Query psy10746
Match_columns 59
No_of_seqs 109 out of 160
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 17:29:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10746.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10746hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00292 PAX: 'Paired box' dom 99.8 1.6E-20 3.5E-25 124.4 2.0 38 16-53 1-38 (125)
2 KOG3862|consensus 99.8 2.9E-20 6.2E-25 139.4 3.2 43 11-53 4-46 (327)
3 KOG3517|consensus 99.7 3.4E-18 7.3E-23 128.4 2.7 40 14-53 2-41 (334)
4 KOG0849|consensus 99.1 7.4E-12 1.6E-16 92.1 0.5 36 18-53 1-36 (354)
5 cd00131 PAX Paired Box domain 99.1 2.7E-11 5.9E-16 77.9 2.9 37 16-52 1-37 (128)
6 smart00351 PAX Paired Box doma 98.9 1.6E-09 3.4E-14 69.0 2.9 36 16-51 1-36 (125)
7 PLN00061 photosystem II protei 88.7 0.16 3.4E-06 35.5 0.4 28 17-44 115-145 (150)
8 cd03482 MutL_Trans_MutL MutL_T 87.2 0.38 8.2E-06 30.3 1.5 31 25-55 47-77 (123)
9 PF08069 Ribosomal_S13_N: Ribo 83.6 0.28 6E-06 29.5 -0.4 20 34-53 30-49 (60)
10 TIGR03044 PS_II_psb27 photosys 83.2 0.59 1.3E-05 32.0 1.0 27 17-43 95-123 (135)
11 PF01119 DNA_mis_repair: DNA m 83.1 0.86 1.9E-05 28.1 1.7 30 26-55 44-73 (119)
12 PF13326 PSII_Pbs27: Photosyst 82.2 0.39 8.5E-06 32.3 -0.1 27 17-43 107-136 (145)
13 cd00782 MutL_Trans MutL_Trans: 82.0 0.91 2E-05 27.5 1.4 26 26-51 48-73 (122)
14 cd03483 MutL_Trans_MLH1 MutL_T 79.9 1.2 2.7E-05 28.1 1.6 29 26-54 52-80 (127)
15 KOG0400|consensus 78.7 1.6 3.4E-05 30.7 1.9 20 34-53 30-49 (151)
16 PF12759 HTH_Tnp_IS1: InsA C-t 78.4 1.6 3.4E-05 25.3 1.5 14 36-49 9-22 (46)
17 PRK10339 DNA-binding transcrip 76.0 3.5 7.6E-05 27.8 2.9 26 28-53 22-51 (327)
18 PRK12794 flaF flagellar biosyn 75.7 2.7 5.8E-05 27.6 2.3 18 29-46 68-85 (122)
19 PRK08561 rps15p 30S ribosomal 75.5 2 4.4E-05 29.9 1.7 20 34-53 30-49 (151)
20 PF07309 FlaF: Flagellar prote 73.9 3.3 7E-05 26.6 2.3 18 29-46 65-82 (113)
21 PRK12793 flaF flagellar biosyn 72.2 3.4 7.4E-05 27.0 2.1 18 29-46 66-83 (115)
22 PLN00064 photosystem II protei 70.0 2.2 4.8E-05 30.3 0.9 27 17-43 124-153 (166)
23 TIGR02417 fruct_sucro_rep D-fr 70.0 6 0.00013 26.5 2.9 25 28-52 20-49 (327)
24 PTZ00072 40S ribosomal protein 69.9 3.3 7.2E-05 28.9 1.7 20 34-53 27-46 (148)
25 cd03485 MutL_Trans_hPMS_1_like 69.8 2.9 6.3E-05 26.3 1.4 19 26-44 53-73 (132)
26 cd03486 MutL_Trans_MLH3 MutL_T 69.2 3.2 6.9E-05 26.6 1.4 23 26-48 47-69 (141)
27 cd00329 TopoII_MutL_Trans MutL 66.7 3.3 7.1E-05 23.4 1.0 21 26-46 48-69 (107)
28 cd03484 MutL_Trans_hPMS_2_like 65.7 4.7 0.0001 26.0 1.7 24 25-48 67-90 (142)
29 PRK11303 DNA-binding transcrip 64.5 6.5 0.00014 26.2 2.2 25 28-52 21-50 (328)
30 TIGR00585 mutl DNA mismatch re 62.0 5.4 0.00012 28.3 1.6 31 25-55 256-286 (312)
31 PRK10703 DNA-binding transcrip 60.6 11 0.00024 25.3 2.9 24 29-52 23-48 (341)
32 cd00569 HTH_Hin_like Helix-tur 60.0 14 0.00029 15.7 2.7 17 33-49 6-22 (42)
33 PRK10727 DNA-binding transcrip 59.9 12 0.00027 25.3 3.0 25 28-52 22-48 (343)
34 PF00356 LacI: Bacterial regul 58.3 14 0.0003 20.4 2.6 24 28-51 20-45 (46)
35 PRK10423 transcriptional repre 55.6 16 0.00035 24.2 2.9 25 28-52 19-45 (327)
36 cd01392 HTH_LacI Helix-turn-he 52.5 21 0.00046 18.3 2.6 26 27-52 17-44 (52)
37 PF00498 FHA: FHA domain; Int 52.2 3.2 6.9E-05 22.5 -0.7 14 22-35 40-53 (68)
38 COG0103 RpsI Ribosomal protein 50.0 9.4 0.0002 26.0 1.2 21 23-43 25-50 (130)
39 PF06440 DNA_pol3_theta: DNA p 49.6 7.3 0.00016 24.7 0.6 18 33-50 8-26 (75)
40 PF06543 Lac_bphage_repr: Lact 49.1 13 0.00028 22.0 1.5 16 27-42 25-40 (49)
41 PF13911 AhpC-TSA_2: AhpC/TSA 48.7 6.8 0.00015 23.3 0.3 13 17-29 89-101 (115)
42 PF13279 4HBT_2: Thioesterase- 47.8 12 0.00025 21.9 1.2 11 31-41 111-121 (121)
43 PRK00095 mutL DNA mismatch rep 46.8 13 0.00029 29.3 1.7 31 25-55 250-280 (617)
44 KOG0634|consensus 46.0 18 0.00038 29.4 2.3 20 28-47 216-235 (472)
45 PF10752 DUF2533: Protein of u 45.9 23 0.00051 22.8 2.5 30 27-56 39-72 (84)
46 smart00240 FHA Forkhead associ 45.0 7 0.00015 19.9 -0.0 11 23-33 42-52 (52)
47 cd08051 gp6_gp15_like Head-Tai 44.8 22 0.00047 22.0 2.1 24 25-48 35-60 (94)
48 PRK03170 dihydrodipicolinate s 44.8 19 0.00042 25.0 2.1 27 24-50 37-68 (292)
49 PRK09526 lacI lac repressor; R 43.9 23 0.00051 23.7 2.3 24 29-52 27-52 (342)
50 PF14377 DUF4414: Domain of un 42.8 19 0.00041 22.4 1.7 13 33-45 9-21 (108)
51 PF14304 CSTF_C: Transcription 42.6 16 0.00036 21.0 1.3 15 32-46 24-38 (46)
52 PLN02512 acetylglutamate kinas 42.3 19 0.00042 25.9 1.8 36 16-51 47-82 (309)
53 PF04806 EspF: EspF protein re 42.1 23 0.00049 20.8 1.8 19 30-48 29-47 (47)
54 cd00950 DHDPS Dihydrodipicolin 41.9 22 0.00049 24.4 2.1 28 23-50 35-67 (284)
55 cd02135 Arsenite_oxidase Nitro 41.6 33 0.00072 20.8 2.6 26 26-54 12-37 (160)
56 TIGR01481 ccpA catabolite cont 40.1 30 0.00064 23.1 2.4 25 28-52 22-48 (329)
57 COG1244 Predicted Fe-S oxidore 39.6 22 0.00048 27.9 1.9 22 24-45 109-130 (358)
58 CHL00079 rps9 ribosomal protei 39.3 20 0.00043 23.9 1.4 12 24-35 25-36 (130)
59 PF11011 DUF2849: Protein of u 39.1 20 0.00043 22.6 1.4 15 28-42 65-79 (90)
60 PF02796 HTH_7: Helix-turn-hel 38.5 22 0.00047 18.8 1.3 17 34-50 7-23 (45)
61 PRK10014 DNA-binding transcrip 37.7 46 0.00099 22.3 3.0 24 29-52 28-53 (342)
62 PF09372 PRANC: PRANC domain; 36.8 25 0.00053 21.0 1.5 13 32-44 74-86 (97)
63 PRK14987 gluconate operon tran 36.6 37 0.0008 22.8 2.4 24 29-52 27-52 (331)
64 TIGR03553 F420_FbiB_CTERM F420 36.5 42 0.0009 21.5 2.6 26 26-54 11-36 (194)
65 TIGR00375 conserved hypothetic 36.4 34 0.00073 26.3 2.4 38 22-59 257-297 (374)
66 COG1765 Predicted redox protei 36.1 35 0.00076 22.0 2.2 19 28-47 96-114 (137)
67 PF01022 HTH_5: Bacterial regu 36.1 31 0.00067 18.1 1.6 14 35-48 1-14 (47)
68 PF01479 S4: S4 domain; Inter 35.9 10 0.00022 19.7 -0.3 13 22-34 24-36 (48)
69 COG1609 PurR Transcriptional r 35.8 35 0.00075 24.3 2.3 25 28-52 21-47 (333)
70 PRK10401 DNA-binding transcrip 35.6 36 0.00079 23.1 2.3 24 29-52 23-48 (346)
71 PF04423 Rad50_zn_hook: Rad50 35.3 21 0.00045 19.6 0.9 18 27-44 24-41 (54)
72 KOG0975|consensus 34.9 26 0.00057 27.6 1.7 22 26-47 277-298 (379)
73 PRK08636 aspartate aminotransf 34.8 37 0.00081 24.2 2.3 20 28-47 187-206 (403)
74 COG1167 ARO8 Transcriptional r 34.8 39 0.00085 25.4 2.5 21 27-47 238-258 (459)
75 PF04664 OGFr_N: Opioid growth 34.5 35 0.00076 24.3 2.1 22 34-55 181-202 (213)
76 PF07460 NUMOD3: NUMOD3 motif 34.4 15 0.00033 19.4 0.2 14 29-42 23-36 (37)
77 PF13562 NTP_transf_4: Sugar n 34.4 24 0.00051 23.5 1.2 18 26-43 68-85 (156)
78 PF12039 DUF3525: Protein of u 34.3 25 0.00055 28.1 1.5 21 26-46 301-321 (453)
79 cd02062 Nitro_FMN_reductase Pr 34.1 53 0.0011 18.8 2.5 20 29-48 11-30 (122)
80 COG0323 MutL DNA mismatch repa 34.1 32 0.0007 27.7 2.1 26 25-50 255-280 (638)
81 TIGR00674 dapA dihydrodipicoli 33.2 38 0.00081 23.6 2.1 24 24-47 34-62 (285)
82 PRK09492 treR trehalose repres 31.0 52 0.0011 21.8 2.4 24 29-52 26-51 (315)
83 PF02234 CDI: Cyclin-dependent 30.9 17 0.00036 20.5 0.0 9 26-34 34-42 (51)
84 smart00496 IENR2 Intron-encode 30.3 58 0.0012 16.8 2.0 17 30-46 2-18 (26)
85 TIGR03679 arCOG00187 arCOG0018 30.1 55 0.0012 22.4 2.5 32 22-54 147-179 (218)
86 PF02878 PGM_PMM_I: Phosphoglu 30.0 52 0.0011 20.4 2.2 20 28-47 114-133 (137)
87 PRK10969 DNA polymerase III su 29.9 31 0.00067 21.8 1.1 19 32-50 7-26 (75)
88 PF11521 TFIIE-A_C-term: C-ter 29.8 25 0.00054 22.1 0.7 11 26-36 43-53 (86)
89 PF13265 DUF4056: Protein of u 29.5 22 0.00048 26.9 0.5 12 45-56 9-20 (270)
90 PRK00132 rpsI 30S ribosomal pr 28.9 40 0.00086 22.4 1.6 20 24-43 26-50 (130)
91 PLN00210 40S ribosomal protein 27.5 55 0.0012 22.1 2.1 19 24-42 25-47 (141)
92 cd04250 AAK_NAGK-C AAK_NAGK-C: 27.3 47 0.001 23.2 1.8 35 17-51 15-49 (279)
93 PRK11753 DNA-binding transcrip 27.1 55 0.0012 20.6 1.9 19 27-45 2-20 (211)
94 PRK06425 histidinol-phosphate 27.0 70 0.0015 22.2 2.6 20 30-49 136-156 (332)
95 PRK07681 aspartate aminotransf 26.9 63 0.0014 22.9 2.4 18 30-47 180-197 (399)
96 cd00060 FHA Forkhead associate 26.5 21 0.00046 19.7 -0.0 11 25-35 67-77 (102)
97 smart00363 S4 S4 RNA-binding d 26.5 20 0.00042 17.6 -0.2 11 23-33 25-35 (60)
98 TIGR03249 KdgD 5-dehydro-4-deo 26.3 59 0.0013 22.9 2.1 25 24-48 41-70 (296)
99 COG1423 ATP-dependent DNA liga 26.2 51 0.0011 26.2 2.0 16 29-44 178-193 (382)
100 cd03567 VHS_GGA VHS domain fam 26.1 71 0.0015 21.0 2.4 18 29-46 95-112 (139)
101 cd00951 KDGDH 5-dehydro-4-deox 26.1 58 0.0013 22.9 2.1 26 24-49 36-66 (289)
102 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 26.1 79 0.0017 18.1 2.3 22 29-50 1-22 (50)
103 PF15027 DUF4525: Domain of un 25.8 48 0.001 23.1 1.6 21 29-49 34-55 (138)
104 PLN00143 tyrosine/nicotianamin 25.7 72 0.0016 23.0 2.5 20 30-49 184-204 (409)
105 cd01360 Adenylsuccinate_lyase_ 25.7 90 0.0019 23.2 3.1 37 19-57 173-209 (387)
106 cd02144 iodotyrosine_dehalogen 25.6 93 0.002 19.5 2.8 27 25-54 12-38 (193)
107 PRK06836 aspartate aminotransf 25.6 81 0.0018 22.4 2.7 22 26-47 178-199 (394)
108 PF00380 Ribosomal_S9: Ribosom 25.4 4.9 0.00011 26.3 -3.2 10 24-33 17-26 (121)
109 cd00165 S4 S4/Hsp/ tRNA synthe 25.1 21 0.00047 17.9 -0.2 11 23-33 25-35 (70)
110 cd02136 Nitroreductase Nitrore 24.8 1.2E+02 0.0025 18.9 3.1 26 26-54 13-38 (178)
111 PF13699 DUF4157: Domain of un 24.8 52 0.0011 19.7 1.4 12 32-43 1-12 (79)
112 PRK07590 L,L-diaminopimelate a 24.5 75 0.0016 22.7 2.4 18 30-47 190-207 (409)
113 PRK08068 transaminase; Reviewe 24.5 73 0.0016 22.4 2.3 20 28-47 179-198 (389)
114 PRK14982 acyl-ACP reductase; P 24.4 86 0.0019 23.6 2.8 27 27-53 310-338 (340)
115 PRK09257 aromatic amino acid a 24.3 77 0.0017 22.5 2.4 21 29-49 185-206 (396)
116 PF04566 RNA_pol_Rpb2_4: RNA p 24.2 56 0.0012 19.0 1.5 26 26-51 1-31 (63)
117 PRK09440 avtA valine--pyruvate 24.2 72 0.0016 22.6 2.2 22 28-49 191-213 (416)
118 PRK03620 5-dehydro-4-deoxygluc 24.0 66 0.0014 22.9 2.0 26 24-49 43-73 (303)
119 PF04218 CENP-B_N: CENP-B N-te 23.8 1.1E+02 0.0024 16.8 2.6 19 31-49 5-23 (53)
120 cd02151 NADPH_oxidoreductase_2 23.7 95 0.002 19.3 2.5 21 26-47 13-33 (162)
121 PHA02554 13 neck protein; Prov 23.6 44 0.00094 25.9 1.1 31 16-46 267-297 (311)
122 PTZ00086 40S ribosomal protein 23.5 67 0.0014 21.9 1.9 19 24-42 31-53 (147)
123 PF02836 Glyco_hydro_2_C: Glyc 23.5 18 0.0004 24.9 -0.8 10 24-33 6-15 (298)
124 PF06236 MelC1: Tyrosinase co- 23.4 18 0.00039 24.5 -0.8 9 26-34 73-81 (125)
125 PF11010 DUF2848: Protein of u 23.4 77 0.0017 22.8 2.3 21 34-54 8-28 (194)
126 PRK10281 hypothetical protein; 23.1 60 0.0013 23.3 1.7 24 19-43 17-40 (299)
127 PF13565 HTH_32: Homeodomain-l 23.1 1.1E+02 0.0025 16.7 2.6 20 29-48 26-46 (77)
128 PRK07366 succinyldiaminopimela 23.0 80 0.0017 22.1 2.3 18 30-47 179-196 (388)
129 TIGR02988 YaaA_near_RecF S4 do 22.9 26 0.00056 19.2 -0.1 12 22-33 32-43 (59)
130 PRK07865 N-succinyldiaminopime 22.9 81 0.0018 21.9 2.3 19 29-47 161-179 (364)
131 PF10615 DUF2470: Protein of u 22.9 34 0.00075 20.0 0.4 11 35-45 73-83 (83)
132 PRK07570 succinate dehydrogena 22.7 23 0.0005 25.3 -0.4 20 17-36 59-79 (250)
133 PRK06207 aspartate aminotransf 22.5 91 0.002 22.4 2.5 18 30-47 192-209 (405)
134 PRK00942 acetylglutamate kinas 22.4 68 0.0015 22.4 1.8 34 18-51 25-58 (283)
135 PF06097 DUF945: Bacterial pro 22.4 33 0.00073 24.6 0.3 13 24-36 446-458 (460)
136 PF04829 PT-VENN: Pre-toxin do 22.3 93 0.002 17.9 2.1 15 32-46 4-18 (55)
137 PRK06348 aspartate aminotransf 22.3 86 0.0019 22.1 2.3 19 29-47 175-193 (384)
138 PF03450 CO_deh_flav_C: CO deh 22.3 55 0.0012 19.3 1.2 28 27-54 53-80 (103)
139 PRK06855 aminotransferase; Val 22.0 84 0.0018 23.0 2.3 18 30-47 185-202 (433)
140 PF14787 zf-CCHC_5: GAG-polypr 22.0 30 0.00065 19.2 0.0 9 28-36 24-32 (36)
141 PF14069 SpoVIF: Stage VI spor 21.9 1.4E+02 0.003 18.5 3.0 23 29-52 44-67 (79)
142 PHA00738 putative HTH transcri 21.7 68 0.0015 21.2 1.7 16 33-48 9-24 (108)
143 TIGR03542 DAPAT_plant LL-diami 21.7 87 0.0019 22.3 2.3 18 30-47 187-204 (402)
144 PF13518 HTH_28: Helix-turn-he 21.6 86 0.0019 15.8 1.7 12 38-49 2-13 (52)
145 PF12298 Bot1p: Eukaryotic mit 21.6 1.2E+02 0.0026 21.0 2.9 23 26-48 10-32 (172)
146 PRK06290 aspartate aminotransf 21.5 87 0.0019 22.8 2.3 19 29-47 192-210 (410)
147 PRK13884 conjugal transfer pep 21.5 29 0.00063 23.5 -0.1 12 24-35 105-116 (178)
148 PF11436 DUF3199: Protein of u 21.4 81 0.0018 21.5 2.0 23 24-46 41-65 (124)
149 TIGR03540 DapC_direct LL-diami 21.4 91 0.002 21.8 2.3 21 27-47 175-195 (383)
150 PRK08558 adenine phosphoribosy 21.2 65 0.0014 22.7 1.5 17 27-43 43-60 (238)
151 cd00408 DHDPS-like Dihydrodipi 21.2 87 0.0019 21.4 2.1 26 24-49 33-63 (281)
152 COG2055 Malate/L-lactate dehyd 21.2 91 0.002 24.1 2.4 34 15-48 310-343 (349)
153 PRK13838 conjugal transfer pil 21.2 29 0.00062 23.6 -0.2 17 20-36 100-116 (176)
154 KOG1052|consensus 21.0 65 0.0014 24.8 1.6 29 20-49 534-562 (656)
155 PRK05839 hypothetical protein; 20.8 88 0.0019 22.1 2.2 18 30-47 169-186 (374)
156 PRK09147 succinyldiaminopimela 20.6 95 0.0021 21.9 2.3 21 29-49 179-200 (396)
157 cd00197 VHS_ENTH_ANTH VHS, ENT 20.6 1.3E+02 0.0027 18.0 2.5 19 28-46 93-111 (115)
158 PRK11053 dihydropteridine redu 20.3 1.3E+02 0.0027 19.9 2.7 24 25-48 14-37 (217)
159 cd02146 NfsA_FRP This family c 20.3 1.2E+02 0.0026 20.3 2.6 25 26-53 13-37 (229)
160 PRK08960 hypothetical protein; 20.3 1.1E+02 0.0023 21.6 2.5 23 27-49 176-199 (387)
161 PRK08637 hypothetical protein; 20.3 1.1E+02 0.0024 21.7 2.5 19 28-46 158-176 (388)
162 PRK07682 hypothetical protein; 20.2 1.1E+02 0.0023 21.4 2.4 20 28-47 166-185 (378)
163 PF07637 PSD5: Protein of unkn 20.1 1.1E+02 0.0025 17.3 2.2 18 31-48 17-34 (64)
No 1
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=99.80 E-value=1.6e-20 Score=124.40 Aligned_cols=38 Identities=63% Similarity=0.997 Sum_probs=31.1
Q ss_pred CCcceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746 16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~ 53 (59)
||++||||||+|+||||||+++|++|||||++|+|||+
T Consensus 1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~ 38 (125)
T PF00292_consen 1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCD 38 (125)
T ss_dssp S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHH
T ss_pred CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHH
Confidence 78999999999999999999999999999999999986
No 2
>KOG3862|consensus
Probab=99.79 E-value=2.9e-20 Score=139.45 Aligned_cols=43 Identities=77% Similarity=1.105 Sum_probs=40.2
Q ss_pred chhccCCcceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746 11 NIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 11 ~~~~~g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~ 53 (59)
+.+..||+|||||||||||||||||.+|++|||||++|||||.
T Consensus 4 ~s~~~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcd 46 (327)
T KOG3862|consen 4 NSIHSGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCD 46 (327)
T ss_pred cCCCCCccchhhccceeecCccCchHHHHHHHHHHHcCCcchh
Confidence 3456799999999999999999999999999999999999995
No 3
>KOG3517|consensus
Probab=99.71 E-value=3.4e-18 Score=128.35 Aligned_cols=40 Identities=63% Similarity=0.856 Sum_probs=37.4
Q ss_pred ccCCcceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746 14 KWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 14 ~~g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~ 53 (59)
.+..+.|||||||||||||||+.+|.||||||+.|+|||.
T Consensus 2 ~~~~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCD 41 (334)
T KOG3517|consen 2 EPSYGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCD 41 (334)
T ss_pred CccccchhhccceeEcCccCcchhhhhHHHHHHcCCCccc
Confidence 3456899999999999999999999999999999999996
No 4
>KOG0849|consensus
Probab=99.15 E-value=7.4e-12 Score=92.08 Aligned_cols=36 Identities=64% Similarity=1.032 Sum_probs=34.6
Q ss_pred cceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746 18 GGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 18 ~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~ 53 (59)
+++|||||+|+||||||+++|++|++||+.|+|||.
T Consensus 1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~ 36 (354)
T KOG0849|consen 1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCV 36 (354)
T ss_pred CCcccCCcccccCCCCCCchhhccccccccccCccc
Confidence 579999999999999999999999999999999985
No 5
>cd00131 PAX Paired Box domain
Probab=99.14 E-value=2.7e-11 Score=77.89 Aligned_cols=37 Identities=73% Similarity=1.135 Sum_probs=34.2
Q ss_pred CCcceecccccccCCCCCChHHHHHHHHHHHcCCCCC
Q psy10746 16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLS 52 (59)
Q Consensus 16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps 52 (59)
|++++|||||+|+||+||+.++|.+||+|++.|..+.
T Consensus 1 ~~~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~ 37 (128)
T cd00131 1 GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPC 37 (128)
T ss_pred CCccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHH
Confidence 6789999999999999999999999999999997543
No 6
>smart00351 PAX Paired Box domain.
Probab=98.87 E-value=1.6e-09 Score=69.03 Aligned_cols=36 Identities=81% Similarity=1.193 Sum_probs=33.0
Q ss_pred CCcceecccccccCCCCCChHHHHHHHHHHHcCCCC
Q psy10746 16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLL 51 (59)
Q Consensus 16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRp 51 (59)
+++++|||||.|++|+||+.+.|.+||+|++.|...
T Consensus 1 ~~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~ 36 (125)
T smart00351 1 GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRP 36 (125)
T ss_pred CCCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCH
Confidence 478999999999999999999999999999988643
No 7
>PLN00061 photosystem II protein Psb27; Provisional
Probab=88.73 E-value=0.16 Score=35.50 Aligned_cols=28 Identities=21% Similarity=0.517 Sum_probs=23.9
Q ss_pred CcceecccccccCC---CCCChHHHHHHHHH
Q psy10746 17 HGGVNQLGGVFVNG---RPLPDVVRQRIVEL 44 (59)
Q Consensus 17 ~~~vNQLGG~FvNG---RPLP~~~R~kIveL 44 (59)
+.-+|.|+|-|.+= ||||+.+|.+|.+-
T Consensus 115 qtALnsLAghYssyGpnrPLPe~lK~Rll~E 145 (150)
T PLN00061 115 EKAIRSLASFYSKAGPSAPLPEDVKSEILDD 145 (150)
T ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence 46789999998765 99999999999863
No 8
>cd03482 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.
Probab=87.21 E-value=0.38 Score=30.30 Aligned_cols=31 Identities=26% Similarity=0.262 Sum_probs=23.7
Q ss_pred ccccCCCCCChHHHHHHHHHHHcCCCCCccc
Q psy10746 25 GVFVNGRPLPDVVRQRIVELAHNGGLLSAKY 55 (59)
Q Consensus 25 G~FvNGRPLP~~~R~kIveLA~~GvRps~~~ 55 (59)
=.||||||.-+..=.+.|+-|-++.-|..+|
T Consensus 47 ~ifVN~R~V~~~~l~~ai~~~y~~~~~~~~~ 77 (123)
T cd03482 47 YFYVNGRMVRDKLISHAVRQAYSDVLHGGRH 77 (123)
T ss_pred EEEEcCcEECChHHHHHHHHHHHHhccCCCC
Confidence 3799999999888888888777666655443
No 9
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=83.63 E-value=0.28 Score=29.50 Aligned_cols=20 Identities=40% Similarity=0.479 Sum_probs=18.3
Q ss_pred ChHHHHHHHHHHHcCCCCCc
Q psy10746 34 PDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 34 P~~~R~kIveLA~~GvRps~ 53 (59)
|+++-..|++||.+|.-||.
T Consensus 30 ~~eVe~~I~klakkG~tpSq 49 (60)
T PF08069_consen 30 PEEVEELIVKLAKKGLTPSQ 49 (60)
T ss_dssp HHHHHHHHHHHCCTTHCHHH
T ss_pred HHHHHHHHHHHHHcCCCHHH
Confidence 68999999999999999874
No 10
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=83.24 E-value=0.59 Score=32.03 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=22.6
Q ss_pred CcceecccccccC--CCCCChHHHHHHHH
Q psy10746 17 HGGVNQLGGVFVN--GRPLPDVVRQRIVE 43 (59)
Q Consensus 17 ~~~vNQLGG~FvN--GRPLP~~~R~kIve 43 (59)
+.-+|.|.|-|.+ -||||+..+.+|.+
T Consensus 95 ~TALNsLAGHY~sy~~rPlPeklk~Rl~~ 123 (135)
T TIGR03044 95 QTALNSLAGHYKSYANRPLPEKLKERLEK 123 (135)
T ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHHH
Confidence 5678999997665 59999999999964
No 11
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=83.15 E-value=0.86 Score=28.12 Aligned_cols=30 Identities=30% Similarity=0.564 Sum_probs=19.9
Q ss_pred cccCCCCCChHHHHHHHHHHHcCCCCCccc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNGGLLSAKY 55 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~GvRps~~~ 55 (59)
+||||||.-+..=.+.|+-+-++.-|..+|
T Consensus 44 ifVN~R~V~~~~l~~~I~~~y~~~~~~~~~ 73 (119)
T PF01119_consen 44 IFVNGRPVENKALSKAINEAYRERLPKGRY 73 (119)
T ss_dssp EEETTEEE--HHHHHHHHHHHHCTTCTTSB
T ss_pred EEeCCCeEeChHHHHHHHHHHhhcccCCCC
Confidence 799999998876666666666555555554
No 12
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=82.21 E-value=0.39 Score=32.29 Aligned_cols=27 Identities=30% Similarity=0.725 Sum_probs=20.3
Q ss_pred CcceecccccccC--CC-CCChHHHHHHHH
Q psy10746 17 HGGVNQLGGVFVN--GR-PLPDVVRQRIVE 43 (59)
Q Consensus 17 ~~~vNQLGG~FvN--GR-PLP~~~R~kIve 43 (59)
..-+|.|+|-|.. =| |||+..|.+|.+
T Consensus 107 ~tAln~LaghY~s~g~raPlP~k~k~rll~ 136 (145)
T PF13326_consen 107 YTALNALAGHYSSYGNRAPLPEKLKERLLK 136 (145)
T ss_dssp HHHHHHHHHHCHHHTTS-S--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHHHH
Confidence 3679999998764 36 999999999975
No 13
>cd00782 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot synd
Probab=81.98 E-value=0.91 Score=27.51 Aligned_cols=26 Identities=35% Similarity=0.517 Sum_probs=18.1
Q ss_pred cccCCCCCChHHHHHHHHHHHcCCCC
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNGGLL 51 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~GvRp 51 (59)
.||||||+-+..=.+.|.-+-++.-+
T Consensus 48 ~fVN~R~v~~~~l~~ai~~~y~~~~~ 73 (122)
T cd00782 48 LFVNGRPVRDKLLSKAINEAYRSYLP 73 (122)
T ss_pred EEECCeEecCHHHHHHHHHHHHHhCc
Confidence 79999999876666666655544443
No 14
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=79.88 E-value=1.2 Score=28.09 Aligned_cols=29 Identities=21% Similarity=0.214 Sum_probs=21.5
Q ss_pred cccCCCCCChHHHHHHHHHHHcCCCCCcc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNGGLLSAK 54 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~GvRps~~ 54 (59)
.||||||.-+..=.+.|+-|-++.=|..+
T Consensus 52 ~fVNgR~V~~~~l~~aI~~~Y~~~l~~~~ 80 (127)
T cd03483 52 LFINNRLVECSALRRAIENVYANYLPKGA 80 (127)
T ss_pred EEEcCCEecCHHHHHHHHHHHHHhCcCCC
Confidence 79999999988878877777655544333
No 15
>KOG0400|consensus
Probab=78.71 E-value=1.6 Score=30.72 Aligned_cols=20 Identities=35% Similarity=0.400 Sum_probs=18.5
Q ss_pred ChHHHHHHHHHHHcCCCCCc
Q psy10746 34 PDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 34 P~~~R~kIveLA~~GvRps~ 53 (59)
+|++..+|++||..|+.||.
T Consensus 30 ~ddvkeqI~K~akKGltpsq 49 (151)
T KOG0400|consen 30 ADDVKEQIYKLAKKGLTPSQ 49 (151)
T ss_pred HHHHHHHHHHHHHcCCChhH
Confidence 58999999999999999985
No 16
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=78.42 E-value=1.6 Score=25.31 Aligned_cols=14 Identities=43% Similarity=0.776 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHcCC
Q psy10746 36 VVRQRIVELAHNGG 49 (59)
Q Consensus 36 ~~R~kIveLA~~Gv 49 (59)
.+.++|||||..|.
T Consensus 9 gikeqIvema~nG~ 22 (46)
T PF12759_consen 9 GIKEQIVEMAFNGS 22 (46)
T ss_pred cHHHHHHHHHhcCC
Confidence 57889999998775
No 17
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=76.05 E-value=3.5 Score=27.77 Aligned_cols=26 Identities=27% Similarity=0.397 Sum_probs=21.1
Q ss_pred cCCCC---CChHHHHHHHHHH-HcCCCCCc
Q psy10746 28 VNGRP---LPDVVRQRIVELA-HNGGLLSA 53 (59)
Q Consensus 28 vNGRP---LP~~~R~kIveLA-~~GvRps~ 53 (59)
+||+| ..+++|+||.+.| ..|-+|+.
T Consensus 22 ln~~~~~~vs~~tr~rV~~~a~~lgY~pn~ 51 (327)
T PRK10339 22 LNDDPTLNVKEETKHRILEIAEKLEYKTSS 51 (327)
T ss_pred hcCCCCCCcCHHHHHHHHHHHHHhCCCCch
Confidence 58887 8899999999988 66766653
No 18
>PRK12794 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=75.70 E-value=2.7 Score=27.56 Aligned_cols=18 Identities=39% Similarity=0.597 Sum_probs=15.8
Q ss_pred CCCCCChHHHHHHHHHHH
Q psy10746 29 NGRPLPDVVRQRIVELAH 46 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~ 46 (59)
.+-|||+++|..|+.|+.
T Consensus 68 ~~N~LP~eLRa~lisL~~ 85 (122)
T PRK12794 68 PDNPLPIELRARIFNLSL 85 (122)
T ss_pred CCCCCCHHHHHHHHHHHH
Confidence 466999999999999985
No 19
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=75.47 E-value=2 Score=29.87 Aligned_cols=20 Identities=35% Similarity=0.483 Sum_probs=18.4
Q ss_pred ChHHHHHHHHHHHcCCCCCc
Q psy10746 34 PDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 34 P~~~R~kIveLA~~GvRps~ 53 (59)
|+++-..|++||.+|.-||.
T Consensus 30 ~eeve~~I~~lakkG~~pSq 49 (151)
T PRK08561 30 PEEIEELVVELAKQGYSPSM 49 (151)
T ss_pred HHHHHHHHHHHHHCCCCHHH
Confidence 78999999999999999884
No 20
>PF07309 FlaF: Flagellar protein FlaF; InterPro: IPR010845 This family consists of several bacterial FlaF flagellar proteins. FlaF and FlaG are trans-acting, regulatory factors that modulate flagellin synthesis during flagellum biogenesis [].
Probab=73.92 E-value=3.3 Score=26.60 Aligned_cols=18 Identities=33% Similarity=0.682 Sum_probs=15.8
Q ss_pred CCCCCChHHHHHHHHHHH
Q psy10746 29 NGRPLPDVVRQRIVELAH 46 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~ 46 (59)
.+-|||+++|..|+.|+.
T Consensus 65 ~~n~LP~~LRa~LisL~~ 82 (113)
T PF07309_consen 65 PDNPLPDELRANLISLGL 82 (113)
T ss_pred ccCCCCHHHHHHHHHHHH
Confidence 466999999999999985
No 21
>PRK12793 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=72.22 E-value=3.4 Score=26.98 Aligned_cols=18 Identities=17% Similarity=0.460 Sum_probs=15.7
Q ss_pred CCCCCChHHHHHHHHHHH
Q psy10746 29 NGRPLPDVVRQRIVELAH 46 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~ 46 (59)
.+-|||+++|..|+.|+.
T Consensus 66 p~N~LP~eLRa~lisL~~ 83 (115)
T PRK12793 66 PENALPEELRADLISIGL 83 (115)
T ss_pred CCCCCCHHHHHHHHHHHH
Confidence 467999999999999874
No 22
>PLN00064 photosystem II protein Psb27; Provisional
Probab=70.00 E-value=2.2 Score=30.30 Aligned_cols=27 Identities=26% Similarity=0.604 Sum_probs=22.8
Q ss_pred CcceecccccccC---CCCCChHHHHHHHH
Q psy10746 17 HGGVNQLGGVFVN---GRPLPDVVRQRIVE 43 (59)
Q Consensus 17 ~~~vNQLGG~FvN---GRPLP~~~R~kIve 43 (59)
++-+|+|.|-|.+ -||||+..+.+|.+
T Consensus 124 yTALNaLAGHY~SfgpnrPlPeKlK~RL~q 153 (166)
T PLN00064 124 YSALNAVSGHYISFGPTAPIPAKRKARILE 153 (166)
T ss_pred HHHHHHHHHHhhccCCCCCCcHHHHHHHHH
Confidence 5779999998854 59999999999864
No 23
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=69.98 E-value=6 Score=26.45 Aligned_cols=25 Identities=16% Similarity=0.407 Sum_probs=20.6
Q ss_pred cCCCC----CChHHHHHHHHHH-HcCCCCC
Q psy10746 28 VNGRP----LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 28 vNGRP----LP~~~R~kIveLA-~~GvRps 52 (59)
.||++ .++++|+||.+.| ..|-+|.
T Consensus 20 Ln~~~~~~~vs~~tr~rV~~~a~~lgY~pn 49 (327)
T TIGR02417 20 INGKAKEYRISQETVERVMAVVREQGYQPN 49 (327)
T ss_pred HcCCCCCCccCHHHHHHHHHHHHHhCCCCC
Confidence 47886 9999999999998 5577665
No 24
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=69.88 E-value=3.3 Score=28.89 Aligned_cols=20 Identities=30% Similarity=0.315 Sum_probs=18.1
Q ss_pred ChHHHHHHHHHHHcCCCCCc
Q psy10746 34 PDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 34 P~~~R~kIveLA~~GvRps~ 53 (59)
|+++-..|++||..|..||.
T Consensus 27 ~eeVe~~I~klaKkG~~pSq 46 (148)
T PTZ00072 27 SSEVEDQICKLAKKGLTPSQ 46 (148)
T ss_pred HHHHHHHHHHHHHCCCCHhH
Confidence 68999999999999998874
No 25
>cd03485 MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.
Probab=69.77 E-value=2.9 Score=26.33 Aligned_cols=19 Identities=21% Similarity=0.363 Sum_probs=13.0
Q ss_pred cccCCCCCCh-H-HHHHHHHH
Q psy10746 26 VFVNGRPLPD-V-VRQRIVEL 44 (59)
Q Consensus 26 ~FvNGRPLP~-~-~R~kIveL 44 (59)
+||||||.-+ . +.+.|.+.
T Consensus 53 ~fVN~R~v~~~~~l~k~i~~~ 73 (132)
T cd03485 53 ISVNSRPVSLGKDIGKLLRQY 73 (132)
T ss_pred EEECCeecccchHHHHHHHHH
Confidence 8999999976 4 34444443
No 26
>cd03486 MutL_Trans_MLH3 MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH3 (MutL homologue 3). MLH3 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with MLH3. The MLH1-MLH3 complex plays a role in meiosis. A role for hMLH1-hMLH3 in DNA mismatch repair (MMR) has not been established. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC.
Probab=69.19 E-value=3.2 Score=26.58 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=17.7
Q ss_pred cccCCCCCChHHHHHHHHHHHcC
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~G 48 (59)
+||||||.-+..=.+.|+-|-++
T Consensus 47 ifVN~R~v~~~~l~~aI~~~y~~ 69 (141)
T cd03486 47 IYVNGRLYLKTRFHKLINKLFRK 69 (141)
T ss_pred EEECCEEechHHHHHHHHHHHhh
Confidence 69999999887777777666444
No 27
>cd00329 TopoII_MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch
Probab=66.74 E-value=3.3 Score=23.38 Aligned_cols=21 Identities=38% Similarity=0.509 Sum_probs=14.1
Q ss_pred cccCCCCCC-hHHHHHHHHHHH
Q psy10746 26 VFVNGRPLP-DVVRQRIVELAH 46 (59)
Q Consensus 26 ~FvNGRPLP-~~~R~kIveLA~ 46 (59)
.||||||.. ...=.+.+.-|-
T Consensus 48 ~fvN~r~v~~~~~~~~~i~~~~ 69 (107)
T cd00329 48 SFVNGRPVREGGTHVKAVREAY 69 (107)
T ss_pred EEEcCeEEcCCHHHHHHHHHHH
Confidence 799999998 544444444443
No 28
>cd03484 MutL_Trans_hPMS_2_like MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome.
Probab=65.72 E-value=4.7 Score=25.98 Aligned_cols=24 Identities=17% Similarity=0.322 Sum_probs=18.0
Q ss_pred ccccCCCCCChHHHHHHHHHHHcC
Q psy10746 25 GVFVNGRPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 25 G~FvNGRPLP~~~R~kIveLA~~G 48 (59)
=+||||||.-+..=.+.|.-|-++
T Consensus 67 ~~fVN~R~V~~~~l~~aI~~~y~~ 90 (142)
T cd03484 67 FFYINGRPVDLKKVAKLINEVYKS 90 (142)
T ss_pred EEEECCeecCCHHHHHHHHHHHHH
Confidence 479999999887666666666544
No 29
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=64.51 E-value=6.5 Score=26.23 Aligned_cols=25 Identities=12% Similarity=0.340 Sum_probs=20.4
Q ss_pred cCCCC----CChHHHHHHHHHH-HcCCCCC
Q psy10746 28 VNGRP----LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 28 vNGRP----LP~~~R~kIveLA-~~GvRps 52 (59)
+||+| .++++|+||.+.| ..|-+|.
T Consensus 21 Ln~~~~~~~Vs~~tr~rV~~~a~elgY~pn 50 (328)
T PRK11303 21 INGKAKQYRVSDKTVEKVMAVVREHNYHPN 50 (328)
T ss_pred HcCCCCCCCcCHHHHHHHHHHHHHhCCCCC
Confidence 47886 9999999999988 5576664
No 30
>TIGR00585 mutl DNA mismatch repair protein MutL. All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.96 E-value=5.4 Score=28.27 Aligned_cols=31 Identities=23% Similarity=0.340 Sum_probs=21.5
Q ss_pred ccccCCCCCChHHHHHHHHHHHcCCCCCccc
Q psy10746 25 GVFVNGRPLPDVVRQRIVELAHNGGLLSAKY 55 (59)
Q Consensus 25 G~FvNGRPLP~~~R~kIveLA~~GvRps~~~ 55 (59)
-+||||||.....=.|.|+=+-+...|..+|
T Consensus 256 ~ifvNgR~v~~~~l~k~I~~~y~~~~~~~~~ 286 (312)
T TIGR00585 256 FLFINGRPVELKLLLKAIREVYHEYLPKGQY 286 (312)
T ss_pred EEEECCcEecchHHHHHHHHHHHHhccCCCC
Confidence 5899999998876666666655555444444
No 31
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=60.59 E-value=11 Score=25.32 Aligned_cols=24 Identities=13% Similarity=-0.031 Sum_probs=19.1
Q ss_pred CCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 29 NGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 29 NGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
||++ +.+++|+||.+.| ..|-.|.
T Consensus 23 n~~~~vs~~tr~~V~~~a~elgY~pn 48 (341)
T PRK10703 23 NKTRFVAEETRNAVWAAIKELHYSPS 48 (341)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence 5554 9999999999999 5676664
No 32
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=60.02 E-value=14 Score=15.66 Aligned_cols=17 Identities=18% Similarity=0.096 Sum_probs=13.2
Q ss_pred CChHHHHHHHHHHHcCC
Q psy10746 33 LPDVVRQRIVELAHNGG 49 (59)
Q Consensus 33 LP~~~R~kIveLA~~Gv 49 (59)
++++.+..|+++...|.
T Consensus 6 ~~~~~~~~i~~~~~~~~ 22 (42)
T cd00569 6 LTPEQIEEARRLLAAGE 22 (42)
T ss_pred CCHHHHHHHHHHHHcCC
Confidence 67788888888887664
No 33
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=59.88 E-value=12 Score=25.33 Aligned_cols=25 Identities=12% Similarity=0.102 Sum_probs=19.8
Q ss_pred cCCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 28 VNGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 28 vNGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
+||++ ..+++|+||.+.| ..|-+|.
T Consensus 22 Ln~~~~Vs~~tr~rV~~~a~elgY~pn 48 (343)
T PRK10727 22 INNSPKASEASRLAVHSAMESLSYHPN 48 (343)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 46665 8999999999998 5676664
No 34
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=58.28 E-value=14 Score=20.36 Aligned_cols=24 Identities=33% Similarity=0.426 Sum_probs=17.2
Q ss_pred cCC-CCCChHHHHHHHHHHH-cCCCC
Q psy10746 28 VNG-RPLPDVVRQRIVELAH-NGGLL 51 (59)
Q Consensus 28 vNG-RPLP~~~R~kIveLA~-~GvRp 51 (59)
+|| ..+.+++|+||.+.|. .|-+|
T Consensus 20 ln~~~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 20 LNGPPRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp HTTCSSSTHHHHHHHHHHHHHHTB-S
T ss_pred HhCCCCCCHHHHHHHHHHHHHHCCCC
Confidence 344 5589999999999984 45444
No 35
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=55.61 E-value=16 Score=24.24 Aligned_cols=25 Identities=8% Similarity=0.092 Sum_probs=19.6
Q ss_pred cCCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 28 VNGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 28 vNGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
+||++ ..+++|+||.+.| ..|=+|+
T Consensus 19 Ln~~~~vs~~tr~rV~~~a~~lgY~pn 45 (327)
T PRK10423 19 INKDRFVSEAITAKVEAAIKELNYAPS 45 (327)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHCCCcc
Confidence 36665 8999999999998 5676664
No 36
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=52.45 E-value=21 Score=18.32 Aligned_cols=26 Identities=27% Similarity=0.553 Sum_probs=19.4
Q ss_pred ccCCCC-CChHHHHHHHHHHHc-CCCCC
Q psy10746 27 FVNGRP-LPDVVRQRIVELAHN-GGLLS 52 (59)
Q Consensus 27 FvNGRP-LP~~~R~kIveLA~~-GvRps 52 (59)
..||++ ....++.+|.+++.. |.+|.
T Consensus 17 ~l~g~~~vs~~~~~~i~~~~~~l~~~~~ 44 (52)
T cd01392 17 VLNGKPRVSEETRERVLAAAEELGYRPN 44 (52)
T ss_pred HHcCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence 346664 577899999999965 87765
No 37
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=52.20 E-value=3.2 Score=22.49 Aligned_cols=14 Identities=43% Similarity=0.691 Sum_probs=10.6
Q ss_pred cccccccCCCCCCh
Q psy10746 22 QLGGVFVNGRPLPD 35 (59)
Q Consensus 22 QLGG~FvNGRPLP~ 35 (59)
--.|+|+||++|+.
T Consensus 40 s~ngt~vng~~l~~ 53 (68)
T PF00498_consen 40 STNGTFVNGQRLGP 53 (68)
T ss_dssp SSS-EEETTEEESS
T ss_pred CCCcEEECCEEcCC
Confidence 35699999999884
No 38
>COG0103 RpsI Ribosomal protein S9 [Translation, ribosomal structure and biogenesis]
Probab=49.99 E-value=9.4 Score=26.04 Aligned_cols=21 Identities=43% Similarity=0.820 Sum_probs=15.4
Q ss_pred ccccccCCCCC-----ChHHHHHHHH
Q psy10746 23 LGGVFVNGRPL-----PDVVRQRIVE 43 (59)
Q Consensus 23 LGG~FvNGRPL-----P~~~R~kIve 43 (59)
=|-+.|||+|+ ++-.|.+|.|
T Consensus 25 ~G~i~vNg~~~e~yf~~e~~r~~i~~ 50 (130)
T COG0103 25 KGKITVNGRPLELYFPRETLRMKIMQ 50 (130)
T ss_pred CcEEEECCcCHHHhcchHHHHHHHhh
Confidence 37789999998 4556666655
No 39
>PF06440 DNA_pol3_theta: DNA polymerase III, theta subunit; InterPro: IPR009052 This entry represents the theta subunit of DNA polymerase III from bacteria, whose core structure consists of an irregular array of three helices []. DNA polymerase III (Pol III) is the primary enzyme responsible for replication of Escherichia coli chromosomal DNA. The holoenzyme consists of 17 proteins and contains two core polymerases. The Pol III catalytic core has three tightly associated subunits: alpha, epsilon and theta. The alpha subunit is responsible for the DNA polymerase activity, while the epsilon subunit is the 3'-5' proofreading exonuclease. The epsilon subunit binds to both the alpha and theta subunits in the linear order alpha-epsilon-theta. The theta subunit is the smallest, and may act to enhance the proofreading activity of epsilon, especially under extreme conditions []. This entry also includes a homologue of polymerase III theta called HOT (homologue of theta) from Bacteriophage P1. HOT contains three alpha-helices, as reported for theta, but the folding topology of the two is different, which could account for the suggested greater heat stability of HOT as compared to theta [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1SE7_A 2IDO_D 2AE9_A 1DU2_A 2XY8_B 2AXD_S.
Probab=49.65 E-value=7.3 Score=24.68 Aligned_cols=18 Identities=28% Similarity=0.387 Sum_probs=15.2
Q ss_pred CChHHHHHH-HHHHHcCCC
Q psy10746 33 LPDVVRQRI-VELAHNGGL 50 (59)
Q Consensus 33 LP~~~R~kI-veLA~~GvR 50 (59)
||.+.|.|| |+||++||-
T Consensus 8 lskee~dKvnvDLaAsgVa 26 (75)
T PF06440_consen 8 LSKEEMDKVNVDLAASGVA 26 (75)
T ss_dssp STCHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHHHHH
Confidence 678888887 899999984
No 40
>PF06543 Lac_bphage_repr: Lactococcus bacteriophage repressor; InterPro: IPR009498 This entry represents the C terminus of various Lactococcus bacteriophage repressor proteins.
Probab=49.13 E-value=13 Score=22.02 Aligned_cols=16 Identities=38% Similarity=0.694 Sum_probs=12.3
Q ss_pred ccCCCCCChHHHHHHH
Q psy10746 27 FVNGRPLPDVVRQRIV 42 (59)
Q Consensus 27 FvNGRPLP~~~R~kIv 42 (59)
-..||||+++...-|-
T Consensus 25 Sf~GrPltdevK~a~k 40 (49)
T PF06543_consen 25 SFDGRPLTDEVKEAMK 40 (49)
T ss_pred eeCCeeCCHHHHHHHH
Confidence 4689999999876553
No 41
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=48.65 E-value=6.8 Score=23.33 Aligned_cols=13 Identities=54% Similarity=0.723 Sum_probs=11.4
Q ss_pred CcceecccccccC
Q psy10746 17 HGGVNQLGGVFVN 29 (59)
Q Consensus 17 ~~~vNQLGG~FvN 29 (59)
.+.+.|+||.||=
T Consensus 89 ~g~~~q~GG~fv~ 101 (115)
T PF13911_consen 89 QGDGWQLGGTFVF 101 (115)
T ss_pred CCCceecCeEEEE
Confidence 6889999999984
No 42
>PF13279 4HBT_2: Thioesterase-like superfamily; PDB: 2W3X_E 3CK1_A 2GF6_C 2NUJ_A 2HLJ_A 2XFL_B 2XEM_B 2OIW_B 2HX5_A 2FUJ_A ....
Probab=47.76 E-value=12 Score=21.87 Aligned_cols=11 Identities=36% Similarity=0.884 Sum_probs=7.0
Q ss_pred CCCChHHHHHH
Q psy10746 31 RPLPDVVRQRI 41 (59)
Q Consensus 31 RPLP~~~R~kI 41 (59)
+|||+++|.+|
T Consensus 111 ~~~P~~~~~~l 121 (121)
T PF13279_consen 111 VPIPDELREAL 121 (121)
T ss_dssp -B--HHHHHHH
T ss_pred CCCCHHHHhcC
Confidence 79999999876
No 43
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=46.80 E-value=13 Score=29.34 Aligned_cols=31 Identities=29% Similarity=0.385 Sum_probs=22.7
Q ss_pred ccccCCCCCChHHHHHHHHHHHcCCCCCccc
Q psy10746 25 GVFVNGRPLPDVVRQRIVELAHNGGLLSAKY 55 (59)
Q Consensus 25 G~FvNGRPLP~~~R~kIveLA~~GvRps~~~ 55 (59)
=.||||||..+..=.+.|+-|-.+.-|..+|
T Consensus 250 ~~fvN~R~v~~~~l~~ai~~~y~~~~~~~~~ 280 (617)
T PRK00095 250 YLFVNGRYVRDKLLNHAIRQAYHDLLPRGRY 280 (617)
T ss_pred EEEECCcEecCHHHHHHHHHHHHHhccCCCC
Confidence 3799999999877777777676555555554
No 44
>KOG0634|consensus
Probab=45.98 E-value=18 Score=29.37 Aligned_cols=20 Identities=30% Similarity=0.393 Sum_probs=17.3
Q ss_pred cCCCCCChHHHHHHHHHHHc
Q psy10746 28 VNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~~ 47 (59)
.-|--|+.+.|++|++||+.
T Consensus 216 PTG~tls~errk~iy~LArK 235 (472)
T KOG0634|consen 216 PTGNTLSLERRKKIYQLARK 235 (472)
T ss_pred CCCCccCHHHHHHHHHHHHH
Confidence 34778999999999999974
No 45
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=45.90 E-value=23 Score=22.84 Aligned_cols=30 Identities=30% Similarity=0.497 Sum_probs=23.8
Q ss_pred ccCCCCCC----hHHHHHHHHHHHcCCCCCcccc
Q psy10746 27 FVNGRPLP----DVVRQRIVELAHNGGLLSAKYS 56 (59)
Q Consensus 27 FvNGRPLP----~~~R~kIveLA~~GvRps~~~~ 56 (59)
|-+|.|.. +++-.+|=|||..|+-|.-||-
T Consensus 39 c~~g~pFs~d~IN~vT~~mN~LAk~givP~Rk~V 72 (84)
T PF10752_consen 39 CKQGEPFSTDKINEVTKEMNELAKQGIVPTRKYV 72 (84)
T ss_pred HHCCCCCcHHHHHHHHHHHHHHHHcCCCCcchhc
Confidence 45677765 4567889999999999998873
No 46
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=45.02 E-value=7 Score=19.88 Aligned_cols=11 Identities=45% Similarity=0.942 Sum_probs=8.5
Q ss_pred ccccccCCCCC
Q psy10746 23 LGGVFVNGRPL 33 (59)
Q Consensus 23 LGG~FvNGRPL 33 (59)
-.|+|+||+++
T Consensus 42 ~~gt~vng~~v 52 (52)
T smart00240 42 TNGTFVNGKRI 52 (52)
T ss_pred CCCeeECCEEC
Confidence 46889999864
No 47
>cd08051 gp6_gp15_like Head-Tail Connector Proteins gp6 and gp15, and similar proteins. Members of this family include the proteins gp6 and gp15 from bacteriophage HK97 and SPP1, respectively. They are critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. They form dodecameric ring structures that comprise the middle ring of the connector, located between the portal protein (attached to the head) and the gp7/gp16 ring (attached to the tail). They are components of the mature phage and the absence or mutation of HK97 gp6 or SPP1 gp15, respectively, result in defective head-tail joining and the absence of mature phage particles. The genome maps of HK97 and SPP1 show that genes encoding gp6 and gp15 are in the same relative position on the genome, located adjacent to the major capsid protein (MCP) gene and in between head and tail gene
Probab=44.84 E-value=22 Score=21.99 Aligned_cols=24 Identities=13% Similarity=0.246 Sum_probs=19.6
Q ss_pred ccccC--CCCCChHHHHHHHHHHHcC
Q psy10746 25 GVFVN--GRPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 25 G~FvN--GRPLP~~~R~kIveLA~~G 48 (59)
..|.. +-+||+.+|.-++.|+.+.
T Consensus 35 ~~~~~~~~~~lp~~vk~A~l~li~~~ 60 (94)
T cd08051 35 EPFWDAVAADIPAAVKGAVLKVFQFY 60 (94)
T ss_pred cccccccccCCCHHHHHHHHHHHHHH
Confidence 33544 8899999999999999765
No 48
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=44.79 E-value=19 Score=24.96 Aligned_cols=27 Identities=15% Similarity=0.224 Sum_probs=21.9
Q ss_pred cccccCCC-----CCChHHHHHHHHHHHcCCC
Q psy10746 24 GGVFVNGR-----PLPDVVRQRIVELAHNGGL 50 (59)
Q Consensus 24 GG~FvNGR-----PLP~~~R~kIveLA~~GvR 50 (59)
-|+|++|. -|.+++|.+++|.+..-+.
T Consensus 37 ~gi~~~Gs~GE~~~ls~~Er~~~~~~~~~~~~ 68 (292)
T PRK03170 37 DGLVVVGTTGESPTLTHEEHEELIRAVVEAVN 68 (292)
T ss_pred CEEEECCcCCccccCCHHHHHHHHHHHHHHhC
Confidence 37788887 6999999999998876443
No 49
>PRK09526 lacI lac repressor; Reviewed
Probab=43.88 E-value=23 Score=23.71 Aligned_cols=24 Identities=8% Similarity=0.077 Sum_probs=18.3
Q ss_pred CCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 29 NGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 29 NGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
||++ ..+++|+||.+.| ..|-+|.
T Consensus 27 n~~~~vs~~tr~rV~~~a~elgY~pn 52 (342)
T PRK09526 27 NQASHVSAKTREKVEAAMAELNYVPN 52 (342)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence 5555 8999999999988 5565554
No 50
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=42.81 E-value=19 Score=22.39 Aligned_cols=13 Identities=23% Similarity=0.626 Sum_probs=10.9
Q ss_pred CChHHHHHHHHHH
Q psy10746 33 LPDVVRQRIVELA 45 (59)
Q Consensus 33 LP~~~R~kIveLA 45 (59)
||+++|.+|+.=.
T Consensus 9 LPeDiR~Evl~~~ 21 (108)
T PF14377_consen 9 LPEDIREEVLAQQ 21 (108)
T ss_pred CCHHHHHHHHHHH
Confidence 8999999997543
No 51
>PF14304 CSTF_C: Transcription termination and cleavage factor C-terminal; PDB: 2J8P_A.
Probab=42.56 E-value=16 Score=20.97 Aligned_cols=15 Identities=40% Similarity=0.618 Sum_probs=11.7
Q ss_pred CCChHHHHHHHHHHH
Q psy10746 32 PLPDVVRQRIVELAH 46 (59)
Q Consensus 32 PLP~~~R~kIveLA~ 46 (59)
-||.+.|..|++|-+
T Consensus 24 ~LPp~qR~~I~~Lr~ 38 (46)
T PF14304_consen 24 ALPPDQRQQILQLRQ 38 (46)
T ss_dssp TS-HHHHTHHHHHHH
T ss_pred hCCHHHHHHHHHHHH
Confidence 389999999999854
No 52
>PLN02512 acetylglutamate kinase
Probab=42.28 E-value=19 Score=25.95 Aligned_cols=36 Identities=22% Similarity=0.151 Sum_probs=30.7
Q ss_pred CCcceecccccccCCCCCChHHHHHHHHHHHcCCCC
Q psy10746 16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLL 51 (59)
Q Consensus 16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRp 51 (59)
++.-|=.|||..+....+|......|..|...|.++
T Consensus 47 ~~tiVIKlGGs~i~d~~~~~~~~~di~~l~~~g~~i 82 (309)
T PLN02512 47 GKTVVVKYGGAAMKDPELKAGVIRDLVLLSCVGLRP 82 (309)
T ss_pred CCeEEEEECCeeccChhHHHHHHHHHHHHHHCCCCE
Confidence 455677799999999999999999999999988764
No 53
>PF04806 EspF: EspF protein repeat; InterPro: IPR006891 Enteropathogenic Escherichia coli O127:H6 attaches to the intestinal muscosa through actin pedestals that are created after it has injected the Type III secretion protein EspF (E. coli secreted protein F-like protein from prophage U) into the cells. EspF recruits the actin machinery by activating the WASP (Wiscott-Aldrich syndrome protein) family of actin nucleating factors []. Subsequent cell-death (apoptosis) is caused by EspF being targeted to the mitochondria as a consequence of its mitochondrial targeting sequence. Import into mitochondria leads to a loss of membrane potential, leakage of cytochrome c and activation of the apoptotic caspase cascade. Mutation of leucine to glutamic at position 16 of EspF (L16E) resulted in the failure of EspF import into mitochondria; mitochondrial membrane potential was not affected and cell death abolished. This suggests that the targeting of EspF to mitochondria is essential for bacterial pathogenesis and apoptosis [, ].; PDB: 2KXC_B 2K42_B.
Probab=42.09 E-value=23 Score=20.82 Aligned_cols=19 Identities=42% Similarity=0.665 Sum_probs=10.8
Q ss_pred CCCCChHHHHHHHHHHHcC
Q psy10746 30 GRPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~G 48 (59)
-||||+--.+-|-.||++|
T Consensus 29 s~~lp~vaq~l~~hla~hg 47 (47)
T PF04806_consen 29 SRPLPPVAQRLKDHLAEHG 47 (47)
T ss_dssp ----SSHHHHHHHHHHTTT
T ss_pred cCCCchHHHHHHHHHHhcC
Confidence 4899976666666688876
No 54
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=41.95 E-value=22 Score=24.40 Aligned_cols=28 Identities=21% Similarity=0.290 Sum_probs=22.7
Q ss_pred ccccccCCC-----CCChHHHHHHHHHHHcCCC
Q psy10746 23 LGGVFVNGR-----PLPDVVRQRIVELAHNGGL 50 (59)
Q Consensus 23 LGG~FvNGR-----PLP~~~R~kIveLA~~GvR 50 (59)
.-|+|++|. -|.+++|++++|.+..-+.
T Consensus 35 v~gl~v~GstGE~~~lt~~Er~~l~~~~~~~~~ 67 (284)
T cd00950 35 TDGLVVCGTTGESPTLSDEEHEAVIEAVVEAVN 67 (284)
T ss_pred CCEEEECCCCcchhhCCHHHHHHHHHHHHHHhC
Confidence 347788887 6999999999999876554
No 55
>cd02135 Arsenite_oxidase Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a beta-proteobacterial strain is able to oxidize arsenite to arsenate.
Probab=41.61 E-value=33 Score=20.80 Aligned_cols=26 Identities=12% Similarity=-0.036 Sum_probs=20.5
Q ss_pred cccCCCCCChHHHHHHHHHHHcCCCCCcc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNGGLLSAK 54 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~GvRps~~ 54 (59)
.| .++|+|+++-.+|++.|..- ||..
T Consensus 12 ~f-~~~~v~~e~l~~il~aA~~A--Ps~~ 37 (160)
T cd02135 12 KL-TLPAPDREQLEQILEAAARA--PDHG 37 (160)
T ss_pred hc-CCCCCCHHHHHHHHHHHHhC--CCcC
Confidence 35 46899999999999999763 6654
No 56
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=40.09 E-value=30 Score=23.10 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=19.6
Q ss_pred cCCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 28 VNGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 28 vNGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
.||++ ..+++|+||.+.| ..|=+|.
T Consensus 22 Ln~~~~vs~~tr~rV~~~a~~lgY~pn 48 (329)
T TIGR01481 22 VNGNPNVKPATRKKVLEVIKRLDYRPN 48 (329)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 36665 8999999999988 5676664
No 57
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=39.61 E-value=22 Score=27.94 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=19.7
Q ss_pred cccccCCCCCChHHHHHHHHHH
Q psy10746 24 GGVFVNGRPLPDVVRQRIVELA 45 (59)
Q Consensus 24 GG~FvNGRPLP~~~R~kIveLA 45 (59)
-|+|.|.+-.|++.|..|++=-
T Consensus 109 SGSFLD~~EVP~e~R~~Il~~i 130 (358)
T COG1244 109 SGSFLDPEEVPREARRYILERI 130 (358)
T ss_pred ccccCChhhCCHHHHHHHHHHH
Confidence 5899999999999999999743
No 58
>CHL00079 rps9 ribosomal protein S9
Probab=39.33 E-value=20 Score=23.91 Aligned_cols=12 Identities=33% Similarity=0.963 Sum_probs=9.5
Q ss_pred cccccCCCCCCh
Q psy10746 24 GGVFVNGRPLPD 35 (59)
Q Consensus 24 GG~FvNGRPLP~ 35 (59)
|-++|||+||-+
T Consensus 25 G~i~INg~~~~~ 36 (130)
T CHL00079 25 GEIIINGKPAEE 36 (130)
T ss_pred cEEEECCCcHHH
Confidence 568999999744
No 59
>PF11011 DUF2849: Protein of unknown function (DUF2849); InterPro: IPR021270 This bacterial family of proteins has no known function.
Probab=39.06 E-value=20 Score=22.59 Aligned_cols=15 Identities=47% Similarity=0.813 Sum_probs=13.1
Q ss_pred cCCCCCChHHHHHHH
Q psy10746 28 VNGRPLPDVVRQRIV 42 (59)
Q Consensus 28 vNGRPLP~~~R~kIv 42 (59)
.+|+|-|.+.|.+|=
T Consensus 65 ~dG~~~P~~~RE~iR 79 (90)
T PF11011_consen 65 ADGRPRPVHLRERIR 79 (90)
T ss_pred CCCCccchhHHHhhh
Confidence 479999999999984
No 60
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=38.53 E-value=22 Score=18.82 Aligned_cols=17 Identities=24% Similarity=0.120 Sum_probs=11.7
Q ss_pred ChHHHHHHHHHHHcCCC
Q psy10746 34 PDVVRQRIVELAHNGGL 50 (59)
Q Consensus 34 P~~~R~kIveLA~~GvR 50 (59)
-++...+|++|..+|.-
T Consensus 7 ~~~~~~~i~~l~~~G~s 23 (45)
T PF02796_consen 7 SKEQIEEIKELYAEGMS 23 (45)
T ss_dssp SHCCHHHHHHHHHTT--
T ss_pred CHHHHHHHHHHHHCCCC
Confidence 34456899999999843
No 61
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=37.68 E-value=46 Score=22.33 Aligned_cols=24 Identities=13% Similarity=0.241 Sum_probs=18.5
Q ss_pred CCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 29 NGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 29 NGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
||++ ..+++|+||.+.| ..|-.|.
T Consensus 28 n~~~~vs~~tr~~V~~~a~elgY~p~ 53 (342)
T PRK10014 28 SGKGRISTATGERVNQAIEELGFVRN 53 (342)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence 4544 8999999999988 5666664
No 62
>PF09372 PRANC: PRANC domain; InterPro: IPR018272 This presumed domain is found at the C terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin, C-terminal) domain is also found on its own in some proteins []. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role.
Probab=36.78 E-value=25 Score=20.97 Aligned_cols=13 Identities=31% Similarity=0.501 Sum_probs=11.4
Q ss_pred CCChHHHHHHHHH
Q psy10746 32 PLPDVVRQRIVEL 44 (59)
Q Consensus 32 PLP~~~R~kIveL 44 (59)
-||.+++.+|++.
T Consensus 74 ~LP~EIk~~Il~~ 86 (97)
T PF09372_consen 74 ILPIEIKYKILEY 86 (97)
T ss_pred hCCHHHHHHHHHc
Confidence 4899999999975
No 63
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=36.61 E-value=37 Score=22.81 Aligned_cols=24 Identities=13% Similarity=0.141 Sum_probs=19.0
Q ss_pred CCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 29 NGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 29 NGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
||++ ..+++|+||.+.| ..|-+|.
T Consensus 27 n~~~~vs~~tr~rV~~~a~elgY~pn 52 (331)
T PRK14987 27 RNPEQVSVALRGKIAAALDELGYIPN 52 (331)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcc
Confidence 5655 8899999999998 5566664
No 64
>TIGR03553 F420_FbiB_CTERM F420 biosynthesis protein FbiB, C-terminal domain. Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5-6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems likely that the C-terminal domain of FbiB, modeled by this alignment, is involved in additional glutamate ligation.
Probab=36.46 E-value=42 Score=21.48 Aligned_cols=26 Identities=15% Similarity=0.115 Sum_probs=20.4
Q ss_pred cccCCCCCChHHHHHHHHHHHcCCCCCcc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNGGLLSAK 54 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~GvRps~~ 54 (59)
-|- ++|+|+++-.+|++.|.. -||++
T Consensus 11 ~f~-~~~V~~e~l~~il~aA~~--APS~~ 36 (194)
T TIGR03553 11 RFS-DDPVDPDAVRAAVAAALT--APAPH 36 (194)
T ss_pred cCC-CCCCCHHHHHHHHHHHHh--CCCCC
Confidence 454 689999999999999986 35543
No 65
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=36.38 E-value=34 Score=26.29 Aligned_cols=38 Identities=21% Similarity=0.197 Sum_probs=30.1
Q ss_pred cccccccCCCCCChHHHHHHHHHHH-cCCCCC--ccccccC
Q psy10746 22 QLGGVFVNGRPLPDVVRQRIVELAH-NGGLLS--AKYSHVI 59 (59)
Q Consensus 22 QLGG~FvNGRPLP~~~R~kIveLA~-~GvRps--~~~~~~~ 59 (59)
++++.|.=|.++-.-+..||.|||- .+.+|. ..|.|.|
T Consensus 257 ~~~~~CpCG~~i~~GV~~Rv~eLad~~~~~p~~rppy~~~i 297 (374)
T TIGR00375 257 TACANCPCGGRIKKGVSDRLRELSDQKLEHPVPRPPYVHLI 297 (374)
T ss_pred hcCCCCCCCCcceechHHHHHHHhcCCCCCCCCCCCeeeeC
Confidence 4578888899999999999999997 777774 4466654
No 66
>COG1765 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=36.10 E-value=35 Score=21.96 Aligned_cols=19 Identities=42% Similarity=0.534 Sum_probs=17.1
Q ss_pred cCCCCCChHHHHHHHHHHHc
Q psy10746 28 VNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~~ 47 (59)
+.| .+.++.+.+++++|..
T Consensus 96 v~g-d~~~e~~~~~i~~a~e 114 (137)
T COG1765 96 VKG-DLDEEKLKRAVELAEE 114 (137)
T ss_pred Eec-CCCHHHHHHHHHHHhc
Confidence 567 9999999999999976
No 67
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=36.06 E-value=31 Score=18.09 Aligned_cols=14 Identities=43% Similarity=0.662 Sum_probs=11.6
Q ss_pred hHHHHHHHHHHHcC
Q psy10746 35 DVVRQRIVELAHNG 48 (59)
Q Consensus 35 ~~~R~kIveLA~~G 48 (59)
|++|.+|+.+-..|
T Consensus 1 d~~R~~Il~~L~~~ 14 (47)
T PF01022_consen 1 DPTRLRILKLLSEG 14 (47)
T ss_dssp SHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHhC
Confidence 57899999988774
No 68
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=35.92 E-value=10 Score=19.70 Aligned_cols=13 Identities=38% Similarity=0.552 Sum_probs=10.3
Q ss_pred cccccccCCCCCC
Q psy10746 22 QLGGVFVNGRPLP 34 (59)
Q Consensus 22 QLGG~FvNGRPLP 34 (59)
.-|+++|||++..
T Consensus 24 ~~g~V~VNg~~v~ 36 (48)
T PF01479_consen 24 KQGRVKVNGKVVK 36 (48)
T ss_dssp HTTTEEETTEEES
T ss_pred CCCEEEECCEEEc
Confidence 3489999998765
No 69
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=35.80 E-value=35 Score=24.31 Aligned_cols=25 Identities=20% Similarity=0.414 Sum_probs=19.4
Q ss_pred cCCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 28 VNGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 28 vNGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
+||.| ..+++|+||.+.| ..|=+|.
T Consensus 21 ln~~~~Vs~eTr~kV~~a~~elgY~pN 47 (333)
T COG1609 21 LNGSPYVSEETREKVLAAIKELGYRPN 47 (333)
T ss_pred HcCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 46665 9999999999987 4566654
No 70
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=35.59 E-value=36 Score=23.07 Aligned_cols=24 Identities=13% Similarity=0.145 Sum_probs=18.7
Q ss_pred CCCC-CChHHHHHHHHHH-HcCCCCC
Q psy10746 29 NGRP-LPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 29 NGRP-LP~~~R~kIveLA-~~GvRps 52 (59)
||++ ..+++|+||.+-| ..|-+|.
T Consensus 23 n~~~~Vs~~tr~kV~~~a~elgY~pn 48 (346)
T PRK10401 23 NNSALVSADTREAVMKAVSELGYRPN 48 (346)
T ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 5544 8999999999999 4576665
No 71
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=35.26 E-value=21 Score=19.58 Aligned_cols=18 Identities=33% Similarity=0.556 Sum_probs=12.1
Q ss_pred ccCCCCCChHHHHHHHHH
Q psy10746 27 FVNGRPLPDVVRQRIVEL 44 (59)
Q Consensus 27 FvNGRPLP~~~R~kIveL 44 (59)
-|=||||.++-|++|++=
T Consensus 24 PlC~r~l~~e~~~~li~~ 41 (54)
T PF04423_consen 24 PLCGRPLDEEHRQELIKK 41 (54)
T ss_dssp TTT--EE-HHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHH
Confidence 356899999999998864
No 72
>KOG0975|consensus
Probab=34.94 E-value=26 Score=27.58 Aligned_cols=22 Identities=41% Similarity=0.635 Sum_probs=18.7
Q ss_pred cccCCCCCChHHHHHHHHHHHc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~ 47 (59)
.=.+|.-||=-+|+.|+|||++
T Consensus 277 Pp~dg~ILpGvTR~sileLa~~ 298 (379)
T KOG0975|consen 277 PPLDGTILPGVTRKSILELARD 298 (379)
T ss_pred CCCCCcccCCccHHHHHHHHHH
Confidence 3457789999999999999964
No 73
>PRK08636 aspartate aminotransferase; Provisional
Probab=34.78 E-value=37 Score=24.16 Aligned_cols=20 Identities=20% Similarity=0.278 Sum_probs=17.5
Q ss_pred cCCCCCChHHHHHHHHHHHc
Q psy10746 28 VNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~~ 47 (59)
+-|+-+|.+.|++|+++|++
T Consensus 187 PTG~~~s~~~~~~l~~~a~~ 206 (403)
T PRK08636 187 PTTATVEKSFYERLVALAKK 206 (403)
T ss_pred CCCccCCHHHHHHHHHHHHH
Confidence 44888999999999999965
No 74
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]
Probab=34.75 E-value=39 Score=25.39 Aligned_cols=21 Identities=19% Similarity=0.215 Sum_probs=18.0
Q ss_pred ccCCCCCChHHHHHHHHHHHc
Q psy10746 27 FVNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 27 FvNGRPLP~~~R~kIveLA~~ 47 (59)
++-|.-++.+-|++|++||++
T Consensus 238 NPtG~tms~~rR~~Ll~lA~~ 258 (459)
T COG1167 238 NPTGVTMSLERRKALLALAEK 258 (459)
T ss_pred CCCCCccCHHHHHHHHHHHHH
Confidence 455889999999999999953
No 75
>PF04664 OGFr_N: Opioid growth factor receptor (OGFr) conserved region; InterPro: IPR006757 Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving in neurotransmission/neuromodulation in the nervous system. The opioid growth factor receptor is an integral membrane protein associated with the nucleus. This conserved domain is situated at the N terminus of the member proteins with a series of imperfect repeats lying immediately to its C-terminal [].; GO: 0004872 receptor activity, 0016020 membrane
Probab=34.51 E-value=35 Score=24.31 Aligned_cols=22 Identities=18% Similarity=0.163 Sum_probs=19.7
Q ss_pred ChHHHHHHHHHHHcCCCCCccc
Q psy10746 34 PDVVRQRIVELAHNGGLLSAKY 55 (59)
Q Consensus 34 P~~~R~kIveLA~~GvRps~~~ 55 (59)
-++.|++++.+|-.+-+|.+++
T Consensus 181 ~~~~r~~l~~~~~~~~~~~~~f 202 (213)
T PF04664_consen 181 DKEERRELVRFAWKHFRPREKF 202 (213)
T ss_pred CHHHHHHHHHHHHHhcCCcccc
Confidence 3678999999999999999886
No 76
>PF07460 NUMOD3: NUMOD3 motif (2 copies); InterPro: IPR003611 This is a short helical motif of unknown function found in intron-associated nuclease 2, which is involved in intron homing.; GO: 0004519 endonuclease activity; PDB: 1I3J_A 1T2T_A.
Probab=34.38 E-value=15 Score=19.44 Aligned_cols=14 Identities=14% Similarity=0.394 Sum_probs=2.2
Q ss_pred CCCCCChHHHHHHH
Q psy10746 29 NGRPLPDVVRQRIV 42 (59)
Q Consensus 29 NGRPLP~~~R~kIv 42 (59)
=|+++++++|++|=
T Consensus 23 ~GK~~Seetk~kiS 36 (37)
T PF07460_consen 23 YGKKHSEETKKKIS 36 (37)
T ss_dssp TT---T--------
T ss_pred cCCccCcccccccc
Confidence 48899999988873
No 77
>PF13562 NTP_transf_4: Sugar nucleotidyl transferase
Probab=34.36 E-value=24 Score=23.50 Aligned_cols=18 Identities=33% Similarity=0.610 Sum_probs=13.6
Q ss_pred cccCCCCCChHHHHHHHH
Q psy10746 26 VFVNGRPLPDVVRQRIVE 43 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIve 43 (59)
+|||||-||++.-..+|.
T Consensus 68 l~INgr~lp~~~l~~~i~ 85 (156)
T PF13562_consen 68 LLINGRFLPDEALVEAIK 85 (156)
T ss_pred EEEeccccCCHHHHHHHH
Confidence 899999999985444443
No 78
>PF12039 DUF3525: Protein of unknown function (DUF3525); InterPro: IPR021912 This family of proteins is functionally uncharacterised. This protein is found in viruses. Proteins in this family are about 360 amino acids in length.
Probab=34.32 E-value=25 Score=28.06 Aligned_cols=21 Identities=33% Similarity=0.596 Sum_probs=19.6
Q ss_pred cccCCCCCChHHHHHHHHHHH
Q psy10746 26 VFVNGRPLPDVVRQRIVELAH 46 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~ 46 (59)
+|.-|.-+|+++|..+||||-
T Consensus 301 SFLkdT~IPEdvkLdvVELay 321 (453)
T PF12039_consen 301 SFLKDTAIPEDVKLDVVELAY 321 (453)
T ss_pred HHhccCCCchhhhhhHHHHHH
Confidence 589999999999999999984
No 79
>cd02062 Nitro_FMN_reductase Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase.
Probab=34.13 E-value=53 Score=18.85 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=16.9
Q ss_pred CCCCCChHHHHHHHHHHHcC
Q psy10746 29 NGRPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~~G 48 (59)
+.+|++++...+|++.|..-
T Consensus 11 ~~~~i~~~~l~~l~~~~~~a 30 (122)
T cd02062 11 TDEPVPEEVLEKILEAARYA 30 (122)
T ss_pred CCCCCCHHHHHHHHHHHHhC
Confidence 46799999999999988643
No 80
>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]
Probab=34.06 E-value=32 Score=27.75 Aligned_cols=26 Identities=35% Similarity=0.441 Sum_probs=18.1
Q ss_pred ccccCCCCCChHHHHHHHHHHHcCCC
Q psy10746 25 GVFVNGRPLPDVVRQRIVELAHNGGL 50 (59)
Q Consensus 25 G~FvNGRPLP~~~R~kIveLA~~GvR 50 (59)
-+||||||+-+.+=.+-|.-|-+-.-
T Consensus 255 ~~fVNgR~V~~~~l~~Ai~~aY~~~L 280 (638)
T COG0323 255 YLFVNGRPVRDKLLNHALREAYADYL 280 (638)
T ss_pred EEEECCCEeccHHHHHHHHHHHHhhc
Confidence 47999999998766665555544333
No 81
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=33.17 E-value=38 Score=23.59 Aligned_cols=24 Identities=17% Similarity=0.409 Sum_probs=19.6
Q ss_pred cccccCCC-----CCChHHHHHHHHHHHc
Q psy10746 24 GGVFVNGR-----PLPDVVRQRIVELAHN 47 (59)
Q Consensus 24 GG~FvNGR-----PLP~~~R~kIveLA~~ 47 (59)
-|+|++|. -|.+++|.++++.+.+
T Consensus 34 ~Gi~~~GstGE~~~Ls~~Er~~~~~~~~~ 62 (285)
T TIGR00674 34 DAIVVVGTTGESPTLSHEEHKKVIEFVVD 62 (285)
T ss_pred CEEEECccCcccccCCHHHHHHHHHHHHH
Confidence 36777775 7999999999998765
No 82
>PRK09492 treR trehalose repressor; Provisional
Probab=30.98 E-value=52 Score=21.80 Aligned_cols=24 Identities=21% Similarity=0.292 Sum_probs=17.9
Q ss_pred CCC-CCChHHHHHHHHHH-HcCCCCC
Q psy10746 29 NGR-PLPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 29 NGR-PLP~~~R~kIveLA-~~GvRps 52 (59)
||+ ...+++|+||.+.| ..|-+|.
T Consensus 26 n~~~~vs~~tr~rV~~~a~elgY~pn 51 (315)
T PRK09492 26 NNESGVSEETRERVEAVINQHGFSPS 51 (315)
T ss_pred CCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence 443 48899999999988 5566654
No 83
>PF02234 CDI: Cyclin-dependent kinase inhibitor; InterPro: IPR003175 Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.; GO: 0004861 cyclin-dependent protein kinase inhibitor activity, 0007050 cell cycle arrest, 0005634 nucleus; PDB: 1H27_E 1JSU_C.
Probab=30.86 E-value=17 Score=20.52 Aligned_cols=9 Identities=67% Similarity=1.125 Sum_probs=6.5
Q ss_pred cccCCCCCC
Q psy10746 26 VFVNGRPLP 34 (59)
Q Consensus 26 ~FvNGRPLP 34 (59)
=|.+|+|||
T Consensus 34 DF~~~~PL~ 42 (51)
T PF02234_consen 34 DFVNDTPLP 42 (51)
T ss_dssp ETTTTEE-S
T ss_pred CCCCCccCC
Confidence 388999997
No 84
>smart00496 IENR2 Intron-encoded nuclease repeat 2. Short helical motif of unknown function (unpublished results).
Probab=30.29 E-value=58 Score=16.77 Aligned_cols=17 Identities=18% Similarity=0.401 Sum_probs=14.6
Q ss_pred CCCCChHHHHHHHHHHH
Q psy10746 30 GRPLPDVVRQRIVELAH 46 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~ 46 (59)
|+.+.++++++|-+.+.
T Consensus 2 GkkhSEETK~KMSea~~ 18 (26)
T smart00496 2 GKKHSEETKKKMSEAAX 18 (26)
T ss_pred CCCCCHHHHHHHHHhhc
Confidence 78899999999998644
No 85
>TIGR03679 arCOG00187 arCOG00187 universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein. This model has the same scope as an archaeal COG (arCOG00187) and is found in all completely sequenced archaea and does not recognize any known non-archaeal genes.
Probab=30.11 E-value=55 Score=22.38 Aligned_cols=32 Identities=16% Similarity=0.263 Sum_probs=25.6
Q ss_pred cccccccCCCCCChHHHHHHHHHHH-cCCCCCcc
Q psy10746 22 QLGGVFVNGRPLPDVVRQRIVELAH-NGGLLSAK 54 (59)
Q Consensus 22 QLGG~FvNGRPLP~~~R~kIveLA~-~GvRps~~ 54 (59)
.|+..|+ ||++-.+...++.+|+. .|+-||-.
T Consensus 147 ~l~~~~l-G~~~~~~~~~~l~~l~~~~~~~~~GE 179 (218)
T TIGR03679 147 GLDESWL-GREIDEKYIEKLKALNKRYGINPAGE 179 (218)
T ss_pred CCChHHC-CCccCHHHHHHHHHHHhhcCccccCC
Confidence 4777787 89999999999888875 48988843
No 86
>PF02878 PGM_PMM_I: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I; InterPro: IPR005844 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 3I3W_B 1WQA_C 1KFQ_B 1KFI_A 2Z0F_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=30.01 E-value=52 Score=20.42 Aligned_cols=20 Identities=20% Similarity=0.449 Sum_probs=15.2
Q ss_pred cCCCCCChHHHHHHHHHHHc
Q psy10746 28 VNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~~ 47 (59)
-||.|++.+.-++|.++...
T Consensus 114 ~~G~~~~~~~~~~I~~~~~~ 133 (137)
T PF02878_consen 114 ANGGPISPEEERKIEQIIER 133 (137)
T ss_dssp TTSSB--HHHHHHHHHHHHH
T ss_pred CCCCcCCHHHHHHHHHHHHh
Confidence 46899999999999998764
No 87
>PRK10969 DNA polymerase III subunit theta; Reviewed
Probab=29.88 E-value=31 Score=21.77 Aligned_cols=19 Identities=26% Similarity=0.363 Sum_probs=16.1
Q ss_pred CCChHHHHHH-HHHHHcCCC
Q psy10746 32 PLPDVVRQRI-VELAHNGGL 50 (59)
Q Consensus 32 PLP~~~R~kI-veLA~~GvR 50 (59)
-||.+.|.|| |+||++||-
T Consensus 7 ~l~qee~dKvnvDLaASgVa 26 (75)
T PRK10969 7 KLSQEEMDKVNVDLAASGVA 26 (75)
T ss_pred hcCHHHHHHHHHHHHHHHHH
Confidence 4788888888 899999974
No 88
>PF11521 TFIIE-A_C-term: C-terminal general transcription factor TFIIE alpha; InterPro: IPR021600 TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C-terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C-terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo []. ; PDB: 2RNR_A 2RNQ_A 2JTX_A.
Probab=29.83 E-value=25 Score=22.14 Aligned_cols=11 Identities=55% Similarity=0.933 Sum_probs=9.6
Q ss_pred cccCCCCCChH
Q psy10746 26 VFVNGRPLPDV 36 (59)
Q Consensus 26 ~FvNGRPLP~~ 36 (59)
|+|+|||+|-+
T Consensus 43 V~V~Gr~~~~~ 53 (86)
T PF11521_consen 43 VMVAGRPYPYS 53 (86)
T ss_dssp EEETTEEEEHH
T ss_pred EEECCEEeehh
Confidence 78999999965
No 89
>PF13265 DUF4056: Protein of unknown function (DUF4056)
Probab=29.52 E-value=22 Score=26.95 Aligned_cols=12 Identities=8% Similarity=0.014 Sum_probs=9.5
Q ss_pred HHcCCCCCcccc
Q psy10746 45 AHNGGLLSAKYS 56 (59)
Q Consensus 45 A~~GvRps~~~~ 56 (59)
+=.|+||||.+-
T Consensus 9 ~P~glRpCCAFG 20 (270)
T PF13265_consen 9 PPVGLRPCCAFG 20 (270)
T ss_pred CCcccccccccC
Confidence 457999999763
No 90
>PRK00132 rpsI 30S ribosomal protein S9; Reviewed
Probab=28.86 E-value=40 Score=22.43 Aligned_cols=20 Identities=35% Similarity=0.606 Sum_probs=13.6
Q ss_pred cccccCCCCC-----ChHHHHHHHH
Q psy10746 24 GGVFVNGRPL-----PDVVRQRIVE 43 (59)
Q Consensus 24 GG~FvNGRPL-----P~~~R~kIve 43 (59)
|-++|||+|| ++..|.+|.|
T Consensus 26 G~i~INg~~~~~yf~~~~~r~~i~~ 50 (130)
T PRK00132 26 GKITVNGRDLEEYFPRETLRMVVRQ 50 (130)
T ss_pred cEEEECCEeHHHHcCCHHHHHHHHH
Confidence 6789999993 3445666543
No 91
>PLN00210 40S ribosomal protein S16; Provisional
Probab=27.53 E-value=55 Score=22.09 Aligned_cols=19 Identities=32% Similarity=0.754 Sum_probs=13.1
Q ss_pred cccccCCCCC----ChHHHHHHH
Q psy10746 24 GGVFVNGRPL----PDVVRQRIV 42 (59)
Q Consensus 24 GG~FvNGRPL----P~~~R~kIv 42 (59)
|-++|||+|| |+..|.+|.
T Consensus 25 G~i~INg~~~~~y~~~~~r~~i~ 47 (141)
T PLN00210 25 GLIKINGCPIELVQPEILRFKAF 47 (141)
T ss_pred ceEEECCCcHHHHCCHHHHHHHH
Confidence 6789999997 344455553
No 92
>cd04250 AAK_NAGK-C AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the non-acetylated, cyclic route of ornithine biosynthesis. In this pathway, glutamate is first N-acetylated and then phosphorylated by NAGK to give phosphoryl NAG, which is converted to NAG-ornithine. There are two variants of this pathway. In one, typified by the pathway in Thermotoga maritima and Pseudomonas aeruginosa, the acetyl group is recycled by reversible transacetylation from acetylornithine to glutamate. The phosphorylation of NAG by NAGK is feedback inhibited by arginine. In photosynthetic organisms, NAGK is the target of the nitrogen-signaling protein PII. Hexameric formation of NAGK domains appears to be essential to both arginine inhibition and NAGK-PII complex formation. NAGK-C are members of the Amino A
Probab=27.30 E-value=47 Score=23.18 Aligned_cols=35 Identities=23% Similarity=0.152 Sum_probs=28.9
Q ss_pred CcceecccccccCCCCCChHHHHHHHHHHHcCCCC
Q psy10746 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLL 51 (59)
Q Consensus 17 ~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRp 51 (59)
+--|=.|||..+....+++.....|.+|...|.++
T Consensus 15 ~~~ViKlGGs~i~~~~~~~~~~~~i~~l~~~g~~~ 49 (279)
T cd04250 15 KTVVIKYGGNAMKDEELKESFARDIVLLKYVGINP 49 (279)
T ss_pred CEEEEEEChHHhcCccHHHHHHHHHHHHHHCCCCE
Confidence 34566799999999999999999999888887653
No 93
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=27.08 E-value=55 Score=20.61 Aligned_cols=19 Identities=21% Similarity=0.349 Sum_probs=16.1
Q ss_pred ccCCCCCChHHHHHHHHHH
Q psy10746 27 FVNGRPLPDVVRQRIVELA 45 (59)
Q Consensus 27 FvNGRPLP~~~R~kIveLA 45 (59)
.|=|.||+++...++.+.+
T Consensus 2 ~~~~~~~~~~~~~~l~~~~ 20 (211)
T PRK11753 2 MVLGKPQTDPTLEWFLSHC 20 (211)
T ss_pred ccccCCCCHHHHHHHHhhC
Confidence 4679999999999998765
No 94
>PRK06425 histidinol-phosphate aminotransferase; Validated
Probab=26.96 E-value=70 Score=22.15 Aligned_cols=20 Identities=20% Similarity=0.302 Sum_probs=17.3
Q ss_pred CCCCChHHHHHHHHHHHc-CC
Q psy10746 30 GRPLPDVVRQRIVELAHN-GG 49 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~-Gv 49 (59)
|.-+|.+.|.+|+++|.. |+
T Consensus 136 G~~~s~~~~~~l~~~a~~~~~ 156 (332)
T PRK06425 136 GNLISRDSLLTISEICRKKGA 156 (332)
T ss_pred CCccCHHHHHHHHHHHHHcCC
Confidence 889999999999999964 53
No 95
>PRK07681 aspartate aminotransferase; Provisional
Probab=26.85 E-value=63 Score=22.92 Aligned_cols=18 Identities=6% Similarity=0.071 Sum_probs=16.6
Q ss_pred CCCCChHHHHHHHHHHHc
Q psy10746 30 GRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~ 47 (59)
|.-+|.+.+++|+++|+.
T Consensus 180 G~~~s~~~~~~i~~~a~~ 197 (399)
T PRK07681 180 PAMAHEDFFKEVIAFAKK 197 (399)
T ss_pred CcCCCHHHHHHHHHHHHH
Confidence 899999999999999974
No 96
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=26.48 E-value=21 Score=19.70 Aligned_cols=11 Identities=45% Similarity=0.894 Sum_probs=9.7
Q ss_pred ccccCCCCCCh
Q psy10746 25 GVFVNGRPLPD 35 (59)
Q Consensus 25 G~FvNGRPLP~ 35 (59)
|+|+||++++.
T Consensus 67 g~~vn~~~~~~ 77 (102)
T cd00060 67 GTFVNGQRVSP 77 (102)
T ss_pred CeEECCEECCC
Confidence 89999999883
No 97
>smart00363 S4 S4 RNA-binding domain.
Probab=26.48 E-value=20 Score=17.60 Aligned_cols=11 Identities=45% Similarity=0.661 Sum_probs=9.2
Q ss_pred ccccccCCCCC
Q psy10746 23 LGGVFVNGRPL 33 (59)
Q Consensus 23 LGG~FvNGRPL 33 (59)
-|.+++||++.
T Consensus 25 ~g~i~vng~~~ 35 (60)
T smart00363 25 QGRVKVNGKKV 35 (60)
T ss_pred cCCEEECCEEe
Confidence 47899999886
No 98
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=26.31 E-value=59 Score=22.89 Aligned_cols=25 Identities=24% Similarity=0.406 Sum_probs=20.6
Q ss_pred cccccCCC-----CCChHHHHHHHHHHHcC
Q psy10746 24 GGVFVNGR-----PLPDVVRQRIVELAHNG 48 (59)
Q Consensus 24 GG~FvNGR-----PLP~~~R~kIveLA~~G 48 (59)
-|+|++|. -|.++.|.+++|.+..-
T Consensus 41 ~gi~v~GstGE~~~Lt~eEr~~v~~~~~~~ 70 (296)
T TIGR03249 41 EALFAAGGTGEFFSLTPAEYEQVVEIAVST 70 (296)
T ss_pred CEEEECCCCcCcccCCHHHHHHHHHHHHHH
Confidence 47788876 79999999999987653
No 99
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=26.19 E-value=51 Score=26.19 Aligned_cols=16 Identities=44% Similarity=0.671 Sum_probs=13.8
Q ss_pred CCCCCChHHHHHHHHH
Q psy10746 29 NGRPLPDVVRQRIVEL 44 (59)
Q Consensus 29 NGRPLP~~~R~kIveL 44 (59)
-|||||.+.|.+|.|=
T Consensus 178 tgr~Lp~eer~~l~ek 193 (382)
T COG1423 178 TGRPLPVEERLELAEK 193 (382)
T ss_pred CCCCCCHHHHHHHHHH
Confidence 5899999999999763
No 100
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=26.11 E-value=71 Score=20.98 Aligned_cols=18 Identities=28% Similarity=0.421 Sum_probs=15.5
Q ss_pred CCCCCChHHHHHHHHHHH
Q psy10746 29 NGRPLPDVVRQRIVELAH 46 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~ 46 (59)
+|...|..++.||++|.+
T Consensus 95 ~~~~~~~~Vk~kil~li~ 112 (139)
T cd03567 95 LGSRTSEKVKTKIIELLY 112 (139)
T ss_pred CCCCCCHHHHHHHHHHHH
Confidence 477789999999999975
No 101
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=26.10 E-value=58 Score=22.91 Aligned_cols=26 Identities=19% Similarity=0.215 Sum_probs=20.6
Q ss_pred cccccCC-----CCCChHHHHHHHHHHHcCC
Q psy10746 24 GGVFVNG-----RPLPDVVRQRIVELAHNGG 49 (59)
Q Consensus 24 GG~FvNG-----RPLP~~~R~kIveLA~~Gv 49 (59)
-|+|++| --|.+++|.++++.+..-+
T Consensus 36 ~gi~v~GstGE~~~Ls~eEr~~l~~~~~~~~ 66 (289)
T cd00951 36 AALFAAGGTGEFFSLTPDEYAQVVRAAVEET 66 (289)
T ss_pred CEEEECcCCcCcccCCHHHHHHHHHHHHHHh
Confidence 3677777 5899999999999876543
No 102
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=26.08 E-value=79 Score=18.07 Aligned_cols=22 Identities=23% Similarity=0.303 Sum_probs=14.1
Q ss_pred CCCCCChHHHHHHHHHHHcCCC
Q psy10746 29 NGRPLPDVVRQRIVELAHNGGL 50 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~~GvR 50 (59)
.|.+|-+.++-+|.-|-+.|..
T Consensus 1 RG~~Lt~~Eqaqid~m~qlG~s 22 (50)
T PF11427_consen 1 RGKTLTDAEQAQIDVMHQLGMS 22 (50)
T ss_dssp -S----HHHHHHHHHHHHTT--
T ss_pred CCCcCCHHHHHHHHHHHHhchh
Confidence 4889999999999999998875
No 103
>PF15027 DUF4525: Domain of unknown function (DUF4525)
Probab=25.79 E-value=48 Score=23.10 Aligned_cols=21 Identities=19% Similarity=0.251 Sum_probs=15.5
Q ss_pred CCCC-CChHHHHHHHHHHHcCC
Q psy10746 29 NGRP-LPDVVRQRIVELAHNGG 49 (59)
Q Consensus 29 NGRP-LP~~~R~kIveLA~~Gv 49 (59)
+.|+ =+.++|.+|++|+..=|
T Consensus 34 q~~~~ss~~LR~QILdLSkrYV 55 (138)
T PF15027_consen 34 QPRHQSSAELREQILDLSKRYV 55 (138)
T ss_pred CCCccChHHHHHHHHHHHHHHH
Confidence 3443 67899999999987533
No 104
>PLN00143 tyrosine/nicotianamine aminotransferase; Provisional
Probab=25.70 E-value=72 Score=22.97 Aligned_cols=20 Identities=25% Similarity=0.199 Sum_probs=17.7
Q ss_pred CCCCChHHHHHHHHHHHc-CC
Q psy10746 30 GRPLPDVVRQRIVELAHN-GG 49 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~-Gv 49 (59)
|+-++.+.+++|+++|++ ++
T Consensus 184 G~~~s~~~~~~l~~~a~~~~~ 204 (409)
T PLN00143 184 GSVYSYEHLNKIAETARKLGI 204 (409)
T ss_pred CCccCHHHHHHHHHHHHHcCC
Confidence 899999999999999975 54
No 105
>cd01360 Adenylsuccinate_lyase_1 Adenylsuccinate lyase (ASL)_subgroup 1. This subgroup contains bacterial and archeal proteins similar to ASL, a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASL catalyzes two steps in the de novo purine biosynthesis: the conversion of 5-aminoimidazole-(N-succinylocarboxamide) ribotide (SAICAR) into 5-aminoimidazole-4-carboxamide ribotide (AICAR) and, the conversion of adenylsuccinate (SAMP) into adenosine monophosphate (AMP).
Probab=25.68 E-value=90 Score=23.20 Aligned_cols=37 Identities=19% Similarity=0.104 Sum_probs=28.8
Q ss_pred ceecccccccCCCCCChHHHHHHHHHHHcCCCCCccccc
Q psy10746 19 GVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSAKYSH 57 (59)
Q Consensus 19 ~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~~~~~ 57 (59)
.+++|||.--+|-++|...|.+..++ -|..+..-.+|
T Consensus 173 ~~~~lgga~Gt~~~~~~~~~~~~a~~--LG~~~~~~~~~ 209 (387)
T cd01360 173 LVGKISGAVGTYANLGPEVEERVAEK--LGLKPEPISTQ 209 (387)
T ss_pred HhhccchHhhcCccCCHHHHHHHHHH--cCCCCCCCCCc
Confidence 56899998889999997788888876 57776655555
No 106
>cd02144 iodotyrosine_dehalogenase Iodotyrosine dehalogenase catalyzes the removal of iodine from the 3, 5 positions of L-tyosine in thyroid, liver and kidney, using NADPH as electron donor. This enzyme is a homolog of the nitroreductase family. These enzymes are usually homodimers.
Probab=25.61 E-value=93 Score=19.50 Aligned_cols=27 Identities=22% Similarity=0.286 Sum_probs=21.1
Q ss_pred ccccCCCCCChHHHHHHHHHHHcCCCCCcc
Q psy10746 25 GVFVNGRPLPDVVRQRIVELAHNGGLLSAK 54 (59)
Q Consensus 25 G~FvNGRPLP~~~R~kIveLA~~GvRps~~ 54 (59)
..|- ++|+|+++=.+|+++|.. -||..
T Consensus 12 R~f~-~~~v~~e~l~~il~aa~~--APS~~ 38 (193)
T cd02144 12 RKFS-DEPVPREVIENCIRTAGT--APSGA 38 (193)
T ss_pred cCCC-CCCCCHHHHHHHHHHHHh--CCCcC
Confidence 3465 579999999999999985 45554
No 107
>PRK06836 aspartate aminotransferase; Provisional
Probab=25.59 E-value=81 Score=22.39 Aligned_cols=22 Identities=9% Similarity=0.049 Sum_probs=19.1
Q ss_pred cccCCCCCChHHHHHHHHHHHc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~ 47 (59)
..+-|..+|.+.+.+|++||+.
T Consensus 178 ~NPtG~~~~~~~~~~l~~la~~ 199 (394)
T PRK06836 178 NNPTGVVYSEETLKALAALLEE 199 (394)
T ss_pred CCCCCcCCCHHHHHHHHHHHHH
Confidence 3556999999999999999975
No 108
>PF00380 Ribosomal_S9: Ribosomal protein S9/S16; InterPro: IPR000754 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S9 is one of the proteins from the small ribosomal subunit. It belongs to the S9P family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial; algal chloroplast; cyanelle and archaeal S9 proteins; and mammalian; plant; and yeast mitochondrial ribosomal S9 proteins. These proteins adopt a beta-alpha-beta fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V46_I 3T1H_I 3MR8_I 3F1G_I 3D5C_I 3D5A_I 2WDG_I 3MS0_I 2WDM_I 2J02_I ....
Probab=25.42 E-value=4.9 Score=26.27 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=8.8
Q ss_pred cccccCCCCC
Q psy10746 24 GGVFVNGRPL 33 (59)
Q Consensus 24 GG~FvNGRPL 33 (59)
|-+.|||+||
T Consensus 17 G~i~INg~~l 26 (121)
T PF00380_consen 17 GKIRINGKPL 26 (121)
T ss_dssp SEEEETTSEH
T ss_pred eEEEECCEEH
Confidence 6679999999
No 109
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=25.09 E-value=21 Score=17.92 Aligned_cols=11 Identities=45% Similarity=0.764 Sum_probs=9.1
Q ss_pred ccccccCCCCC
Q psy10746 23 LGGVFVNGRPL 33 (59)
Q Consensus 23 LGG~FvNGRPL 33 (59)
-|++++||+..
T Consensus 25 ~g~V~vn~~~~ 35 (70)
T cd00165 25 HGHVLVNGKVV 35 (70)
T ss_pred cCCEEECCEEc
Confidence 57899999876
No 110
>cd02136 Nitroreductase Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source of reducing equivalents in an obligatory two-election transfer mechanism. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=24.76 E-value=1.2e+02 Score=18.94 Aligned_cols=26 Identities=23% Similarity=0.362 Sum_probs=19.8
Q ss_pred cccCCCCCChHHHHHHHHHHHcCCCCCcc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNGGLLSAK 54 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~GvRps~~ 54 (59)
.|- ++|+|++.-.+|++.|..- ||..
T Consensus 13 ~f~-~~~v~~e~l~~il~~a~~a--Ps~~ 38 (178)
T cd02136 13 AFL-PDPVPRETIEEILAAAQRA--PSGC 38 (178)
T ss_pred cCC-CCCCCHHHHHHHHHHHHhC--cccc
Confidence 344 6799999999999998743 5544
No 111
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=24.76 E-value=52 Score=19.67 Aligned_cols=12 Identities=42% Similarity=0.969 Sum_probs=9.9
Q ss_pred CCChHHHHHHHH
Q psy10746 32 PLPDVVRQRIVE 43 (59)
Q Consensus 32 PLP~~~R~kIve 43 (59)
|||..+|.++=.
T Consensus 1 PLp~~~r~~~e~ 12 (79)
T PF13699_consen 1 PLPESIRSRLER 12 (79)
T ss_pred CCCHHHHHHHHH
Confidence 899999988753
No 112
>PRK07590 L,L-diaminopimelate aminotransferase; Validated
Probab=24.53 E-value=75 Score=22.68 Aligned_cols=18 Identities=22% Similarity=0.237 Sum_probs=16.7
Q ss_pred CCCCChHHHHHHHHHHHc
Q psy10746 30 GRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~ 47 (59)
|+-++.+.|++|+++|+.
T Consensus 190 G~~~s~~~~~~l~~~a~~ 207 (409)
T PRK07590 190 GTVLTKEQLKAWVDYAKE 207 (409)
T ss_pred CCcCCHHHHHHHHHHHHH
Confidence 999999999999999964
No 113
>PRK08068 transaminase; Reviewed
Probab=24.47 E-value=73 Score=22.44 Aligned_cols=20 Identities=15% Similarity=0.169 Sum_probs=17.4
Q ss_pred cCCCCCChHHHHHHHHHHHc
Q psy10746 28 VNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~~ 47 (59)
+-|.-+|.+.+++|+++|++
T Consensus 179 PTG~~~s~~~~~~l~~la~~ 198 (389)
T PRK08068 179 PTGAVATKAFFEETVAFAKK 198 (389)
T ss_pred CCCCcCCHHHHHHHHHHHHH
Confidence 45888999999999999875
No 114
>PRK14982 acyl-ACP reductase; Provisional
Probab=24.37 E-value=86 Score=23.59 Aligned_cols=27 Identities=22% Similarity=0.059 Sum_probs=22.3
Q ss_pred ccCCCC-CChHHHHHHHHHH-HcCCCCCc
Q psy10746 27 FVNGRP-LPDVVRQRIVELA-HNGGLLSA 53 (59)
Q Consensus 27 FvNGRP-LP~~~R~kIveLA-~~GvRps~ 53 (59)
|-=||. |+.+.=++|-+|| +||.+|.-
T Consensus 310 fS~Gr~~i~~~~v~~i~~~a~kHGf~~~~ 338 (340)
T PRK14982 310 FSWGRNQITLEKMEFIGEASVKHGFSPLL 338 (340)
T ss_pred CCcCccccCHHHHHHHHHHHHHcCCcccc
Confidence 444898 9999999999999 78888863
No 115
>PRK09257 aromatic amino acid aminotransferase; Provisional
Probab=24.33 E-value=77 Score=22.45 Aligned_cols=21 Identities=24% Similarity=0.295 Sum_probs=17.9
Q ss_pred CCCCCChHHHHHHHHHHHc-CC
Q psy10746 29 NGRPLPDVVRQRIVELAHN-GG 49 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~~-Gv 49 (59)
-|+-++.+.|++|+++|.. ++
T Consensus 185 TG~~~s~~~~~~l~~~a~~~~~ 206 (396)
T PRK09257 185 TGADLTPEQWDELAELLKERGL 206 (396)
T ss_pred CCCCCCHHHHHHHHHHHHhCCc
Confidence 4888999999999999964 54
No 116
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 4, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=24.24 E-value=56 Score=19.00 Aligned_cols=26 Identities=27% Similarity=0.523 Sum_probs=19.4
Q ss_pred cccCCCCC-----ChHHHHHHHHHHHcCCCC
Q psy10746 26 VFVNGRPL-----PDVVRQRIVELAHNGGLL 51 (59)
Q Consensus 26 ~FvNGRPL-----P~~~R~kIveLA~~GvRp 51 (59)
+|+||..+ |..+-..+-+|-.+|.-+
T Consensus 1 VFlNG~~iG~~~~p~~l~~~lr~~RR~g~i~ 31 (63)
T PF04566_consen 1 VFLNGVWIGIHSDPEELVKTLRNLRRSGKIS 31 (63)
T ss_dssp EEETTEEEEEESSHHHHHHHHHHHHHTTSS-
T ss_pred CEECCEEEEEEcCHHHHHHHHHHHhhccCCc
Confidence 68888876 677888888888887543
No 117
>PRK09440 avtA valine--pyruvate transaminase; Provisional
Probab=24.17 E-value=72 Score=22.63 Aligned_cols=22 Identities=23% Similarity=0.222 Sum_probs=18.5
Q ss_pred cCCCCCChHHHHHHHHHHHc-CC
Q psy10746 28 VNGRPLPDVVRQRIVELAHN-GG 49 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~~-Gv 49 (59)
+-|+-++.+.|++|+++|.+ ++
T Consensus 191 PTG~~~s~~~~~~l~~~a~~~~~ 213 (416)
T PRK09440 191 PTGNVLTDEELEKLDALARQHNI 213 (416)
T ss_pred CCCccCCHHHHHHHHHHHHHcCC
Confidence 45899999999999999964 54
No 118
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=24.04 E-value=66 Score=22.85 Aligned_cols=26 Identities=19% Similarity=0.216 Sum_probs=21.0
Q ss_pred cccccCC-----CCCChHHHHHHHHHHHcCC
Q psy10746 24 GGVFVNG-----RPLPDVVRQRIVELAHNGG 49 (59)
Q Consensus 24 GG~FvNG-----RPLP~~~R~kIveLA~~Gv 49 (59)
-|+|++| --|..++|.++++.+..-+
T Consensus 43 ~Gi~~~GstGE~~~Lt~eEr~~~~~~~~~~~ 73 (303)
T PRK03620 43 AALFAAGGTGEFFSLTPDEYSQVVRAAVETT 73 (303)
T ss_pred CEEEECcCCcCcccCCHHHHHHHHHHHHHHh
Confidence 4788888 4799999999999875433
No 119
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=23.79 E-value=1.1e+02 Score=16.78 Aligned_cols=19 Identities=16% Similarity=0.228 Sum_probs=15.2
Q ss_pred CCCChHHHHHHHHHHHcCC
Q psy10746 31 RPLPDVVRQRIVELAHNGG 49 (59)
Q Consensus 31 RPLP~~~R~kIveLA~~Gv 49 (59)
+.|..+.+.+||++...|.
T Consensus 5 ~~LTl~eK~~iI~~~e~g~ 23 (53)
T PF04218_consen 5 KSLTLEEKLEIIKRLEEGE 23 (53)
T ss_dssp SS--HHHHHHHHHHHHCTT
T ss_pred ccCCHHHHHHHHHHHHcCC
Confidence 4678899999999999998
No 120
>cd02151 NADPH_oxidoreductase_2 NAD(P)H:flavin oxidoreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=23.66 E-value=95 Score=19.31 Aligned_cols=21 Identities=14% Similarity=0.252 Sum_probs=17.9
Q ss_pred cccCCCCCChHHHHHHHHHHHc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~ 47 (59)
.| .++|+|++.-++|++.|..
T Consensus 13 ~f-~~~~v~~e~l~~il~aa~~ 33 (162)
T cd02151 13 KF-TDEPVEKEKVDALLKAALR 33 (162)
T ss_pred cC-CCCCCCHHHHHHHHHHHHh
Confidence 45 4789999999999998875
No 121
>PHA02554 13 neck protein; Provisional
Probab=23.63 E-value=44 Score=25.85 Aligned_cols=31 Identities=35% Similarity=0.538 Sum_probs=27.2
Q ss_pred CCcceecccccccCCCCCChHHHHHHHHHHH
Q psy10746 16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAH 46 (59)
Q Consensus 16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~ 46 (59)
-+.|+=..||+-+|||-|=++-|++|=+|-.
T Consensus 267 K~qGmqLPGGITldG~~i~eeA~~eie~Lr~ 297 (311)
T PHA02554 267 KHQGMQLPGGVTLDGRRLIEEARQEKEKLRE 297 (311)
T ss_pred HccCcccCCceeechHhHHHHHHHHHHHHHH
Confidence 4678889999999999999999999987753
No 122
>PTZ00086 40S ribosomal protein S16; Provisional
Probab=23.50 E-value=67 Score=21.86 Aligned_cols=19 Identities=42% Similarity=0.842 Sum_probs=13.3
Q ss_pred cccccCCCCC----ChHHHHHHH
Q psy10746 24 GGVFVNGRPL----PDVVRQRIV 42 (59)
Q Consensus 24 GG~FvNGRPL----P~~~R~kIv 42 (59)
|-++|||+|| |+..|.+|.
T Consensus 31 G~i~INg~~l~~y~~~~~r~~i~ 53 (147)
T PTZ00086 31 GLIRVNGVPLDLINPETLRAKVF 53 (147)
T ss_pred ceEEECCcCHHHhCcHHHHHHHH
Confidence 6789999996 444555554
No 123
>PF02836 Glyco_hydro_2_C: Glycosyl hydrolases family 2, TIM barrel domain; InterPro: IPR006103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. Beta-galactosidase from E. coli has a TIM-barrel-like core surrounded by four other largely beta domains [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3CMG_A 3FN9_C 1YQ2_A 3K4D_B 3LPG_B 3LPF_A 3K4A_B 3K46_B 3GM8_A 3DEC_A ....
Probab=23.46 E-value=18 Score=24.91 Aligned_cols=10 Identities=50% Similarity=1.454 Sum_probs=6.2
Q ss_pred cccccCCCCC
Q psy10746 24 GGVFVNGRPL 33 (59)
Q Consensus 24 GG~FvNGRPL 33 (59)
||.|+||+|+
T Consensus 6 ~~~~lNGk~~ 15 (298)
T PF02836_consen 6 GGFYLNGKPI 15 (298)
T ss_dssp TEEEETTEEE
T ss_pred CEEEECCEEE
Confidence 4566776654
No 124
>PF06236 MelC1: Tyrosinase co-factor MelC1; InterPro: IPR010928 This family consists of several tyrosinase co-factor MELC1 proteins from a number of Streptomyces species. The melanin operon (melC) of Streptomyces antibioticus contains two genes, melC1 and melC2 (apotyrosinase). It is thought that MelC1 forms a transient binary complex with the downstream apotyrosinase MelC2 to facilitate the incorporation of copper ion and the secretion of tyrosinase indicating that MelC1 is a chaperone for the apotyrosinase MelC2 [].; GO: 0005507 copper ion binding, 0042438 melanin biosynthetic process; PDB: 1WX4_B 2ZWD_B 2ZMZ_B 1WX2_B 1WX5_D 3AWX_B 3AWS_B 2ZMY_B 3AX0_B 2ZWG_B ....
Probab=23.44 E-value=18 Score=24.55 Aligned_cols=9 Identities=56% Similarity=1.047 Sum_probs=7.6
Q ss_pred cccCCCCCC
Q psy10746 26 VFVNGRPLP 34 (59)
Q Consensus 26 ~FvNGRPLP 34 (59)
|||+||||.
T Consensus 73 V~IDGr~Lh 81 (125)
T PF06236_consen 73 VTIDGRPLH 81 (125)
T ss_dssp EEETTEEE-
T ss_pred EEECCeEee
Confidence 899999996
No 125
>PF11010 DUF2848: Protein of unknown function (DUF2848); InterPro: IPR021269 This bacterial family of proteins has no known function.
Probab=23.40 E-value=77 Score=22.79 Aligned_cols=21 Identities=29% Similarity=0.268 Sum_probs=17.9
Q ss_pred ChHHHHHHHHHHHcCCCCCcc
Q psy10746 34 PDVVRQRIVELAHNGGLLSAK 54 (59)
Q Consensus 34 P~~~R~kIveLA~~GvRps~~ 54 (59)
++.+...|-|||+-||-|+.+
T Consensus 8 ~~av~~HI~EL~~lGVp~Ps~ 28 (194)
T PF11010_consen 8 QEAVEHHIEELAALGVPPPSS 28 (194)
T ss_pred HHHHHHHHHHHHHhCCCCCCC
Confidence 467889999999999988764
No 126
>PRK10281 hypothetical protein; Provisional
Probab=23.09 E-value=60 Score=23.34 Aligned_cols=24 Identities=29% Similarity=0.304 Sum_probs=19.5
Q ss_pred ceecccccccCCCCCChHHHHHHHH
Q psy10746 19 GVNQLGGVFVNGRPLPDVVRQRIVE 43 (59)
Q Consensus 19 ~vNQLGG~FvNGRPLP~~~R~kIve 43 (59)
+=|++ +|+++...|+++..|+|-.
T Consensus 17 ~GNpa-aVv~~a~~L~~~~Mq~IAr 40 (299)
T PRK10281 17 RGNSA-GVVLNADGLSEAQMQLIAR 40 (299)
T ss_pred CCCce-EEEcCCCCCCHHHHHHHHH
Confidence 34887 6778889999999999954
No 127
>PF13565 HTH_32: Homeodomain-like domain
Probab=23.06 E-value=1.1e+02 Score=16.66 Aligned_cols=20 Identities=35% Similarity=0.539 Sum_probs=15.8
Q ss_pred CCCCC-ChHHHHHHHHHHHcC
Q psy10746 29 NGRPL-PDVVRQRIVELAHNG 48 (59)
Q Consensus 29 NGRPL-P~~~R~kIveLA~~G 48 (59)
.|||. ++++++.|+++....
T Consensus 26 ~Grp~~~~e~~~~i~~~~~~~ 46 (77)
T PF13565_consen 26 PGRPRKDPEQRERIIALIEEH 46 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHhC
Confidence 67775 488889999997654
No 128
>PRK07366 succinyldiaminopimelate transaminase; Validated
Probab=23.05 E-value=80 Score=22.15 Aligned_cols=18 Identities=17% Similarity=0.078 Sum_probs=16.7
Q ss_pred CCCCChHHHHHHHHHHHc
Q psy10746 30 GRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~ 47 (59)
|.-++.+.+++|+++|..
T Consensus 179 G~~~s~~~~~~l~~~a~~ 196 (388)
T PRK07366 179 TAIAPLSFFQEAVAFCQQ 196 (388)
T ss_pred CccCCHHHHHHHHHHHHH
Confidence 999999999999999974
No 129
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=22.93 E-value=26 Score=19.19 Aligned_cols=12 Identities=42% Similarity=0.390 Sum_probs=9.7
Q ss_pred cccccccCCCCC
Q psy10746 22 QLGGVFVNGRPL 33 (59)
Q Consensus 22 QLGG~FvNGRPL 33 (59)
+=|.++|||.+.
T Consensus 32 ~~G~V~VNg~~~ 43 (59)
T TIGR02988 32 QENEVLVNGELE 43 (59)
T ss_pred HcCCEEECCEEc
Confidence 448899999876
No 130
>PRK07865 N-succinyldiaminopimelate aminotransferase; Reviewed
Probab=22.91 E-value=81 Score=21.92 Aligned_cols=19 Identities=26% Similarity=0.288 Sum_probs=16.6
Q ss_pred CCCCCChHHHHHHHHHHHc
Q psy10746 29 NGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~~ 47 (59)
-|.-++.+.|++|+++|++
T Consensus 161 tG~~~~~~~~~~i~~~a~~ 179 (364)
T PRK07865 161 TGRVLGVDHLRKVVAWARE 179 (364)
T ss_pred CCccCCHHHHHHHHHHHHH
Confidence 4888999999999999974
No 131
>PF10615 DUF2470: Protein of unknown function (DUF2470); InterPro: IPR019595 This entry represents a putative haem-iron utilisation family of proteins, as many members are annotated as being pyridoxamine 5'-phosphate oxidase-related, FMN-binding; however the function of this domain is not known. ; PDB: 3GAS_D 3SWJ_A 2ARZ_B.
Probab=22.88 E-value=34 Score=19.97 Aligned_cols=11 Identities=36% Similarity=0.634 Sum_probs=9.2
Q ss_pred hHHHHHHHHHH
Q psy10746 35 DVVRQRIVELA 45 (59)
Q Consensus 35 ~~~R~kIveLA 45 (59)
.+.|.++|+||
T Consensus 73 ~e~r~~lV~ma 83 (83)
T PF10615_consen 73 EEARDALVEMA 83 (83)
T ss_dssp CCHHHHHHHHH
T ss_pred HHHHHHHHHhC
Confidence 47899999987
No 132
>PRK07570 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated
Probab=22.67 E-value=23 Score=25.34 Aligned_cols=20 Identities=40% Similarity=0.795 Sum_probs=14.2
Q ss_pred CcceecccccccCCCC-CChH
Q psy10746 17 HGGVNQLGGVFVNGRP-LPDV 36 (59)
Q Consensus 17 ~~~vNQLGG~FvNGRP-LP~~ 36 (59)
..+|+=-=++-|||+| ||..
T Consensus 59 r~~iCGsCam~ING~p~~~~~ 79 (250)
T PRK07570 59 REGICGMCGLVINGRPHGPDR 79 (250)
T ss_pred cCCcCCcceeEECCccCCCCc
Confidence 4566666689999999 4443
No 133
>PRK06207 aspartate aminotransferase; Provisional
Probab=22.50 E-value=91 Score=22.43 Aligned_cols=18 Identities=22% Similarity=0.176 Sum_probs=16.7
Q ss_pred CCCCChHHHHHHHHHHHc
Q psy10746 30 GRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~ 47 (59)
|+-+|.+.+++|+++|++
T Consensus 192 G~~~s~e~l~~l~~~a~~ 209 (405)
T PRK06207 192 GVVYSAEEIAQIAALARR 209 (405)
T ss_pred CcCCCHHHHHHHHHHHHH
Confidence 899999999999999965
No 134
>PRK00942 acetylglutamate kinase; Provisional
Probab=22.39 E-value=68 Score=22.35 Aligned_cols=34 Identities=24% Similarity=0.180 Sum_probs=28.5
Q ss_pred cceecccccccCCCCCChHHHHHHHHHHHcCCCC
Q psy10746 18 GGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLL 51 (59)
Q Consensus 18 ~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRp 51 (59)
--|=.+||..+...-.++.+...|..|...|.++
T Consensus 25 ~iViK~GGs~l~~~~~~~~l~~~i~~l~~~g~~v 58 (283)
T PRK00942 25 TIVIKYGGNAMTDEELKEAFARDIVLLKQVGINP 58 (283)
T ss_pred eEEEEEChHHhcCcchHHHHHHHHHHHHHCCCCE
Confidence 3466799999988888889999999999998764
No 135
>PF06097 DUF945: Bacterial protein of unknown function (DUF945); InterPro: IPR010352 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.36 E-value=33 Score=24.55 Aligned_cols=13 Identities=38% Similarity=0.797 Sum_probs=10.4
Q ss_pred cccccCCCCCChH
Q psy10746 24 GGVFVNGRPLPDV 36 (59)
Q Consensus 24 GG~FvNGRPLP~~ 36 (59)
|-+.+||+|+|.+
T Consensus 446 g~l~lNG~~ipl~ 458 (460)
T PF06097_consen 446 GQLTLNGQPIPLP 458 (460)
T ss_pred CEEEECCeECchh
Confidence 5677899999964
No 136
>PF04829 PT-VENN: Pre-toxin domain with VENN motif; InterPro: IPR006914 This group of proteins, mainly from Neisseria meningitidis, may have haemagglutinin or haemolysin activity. A number of them have a second conserved domain, IPR006915 from INTERPRO, which is found in possible Pseudomonas aeruginosa haemagglutinins []. Filamentous haemagglutinin (FHA) is a major virulence attachment factor produced by certain bacterial species that functions as both a primary adhesin and an immunomodulator. Haemolysin is pore-forming toxin.
Probab=22.30 E-value=93 Score=17.95 Aligned_cols=15 Identities=20% Similarity=0.423 Sum_probs=13.0
Q ss_pred CCChHHHHHHHHHHH
Q psy10746 32 PLPDVVRQRIVELAH 46 (59)
Q Consensus 32 PLP~~~R~kIveLA~ 46 (59)
.|+++.|++|..|+.
T Consensus 4 ~Lte~eK~~v~~ls~ 18 (55)
T PF04829_consen 4 ELTEEEKQKVSALSQ 18 (55)
T ss_pred hcCHHHHHHHHHHHH
Confidence 589999999998875
No 137
>PRK06348 aspartate aminotransferase; Provisional
Probab=22.27 E-value=86 Score=22.10 Aligned_cols=19 Identities=16% Similarity=0.261 Sum_probs=17.0
Q ss_pred CCCCCChHHHHHHHHHHHc
Q psy10746 29 NGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~~ 47 (59)
-|..++.+.+++|+++|++
T Consensus 175 tG~~~s~~~~~~l~~~a~~ 193 (384)
T PRK06348 175 TGAVFSKETLEEIAKIAIE 193 (384)
T ss_pred CCcCCCHHHHHHHHHHHHH
Confidence 4999999999999999964
No 138
>PF03450 CO_deh_flav_C: CO dehydrogenase flavoprotein C-terminal domain; InterPro: IPR005107 Proteins containing this domain form structural complexes with other known families, such as IPR008274 from INTERPRO and IPR001041 from INTERPRO]. The carbon monoxide (CO) dehydrogenase of Oligotropha carboxidovorans is a heterotrimeric complex composed of a apoflavoprotein, a molybdoprotein, and an iron-sulphur protein. It can be dissociated with sodium dodecylsulphate []. CO dehydrogenase catalyzes the oxidation of CO according to the following equation []: CO + H2O = CO2 + 2e + 2H+ Subunit S represents the iron-sulphur protein of CO dehydrogenase and is clearly divided into a C- and an N-terminal domain, each binding a [2Fe-2S] cluster [].; PDB: 3EUB_K 3NS1_K 3NVV_B 1FO4_B 3AM9_A 3AX7_B 3BDJ_A 3ETR_B 3UNI_A 3AMZ_A ....
Probab=22.27 E-value=55 Score=19.32 Aligned_cols=28 Identities=14% Similarity=0.114 Sum_probs=22.7
Q ss_pred ccCCCCCChHHHHHHHHHHHcCCCCCcc
Q psy10746 27 FVNGRPLPDVVRQRIVELAHNGGLLSAK 54 (59)
Q Consensus 27 FvNGRPLP~~~R~kIveLA~~GvRps~~ 54 (59)
+..|++|.+++=+++.+.....+.|...
T Consensus 53 ~L~g~~~~~~~~~~~~~~~~~~~~~~~d 80 (103)
T PF03450_consen 53 ALIGKPLSEETLEEAAEAVSEEIDPISD 80 (103)
T ss_dssp HTTTSBSSHHHHHHHHHHHHHHTHHCTT
T ss_pred HHhhcchhhhhHHHHHHHHHhcCCCCCC
Confidence 5789999999999999988877766543
No 139
>PRK06855 aminotransferase; Validated
Probab=22.03 E-value=84 Score=22.97 Aligned_cols=18 Identities=28% Similarity=0.556 Sum_probs=16.7
Q ss_pred CCCCChHHHHHHHHHHHc
Q psy10746 30 GRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~ 47 (59)
|+-+|.+.|++|+++|.+
T Consensus 185 G~~~s~~~~~~l~~~a~~ 202 (433)
T PRK06855 185 GAVYPKEILREIVDIARE 202 (433)
T ss_pred CcCCCHHHHHHHHHHHHH
Confidence 999999999999999964
No 140
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=21.96 E-value=30 Score=19.20 Aligned_cols=9 Identities=56% Similarity=1.080 Sum_probs=5.4
Q ss_pred cCCCCCChH
Q psy10746 28 VNGRPLPDV 36 (59)
Q Consensus 28 vNGRPLP~~ 36 (59)
++|+|||..
T Consensus 24 ~~G~pl~p~ 32 (36)
T PF14787_consen 24 VDGNPLPPP 32 (36)
T ss_dssp CCCEE-S--
T ss_pred ccCCCCcCc
Confidence 789999954
No 141
>PF14069 SpoVIF: Stage VI sporulation protein F
Probab=21.92 E-value=1.4e+02 Score=18.55 Aligned_cols=23 Identities=13% Similarity=0.212 Sum_probs=18.2
Q ss_pred CCCCCChHHHHHHHHHH-HcCCCCC
Q psy10746 29 NGRPLPDVVRQRIVELA-HNGGLLS 52 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA-~~GvRps 52 (59)
=|+|+|++.=.+||+.- .+|+ |.
T Consensus 44 an~~Vs~~~ed~IV~~I~~~~~-p~ 67 (79)
T PF14069_consen 44 ANKPVSKEQEDQIVQAIINQKI-PN 67 (79)
T ss_pred hCCCCCHHHHHHHHHHHHhCCC-Cc
Confidence 47999999999999987 4455 54
No 142
>PHA00738 putative HTH transcription regulator
Probab=21.74 E-value=68 Score=21.19 Aligned_cols=16 Identities=25% Similarity=0.532 Sum_probs=12.1
Q ss_pred CChHHHHHHHHHHHcC
Q psy10746 33 LPDVVRQRIVELAHNG 48 (59)
Q Consensus 33 LP~~~R~kIveLA~~G 48 (59)
-.|.+|++|+++-..|
T Consensus 9 ~~dptRr~IL~lL~~~ 24 (108)
T PHA00738 9 RAKILRRKILELIAEN 24 (108)
T ss_pred cCCHHHHHHHHHHHHc
Confidence 3588999999965554
No 143
>TIGR03542 DAPAT_plant LL-diaminopimelate aminotransferase. This clade of the pfam00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). This clade includes characterized species in plants and Chlamydia. Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh).
Probab=21.72 E-value=87 Score=22.30 Aligned_cols=18 Identities=22% Similarity=0.351 Sum_probs=16.8
Q ss_pred CCCCChHHHHHHHHHHHc
Q psy10746 30 GRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~ 47 (59)
|..++.+.+++|+++|++
T Consensus 187 G~~~s~~~~~~l~~~a~~ 204 (402)
T TIGR03542 187 GTVLTKEQLKELVDYANE 204 (402)
T ss_pred CccCCHHHHHHHHHHHHH
Confidence 999999999999999974
No 144
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.63 E-value=86 Score=15.79 Aligned_cols=12 Identities=50% Similarity=0.617 Sum_probs=10.2
Q ss_pred HHHHHHHHHcCC
Q psy10746 38 RQRIVELAHNGG 49 (59)
Q Consensus 38 R~kIveLA~~Gv 49 (59)
|.+||++..+|.
T Consensus 2 r~~iv~~~~~g~ 13 (52)
T PF13518_consen 2 RLQIVELYLEGE 13 (52)
T ss_pred HHHHHHHHHcCC
Confidence 678999998886
No 145
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=21.62 E-value=1.2e+02 Score=20.98 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=19.5
Q ss_pred cccCCCCCChHHHHHHHHHHHcC
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~G 48 (59)
.|..-.+|++++|.+|.++...+
T Consensus 10 ~f~~~~~lse~~r~~Iy~~~~~~ 32 (172)
T PF12298_consen 10 SFRSNPVLSEELREQIYEDVMQD 32 (172)
T ss_pred CCCCCCcCCHHHHHHHHHHHHhC
Confidence 47777899999999999998654
No 146
>PRK06290 aspartate aminotransferase; Provisional
Probab=21.52 E-value=87 Score=22.84 Aligned_cols=19 Identities=16% Similarity=0.312 Sum_probs=16.8
Q ss_pred CCCCCChHHHHHHHHHHHc
Q psy10746 29 NGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~~ 47 (59)
-|.-+|.+.+++|+++|++
T Consensus 192 TG~v~s~e~l~~l~~la~~ 210 (410)
T PRK06290 192 TGAVATKEFYEEVVDFAKE 210 (410)
T ss_pred CCcCCCHHHHHHHHHHHHH
Confidence 3888999999999999964
No 147
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=21.46 E-value=29 Score=23.46 Aligned_cols=12 Identities=58% Similarity=0.733 Sum_probs=10.1
Q ss_pred cccccCCCCCCh
Q psy10746 24 GGVFVNGRPLPD 35 (59)
Q Consensus 24 GG~FvNGRPLP~ 35 (59)
+++||||++++.
T Consensus 105 ~~l~VNG~~v~~ 116 (178)
T PRK13884 105 DGVRVNGELLPL 116 (178)
T ss_pred CEEEECCEEccc
Confidence 459999999975
No 148
>PF11436 DUF3199: Protein of unknown function (DUF3199); InterPro: IPR013514 This entry represents the hypothetical protein YqbG from Bacillus species, as well as related proteins from other bacteria. YqbG exists as a monomer, consisting of four alpha-helices with a right-handed twist, arranged in a left-handed superhelix [].; PDB: 1XN8_A 1ZTS_A.
Probab=21.42 E-value=81 Score=21.47 Aligned_cols=23 Identities=39% Similarity=0.752 Sum_probs=12.0
Q ss_pred cccccCC--CCCChHHHHHHHHHHH
Q psy10746 24 GGVFVNG--RPLPDVVRQRIVELAH 46 (59)
Q Consensus 24 GG~FvNG--RPLP~~~R~kIveLA~ 46 (59)
|--|.|= .|||+.+|.-.+.||+
T Consensus 41 ~~~F~~~~~~p~pe~v~lA~~kLAq 65 (124)
T PF11436_consen 41 GHDFSDEDYKPLPEKVRLALLKLAQ 65 (124)
T ss_dssp T-----CCG----HHHHHHHHHHHH
T ss_pred CCCCCCcccccChHHHHHHHHHHHH
Confidence 3345443 4799999999999986
No 149
>TIGR03540 DapC_direct LL-diaminopimelate aminotransferase. This clade of the pfam00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known aminotransferases, succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh). Although there is no experimental characterization of any of the sequences in this clade, a direct pathway is known in plants and Chlamydia, so it seems quite reasonable that these enzymes catalyze the same transformation.
Probab=21.39 E-value=91 Score=21.76 Aligned_cols=21 Identities=24% Similarity=0.240 Sum_probs=17.8
Q ss_pred ccCCCCCChHHHHHHHHHHHc
Q psy10746 27 FVNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 27 FvNGRPLP~~~R~kIveLA~~ 47 (59)
.+-|.-++.+.+++|+++|++
T Consensus 175 NPtG~~~~~~~~~~i~~~a~~ 195 (383)
T TIGR03540 175 NPTGAVAPLKFFKELVEFAKE 195 (383)
T ss_pred CCcCccCCHHHHHHHHHHHHH
Confidence 345888999999999999964
No 150
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=21.21 E-value=65 Score=22.70 Aligned_cols=17 Identities=53% Similarity=0.854 Sum_probs=13.7
Q ss_pred ccCCCCCChHH-HHHHHH
Q psy10746 27 FVNGRPLPDVV-RQRIVE 43 (59)
Q Consensus 27 FvNGRPLP~~~-R~kIve 43 (59)
||||+.||... .++|++
T Consensus 43 Yv~g~~~P~~~~a~~~~~ 60 (238)
T PRK08558 43 YVNGHVLPSVERAREIVE 60 (238)
T ss_pred HHcCCcCCCHHHHHHHHH
Confidence 79999999877 556665
No 151
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=21.17 E-value=87 Score=21.35 Aligned_cols=26 Identities=27% Similarity=0.410 Sum_probs=20.5
Q ss_pred cccccCCC-----CCChHHHHHHHHHHHcCC
Q psy10746 24 GGVFVNGR-----PLPDVVRQRIVELAHNGG 49 (59)
Q Consensus 24 GG~FvNGR-----PLP~~~R~kIveLA~~Gv 49 (59)
.|+|++|. -|..++|+++++.+..-+
T Consensus 33 ~gi~~~GstGE~~~ls~~Er~~l~~~~~~~~ 63 (281)
T cd00408 33 DGLVVLGTTGEAPTLTDEERKEVIEAVVEAV 63 (281)
T ss_pred CEEEECCCCcccccCCHHHHHHHHHHHHHHh
Confidence 46777775 799999999999886544
No 152
>COG2055 Malate/L-lactate dehydrogenases [Energy production and conversion]
Probab=21.16 E-value=91 Score=24.14 Aligned_cols=34 Identities=18% Similarity=0.079 Sum_probs=24.3
Q ss_pred cCCcceecccccccCCCCCChHHHHHHHHHHHcC
Q psy10746 15 WSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 15 ~g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~G 48 (59)
+|+......--.--||=||++.+-++|.+||...
T Consensus 310 PG~~~~~~~~~~~~~GI~i~~~~~~~l~~la~~~ 343 (349)
T COG2055 310 PGEREFAAREKRQKEGIPIDEDVWAELKELAEEL 343 (349)
T ss_pred CCcHHHHHHHHHHhcCCccCHHHHHHHHHHHHHc
Confidence 3444333333444689999999999999999764
No 153
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=21.16 E-value=29 Score=23.57 Aligned_cols=17 Identities=47% Similarity=0.802 Sum_probs=13.0
Q ss_pred eecccccccCCCCCChH
Q psy10746 20 VNQLGGVFVNGRPLPDV 36 (59)
Q Consensus 20 vNQLGG~FvNGRPLP~~ 36 (59)
|.--+.+|+||+++++.
T Consensus 100 V~i~~~v~iNg~~~~~~ 116 (176)
T PRK13838 100 VEIGGSVSIDGRPLPSS 116 (176)
T ss_pred EEECCEEEECCEEcccc
Confidence 44446899999999864
No 154
>KOG1052|consensus
Probab=21.02 E-value=65 Score=24.76 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=25.2
Q ss_pred eecccccccCCCCCChHHHHHHHHHHHcCC
Q psy10746 20 VNQLGGVFVNGRPLPDVVRQRIVELAHNGG 49 (59)
Q Consensus 20 vNQLGG~FvNGRPLP~~~R~kIveLA~~Gv 49 (59)
-+.+| .|.-|.||-+.+..+|.+|+..|+
T Consensus 534 ~~~~~-~~~~~Spl~~~is~~Il~l~e~g~ 562 (656)
T KOG1052|consen 534 YKGYG-AFPKGSPLRSLISRAILKLQETGI 562 (656)
T ss_pred CCCcc-eecCCCccHHHHHHHHHhhccccH
Confidence 34566 899999999999999999998875
No 155
>PRK05839 hypothetical protein; Provisional
Probab=20.82 E-value=88 Score=22.10 Aligned_cols=18 Identities=33% Similarity=0.231 Sum_probs=16.5
Q ss_pred CCCCChHHHHHHHHHHHc
Q psy10746 30 GRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 30 GRPLP~~~R~kIveLA~~ 47 (59)
|.-++.+.+.+|+++|++
T Consensus 169 G~~~s~~~l~~i~~~~~~ 186 (374)
T PRK05839 169 GRTLSLEELIEWVKLALK 186 (374)
T ss_pred CcccCHHHHHHHHHHHHH
Confidence 899999999999999864
No 156
>PRK09147 succinyldiaminopimelate transaminase; Provisional
Probab=20.61 E-value=95 Score=21.93 Aligned_cols=21 Identities=24% Similarity=0.306 Sum_probs=17.8
Q ss_pred CCCCCChHHHHHHHHHHHc-CC
Q psy10746 29 NGRPLPDVVRQRIVELAHN-GG 49 (59)
Q Consensus 29 NGRPLP~~~R~kIveLA~~-Gv 49 (59)
-|+-++.+.+++|+++|.+ ++
T Consensus 179 TG~~~s~~~~~~l~~~a~~~~~ 200 (396)
T PRK09147 179 TGAVLPLDDWKKLFALSDRYGF 200 (396)
T ss_pred cCccCCHHHHHHHHHHHHHcCe
Confidence 3889999999999999964 53
No 157
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=20.60 E-value=1.3e+02 Score=18.05 Aligned_cols=19 Identities=26% Similarity=0.494 Sum_probs=16.2
Q ss_pred cCCCCCChHHHHHHHHHHH
Q psy10746 28 VNGRPLPDVVRQRIVELAH 46 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~ 46 (59)
..|+..+..+|.++.+|.+
T Consensus 93 ~~~~~~~~~Vr~k~~~l~~ 111 (115)
T cd00197 93 LLGDDVSTNVREKAIELVQ 111 (115)
T ss_pred cccCCCChHHHHHHHHHHH
Confidence 3688889999999999865
No 158
>PRK11053 dihydropteridine reductase; Provisional
Probab=20.33 E-value=1.3e+02 Score=19.86 Aligned_cols=24 Identities=21% Similarity=0.228 Sum_probs=19.9
Q ss_pred ccccCCCCCChHHHHHHHHHHHcC
Q psy10746 25 GVFVNGRPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 25 G~FvNGRPLP~~~R~kIveLA~~G 48 (59)
..|-...|+|++.=++|+|.|..-
T Consensus 14 R~f~~~~~v~~e~l~~ileaa~~A 37 (217)
T PRK11053 14 KAFDPSKKLPAEQIEQIKTLLRFS 37 (217)
T ss_pred eccCCCCCCCHHHHHHHHHHHHhC
Confidence 347667899999999999999753
No 159
>cd02146 NfsA_FRP This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as an electron donor. Oxygen-insensitive nitroreductase, such as NfsA protein in Escherichia coli, catalyzes reduction of nitrocompounds using NADPH as electron donor.
Probab=20.29 E-value=1.2e+02 Score=20.34 Aligned_cols=25 Identities=20% Similarity=0.490 Sum_probs=20.0
Q ss_pred cccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746 26 VFVNGRPLPDVVRQRIVELAHNGGLLSA 53 (59)
Q Consensus 26 ~FvNGRPLP~~~R~kIveLA~~GvRps~ 53 (59)
.| .++|+|++.-.+|++.|..- ||.
T Consensus 13 ~f-~~~~V~~e~l~~ileaa~~A--PS~ 37 (229)
T cd02146 13 KF-KDEPIPDETLETLIAAAQSA--PTS 37 (229)
T ss_pred CC-CCCCCCHHHHHHHHHHHHHc--CCc
Confidence 45 37899999999999999753 554
No 160
>PRK08960 hypothetical protein; Provisional
Probab=20.29 E-value=1.1e+02 Score=21.60 Aligned_cols=23 Identities=17% Similarity=0.156 Sum_probs=19.5
Q ss_pred ccCCCCCChHHHHHHHHHHHc-CC
Q psy10746 27 FVNGRPLPDVVRQRIVELAHN-GG 49 (59)
Q Consensus 27 FvNGRPLP~~~R~kIveLA~~-Gv 49 (59)
.+-|.-+|.+.+.+|+++|++ |+
T Consensus 176 NPtG~~~~~~~~~~l~~~~~~~~~ 199 (387)
T PRK08960 176 NPTGTLLSRDELAALSQALRARGG 199 (387)
T ss_pred CCCCcCcCHHHHHHHHHHHHHcCC
Confidence 467999999999999999964 55
No 161
>PRK08637 hypothetical protein; Provisional
Probab=20.29 E-value=1.1e+02 Score=21.68 Aligned_cols=19 Identities=21% Similarity=0.158 Sum_probs=16.6
Q ss_pred cCCCCCChHHHHHHHHHHH
Q psy10746 28 VNGRPLPDVVRQRIVELAH 46 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~ 46 (59)
+-|+.++.+.|++|+++|+
T Consensus 158 PTG~~~s~~~~~~l~~~~~ 176 (388)
T PRK08637 158 PTGYTPTEKEATAIVEAIK 176 (388)
T ss_pred CCCCCCCHHHHHHHHHHHH
Confidence 3489999999999999875
No 162
>PRK07682 hypothetical protein; Validated
Probab=20.20 E-value=1.1e+02 Score=21.37 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=17.2
Q ss_pred cCCCCCChHHHHHHHHHHHc
Q psy10746 28 VNGRPLPDVVRQRIVELAHN 47 (59)
Q Consensus 28 vNGRPLP~~~R~kIveLA~~ 47 (59)
+-|..+|.+.+++|+++|+.
T Consensus 166 PtG~~~s~~~~~~l~~~~~~ 185 (378)
T PRK07682 166 PTGAVLNKSELEEIAVIVEK 185 (378)
T ss_pred CcCcCcCHHHHHHHHHHHHH
Confidence 35788999999999999975
No 163
>PF07637 PSD5: Protein of unknown function (DUF1595); InterPro: IPR013043 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013042 from INTERPRO.
Probab=20.14 E-value=1.1e+02 Score=17.33 Aligned_cols=18 Identities=33% Similarity=0.475 Sum_probs=15.1
Q ss_pred CCCChHHHHHHHHHHHcC
Q psy10746 31 RPLPDVVRQRIVELAHNG 48 (59)
Q Consensus 31 RPLP~~~R~kIveLA~~G 48 (59)
||++++....++++..+.
T Consensus 17 Rp~~~~e~~~~~~~~~~~ 34 (64)
T PF07637_consen 17 RPLTDEEVDRYLALYDSA 34 (64)
T ss_pred CCCCHHHHHHHHHHHHHH
Confidence 899999999998887643
Done!