe--ccccHHHHHHHHHHCCCCeeecccceee-cC----cccccCHHHHHHHHHHHHHHccCCCcceee
Q 026745 166 YKVVS--TSDNYTDITTKLREAGIPFETDNGSELL-PI----TTIEVDDEAMELNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 166 ~~~~~--~p~~~~~v~~~L~~~g~~i~~~~~~~~i-P~----~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy 230 (234)
+.+.+ .|.-|..+...|.+.|..+..- ...-. +. -.+.+.=.+.+.+..++++|+.+++|..|+
T Consensus 9 l~i~~~dr~GlL~dI~~~i~~~~~nI~~i-~~~~~~~~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 9 LRIEAEDRPGLLADITSVISENGVNIRSI-NARTNKDDGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEE--TTHHHHHHHHHHCSSSEEEEE-EEEE--ETTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEcCCCHHHHHHHHHHHCCCCeEEE-EeEEeccCCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 34444 5667999999999999988632 22221 11 112222234566789999999999999986
No 12
>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=70.71 E-value=14 Score=24.46 Aligned_cols=57 Identities=19% Similarity=0.201 Sum_probs=38.0
Q ss_pred ccccHHHHHHHHHHCCCCeeecccceeecC-c----ccccCHHHHHHHHHHHHHHccCCCccee
Q 026745 171 TSDNYTDITTKLREAGIPFETDNGSELLPI-T----TIEVDDEAMELNKELIAKLLELDDVDAV 229 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~-~----~V~l~~e~~~~~~~li~~Lee~dDV~~V 229 (234)
.|..+..+...|.+.|+.+... ...-.|. . .+.+.... ..+..+++.|+..++|..|
T Consensus 10 ~~g~l~~i~~~l~~~~~~i~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 10 EPGVLNRISGLFARRGFNIESL-TVGPTEDPGISRITIVVEGDD-DVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred CCcHHHHHHHHHHhCCCCEEEE-EeeecCCCCeEEEEEEEECCH-HHHHHHHHHHhCCccEEEe
Confidence 4456889999999999988632 2111111 1 23333334 6688999999999999987
No 13
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=69.50 E-value=63 Score=26.68 Aligned_cols=134 Identities=16% Similarity=0.109 Sum_probs=74.5
Q ss_pred EEEEecCCchhhHHHHHHHHhhcCccccCCcceeeec-ceeEEEEEeCCCCCHHHHHHHHHH--CCCcccccCCCCCCCC
Q 026745 81 VVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKF-RRARVVNIKFTDADKDQLLDIALD--AGAEDVIEPPVNEDDT 157 (234)
Q Consensus 81 IVe~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~F-~~~g~i~~~~~~~~~d~~~e~AIE--~GAeDv~~~~~~ed~~ 157 (234)
++.++.+|....++.|-.+|+++|.++- +-.+...= ...-.+.+.... + |..++.... .-..||-....-.+++
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~-Sl~v~~t~~~~~sriti~V~~-d-~~~i~qi~kQl~Kli~V~~V~~~~~~~ 79 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIE-SLTVGPTEDPDLSRMTIVVVG-D-DKVLEQITKQLNKLVDVIKVSDLTESA 79 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEE-EEEEeecCCCCEEEEEEEEEC-C-HHHHHHHHHHHhcCccEEEEEecCCCc
Confidence 5678999999999999999999999773 11222210 111122222222 2 333433332 2333332210000000
Q ss_pred ccccCCceEEEEeccccHHHHHHHHHHCCCCeeecccceeecC-cccccCHHHHHHHHHHHHHHccC
Q 026745 158 DEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI-TTIEVDDEAMELNKELIAKLLEL 223 (234)
Q Consensus 158 ~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~-~~V~l~~e~~~~~~~li~~Lee~ 223 (234)
--..+--.+.|.|++.+-..+..-.+.++-.+... -|. -.++++... +++..|++.|+..
T Consensus 80 ~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~ivdv-----~~~~~~ie~tG~~-~ki~~~~~~l~~~ 140 (157)
T TIGR00119 80 IVERELCLVKVSAPGEGRDEIIRLTNIFRGRIVDV-----SPDSYTVEVTGDS-DKIDAFLELLRPF 140 (157)
T ss_pred ceeeEEEEEEEECCccCHHHHHHHHHHhCCEEEEe-----cCCEEEEEEcCCH-HHHHHHHHHhhhc
Confidence 01122246788899988888888888776666432 243 357776533 4567788888765
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=69.41 E-value=18 Score=22.99 Aligned_cols=60 Identities=18% Similarity=0.176 Sum_probs=36.9
Q ss_pred EeccccHHHHHHHHHHCCCCeeecccceeec-C---cccccCHHHHHHHHHHHHHHccCCCccee
Q 026745 169 VSTSDNYTDITTKLREAGIPFETDNGSELLP-I---TTIEVDDEAMELNKELIAKLLELDDVDAV 229 (234)
Q Consensus 169 ~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP-~---~~V~l~~e~~~~~~~li~~Lee~dDV~~V 229 (234)
.-.|..+..+...|.+.++.+... ...-.. . -.+.+.......+..+++.|...++|..|
T Consensus 6 ~~~~~~l~~i~~~l~~~~~~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~v 69 (71)
T cd04876 6 IDRPGLLADITTVIAEEKINILSV-NTRTDDDGLATIRLTLEVRDLEHLARIMRKLRQIPGVIDV 69 (71)
T ss_pred eccCcHHHHHHHHHHhCCCCEEEE-EeEECCCCEEEEEEEEEECCHHHHHHHHHHHhCCCCcEEE
Confidence 345667889999999999988532 111110 1 12223211223467899999999998775
No 15
>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=68.06 E-value=17 Score=25.44 Aligned_cols=57 Identities=18% Similarity=0.159 Sum_probs=38.9
Q ss_pred ccccHHHHHHHHHHCCCCeeecccceeecCcccc--cCHHHHHHHHHHHHHHccCCCcceee
Q 026745 171 TSDNYTDITTKLREAGIPFETDNGSELLPITTIE--VDDEAMELNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~--l~~e~~~~~~~li~~Lee~dDV~~Vy 230 (234)
.+--++.+...|.+.|+.+... + ..+...+. +.-.+.+.+..++++|+.+++|..|+
T Consensus 10 r~Gll~dI~~~i~~~~~nI~~~-~--~~~~~~i~l~i~v~~~~~L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 10 RLGITQEVLDLLVEHNIDLRGI-E--IDPKGRIYLNFPTIEFEKLQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred cchHHHHHHHHHHHCCCceEEE-E--EecCCeEEEEeEecCHHHHHHHHHHHhCCCCceEEE
Confidence 3445889999999999988532 2 22211122 22234556789999999999999986
No 16
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=66.89 E-value=73 Score=26.43 Aligned_cols=133 Identities=16% Similarity=0.112 Sum_probs=74.6
Q ss_pred EEEEecCCchhhHHHHHHHHhhcCccccCCcceeee-cceeE--EEEEeCCCCCHHHHHHHHHH--CCCcccccCCCCCC
Q 026745 81 VVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFK-FRRAR--VVNIKFTDADKDQLLDIALD--AGAEDVIEPPVNED 155 (234)
Q Consensus 81 IVe~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~-F~~~g--~i~~~~~~~~~d~~~e~AIE--~GAeDv~~~~~~ed 155 (234)
++.++.+|+...++.|-.+|+++|.++- +-++... ....- .+.+.. + |+.++..+- ....||-....-.+
T Consensus 4 ~IsV~veN~pGvL~rI~~lf~rrg~NI~-Sl~v~~te~~~~sriti~V~~---~-~~~i~qi~kQl~KLidV~~V~~~~~ 78 (161)
T PRK11895 4 TLSVLVENEPGVLSRVAGLFSRRGYNIE-SLTVGPTEDPGLSRMTIVTSG---D-EQVIEQITKQLNKLIDVLKVVDLTE 78 (161)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCcEE-EEEeeecCCCCEEEEEEEEEC---C-HHHHHHHHHHHhccccEEEEEecCC
Confidence 5678999999999999999999999773 1222221 01111 133333 2 333333332 23333322100000
Q ss_pred CCccccCCceEEEEeccccHHHHHHHHHHCCCCeeecccceeecC-cccccCHHHHHHHHHHHHHHccCC
Q 026745 156 DTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI-TTIEVDDEAMELNKELIAKLLELD 224 (234)
Q Consensus 156 ~~~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~-~~V~l~~e~~~~~~~li~~Lee~d 224 (234)
++--..+--.+.|.|++..-.++..-.+.++-.+... -|. -.++++... +++..|++.|+...
T Consensus 79 ~~~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~ivdv-----~~~~~~iE~tG~~-~ki~~~~~~l~~~g 142 (161)
T PRK11895 79 EAHVERELALVKVRASGENRAEILRLADIFRAKIVDV-----TPESLTIEVTGDS-DKIDAFIDLLRPYG 142 (161)
T ss_pred cchhheEEEEEEEECCcccHHHHHHHHHHhCCEEEEe-----cCCEEEEEEeCCH-HHHHHHHHHhhhcC
Confidence 1101122356788899888888888888776666432 233 357776533 45677888887643
No 17
>PRK04435 hypothetical protein; Provisional
Probab=65.02 E-value=14 Score=29.98 Aligned_cols=61 Identities=31% Similarity=0.406 Sum_probs=42.2
Q ss_pred EEeccccHHHHHHHHHHCCCCeeecccceeecCc-----ccccCHHHHH-HHHHHHHHHccCCCcceee
Q 026745 168 VVSTSDNYTDITTKLREAGIPFETDNGSELLPIT-----TIEVDDEAME-LNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 168 ~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~-----~V~l~~e~~~-~~~~li~~Lee~dDV~~Vy 230 (234)
....|.-|++|...|.+.|.++..- . .-+|.. .+.++-..++ .+..|+++|+.+++|.+|.
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 3455777999999999999988631 1 124431 2333333343 6889999999999999885
No 18
>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=63.27 E-value=35 Score=22.32 Aligned_cols=26 Identities=12% Similarity=0.290 Sum_probs=23.3
Q ss_pred EEecCCchhhHHHHHHHHhhcCcccc
Q 026745 83 EVLTDKITRSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 83 e~~TdN~nRt~~~vr~~~~K~gg~l~ 108 (234)
...++|+.+.+++|-.+|+++|.++.
T Consensus 3 ~v~~~d~~g~l~~i~~~l~~~~~nI~ 28 (71)
T cd04879 3 LIVHKDVPGVIGKVGTILGEHGINIA 28 (71)
T ss_pred EEEecCCCCHHHHHHHHHHhcCCCee
Confidence 45788999999999999999999885
No 19
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=63.05 E-value=15 Score=27.49 Aligned_cols=65 Identities=25% Similarity=0.266 Sum_probs=45.3
Q ss_pred eEEEEeccccHHHHHHHHHHC-CCCeeec-ccceeecCcccccCHHHHHHHHHHHHHHccCCCcce---eecc
Q 026745 165 YYKVVSTSDNYTDITTKLREA-GIPFETD-NGSELLPITTIEVDDEAMELNKELIAKLLELDDVDA---VYTD 232 (234)
Q Consensus 165 ~~~~~~~p~~~~~v~~~L~~~-g~~i~~~-~~~~~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~---Vy~N 232 (234)
.+.|.|.|..+..|+..|.+. |.+|... .+. =+--|.|..+........++.++.+|.|.. |||+
T Consensus 9 SlVV~~~Pe~~~~V~~~l~~ipg~Evh~~d~~~---GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVYh~ 78 (87)
T PRK10553 9 SLVVQAKSERISDISTQLNAFPGCEVAVSDAPS---GQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVYHQ 78 (87)
T ss_pred EEEEEeChHHHHHHHHHHHcCCCcEEEeecCCC---CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEEEE
Confidence 467899999999999999984 6666521 000 012366665555556678899999999766 5776
No 20
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=62.33 E-value=6.9 Score=28.48 Aligned_cols=52 Identities=27% Similarity=0.195 Sum_probs=34.1
Q ss_pred ccccHHHHHHHHHHCCCCeeecccceeecCcccccCHHHHHHHHHHHHHHcc
Q 026745 171 TSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLE 222 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~Lee 222 (234)
+...+.+-.+.|++.||--.......-.|.+.+.|++.-.+.+.+.++.|++
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 4456777778899999943221122335999999999888888888888765
No 21
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=62.08 E-value=26 Score=30.79 Aligned_cols=66 Identities=17% Similarity=0.174 Sum_probs=42.7
Q ss_pred EEEEeccccH----HHHHHHHHHCCCCeeecccceeec-Cccccc------CHHHHHHHHHHHHHHccCCCcceeecc
Q 026745 166 YKVVSTSDNY----TDITTKLREAGIPFETDNGSELLP-ITTIEV------DDEAMELNKELIAKLLELDDVDAVYTD 232 (234)
Q Consensus 166 ~~~~~~p~~~----~~v~~~L~~~g~~i~~~~~~~~iP-~~~V~l------~~e~~~~~~~li~~Lee~dDV~~Vy~N 232 (234)
+.++|.+.+- ..+.+.|++.+|.+.+- ++.-.+ .+.+++ ...+...+++++..|...|.|++|+.|
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 4788988774 44455566778888632 332233 233333 112334578899999999999999887
No 22
>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=61.61 E-value=43 Score=21.98 Aligned_cols=27 Identities=22% Similarity=0.251 Sum_probs=23.9
Q ss_pred EEEecCCchhhHHHHHHHHhhcCcccc
Q 026745 82 VEVLTDKITRSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 82 Ve~~TdN~nRt~~~vr~~~~K~gg~l~ 108 (234)
+.+.++|+...++++-.+|.++|.++.
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~ 28 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIA 28 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCee
Confidence 456888999999999999999999885
No 23
>PF14502 HTH_41: Helix-turn-helix domain
Probab=60.01 E-value=12 Score=25.06 Aligned_cols=43 Identities=19% Similarity=0.265 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcE
Q 026745 32 VLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVS 79 (234)
Q Consensus 32 ~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGva 79 (234)
||.++-+-+.+.++..-+|++||+.=...+. +..|-+|.-|..
T Consensus 5 Ri~tI~e~~~~~~vs~GtiQ~Alk~Le~~ga-----I~Le~rGh~GTf 47 (48)
T PF14502_consen 5 RIPTISEYSEKFGVSRGTIQNALKFLEENGA-----IKLESRGHLGTF 47 (48)
T ss_pred ccCCHHHHHHHhCcchhHHHHHHHHHHHCCc-----EEeeecCcCccc
Confidence 7788889999999999999999996443332 577788877764
No 24
>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=59.17 E-value=71 Score=25.12 Aligned_cols=92 Identities=16% Similarity=0.257 Sum_probs=48.4
Q ss_pred eeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCceEEEEe---ccccHHHHHHHHHHCCCCeeecccc
Q 026745 119 RARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVS---TSDNYTDITTKLREAGIPFETDNGS 195 (234)
Q Consensus 119 ~~g~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~~~~~~~---~p~~~~~v~~~L~~~g~~i~~~~~~ 195 (234)
...+|.++..+.-....+..|++.||+-|-..- ...++-.|. .. -..-+..+++.|++.|++..- -.+
T Consensus 28 ~vriIrvpC~Grv~~~~il~Af~~GADGV~V~g-------C~~g~Ch~~-~Gn~~a~~Rv~~~k~~L~~~Gi~~eR-v~~ 98 (124)
T PF02662_consen 28 NVRIIRVPCSGRVDPEFILRAFEKGADGVLVAG-------CHPGDCHYR-EGNYRAEKRVERLKKLLEELGIEPER-VRL 98 (124)
T ss_pred CeEEEEccCCCccCHHHHHHHHHcCCCEEEEeC-------CCCCCCCcc-hhhHHHHHHHHHHHHHHHHcCCChhH-eEE
Confidence 355777776654445678899999998875420 000111111 01 112345577789999998642 122
Q ss_pred eeecCcccccCHH-HHHHHHHHHHHHccC
Q 026745 196 ELLPITTIEVDDE-AMELNKELIAKLLEL 223 (234)
Q Consensus 196 ~~iP~~~V~l~~e-~~~~~~~li~~Lee~ 223 (234)
.|+... +.+ =.+.+..|.+.|+++
T Consensus 99 ~~~~~~----~~~~fa~~~~~f~~~i~~l 123 (124)
T PF02662_consen 99 YWISAP----EGKRFAEIVNEFTERIKEL 123 (124)
T ss_pred EEeCcc----cHHHHHHHHHHHHHHHHHc
Confidence 233221 011 234566677776653
No 25
>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=59.04 E-value=28 Score=23.03 Aligned_cols=55 Identities=20% Similarity=0.134 Sum_probs=37.8
Q ss_pred ccccHHHHHHHHHHCCCCeeecccceeecC------cccccCHHHHHHHHHHHHHHccCCCcceee
Q 026745 171 TSDNYTDITTKLREAGIPFETDNGSELLPI------TTIEVDDEAMELNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~------~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy 230 (234)
.|..+.++...|.+.++.+... . ..+. -.+.++.. ..+..+++.|++.++|..|+
T Consensus 10 ~~g~l~~i~~~l~~~~~~i~~~-~--~~~~~~~~~~~~i~~~~~--~~~~~~~~~L~~~~~v~~v~ 70 (72)
T cd04874 10 KPGVLRDLTGVIAEHGGNITYT-Q--QFIEREGKARIYMELEGV--GDIEELVEELRSLPIVREVE 70 (72)
T ss_pred CCChHHHHHHHHHhCCCCEEEE-E--EeccCCCeEEEEEEEecc--ccHHHHHHHHhCCCCeEEEE
Confidence 4556899999999999988631 1 1121 12444432 45568999999999999885
No 26
>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=57.22 E-value=19 Score=23.39 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=31.2
Q ss_pred EEeccccHHHHHHHHHHCCCCeeecccceeecC--cccccCHHHHHHHHHHH
Q 026745 168 VVSTSDNYTDITTKLREAGIPFETDNGSELLPI--TTIEVDDEAMELNKELI 217 (234)
Q Consensus 168 ~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~--~~V~l~~e~~~~~~~li 217 (234)
+.|+-..++.|+..|++.++.+.. ..|--. -.+.+++++.+.+.+.+
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 468899999999999999998863 456444 23555555555444443
No 27
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=56.25 E-value=20 Score=26.70 Aligned_cols=60 Identities=20% Similarity=0.101 Sum_probs=39.7
Q ss_pred eccccHHHHHHHHHHCCCCeeeccccee--ecC-ccc--ccCHHHHHHHHHHHHHHccCCCcceee
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSEL--LPI-TTI--EVDDEAMELNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~--iP~-~~V--~l~~e~~~~~~~li~~Lee~dDV~~Vy 230 (234)
=.|--|+.+...+...||.|.+- .+.. .|. +.. -++..+...++.++..|+.+.||.+|+
T Consensus 11 N~~GVL~Rit~lFsRRg~NI~SL-tvg~Te~~~iSRmtivv~~~d~~~ieqI~kQL~KlidVikV~ 75 (84)
T PRK13562 11 DQVSTLNRITSAFVRLQYNIDTL-HVTHSEQPGISNMEIQVDIQDDTSLHILIKKLKQQINVLTVE 75 (84)
T ss_pred CCCCHHHHHHHHHhccCcCeeeE-EecccCCCCceEEEEEEeCCCHHHHHHHHHHHhCCccEEEEE
Confidence 34667899999999999998631 1111 233 222 222123345678899999999999998
No 28
>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=55.83 E-value=27 Score=23.46 Aligned_cols=58 Identities=21% Similarity=0.189 Sum_probs=37.3
Q ss_pred ccccHHHHHHHHHHCCCCeeecccceeecC-c--ccc--cCHHHHHHHHHHHHHHccCCCccee
Q 026745 171 TSDNYTDITTKLREAGIPFETDNGSELLPI-T--TIE--VDDEAMELNKELIAKLLELDDVDAV 229 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~-~--~V~--l~~e~~~~~~~li~~Lee~dDV~~V 229 (234)
.|..+.++...|.+.|..+... .....+. . .+. +.....+.+..++++|+..++|+.+
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 3446889999999999988642 1111111 1 121 2233456678899999999999875
No 29
>COG2605 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]
Probab=54.48 E-value=30 Score=31.89 Aligned_cols=53 Identities=13% Similarity=0.230 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCceEEEEeccccHHHHHHHHHH-CCCCe
Q 026745 129 DADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLRE-AGIPF 189 (234)
Q Consensus 129 ~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~~~~~~~~p~~~~~v~~~L~~-~g~~i 189 (234)
+...|.+.+.|++.||-==... .-++.+++-|+|+|+....+.++|+. .|+.+
T Consensus 265 N~~IDriy~~A~~~GA~~gKl~--------GaG~gGFllf~~~p~k~~~l~r~l~~~~~~~~ 318 (333)
T COG2605 265 NDAIDRIYELALKNGAYGGKLS--------GAGGGGFLLFFCDPSKRNELARALEKEQGFVV 318 (333)
T ss_pred cHHHHHHHHHHHhcCchhceee--------ccCCccEEEEEeCccchHHHHHHHHHhcCCeE
Confidence 3457999999999999764432 12345788899999999999999987 45543
No 30
>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=54.23 E-value=38 Score=23.09 Aligned_cols=59 Identities=20% Similarity=0.168 Sum_probs=38.1
Q ss_pred EEeccccHHHHHHHHHHCCCCeeecccceeecCc----ccccCHHHHHHHHHHHHHHccCCCcc
Q 026745 168 VVSTSDNYTDITTKLREAGIPFETDNGSELLPIT----TIEVDDEAMELNKELIAKLLELDDVD 227 (234)
Q Consensus 168 ~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~----~V~l~~e~~~~~~~li~~Lee~dDV~ 227 (234)
..-.|..|..+...|.+.|..+... ...-.+.. .+.+.-...+.+..++++|+..++|.
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 3445677999999999999998632 22222111 12222223455678999999999975
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=54.11 E-value=9.6 Score=26.11 Aligned_cols=24 Identities=29% Similarity=0.282 Sum_probs=15.5
Q ss_pred HHHHHHHHHHH-HccCCCcceeecc
Q 026745 209 AMELNKELIAK-LLELDDVDAVYTD 232 (234)
Q Consensus 209 ~~~~~~~li~~-Lee~dDV~~Vy~N 232 (234)
+++.+..|+.. |..+|.|.++.+.
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 45556666666 7777777766654
No 32
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=52.41 E-value=22 Score=25.86 Aligned_cols=60 Identities=12% Similarity=0.031 Sum_probs=38.5
Q ss_pred eccccHHHHHHHHHHCCCCeeeccccee--ecC-cccccC-HHHHHHHHHHHHHHccCCCcceee
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSEL--LPI-TTIEVD-DEAMELNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~--iP~-~~V~l~-~e~~~~~~~li~~Lee~dDV~~Vy 230 (234)
=.|.-|..+...+...||.+.+- .+.. .|. +.+.+. ..+-..+..++..|+.+.||.+|-
T Consensus 11 n~pGVL~Ri~~lf~rRgfNI~Sl-~vg~te~~~~sriti~~~~~~~~i~qi~kQL~KLidV~~V~ 74 (76)
T PRK06737 11 NDPSVLLRISGIFARRGYYISSL-NLNERDTSGVSEMKLTAVCTENEATLLVSQLKKLINVLQVN 74 (76)
T ss_pred cCCCHHHHHHHHHhccCcceEEE-EecccCCCCeeEEEEEEECCHHHHHHHHHHHhCCcCEEEEE
Confidence 35667899999999999998642 2221 232 122221 112234668899999999999885
No 33
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=52.06 E-value=21 Score=27.26 Aligned_cols=60 Identities=13% Similarity=0.088 Sum_probs=40.6
Q ss_pred ccccHHHHHHHHHHCCCCeeec-ccceeecC-cc--cccCHHHHHHHHHHHHHHccCCCcceeecc
Q 026745 171 TSDNYTDITTKLREAGIPFETD-NGSELLPI-TT--IEVDDEAMELNKELIAKLLELDDVDAVYTD 232 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~-~~~~~iP~-~~--V~l~~e~~~~~~~li~~Lee~dDV~~Vy~N 232 (234)
.|--|..+..-+...||.|++- ++-.-.|. +. +-+.+ + ..+++++..|+.+.||.+|+..
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 4566899999999999998631 11111233 22 22232 2 4678899999999999999864
No 34
>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=51.80 E-value=16 Score=23.69 Aligned_cols=22 Identities=23% Similarity=0.508 Sum_probs=16.2
Q ss_pred HHHHHHHcCCCHHHHHHHHHHh
Q 026745 36 VLEKAKELDVPKDIVERNIKRA 57 (234)
Q Consensus 36 ai~~Ak~~nmPk~~Ie~AIkr~ 57 (234)
+-..|+..|||+.+|.+-++..
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 4467899999999999888753
No 35
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=50.07 E-value=56 Score=30.81 Aligned_cols=61 Identities=16% Similarity=0.176 Sum_probs=44.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.++---|+.-+.+-++++
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 56788889999999999999999765422 1444433 2567788887666777777777765
No 36
>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=49.61 E-value=37 Score=23.51 Aligned_cols=52 Identities=15% Similarity=0.199 Sum_probs=36.5
Q ss_pred eccccHHHHHHHHHHCCCCeeecccceeecCcc--------cccCHH-HHHHHHHHHHHHccCC
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSELLPITT--------IEVDDE-AMELNKELIAKLLELD 224 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~--------V~l~~e-~~~~~~~li~~Lee~d 224 (234)
-.|-.|..|.+.+++.|+.+.+ ++-+|... |+++.. +...++.+++.|++.-
T Consensus 8 d~pG~L~~vL~~f~~~~vni~~---I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~~~ 68 (75)
T cd04880 8 NKPGALAKALKVFAERGINLTK---IESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKRVT 68 (75)
T ss_pred CcCCHHHHHHHHHHHCCCCEEE---EEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhC
Confidence 3577899999999999999863 45556532 666543 3456778888888753
No 37
>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=49.54 E-value=64 Score=30.17 Aligned_cols=61 Identities=15% Similarity=0.200 Sum_probs=44.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+.-.+-.. +.|....+|+.+|+++.--|+.-+.+-|.++
T Consensus 259 ~laAia~~~~lGi~~~~i~~~l~~~~~~~g------R~e~~~~~~~~vidDsya~np~s~~~al~~l 319 (417)
T TIGR01143 259 ALAAAALALELGIPLEEIAEGLAELKLVKG------RFEIQTKNGLTLIDDTYNANPDSMRAALDAL 319 (417)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCC------ceeEEcCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence 566778888999999999999987654221 3332335789999998877887766666655
No 38
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=49.50 E-value=44 Score=31.33 Aligned_cols=60 Identities=17% Similarity=0.163 Sum_probs=42.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVRE 98 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~ 98 (234)
+..||..|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.++--.|+.-+..-++.
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 56778888899999999999998654322 2444443 367889999866677766665554
No 39
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase.
Probab=48.41 E-value=57 Score=30.53 Aligned_cols=61 Identities=16% Similarity=0.223 Sum_probs=44.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+...+-.. ++|..+ .+|+.+|.+.--.|+.-|..-++++
T Consensus 269 a~aAia~a~~lgi~~~~i~~~L~~f~g~~~------R~e~v~~~~g~~~idD~~atn~~a~~~al~~~ 330 (433)
T TIGR01087 269 ILAAIALAKSLGLNLEAILEALRSFKGLPH------RLEYVGQKNGVHFYNDSKATNVHATLAALSAF 330 (433)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCC------ceEEEEEECCEEEEEcCCCCCHHHHHHHHHhC
Confidence 567888899999999999999997654221 444433 3688888887677777777777654
No 40
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=47.42 E-value=67 Score=30.12 Aligned_cols=61 Identities=13% Similarity=0.183 Sum_probs=44.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+..++-. -++|..+ .+|+.+|.++--.|+.-+..-++.+
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 56788889999999999999999654322 1444443 3678888888777777777666654
No 41
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=47.35 E-value=63 Score=30.43 Aligned_cols=61 Identities=10% Similarity=0.191 Sum_probs=43.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEec-CCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGY-GGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gP-gGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|++-.+-. -++|..+- +|+.+|.++---|+.-+..-++++
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 56677888888999999999999754422 14444332 578899997667777666666544
No 42
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=47.26 E-value=17 Score=26.44 Aligned_cols=59 Identities=17% Similarity=0.089 Sum_probs=37.9
Q ss_pred eccccHHHHHHHHHHCCCCeeeccccee--ecC-cccccCHHHHHHHHHHHHHHccCCCccee
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSEL--LPI-TTIEVDDEAMELNKELIAKLLELDDVDAV 229 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~--iP~-~~V~l~~e~~~~~~~li~~Lee~dDV~~V 229 (234)
=.|.-|..+..-++..||.|.+- .... -|. ..+.+.-+.-..++.++..|+.+.||.+|
T Consensus 12 n~pGVL~Ri~~lf~rRGfnI~sl-~v~~t~~~~~sriti~v~~~~~i~ql~kQL~KL~dV~~V 73 (76)
T PRK11152 12 FRPEVLERVLRVVRHRGFQVCSM-NMTQNTDAQNINIELTVASERPIDLLSSQLNKLVDVAHV 73 (76)
T ss_pred CCccHHHHHHHHHhcCCeeeeeE-EeeecCCCCEEEEEEEECCCchHHHHHHHHhcCcCeEEE
Confidence 35667889999999999998642 2333 222 22222111223466788999999999887
No 43
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=46.91 E-value=60 Score=30.63 Aligned_cols=61 Identities=15% Similarity=0.139 Sum_probs=44.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
...|+..|...++|.+.|.++|+.-++-.. ++|..+ .+|+.+|-++.--|+.-+.+-++.+
T Consensus 274 alaAia~a~~lGi~~~~i~~~L~~f~g~~~------R~e~v~~~~g~~~idDs~~tn~~s~~~Al~~~ 335 (438)
T PRK04663 274 VLVVLALLDAAGVDYRKALDALKSYTGLTH------RCQVVADNHGIKWVNDSKATNVASTLAALSGL 335 (438)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCC------ceEEeeeeCCcEEEeCCCcCCHHHHHHHHHhc
Confidence 466778889999999999999987654322 333332 2688889888777777777777754
No 44
>TIGR01081 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase. Alternate name: murein tripeptide ligase
Probab=45.81 E-value=88 Score=29.53 Aligned_cols=60 Identities=12% Similarity=0.160 Sum_probs=43.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...+++.+.|.++|+...+-. -++|..+ .+|+.+|.++ .-|+.-+.+-++++
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 45677888888999999999998654321 2445443 3678899998 77888777766665
No 45
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=45.03 E-value=74 Score=32.77 Aligned_cols=61 Identities=11% Similarity=0.115 Sum_probs=45.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+.-++-. -++|..+ .+|+.+|.++.--|+.-+.+-|+++
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 45677788999999999999998655422 2455554 4789999998777877777777666
No 46
>PRK14106 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=44.75 E-value=63 Score=30.32 Aligned_cols=61 Identities=15% Similarity=0.175 Sum_probs=43.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|..+|+..++-.. ++|... .+|+.+|+++.-.|+.-+.+-++++
T Consensus 284 a~aAia~~~~lgi~~~~i~~~L~~~~~~~g------R~e~i~~~~~~~vi~D~~ahNP~s~~~~l~~l 345 (450)
T PRK14106 284 ALAATAAAYLLGISPDVIANTLKTFKGVEH------RIEFVAEINGVKFINDSKGTNPDAAIKALEAY 345 (450)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCc------ceEEEeeECCEEEEeCCCccCHHHHHHHHHhC
Confidence 677888899999999999999987543221 333332 3567899998888887666655544
No 47
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=44.67 E-value=79 Score=29.89 Aligned_cols=60 Identities=18% Similarity=0.226 Sum_probs=43.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVRE 98 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~ 98 (234)
+..|+..|...++|.+.|.++|+...+-. -++|..+ .+|+.+|.++-.-|+.-+.+.|+.
T Consensus 292 a~aAiaa~~~lgi~~~~i~~gL~~~~~~~------gR~e~i~~~~g~~vIdDs~ahNp~s~~~aL~~ 352 (460)
T PRK01390 292 AAAAYAAARALGLSPEEIAAGLASFPGLA------HRMEQVGRRGGVLFVNDSKATNADAAAKALSS 352 (460)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCC------CceEEEeeeCCcEEEEcCCCCCHHHHHHHHHh
Confidence 46677778888999999999999764322 1444443 367888889888888888766653
No 48
>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed
Probab=44.29 E-value=82 Score=29.93 Aligned_cols=61 Identities=11% Similarity=0.013 Sum_probs=42.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEE-ecCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVY-GYGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~-gPgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+.-++-.. ++|.. .++|+.+|-+|.--|+.-...-|..+
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 556778889999999999999997654222 22322 24777777777887777666666554
No 49
>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=44.29 E-value=97 Score=20.84 Aligned_cols=59 Identities=17% Similarity=0.256 Sum_probs=39.5
Q ss_pred EEEecCCchhhHHHHHHHHhhcCccccCCcceeeecceeEEEEEeCCCCCHHHHHHHHHHCCC
Q 026745 82 VEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGA 144 (234)
Q Consensus 82 Ve~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~~~~~~d~~~e~AIE~GA 144 (234)
+.+..+|....++.|-.+|.++|.++-. - +.+.-..++++.+..+ +.+.+.+..-+.|.
T Consensus 4 i~v~v~d~pG~La~v~~~l~~~~inI~~-i-~~~~~~~~~~~rl~~~--~~~~~~~~L~~~G~ 62 (66)
T cd04908 4 LSVFLENKPGRLAAVTEILSEAGINIRA-L-SIADTSEFGILRLIVS--DPDKAKEALKEAGF 62 (66)
T ss_pred EEEEEcCCCChHHHHHHHHHHCCCCEEE-E-EEEecCCCCEEEEEEC--CHHHHHHHHHHCCC
Confidence 3457889999999999999999998741 1 1222233566666542 45666666556664
No 50
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=44.26 E-value=1.4e+02 Score=27.70 Aligned_cols=57 Identities=16% Similarity=0.247 Sum_probs=33.7
Q ss_pred HHHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCCch-------hhHHHHHHHHhhcCccc
Q 026745 48 DIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKIT-------RSVAAVREVVKDCGGKM 107 (234)
Q Consensus 48 ~~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGvaiIVe~~TdN~n-------Rt~~~vr~~~~K~gg~l 107 (234)
+.|.+||..|...+... ..+..-..||.-.. |.+.|.++. .++..+...++|+||++
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-CKITIKLIAPPQYV--IVTTCSDKDKGMEIIGAALEAIKEVIKKKGGDF 263 (319)
T ss_pred HHHHHHHHHHHhcCCCc-CcEEEEEEcCCeEE--EEEEeCCHHHHHHHHHHHHHHHHHHHHHcCCeE
Confidence 45667777765433321 23555567777654 455566665 45555666667777774
No 51
>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=43.99 E-value=55 Score=19.63 Aligned_cols=25 Identities=16% Similarity=0.251 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH
Q 026745 32 VLAAVLEKAKELDVPKDIVERNIKR 56 (234)
Q Consensus 32 ~L~~ai~~Ak~~nmPk~~Ie~AIkr 56 (234)
..-.+|..|+..|++++-|..-++.
T Consensus 4 EW~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 4 EWVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4567899999999999999988774
No 52
>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=42.10 E-value=30 Score=23.18 Aligned_cols=56 Identities=21% Similarity=0.253 Sum_probs=36.7
Q ss_pred ccccHHHHHHHHHHCCCCeeecccce---eecCcccccCHHHHHHHHHHHHHHccCCCcceee
Q 026745 171 TSDNYTDITTKLREAGIPFETDNGSE---LLPITTIEVDDEAMELNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~~~~~---~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy 230 (234)
.|-.++++...|.+.|+.+... ... -.+...++++.. ....++++|...++|.+|+
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 4667899999999998887421 110 011122344433 4567999999999999885
No 53
>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional
Probab=41.63 E-value=1e+02 Score=29.52 Aligned_cols=59 Identities=12% Similarity=0.094 Sum_probs=42.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+. .+-. -+.|..+ .+|+.+|++ .-.|+.-..+-+.++
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 566778888899999999999986 4322 2445554 368889999 677776666666555
No 54
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=41.31 E-value=22 Score=24.58 Aligned_cols=56 Identities=23% Similarity=0.229 Sum_probs=35.6
Q ss_pred cccHHHHHHHHHHCCCCeeeccccee--ecC-ccccc--CHHHHHHHHHHHHHHccCCCccee
Q 026745 172 SDNYTDITTKLREAGIPFETDNGSEL--LPI-TTIEV--DDEAMELNKELIAKLLELDDVDAV 229 (234)
Q Consensus 172 p~~~~~v~~~L~~~g~~i~~~~~~~~--iP~-~~V~l--~~e~~~~~~~li~~Lee~dDV~~V 229 (234)
|--|..+..-+...||.+.+- .+.. .|. ..+.+ +.+ ...+..|+..|+.+.||.+|
T Consensus 3 ~GvL~Ri~~vf~rRg~nI~sl-~v~~~~~~~~~riti~v~~~-~~~i~~l~~Ql~KlidV~~V 63 (63)
T PF13710_consen 3 PGVLNRITGVFRRRGFNIESL-SVGPTEDPGISRITIVVSGD-DREIEQLVKQLEKLIDVVKV 63 (63)
T ss_dssp TTHHHHHHHHHHTTT-EECEE-EEEE-SSTTEEEEEEEEES--CCHHHHHHHHHHCSTTEEEE
T ss_pred cHHHHHHHHHHhcCCeEEeeE-EeeecCCCCEEEEEEEEeeC-chhHHHHHHHHhccCCeEeC
Confidence 456788888999999998642 3333 232 22333 322 23456799999999999876
No 55
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=40.33 E-value=48 Score=29.08 Aligned_cols=62 Identities=18% Similarity=0.303 Sum_probs=43.8
Q ss_pred EEEecCCchhhHHHHHHHHhhcCccccCCcce---eeecceeEEEEEeCCCCCHHHHHHHHHHCC
Q 026745 82 VEVLTDKITRSVAAVREVVKDCGGKMADPGSV---MFKFRRARVVNIKFTDADKDQLLDIALDAG 143 (234)
Q Consensus 82 Ve~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv---~~~F~~~g~i~~~~~~~~~d~~~e~AIE~G 143 (234)
+...|++...+...|+.++.++||-+...... .....+.+.+.+.-+...+|.+++..-+.|
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 56777999999999999999999987632221 122345566666555556788777777666
No 56
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=39.53 E-value=1.2e+02 Score=28.86 Aligned_cols=60 Identities=15% Similarity=0.107 Sum_probs=43.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
...|+..|...++|.+.|..+|+...+-.. ++|... .+|+.+|++ .-.|+.-+.+-++++
T Consensus 283 alaAia~a~~lgi~~~~i~~~L~~~~~~~g------R~e~~~~~~~~~iI~D-yahNP~s~~aal~~l 343 (460)
T PRK00139 283 LLAALAALLALGVPLEDALAALAKLQGVPG------RMERVDAGQGPLVIVD-YAHTPDALEKVLEAL 343 (460)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCC------CcEEEEcCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 456777788899999999999997654221 444444 368899999 777887777777665
No 57
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=38.69 E-value=31 Score=22.00 Aligned_cols=20 Identities=40% Similarity=0.537 Sum_probs=15.5
Q ss_pred HHHHHcCCCHHHHHHHHHHh
Q 026745 38 EKAKELDVPKDIVERNIKRA 57 (234)
Q Consensus 38 ~~Ak~~nmPk~~Ie~AIkr~ 57 (234)
+-|+..|+++.+|-+-|+|+
T Consensus 25 ~IA~~lg~s~sTV~relkR~ 44 (44)
T PF13936_consen 25 EIAKRLGRSRSTVSRELKRN 44 (44)
T ss_dssp HHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHCcCcHHHHHHHhcC
Confidence 46789999999999999985
No 58
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=38.61 E-value=94 Score=29.72 Aligned_cols=61 Identities=15% Similarity=0.169 Sum_probs=45.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEec-CCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGY-GGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gP-gGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+.-++-. .++|..+- +|+.+|.++---|+.-+...++++
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 46677888888999999999999754422 23443332 688999997777988888877776
No 59
>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=38.48 E-value=81 Score=21.27 Aligned_cols=21 Identities=24% Similarity=0.414 Sum_probs=11.4
Q ss_pred HHHHHHHHHHccCCCcceeec
Q 026745 211 ELNKELIAKLLELDDVDAVYT 231 (234)
Q Consensus 211 ~~~~~li~~Lee~dDV~~Vy~ 231 (234)
+.+.+|.+.|.++|+|..+|.
T Consensus 10 ~~~~~~~~~l~~~p~V~~~~~ 30 (74)
T PF01037_consen 10 DAYDEFAEALAEIPEVVECYS 30 (74)
T ss_dssp THHHHHHHHHHTSTTEEEEEE
T ss_pred chHHHHHHHHHcCCCEEEEEE
Confidence 334555555556666555553
No 60
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=37.26 E-value=67 Score=26.53 Aligned_cols=58 Identities=19% Similarity=0.198 Sum_probs=40.4
Q ss_pred eccccHHHHHHHHHHCCCCeeecccceeecCc-------ccccCHHHHHHHHHHHHHHccCCCcceeec
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSELLPIT-------TIEVDDEAMELNKELIAKLLELDDVDAVYT 231 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~-------~V~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 231 (234)
-.|--|+.+...+...||.+.+ +.-.|.. ++-++. +-..++.+...|+.+.||.+|++
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 3566799999999999999963 2222221 123333 22457789999999999999976
No 61
>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=37.23 E-value=47 Score=23.29 Aligned_cols=28 Identities=14% Similarity=0.139 Sum_probs=26.5
Q ss_pred EEEEecCCchhhHHHHHHHHhhcCcccc
Q 026745 81 VVEVLTDKITRSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 81 IVe~~TdN~nRt~~~vr~~~~K~gg~l~ 108 (234)
++|+.|.++...++.|-.+|..+|+++.
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~ 29 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVV 29 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEE
Confidence 6899999999999999999999999985
No 62
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=36.79 E-value=92 Score=29.58 Aligned_cols=58 Identities=16% Similarity=0.164 Sum_probs=41.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHH
Q 026745 34 AAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVRE 98 (234)
Q Consensus 34 ~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~ 98 (234)
..|+..|... +|.+.|.++|+.-++... +.|.++ .+|+-+|.++.--|+.-+.+-|+.
T Consensus 289 laA~a~a~~~-i~~~~i~~~L~~f~~~~~------R~e~~~~~~g~~~i~Dsy~~np~s~~~al~~ 347 (458)
T PRK01710 289 LAAFCAVNDD-VSIESMKKVATTFSGVEH------RCEFVREINGVKYYNDSIASSPTRTLAGLKA 347 (458)
T ss_pred HHHHHHHHhC-CCHHHHHHHHHhCCCCCc------ceEEEEEECCEEEecccccCCHHHHHHHHHh
Confidence 3455566666 999999999987654332 444443 478999999888899877776653
No 63
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=36.51 E-value=17 Score=28.29 Aligned_cols=28 Identities=21% Similarity=0.452 Sum_probs=22.4
Q ss_pred CCCCCCCCHHHHHHHHHH--HHcCCCHHHH
Q 026745 23 GGPNPTSNTVLAAVLEKA--KELDVPKDIV 50 (234)
Q Consensus 23 GG~DP~~N~~L~~ai~~A--k~~nmPk~~I 50 (234)
|+.+|+.|.+|...|-.. +..++|++.|
T Consensus 67 G~~~~~~n~~~s~~i~~~l~~~LgIp~dRi 96 (113)
T PTZ00450 67 GEYAPSKPKMMTPRITAAITKECGIPAERI 96 (113)
T ss_pred cCcCHHHHHHHHHHHHHHHHHHcCCCcccE
Confidence 778899999999998875 5678887654
No 64
>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=36.12 E-value=1.5e+02 Score=25.64 Aligned_cols=71 Identities=10% Similarity=0.015 Sum_probs=47.5
Q ss_pred HHHHHHHHHH-CCCcccccCCCCCCCCccccCCceEEEEeccccHHHHHHHHHHCCCCeeecccceeecC--cccccCHH
Q 026745 132 KDQLLDIALD-AGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI--TTIEVDDE 208 (234)
Q Consensus 132 ~d~~~e~AIE-~GAeDv~~~~~~ed~~~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~--~~V~l~~e 208 (234)
.-.....||+ ++...... ...+.|.|+...+..+...|.+.++.+. +..|-.. -.+.++.+
T Consensus 117 Y~~aa~~al~~a~~~~~~~-------------~~~~~~~~~y~~~~~v~~~l~~~~~~i~---~~~y~~~V~~~~~v~~~ 180 (204)
T TIGR00257 117 YGKSVLEALNNIQKEEKLE-------------LEILSLHCDYKQLDALERELKKFQLEII---KSNFSNNVVLVEISGTK 180 (204)
T ss_pred HHHHHHHHHHhCCeEEEEE-------------EEEEEEEechhHHHHHHHHHHHCCCEEE---eeEecCCEEEEEEECHH
Confidence 3456677776 67666543 1468899999999999999999998875 3456444 23445666
Q ss_pred HHHHHHHHHH
Q 026745 209 AMELNKELIA 218 (234)
Q Consensus 209 ~~~~~~~li~ 218 (234)
+.+.+.+.+.
T Consensus 181 ~~~~~~~~l~ 190 (204)
T TIGR00257 181 ENLAFSEQLT 190 (204)
T ss_pred HHHHHHHHHH
Confidence 6555444433
No 65
>PRK10858 nitrogen regulatory protein P-II 1; Provisional
Probab=35.95 E-value=83 Score=24.41 Aligned_cols=24 Identities=21% Similarity=0.290 Sum_probs=21.0
Q ss_pred eEEEEeccccHHHHHHHHHHCCCC
Q 026745 165 YYKVVSTSDNYTDITTKLREAGIP 188 (234)
Q Consensus 165 ~~~~~~~p~~~~~v~~~L~~~g~~ 188 (234)
.+..+..|..+..|+++|.+.|+.
T Consensus 3 ~I~AIIRp~kl~~v~~aL~~~G~~ 26 (112)
T PRK10858 3 KIDAIIKPFKLDDVREALAEVGIT 26 (112)
T ss_pred EEEEEECHHHHHHHHHHHHHCCCC
Confidence 366789999999999999998875
No 66
>PRK09977 putative Mg(2+) transport ATPase; Provisional
Probab=35.84 E-value=52 Score=28.66 Aligned_cols=63 Identities=11% Similarity=0.057 Sum_probs=42.0
Q ss_pred eEEEEeccccHHHHHHHHHHCCCCeeecccceeecC-c--c--cccCHHHHHHHHHHHHHHccCCCcceee
Q 026745 165 YYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI-T--T--IEVDDEAMELNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 165 ~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~-~--~--V~l~~e~~~~~~~li~~Lee~dDV~~Vy 230 (234)
.+.+.|.+.+...+.+.|.+.++.+.+- +++.... . . +.+.. .....++++.|.+.|+|+.|-
T Consensus 146 ~~~i~~~~~~~~~i~~~l~~~~i~i~~~-~~~~~~~~~~~~~~~~~~~--~~~~~~l~~~L~~~~~V~~v~ 213 (215)
T PRK09977 146 HLQLTLVNGNVVSMLDWFKQQKIKTDLV-SLQENEDHEVVAIDITLHA--TTSIEDLYRLLKGIAGVKGVS 213 (215)
T ss_pred EEEEEEccccHHHHHHHHHHcCceEEEE-EEEecCCCcEEEEEEEECC--CCCHHHHHHHHhcCCCceEEE
Confidence 4678899999999999999999987632 2222211 1 1 22222 123457899999999999874
No 67
>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=34.66 E-value=1.6e+02 Score=27.84 Aligned_cols=60 Identities=13% Similarity=0.112 Sum_probs=42.7
Q ss_pred HHHHHHHHHHcC-CCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELD-VPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~n-mPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...+ +|.+.|..+|+..++... ++|... .+|+.+|.+ ...|+.-..+-+.++
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 456777788888 999999999997654322 223322 368899999 777887777766665
No 68
>PRK08577 hypothetical protein; Provisional
Probab=34.16 E-value=77 Score=24.99 Aligned_cols=57 Identities=23% Similarity=0.267 Sum_probs=38.2
Q ss_pred cccHHHHHHHHHHCCCCeeecccceeec-------CcccccCHHHHHHHHHHHHHHccCCCcceee
Q 026745 172 SDNYTDITTKLREAGIPFETDNGSELLP-------ITTIEVDDEAMELNKELIAKLLELDDVDAVY 230 (234)
Q Consensus 172 p~~~~~v~~~L~~~g~~i~~~~~~~~iP-------~~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy 230 (234)
|--|+.+...|.+.|+.+... ...-.+ .-.+++++.+ ..+..+++.|+.+++|..|+
T Consensus 67 ~GvLa~I~~~l~~~~inI~~i-~~~~~~~~~~~~i~l~vev~~~~-~~l~~l~~~L~~l~~V~~V~ 130 (136)
T PRK08577 67 PGVLAKITGLLAEHGVDILAT-ECEELKRGELAECVIIVDLSKSD-IDLEELEEELKKLEEVKEVE 130 (136)
T ss_pred CCHHHHHHHHHHHCCCCEEEE-EEEEecCCCEEEEEEEEEeCCch-hhHHHHHHHHHcCCCEEEEE
Confidence 335889999999999987632 222222 1124555421 34678999999999999886
No 69
>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=32.48 E-value=93 Score=21.82 Aligned_cols=53 Identities=19% Similarity=0.232 Sum_probs=35.0
Q ss_pred eccccHHHHHHHHHHCCCCeeecccceeecCc--------ccccCHH-HHHHHHHHHHHHccCCC
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSELLPIT--------TIEVDDE-AMELNKELIAKLLELDD 225 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~--------~V~l~~e-~~~~~~~li~~Lee~dD 225 (234)
-.|-.|..+.+.+.+.|+.+.+ ++-.|.. .|+++.. +...+.++++.|+++.+
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 4567789999999999999863 4455542 1444432 24566788888887543
No 70
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=31.94 E-value=1.6e+02 Score=19.68 Aligned_cols=59 Identities=17% Similarity=0.242 Sum_probs=35.3
Q ss_pred EEecCCchhhHHHHHHHHhhcCccccCCcceeeecc---eeEEEEEeCCCCCHHHHHHHHHHCCC
Q 026745 83 EVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFR---RARVVNIKFTDADKDQLLDIALDAGA 144 (234)
Q Consensus 83 e~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~F~---~~g~i~~~~~~~~~d~~~e~AIE~GA 144 (234)
.+.-++....++.+-.+|.++|.++. ++..... ..+.+.+.....+.+++.+..-+.|.
T Consensus 5 ~v~~~d~pG~l~~i~~~l~~~~inI~---~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~ 66 (72)
T cd04883 5 EVRVPDRPGQLADIAAIFKDRGVNIV---SVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGY 66 (72)
T ss_pred EEEECCCCCHHHHHHHHHHHcCCCEE---EEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCC
Confidence 34455666799999999999999885 2222122 23334443333455666666556664
No 71
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=31.63 E-value=87 Score=25.99 Aligned_cols=58 Identities=16% Similarity=0.181 Sum_probs=39.3
Q ss_pred eccccHHHHHHHHHHCCCCeeecccceeecCc-----c--cccCHHHHHHHHHHHHHHccCCCcceeec
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSELLPIT-----T--IEVDDEAMELNKELIAKLLELDDVDAVYT 231 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~-----~--V~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 231 (234)
-.|--|..+...+...||.|.+ +.-.|.. . +.++. +...++.++..|+.+.||.+|++
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 3566789999999999999863 2222321 1 22322 22346678889999999999976
No 72
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=31.50 E-value=2.3e+02 Score=21.50 Aligned_cols=88 Identities=13% Similarity=0.223 Sum_probs=50.5
Q ss_pred CchhhHHHHHHHHhhcCccccCCcceeeecceeEEEEEeC---CCCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCc
Q 026745 88 KITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKF---TDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAER 164 (234)
Q Consensus 88 N~nRt~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~---~~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~ 164 (234)
...++..++..++. +||++- .|.+...-.|.+.... +..|.+..++..=+..|.-+... -+ +-=
T Consensus 6 ~~~~~~~EL~~IVd-~Gg~V~---DV~veHp~YG~i~~~L~i~sr~Dv~~Fi~~l~~~~~~~Ls~L--------T~-GvH 72 (98)
T PF02829_consen 6 TPDEIEDELEIIVD-NGGRVL---DVIVEHPVYGEITGNLNISSRRDVDKFIEKLEKSKAKPLSSL--------TG-GVH 72 (98)
T ss_dssp -GGGHHHHHHHHHH-TT-EEE---EEEEEETTTEEEEEEEEE-SHHHHHHHHHHHHH--S--STTG--------GG-GEE
T ss_pred CHHHHHHHHHHHHH-CCCEEE---EEEEeCCCCcEEEEEEecCCHHHHHHHHHHHhccCCcchHHh--------cC-CEe
Confidence 45567788888877 999986 5777776666554432 12345565555555677755432 11 222
Q ss_pred eEEEEeccc-cHHHHHHHHHHCCCC
Q 026745 165 YYKVVSTSD-NYTDITTKLREAGIP 188 (234)
Q Consensus 165 ~~~~~~~p~-~~~~v~~~L~~~g~~ 188 (234)
...|.|+.. .|.++.++|+++||=
T Consensus 73 ~HtI~a~~~e~l~~I~~~L~~~G~L 97 (98)
T PF02829_consen 73 YHTIEAPDEEDLDKIEEALKKKGFL 97 (98)
T ss_dssp EEEEEESSHHHHHHHHHHHHHTT-B
T ss_pred eEEEEECCHHHHHHHHHHHHHCCCc
Confidence 344555444 689999999999983
No 73
>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=31.16 E-value=2e+02 Score=26.71 Aligned_cols=57 Identities=7% Similarity=0.060 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCceEEEEeccccHHHHHHHHHHCCCCe
Q 026745 129 DADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPF 189 (234)
Q Consensus 129 ~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i 189 (234)
....|.+.+...+.+.|.+.....++ +...+..+.|..+..+...|-++|++.|+.-
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 34677777776667774443321111 1112357888999999999999999998764
No 74
>PRK11568 hypothetical protein; Provisional
Probab=30.86 E-value=2.3e+02 Score=24.35 Aligned_cols=71 Identities=11% Similarity=0.050 Sum_probs=47.1
Q ss_pred HHHHHHHHH-CCCcccccCCCCCCCCccccCCceEEEEeccccHHHHHHHHHHCCCCeeecccceeecC--cccccCHHH
Q 026745 133 DQLLDIALD-AGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI--TTIEVDDEA 209 (234)
Q Consensus 133 d~~~e~AIE-~GAeDv~~~~~~ed~~~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~--~~V~l~~e~ 209 (234)
-.....||+ ++...... ...+.|.|+...++.+...|.+.++.+. +..|--. -.+.++.++
T Consensus 118 ~~aa~~al~~a~~~~~~~-------------~~~~~i~~~y~~~~~v~~~l~~~~~~i~---~~~y~~~V~~~~~v~~~~ 181 (204)
T PRK11568 118 GGGVQQALRQLTTQRKVP-------------LTEYTLQCEYAQLAGIEALLGQFDGKIV---NSEYQAFVTLRVALPAAK 181 (204)
T ss_pred HHHHHHHHHhCCeEEEEE-------------eEEEEEEECcchHHHHHHHHHHCCCEEE---cceecCCEEEEEEECHHH
Confidence 455666666 66655543 1458899999999999999999998875 3455433 235556666
Q ss_pred HHHHHHHHHH
Q 026745 210 MELNKELIAK 219 (234)
Q Consensus 210 ~~~~~~li~~ 219 (234)
.+.+...+..
T Consensus 182 ~~~~~~~l~~ 191 (204)
T PRK11568 182 VAEFSAKLAD 191 (204)
T ss_pred HHHHHHHHHH
Confidence 6655554433
No 75
>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=30.32 E-value=1.5e+02 Score=28.37 Aligned_cols=60 Identities=17% Similarity=0.211 Sum_probs=40.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVRE 98 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~ 98 (234)
+..|+..|...++|.+.|.++|+...+-.. ++|..+ .+|+.+|-++--.|..-+.+-++.
T Consensus 325 alaAia~~~~lgi~~~~i~~aL~~f~~~~g------R~e~~~~~~g~~~idDs~~tn~~s~~~al~~ 385 (498)
T PRK02006 325 ALAALALARAIGLPAAPLLHGLREYRGEPH------RVELVATIDGVDYYDDSKGTNVGATVAALDG 385 (498)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCCCC------ceEEEEEECCEEEEEcCCCCCHHHHHHHHHh
Confidence 456778888999999999999997644221 444443 267777777755566666666664
No 76
>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=30.14 E-value=1.1e+02 Score=28.81 Aligned_cols=45 Identities=22% Similarity=0.409 Sum_probs=31.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEE
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVE 83 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe 83 (234)
+..|+..|...++|.+.|..+|+...+-.. ++|..+ .+|+.+|.+
T Consensus 278 ~~aA~a~~~~lgi~~~~i~~~l~~f~~~~~------R~e~~~~~~gv~~i~D 323 (448)
T TIGR01082 278 ALAAIAVALELGIDFEAILRALANFQGVKR------RFEILGEFGGVLLIDD 323 (448)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCc------cceEEEEeCCeEEEEc
Confidence 557778888899999999999997654221 333332 357878777
No 77
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=29.88 E-value=1.6e+02 Score=30.85 Aligned_cols=61 Identities=11% Similarity=0.057 Sum_probs=43.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+.-++-.. +.|.+. .+|+.+|.++.--|+.-+.+-|.++
T Consensus 796 alaAia~a~~lGi~~~~i~~~L~~f~~~~g------R~e~~~~~~~~~iidDsya~np~s~~aaL~~l 857 (958)
T PRK11929 796 ALAAIACALAAGASLKQIRAGLERFQPVAG------RMQRRRLSCGTRIIDDTYNANPDSMRAAIDVL 857 (958)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCCCC------CceEEEcCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence 566788899999999999999997654221 222222 4788999998877887666666554
No 78
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=29.28 E-value=45 Score=24.60 Aligned_cols=19 Identities=21% Similarity=0.440 Sum_probs=16.5
Q ss_pred ccHHHHHHHHHHCCCCeee
Q 026745 173 DNYTDITTKLREAGIPFET 191 (234)
Q Consensus 173 ~~~~~v~~~L~~~g~~i~~ 191 (234)
..|..|+.+|+++||++..
T Consensus 8 ~~Ls~v~~~L~~~GyeVv~ 26 (80)
T PF03698_consen 8 EGLSNVKEALREKGYEVVD 26 (80)
T ss_pred CCchHHHHHHHHCCCEEEe
Confidence 5688999999999999853
No 79
>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=29.01 E-value=2.2e+02 Score=27.25 Aligned_cols=99 Identities=15% Similarity=0.210 Sum_probs=60.2
Q ss_pred ecceeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCCCccccCCceEEEEeccccHHH-HHHHHHHCCCCeeecc-
Q 026745 116 KFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTD-ITTKLREAGIPFETDN- 193 (234)
Q Consensus 116 ~F~~~g~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~~ed~~~ed~~~~~~~~~~~p~~~~~-v~~~L~~~g~~i~~~~- 193 (234)
.|++.|++.+. +.|++++.+-=..-.-.- .+ ..+-|++..--+.. +.+.+...|+++-.-+
T Consensus 265 ~~~~~Gv~~~~----~~~el~~~~~~l~~~~~~------------~g-~rvaivs~sGG~g~l~aD~~~~~Gl~lp~ls~ 327 (447)
T TIGR02717 265 AFKQAGVIRAD----SIEELFDLARLLSNQPLP------------KG-NRVAIITNAGGPGVIATDACEENGLELAELSE 327 (447)
T ss_pred HHHHCCeEEeC----CHHHHHHHHHHHhcCCCC------------CC-CeEEEEECCchHHHHHHHHHHHcCCCcCCCCH
Confidence 47788887774 567777765543322211 01 34566777666544 5667788888753100
Q ss_pred c----c-ee-----ecCcccccCH-HHHHHHHHHHHHHccCCCcceeec
Q 026745 194 G----S-EL-----LPITTIEVDD-EAMELNKELIAKLLELDDVDAVYT 231 (234)
Q Consensus 194 ~----~-~~-----iP~~~V~l~~-e~~~~~~~li~~Lee~dDV~~Vy~ 231 (234)
+ + .+ .+.+++++.. ..-+.+...++.|.++|+|..|..
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 0 11 2347888732 345678889999999999887763
No 80
>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=28.99 E-value=79 Score=21.13 Aligned_cols=28 Identities=21% Similarity=0.230 Sum_probs=25.4
Q ss_pred EEEEecCCchhhHHHHHHHHhhcCcccc
Q 026745 81 VVEVLTDKITRSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 81 IVe~~TdN~nRt~~~vr~~~~K~gg~l~ 108 (234)
++.+.+.++...+++|-.+|+++|+++.
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~ 29 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIH 29 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEE
Confidence 4678899999999999999999999885
No 81
>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=28.96 E-value=1.7e+02 Score=19.13 Aligned_cols=28 Identities=29% Similarity=0.343 Sum_probs=25.0
Q ss_pred EEEEecCCchhhHHHHHHHHhhcCcccc
Q 026745 81 VVEVLTDKITRSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 81 IVe~~TdN~nRt~~~vr~~~~K~gg~l~ 108 (234)
.+.+.++++...+++|-.+|+.+|+++.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~ 29 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIH 29 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEE
Confidence 4567889999999999999999999885
No 82
>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=28.83 E-value=1.5e+02 Score=20.65 Aligned_cols=50 Identities=14% Similarity=0.129 Sum_probs=34.7
Q ss_pred ccccHHHHHHHHHHCCCCeeecccceeecCcc--------cccCHHHHHHHHHHHHHHccCC
Q 026745 171 TSDNYTDITTKLREAGIPFETDNGSELLPITT--------IEVDDEAMELNKELIAKLLELD 224 (234)
Q Consensus 171 ~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~--------V~l~~e~~~~~~~li~~Lee~d 224 (234)
.|-.|..+.+.+.+.|+.+. .++-+|... |+++. +.+.+.++++.|...-
T Consensus 10 ~pG~L~~vL~~f~~~~iNlt---~IeSRP~~~~~~~y~Ffvd~~~-~~~~~~~~l~~L~~~~ 67 (74)
T cd04904 10 EVGALARALKLFEEFGVNLT---HIESRPSRRNGSEYEFFVDCEV-DRGDLDQLISSLRRVV 67 (74)
T ss_pred CCcHHHHHHHHHHHCCCcEE---EEECCCCCCCCceEEEEEEEEc-ChHHHHHHHHHHHHhc
Confidence 46778889999999999986 356666532 66654 2244778888887643
No 83
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=28.71 E-value=46 Score=28.98 Aligned_cols=24 Identities=29% Similarity=0.403 Sum_probs=18.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Q 026745 34 AAVLEKAKELDVPKDIVERNIKRA 57 (234)
Q Consensus 34 ~~ai~~Ak~~nmPk~~Ie~AIkr~ 57 (234)
..+|.-|+..|+|++.|+||-...
T Consensus 206 S~ai~iA~~~g~p~~II~rA~~i~ 229 (235)
T PF00488_consen 206 SYAIEIAKLAGLPEEIIERAKEIL 229 (235)
T ss_dssp TCHHHHHHHTT--HHHHHHHHHHH
T ss_pred cHHHHHHHHhCcCHHHHHHHHHHH
Confidence 358999999999999999996643
No 84
>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=27.93 E-value=1.9e+02 Score=19.27 Aligned_cols=27 Identities=19% Similarity=0.217 Sum_probs=23.3
Q ss_pred EEEecCCchhhHHHHHHHHhhcCcccc
Q 026745 82 VEVLTDKITRSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 82 Ve~~TdN~nRt~~~vr~~~~K~gg~l~ 108 (234)
+.+..+++...+..|-.+|.++|.++.
T Consensus 4 ~~v~~~d~~G~L~~l~~~l~~~~i~i~ 30 (69)
T cd04909 4 LYVDVPDEPGVIAEVTQILGDAGISIK 30 (69)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCce
Confidence 455678888899999999999999885
No 85
>PF07942 N2227: N2227-like protein; InterPro: IPR012901 This family features sequences that are similar to a region of hypothetical yeast gene product N2227 (P53934 from SWISSPROT). This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions [].
Probab=27.70 E-value=73 Score=28.73 Aligned_cols=68 Identities=15% Similarity=0.310 Sum_probs=46.9
Q ss_pred EEEEEecCCchhhHHHHHHHHhhcCccccCCcceeeecceeEEEEEeCCCCCHHHHHHHHHHCCCccccc
Q 026745 80 IVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIE 149 (234)
Q Consensus 80 iIVe~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~F~~~g~i~~~~~~~~~d~~~e~AIE~GAeDv~~ 149 (234)
+.|++ ..|.-.-+..|.++++ -||-+-.-|++.|.|...+.-....-.++.|++..++...|-+++.+
T Consensus 173 FFIDT-A~Ni~~Yi~tI~~lLk-pgG~WIN~GPLlyh~~~~~~~~~~sveLs~eEi~~l~~~~GF~~~~~ 240 (270)
T PF07942_consen 173 FFIDT-AENIIEYIETIEHLLK-PGGYWINFGPLLYHFEPMSIPNEMSVELSLEEIKELIEKLGFEIEKE 240 (270)
T ss_pred EEeec-hHHHHHHHHHHHHHhc-cCCEEEecCCccccCCCCCCCCCcccCCCHHHHHHHHHHCCCEEEEE
Confidence 44444 4567777777777775 46766667789999987641000001467899999999999999864
No 86
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=27.63 E-value=1.8e+02 Score=27.58 Aligned_cols=61 Identities=16% Similarity=0.167 Sum_probs=40.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..||..|...++|.+.|.++|++.++... ++|..+ .+|+.+|-++---|+.-+.+-|+.+
T Consensus 305 a~aAia~~~~lgi~~~~i~~~L~~~~~~~g------R~E~i~~~~~~~iiDDs~ahNp~a~~aaL~~l 366 (480)
T PRK01438 305 ALAAAALARSFGVPPAAVRDGLRAFRPDAH------RIEHVADADGVTWVDDSKATNPHAAAASLAAY 366 (480)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCC------ceEEEEEECCEEEEecCccCCHHHHHHHHHhC
Confidence 456667778889999999999997654321 333322 2466566667777877777766654
No 87
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=27.55 E-value=43 Score=21.45 Aligned_cols=26 Identities=15% Similarity=0.318 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHh
Q 026745 32 VLAAVLEKAKELDVPKDIVERNIKRA 57 (234)
Q Consensus 32 ~L~~ai~~Ak~~nmPk~~Ie~AIkr~ 57 (234)
...++-+.|+..|+...+|-++|+.+
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~~ 41 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNTG 41 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhCC
Confidence 36788899999999999999999963
No 88
>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=27.48 E-value=52 Score=31.02 Aligned_cols=34 Identities=15% Similarity=0.107 Sum_probs=15.5
Q ss_pred EEeccccHHHHHHHHHHCCCCeeecccceeecCc
Q 026745 168 VVSTSDNYTDITTKLREAGIPFETDNGSELLPIT 201 (234)
Q Consensus 168 ~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~ 201 (234)
|.|+|..|..-.+.|.+.||.+....-+.++|+|
T Consensus 394 vsc~p~tlard~~~l~~~gy~~~~~~~~DmFP~T 427 (431)
T TIGR00479 394 VSCNPATLARDLEFLCKEGYGITWVQPVDMFPHT 427 (431)
T ss_pred EcCCHHHHHHHHHHHHHCCeeEEEEEEeccCCCC
Confidence 4455555444444454445544332233444544
No 89
>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=27.29 E-value=53 Score=25.89 Aligned_cols=23 Identities=26% Similarity=0.411 Sum_probs=19.9
Q ss_pred hCCCCCCCCHHHHHHHHHHHHcC
Q 026745 22 KGGPNPTSNTVLAAVLEKAKELD 44 (234)
Q Consensus 22 ~GG~DP~~N~~L~~ai~~Ak~~n 44 (234)
.|.+|-+....|+.||.+||.+|
T Consensus 76 TGD~DIDhDqaLa~aI~eAk~q~ 98 (114)
T PF05902_consen 76 TGDADIDHDQALAQAIKEAKEQH 98 (114)
T ss_pred ecCCCcchHHHHHHHHHHHHHhC
Confidence 46788888999999999999865
No 90
>KOG2121 consensus Predicted metal-dependent hydrolase (beta-lactamase superfamily) [General function prediction only]
Probab=27.27 E-value=27 Score=35.67 Aligned_cols=54 Identities=28% Similarity=0.303 Sum_probs=38.8
Q ss_pred HHHHHHcCCCHHHHHHHHHHhccCCccceeEEEE-EEEec---CCcEEEEEEecCCch
Q 026745 37 LEKAKELDVPKDIVERNIKRASEKGQEAFIEKVY-EVYGY---GGVSIVVEVLTDKIT 90 (234)
Q Consensus 37 i~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~y-E~~gP---gGvaiIVe~~TdN~n 90 (234)
+++|++.|+|+--+-+.+++|+.-.-..-.-.++ |.+|| |-+.+|++|-+++.-
T Consensus 223 ~~kA~~lGvp~Gp~~~~L~~G~~vt~~~g~i~~~~ev~gp~~~~~~f~il~cp~e~~l 280 (746)
T KOG2121|consen 223 VEKAKELGVPKGPLIGKLKSGESVTLDDGTIVVPSEVVGPSRPGASFLILDCPDESYL 280 (746)
T ss_pred HHHHHHhCCCCCcchhhhcCCCceeccCCcEEehhhhcCCCCCccEEEEecCCcHHHH
Confidence 6788999999999999999886421111122344 88887 568899999887643
No 91
>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=27.00 E-value=1.9e+02 Score=19.13 Aligned_cols=24 Identities=13% Similarity=0.207 Sum_probs=21.4
Q ss_pred ecCCchhhHHHHHHHHhhcCcccc
Q 026745 85 LTDKITRSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 85 ~TdN~nRt~~~vr~~~~K~gg~l~ 108 (234)
...+....++.+..+|.++|.++.
T Consensus 5 ~~~d~~G~l~~i~~~l~~~~inI~ 28 (73)
T cd04902 5 RNTDRPGVIGKVGTILGEAGINIA 28 (73)
T ss_pred EeCCCCCHHHHHHHHHHHcCcChh
Confidence 667888999999999999999885
No 92
>COG0347 GlnK Nitrogen regulatory protein PII [Amino acid transport and metabolism]
Probab=26.98 E-value=72 Score=25.06 Aligned_cols=57 Identities=21% Similarity=0.321 Sum_probs=37.9
Q ss_pred eEEEEeccccHHHHHHHHHHCCCCeeecc--------------------cceeecCccccc--CHHHHH-HHHHHHHHHc
Q 026745 165 YYKVVSTSDNYTDITTKLREAGIPFETDN--------------------GSELLPITTIEV--DDEAME-LNKELIAKLL 221 (234)
Q Consensus 165 ~~~~~~~p~~~~~v~~~L~~~g~~i~~~~--------------------~~~~iP~~~V~l--~~e~~~-~~~~li~~Le 221 (234)
.++.+..|..|..|+++|++.|+.-.... ...|+|+..+++ +++..+ .++.+...++
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 47789999999999999999887521000 224578877666 666544 4555555555
No 93
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=26.29 E-value=74 Score=24.47 Aligned_cols=27 Identities=19% Similarity=0.394 Sum_probs=17.6
Q ss_pred hhhHHHHhhCCCCCCCCHHHHHHHHHHHHcCC
Q 026745 14 KSYLRNVKKGGPNPTSNTVLAAVLEKAKELDV 45 (234)
Q Consensus 14 keI~~Avk~GG~DP~~N~~L~~ai~~Ak~~nm 45 (234)
--+..|-+.| .||++.+++.-+|+.|+
T Consensus 64 e~LYkaLS~~-----GNPtf~Til~V~kAlG~ 90 (100)
T COG3636 64 EGLYKALSPG-----GNPTFDTILAVLKALGL 90 (100)
T ss_pred HHHHHHhCCC-----CCCcHHHHHHHHHHcCc
Confidence 3444444433 47788888888887776
No 94
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=26.12 E-value=87 Score=21.97 Aligned_cols=30 Identities=30% Similarity=0.417 Sum_probs=24.5
Q ss_pred EEEEEecCCchhhHHHHHHHHhhcCccccC
Q 026745 80 IVVEVLTDKITRSVAAVREVVKDCGGKMAD 109 (234)
Q Consensus 80 iIVe~~TdN~nRt~~~vr~~~~K~gg~l~~ 109 (234)
+||-+.-.++...++.|-.++.++||++.+
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d 32 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIED 32 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEE
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEE
Confidence 688888899999999999999999999874
No 95
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=26.10 E-value=1.5e+02 Score=22.53 Aligned_cols=62 Identities=21% Similarity=0.189 Sum_probs=41.8
Q ss_pred eEEEEeccccHHHHHHHHHHC-CCCeeecccceeecCcccccCHHHHHHHHHHHHHHccCCCccee
Q 026745 165 YYKVVSTSDNYTDITTKLREA-GIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAV 229 (234)
Q Consensus 165 ~~~~~~~p~~~~~v~~~L~~~-g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~Lee~dDV~~V 229 (234)
...+-|-|..+.+|+.+|... |.+|.. ++-+ -+--|=+..+..+.+..-++.++.+|.|.+|
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 356789999999999999985 555532 2210 1223444555566677788888899988775
No 96
>PF11588 DUF3243: Protein of unknown function (DUF3243); InterPro: IPR021637 This family of proteins with unknown function includes uncharacterised proteins ymfJ and yflH. The family appears to be restricted to Firmicutes.; PDB: 3D0W_B.
Probab=25.94 E-value=23 Score=26.29 Aligned_cols=26 Identities=15% Similarity=0.279 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHh
Q 026745 32 VLAAVLEKAKELDVPKDIVERNIKRA 57 (234)
Q Consensus 32 ~L~~ai~~Ak~~nmPk~~Ie~AIkr~ 57 (234)
-|...+..|++.||+.++|.....+-
T Consensus 13 ~Lg~~v~~ae~~Gms~e~i~~~A~~i 38 (81)
T PF11588_consen 13 FLGDRVEQAEKLGMSEETIANLAYQI 38 (81)
T ss_dssp HHHHHHHHHHHHHHHTT----HHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 48899999999999999999877654
No 97
>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=25.92 E-value=4.9e+02 Score=23.38 Aligned_cols=95 Identities=17% Similarity=0.197 Sum_probs=59.5
Q ss_pred CCcEEEEEEecCCchhhHHHHHHHHhh-cCccccCCcceeeecc-eeEEEEEeCCCCCHHHHHHHHHHCCCcccccCCCC
Q 026745 76 GGVSIVVEVLTDKITRSVAAVREVVKD-CGGKMADPGSVMFKFR-RARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVN 153 (234)
Q Consensus 76 gGvaiIVe~~TdN~nRt~~~vr~~~~K-~gg~l~~~gsv~~~F~-~~g~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~~ 153 (234)
|=-+|++++-.++.+.....++..|.. .+-.++-..++.+.=+ .+-.|.+++.+..+.++++ ++..|.-+.+
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 444566677777656788999999999 7777753333333312 2334566666667777776 4666654432
Q ss_pred CCCCccccCCceEEEEeccccHHHHHHHHHHCCCCee
Q 026745 154 EDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFE 190 (234)
Q Consensus 154 ed~~~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i~ 190 (234)
...++|+..++..+ .++.|+.+.
T Consensus 114 -----------i~~visn~~~~~~~---A~~~gIp~~ 136 (280)
T TIGR00655 114 -----------IALVISNHEDLRSL---VERFGIPFH 136 (280)
T ss_pred -----------EEEEEEcChhHHHH---HHHhCCCEE
Confidence 24467888777653 456787764
No 98
>PF14501 HATPase_c_5: GHKL domain
Probab=25.54 E-value=2.7e+02 Score=20.23 Aligned_cols=59 Identities=15% Similarity=0.302 Sum_probs=33.0
Q ss_pred HHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCCch--------------hhHHHHHHHHhhcCcccc
Q 026745 49 IVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKIT--------------RSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 49 ~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGvaiIVe~~TdN~n--------------Rt~~~vr~~~~K~gg~l~ 108 (234)
.+++||+-+.......+..+.+.-.. +-+.+.|+=-++... ==+..|+.+++|.+|++.
T Consensus 13 lldNAiea~~~~~~~~~I~i~~~~~~-~~~~i~i~N~~~~~~~~~~~~~~~~~~~G~GL~~v~~i~~~y~g~~~ 85 (100)
T PF14501_consen 13 LLDNAIEACKKYEDKRFISISIREEN-GFLVIIIENSCEKEIEKLESSSSKKKGHGIGLKNVKKILEKYNGSLS 85 (100)
T ss_pred HHHHHHHHHHhcCCCcEEEEEEEecC-CEEEEEEEECCCCccccccccccCCCCCCcCHHHHHHHHHHCCCEEE
Confidence 46778876554332445555443332 445555544443321 135789999999988763
No 99
>COG3453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.43 E-value=2e+02 Score=23.17 Aligned_cols=41 Identities=15% Similarity=0.359 Sum_probs=31.3
Q ss_pred cHHHHHHHHHHCCCCeeecccceeecCcccccCHHHHHHHHHHHHHH
Q 026745 174 NYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKL 220 (234)
Q Consensus 174 ~~~~v~~~L~~~g~~i~~~~~~~~iP~~~V~l~~e~~~~~~~li~~L 220 (234)
.+.+++.+.++.|+.+ .|+|.+.-.+++++.+.+...++.+
T Consensus 46 ~~~~i~~aa~~aGl~y------~~iPV~~~~iT~~dV~~f~~Al~ea 86 (130)
T COG3453 46 GFAAIAAAAEAAGLTY------THIPVTGGGITEADVEAFQRALDEA 86 (130)
T ss_pred ChHHHHHHHHhcCCce------EEeecCCCCCCHHHHHHHHHHHHHh
Confidence 5889999999999865 4689999899988766555555444
No 100
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=25.37 E-value=97 Score=26.06 Aligned_cols=60 Identities=18% Similarity=0.148 Sum_probs=39.7
Q ss_pred eccccHHHHHHHHHHCCCCeeecccceeecC-----cccccCHHHHHHHHHHHHHHccCCCcceeec
Q 026745 170 STSDNYTDITTKLREAGIPFETDNGSELLPI-----TTIEVDDEAMELNKELIAKLLELDDVDAVYT 231 (234)
Q Consensus 170 ~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~-----~~V~l~~e~~~~~~~li~~Lee~dDV~~Vy~ 231 (234)
=.|--+..+...|...||++.+- ...-.+. -++.++..+.. ++.|.+.|+.+.||.+|..
T Consensus 11 n~PGVL~RIt~lFsrRg~NIesL-sv~~t~~~~~sr~TIvv~~~~~~-ieqL~kQL~KLidVl~V~~ 75 (174)
T CHL00100 11 DESGVLTRIAGLFARRGFNIESL-AVGPAEQKGISRITMVVPGDDRT-IEQLTKQLYKLVNILKVQD 75 (174)
T ss_pred CcCCHHHHHHHHHHhCCCCeeEE-EeeEcCCCCccEEEEEEECCHHH-HHHHHHHHHHHhHhhEEEe
Confidence 35667899999999999999742 2322112 12334432222 6788889999999888865
No 101
>cd04927 ACT_ACR-like_2 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). 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 (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.97 E-value=87 Score=22.13 Aligned_cols=29 Identities=10% Similarity=0.162 Sum_probs=26.7
Q ss_pred EEEEEecCCchhhHHHHHHHHhhcCcccc
Q 026745 80 IVVEVLTDKITRSVAAVREVVKDCGGKMA 108 (234)
Q Consensus 80 iIVe~~TdN~nRt~~~vr~~~~K~gg~l~ 108 (234)
+++|+.|.++.+..+.+-.+|..+|.++.
T Consensus 1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~ 29 (76)
T cd04927 1 FLLKLFCSDRKGLLHDVTEVLYELELTIE 29 (76)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHCCCeEE
Confidence 47899999999999999999999999874
No 102
>PRK03094 hypothetical protein; Provisional
Probab=24.83 E-value=59 Score=24.04 Aligned_cols=18 Identities=22% Similarity=0.433 Sum_probs=16.1
Q ss_pred ccHHHHHHHHHHCCCCee
Q 026745 173 DNYTDITTKLREAGIPFE 190 (234)
Q Consensus 173 ~~~~~v~~~L~~~g~~i~ 190 (234)
+.|..|+..|+++||++.
T Consensus 8 ~~Ls~i~~~L~~~GYeVv 25 (80)
T PRK03094 8 QSLTDVQQALKQKGYEVV 25 (80)
T ss_pred cCcHHHHHHHHHCCCEEE
Confidence 578899999999999985
No 103
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=24.77 E-value=4.2e+02 Score=22.22 Aligned_cols=129 Identities=12% Similarity=0.048 Sum_probs=73.8
Q ss_pred EEEEecCCchhhHHHHHHHHhhcCccccCCcceee----ecceeEEEEEeCCCCCHHHHH---HHHHH-CCCcccccCCC
Q 026745 81 VVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMF----KFRRARVVNIKFTDADKDQLL---DIALD-AGAEDVIEPPV 152 (234)
Q Consensus 81 IVe~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~----~F~~~g~i~~~~~~~~~d~~~---e~AIE-~GAeDv~~~~~ 152 (234)
.+.++..|+...+..|-.+|++.|=++- .=++.- ...+. .|.++......+++. +.-++ .-++++...
T Consensus 4 ~isvlv~n~PGVL~RIt~lFsrRg~NIe-sLsv~~t~~~~~sr~-TIvv~~~~~~ieqL~kQL~KLidVl~V~~~~~~-- 79 (174)
T CHL00100 4 TLSVLVEDESGVLTRIAGLFARRGFNIE-SLAVGPAEQKGISRI-TMVVPGDDRTIEQLTKQLYKLVNILKVQDITNI-- 79 (174)
T ss_pred EEEEEEeCcCCHHHHHHHHHHhCCCCee-EEEeeEcCCCCccEE-EEEEECCHHHHHHHHHHHHHHhHhhEEEecCCc--
Confidence 5788999999999999999999998653 111211 11121 233443211133322 22222 344444321
Q ss_pred CCCCCccccCCceEEEEeccccHHHHHHHHHHCCCCeeecccceeecC-cccccCHHHHHHHHHHHHHHccC
Q 026745 153 NEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPI-TTIEVDDEAMELNKELIAKLLEL 223 (234)
Q Consensus 153 ~ed~~~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~-~~V~l~~e~~~~~~~li~~Lee~ 223 (234)
+-. .++=-.+.|.|++.+-..+..-...++-.+... -|. -.++++... +++..|++.|+..
T Consensus 80 ---~~v-~rEl~LiKv~~~~~~r~ei~~~~~~f~a~ivdv-----~~~~~~ie~tG~~-~ki~a~~~~l~~~ 141 (174)
T CHL00100 80 ---PCV-ERELMLIKINVNSQTRPEILEIAQIFRAKVVDL-----SEESLILEVTGDP-GKIVAIEQLLEKF 141 (174)
T ss_pred ---cce-eeEEEEEEEecCCcCHHHHHHHHHHhCCEEEEe-----cCCEEEEEEcCCH-HHHHHHHHHhhhc
Confidence 111 122346788898888888888887776666432 233 357776533 4567788877765
No 104
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=24.76 E-value=3e+02 Score=26.01 Aligned_cols=51 Identities=20% Similarity=0.298 Sum_probs=34.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCch
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKIT 90 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~n 90 (234)
+..|+..|...++|.+.|.++|+..++-.. ++|..+ .+|+.+|.+. -.|+.
T Consensus 284 ~~aA~a~~~~lgv~~~~i~~~l~~f~~~~~------R~e~~~~~~g~~~i~D~-aHnp~ 335 (461)
T PRK00421 284 ALAAIAVALELGIDDEAIREALATFKGVKR------RFEEKGEVGGVVLIDDY-AHHPT 335 (461)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCc------ccEEEEecCCcEEEEeC-CCCHH
Confidence 456777888899999999999997654221 333333 3588888883 33443
No 105
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=24.48 E-value=97 Score=20.84 Aligned_cols=28 Identities=14% Similarity=0.385 Sum_probs=20.9
Q ss_pred CcEEEEEEecCCchhhHHHHHHHHhhcCccc
Q 026745 77 GVSIVVEVLTDKITRSVAAVREVVKDCGGKM 107 (234)
Q Consensus 77 GvaiIVe~~TdN~nRt~~~vr~~~~K~gg~l 107 (234)
|+.+.+ +....-....++.+++++||++
T Consensus 8 g~~f~i---~~~~~~~~~~l~~~i~~~GG~v 35 (78)
T PF00533_consen 8 GCTFCI---SGFDSDEREELEQLIKKHGGTV 35 (78)
T ss_dssp TEEEEE---SSTSSSHHHHHHHHHHHTTEEE
T ss_pred CEEEEE---ccCCCCCHHHHHHHHHHcCCEE
Confidence 444444 6666777778899999999987
No 106
>COG2605 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]
Probab=24.16 E-value=3.8e+02 Score=24.86 Aligned_cols=79 Identities=15% Similarity=0.176 Sum_probs=44.9
Q ss_pred HHHHHHHHHH------HHcCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCCchhhHHHHHHHHhhcC
Q 026745 31 TVLAAVLEKA------KELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCG 104 (234)
Q Consensus 31 ~~L~~ai~~A------k~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGvaiIVe~~TdN~nRt~~~vr~~~~K~g 104 (234)
+.++.+|.+. -...++.+-|+|.++.|..++.-.-+ .-|-|-|| ++++-|--.++++ |...|.++.
T Consensus 243 ~~f~~~l~~gW~~KK~ls~~ISN~~IDriy~~A~~~GA~~gK---l~GaG~gG-Fllf~~~p~k~~~----l~r~l~~~~ 314 (333)
T COG2605 243 PEFGQILDRGWEAKKKLSSRISNDAIDRIYELALKNGAYGGK---LSGAGGGG-FLLFFCDPSKRNE----LARALEKEQ 314 (333)
T ss_pred HHHHHHHHhHHHhhhhhccCcCcHHHHHHHHHHHhcCchhce---eeccCCcc-EEEEEeCccchHH----HHHHHHHhc
Confidence 3566666543 23578899999999988765542111 22444333 4555665555554 344555665
Q ss_pred ccccCCcceeeecceeEE
Q 026745 105 GKMADPGSVMFKFRRARV 122 (234)
Q Consensus 105 g~l~~~gsv~~~F~~~g~ 122 (234)
|-+ +.|.|+..|.
T Consensus 315 ~~~-----~~~~Fd~~Gs 327 (333)
T COG2605 315 GFV-----VDTSFDKEGS 327 (333)
T ss_pred CCe-----EEEEecCCCe
Confidence 553 4466665553
No 107
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=23.40 E-value=1.8e+02 Score=27.59 Aligned_cols=39 Identities=21% Similarity=0.203 Sum_probs=30.9
Q ss_pred ceEEEEeccccHHHHHHHHHHCCCCeeecccceeecCcc
Q 026745 164 RYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITT 202 (234)
Q Consensus 164 ~~~~~~~~p~~~~~v~~~L~~~g~~i~~~~~~~~iP~~~ 202 (234)
..+-|.|+|..|..=...|.+.||.+....-+.++|+|+
T Consensus 394 ~ivyvSCnp~tlaRDl~~L~~~gY~l~~i~~~DmFP~T~ 432 (443)
T PRK13168 394 RIVYVSCNPATLARDAGVLVEAGYRLKRAGMLDMFPHTG 432 (443)
T ss_pred eEEEEEeChHHhhccHHHHhhCCcEEEEEEEeccCCCCC
Confidence 456689999999887778888899987655677889974
No 108
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.26 E-value=56 Score=24.90 Aligned_cols=21 Identities=24% Similarity=0.349 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHccCCCccee
Q 026745 209 AMELNKELIAKLLELDDVDAV 229 (234)
Q Consensus 209 ~~~~~~~li~~Lee~dDV~~V 229 (234)
+...+..|++-|++..|||+|
T Consensus 15 eAAaFRrLv~HL~~rsdvQNI 35 (104)
T COG3492 15 EAAAFRRLVEHLQERSDVQNI 35 (104)
T ss_pred HHHHHHHHHHHHHHhcccchh
Confidence 355788999999999999987
No 109
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=22.78 E-value=77 Score=23.72 Aligned_cols=34 Identities=21% Similarity=0.323 Sum_probs=26.8
Q ss_pred hhCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHH
Q 026745 21 KKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIK 55 (234)
Q Consensus 21 k~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIk 55 (234)
|.||. +..--.|..+|+-|-+.+||-+.|-+.++
T Consensus 32 ~~Gg~-~~~~~ai~rliS~~Lr~G~~~~~ii~~L~ 65 (95)
T PF12637_consen 32 KAGGC-SGNLEAIARLISLALRSGVPPEEIIDQLR 65 (95)
T ss_pred cCCCc-hHHHHHHHHHHHHHHHcCCCHHHHHHHhc
Confidence 35665 55556799999999999999887777776
No 110
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=22.08 E-value=5.8e+02 Score=22.89 Aligned_cols=93 Identities=19% Similarity=0.207 Sum_probs=55.6
Q ss_pred cEEEEEEecCCchhhHHHHHHHHhhcCccccCCcceeeeccee-EEEEEeCCCCCHHHHHHHHHHCCCcccccCCCCCCC
Q 026745 78 VSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRA-RVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDD 156 (234)
Q Consensus 78 vaiIVe~~TdN~nRt~~~vr~~~~K~gg~l~~~gsv~~~F~~~-g~i~~~~~~~~~d~~~e~AIE~GAeDv~~~~~~ed~ 156 (234)
..+++++-.+........|+..|...+..++-..++...-.++ -.|..++.+..+..+++ +++.|--..
T Consensus 48 F~m~i~v~~~~~~~~~~~L~~~L~~l~~~l~l~i~l~~~~~~~ri~vl~Sg~gsnl~al~~-~~~~~~~~~--------- 117 (286)
T PRK06027 48 FFMRVEFEGDGLIFNLETLRADFAALAEEFEMDWRLLDSAERKRVVILVSKEDHCLGDLLW-RWRSGELPV--------- 117 (286)
T ss_pred EEEEEEEEeCCCCCCHHHHHHHHHHHHHHhCCEEEEcccccCcEEEEEEcCCCCCHHHHHH-HHHcCCCCc---------
Confidence 4455666664434458888888888887765333333322333 34556666677887776 456553322
Q ss_pred CccccCCceEEEEeccccHHHHHHHHHHCCCCee
Q 026745 157 TDEDRAERYYKVVSTSDNYTDITTKLREAGIPFE 190 (234)
Q Consensus 157 ~~ed~~~~~~~~~~~p~~~~~v~~~L~~~g~~i~ 190 (234)
....++|++.+...+ .++.|+.+.
T Consensus 118 -------~i~~visn~~~~~~l---A~~~gIp~~ 141 (286)
T PRK06027 118 -------EIAAVISNHDDLRSL---VERFGIPFH 141 (286)
T ss_pred -------EEEEEEEcChhHHHH---HHHhCCCEE
Confidence 134578888877665 556687764
No 111
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=22.00 E-value=63 Score=23.83 Aligned_cols=33 Identities=12% Similarity=0.012 Sum_probs=22.8
Q ss_pred cHHHHHHHHHHCCCCeeecccceeecC-cccccCH
Q 026745 174 NYTDITTKLREAGIPFETDNGSELLPI-TTIEVDD 207 (234)
Q Consensus 174 ~~~~v~~~L~~~g~~i~~~~~~~~iP~-~~V~l~~ 207 (234)
-|..|-.+|+++||...+. -+.|+=. .|.-++.
T Consensus 20 iL~~Vy~AL~EKGYnPinQ-ivGYllSGDPaYIts 53 (79)
T PF06135_consen 20 ILKQVYAALEEKGYNPINQ-IVGYLLSGDPAYITS 53 (79)
T ss_pred HHHHHHHHHHHcCCChHHH-HHhheecCCCccccC
Confidence 4678999999999997653 5677533 4544543
No 112
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=21.94 E-value=2.8e+02 Score=26.07 Aligned_cols=60 Identities=15% Similarity=0.244 Sum_probs=38.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEec-CCcEEEEEEecCCchhhHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGY-GGVSIVVEVLTDKITRSVAAVRE 98 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gP-gGvaiIVe~~TdN~nRt~~~vr~ 98 (234)
+..|+..|...+++.+.|..+|+..++-.. ++|..+- +|+.+|-++--.|..-+..-++.
T Consensus 280 alaAia~a~~lgi~~~~i~~~L~~f~~~~~------R~e~~~~~~~~~~iDDs~~~n~~s~~~al~~ 340 (445)
T PRK04308 280 VMAAVALCEAVGLPREALLEHVKTFQGLPH------RVEKIGEKNGVVFIDDSKGTNVGATAAAIAG 340 (445)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCCCC------ceEEEEeeCCeEEEEcCCCCCHHHHHHHHHh
Confidence 567888889999999999999997654322 3333321 46666667644555444444443
No 113
>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=21.80 E-value=2.5e+02 Score=27.07 Aligned_cols=59 Identities=15% Similarity=0.144 Sum_probs=39.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVR 97 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr 97 (234)
...|+..|+..++|.+.|.++|+..++... ++|..+ .+|+.+|=++---|+.-+.+-|+
T Consensus 288 alaAla~a~~lGi~~e~i~~~L~~f~~~~g------R~E~v~~~~gv~iIDDS~AhNp~s~~aal~ 347 (488)
T PRK03369 288 ALAAAALARAVGVPAGAIADALASFRVGRH------RAEVVAVADGITYVDDSKATNPHAARASIL 347 (488)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCCCCC------ccEEEEcCCCEEEEECCCCCCHHHHHHHHH
Confidence 456778888999999999999997654221 333332 36775555566666666666665
No 114
>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=21.49 E-value=94 Score=26.67 Aligned_cols=25 Identities=20% Similarity=0.310 Sum_probs=22.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRA 57 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~ 57 (234)
-..+|.-|+..++|++.|+||-+.+
T Consensus 194 ~s~a~~~a~~~g~p~~vi~~A~~~~ 218 (222)
T cd03285 194 QSFGIHVAELANFPKEVIEMAKQKA 218 (222)
T ss_pred CcHHHHHHHHhCcCHHHHHHHHHHH
Confidence 4789999999999999999997754
No 115
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=21.37 E-value=1.6e+02 Score=21.47 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=22.1
Q ss_pred HHHHHHCCCCe---------eeccccee--ecCccc-ccCHHHHHHH
Q 026745 179 TTKLREAGIPF---------ETDNGSEL--LPITTI-EVDDEAMELN 213 (234)
Q Consensus 179 ~~~L~~~g~~i---------~~~~~~~~--iP~~~V-~l~~e~~~~~ 213 (234)
+.+|.+.||.+ +++.+..| +|..+- ++++++++.+
T Consensus 28 raaL~e~G~~~P~~~~i~VvE~t~~~~~lVlP~~P~~~lse~~L~~v 74 (77)
T TIGR03793 28 KEALEREGVQVPAEVEVKVVEESPTVLYLVLPVNPDIELTDEQLDAV 74 (77)
T ss_pred HHHHHHhCCCCCCceEEEEEEcCCCeEEEEecCCCCCCCCHHHHHHh
Confidence 66788888864 22233444 476554 8898887765
No 116
>PF13730 HTH_36: Helix-turn-helix domain
Probab=21.31 E-value=88 Score=20.20 Aligned_cols=28 Identities=43% Similarity=0.640 Sum_probs=19.7
Q ss_pred hCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 026745 22 KGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKR 56 (234)
Q Consensus 22 ~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr 56 (234)
.||.-| ++.+|+. ..|+.+.+|.++|+.
T Consensus 21 ~~~~~p-S~~~la~------~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 21 NGGCFP-SQETLAK------DLGVSRRTVQRAIKE 48 (55)
T ss_pred CCCCCc-CHHHHHH------HHCcCHHHHHHHHHH
Confidence 345555 4555544 459999999999985
No 117
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=21.01 E-value=86 Score=24.10 Aligned_cols=23 Identities=35% Similarity=0.374 Sum_probs=18.7
Q ss_pred HHHHHHcCCCHHHHHHHHHHhcc
Q 026745 37 LEKAKELDVPKDIVERNIKRASE 59 (234)
Q Consensus 37 i~~Ak~~nmPk~~Ie~AIkr~~~ 59 (234)
.+-|++.+.+...+||||..|-.
T Consensus 44 p~IA~k~~TT~s~VERaIR~aI~ 66 (106)
T PF08769_consen 44 PDIAKKYGTTPSRVERAIRHAIE 66 (106)
T ss_dssp HHHHHHTTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 45689999999999999998853
No 118
>PF05423 Mycobact_memb: Mycobacterium membrane protein; InterPro: IPR008693 This family contains several membrane proteins from Mycobacterium species [].
Probab=21.00 E-value=1.4e+02 Score=24.11 Aligned_cols=20 Identities=30% Similarity=0.391 Sum_probs=15.7
Q ss_pred eEEEEEEEecCCcEEEEEEe
Q 026745 66 IEKVYEVYGYGGVSIVVEVL 85 (234)
Q Consensus 66 ~~~~yE~~gPgGvaiIVe~~ 85 (234)
+.++||..||.|...-|.-+
T Consensus 51 k~V~YEV~G~~G~~~~I~Y~ 70 (140)
T PF05423_consen 51 KTVTYEVTGPPGSTATISYL 70 (140)
T ss_pred cEEEEEEEcCCCCeEEEEEE
Confidence 67899999997776666555
No 119
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=20.99 E-value=3.2e+02 Score=28.63 Aligned_cols=60 Identities=22% Similarity=0.229 Sum_probs=42.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe----cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG----YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g----PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|..+|+..++-.. ++|..+ .+|..+|++ .--|+.-..+-++++
T Consensus 312 alaAia~a~~lgi~~~~I~~~L~~~~~~~g------R~e~i~~~~~~~~~~vi~D-yahnP~s~~a~l~~l 375 (958)
T PRK11929 312 LLLVAAALKKLGLPLAQIARALAAVSPVPG------RMERVGPTAGAQGPLVVVD-YAHTPDALAKALTAL 375 (958)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhcCCCCCC------CcEEeccccCCCCCEEEEE-CCCCHHHHHHHHHHH
Confidence 566778888899999999999987643221 444442 368889999 566776655555555
No 120
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=20.91 E-value=1.4e+02 Score=28.88 Aligned_cols=60 Identities=23% Similarity=0.286 Sum_probs=35.9
Q ss_pred HHHHhhCCCCCCCCHHHHHHHHHHHHc---------------CCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcE
Q 026745 17 LRNVKKGGPNPTSNTVLAAVLEKAKEL---------------DVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVS 79 (234)
Q Consensus 17 ~~Avk~GG~DP~~N~~L~~ai~~Ak~~---------------nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGva 79 (234)
...+.-||+|+ +..|+++++.+|.- -+- +-+.+-+++.+.........+...++|++|..
T Consensus 339 L~~~f~GGTD~--~~~l~~al~~~k~~~~~~adiv~ITDg~~~~~-~~~~~~v~e~~k~~~~rl~aV~I~~~~~~~l~ 413 (437)
T COG2425 339 LSYVFGGGTDI--TKALRSALEDLKSRELFKADIVVITDGEDERL-DDFLRKVKELKKRRNARLHAVLIGGYGKPGLM 413 (437)
T ss_pred HhhhcCCCCCh--HHHHHHHHHHhhcccccCCCEEEEeccHhhhh-hHHHHHHHHHHHHhhceEEEEEecCCCCcccc
Confidence 34445688875 89999999999822 222 33344444433333333556788899955543
No 121
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=20.86 E-value=1.3e+02 Score=20.20 Aligned_cols=41 Identities=22% Similarity=0.216 Sum_probs=29.7
Q ss_pred hHHHHhhCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHhcc
Q 026745 16 YLRNVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASE 59 (234)
Q Consensus 16 I~~Avk~GG~DP~~N~~L~~ai~~Ak~~nmPk~~Ie~AIkr~~~ 59 (234)
+..|...|=-| .||=.++=+-|+..||++.++..-|.||..
T Consensus 9 L~~A~~~GYfd---~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 9 LKAAYELGYFD---VPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred HHHHHHcCCCC---CCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 44455554455 346666778899999999999999988753
No 122
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=20.66 E-value=2.9e+02 Score=26.37 Aligned_cols=61 Identities=18% Similarity=0.163 Sum_probs=40.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhccCCccceeEEEEEEEe-cCCcEEEEEEecCCchhhHHHHHHH
Q 026745 33 LAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYG-YGGVSIVVEVLTDKITRSVAAVREV 99 (234)
Q Consensus 33 L~~ai~~Ak~~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~g-PgGvaiIVe~~TdN~nRt~~~vr~~ 99 (234)
+..|+..|...++|.+.|.++|+.....+. +.|..+ .+|+.+|-++...|+.-+.+-++.+
T Consensus 294 a~aA~a~~~~lgi~~~~i~~~l~~~~~~~~------R~e~~~~~~~~~iiDdsyahNp~s~~~~l~~l 355 (473)
T PRK00141 294 ALAAAAVARSQGVAPEAIARALSSFEVAGH------RGQVVAEHGGVTWIDNSKATNPHAADAALAGH 355 (473)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhhCCCCCC------ceEEEEEeCCEEEEEcCCCCCHHHHHHHHHhc
Confidence 567778888999999999999997764332 223232 2456444445577877777766653
No 123
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=20.32 E-value=1.3e+02 Score=20.43 Aligned_cols=53 Identities=21% Similarity=0.206 Sum_probs=29.8
Q ss_pred EeccccHHHHHHHHHHCCCCeeec----ccc-eeecC---cccccCHHHHHHHHHHHHHHc
Q 026745 169 VSTSDNYTDITTKLREAGIPFETD----NGS-ELLPI---TTIEVDDEAMELNKELIAKLL 221 (234)
Q Consensus 169 ~~~p~~~~~v~~~L~~~g~~i~~~----~~~-~~iP~---~~V~l~~e~~~~~~~li~~Le 221 (234)
..++-...-++..|++.|+..... +.. .+.|. ..|-+.+++.++...+++.++
T Consensus 6 ~~~~~ea~~i~~~L~~~gI~~~v~~~~~~~~~g~~g~~~~~~v~V~~~d~~~A~~il~~~~ 66 (67)
T PF09413_consen 6 AGDPIEAELIKGLLEENGIPAFVKNEHMSGYAGEPGTGGQVEVYVPEEDYERAREILEEFE 66 (67)
T ss_dssp E--HHHHHHHHHHHHHTT--EE--S----SS---S--SSSEEEEEEGGGHHHHHHHHHHTT
T ss_pred cCCHHHHHHHHHHHHhCCCcEEEECCccchhhcccCccCceEEEECHHHHHHHHHHHHHhc
Confidence 445556777999999999985221 111 22344 335557788888888888765
No 124
>PF00675 Peptidase_M16: Insulinase (Peptidase family M16) This is family M16 in the peptidase classification. ; InterPro: IPR011765 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. The majority of the sequences in this entry are metallopeptidases and non-peptidase homologs belong to MEROPS peptidase family M16 (clan ME), subfamilies M16A, M16B and M16C; they include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The proteins classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3P7L_A 3P7O_A 3TUV_A 3GO9_A 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B ....
Probab=20.23 E-value=3.3e+02 Score=20.96 Aligned_cols=77 Identities=16% Similarity=0.236 Sum_probs=55.8
Q ss_pred HHHhhCC-CCCCCCHHHHHHHHHHHH---cCCCHHHHHHHHHHhccCCccceeEEEEEEEecCCcEEEEEEecCCchhhH
Q 026745 18 RNVKKGG-PNPTSNTVLAAVLEKAKE---LDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSV 93 (234)
Q Consensus 18 ~Avk~GG-~DP~~N~~L~~ai~~Ak~---~nmPk~~Ie~AIkr~~~~~~~~~~~~~yE~~gPgGvaiIVe~~TdN~nRt~ 93 (234)
+.++.|. -||..++-|+.+++..-- .+.|...|.+.+.+-.+ .+ .-..+...+.+-+.|++++...++
T Consensus 17 l~~~~Gs~~e~~~~~G~a~ll~~l~~~gs~~~~~~~l~~~l~~~G~----~~----~~~t~~d~t~~~~~~~~~~~~~~l 88 (149)
T PF00675_consen 17 LVFKAGSRYEPPGKPGLAHLLEHLLFRGSKKYSSDELQEELESLGA----SF----NASTSRDSTSYSASVLSEDLEKAL 88 (149)
T ss_dssp EEES-SGGGSCTTTTTHHHHHHHHTTSBBSSSBHHHHHHHHHHTTC----EE----EEEEESSEEEEEEEEEGGGHHHHH
T ss_pred EEEeeccCCCCCCCCchhhhhhhhcccccchhhhhhhHHHhhhhcc----cc----ceEecccceEEEEEEecccchhHH
Confidence 3344443 489999999999987543 45888888888886321 11 123456778899999999999999
Q ss_pred HHHHHHHhh
Q 026745 94 AAVREVVKD 102 (234)
Q Consensus 94 ~~vr~~~~K 102 (234)
..+..++..
T Consensus 89 ~~l~~~~~~ 97 (149)
T PF00675_consen 89 ELLADMLFN 97 (149)
T ss_dssp HHHHHHHHS
T ss_pred HHHHHHHhC
Confidence 999888876
Done!