Query 039148
Match_columns 82
No_of_seqs 108 out of 602
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 06:46:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039148.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039148hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00212 glutelin; Provisional 99.8 1.4E-18 3E-23 135.2 8.6 73 6-81 150-249 (493)
2 PF00190 Cupin_1: Cupin; Inte 99.5 4.4E-14 9.5E-19 93.3 8.8 61 3-75 81-143 (144)
3 TIGR03404 bicupin_oxalic bicup 99.5 1.6E-13 3.4E-18 103.6 8.4 74 3-80 288-361 (367)
4 TIGR03404 bicupin_oxalic bicup 99.4 6.2E-13 1.3E-17 100.4 8.0 76 1-81 107-185 (367)
5 PLN00212 glutelin; Provisional 99.4 5.6E-13 1.2E-17 104.1 6.2 71 1-81 390-468 (493)
6 smart00835 Cupin_1 Cupin. This 99.2 6.3E-11 1.4E-15 78.4 8.4 69 3-75 74-145 (146)
7 COG2140 Thermophilic glucose-6 98.1 3.1E-06 6.8E-11 60.3 4.2 72 3-78 125-196 (209)
8 PF07883 Cupin_2: Cupin domain 97.8 8.7E-05 1.9E-09 42.4 5.0 34 5-38 38-71 (71)
9 COG0662 {ManC} Mannose-6-phosp 97.6 0.00014 3E-09 47.3 4.9 39 5-43 76-114 (127)
10 PRK04190 glucose-6-phosphate i 97.5 0.00031 6.8E-09 49.3 5.7 37 5-41 121-157 (191)
11 COG1917 Uncharacterized conser 97.5 0.00019 4.1E-09 46.2 4.4 36 5-40 83-118 (131)
12 PF06560 GPI: Glucose-6-phosph 97.4 0.00057 1.2E-08 47.8 6.0 39 2-40 108-146 (182)
13 COG4101 Predicted mannose-6-ph 97.2 0.00067 1.5E-08 45.3 4.3 44 1-44 84-128 (142)
14 PF02373 JmjC: JmjC domain, hy 97.1 0.0013 2.8E-08 40.7 4.6 31 3-33 80-110 (114)
15 TIGR03214 ura-cupin putative a 97.0 0.0012 2.6E-08 47.8 4.6 34 6-39 220-253 (260)
16 PRK13290 ectC L-ectoine syntha 96.9 0.003 6.6E-08 41.4 5.5 38 6-45 77-114 (125)
17 PRK09943 DNA-binding transcrip 96.5 0.0062 1.3E-07 41.5 5.0 34 5-38 147-180 (185)
18 PRK15460 cpsB mannose-1-phosph 96.4 0.0061 1.3E-07 47.9 5.0 35 5-39 425-459 (478)
19 PF01050 MannoseP_isomer: Mann 96.4 0.0065 1.4E-07 41.1 4.5 33 5-37 103-135 (151)
20 TIGR01479 GMP_PMI mannose-1-ph 96.4 0.0075 1.6E-07 46.9 5.2 35 5-39 416-450 (468)
21 PF13621 Cupin_8: Cupin-like d 96.4 0.011 2.3E-07 40.7 5.5 33 3-35 208-241 (251)
22 COG3837 Uncharacterized conser 96.4 0.0072 1.6E-07 41.7 4.5 37 6-42 84-122 (161)
23 PRK11171 hypothetical protein; 96.1 0.016 3.5E-07 42.0 5.2 35 5-39 102-136 (266)
24 PF08007 Cupin_4: Cupin superf 96.0 0.017 3.6E-07 42.9 5.1 25 4-28 176-200 (319)
25 PRK11171 hypothetical protein; 95.9 0.016 3.5E-07 42.0 4.8 35 5-39 224-258 (266)
26 TIGR03214 ura-cupin putative a 95.7 0.029 6.3E-07 40.6 5.2 35 5-39 99-133 (260)
27 PF03079 ARD: ARD/ARD' family; 94.7 0.15 3.3E-06 34.7 6.2 36 5-40 116-151 (157)
28 PF11699 CENP-C_C: Mif2/CENP-C 94.6 0.097 2.1E-06 32.4 4.6 30 7-36 54-83 (85)
29 TIGR02272 gentisate_1_2 gentis 94.3 0.055 1.2E-06 41.0 3.6 35 6-40 122-156 (335)
30 PF02311 AraC_binding: AraC-li 93.4 0.23 4.9E-06 30.3 4.6 31 6-36 43-73 (136)
31 PF05899 Cupin_3: Protein of u 92.8 0.1 2.2E-06 31.0 2.2 17 5-21 45-61 (74)
32 TIGR03037 anthran_nbaC 3-hydro 91.8 0.19 4.1E-06 34.6 2.9 26 5-30 71-96 (159)
33 PRK15457 ethanolamine utilizat 91.6 0.34 7.4E-06 35.2 4.2 23 5-28 194-217 (233)
34 KOG3706 Uncharacterized conser 91.3 0.072 1.6E-06 42.8 0.5 26 3-28 380-405 (629)
35 PRK13264 3-hydroxyanthranilate 91.3 0.31 6.6E-06 34.1 3.6 25 5-29 77-101 (177)
36 PF12852 Cupin_6: Cupin 91.1 0.22 4.7E-06 33.6 2.6 25 6-30 57-81 (186)
37 COG1791 Uncharacterized conser 91.0 0.92 2E-05 31.9 5.7 40 2-41 116-155 (181)
38 COG3450 Predicted enzyme of th 89.2 0.36 7.8E-06 31.6 2.4 16 6-21 84-99 (116)
39 TIGR02451 anti_sig_ChrR anti-s 87.3 0.68 1.5E-05 32.7 3.0 37 6-42 163-199 (215)
40 PF13759 2OG-FeII_Oxy_5: Putat 87.2 2 4.4E-05 26.3 4.8 33 4-36 66-99 (101)
41 KOG2107 Uncharacterized conser 86.8 0.46 1E-05 33.2 1.8 20 6-25 118-137 (179)
42 PRK05341 homogentisate 1,2-dio 86.4 1.4 2.9E-05 34.9 4.4 32 7-39 175-206 (438)
43 PLN02658 homogentisate 1,2-dio 85.2 1.7 3.7E-05 34.3 4.4 32 7-39 168-199 (435)
44 COG4297 Uncharacterized protei 82.1 0.95 2E-05 31.0 1.7 19 7-25 88-106 (163)
45 TIGR00218 manA mannose-6-phosp 81.5 1.2 2.7E-05 32.6 2.3 24 5-30 152-175 (302)
46 COG3435 Gentisate 1,2-dioxygen 81.2 1.5 3.3E-05 33.5 2.7 35 6-40 133-167 (351)
47 PRK14585 pgaD putative PGA bio 81.1 2.1 4.6E-05 28.9 3.1 25 57-81 88-112 (137)
48 PRK10296 DNA-binding transcrip 79.5 3.9 8.6E-05 28.8 4.2 21 7-27 64-84 (278)
49 TIGR02297 HpaA 4-hydroxyphenyl 78.9 2.9 6.2E-05 29.5 3.4 26 6-31 64-89 (287)
50 PF05118 Asp_Arg_Hydrox: Aspar 78.3 6 0.00013 26.5 4.7 31 5-35 125-155 (163)
51 PRK14584 hmsS hemin storage sy 77.4 3.3 7.2E-05 28.4 3.2 25 57-81 97-121 (153)
52 PF13994 PgaD: PgaD-like prote 76.8 3.7 7.9E-05 27.0 3.2 23 59-81 101-123 (138)
53 PF02787 CPSase_L_D3: Carbamoy 76.4 3.1 6.8E-05 27.1 2.7 24 58-81 72-95 (123)
54 PRK15131 mannose-6-phosphate i 76.2 1.9 4.1E-05 33.2 1.9 24 5-29 238-261 (389)
55 PF13464 DUF4115: Domain of un 75.9 10 0.00022 22.2 4.7 35 2-37 20-54 (77)
56 PRK10572 DNA-binding transcrip 75.4 3.8 8.2E-05 29.1 3.2 25 5-29 68-92 (290)
57 PF04209 HgmA: homogentisate 1 73.7 6 0.00013 31.1 4.1 30 7-38 167-196 (424)
58 COG2850 Uncharacterized conser 73.7 1.6 3.4E-05 33.9 0.9 24 6-29 181-204 (383)
59 TIGR01015 hmgA homogentisate 1 73.0 2.8 6E-05 33.1 2.1 27 7-35 169-195 (429)
60 PF13348 Y_phosphatase3C: Tyro 73.0 2.6 5.6E-05 24.0 1.5 22 60-81 45-66 (68)
61 PF02041 Auxin_BP: Auxin bindi 72.1 10 0.00022 26.3 4.5 33 8-40 95-128 (167)
62 PRK13500 transcriptional activ 71.5 5.4 0.00012 29.0 3.3 24 6-29 88-111 (312)
63 PRK13502 transcriptional activ 71.4 6.5 0.00014 27.7 3.6 24 6-29 58-81 (282)
64 TIGR02272 gentisate_1_2 gentis 71.3 6.6 0.00014 29.9 3.8 30 7-38 291-320 (335)
65 COG1482 ManA Phosphomannose is 70.4 3 6.6E-05 31.5 1.8 20 6-25 160-179 (312)
66 KOG2130 Phosphatidylserine-spe 69.7 7.9 0.00017 30.0 3.9 41 6-46 265-305 (407)
67 PF06249 EutQ: Ethanolamine ut 69.3 3.5 7.6E-05 28.1 1.8 17 7-23 116-133 (152)
68 PF13384 HTH_23: Homeodomain-l 69.1 8.2 0.00018 20.3 2.9 24 59-82 18-41 (50)
69 PRK13501 transcriptional activ 67.4 7.2 0.00016 27.8 3.1 25 5-29 57-81 (290)
70 PF06052 3-HAO: 3-hydroxyanthr 64.8 13 0.00028 25.5 3.8 25 6-30 77-101 (151)
71 PRK13503 transcriptional activ 63.8 6.9 0.00015 27.3 2.4 23 6-28 55-77 (278)
72 PF06413 Neugrin: Neugrin; In 60.2 10 0.00022 27.3 2.8 28 52-79 22-50 (225)
73 PF05995 CDO_I: Cysteine dioxy 58.5 37 0.0008 23.0 5.3 33 7-39 130-163 (175)
74 PF06971 Put_DNA-bind_N: Putat 58.4 11 0.00023 21.1 2.1 19 59-77 29-47 (50)
75 COG4847 Uncharacterized protei 57.9 5.4 0.00012 25.6 1.0 20 5-24 13-33 (103)
76 PRK10371 DNA-binding transcrip 57.0 17 0.00036 26.5 3.5 25 6-30 66-90 (302)
77 PF04970 LRAT: Lecithin retino 55.0 12 0.00025 23.8 2.2 32 5-36 4-36 (125)
78 PF08279 HTH_11: HTH domain; 54.0 13 0.00029 19.9 2.0 23 55-77 12-34 (55)
79 PF13613 HTH_Tnp_4: Helix-turn 52.5 15 0.00033 20.0 2.1 21 59-79 20-40 (53)
80 PF07385 DUF1498: Protein of u 52.5 38 0.00083 24.6 4.7 33 7-41 157-189 (225)
81 KOG1633 F-box protein JEMMA an 51.8 17 0.00036 30.8 3.1 41 4-44 196-236 (776)
82 PF02796 HTH_7: Helix-turn-hel 51.8 25 0.00055 18.5 2.9 24 58-81 21-44 (45)
83 PF12973 Cupin_7: ChrR Cupin-l 49.3 35 0.00076 20.3 3.6 21 6-26 60-80 (91)
84 KOG2131 Uncharacterized conser 49.2 10 0.00022 29.8 1.4 22 9-30 273-294 (427)
85 PLN02288 mannose-6-phosphate i 48.7 11 0.00025 29.1 1.6 20 6-25 253-272 (394)
86 PF05523 FdtA: WxcM-like, C-te 48.6 38 0.00082 22.0 3.9 24 12-36 85-108 (131)
87 PRK13285 flagellar assembly pr 45.8 56 0.0012 21.9 4.5 59 7-65 12-80 (148)
88 smart00550 Zalpha Z-DNA-bindin 45.7 33 0.00071 19.7 2.9 21 58-78 22-42 (68)
89 PF08220 HTH_DeoR: DeoR-like h 45.7 26 0.00056 19.4 2.4 20 58-77 14-33 (57)
90 PF00856 SET: SET domain; Int 44.3 8.7 0.00019 23.6 0.3 17 5-21 7-23 (162)
91 COG5553 Predicted metal-depend 44.2 42 0.00091 23.7 3.7 30 8-38 126-155 (191)
92 PF00908 dTDP_sugar_isom: dTDP 43.7 96 0.0021 21.3 5.5 43 3-45 95-139 (176)
93 PF12937 F-box-like: F-box-lik 43.4 43 0.00093 17.3 3.0 21 58-78 3-24 (47)
94 COG4766 EutQ Ethanolamine util 43.0 15 0.00033 25.5 1.4 13 9-21 141-153 (176)
95 PF09943 DUF2175: Uncharacteri 42.0 15 0.00033 23.6 1.2 19 6-24 10-29 (101)
96 PF05721 PhyH: Phytanoyl-CoA d 41.8 20 0.00043 23.1 1.7 23 5-27 181-203 (211)
97 PF11948 DUF3465: Protein of u 41.7 21 0.00046 23.9 1.9 21 7-27 85-113 (131)
98 COG3257 GlxB Uncharacterized p 41.3 50 0.0011 24.4 3.8 32 5-36 102-133 (264)
99 TIGR02466 conserved hypothetic 41.2 43 0.00093 23.5 3.5 30 7-36 165-195 (201)
100 PF10668 Phage_terminase: Phag 40.9 29 0.00064 20.1 2.2 23 59-81 23-45 (60)
101 PF07506 RepB: RepB plasmid pa 40.5 39 0.00084 23.0 3.1 21 58-78 21-41 (185)
102 PRK09685 DNA-binding transcrip 39.4 51 0.0011 23.3 3.7 27 6-32 91-117 (302)
103 PF15428 Imm14: Immunity prote 38.6 27 0.00058 22.1 1.9 11 9-19 1-11 (129)
104 COG3508 HmgA Homogentisate 1,2 37.8 25 0.00054 27.6 2.0 31 6-37 166-196 (427)
105 COG3435 Gentisate 1,2-dioxygen 37.8 39 0.00085 26.0 3.0 32 7-39 302-333 (351)
106 smart00351 PAX Paired Box doma 36.0 42 0.00091 21.5 2.6 24 58-81 33-56 (125)
107 PF06806 DUF1233: Putative exc 35.5 41 0.00088 20.3 2.3 23 59-81 10-32 (72)
108 PF13412 HTH_24: Winged helix- 35.5 68 0.0015 16.6 3.1 23 56-78 15-37 (48)
109 cd00131 PAX Paired Box domain 35.5 42 0.00092 21.7 2.5 25 58-82 33-57 (128)
110 cd00248 Mth938-like Mth938-lik 34.8 26 0.00056 22.1 1.4 23 5-27 13-35 (109)
111 PF13518 HTH_28: Helix-turn-he 34.6 54 0.0012 16.9 2.5 23 59-81 13-35 (52)
112 PF11256 DUF3055: Protein of u 34.2 45 0.00097 20.6 2.3 30 51-80 47-76 (81)
113 PF02678 Pirin: Pirin; InterP 34.1 1.2E+02 0.0026 19.1 4.5 31 5-35 70-103 (107)
114 PHA00675 hypothetical protein 33.6 71 0.0015 19.6 3.1 24 58-81 39-62 (78)
115 PF13551 HTH_29: Winged helix- 33.5 51 0.0011 19.6 2.6 24 59-82 12-36 (112)
116 PF04545 Sigma70_r4: Sigma-70, 33.4 75 0.0016 16.6 3.0 22 59-80 21-42 (50)
117 COG3822 ABC-type sugar transpo 32.6 92 0.002 22.5 4.0 32 7-40 156-187 (225)
118 PF01476 LysM: LysM domain; I 32.6 11 0.00024 19.2 -0.5 11 7-17 34-44 (44)
119 smart00421 HTH_LUXR helix_turn 32.6 74 0.0016 16.1 3.1 23 58-80 18-40 (58)
120 PF04354 ZipA_C: ZipA, C-termi 32.5 54 0.0012 21.4 2.7 33 16-48 34-66 (131)
121 PRK05467 Fe(II)-dependent oxyg 30.8 38 0.00082 24.3 1.9 22 6-27 143-164 (226)
122 cd06171 Sigma70_r4 Sigma70, re 30.7 75 0.0016 15.6 3.0 23 58-80 26-48 (55)
123 PRK09956 hypothetical protein; 30.6 56 0.0012 24.3 2.8 30 48-79 278-307 (308)
124 PF08822 DUF1804: Protein of u 30.4 66 0.0014 22.3 2.9 27 51-80 15-41 (165)
125 COG1898 RfbC dTDP-4-dehydrorha 30.3 92 0.002 21.6 3.6 30 11-40 105-134 (173)
126 PF05257 CHAP: CHAP domain; I 30.1 1.4E+02 0.003 18.5 4.3 12 5-16 60-71 (124)
127 PF02362 B3: B3 DNA binding do 30.0 25 0.00054 20.8 0.7 12 6-17 72-83 (100)
128 COG4001 Predicted metal-bindin 29.9 32 0.0007 21.9 1.2 13 65-77 69-81 (102)
129 PHA02591 hypothetical protein; 29.9 88 0.0019 19.4 3.1 31 48-80 51-81 (83)
130 COG4296 Uncharacterized protei 29.9 92 0.002 21.3 3.5 26 12-37 115-143 (156)
131 PF08830 DUF1806: Protein of u 29.6 86 0.0019 20.6 3.2 37 4-42 64-100 (114)
132 smart00530 HTH_XRE Helix-turn- 29.2 76 0.0017 15.1 3.2 23 58-80 10-32 (56)
133 cd04762 HTH_MerR-trunc Helix-T 29.1 81 0.0018 15.5 3.0 20 61-80 3-22 (49)
134 PF00054 Laminin_G_1: Laminin 28.9 60 0.0013 20.4 2.4 27 13-39 23-49 (131)
135 PF01238 PMI_typeI: Phosphoman 28.8 31 0.00067 26.2 1.2 21 6-26 252-272 (373)
136 PLN02499 glycerol-3-phosphate 28.5 28 0.00062 28.0 1.0 17 6-22 348-364 (498)
137 PF01381 HTH_3: Helix-turn-hel 28.5 93 0.002 16.2 2.8 23 58-80 9-31 (55)
138 PF03152 UFD1: Ubiquitin fusio 28.0 42 0.00091 23.3 1.6 36 6-41 132-168 (176)
139 cd00092 HTH_CRP helix_turn_hel 27.7 1.1E+02 0.0023 16.4 3.2 22 57-78 24-45 (67)
140 PF11142 DUF2917: Protein of u 27.6 49 0.0011 19.0 1.7 17 7-23 39-55 (63)
141 PHA02752 hypothetical protein; 27.5 35 0.00076 24.5 1.2 22 20-41 161-182 (242)
142 TIGR02937 sigma70-ECF RNA poly 27.4 89 0.0019 18.7 3.0 22 59-80 127-148 (158)
143 PF13320 DUF4091: Domain of un 27.1 25 0.00055 20.6 0.4 12 18-29 4-15 (68)
144 cd00231 ZipA ZipA C-terminal d 27.0 92 0.002 20.4 3.1 30 18-47 35-64 (130)
145 PRK10926 ferredoxin-NADP reduc 26.9 88 0.0019 21.9 3.2 33 7-39 81-116 (248)
146 PF13404 HTH_AsnC-type: AsnC-t 26.8 1.1E+02 0.0023 16.0 2.8 20 57-76 16-35 (42)
147 cd05560 Xcc1710_like Xcc1710_l 26.8 47 0.001 20.9 1.6 22 5-26 13-35 (109)
148 PRK05713 hypothetical protein; 26.7 88 0.0019 22.7 3.2 34 6-39 166-202 (312)
149 PRK08158 type III secretion sy 26.7 57 0.0012 24.6 2.3 23 6-28 167-199 (303)
150 PF13936 HTH_38: Helix-turn-he 26.6 82 0.0018 16.4 2.3 21 58-78 20-40 (44)
151 cd03703 aeIF5B_II aeIF5B_II: T 26.3 48 0.001 21.4 1.6 14 3-16 22-35 (110)
152 smart00531 TFIIE Transcription 26.3 83 0.0018 20.7 2.8 23 58-80 15-37 (147)
153 PF13730 HTH_36: Helix-turn-he 26.0 93 0.002 16.4 2.6 20 60-79 27-46 (55)
154 PRK13284 flagellar assembly pr 25.9 1.8E+02 0.0039 19.4 4.4 17 7-23 12-28 (145)
155 PF04703 FaeA: FaeA-like prote 25.9 80 0.0017 18.2 2.4 22 58-79 15-36 (62)
156 cd06170 LuxR_C_like C-terminal 25.6 1.1E+02 0.0023 15.6 3.1 22 58-79 15-36 (57)
157 cd04761 HTH_MerR-SF Helix-Turn 25.4 1.1E+02 0.0023 15.5 3.0 20 61-80 3-22 (49)
158 PRK12815 carB carbamoyl phosph 25.3 80 0.0017 27.4 3.1 24 58-81 492-515 (1068)
159 TIGR02675 tape_meas_nterm tape 25.0 97 0.0021 18.2 2.7 20 61-80 47-66 (75)
160 PF07734 FBA_1: F-box associat 25.0 1E+02 0.0023 20.1 3.1 28 15-42 2-30 (164)
161 smart00420 HTH_DEOR helix_turn 24.7 1.1E+02 0.0023 15.3 3.0 21 58-78 14-34 (53)
162 PF03144 GTP_EFTU_D2: Elongati 24.7 74 0.0016 17.7 2.1 15 2-16 7-21 (74)
163 COG3093 VapI Plasmid maintenan 24.5 64 0.0014 20.8 1.9 18 64-81 58-75 (104)
164 PF04430 DUF498: Protein of un 24.3 69 0.0015 19.9 2.0 27 7-34 14-40 (110)
165 PF13545 HTH_Crp_2: Crp-like h 24.0 79 0.0017 17.6 2.1 21 59-79 29-49 (76)
166 cd00468 HIT_like HIT family: H 23.8 1.5E+02 0.0032 16.7 3.9 49 29-80 4-56 (86)
167 smart00256 FBOX A Receptor for 23.8 1E+02 0.0022 14.7 2.7 21 59-79 1-22 (41)
168 TIGR03070 couple_hipB transcri 23.7 1.2E+02 0.0026 15.5 3.1 23 58-80 15-37 (58)
169 PRK05294 carB carbamoyl phosph 23.6 90 0.0019 27.0 3.1 24 58-81 492-515 (1066)
170 PF14173 ComGG: ComG operon pr 23.5 1.8E+02 0.0038 17.6 3.8 25 12-36 42-66 (95)
171 COG2094 Mpg 3-methyladenine DN 23.5 1.5E+02 0.0033 21.2 3.8 61 11-75 64-143 (200)
172 PF02298 Cu_bind_like: Plastoc 23.4 45 0.00097 20.1 1.0 23 6-35 17-39 (85)
173 COG2150 Predicted regulator of 23.3 70 0.0015 22.3 2.0 25 53-77 36-60 (167)
174 PF02002 TFIIE_alpha: TFIIE al 23.3 77 0.0017 19.3 2.1 23 58-80 27-49 (105)
175 PRK09857 putative transposase; 23.2 96 0.0021 22.9 2.9 30 48-79 262-291 (292)
176 PF13560 HTH_31: Helix-turn-he 23.2 1.4E+02 0.0031 16.3 3.0 23 58-80 14-36 (64)
177 PLN02735 carbamoyl-phosphate s 23.2 92 0.002 27.3 3.1 24 58-81 512-535 (1102)
178 KOG1314 DHHC-type Zn-finger pr 23.1 42 0.00091 26.3 1.0 20 7-26 335-354 (414)
179 PF13411 MerR_1: MerR HTH fami 23.0 1.1E+02 0.0023 16.8 2.5 19 63-81 5-23 (69)
180 KOG4736 Uncharacterized conser 23.0 2.4E+02 0.0051 21.5 4.9 49 30-78 189-239 (302)
181 PF06970 RepA_N: Replication i 22.9 1.2E+02 0.0025 18.1 2.7 28 51-81 48-75 (76)
182 PRK00135 scpB segregation and 22.5 1.4E+02 0.003 20.8 3.4 28 50-77 11-39 (188)
183 TIGR01221 rmlC dTDP-4-dehydror 22.3 2.7E+02 0.0058 19.1 5.5 41 4-45 96-139 (176)
184 TIGR01784 T_den_put_tspse cons 21.9 93 0.002 21.5 2.5 29 48-78 242-270 (270)
185 PRK10681 DNA-binding transcrip 21.7 1E+02 0.0022 22.0 2.7 20 58-77 21-40 (252)
186 PF00962 A_deaminase: Adenosin 21.6 66 0.0014 23.2 1.7 35 37-80 276-312 (331)
187 PF13275 S4_2: S4 domain; PDB: 21.5 63 0.0014 18.9 1.3 13 6-18 47-59 (65)
188 smart00345 HTH_GNTR helix_turn 21.4 1.3E+02 0.0029 15.4 2.6 21 58-78 19-40 (60)
189 TIGR02531 yecD_yerC TrpR-relat 21.4 1.5E+02 0.0033 18.2 3.1 23 58-80 50-72 (88)
190 TIGR01451 B_ant_repeat conserv 21.2 1.6E+02 0.0034 16.0 3.3 42 6-51 6-47 (53)
191 smart00753 PAM PCI/PINT associ 21.0 1.2E+02 0.0025 17.5 2.5 20 59-78 25-44 (88)
192 smart00088 PINT motif in prote 21.0 1.2E+02 0.0025 17.5 2.5 20 59-78 25-44 (88)
193 PLN02177 glycerol-3-phosphate 20.8 46 0.00099 26.6 0.8 16 6-21 361-376 (497)
194 COG1349 GlpR Transcriptional r 20.6 78 0.0017 22.6 1.9 19 59-77 20-38 (253)
195 TIGR01369 CPSaseII_lrg carbamo 20.5 1.1E+02 0.0025 26.4 3.1 24 58-81 491-514 (1050)
196 PF13443 HTH_26: Cro/C1-type H 20.5 1.6E+02 0.0034 15.8 2.9 23 58-80 10-32 (63)
197 KOG3995 3-hydroxyanthranilate 20.3 70 0.0015 23.6 1.6 24 7-30 78-101 (279)
198 PF00122 E1-E2_ATPase: E1-E2 A 20.3 40 0.00087 22.9 0.3 16 5-20 49-64 (230)
199 PF01052 SpoA: Surface present 20.1 69 0.0015 18.4 1.3 13 7-19 28-40 (77)
200 PF13542 HTH_Tnp_ISL3: Helix-t 20.0 1.1E+02 0.0025 15.8 2.1 21 59-79 28-48 (52)
No 1
>PLN00212 glutelin; Provisional
Probab=99.77 E-value=1.4e-18 Score=135.19 Aligned_cols=73 Identities=25% Similarity=0.432 Sum_probs=63.9
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCcce--------ee-------------------ccccccCCCC
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGVV--------TI-------------------ANTAFGSNPA 58 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~~--------~~-------------------~~~~F~~~p~ 58 (82)
++|++||||++|+|++||+||+|++|+++++++|..|+..| .+ +.|+|++
T Consensus 150 ~~lr~GDViaiPaG~~hw~yN~Gd~~~v~v~~~d~~n~~Nqld~~~r~F~LaG~~~~~~~~~~~~~~~~~~~nifsG--- 226 (493)
T PLN00212 150 HQFRQGDVVALPAGVAHWFYNDGDAPVVALYVYDINNNANQLEPRQREFLLAGNNNRQQQVYGRSIEQHSGQNIFSG--- 226 (493)
T ss_pred eEeccCCEEEECCCCeEEEEeCCCCcEEEEEEEeccccccccCCCcceeeccCCCccccccccccccccccCchhhc---
Confidence 58999999999999999999999999999999997764322 11 2469997
Q ss_pred CcHHHHHHHhCCCHHHHHHHHhc
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
|++++|++||+++.++++||+++
T Consensus 227 F~~e~La~Afnv~~e~~~klq~~ 249 (493)
T PLN00212 227 FSTELLSEALGINAQVAKRLQSQ 249 (493)
T ss_pred CCHHHHHHHHCCCHHHHHHHhcc
Confidence 99999999999999999999864
No 2
>PF00190 Cupin_1: Cupin; InterPro: IPR006045 This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. ; GO: 0045735 nutrient reservoir activity; PDB: 2E9Q_A 2EVX_A 1OD5_A 1UCX_A 1UD1_C 1FXZ_C 3KGL_C 3KSC_D 1UIJ_F 1IPK_B ....
Probab=99.55 E-value=4.4e-14 Score=93.33 Aligned_cols=61 Identities=31% Similarity=0.394 Sum_probs=54.6
Q ss_pred eEEEe--ecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCcceeeccccccCCCCCcHHHHHHHhCCCHHHH
Q 039148 3 LIIMV--LKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGVVTIANTAFGSNPAIVTDMLAKAFQAEKKIV 75 (82)
Q Consensus 3 ~~~~~--l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~~~~~~~~F~~~p~~~~~vLa~af~~d~~~i 75 (82)
.+.++ +++|||+++|+|.+||++|.||.++..+.+|++.+|..+ +|+++++++|+++++.+
T Consensus 81 ~~~~~v~l~~Gdv~~vP~G~~h~~~n~~~~~~~~~~~f~~~~~~~~------------l~~~v~~~~F~~~~~~~ 143 (144)
T PF00190_consen 81 DFSQKVRLKAGDVFVVPAGHPHWIINDGDDEALVLIIFDTNNPPNQ------------LPPEVLAKAFFLSGEEV 143 (144)
T ss_dssp EEEEEEEEETTEEEEE-TT-EEEEEECSSSSEEEEEEEEESSTTGE------------SSHHHHHHHEESSHHHH
T ss_pred eeeceeeeecccceeeccceeEEEEcCCCCCCEEEEEEECCCCccc------------CCcHHHHHhcCCCcCcC
Confidence 55666 999999999999999999999999999999999999886 88999999999999865
No 3
>TIGR03404 bicupin_oxalic bicupin, oxalate decarboxylase family. Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.
Probab=99.48 E-value=1.6e-13 Score=103.59 Aligned_cols=74 Identities=15% Similarity=0.234 Sum_probs=67.4
Q ss_pred eEEEeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCcceeeccccccCCCCCcHHHHHHHhCCCHHHHHHHHh
Q 039148 3 LIIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGVVTIANTAFGSNPAIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 3 ~~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~~~~~~~~F~~~p~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
..+..|++||+++||+|..|+..|.|++++.++++|++..++.+.++..+ +. +|+++|+++|+++.+++++|++
T Consensus 288 ~~~~~l~~GD~~~iP~g~~H~i~N~G~e~l~fL~if~s~~~~~i~l~~~l-~~---~p~~vl~~~~~~~~~~~~~l~~ 361 (367)
T TIGR03404 288 ARTFDYQAGDVGYVPRNMGHYVENTGDETLVFLEVFKADRFADVSLNQWL-AL---TPPQLVAAHLNLDDEVIDSLKK 361 (367)
T ss_pred EEEEEECCCCEEEECCCCeEEEEECCCCCEEEEEEECCCCCceeEHHHHH-hh---CCHHHHHHHhCcCHHHHHhccc
Confidence 34678999999999999999999999999999999999999999886644 44 9999999999999999999985
No 4
>TIGR03404 bicupin_oxalic bicupin, oxalate decarboxylase family. Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.
Probab=99.42 E-value=6.2e-13 Score=100.38 Aligned_cols=76 Identities=21% Similarity=0.288 Sum_probs=65.2
Q ss_pred CeeEEEeecCCcEEEEccCceeEEEecCCcceEEEEeeecCC---CcceeeccccccCCCCCcHHHHHHHhCCCHHHHHH
Q 039148 1 NRLIIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQN---LGVVTIANTAFGSNPAIVTDMLAKAFQAEKKIVKQ 77 (82)
Q Consensus 1 n~~~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~n---pg~~~~~~~~F~~~p~~~~~vLa~af~~d~~~i~k 77 (82)
+|.|.+.|++||+++||+|++|++.|.+ +.+.++.+|++.+ +.++.+.. .|+. +|++||+++|++|.+++++
T Consensus 107 g~~~~~~L~~GD~~~fP~g~~H~~~n~~-~~~~~l~vf~~~~f~~~~~~~~~~-~l~~---~p~~Vla~~f~l~~~~~~~ 181 (367)
T TIGR03404 107 GRNYIDDVGAGDLWYFPPGIPHSLQGLD-EGCEFLLVFDDGNFSEDGTFLVTD-WLAH---TPKDVLAKNFGVPESAFDN 181 (367)
T ss_pred CcEEEeEECCCCEEEECCCCeEEEEECC-CCeEEEEEeCCcccCCcceeeHHH-HHHh---CCHHHHHHHhCCCHHHHHh
Confidence 4678889999999999999999999996 4577888888764 56777766 4676 9999999999999999999
Q ss_pred HHhc
Q 039148 78 LQNT 81 (82)
Q Consensus 78 l~~~ 81 (82)
|+++
T Consensus 182 l~~~ 185 (367)
T TIGR03404 182 LPLK 185 (367)
T ss_pred cccc
Confidence 9864
No 5
>PLN00212 glutelin; Provisional
Probab=99.39 E-value=5.6e-13 Score=104.07 Aligned_cols=71 Identities=20% Similarity=0.291 Sum_probs=64.6
Q ss_pred CeeEEEeecCCcEEEEccCcee--------EEEecCCcceEEEEeeecCCCcceeeccccccCCCCCcHHHHHHHhCCCH
Q 039148 1 NRLIIMVLKKGDVFVFLVGLVH--------FKCNVGYGNVVAIVAFSSQNLGVVTIANTAFGSNPAIVTDMLAKAFQAEK 72 (82)
Q Consensus 1 n~~~~~~l~~GDv~vfP~G~~H--------~~~N~G~~~av~i~~~~s~npg~~~~~~~~F~~~p~~~~~vLa~af~~d~ 72 (82)
|++|.++|++|||||||+|.+| |+||.+.+++ .++.++.||. .++|.. +|.+||++||++|.
T Consensus 390 ~~vf~~~L~~GdvfVVPqg~~v~~~A~~egfe~v~F~tna---~~~~s~laG~----~Sv~~a---lp~eVla~Af~is~ 459 (493)
T PLN00212 390 KTVFNGVLRPGQLLIIPQHYAVLKKAEREGCQYIAFKTNA---NAMVSHIAGK----NSIFRA---LPVDVIANAYRISR 459 (493)
T ss_pred CEEEEEEEcCCCEEEECCCCeEEEeecCCceEEEEeecCC---CccccccccH----HHHHHh---CCHHHHHHHcCCCH
Confidence 5799999999999999999999 9999999888 3577888997 678986 99999999999999
Q ss_pred HHHHHHHhc
Q 039148 73 KIVKQLQNT 81 (82)
Q Consensus 73 ~~i~kl~~~ 81 (82)
+.+++||..
T Consensus 460 eea~~lk~n 468 (493)
T PLN00212 460 EEARRLKNN 468 (493)
T ss_pred HHHHHHHhc
Confidence 999999975
No 6
>smart00835 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.
Probab=99.24 E-value=6.3e-11 Score=78.36 Aligned_cols=69 Identities=29% Similarity=0.430 Sum_probs=58.5
Q ss_pred eEEEeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCccee-e--ccccccCCCCCcHHHHHHHhCCCHHHH
Q 039148 3 LIIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGVVT-I--ANTAFGSNPAIVTDMLAKAFQAEKKIV 75 (82)
Q Consensus 3 ~~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~~~-~--~~~~F~~~p~~~~~vLa~af~~d~~~i 75 (82)
-+...+++||++.+|+|..||..|.++++++.+ ++++++|..-. . ..++|++ +++++++++|+++.+++
T Consensus 74 ~~~~~l~~GD~~~ip~g~~H~~~n~~~~~~~~l-~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~ 145 (146)
T smart00835 74 VYDARLREGDVFVVPQGHPHFQVNSGDENLEFV-AFNTNDPNRRFFLAGRNSVLRG---LPPEVLAAAFGVSAEEV 145 (146)
T ss_pred EEEEEecCCCEEEECCCCEEEEEcCCCCCEEEE-EEecCCCCceeEeecccchhhc---CCHHHHHHHhCcChHHc
Confidence 457789999999999999999999999999888 68888876421 1 2468886 99999999999999875
No 7
>COG2140 Thermophilic glucose-6-phosphate isomerase and related metalloenzymes [Carbohydrate transport and metabolism / General function prediction only]
Probab=98.14 E-value=3.1e-06 Score=60.29 Aligned_cols=72 Identities=15% Similarity=0.210 Sum_probs=54.6
Q ss_pred eEEEeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCcceeeccccccCCCCCcHHHHHHHhCCCHHHHHHH
Q 039148 3 LIIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGVVTIANTAFGSNPAIVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 3 ~~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~~~~~~~~F~~~p~~~~~vLa~af~~d~~~i~kl 78 (82)
+..-.+++||++.+|++..|...|+|++|.+.+..+....+.......-+++ ++..+++.-++.+....+.+
T Consensus 125 ~~v~~~~~Gd~iyVPp~~gH~t~N~Gd~pLvf~~v~~~~~~~~y~~~~~~~~----~~~~~~~~~~~~~~~~~D~p 196 (209)
T COG2140 125 ARVIAVRAGDVIYVPPGYGHYTINTGDEPLVFLNVYPADAGQDYDLIAWLGG----MPPVLVENGLNKNPKYVDVP 196 (209)
T ss_pred EEEEEecCCcEEEeCCCcceEeecCCCCCEEEEEEEeCCCCceeeeeehhcc----CCceeeccccccCcccccCc
Confidence 4566789999999999999999999999999999999876655544433444 56666666666665555544
No 8
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=97.76 E-value=8.7e-05 Score=42.38 Aligned_cols=34 Identities=26% Similarity=0.291 Sum_probs=31.1
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEee
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAF 38 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~ 38 (82)
...+++||.+.+|+|..|...|.++++++++..+
T Consensus 38 ~~~l~~Gd~~~i~~~~~H~~~n~~~~~~~~l~V~ 71 (71)
T PF07883_consen 38 RVELKPGDAIYIPPGVPHQVRNPGDEPARFLVVY 71 (71)
T ss_dssp EEEEETTEEEEEETTSEEEEEEESSSEEEEEEEE
T ss_pred EeEccCCEEEEECCCCeEEEEECCCCCEEEEEEC
Confidence 4578999999999999999999999999998764
No 9
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=97.61 E-value=0.00014 Score=47.32 Aligned_cols=39 Identities=28% Similarity=0.204 Sum_probs=33.8
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCC
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNL 43 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~np 43 (82)
...|++||++++|+|..|...|.|..|+.++..-.....
T Consensus 76 ~~~v~~gd~~~iP~g~~H~~~N~G~~~L~liei~~p~~~ 114 (127)
T COG0662 76 EVEVKAGDSVYIPAGTPHRVRNTGKIPLVLIEVQSPPYL 114 (127)
T ss_pred EEEecCCCEEEECCCCcEEEEcCCCcceEEEEEecCCcC
Confidence 457899999999999999999999999998887665443
No 10
>PRK04190 glucose-6-phosphate isomerase; Provisional
Probab=97.50 E-value=0.00031 Score=49.26 Aligned_cols=37 Identities=16% Similarity=0.229 Sum_probs=34.0
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeeecC
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQ 41 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~ 41 (82)
.-.+++||++.+|+|..|...|.|++|++.++.....
T Consensus 121 ~~~v~pGd~v~IPpg~~H~~iN~G~epl~fl~v~p~~ 157 (191)
T PRK04190 121 WIEMEPGTVVYVPPYWAHRSVNTGDEPLVFLACYPAD 157 (191)
T ss_pred EEEECCCCEEEECCCCcEEeEECCCCCEEEEEEEcCC
Confidence 4578999999999999999999999999999988864
No 11
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=97.50 E-value=0.00019 Score=46.24 Aligned_cols=36 Identities=31% Similarity=0.338 Sum_probs=31.4
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeeec
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSS 40 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s 40 (82)
.+.+++||++.+|+|..||..|.++.+.+.++.+..
T Consensus 83 ~~~l~~Gd~i~ip~g~~H~~~a~~~~~~~~l~v~~~ 118 (131)
T COG1917 83 KKELKAGDVIIIPPGVVHGLKAVEDEPMVLLLVFPL 118 (131)
T ss_pred ceEecCCCEEEECCCCeeeeccCCCCceeEEEEeee
Confidence 468999999999999999999999998677776665
No 12
>PF06560 GPI: Glucose-6-phosphate isomerase (GPI); InterPro: IPR010551 This entry consists of several bacterial and archaeal glucose-6-phosphate isomerase (GPI) proteins (5.3.1.9 from EC), which are involved in glycolysis and in gluconeogenesis and catalyse the conversion of D-glucose 6-phosphate to D-fructose 6-phosphate. The deduced amino acid sequence of the first archaeal PGI isolated from Pyrococcus furiosus revealed that it is not related to its eukaryotic and many of its bacterial counterparts. In contrast, this archaeal PGI shares similarity with the cupin superfamily that consists of a variety of proteins that are generally involved in sugar metabolism in both prokaryotes and eukaryotes [].; GO: 0004347 glucose-6-phosphate isomerase activity, 0006094 gluconeogenesis, 0006096 glycolysis, 0005737 cytoplasm; PDB: 1J3Q_B 1J3R_B 1J3P_A 2GC0_A 1X8E_A 1X82_A 1QY4_B 2GC2_B 1QXJ_A 1QXR_B ....
Probab=97.40 E-value=0.00057 Score=47.80 Aligned_cols=39 Identities=26% Similarity=0.255 Sum_probs=30.0
Q ss_pred eeEEEeecCCcEEEEccCceeEEEecCCcceEEEEeeec
Q 039148 2 RLIIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSS 40 (82)
Q Consensus 2 ~~~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s 40 (82)
+++.-..++||++.+|.|.+|...|+|++|++..+..++
T Consensus 108 ~~~~v~~~~G~~v~IPp~yaH~tIN~g~~~L~~~~~~~~ 146 (182)
T PF06560_consen 108 DVIAVEAKPGDVVYIPPGYAHRTINTGDEPLVFAAWVPR 146 (182)
T ss_dssp -EEEEEE-TTEEEEE-TT-EEEEEE-SSS-EEEEEEEET
T ss_pred eEEEEEeCCCCEEEECCCceEEEEECCCCcEEEEEEEec
Confidence 456778999999999999999999999999998888875
No 13
>COG4101 Predicted mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=97.20 E-value=0.00067 Score=45.29 Aligned_cols=44 Identities=30% Similarity=0.329 Sum_probs=36.7
Q ss_pred Cee-EEEeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCc
Q 039148 1 NRL-IIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLG 44 (82)
Q Consensus 1 n~~-~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg 44 (82)
||| +.-+.++||.|.+|.|+-|--+|..++|+.++-+-..-||.
T Consensus 84 ~rLE~ha~~~pGDf~YiPpgVPHqp~N~S~ep~s~vIaRsDp~~~ 128 (142)
T COG4101 84 NRLEEHAEVGPGDFFYIPPGVPHQPANLSTEPLSAVIARSDPNPQ 128 (142)
T ss_pred cceeeeEEecCCCeEEcCCCCCCcccccCCCCeEEEEEccCCCCC
Confidence 344 56678999999999999999999999999998887755543
No 14
>PF02373 JmjC: JmjC domain, hydroxylase; InterPro: IPR013129 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with jmjN (see IPR003349 from INTERPRO) and belongs to the Cupin superfamily [].; PDB: 2YU2_A 2YU1_A 3AVR_A 3AVS_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=97.07 E-value=0.0013 Score=40.66 Aligned_cols=31 Identities=23% Similarity=0.222 Sum_probs=23.0
Q ss_pred eEEEeecCCcEEEEccCceeEEEecCCcceE
Q 039148 3 LIIMVLKKGDVFVFLVGLVHFKCNVGYGNVV 33 (82)
Q Consensus 3 ~~~~~l~~GDv~vfP~G~~H~~~N~G~~~av 33 (82)
.+.-+-++||.+++|+|..|+.+|.|..=++
T Consensus 80 ~~~~~Q~~Ge~V~i~pg~~H~v~n~g~~i~~ 110 (114)
T PF02373_consen 80 VYRFVQKPGEFVFIPPGAYHQVFNLGDNISE 110 (114)
T ss_dssp -EEEEEETT-EEEE-TT-EEEEEESSSEEEE
T ss_pred cccceECCCCEEEECCCceEEEEeCCceEEE
Confidence 5667789999999999999999999975443
No 15
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=97.03 E-value=0.0012 Score=47.85 Aligned_cols=34 Identities=12% Similarity=0.010 Sum_probs=30.3
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
..+++||++.+|+|..||+||.|++|+..+--=|
T Consensus 220 ~~V~~GD~i~i~~~~~h~~~~~G~~~~~~l~ykd 253 (260)
T TIGR03214 220 VPVEAGDYIWMGAYCPQACYAGGRGEFRYLLYKD 253 (260)
T ss_pred EEecCCCEEEECCCCCEEEEecCCCcEEEEEEcc
Confidence 5689999999999999999999999998776544
No 16
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=96.92 E-value=0.003 Score=41.40 Aligned_cols=38 Identities=11% Similarity=0.166 Sum_probs=33.3
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCcc
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGV 45 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~ 45 (82)
..|++||.+.||.+..|...|. +++.++++++-.-+|.
T Consensus 77 ~~L~aGD~i~~~~~~~H~~~N~--e~~~~l~v~tP~~~~~ 114 (125)
T PRK13290 77 HPIRPGTMYALDKHDRHYLRAG--EDMRLVCVFNPPLTGR 114 (125)
T ss_pred EEeCCCeEEEECCCCcEEEEcC--CCEEEEEEECCCCCCc
Confidence 5789999999999999999998 8999999988655554
No 17
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=96.53 E-value=0.0062 Score=41.46 Aligned_cols=34 Identities=24% Similarity=0.213 Sum_probs=30.8
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEee
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAF 38 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~ 38 (82)
...|++||.+.||.+..|...|.|++++.++.+.
T Consensus 147 ~~~l~~Gd~~~~~~~~~H~~~n~~~~~~~~l~~~ 180 (185)
T PRK09943 147 DYHLVAGQSYAINTGIPHSFSNTSAGICRIISAH 180 (185)
T ss_pred EEEecCCCEEEEcCCCCeeeeCCCCCCeEEEEEe
Confidence 3578999999999999999999999999888864
No 18
>PRK15460 cpsB mannose-1-phosphate guanyltransferase; Provisional
Probab=96.44 E-value=0.0061 Score=47.93 Aligned_cols=35 Identities=23% Similarity=0.159 Sum_probs=32.1
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
...|++||.+.||+|..|...|.|++|+.++.+.-
T Consensus 425 ~~~L~~GDSi~ip~g~~H~~~N~g~~~l~iI~V~~ 459 (478)
T PRK15460 425 IKLLGENESIYIPLGATHCLENPGKIPLDLIEVRS 459 (478)
T ss_pred EEEecCCCEEEECCCCcEEEEcCCCCCEEEEEEEc
Confidence 46789999999999999999999999999998854
No 19
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=96.42 E-value=0.0065 Score=41.12 Aligned_cols=33 Identities=27% Similarity=0.209 Sum_probs=29.9
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEe
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVA 37 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~ 37 (82)
.+.+.+||.+.+|+|..|-..|.|++|+.++=+
T Consensus 103 ~~~~~~g~sv~Ip~g~~H~i~n~g~~~L~~IEV 135 (151)
T PF01050_consen 103 EFTLKEGDSVYIPRGAKHRIENPGKTPLEIIEV 135 (151)
T ss_pred EEEEcCCCEEEECCCCEEEEECCCCcCcEEEEE
Confidence 467899999999999999999999999988754
No 20
>TIGR01479 GMP_PMI mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase. This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in Pseudomonas aeruginosa, Xanthomonas campestris, and Gluconacetobacter xylinus. The literature on the enzyme from E. coli attributes mannose-6-phosphate isomerase activity to an adjacent gene, but the present sequence has not been shown to lack the activity. The PMI domain is C-terminal.
Probab=96.39 E-value=0.0075 Score=46.87 Aligned_cols=35 Identities=20% Similarity=0.187 Sum_probs=32.4
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
...|++||.+.||.|..|...|.|++|+.++.+..
T Consensus 416 ~~~l~~GDsi~ip~~~~H~~~N~g~~~~~~i~v~~ 450 (468)
T TIGR01479 416 TLLLTENESTYIPLGVIHRLENPGKIPLELIEVQS 450 (468)
T ss_pred EEEecCCCEEEECCCCcEEEEcCCCCCEEEEEEEc
Confidence 35789999999999999999999999999999865
No 21
>PF13621 Cupin_8: Cupin-like domain; PDB: 3AL6_C 3AL5_C 2XUM_A 2Y0I_A 1MZE_A 3KCY_A 1MZF_A 1YCI_A 2ILM_A 1H2L_A ....
Probab=96.38 E-value=0.011 Score=40.65 Aligned_cols=33 Identities=24% Similarity=0.319 Sum_probs=23.8
Q ss_pred eEEEeecCCcEEEEccCceeEEEecCCcc-eEEE
Q 039148 3 LIIMVLKKGDVFVFLVGLVHFKCNVGYGN-VVAI 35 (82)
Q Consensus 3 ~~~~~l~~GDv~vfP~G~~H~~~N~G~~~-av~i 35 (82)
.+.-+|++||++.+|+|.-|...|...++ .+++
T Consensus 208 ~~~~~l~pGD~LfiP~gWwH~V~~~~~~~~sisv 241 (251)
T PF13621_consen 208 PYEVVLEPGDVLFIPPGWWHQVENLSDDDLSISV 241 (251)
T ss_dssp EEEEEEETT-EEEE-TT-EEEEEESTTSSCEEEE
T ss_pred eeEEEECCCeEEEECCCCeEEEEEcCCCCeEEEE
Confidence 46778999999999999999999995444 4444
No 22
>COG3837 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=96.38 E-value=0.0072 Score=41.68 Aligned_cols=37 Identities=19% Similarity=0.076 Sum_probs=33.7
Q ss_pred EeecCCcEEEEccC--ceeEEEecCCcceEEEEeeecCC
Q 039148 6 MVLKKGDVFVFLVG--LVHFKCNVGYGNVVAIVAFSSQN 42 (82)
Q Consensus 6 ~~l~~GDv~vfP~G--~~H~~~N~G~~~av~i~~~~s~n 42 (82)
..|++||.+-||+| ..|+..|.++.+++.+++-+...
T Consensus 84 ~~lrpGD~~gFpAG~~~aHhliN~s~~~~~yL~vG~r~~ 122 (161)
T COG3837 84 TRLRPGDSAGFPAGVGNAHHLINRSDVILRYLEVGTREP 122 (161)
T ss_pred EEecCCceeeccCCCcceeEEeecCCceEEEEEeccccc
Confidence 57999999999999 99999999999999998887654
No 23
>PRK11171 hypothetical protein; Provisional
Probab=96.05 E-value=0.016 Score=42.04 Aligned_cols=35 Identities=14% Similarity=-0.048 Sum_probs=31.6
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
+..|++||.+.||.|..|...|.|++++.++.+.-
T Consensus 102 ~~~L~~GDsi~~p~~~~H~~~N~g~~~a~~l~v~~ 136 (266)
T PRK11171 102 THALSEGGYAYLPPGSDWTLRNAGAEDARFHWIRK 136 (266)
T ss_pred EEEECCCCEEEECCCCCEEEEECCCCCEEEEEEEc
Confidence 45799999999999999999999999999988753
No 24
>PF08007 Cupin_4: Cupin superfamily protein; InterPro: IPR022777 This signature represents primarily the cupin fold found in JmjC transcription factors. The fold is also found in lysine-specific demethylase NO66.; PDB: 2XDV_A 1VRB_B 4DIQ_B.
Probab=95.98 E-value=0.017 Score=42.86 Aligned_cols=25 Identities=28% Similarity=0.327 Sum_probs=19.4
Q ss_pred EEEeecCCcEEEEccCceeEEEecC
Q 039148 4 IIMVLKKGDVFVFLVGLVHFKCNVG 28 (82)
Q Consensus 4 ~~~~l~~GDv~vfP~G~~H~~~N~G 28 (82)
..-+|++||++.+|+|.+|.....+
T Consensus 176 ~~~~L~pGD~LYlPrG~~H~~~~~~ 200 (319)
T PF08007_consen 176 EEVVLEPGDVLYLPRGWWHQAVTTD 200 (319)
T ss_dssp EEEEE-TT-EEEE-TT-EEEEEESS
T ss_pred EEEEECCCCEEEECCCccCCCCCCC
Confidence 4568999999999999999999999
No 25
>PRK11171 hypothetical protein; Provisional
Probab=95.93 E-value=0.016 Score=42.03 Aligned_cols=35 Identities=11% Similarity=-0.005 Sum_probs=31.5
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
...|++||++.||.+..||..|.|++++..+.-=|
T Consensus 224 ~~~l~~GD~i~~~~~~~h~~~N~g~~~~~yl~~k~ 258 (266)
T PRK11171 224 WVEVEAGDFIWMRAYCPQACYAGGPGPFRYLLYKD 258 (266)
T ss_pred EEEeCCCCEEEECCCCCEEEECCCCCcEEEEEEcc
Confidence 35789999999999999999999999998887655
No 26
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=95.66 E-value=0.029 Score=40.63 Aligned_cols=35 Identities=11% Similarity=-0.019 Sum_probs=30.9
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
+..|++||.+.||.|..|...|.++++|.++..--
T Consensus 99 ~~~L~~Gd~~y~pa~~~H~~~N~~~~~a~~l~v~k 133 (260)
T TIGR03214 99 THELREGGYAYLPPGSKWTLANAQAEDARFFLYKK 133 (260)
T ss_pred EEEECCCCEEEECCCCCEEEEECCCCCEEEEEEEe
Confidence 35899999999999999999999999998876553
No 27
>PF03079 ARD: ARD/ARD' family; InterPro: IPR004313 The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Q9ZFE7 from SWISSPROT, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+ []. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions []. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [, ]. This family also contains other proteins, whose functions are not well characterised.; GO: 0010309 acireductone dioxygenase [iron(II)-requiring] activity, 0055114 oxidation-reduction process; PDB: 1VR3_A 1ZRR_A 2HJI_A.
Probab=94.74 E-value=0.15 Score=34.74 Aligned_cols=36 Identities=25% Similarity=0.220 Sum_probs=25.0
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEEeeec
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSS 40 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s 40 (82)
+-.+.+||.+++|+|+-||..-.-.....++=.|..
T Consensus 116 ri~~e~GDli~vP~g~~HrF~~~~~~~i~aiRlF~~ 151 (157)
T PF03079_consen 116 RILCEKGDLIVVPAGTYHRFTLGESPYIKAIRLFKD 151 (157)
T ss_dssp EEEEETTCEEEE-TT--EEEEESTTSSEEEEEEESS
T ss_pred EEEEcCCCEEecCCCCceeEEcCCCCcEEEEEeecC
Confidence 356799999999999999998665666666655543
No 28
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=94.63 E-value=0.097 Score=32.40 Aligned_cols=30 Identities=23% Similarity=0.208 Sum_probs=22.6
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEEE
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAIV 36 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i~ 36 (82)
.+.+||+|.+|+|=.+-..|.++++|.++-
T Consensus 54 ~v~~G~~F~VP~gN~Y~i~N~~~~~a~LfF 83 (85)
T PF11699_consen 54 VVTKGGSFQVPRGNYYSIKNIGNEEAKLFF 83 (85)
T ss_dssp EEETT-EEEE-TT-EEEEEE-SSS-EEEEE
T ss_pred EEeCCCEEEECCCCEEEEEECCCCcEEEEE
Confidence 578999999999999999999999998764
No 29
>TIGR02272 gentisate_1_2 gentisate 1,2-dioxygenase. This family consists of gentisate 1,2-dioxygenases. This ring-opening enzyme acts in salicylate degradation that goes via gentisate rather than via catechol. It converts gentisate to maleylpyruvate. Some putative gentisate 1,2-dioxygenases are excluded by a relatively high trusted cutoff score because they are too closely related to known examples of 1-hydroxy-2-naphthoate dioxygenase. Therefore some homologs may be bona fide gentisate 1,2-dioxygenases even if they score below the given cutoffs.
Probab=94.35 E-value=0.055 Score=41.03 Aligned_cols=35 Identities=14% Similarity=0.104 Sum_probs=31.8
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEeeec
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSS 40 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s 40 (82)
-.+++||+|+.|.+.-|-..|.|++|++.+..+|.
T Consensus 122 ~~~~~gD~~~tP~w~wH~H~n~~d~~~~wld~lD~ 156 (335)
T TIGR02272 122 TTMHPGDFIITPSWTWHDHGNPGDEPMIWLDGLDI 156 (335)
T ss_pred EeeeCCCEEEeCCCeeEecccCCCCcEEEEecCCH
Confidence 35789999999999999999999999999888884
No 30
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=93.43 E-value=0.23 Score=30.29 Aligned_cols=31 Identities=23% Similarity=0.117 Sum_probs=20.4
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEE
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIV 36 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~ 36 (82)
-.+++||++.+|+|..|-..-.+.++...+.
T Consensus 43 ~~l~~g~~~li~p~~~H~~~~~~~~~~~~~~ 73 (136)
T PF02311_consen 43 YPLKPGDLFLIPPGQPHSYYPDSNEPWEYYW 73 (136)
T ss_dssp EEE-TT-EEEE-TTS-EEEEE-TTSEEEEEE
T ss_pred EEEECCEEEEecCCccEEEecCCCCCEEEEE
Confidence 4689999999999999998888865554433
No 31
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=92.80 E-value=0.1 Score=30.98 Aligned_cols=17 Identities=29% Similarity=0.554 Sum_probs=14.0
Q ss_pred EEeecCCcEEEEccCce
Q 039148 5 IMVLKKGDVFVFLVGLV 21 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~ 21 (82)
+.++++||+++||+|..
T Consensus 45 ~~~~~aGD~~~~p~G~~ 61 (74)
T PF05899_consen 45 TVTFKAGDAFFLPKGWT 61 (74)
T ss_dssp EEEEETTEEEEE-TTEE
T ss_pred EEEEcCCcEEEECCCCE
Confidence 46899999999999983
No 32
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=91.76 E-value=0.19 Score=34.60 Aligned_cols=26 Identities=15% Similarity=0.232 Sum_probs=21.1
Q ss_pred EEeecCCcEEEEccCceeEEEecCCc
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYG 30 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~ 30 (82)
.-+|++||++++|+|+-|--.-.+++
T Consensus 71 ~v~L~eGd~flvP~gvpHsP~r~~~t 96 (159)
T TIGR03037 71 DVPIREGDIFLLPPHVPHSPQRPAGS 96 (159)
T ss_pred EEEECCCCEEEeCCCCCcccccCCCc
Confidence 35789999999999999987765443
No 33
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=91.58 E-value=0.34 Score=35.25 Aligned_cols=23 Identities=30% Similarity=0.433 Sum_probs=18.6
Q ss_pred EEeecCCcEEEEccCce-eEEEecC
Q 039148 5 IMVLKKGDVFVFLVGLV-HFKCNVG 28 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~-H~~~N~G 28 (82)
+.++++||++.+|+|.. || .+.+
T Consensus 194 t~~l~pGDvlfIPkGs~~hf-~tp~ 217 (233)
T PRK15457 194 TMIAKAGDVMFIPKGSSIEF-GTPS 217 (233)
T ss_pred EEEeCCCcEEEECCCCeEEe-cCCC
Confidence 46789999999999999 77 4444
No 34
>KOG3706 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.32 E-value=0.072 Score=42.80 Aligned_cols=26 Identities=27% Similarity=0.393 Sum_probs=21.0
Q ss_pred eEEEeecCCcEEEEccCceeEEEecC
Q 039148 3 LIIMVLKKGDVFVFLVGLVHFKCNVG 28 (82)
Q Consensus 3 ~~~~~l~~GDv~vfP~G~~H~~~N~G 28 (82)
++.-.|.+||++.||+|.||-.--..
T Consensus 380 V~e~vle~GDllYfPRG~IHQA~t~~ 405 (629)
T KOG3706|consen 380 VHEFVLEPGDLLYFPRGTIHQADTPA 405 (629)
T ss_pred hHHhhcCCCcEEEecCcceeeccccc
Confidence 34567899999999999999765554
No 35
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=91.30 E-value=0.31 Score=34.13 Aligned_cols=25 Identities=12% Similarity=0.189 Sum_probs=20.9
Q ss_pred EEeecCCcEEEEccCceeEEEecCC
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGY 29 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~ 29 (82)
..+|++||++++|+|+-|--....+
T Consensus 77 ~v~L~eGd~fllP~gvpHsP~r~~~ 101 (177)
T PRK13264 77 DVPIREGEMFLLPPHVPHSPQREAG 101 (177)
T ss_pred eEEECCCCEEEeCCCCCcCCccCCC
Confidence 5679999999999999998866433
No 36
>PF12852 Cupin_6: Cupin
Probab=91.12 E-value=0.22 Score=33.56 Aligned_cols=25 Identities=20% Similarity=0.305 Sum_probs=21.3
Q ss_pred EeecCCcEEEEccCceeEEEecCCc
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYG 30 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~ 30 (82)
-.|++||++++|+|..|+..-..+.
T Consensus 57 ~~L~~GDivllp~g~~H~l~~~~~~ 81 (186)
T PF12852_consen 57 IRLEAGDIVLLPRGTAHVLSSDPDS 81 (186)
T ss_pred EEecCCCEEEEcCCCCeEeCCCCCC
Confidence 4689999999999999999766554
No 37
>COG1791 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=91.01 E-value=0.92 Score=31.87 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=34.6
Q ss_pred eeEEEeecCCcEEEEccCceeEEEecCCcceEEEEeeecC
Q 039148 2 RLIIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQ 41 (82)
Q Consensus 2 ~~~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~ 41 (82)
+.|.=.+.+||.+.+|.|.-||+--.-+-.-+|+=.|...
T Consensus 116 ~~~~i~c~~gDLI~vP~gi~HwFtlt~~~~f~AvRlF~~~ 155 (181)
T COG1791 116 KVYQIRCEKGDLISVPPGIYHWFTLTESPNFKAVRLFTEP 155 (181)
T ss_pred cEEEEEEccCCEEecCCCceEEEEccCCCcEEEEEEeeCC
Confidence 5677888999999999999999988888888888887654
No 38
>COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]
Probab=89.22 E-value=0.36 Score=31.62 Aligned_cols=16 Identities=38% Similarity=0.754 Sum_probs=14.3
Q ss_pred EeecCCcEEEEccCce
Q 039148 6 MVLKKGDVFVFLVGLV 21 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~ 21 (82)
.++++||.++||+|.-
T Consensus 84 v~~~aGD~~~~~~G~~ 99 (116)
T COG3450 84 VEVRAGDSFVFPAGFK 99 (116)
T ss_pred EEEcCCCEEEECCCCe
Confidence 5789999999999974
No 39
>TIGR02451 anti_sig_ChrR anti-sigma factor, putative, ChrR family. The member of this family from Rhodobacter sphaeroides has been shown both to form a complex with sigma(E) and to negatively regulate tetrapyrrole biosynthesis. This protein likely contains (at least) two distinct functional domains; several smaller homologs (excluded by the model) show homology only to the C-terminal, including a motif PxHxHxGxE.
Probab=87.34 E-value=0.68 Score=32.71 Aligned_cols=37 Identities=16% Similarity=0.085 Sum_probs=33.6
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEeeecCC
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQN 42 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~n 42 (82)
.++.+||.+..|.|..|--.+.++++.+++++.|...
T Consensus 163 g~y~~Gd~i~~p~~~~H~p~a~~~~~Cicl~v~dapl 199 (215)
T TIGR02451 163 GVYGVGDFEEADGSVQHQPRTVSGGDCLCLAVLDAPL 199 (215)
T ss_pred CccCCCeEEECCCCCCcCcccCCCCCeEEEEEecCCc
Confidence 4678999999999999999999999999999998653
No 40
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=87.15 E-value=2 Score=26.29 Aligned_cols=33 Identities=21% Similarity=0.153 Sum_probs=20.1
Q ss_pred EEEeecCCcEEEEccCceeEEEec-CCcceEEEE
Q 039148 4 IIMVLKKGDVFVFLVGLVHFKCNV-GYGNVVAIV 36 (82)
Q Consensus 4 ~~~~l~~GDv~vfP~G~~H~~~N~-G~~~av~i~ 36 (82)
+.-..++||+++||.-+.|...-. ++++-+.||
T Consensus 66 ~~~~p~~G~lvlFPs~l~H~v~p~~~~~~Risis 99 (101)
T PF13759_consen 66 YIVEPEEGDLVLFPSWLWHGVPPNNSDEERISIS 99 (101)
T ss_dssp EEE---TTEEEEEETTSEEEE----SSS-EEEEE
T ss_pred EEeCCCCCEEEEeCCCCEEeccCcCCCCCEEEEE
Confidence 344568999999999999998755 445665554
No 41
>KOG2107 consensus Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=86.85 E-value=0.46 Score=33.25 Aligned_cols=20 Identities=30% Similarity=0.557 Sum_probs=16.7
Q ss_pred EeecCCcEEEEccCceeEEE
Q 039148 6 MVLKKGDVFVFLVGLVHFKC 25 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~ 25 (82)
=-+++||++++|+|+-|-.-
T Consensus 118 i~vekGDlivlPaGiyHRFT 137 (179)
T KOG2107|consen 118 IFVEKGDLIVLPAGIYHRFT 137 (179)
T ss_pred EEEecCCEEEecCcceeeee
Confidence 34689999999999999653
No 42
>PRK05341 homogentisate 1,2-dioxygenase; Provisional
Probab=86.36 E-value=1.4 Score=34.85 Aligned_cols=32 Identities=19% Similarity=0.302 Sum_probs=23.7
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
.+++||+.|+|+|+. |..+..++|+..+..=+
T Consensus 175 ~v~pgei~VIPRG~~-frv~l~~gp~rgyi~E~ 206 (438)
T PRK05341 175 DVEPGEIAVIPRGVK-FRVELPDGPARGYVCEN 206 (438)
T ss_pred EecCCCEEEEcCccE-EEEecCCCCeeEEEEEe
Confidence 578999999999998 55666566766655443
No 43
>PLN02658 homogentisate 1,2-dioxygenase
Probab=85.19 E-value=1.7 Score=34.29 Aligned_cols=32 Identities=19% Similarity=0.254 Sum_probs=23.3
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
.+++||+.|+|+|+. |..+..++|+..+..=+
T Consensus 168 ~v~pgei~VIPRG~~-frv~l~~gp~rgyv~E~ 199 (435)
T PLN02658 168 QVSPGEIVVIPRGFR-FAVDLPDGPSRGYVLEI 199 (435)
T ss_pred EecCCCEEEecCccE-EEEecCCCCeeEEEEee
Confidence 469999999999998 66665556666544433
No 44
>COG4297 Uncharacterized protein containing double-stranded beta helix domain [Function unknown]
Probab=82.08 E-value=0.95 Score=31.04 Aligned_cols=19 Identities=26% Similarity=0.506 Sum_probs=16.3
Q ss_pred eecCCcEEEEccCceeEEE
Q 039148 7 VLKKGDVFVFLVGLVHFKC 25 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~ 25 (82)
.+.+||++++|+|+-|.-.
T Consensus 88 ~v~~GDvlliPAGvGH~rl 106 (163)
T COG4297 88 EVGEGDVLLIPAGVGHCRL 106 (163)
T ss_pred eecCCCEEEEecCcccccc
Confidence 4689999999999999654
No 45
>TIGR00218 manA mannose-6-phosphate isomerase, class I. The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc.
Probab=81.51 E-value=1.2 Score=32.62 Aligned_cols=24 Identities=33% Similarity=0.311 Sum_probs=19.9
Q ss_pred EEeecCCcEEEEccCceeEEEecCCc
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYG 30 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~ 30 (82)
.-.+++||.+.+|.|.+|- | .|..
T Consensus 152 ~v~v~~Gd~i~ipaGt~HA-~-~g~~ 175 (302)
T TIGR00218 152 RIKLKPGDFFYVPSGTPHA-Y-KGGL 175 (302)
T ss_pred ccccCCCCEEEeCCCCccc-c-cCce
Confidence 3568999999999999998 6 5544
No 46
>COG3435 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=81.24 E-value=1.5 Score=33.47 Aligned_cols=35 Identities=14% Similarity=0.085 Sum_probs=32.7
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEeeec
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSS 40 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s 40 (82)
..+++||.++-|++.-|-.-|.|.+|.+.+=.+|.
T Consensus 133 ~~M~~GDfilTP~w~wHdHgn~g~eP~iWlDgLDi 167 (351)
T COG3435 133 TPMEAGDFILTPAWTWHDHGNEGTEPCIWLDGLDI 167 (351)
T ss_pred eeccCCCEEEccCceeccCCCCCCCceEEEcccch
Confidence 46799999999999999999999999999999986
No 47
>PRK14585 pgaD putative PGA biosynthesis protein; Provisional
Probab=81.12 E-value=2.1 Score=28.89 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=22.4
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 57 PAIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 57 p~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
|..+++-||++|+++++.+++||+.
T Consensus 88 ~~~~~~eLA~Sf~is~el~~qL~~~ 112 (137)
T PRK14585 88 YQYTPQEYAESLAIPDELYQQLQKS 112 (137)
T ss_pred CCCChHHHHHHcCCCHHHHHHHhcC
Confidence 4589999999999999999999864
No 48
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=79.50 E-value=3.9 Score=28.81 Aligned_cols=21 Identities=24% Similarity=0.377 Sum_probs=18.1
Q ss_pred eecCCcEEEEccCceeEEEec
Q 039148 7 VLKKGDVFVFLVGLVHFKCNV 27 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~ 27 (82)
.+.+||++++|+|.+|-.+..
T Consensus 64 ~l~~g~l~~i~p~~~H~~~~~ 84 (278)
T PRK10296 64 LLERGDFVFIPLGSHHQSFYE 84 (278)
T ss_pred EECCCcEEEeCCCCccceeee
Confidence 789999999999999966544
No 49
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=78.92 E-value=2.9 Score=29.47 Aligned_cols=26 Identities=8% Similarity=-0.224 Sum_probs=21.0
Q ss_pred EeecCCcEEEEccCceeEEEecCCcc
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGN 31 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~ 31 (82)
-.+++||++++|+|..|-....+...
T Consensus 64 ~~l~~g~~~ii~~~~~H~~~~~~~~~ 89 (287)
T TIGR02297 64 YSEYAPCFFLTPPSVPHGFVTDLDAD 89 (287)
T ss_pred EEecCCeEEEeCCCCccccccCCCcc
Confidence 36899999999999999877655433
No 50
>PF05118 Asp_Arg_Hydrox: Aspartyl/Asparaginyl beta-hydroxylase; InterPro: IPR007803 The alpha-ketoglutarate-dependent dioxygenase aspartyl (asparaginyl) beta-hydroxylase (1.14.11.16 from EC) specifically hydroxylates one aspartic or asparagine residue in certain epidermal growth factor-like domains of a number of proteins. Its action may be due to histidine-675, which, when mutated to an alanine residue, causes the loss of enzymatic activity in the protein []. An invertebrate alpha-ketoglutarate-dependent aspartyl/asparaginyl beta-hydroxylase, which posttranslationally hydroxylates specific aspartyl or asparaginyl residues within epidermal growth factor-like modules [], activity was found to be similar to that of the purified mammalian aspartyl/asparaginyl beta-hydroxylase with respect to cofactor requirements, stereochemistry and substrate sequence specificity []. This enzyme requires Fe2+ as a cofactor. Some vitamin K-dependent coagulation factors, as well as synthetic peptides based on the structure of the first epidermal growth factor domain of human coagulation factor IX or X, can act as acceptors.; GO: 0018193 peptidyl-amino acid modification, 0030176 integral to endoplasmic reticulum membrane; PDB: 3RCQ_A 1E5S_A 1E5R_B.
Probab=78.32 E-value=6 Score=26.55 Aligned_cols=31 Identities=23% Similarity=0.284 Sum_probs=22.2
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEE
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAI 35 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i 35 (82)
....++|++++|=-...|+.+|.|+++-+.+
T Consensus 125 ~~~w~~G~~~~fD~s~~H~~~N~~~~~Rv~L 155 (163)
T PF05118_consen 125 TRHWREGECWVFDDSFEHEVWNNGDEDRVVL 155 (163)
T ss_dssp EEB--CTEEEEE-TTS-EEEEESSSS-EEEE
T ss_pred EEEeccCcEEEEeCCEEEEEEeCCCCCEEEE
Confidence 3567999999999999999999998866554
No 51
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=77.37 E-value=3.3 Score=28.38 Aligned_cols=25 Identities=28% Similarity=0.500 Sum_probs=22.5
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 57 PAIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 57 p~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
|.++++=+|++|+++++.++++|+.
T Consensus 97 ~~l~~dElA~sF~l~~e~i~qLr~~ 121 (153)
T PRK14584 97 PDLDDDELASSFALSPELIAQLKSG 121 (153)
T ss_pred CCCChHHHHHHcCCCHHHHHHHHhC
Confidence 4599999999999999999999863
No 52
>PF13994 PgaD: PgaD-like protein
Probab=76.83 E-value=3.7 Score=27.05 Aligned_cols=23 Identities=22% Similarity=0.429 Sum_probs=21.2
Q ss_pred CcHHHHHHHhCCCHHHHHHHHhc
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
.+++=+|+.|+++++.++++|+.
T Consensus 101 ~~~~elA~~f~l~~~~l~~lr~~ 123 (138)
T PF13994_consen 101 VSDEELARSFGLSPEQLQQLRQA 123 (138)
T ss_pred CCHHHHHHHcCCCHHHHHHHHhC
Confidence 88999999999999999999863
No 53
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=76.39 E-value=3.1 Score=27.12 Aligned_cols=24 Identities=13% Similarity=0.314 Sum_probs=18.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
||+|..||+..+++++.|++++.+
T Consensus 72 GFsD~~IA~l~~~~e~~vr~~R~~ 95 (123)
T PF02787_consen 72 GFSDRQIARLWGVSEEEVRELRKE 95 (123)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHhccCCCHHHHHHHHHH
Confidence 499999999999999999998854
No 54
>PRK15131 mannose-6-phosphate isomerase; Provisional
Probab=76.25 E-value=1.9 Score=33.23 Aligned_cols=24 Identities=17% Similarity=0.295 Sum_probs=19.0
Q ss_pred EEeecCCcEEEEccCceeEEEecCC
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGY 29 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~ 29 (82)
.-+|++||.+.+|.|.+|-. -.|+
T Consensus 238 ~v~l~pGeaifipAg~~HAy-l~G~ 261 (389)
T PRK15131 238 VVKLNPGEAMFLFAETPHAY-LQGV 261 (389)
T ss_pred EEEeCCCCEEEeCCCCCeEE-cCCe
Confidence 35789999999999999963 3344
No 55
>PF13464 DUF4115: Domain of unknown function (DUF4115)
Probab=75.89 E-value=10 Score=22.21 Aligned_cols=35 Identities=26% Similarity=0.400 Sum_probs=29.4
Q ss_pred eeEEEeecCCcEEEEccCceeEEEecCCcceEEEEe
Q 039148 2 RLIIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVA 37 (82)
Q Consensus 2 ~~~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~ 37 (82)
.+|+..+++||..-+ .+---+....|+.+++.+..
T Consensus 20 ~~~~~~l~~G~~~~~-~~~~~~~i~iGna~~v~v~~ 54 (77)
T PF13464_consen 20 VLFSGTLKAGETKTF-EGKEPFRIRIGNAGAVEVTV 54 (77)
T ss_pred EeeeeeeCCCcEEEE-eCCCCEEEEEeCCCcEEEEE
Confidence 589999999999999 66777888899988876654
No 56
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=75.36 E-value=3.8 Score=29.09 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=20.5
Q ss_pred EEeecCCcEEEEccCceeEEEecCC
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGY 29 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~ 29 (82)
.-.+++||++++|+|.+|......+
T Consensus 68 ~~~~~~g~~i~i~p~~~h~~~~~~~ 92 (290)
T PRK10572 68 AFVCRPGDLLLFPPGEIHHYGRHPD 92 (290)
T ss_pred eEecCCCCEEEECCCCceeeccCCC
Confidence 3468999999999999998666544
No 57
>PF04209 HgmA: homogentisate 1,2-dioxygenase; InterPro: IPR005708 Alkaptonuria (AKU), a rare hereditary disorder, was the first disease to be interpreted as an inborn error of metabolism. The deficiency causes homogentisic aciduria, ochronosis, and arthritis. AKU patients are deficient for homogentisate 1,2 dioxygenase (1.13.11.5 from EC), the enzyme that mediates the conversion of homogentisate to maleylacetoacetate; a step in the catabolism of both tyrosine and phenylalanine. Homogentisate + O(2) = 4-maleylacetoacetate. ; GO: 0004411 homogentisate 1,2-dioxygenase activity, 0006559 L-phenylalanine catabolic process, 0006570 tyrosine metabolic process, 0055114 oxidation-reduction process; PDB: 1EY2_A 1EYB_A.
Probab=73.70 E-value=6 Score=31.13 Aligned_cols=30 Identities=17% Similarity=0.046 Sum_probs=17.9
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEEEee
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAF 38 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~ 38 (82)
.+++||++|+|+|+.|-..=. +|+..+..=
T Consensus 167 ~v~pGd~~VIPRG~~~rv~l~--~p~rgyi~E 196 (424)
T PF04209_consen 167 DVRPGDYVVIPRGTRFRVELP--GPARGYIIE 196 (424)
T ss_dssp EE-TTEEEEE-TT--EEEE-S--SSEEEEEEE
T ss_pred EEcCCeEEEECCeeEEEEEeC--CCceEEEEE
Confidence 479999999999998765444 566555544
No 58
>COG2850 Uncharacterized conserved protein [Function unknown]
Probab=73.68 E-value=1.6 Score=33.93 Aligned_cols=24 Identities=25% Similarity=0.419 Sum_probs=20.4
Q ss_pred EeecCCcEEEEccCceeEEEecCC
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGY 29 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~ 29 (82)
-.+.+|||..+|+|+.|+-+--++
T Consensus 181 ~vlepGDiLYiPp~~~H~gvae~d 204 (383)
T COG2850 181 EVLEPGDILYIPPGFPHYGVAEDD 204 (383)
T ss_pred hhcCCCceeecCCCCCcCCccccc
Confidence 367899999999999999887743
No 59
>TIGR01015 hmgA homogentisate 1,2-dioxygenase. Missing in human disease alkaptonuria.
Probab=72.96 E-value=2.8 Score=33.08 Aligned_cols=27 Identities=7% Similarity=0.081 Sum_probs=19.3
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEE
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAI 35 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i 35 (82)
.+++||+.|+|+|+.+-..=.| |+..+
T Consensus 169 ~v~pgei~VIPRG~~frv~l~g--p~rgy 195 (429)
T TIGR01015 169 LVEPNEICVIPRGVRFRVTVLE--PARGY 195 (429)
T ss_pred EecCCCEEEecCccEEEEeeCC--CceEE
Confidence 5799999999999985444334 54443
No 60
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=72.95 E-value=2.6 Score=24.05 Aligned_cols=22 Identities=14% Similarity=0.312 Sum_probs=16.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHhc
Q 039148 60 VTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 60 ~~~vLa~af~~d~~~i~kl~~~ 81 (82)
.+..|.+.+|++++.+++||..
T Consensus 45 ~e~Yl~~~lgl~~~~i~~Lr~~ 66 (68)
T PF13348_consen 45 VENYLREELGLSEEDIERLRER 66 (68)
T ss_dssp HHHHHHHT-T--HHHHHHHHHH
T ss_pred HHHHHHHcCCCCHHHHHHHHHH
Confidence 5678889999999999999975
No 61
>PF02041 Auxin_BP: Auxin binding protein; InterPro: IPR000526 Auxin binding protein is located in the lumen of the endoplasmic reticulum (ER). The primary structure contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could represent a signal for translocation of the protein to the ER [, ]. The mature protein comprises around 165 residues, and contains a number of potential N-glycosylation sites. In vitro transport studies have demonstrated co-translational glycosylation []. Retention within the lumen of the ER correlates with an additional signal located at the C terminus, represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ER in eukaryotic cells [, ].; GO: 0004872 receptor activity, 0005788 endoplasmic reticulum lumen; PDB: 1LR5_D 1LRH_D.
Probab=72.13 E-value=10 Score=26.27 Aligned_cols=33 Identities=18% Similarity=0.167 Sum_probs=19.8
Q ss_pred ecCCcEEEEccCceeEEEecC-CcceEEEEeeec
Q 039148 8 LKKGDVFVFLVGLVHFKCNVG-YGNVVAIVAFSS 40 (82)
Q Consensus 8 l~~GDv~vfP~G~~H~~~N~G-~~~av~i~~~~s 40 (82)
+-+++.|.+|.+..|-..|.+ .+++.++...+.
T Consensus 95 ~~pnSTf~IPvn~~HQv~NT~e~eDlqvlViiSr 128 (167)
T PF02041_consen 95 IFPNSTFHIPVNDAHQVWNTNEHEDLQVLVIISR 128 (167)
T ss_dssp E-TTEEEEE-TT--EEEE---SSS-EEEEEEEES
T ss_pred ecCCCeEEeCCCCcceeecCCCCcceEEEEEecC
Confidence 457999999999999999999 477766666553
No 62
>PRK13500 transcriptional activator RhaR; Provisional
Probab=71.49 E-value=5.4 Score=29.03 Aligned_cols=24 Identities=21% Similarity=0.272 Sum_probs=19.8
Q ss_pred EeecCCcEEEEccCceeEEEecCC
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGY 29 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~ 29 (82)
-.+.+||++++|+|..|-.....+
T Consensus 88 ~~l~~Gdl~~I~~~~~H~~~~~~~ 111 (312)
T PRK13500 88 YRITRGDLFYIHADDKHSYASVND 111 (312)
T ss_pred EeecCCeEEEECCCCeecccccCC
Confidence 468999999999999998665444
No 63
>PRK13502 transcriptional activator RhaR; Provisional
Probab=71.41 E-value=6.5 Score=27.69 Aligned_cols=24 Identities=21% Similarity=0.242 Sum_probs=19.3
Q ss_pred EeecCCcEEEEccCceeEEEecCC
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGY 29 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~ 29 (82)
-.+++||++++|+|..|.....++
T Consensus 58 ~~l~~g~l~li~~~~~H~~~~~~~ 81 (282)
T PRK13502 58 YRITRGDLFYIRAEDKHSYTSVND 81 (282)
T ss_pred EeecCCcEEEECCCCcccccccCC
Confidence 467999999999999997654343
No 64
>TIGR02272 gentisate_1_2 gentisate 1,2-dioxygenase. This family consists of gentisate 1,2-dioxygenases. This ring-opening enzyme acts in salicylate degradation that goes via gentisate rather than via catechol. It converts gentisate to maleylpyruvate. Some putative gentisate 1,2-dioxygenases are excluded by a relatively high trusted cutoff score because they are too closely related to known examples of 1-hydroxy-2-naphthoate dioxygenase. Therefore some homologs may be bona fide gentisate 1,2-dioxygenases even if they score below the given cutoffs.
Probab=71.34 E-value=6.6 Score=29.90 Aligned_cols=30 Identities=17% Similarity=-0.078 Sum_probs=20.6
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEEEee
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAF 38 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~ 38 (82)
..++||+|++|.-..|-..|. ++++++++-
T Consensus 291 ~W~~gD~f~vPsW~~~~h~a~--~da~Lf~~~ 320 (335)
T TIGR02272 291 RFSPKDVFVVPSWHPVRFEAS--DDAVLFSFS 320 (335)
T ss_pred EecCCCEEEECCCCcEecccC--CCeEEEEec
Confidence 578999999999876655553 455544443
No 65
>COG1482 ManA Phosphomannose isomerase [Carbohydrate transport and metabolism]
Probab=70.40 E-value=3 Score=31.50 Aligned_cols=20 Identities=30% Similarity=0.441 Sum_probs=17.3
Q ss_pred EeecCCcEEEEccCceeEEE
Q 039148 6 MVLKKGDVFVFLVGLVHFKC 25 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~ 25 (82)
=.|++||.|.+|+|.+|-..
T Consensus 160 v~lkpGe~~fl~Agt~HA~~ 179 (312)
T COG1482 160 VKLKPGEAFFLPAGTPHAYL 179 (312)
T ss_pred EecCCCCEEEecCCCceeec
Confidence 46899999999999999643
No 66
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=69.74 E-value=7.9 Score=30.00 Aligned_cols=41 Identities=20% Similarity=0.169 Sum_probs=33.9
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCcce
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGVV 46 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~~ 46 (82)
-...+|++|.+|-|.=|...|...+-||.----+..|.+.+
T Consensus 265 c~q~pGEt~fVP~GWWHvVlNle~TIAiTqNf~s~eNf~~V 305 (407)
T KOG2130|consen 265 CLQKPGETMFVPSGWWHVVLNLEPTIAITQNFASKENFPFV 305 (407)
T ss_pred eeecCCceEEecCCeEEEEeccCceeeeeeccccccCCcee
Confidence 35689999999999999999999888887777777776543
No 67
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=69.30 E-value=3.5 Score=28.14 Aligned_cols=17 Identities=35% Similarity=0.559 Sum_probs=11.1
Q ss_pred eecCCcEEEEccCc-eeE
Q 039148 7 VLKKGDVFVFLVGL-VHF 23 (82)
Q Consensus 7 ~l~~GDv~vfP~G~-~H~ 23 (82)
+-++|||+.||+|. ++|
T Consensus 116 ~A~~GDvi~iPkGs~I~f 133 (152)
T PF06249_consen 116 TAKPGDVIFIPKGSTITF 133 (152)
T ss_dssp EEETT-EEEE-TT-EEEE
T ss_pred EEcCCcEEEECCCCEEEE
Confidence 45899999999997 444
No 68
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=69.08 E-value=8.2 Score=20.33 Aligned_cols=24 Identities=13% Similarity=0.162 Sum_probs=17.5
Q ss_pred CcHHHHHHHhCCCHHHHHHHHhcC
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQNTF 82 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~~~f 82 (82)
.+..-+|+.++++..+|.+....|
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHc
Confidence 788889999999999999987654
No 69
>PRK13501 transcriptional activator RhaR; Provisional
Probab=67.38 E-value=7.2 Score=27.75 Aligned_cols=25 Identities=24% Similarity=0.110 Sum_probs=20.3
Q ss_pred EEeecCCcEEEEccCceeEEEecCC
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGY 29 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~ 29 (82)
.-.+.+||++++|.|..|.....++
T Consensus 57 ~~~l~~g~~~~I~p~~~H~~~~~~~ 81 (290)
T PRK13501 57 PYRITCGDVFYIQAADHHSYESVHD 81 (290)
T ss_pred eeeecCCeEEEEcCCCcccccccCC
Confidence 3568999999999999998765543
No 70
>PF06052 3-HAO: 3-hydroxyanthranilic acid dioxygenase; InterPro: IPR010329 Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase (1.13.11.6 from EC). It is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid [].The prokaryotic homologue is involved in the 2-nitrobenzoate degradation pathway []. The enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.; GO: 0000334 3-hydroxyanthranilate 3,4-dioxygenase activity, 0005506 iron ion binding, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 1ZVF_A 1YFX_A 1YFW_A 1YFY_A 1YFU_A 2QNK_A 3FE5_A.
Probab=64.79 E-value=13 Score=25.49 Aligned_cols=25 Identities=12% Similarity=0.303 Sum_probs=15.8
Q ss_pred EeecCCcEEEEccCceeEEEecCCc
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYG 30 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~ 30 (82)
-.+++||+|.+|.++.|--.-..++
T Consensus 77 i~I~EGe~fLLP~~vpHsP~R~~~t 101 (151)
T PF06052_consen 77 IPIREGEMFLLPANVPHSPQRPADT 101 (151)
T ss_dssp EEE-TTEEEEE-TT--EEEEE-TT-
T ss_pred EEeCCCcEEecCCCCCCCCcCCCCc
Confidence 4689999999999999987776543
No 71
>PRK13503 transcriptional activator RhaS; Provisional
Probab=63.80 E-value=6.9 Score=27.33 Aligned_cols=23 Identities=17% Similarity=0.059 Sum_probs=18.7
Q ss_pred EeecCCcEEEEccCceeEEEecC
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVG 28 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G 28 (82)
-.+++||++++|+|..|......
T Consensus 55 ~~l~~g~~~~i~~~~~h~~~~~~ 77 (278)
T PRK13503 55 YTLSGGTVCFVRDHDRHLYEHTD 77 (278)
T ss_pred ccccCCcEEEECCCccchhhhcc
Confidence 35799999999999999655543
No 72
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=60.23 E-value=10 Score=27.35 Aligned_cols=28 Identities=14% Similarity=0.389 Sum_probs=21.7
Q ss_pred cccCCCC-CcHHHHHHHhCCCHHHHHHHH
Q 039148 52 AFGSNPA-IVTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 52 ~F~~~p~-~~~~vLa~af~~d~~~i~kl~ 79 (82)
|-..+|. ...+.||+.|.|+++.|+++-
T Consensus 22 L~~~~p~~~t~~~Lae~F~vspe~irrIL 50 (225)
T PF06413_consen 22 LHKEDPEEWTVERLAESFKVSPEAIRRIL 50 (225)
T ss_pred HHHhCccccCHHHHHhhCCCCHHHHHHHH
Confidence 3334454 688999999999999999863
No 73
>PF05995 CDO_I: Cysteine dioxygenase type I; InterPro: IPR010300 Cysteine dioxygenase type I (1.13.11.20 from EC) converts cysteine to cysteinesulphinic acid and is the rate-limiting step in sulphate production.; GO: 0005506 iron ion binding, 0017172 cysteine dioxygenase activity, 0046439 L-cysteine metabolic process, 0055114 oxidation-reduction process; PDB: 2IC1_A 3EQE_B 3ELN_A 2B5H_A 2GH2_A 2Q4S_A 2ATF_A 2GM6_A 3USS_B.
Probab=58.51 E-value=37 Score=23.03 Aligned_cols=33 Identities=21% Similarity=0.237 Sum_probs=25.7
Q ss_pred eecCCcEEEEccCceeEEEecC-CcceEEEEeee
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVG-YGNVVAIVAFS 39 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G-~~~av~i~~~~ 39 (82)
.+..|.+.+++.+-+|-..|.+ +++|+.+=++.
T Consensus 130 ~~~~g~~~~~~~~~iH~v~n~s~~~~avSLHvYs 163 (175)
T PF05995_consen 130 LLPGGVTYIFDPHGIHRVENPSGDEPAVSLHVYS 163 (175)
T ss_dssp EETTTEEEEBTTTBEEEEEES-SSS-EEEEEEEE
T ss_pred ecCCCeEEecCCCCeEEeccCCCCCCEEEEEEcC
Confidence 3567788899999999999986 89998876665
No 74
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=58.39 E-value=11 Score=21.08 Aligned_cols=19 Identities=21% Similarity=0.305 Sum_probs=15.4
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 039148 59 IVTDMLAKAFQAEKKIVKQ 77 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~k 77 (82)
++.+-||+.+|+++.+|||
T Consensus 29 vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 29 VSSQELAEALGITPAQVRK 47 (50)
T ss_dssp E-HHHHHHHHTS-HHHHHH
T ss_pred ECHHHHHHHHCCCHHHhcc
Confidence 6678899999999999987
No 75
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=57.93 E-value=5.4 Score=25.58 Aligned_cols=20 Identities=30% Similarity=0.502 Sum_probs=15.9
Q ss_pred EEeecCCcEEEE-ccCceeEE
Q 039148 5 IMVLKKGDVFVF-LVGLVHFK 24 (82)
Q Consensus 5 ~~~l~~GDv~vf-P~G~~H~~ 24 (82)
-+++..|+.|-| |+|.+||.
T Consensus 13 g~~iieGqkFTF~~kGsVH~e 33 (103)
T COG4847 13 GGTIIEGQKFTFTKKGSVHYE 33 (103)
T ss_pred CCEeeeccEEEEeeCCcchHH
Confidence 356788988866 79999995
No 76
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=56.95 E-value=17 Score=26.47 Aligned_cols=25 Identities=16% Similarity=0.276 Sum_probs=20.2
Q ss_pred EeecCCcEEEEccCceeEEEecCCc
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYG 30 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~ 30 (82)
-.+++||+++++.|..|-....++.
T Consensus 66 ~~l~~Gd~ili~s~~~H~~~~~~~~ 90 (302)
T PRK10371 66 VQINQGHITLFWACTPHQLTDPGNC 90 (302)
T ss_pred EEEcCCcEEEEecCCcccccccCCC
Confidence 4689999999999999976655543
No 77
>PF04970 LRAT: Lecithin retinol acyltransferase; InterPro: IPR007053 This entry represents a conserved sequence region found in proteins from viruses, bacteria and eukaryotes. It contains a well-conserved NCEHF motif, though its function in these proteins is unknown.; PDB: 2KYT_A 4DOT_A 4FA0_A.
Probab=55.05 E-value=12 Score=23.76 Aligned_cols=32 Identities=34% Similarity=0.422 Sum_probs=21.4
Q ss_pred EEeecCCcEEEEccCc-eeEEEecCCcceEEEE
Q 039148 5 IMVLKKGDVFVFLVGL-VHFKCNVGYGNVVAIV 36 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~-~H~~~N~G~~~av~i~ 36 (82)
.+.+++||++.+++++ .||-.=.|+...+=++
T Consensus 4 ~~~~~~GD~I~~~r~~y~H~gIYvG~~~ViH~~ 36 (125)
T PF04970_consen 4 KKRLKPGDHIEVPRGLYEHWGIYVGDGEVIHFS 36 (125)
T ss_dssp --S--TT-EEEEEETTEEEEEEEEETTEEEEEE
T ss_pred ccCCCCCCEEEEecCCccEEEEEecCCeEEEec
Confidence 4679999999999875 6888878887665555
No 78
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=53.99 E-value=13 Score=19.89 Aligned_cols=23 Identities=17% Similarity=0.391 Sum_probs=17.9
Q ss_pred CCCCCcHHHHHHHhCCCHHHHHH
Q 039148 55 SNPAIVTDMLAKAFQAEKKIVKQ 77 (82)
Q Consensus 55 ~~p~~~~~vLa~af~~d~~~i~k 77 (82)
.++.++.+-||+.++++..+|++
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRR 34 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHH
T ss_pred cCCCcCHHHHHHHhCCCHHHHHH
Confidence 34458999999999999988765
No 79
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=52.54 E-value=15 Score=20.03 Aligned_cols=21 Identities=19% Similarity=0.221 Sum_probs=18.1
Q ss_pred CcHHHHHHHhCCCHHHHHHHH
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~ 79 (82)
.+.+.||.-|++++.++.+.-
T Consensus 20 ~~~~~La~~FgIs~stvsri~ 40 (53)
T PF13613_consen 20 LTFQDLAYRFGISQSTVSRIF 40 (53)
T ss_pred CcHhHHhhheeecHHHHHHHH
Confidence 778899999999999988764
No 80
>PF07385 DUF1498: Protein of unknown function (DUF1498); InterPro: IPR010864 This family consists of several hypothetical bacterial proteins of around 225 residues in length. The function of this family is unknown.; PDB: 3MPB_B 3KMH_A.
Probab=52.46 E-value=38 Score=24.64 Aligned_cols=33 Identities=24% Similarity=0.298 Sum_probs=22.4
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEEEeeecC
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQ 41 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~ 41 (82)
+|.+|+-+.+|+|+-|+.+=-+.. +++.-.++-
T Consensus 157 ~L~PGESiTL~Pg~yH~Fw~e~g~--vLigEVStv 189 (225)
T PF07385_consen 157 RLNPGESITLPPGIYHWFWGEGGD--VLIGEVSTV 189 (225)
T ss_dssp EE-TT-EEEE-TTEEEEEEE-TTS--EEEEEEEE-
T ss_pred EeCCCCeEeeCCCCeeeEEecCCC--EEEEeeecc
Confidence 689999999999999999876544 666666653
No 81
>KOG1633 consensus F-box protein JEMMA and related proteins with JmjC, PHD, F-box and LRR domains [Chromatin structure and dynamics]
Probab=51.83 E-value=17 Score=30.80 Aligned_cols=41 Identities=17% Similarity=0.121 Sum_probs=35.2
Q ss_pred EEEeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCc
Q 039148 4 IIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLG 44 (82)
Q Consensus 4 ~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg 44 (82)
|.-.|++|+.+.+|.|.||=-|-.-+.-+...-.+.+++-.
T Consensus 196 ~~~~l~~g~T~~iPsGwIhAV~Tp~d~l~fgGnflhsl~i~ 236 (776)
T KOG1633|consen 196 YKCILKQGQTLFIPSGWIHAVLTPTDCLVFGGNFLHSLTIE 236 (776)
T ss_pred EEEEeccCceEecccceeEeeecCcchheeccchhhhhhhH
Confidence 45568999999999999999999999888888888877643
No 82
>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=51.79 E-value=25 Score=18.49 Aligned_cols=24 Identities=21% Similarity=0.292 Sum_probs=18.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
|++..-+|+.|+++..+|-+...+
T Consensus 21 G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 21 GMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp T--HHHHHHHTTS-HHHHHHHHCC
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhc
Confidence 488889999999999999987653
No 83
>PF12973 Cupin_7: ChrR Cupin-like domain; PDB: 3O14_B 2Z2S_F 2Q1Z_B 3EBR_A.
Probab=49.29 E-value=35 Score=20.29 Aligned_cols=21 Identities=19% Similarity=0.082 Sum_probs=17.1
Q ss_pred EeecCCcEEEEccCceeEEEe
Q 039148 6 MVLKKGDVFVFLVGLVHFKCN 26 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N 26 (82)
..+.+||.+..|.|..|--.-
T Consensus 60 ~~~~~G~~~~~p~g~~h~~~s 80 (91)
T PF12973_consen 60 GRYGAGDWLRLPPGSSHTPRS 80 (91)
T ss_dssp CEEETTEEEEE-TTEEEEEEE
T ss_pred ccCCCCeEEEeCCCCccccCc
Confidence 357899999999999998773
No 84
>KOG2131 consensus Uncharacterized conserved protein, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=49.23 E-value=10 Score=29.76 Aligned_cols=22 Identities=23% Similarity=0.294 Sum_probs=21.1
Q ss_pred cCCcEEEEccCceeEEEecCCc
Q 039148 9 KKGDVFVFLVGLVHFKCNVGYG 30 (82)
Q Consensus 9 ~~GDv~vfP~G~~H~~~N~G~~ 30 (82)
++|+++.+|.|.-|-.+|.|++
T Consensus 273 epge~VFvPsGW~hQV~NL~dT 294 (427)
T KOG2131|consen 273 EPGETVFVPSGWHHQVLNLGDT 294 (427)
T ss_pred cCCceeeccCccccccccccce
Confidence 7899999999999999999997
No 85
>PLN02288 mannose-6-phosphate isomerase
Probab=48.72 E-value=11 Score=29.13 Aligned_cols=20 Identities=15% Similarity=0.135 Sum_probs=17.4
Q ss_pred EeecCCcEEEEccCceeEEE
Q 039148 6 MVLKKGDVFVFLVGLVHFKC 25 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~ 25 (82)
-+|++||.+.+|+|.+|--.
T Consensus 253 v~L~PGeaifl~ag~~HAYl 272 (394)
T PLN02288 253 VKLNPGEALYLGANEPHAYL 272 (394)
T ss_pred EecCCCCEEEecCCCCceec
Confidence 57899999999999999643
No 86
>PF05523 FdtA: WxcM-like, C-terminal ; InterPro: IPR008894 This entry includes FdtA (Q6T1W8 from SWISSPROT) from Aneurinibacillus thermoaerophilus, which has been characterised as a dTDP-6-deoxy-3,4-keto-hexulose isomerase []. It also includes WxcM (Q93S92 from SWISSPROT) from Xanthomonas campestris pv campestris) []. ; PDB: 2PAK_A 2PAE_A 2PA7_B 2PAM_A.
Probab=48.56 E-value=38 Score=21.96 Aligned_cols=24 Identities=21% Similarity=0.083 Sum_probs=14.1
Q ss_pred cEEEEccCceeEEEecCCcceEEEE
Q 039148 12 DVFVFLVGLVHFKCNVGYGNVVAIV 36 (82)
Q Consensus 12 Dv~vfP~G~~H~~~N~G~~~av~i~ 36 (82)
..+.+|+|+.|-..|.+.. ++++.
T Consensus 85 ~~L~Ippg~w~~~~~~s~~-svlLv 108 (131)
T PF05523_consen 85 KGLYIPPGVWHGIKNFSED-SVLLV 108 (131)
T ss_dssp EEEEE-TT-EEEEE---TT--EEEE
T ss_pred eEEEECCchhhHhhccCCC-cEEEE
Confidence 5788999999999999877 55554
No 87
>PRK13285 flagellar assembly protein FliW; Provisional
Probab=45.83 E-value=56 Score=21.85 Aligned_cols=59 Identities=15% Similarity=0.193 Sum_probs=30.6
Q ss_pred eecCCcEEEEccCceeEE------Ee--cCCcceEEEEeeecCCCcceeeccccccCC--CCCcHHHHH
Q 039148 7 VLKKGDVFVFLVGLVHFK------CN--VGYGNVVAIVAFSSQNLGVVTIANTAFGSN--PAIVTDMLA 65 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~------~N--~G~~~av~i~~~~s~npg~~~~~~~~F~~~--p~~~~~vLa 65 (82)
.+.+-+++.||+|+.-|. .= .++.|..++-+.+..+.+...+....|..+ |.++++.++
T Consensus 12 ev~e~~ii~Fp~Gi~GFe~~~~f~L~~~~~~~pf~~LqS~dd~~~~F~vi~P~~~~~dY~~~l~~~~~~ 80 (148)
T PRK13285 12 EIDEEDIITFPEGIPGFEDLKKFILLPLEEDSPFLWLQSVEDPDLAFVVIDPFNFFPDYEFDLDEEELE 80 (148)
T ss_pred ecChhceEECCCCCCCCCcccEEEEEecCCCCCEEEEEecCCCceEEEEeCHHHhCCCCccccCHHHHH
Confidence 456779999999996543 21 224455444444333333444433333322 446666554
No 88
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=45.71 E-value=33 Score=19.69 Aligned_cols=21 Identities=29% Similarity=0.227 Sum_probs=18.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 039148 58 AIVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl 78 (82)
++...-||+.++++..+++++
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~ 42 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRV 42 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHH
Confidence 489999999999999988875
No 89
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=45.66 E-value=26 Score=19.41 Aligned_cols=20 Identities=15% Similarity=0.345 Sum_probs=17.1
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 039148 58 AIVTDMLAKAFQAEKKIVKQ 77 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~k 77 (82)
.+..+=|++.|+++..+|++
T Consensus 14 ~~s~~ela~~~~VS~~TiRR 33 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRR 33 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHH
Confidence 46778899999999999876
No 90
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=44.30 E-value=8.7 Score=23.58 Aligned_cols=17 Identities=18% Similarity=0.255 Sum_probs=12.0
Q ss_pred EEeecCCcEEEEccCce
Q 039148 5 IMVLKKGDVFVFLVGLV 21 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~ 21 (82)
++.+++||++++|..++
T Consensus 7 t~dI~~Ge~I~~p~~~~ 23 (162)
T PF00856_consen 7 TRDIKAGEVILIPRPAI 23 (162)
T ss_dssp SS-B-TTEEEEEESEEE
T ss_pred CccCCCCCEEEEECcce
Confidence 46789999888888765
No 91
>COG5553 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]
Probab=44.23 E-value=42 Score=23.67 Aligned_cols=30 Identities=27% Similarity=0.339 Sum_probs=14.2
Q ss_pred ecCCcEEEEccCceeEEEecCCcceEEEEee
Q 039148 8 LKKGDVFVFLVGLVHFKCNVGYGNVVAIVAF 38 (82)
Q Consensus 8 l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~ 38 (82)
..+|+|. +-+|-+|-.-|.|.....+|-++
T Consensus 126 ~apgeV~-lSpgdihsv~n~~sdrs~aiHvy 155 (191)
T COG5553 126 AAPGEVH-LSPGDIHSVANTGSDRSGAIHVY 155 (191)
T ss_pred cCcceEe-eCCCCeeeecccCCCccceEEEE
Confidence 4455555 22255555555554433444333
No 92
>PF00908 dTDP_sugar_isom: dTDP-4-dehydrorhamnose 3,5-epimerase; InterPro: IPR000888 Deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-d-hexulose 3, 5-epimerase (RmlC, 5.1.3.13 from EC) is involved in the biosynthesis of dTDP-l-rhamnose, which is an essential component of the bacterial cell wall, converting dTDP-4-keto-6-deoxy-D-glucose to dTDP-4-keto-L-rhamnose. The crystal structure of RmlC from Methanobacterium thermoautotrophicum was determined in the presence and absence of a substrate analogue. RmlC is a homodimer comprising a central jelly roll motif, which extends in two directions into longer beta-sheets. Binding of dTDP is stabilised by ionic interactions to the phosphate group and by a combination of ionic and hydrophobic interactions with the base. The active site, which is located in the centre of the jelly roll, is formed by residues that are conserved in all known RmlC sequence homologues. The active site is lined with a number of charged residues and a number of residues with hydrogen-bonding potentials, which together comprise a potential network for substrate binding and catalysis. The active site is also lined with aromatic residues which provide favorable environments for the base moiety of dTDP and potentially for the sugar moiety of the substrate [].; GO: 0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity, 0009103 lipopolysaccharide biosynthetic process; PDB: 1EPZ_A 1EP0_A 1NXM_A 1NZC_D 2IXL_C 1NYW_B 2IXC_D 1PM7_B 1UPI_A 3RYK_B ....
Probab=43.68 E-value=96 Score=21.27 Aligned_cols=43 Identities=9% Similarity=-0.070 Sum_probs=25.6
Q ss_pred eEEEeecCC--cEEEEccCceeEEEecCCcceEEEEeeecCCCcc
Q 039148 3 LIIMVLKKG--DVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGV 45 (82)
Q Consensus 3 ~~~~~l~~G--Dv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~ 45 (82)
...-.|.++ -.+.+|+|++|=.+...+.-.+.+-.-+.=+|+.
T Consensus 95 ~~~~~Ls~~n~~~l~IP~G~aHGf~~l~d~a~v~Y~~t~~y~p~~ 139 (176)
T PF00908_consen 95 WVSVELSAENPRQLYIPPGVAHGFQTLEDDAEVLYKVTNYYDPED 139 (176)
T ss_dssp EEEEEEETTT--EEEE-TTEEEEEEESSSEEEEEEEESS---GGG
T ss_pred EEEEEeCccccCEEEeCCcceeeEEeccCceEEEEecCCccCccc
Confidence 344556555 4799999999999999887444443333335554
No 93
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=43.38 E-value=43 Score=17.30 Aligned_cols=21 Identities=14% Similarity=0.362 Sum_probs=14.5
Q ss_pred CCcHHHHHHHhC-CCHHHHHHH
Q 039148 58 AIVTDMLAKAFQ-AEKKIVKQL 78 (82)
Q Consensus 58 ~~~~~vLa~af~-~d~~~i~kl 78 (82)
.+|+|+|.+.|. ++.+++-.+
T Consensus 3 ~LP~Eil~~If~~L~~~dl~~~ 24 (47)
T PF12937_consen 3 SLPDEILLEIFSYLDPRDLLRL 24 (47)
T ss_dssp CS-HHHHHHHHTTS-HHHHHHH
T ss_pred HhHHHHHHHHHhcCCHHHHHHH
Confidence 389999999997 677665544
No 94
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=42.96 E-value=15 Score=25.54 Aligned_cols=13 Identities=31% Similarity=0.381 Sum_probs=11.6
Q ss_pred cCCcEEEEccCce
Q 039148 9 KKGDVFVFLVGLV 21 (82)
Q Consensus 9 ~~GDv~vfP~G~~ 21 (82)
.+|||+.+|+|.-
T Consensus 141 ~aGDvifiPKgss 153 (176)
T COG4766 141 GAGDVIFIPKGSS 153 (176)
T ss_pred CCCcEEEecCCCe
Confidence 7899999999974
No 95
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=41.98 E-value=15 Score=23.56 Aligned_cols=19 Identities=32% Similarity=0.684 Sum_probs=14.9
Q ss_pred EeecCCcEEEEc-cCceeEE
Q 039148 6 MVLKKGDVFVFL-VGLVHFK 24 (82)
Q Consensus 6 ~~l~~GDv~vfP-~G~~H~~ 24 (82)
+.+..|+.|-|+ +|.+||.
T Consensus 10 ~~I~~gqlFTF~~kG~VH~~ 29 (101)
T PF09943_consen 10 KPIYEGQLFTFTKKGPVHYE 29 (101)
T ss_pred CeeeecceEEEecCCcEeHH
Confidence 466788888776 7899995
No 96
>PF05721 PhyH: Phytanoyl-CoA dioxygenase (PhyH); InterPro: IPR008775 This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins as well as a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues [].; PDB: 3GJA_A 3EMR_A 3OBZ_A 2OPW_A 3NNL_B 3NNF_A 3NNM_B 3NNJ_A 2FCV_B 2FCU_A ....
Probab=41.81 E-value=20 Score=23.13 Aligned_cols=23 Identities=30% Similarity=0.372 Sum_probs=17.7
Q ss_pred EEeecCCcEEEEccCceeEEEec
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNV 27 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~ 27 (82)
.-.+++||+++|-.-++|--..+
T Consensus 181 ~~~~~~Gdvl~~~~~~~H~s~~N 203 (211)
T PF05721_consen 181 PVPMKAGDVLFFHSRLIHGSGPN 203 (211)
T ss_dssp EE-BSTTEEEEEETTSEEEEE-B
T ss_pred EeecCCCeEEEEcCCccccCCCC
Confidence 34579999999999999976543
No 97
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=41.68 E-value=21 Score=23.89 Aligned_cols=21 Identities=33% Similarity=0.572 Sum_probs=16.5
Q ss_pred eecCCcEEEEc--------cCceeEEEec
Q 039148 7 VLKKGDVFVFL--------VGLVHFKCNV 27 (82)
Q Consensus 7 ~l~~GDv~vfP--------~G~~H~~~N~ 27 (82)
.|++||.+-|- -|++||+.-+
T Consensus 85 ~l~~GD~V~f~GeYe~n~kggvIHWTH~d 113 (131)
T PF11948_consen 85 WLQKGDQVEFYGEYEWNPKGGVIHWTHHD 113 (131)
T ss_pred CcCCCCEEEEEEEEEECCCCCEEEeeccC
Confidence 37899999885 6889998843
No 98
>COG3257 GlxB Uncharacterized protein, possibly involved in glyoxylate utilization [General function prediction only]
Probab=41.29 E-value=50 Score=24.41 Aligned_cols=32 Identities=13% Similarity=-0.078 Sum_probs=27.8
Q ss_pred EEeecCCcEEEEccCceeEEEecCCcceEEEE
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIV 36 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~ 36 (82)
+..|++|+-..+|+|.-|-.-|...+++.+.-
T Consensus 102 th~l~eggyaylPpgs~~~~~N~~~~~~rfhw 133 (264)
T COG3257 102 THALREGGYAYLPPGSGWTLRNAQKEDSRFHW 133 (264)
T ss_pred EEEeccCCeEEeCCCCcceEeeccCCceEEEE
Confidence 46799999999999999999999988876543
No 99
>TIGR02466 conserved hypothetical protein. This family consists of uncharacterized proteins in Caulobacter crescentus CB15, Bdellovibrio bacteriovorus HD100, Synechococcus sp. WH 8102 (2), Silicibacter pomeroyi DSS-3 (2), and Hyphomonas neptunium ATCC 15444. The context of nearby genes differs substantially between members and does point to any specific biological role.
Probab=41.25 E-value=43 Score=23.53 Aligned_cols=30 Identities=17% Similarity=0.109 Sum_probs=22.1
Q ss_pred eecCCcEEEEccCceeEEEec-CCcceEEEE
Q 039148 7 VLKKGDVFVFLVGLVHFKCNV-GYGNVVAIV 36 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~-G~~~av~i~ 36 (82)
.-++||+++||.=+.|-..=. |+++-+.||
T Consensus 165 ~P~~G~lvlFPS~L~H~v~p~~~~~~RISiS 195 (201)
T TIGR02466 165 PPQEGRVLLFESWLRHEVPPNESEEERISVS 195 (201)
T ss_pred CCCCCeEEEECCCCceecCCCCCCCCEEEEE
Confidence 348999999999999987654 455554443
No 100
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=40.91 E-value=29 Score=20.10 Aligned_cols=23 Identities=9% Similarity=0.224 Sum_probs=20.4
Q ss_pred CcHHHHHHHhCCCHHHHHHHHhc
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
+...=||+.+++++.+|++-+++
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHhhh
Confidence 77888999999999999998764
No 101
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens [, ].
Probab=40.55 E-value=39 Score=22.98 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=19.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 039148 58 AIVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl 78 (82)
|++.+.++.++++|...+.++
T Consensus 21 G~~~~~I~~aL~id~~~ls~~ 41 (185)
T PF07506_consen 21 GFSREEIAAALGIDKSYLSRM 41 (185)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
Confidence 599999999999999999776
No 102
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=39.38 E-value=51 Score=23.29 Aligned_cols=27 Identities=15% Similarity=0.102 Sum_probs=19.7
Q ss_pred EeecCCcEEEEccCceeEEEecCCcce
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNV 32 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~a 32 (82)
-.+++||++++|.+..|...-.++...
T Consensus 91 ~~l~~G~~~l~~~~~p~~~~~~~~~~~ 117 (302)
T PRK09685 91 VQLAAGDITLIDASRPCSIYPQGLSEQ 117 (302)
T ss_pred EEEcCCCEEEEECCCCcEeecCCCcee
Confidence 468999999999998876554444333
No 103
>PF15428 Imm14: Immunity protein 14
Probab=38.62 E-value=27 Score=22.13 Aligned_cols=11 Identities=36% Similarity=0.745 Sum_probs=9.1
Q ss_pred cCCcEEEEccC
Q 039148 9 KKGDVFVFLVG 19 (82)
Q Consensus 9 ~~GDv~vfP~G 19 (82)
++||+|+||-.
T Consensus 1 K~GDIF~ipL~ 11 (129)
T PF15428_consen 1 KPGDIFCIPLD 11 (129)
T ss_pred CCceEEEEEcC
Confidence 58999999944
No 104
>COG3508 HmgA Homogentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=37.82 E-value=25 Score=27.61 Aligned_cols=31 Identities=10% Similarity=-0.035 Sum_probs=21.1
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEe
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVA 37 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~ 37 (82)
-.+++||+-|+|+|+..-..=.+.+ +...-.
T Consensus 166 l~v~pgeiavIPRG~~frve~~~~~-~rgy~~ 196 (427)
T COG3508 166 LEVEPGEIAVIPRGTTFRVELKDGE-ARGYGC 196 (427)
T ss_pred EEecCCcEEEeeCCceEEEEecCCc-eEEEEE
Confidence 4679999999999997655544433 444333
No 105
>COG3435 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=37.77 E-value=39 Score=26.00 Aligned_cols=32 Identities=22% Similarity=0.109 Sum_probs=21.5
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEEEeee
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
..+.||+||+|.=.-|-..|. .+.++++|.-|
T Consensus 302 ~~~~~D~fvVPsW~~~~~~~g-s~da~LFsfsD 333 (351)
T COG3435 302 DWSAGDIFVVPSWAWHEHVNG-SEDAVLFSFSD 333 (351)
T ss_pred eccCCCEEEccCcceeecccC-CcceEEEecCC
Confidence 458899999998655555444 67776665433
No 106
>smart00351 PAX Paired Box domain.
Probab=35.97 E-value=42 Score=21.50 Aligned_cols=24 Identities=4% Similarity=0.094 Sum_probs=20.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
+.+..-+|+.|+++..+|.++..+
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r 56 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGR 56 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 488899999999999999987654
No 107
>PF06806 DUF1233: Putative excisionase (DUF1233); InterPro: IPR009634 This family consists of several putative phage and prophage excisionase proteins of around 80 residues in length.; PDB: 2KVV_A.
Probab=35.55 E-value=41 Score=20.27 Aligned_cols=23 Identities=9% Similarity=0.209 Sum_probs=16.4
Q ss_pred CcHHHHHHHhCCCHHHHHHHHhc
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
+..++|.+.+|+...+|++-|.+
T Consensus 10 V~e~~L~a~tGls~~~I~~yR~~ 32 (72)
T PF06806_consen 10 VTEELLMAITGLSPGTIKRYRKK 32 (72)
T ss_dssp E-HHHHHHHH---HHHHHHHHTT
T ss_pred hhHHHHHHHHCCCHHHHHHHHHH
Confidence 56899999999999999987754
No 108
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=35.53 E-value=68 Score=16.56 Aligned_cols=23 Identities=26% Similarity=0.419 Sum_probs=17.5
Q ss_pred CCCCcHHHHHHHhCCCHHHHHHH
Q 039148 56 NPAIVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 56 ~p~~~~~vLa~af~~d~~~i~kl 78 (82)
+|+++..-||+.++++..++.+.
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~ 37 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRY 37 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHH
Confidence 57799999999999999877654
No 109
>cd00131 PAX Paired Box domain
Probab=35.50 E-value=42 Score=21.68 Aligned_cols=25 Identities=12% Similarity=0.267 Sum_probs=21.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhcC
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNTF 82 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~f 82 (82)
+++..-+|+.|+++..+|.++...|
T Consensus 33 G~s~~~iA~~~~Vs~~tV~r~i~r~ 57 (128)
T cd00131 33 GIRPCDISRQLRVSHGCVSKILNRY 57 (128)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4899999999999999999887643
No 110
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=34.79 E-value=26 Score=22.06 Aligned_cols=23 Identities=17% Similarity=0.274 Sum_probs=18.2
Q ss_pred EEeecCCcEEEEccCceeEEEec
Q 039148 5 IMVLKKGDVFVFLVGLVHFKCNV 27 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H~~~N~ 27 (82)
...-..|+++++|.+..+|....
T Consensus 13 ~g~~y~~~viv~p~~~~~w~~~~ 35 (109)
T cd00248 13 AGQVYRGPLLVLPDGVVPWDGTS 35 (109)
T ss_pred CCEEEeeCEEEeCCceeecCCcC
Confidence 34557899999999999997543
No 111
>PF13518 HTH_28: Helix-turn-helix domain
Probab=34.57 E-value=54 Score=16.89 Aligned_cols=23 Identities=13% Similarity=0.151 Sum_probs=18.8
Q ss_pred CcHHHHHHHhCCCHHHHHHHHhc
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
.+-.-+|+.|+++..++.+....
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHH
Confidence 57788999999999998876543
No 112
>PF11256 DUF3055: Protein of unknown function (DUF3055); InterPro: IPR021415 This family of proteins with unknown function appear to be restricted to Firmicutes.
Probab=34.16 E-value=45 Score=20.60 Aligned_cols=30 Identities=17% Similarity=0.286 Sum_probs=22.8
Q ss_pred ccccCCCCCcHHHHHHHhCCCHHHHHHHHh
Q 039148 51 TAFGSNPAIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 51 ~~F~~~p~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
++.+.+---.+..|+.+|+++++.+..|++
T Consensus 47 ailg~dDlee~gyl~~~f~l~~eea~eL~~ 76 (81)
T PF11256_consen 47 AILGPDDLEEPGYLEHAFGLSEEEAEELRE 76 (81)
T ss_pred EEEChhhcccccHHHHHhCCCHHHHHHHHH
Confidence 455554334567899999999999998875
No 113
>PF02678 Pirin: Pirin; InterPro: IPR003829 This entry represents N-terminal domain of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures []. Pirin is composed of two structurally similar domains arranged face to face. The N-terminal domain additionally features four beta-strands, and the C-terminal domain also includes four additional -strands and a short alpha-helix. Although the two domains are similar, the C-terminal domain of Pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues []. Pirin is confirmed to be a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal beta-barrel of Pirin, may be significant in its role in regulating NFI DNA replication and NF-kappaB transcription factor activity []. Pirin structure has been found to closely resemble members of the cupin superfamily. Pirin contains the two characteristic sequences of the cupin superfamily, namely PG-(X)5-HXH-(X)4-E-(X)6-G and G-(X)5-PXG-(X)2-H-(X)3-N separated by a variable stretch of 15-50 amino acids. These motifs are best conserved in the N-terminal where the conserved histidine and glutamic acid residues correspond to the metal-coordinating residues. The C-terminal domain motifs lack the metal binding residues normally associated with the cupin fold []. Pirin was identified to be a metal-binding protein [], and was found that the metal-binding residues of Pirins are highly conserved across mammals, plants, fungi, and prokaryotic organisms. Pirin acts as a cofactor for the transcription factor NFI, the regulatory mechanism of which is generally believed to require the assistance of a metal ion []. Structural data supports the hypothesis that the bound iron of Pirin may participate in this transcriptional regulation by enhancing and stabilising the formation of the p50,Bcl3,DNA complex []. Metals have been implicated directly or indirectly in the NF-kappaB family of transcription factors that control expression of a number of early response genes associated with inflammatory responses, cell growth, cell cycle progression, and neoplastic transformation []. However, most metal-dependent transcription factors are DNA-binding proteins that bind to specific sequences when the metal binds to the protein. Pirin, on the other hand, appears to function differently and bind to the transcription factor DNA complex [].; PDB: 2VEC_A 1J1L_A 3ACL_A 2P17_A 1TQ5_A.
Probab=34.09 E-value=1.2e+02 Score=19.13 Aligned_cols=31 Identities=32% Similarity=0.409 Sum_probs=22.4
Q ss_pred EEeecCCcEEEEc--cCceeEEEecCC-cceEEE
Q 039148 5 IMVLKKGDVFVFL--VGLVHFKCNVGY-GNVVAI 35 (82)
Q Consensus 5 ~~~l~~GDv~vfP--~G~~H~~~N~G~-~~av~i 35 (82)
..+|++||+-+.- +|+.|=..|..+ +++-.+
T Consensus 70 ~~~l~~G~vq~m~AG~Gi~H~E~~~~~~~~~~~l 103 (107)
T PF02678_consen 70 RGVLRAGDVQWMTAGSGIVHSERNASDGGPLHGL 103 (107)
T ss_dssp EEEEETTEEEEEE-TTTEEEEEEE-TSSS-EEEE
T ss_pred eeEeCCCeEEEEeCCCCceEEEecCCCCCeEEEE
Confidence 3678999988887 567999999987 665543
No 114
>PHA00675 hypothetical protein
Probab=33.62 E-value=71 Score=19.60 Aligned_cols=24 Identities=17% Similarity=0.302 Sum_probs=20.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
+.+.-.||+-|+++..+|.+++..
T Consensus 39 G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 39 GMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred CccHHHHHHHhCCCHHHHHHHHcc
Confidence 356678999999999999998863
No 115
>PF13551 HTH_29: Winged helix-turn helix
Probab=33.51 E-value=51 Score=19.56 Aligned_cols=24 Identities=8% Similarity=0.250 Sum_probs=20.1
Q ss_pred Cc-HHHHHHHhCCCHHHHHHHHhcC
Q 039148 59 IV-TDMLAKAFQAEKKIVKQLQNTF 82 (82)
Q Consensus 59 ~~-~~vLa~af~~d~~~i~kl~~~f 82 (82)
.+ .+-+|+.++++..+|.+....|
T Consensus 12 ~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 12 VSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 64 8889999999999999887643
No 116
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=33.36 E-value=75 Score=16.59 Aligned_cols=22 Identities=9% Similarity=0.308 Sum_probs=18.7
Q ss_pred CcHHHHHHHhCCCHHHHHHHHh
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~~ 80 (82)
.+-+=+|+.+|++.+.|+++..
T Consensus 21 ~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 21 LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp -SHHHHHHHHTSCHHHHHHHHH
T ss_pred CCHHHHHHHHCCcHHHHHHHHH
Confidence 8888999999999999988764
No 117
>COG3822 ABC-type sugar transport system, auxiliary component [General function prediction only]
Probab=32.64 E-value=92 Score=22.54 Aligned_cols=32 Identities=28% Similarity=0.246 Sum_probs=24.3
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEEEEeeec
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSS 40 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s 40 (82)
.|.+|+-+.+|+|+-||..--+.. +++.--++
T Consensus 156 kL~PGesitL~Pg~~HsFwae~g~--vlvgEvSs 187 (225)
T COG3822 156 KLSPGESITLPPGLYHSFWAEEGG--VLVGEVSS 187 (225)
T ss_pred EECCCCcEecCCCceeeeeecCCc--EEEEEEee
Confidence 689999999999999998876544 44444444
No 118
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=32.60 E-value=11 Score=19.15 Aligned_cols=11 Identities=18% Similarity=0.280 Sum_probs=9.1
Q ss_pred eecCCcEEEEc
Q 039148 7 VLKKGDVFVFL 17 (82)
Q Consensus 7 ~l~~GDv~vfP 17 (82)
.|.+|+.+.+|
T Consensus 34 ~l~~G~~l~iP 44 (44)
T PF01476_consen 34 NLQPGQKLCIP 44 (44)
T ss_dssp CGGTTEEEEEC
T ss_pred cCCCCCEEEeC
Confidence 48889998887
No 119
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.55 E-value=74 Score=16.06 Aligned_cols=23 Identities=17% Similarity=0.238 Sum_probs=19.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
+.+..-+|+.++++..+|++...
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 38999999999999998887643
No 120
>PF04354 ZipA_C: ZipA, C-terminal FtsZ-binding domain; InterPro: IPR007449 This entry represents the ZipA C-terminal domain. ZipA is an essential cell division protein involved in septum formation [, ]. Its C-terminal domain binds FtsZ, a major component of the bacterial septal ring []. The structure of this domain is an alpha-beta fold with three alpha helices and a beta sheet of six antiparallel beta strands. The major loops protruding from the beta sheet surface are thought to form a binding site for FtsZ [].; GO: 0000917 barrier septum formation, 0009276 Gram-negative-bacterium-type cell wall, 0016021 integral to membrane; PDB: 1Y2G_B 1S1S_A 1F46_A 1S1J_A 1F47_B 1F7W_A 1Y2F_A 1F7X_A.
Probab=32.49 E-value=54 Score=21.35 Aligned_cols=33 Identities=12% Similarity=-0.000 Sum_probs=24.4
Q ss_pred EccCceeEEEecCCcceEEEEeeecCCCcceee
Q 039148 16 FLVGLVHFKCNVGYGNVVAIVAFSSQNLGVVTI 48 (82)
Q Consensus 16 fP~G~~H~~~N~G~~~av~i~~~~s~npg~~~~ 48 (82)
=..|+-|+..+.+....+.+|+.|.-+||+...
T Consensus 34 g~~~iFHr~~~~~~~g~vlFSvaN~~~PG~F~~ 66 (131)
T PF04354_consen 34 GEMGIFHRHEDPDGSGPVLFSVANMVEPGTFDP 66 (131)
T ss_dssp EGGGEEEEESSTTSSSSEEEEEEESSTT----T
T ss_pred CCCCcEEEeecCCCCCceEEEEEeCCCCCCCCc
Confidence 356778999888888899999999999987543
No 121
>PRK05467 Fe(II)-dependent oxygenase superfamily protein; Provisional
Probab=30.84 E-value=38 Score=24.33 Aligned_cols=22 Identities=23% Similarity=0.326 Sum_probs=18.0
Q ss_pred EeecCCcEEEEccCceeEEEec
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNV 27 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~ 27 (82)
-.+.+||+++||.-++|--.=+
T Consensus 143 Vkp~aG~~vlfps~~lH~v~pV 164 (226)
T PRK05467 143 VKLPAGDLVLYPSTSLHRVTPV 164 (226)
T ss_pred EecCCCeEEEECCCCceeeeec
Confidence 3568999999999999876654
No 122
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=30.71 E-value=75 Score=15.59 Aligned_cols=23 Identities=13% Similarity=0.226 Sum_probs=19.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
+++.+-+|+.++++...|.+...
T Consensus 26 ~~~~~~ia~~~~~s~~~i~~~~~ 48 (55)
T cd06171 26 GLSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 38999999999999998877653
No 123
>PRK09956 hypothetical protein; Provisional
Probab=30.65 E-value=56 Score=24.28 Aligned_cols=30 Identities=17% Similarity=0.047 Sum_probs=24.0
Q ss_pred eccccccCCCCCcHHHHHHHhCCCHHHHHHHH
Q 039148 48 IANTAFGSNPAIVTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 48 ~~~~~F~~~p~~~~~vLa~af~~d~~~i~kl~ 79 (82)
++..+... |++.+.+++++|++.+.++++.
T Consensus 278 iA~~mL~~--G~~~~~i~~~tgLs~eel~~~~ 307 (308)
T PRK09956 278 IALRMLEQ--GFDRDQVLAATQLSEADLAANN 307 (308)
T ss_pred HHHHHHHc--CCCHHHHHHHhCCCHHHHHHhc
Confidence 44555544 4999999999999999998864
No 124
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=30.41 E-value=66 Score=22.28 Aligned_cols=27 Identities=7% Similarity=0.107 Sum_probs=24.0
Q ss_pred ccccCCCCCcHHHHHHHhCCCHHHHHHHHh
Q 039148 51 TAFGSNPAIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 51 ~~F~~~p~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
-+|.. ++-+..|+.+||+..++++-|+
T Consensus 15 YV~~~---~sLe~aA~~~gVs~~TarrWK~ 41 (165)
T PF08822_consen 15 YVFDR---LSLEQAAAKCGVSYATARRWKR 41 (165)
T ss_pred HHhCC---CCHHHHHHHhCCCHHHHHHHHH
Confidence 36776 9999999999999999999886
No 125
>COG1898 RfbC dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]
Probab=30.31 E-value=92 Score=21.61 Aligned_cols=30 Identities=10% Similarity=-0.073 Sum_probs=23.7
Q ss_pred CcEEEEccCceeEEEecCCcceEEEEeeec
Q 039148 11 GDVFVFLVGLVHFKCNVGYGNVVAIVAFSS 40 (82)
Q Consensus 11 GDv~vfP~G~~H~~~N~G~~~av~i~~~~s 40 (82)
..++-+|+|.+|=..|.+++..+.+..-+.
T Consensus 105 ~~~l~IP~G~AHGf~~L~d~~~~~y~~~~~ 134 (173)
T COG1898 105 KRQLYIPPGFAHGFQVLSDDAEVVYKVTEE 134 (173)
T ss_pred ceEEEeCCcccceeEEccCceEEEEEecce
Confidence 378999999999999999998555554443
No 126
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=30.10 E-value=1.4e+02 Score=18.46 Aligned_cols=12 Identities=25% Similarity=0.396 Sum_probs=7.8
Q ss_pred EEeecCCcEEEE
Q 039148 5 IMVLKKGDVFVF 16 (82)
Q Consensus 5 ~~~l~~GDv~vf 16 (82)
..+.++||++++
T Consensus 60 ~~~P~~Gdivv~ 71 (124)
T PF05257_consen 60 GSTPQPGDIVVW 71 (124)
T ss_dssp CS---TTEEEEE
T ss_pred CcccccceEEEe
Confidence 356799999999
No 127
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=30.02 E-value=25 Score=20.78 Aligned_cols=12 Identities=58% Similarity=0.678 Sum_probs=7.0
Q ss_pred EeecCCcEEEEc
Q 039148 6 MVLKKGDVFVFL 17 (82)
Q Consensus 6 ~~l~~GDv~vfP 17 (82)
+.|+.||+++|=
T Consensus 72 n~L~~GD~~~F~ 83 (100)
T PF02362_consen 72 NGLKEGDVCVFE 83 (100)
T ss_dssp CT--TT-EEEEE
T ss_pred cCCCCCCEEEEE
Confidence 468999999874
No 128
>COG4001 Predicted metal-binding protein [General function prediction only]
Probab=29.91 E-value=32 Score=21.88 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=10.2
Q ss_pred HHHhCCCHHHHHH
Q 039148 65 AKAFQAEKKIVKQ 77 (82)
Q Consensus 65 a~af~~d~~~i~k 77 (82)
+.||++|+++|+.
T Consensus 69 arAfgVdee~iRE 81 (102)
T COG4001 69 ARAFGVDEEDIRE 81 (102)
T ss_pred chhcCCCHHHHHH
Confidence 5689999988764
No 129
>PHA02591 hypothetical protein; Provisional
Probab=29.90 E-value=88 Score=19.37 Aligned_cols=31 Identities=6% Similarity=0.157 Sum_probs=23.8
Q ss_pred eccccccCCCCCcHHHHHHHhCCCHHHHHHHHh
Q 039148 48 IANTAFGSNPAIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 48 ~~~~~F~~~p~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
++.-|-.- |+..+-+|+.+|++.++|++.-.
T Consensus 51 vA~eL~eq--GlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARK--GFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHh
Confidence 33444443 59999999999999999998754
No 130
>COG4296 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.90 E-value=92 Score=21.29 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=20.6
Q ss_pred cEEEEccCceeEEEecCC---cceEEEEe
Q 039148 12 DVFVFLVGLVHFKCNVGY---GNVVAIVA 37 (82)
Q Consensus 12 Dv~vfP~G~~H~~~N~G~---~~av~i~~ 37 (82)
-+++-|-|-+-|-||+|+ +..++++.
T Consensus 115 ~v~~~pdGe~efyy~DGdLF~GH~Ilis~ 143 (156)
T COG4296 115 NVMLYPDGEAEFYYSDGDLFAGHVILISV 143 (156)
T ss_pred ceEeccCCcEEEEecCCCeEeeeEEEEEE
Confidence 478999999999999997 45555543
No 131
>PF08830 DUF1806: Protein of unknown function (DUF1806); InterPro: IPR014934 This entry consists of bacterial uncharacterised proteins. The structure of one of the proteins has been solved and it adopts a beta barrel-like structure. ; PDB: 1NJH_A.
Probab=29.63 E-value=86 Score=20.56 Aligned_cols=37 Identities=16% Similarity=0.204 Sum_probs=24.0
Q ss_pred EEEeecCCcEEEEccCceeEEEecCCcceEEEEeeecCC
Q 039148 4 IIMVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQN 42 (82)
Q Consensus 4 ~~~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~n 42 (82)
|+--|+-.+-.|.-+|+.||..+... ..+++..|.+.
T Consensus 64 yRvGLK~~~GWvYaEGLTh~e~d~~~--rLLlAGhd~eG 100 (114)
T PF08830_consen 64 YRVGLKLEIGWVYAEGLTHYEVDEEG--RLLLAGHDYEG 100 (114)
T ss_dssp EEEEEEESSSEEEEEEE-EEEE-TT----EEEEEEETTT
T ss_pred eEEEEecCCCEEEEccceeeEEcCCC--cEEEcccCCCC
Confidence 45556666778888999999987643 45677777653
No 132
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=29.16 E-value=76 Score=15.15 Aligned_cols=23 Identities=13% Similarity=0.384 Sum_probs=18.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
+++..-+++..+++...+.++..
T Consensus 10 ~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 10 GLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHC
Confidence 37778889999999888887653
No 133
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=29.13 E-value=81 Score=15.47 Aligned_cols=20 Identities=10% Similarity=0.119 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCHHHHHHHHh
Q 039148 61 TDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 61 ~~vLa~af~~d~~~i~kl~~ 80 (82)
.+=+|+.++++..++.++.+
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~ 22 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVK 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 34578889999999988743
No 134
>PF00054 Laminin_G_1: Laminin G domain; InterPro: IPR012679 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, which includes a large number of extracellular proteins. The C terminus of laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions has been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each has five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012680 from INTERPRO).; PDB: 1OKQ_A 1DYK_A 2C5D_A 1H30_A 1LHW_A 1KDK_A 1LHU_A 1KDM_A 1LHO_A 1D2S_A ....
Probab=28.88 E-value=60 Score=20.43 Aligned_cols=27 Identities=19% Similarity=0.263 Sum_probs=21.6
Q ss_pred EEEEccCceeEEEecCCcceEEEEeee
Q 039148 13 VFVFLVGLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 13 v~vfP~G~~H~~~N~G~~~av~i~~~~ 39 (82)
.+-+=.|-+++.||.|..++.+.+.-.
T Consensus 23 al~L~~G~l~~~~~~G~~~~~~~~~~~ 49 (131)
T PF00054_consen 23 ALELRDGRLEFRYNLGSGPASLRSPQK 49 (131)
T ss_dssp EEEEETTEEEEEEESSSEEEEEEESSE
T ss_pred EEEEECCEEEEEEeCCCccceecCCCc
Confidence 445568999999999999887776655
No 135
>PF01238 PMI_typeI: Phosphomannose isomerase type I; InterPro: IPR001250 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. Type I includes eukaryotic PMI and the enzyme encoded by the manA gene in enterobacteria. PMI has a bound zinc ion, which is essential for activity. A crystal structure of PMI from Candida albicans shows that the enzyme has three distinct domains []. The active site lies in the central domain, contains a single essential zinc atom, and forms a deep, open cavity of suitable dimensions to contain M6P or F6P The central domain is flanked by a helical domain on one side and a jelly-roll like domain on the other.; GO: 0004476 mannose-6-phosphate isomerase activity, 0008270 zinc ion binding, 0005975 carbohydrate metabolic process; PDB: 1PMI_A 1QWR_B 1ZX5_A 3H1Y_A 2WFP_A 3H1M_A 3H1W_A.
Probab=28.82 E-value=31 Score=26.25 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=16.2
Q ss_pred EeecCCcEEEEccCceeEEEe
Q 039148 6 MVLKKGDVFVFLVGLVHFKCN 26 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N 26 (82)
-+|++|+.+.+|+|.+|--.-
T Consensus 252 v~L~pGeaifl~a~~~HAYl~ 272 (373)
T PF01238_consen 252 VELQPGEAIFLPAGEPHAYLS 272 (373)
T ss_dssp EEE-TT-EEEEHTTHHEEEEE
T ss_pred EEecCCceEEecCCCcccccc
Confidence 478999999999999996554
No 136
>PLN02499 glycerol-3-phosphate acyltransferase
Probab=28.49 E-value=28 Score=28.01 Aligned_cols=17 Identities=29% Similarity=0.360 Sum_probs=14.1
Q ss_pred EeecCCcEEEEccCcee
Q 039148 6 MVLKKGDVFVFLVGLVH 22 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H 22 (82)
+.|++||+++||.|..+
T Consensus 348 ~lL~~G~lvIFPEGTrs 364 (498)
T PLN02499 348 RELARGDLVVCPEGTTC 364 (498)
T ss_pred HHhhCCCEEEcCCCCCC
Confidence 45899999999999644
No 137
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=28.48 E-value=93 Score=16.20 Aligned_cols=23 Identities=13% Similarity=0.343 Sum_probs=17.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
+++..=||+..+++..++.++-+
T Consensus 9 gls~~~la~~~gis~~~i~~~~~ 31 (55)
T PF01381_consen 9 GLSQKELAEKLGISRSTISRIEN 31 (55)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHhCCCcchhHHHhc
Confidence 37778899999999998888753
No 138
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=27.99 E-value=42 Score=23.29 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=25.1
Q ss_pred EeecCCcEEEEccCceeEEEecC-CcceEEEEeeecC
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVG-YGNVVAIVAFSSQ 41 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G-~~~av~i~~~~s~ 41 (82)
.+|.+||++.+.-+=..|.+.+- .+|+-+|+..|+.
T Consensus 132 stLT~Gd~I~i~~~~~~y~l~V~e~kP~~aV~IidTD 168 (176)
T PF03152_consen 132 STLTKGDTISIEYNNKTYELDVVEVKPENAVSIIDTD 168 (176)
T ss_dssp SEEETTSEEEEECTTEEEEEEEEEECSSSCEE-SSS-
T ss_pred ceeecCCEEEEEeCCEEEEEEEEEEcCCCEEEEEeCc
Confidence 57999999999877767766653 4566677776653
No 139
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=27.66 E-value=1.1e+02 Score=16.41 Aligned_cols=22 Identities=9% Similarity=0.149 Sum_probs=18.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHHH
Q 039148 57 PAIVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 57 p~~~~~vLa~af~~d~~~i~kl 78 (82)
+.++..-||+.++++..++.++
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~ 45 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRT 45 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHH
Confidence 3588899999999999887764
No 140
>PF11142 DUF2917: Protein of unknown function (DUF2917); InterPro: IPR021317 This bacterial family of proteins appears to be restricted to Proteobacteria.
Probab=27.60 E-value=49 Score=18.96 Aligned_cols=17 Identities=24% Similarity=0.176 Sum_probs=13.6
Q ss_pred eecCCcEEEEccCceeE
Q 039148 7 VLKKGDVFVFLVGLVHF 23 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~ 23 (82)
.|++||.+.+|+|--=|
T Consensus 39 ~L~~G~~l~l~~g~~vv 55 (63)
T PF11142_consen 39 WLQAGDSLRLRRGGRVV 55 (63)
T ss_pred EECCCCEEEeCCCCEEE
Confidence 58899999999886544
No 141
>PHA02752 hypothetical protein; Provisional
Probab=27.50 E-value=35 Score=24.52 Aligned_cols=22 Identities=41% Similarity=0.543 Sum_probs=15.3
Q ss_pred ceeEEEecCCcceEEEEeeecC
Q 039148 20 LVHFKCNVGYGNVVAIVAFSSQ 41 (82)
Q Consensus 20 ~~H~~~N~G~~~av~i~~~~s~ 41 (82)
+.|||||..++..-++.--++|
T Consensus 161 ~~~fqynindT~~~V~VPsksq 182 (242)
T PHA02752 161 LAHFQYNINDTNVHVVVPSKSQ 182 (242)
T ss_pred HHhheeccCCeEEEEEecCCCC
Confidence 5799999998866554444443
No 142
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=27.37 E-value=89 Score=18.73 Aligned_cols=22 Identities=14% Similarity=0.095 Sum_probs=19.5
Q ss_pred CcHHHHHHHhCCCHHHHHHHHh
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~~ 80 (82)
.+.+=+|+.++++++.|++.+.
T Consensus 127 ~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 127 LSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999998887654
No 143
>PF13320 DUF4091: Domain of unknown function (DUF4091)
Probab=27.11 E-value=25 Score=20.57 Aligned_cols=12 Identities=17% Similarity=0.260 Sum_probs=9.5
Q ss_pred cCceeEEEecCC
Q 039148 18 VGLVHFKCNVGY 29 (82)
Q Consensus 18 ~G~~H~~~N~G~ 29 (82)
.|.+||.||.=.
T Consensus 4 ~G~L~W~~~~w~ 15 (68)
T PF13320_consen 4 DGFLRWAYNFWN 15 (68)
T ss_pred CeEEEecccccc
Confidence 589999999543
No 144
>cd00231 ZipA ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic tubulins, at the prospective division site, followed by the sequential addition of FtsK, FtsQ, FtsL, FtsW, FtsI, and FtsN. ZipA contains three domains: a short N-terminal membrane-anchored domain, a central P/Q domain that is rich in proline and glutamine and a C-terminal domain, which comprises almost half the protein.
Probab=26.97 E-value=92 Score=20.40 Aligned_cols=30 Identities=10% Similarity=0.092 Sum_probs=23.0
Q ss_pred cCceeEEEecCCcceEEEEeeecCCCccee
Q 039148 18 VGLVHFKCNVGYGNVVAIVAFSSQNLGVVT 47 (82)
Q Consensus 18 ~G~~H~~~N~G~~~av~i~~~~s~npg~~~ 47 (82)
.|+-|.......+..+.+|+.|.-+||+..
T Consensus 35 ~~iFHr~~~~~~~g~vlFSlan~~~PG~F~ 64 (130)
T cd00231 35 MNIFHRHLSLSGSGPVLFSVANMVKPGTFD 64 (130)
T ss_pred CCceEeccccCCCCceEEEEeeccCCCCCC
Confidence 567788877666666899999988888653
No 145
>PRK10926 ferredoxin-NADP reductase; Provisional
Probab=26.89 E-value=88 Score=21.89 Aligned_cols=33 Identities=15% Similarity=0.122 Sum_probs=20.8
Q ss_pred eecCCcEEEE--cc-CceeEEEecCCcceEEEEeee
Q 039148 7 VLKKGDVFVF--LV-GLVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 7 ~l~~GDv~vf--P~-G~~H~~~N~G~~~av~i~~~~ 39 (82)
.+++||.+-+ |. |..+.....++.|.++|++-.
T Consensus 81 ~l~~Gd~v~i~gp~~g~f~l~~~~~~~~~vlIagGt 116 (248)
T PRK10926 81 ALKPGDEVQVVSEAAGFFVLDEVPDCETLWMLATGT 116 (248)
T ss_pred hCCCCCEEEEecCCCcceEccCCCCCCeEEEEEeee
Confidence 4899998866 54 543332223457888888654
No 146
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=26.82 E-value=1.1e+02 Score=16.04 Aligned_cols=20 Identities=15% Similarity=0.079 Sum_probs=14.5
Q ss_pred CCCcHHHHHHHhCCCHHHHH
Q 039148 57 PAIVTDMLAKAFQAEKKIVK 76 (82)
Q Consensus 57 p~~~~~vLa~af~~d~~~i~ 76 (82)
+..+-.-||+..|+++.++.
T Consensus 16 ~r~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVR 35 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHH
T ss_pred CCccHHHHHHHHCcCHHHHH
Confidence 45888899999999986654
No 147
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=26.79 E-value=47 Score=20.93 Aligned_cols=22 Identities=9% Similarity=-0.055 Sum_probs=17.5
Q ss_pred EEeecCCcEEEEccCcee-EEEe
Q 039148 5 IMVLKKGDVFVFLVGLVH-FKCN 26 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~~H-~~~N 26 (82)
..+-..|+++++|.+.+. |...
T Consensus 13 ~g~~y~~sviv~p~~~~~~w~~~ 35 (109)
T cd05560 13 NDQRYEHSLIVTPDELITDWPVA 35 (109)
T ss_pred CCEEEecCEEEECCceeeccccC
Confidence 345578999999999988 8754
No 148
>PRK05713 hypothetical protein; Provisional
Probab=26.74 E-value=88 Score=22.70 Aligned_cols=34 Identities=21% Similarity=0.266 Sum_probs=23.5
Q ss_pred EeecCCcEEEE--ccC-ceeEEEecCCcceEEEEeee
Q 039148 6 MVLKKGDVFVF--LVG-LVHFKCNVGYGNVVAIVAFS 39 (82)
Q Consensus 6 ~~l~~GDv~vf--P~G-~~H~~~N~G~~~av~i~~~~ 39 (82)
..+++||.+-+ |.| ..+|..+....|.+.|++-.
T Consensus 166 ~~l~~Gd~v~l~~p~gg~~~~~~~~~~~~~vlIAgGt 202 (312)
T PRK05713 166 RQLQVGDLLRLGELRGGALHYDPDWQERPLWLLAAGT 202 (312)
T ss_pred hcCCCCCEEEEccCCCCceEecCCCCCCcEEEEecCc
Confidence 46899999887 775 55554433457888887654
No 149
>PRK08158 type III secretion system protein SpaO; Validated
Probab=26.68 E-value=57 Score=24.63 Aligned_cols=23 Identities=22% Similarity=0.242 Sum_probs=17.2
Q ss_pred EeecCCcEEEEcc----------CceeEEEecC
Q 039148 6 MVLKKGDVFVFLV----------GLVHFKCNVG 28 (82)
Q Consensus 6 ~~l~~GDv~vfP~----------G~~H~~~N~G 28 (82)
++++.|||..+++ -+.||+++.+
T Consensus 167 ~~l~~GDVLlI~~~~~~l~v~~r~i~~f~~~~~ 199 (303)
T PRK08158 167 GRIGIGDVLLISTSRAEVYCYAKKIGHFNRVEE 199 (303)
T ss_pred hccccCcEEEEcccccEEEEcceEEEEEEEcCC
Confidence 5789999999997 3466666644
No 150
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=26.62 E-value=82 Score=16.45 Aligned_cols=21 Identities=14% Similarity=0.191 Sum_probs=13.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 039148 58 AIVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl 78 (82)
|.+..-+|+.++.+..+|.+-
T Consensus 20 G~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 20 GMSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp ---HHHHHHHTT--HHHHHHH
T ss_pred CCCHHHHHHHHCcCcHHHHHH
Confidence 488889999999999988763
No 151
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=26.31 E-value=48 Score=21.41 Aligned_cols=14 Identities=36% Similarity=0.470 Sum_probs=11.5
Q ss_pred eEEEeecCCcEEEE
Q 039148 3 LIIMVLKKGDVFVF 16 (82)
Q Consensus 3 ~~~~~l~~GDv~vf 16 (82)
||.=+|++||.+|+
T Consensus 22 l~~GtL~~GD~Iv~ 35 (110)
T cd03703 22 LYDGTLREGDTIVV 35 (110)
T ss_pred EECCeEecCCEEEE
Confidence 45668999999987
No 152
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.27 E-value=83 Score=20.68 Aligned_cols=23 Identities=13% Similarity=0.286 Sum_probs=20.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
.+.++-||+.++++...+||+-.
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~ 37 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILY 37 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHH
Confidence 59999999999999999998743
No 153
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.98 E-value=93 Score=16.39 Aligned_cols=20 Identities=20% Similarity=0.331 Sum_probs=16.9
Q ss_pred cHHHHHHHhCCCHHHHHHHH
Q 039148 60 VTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 60 ~~~vLa~af~~d~~~i~kl~ 79 (82)
+.+.||+.++++..+|.+.-
T Consensus 27 S~~~la~~~g~s~~Tv~~~i 46 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAI 46 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57899999999998887753
No 154
>PRK13284 flagellar assembly protein FliW; Provisional
Probab=25.86 E-value=1.8e+02 Score=19.44 Aligned_cols=17 Identities=29% Similarity=0.454 Sum_probs=12.8
Q ss_pred eecCCcEEEEccCceeE
Q 039148 7 VLKKGDVFVFLVGLVHF 23 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~ 23 (82)
.+.+-+++.||+|+.-|
T Consensus 12 ev~e~~ii~Fp~Gi~GF 28 (145)
T PRK13284 12 EVDPEKVITFPAGLPGF 28 (145)
T ss_pred eeCccceEECCCCCCCC
Confidence 34667899999999543
No 155
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=25.86 E-value=80 Score=18.19 Aligned_cols=22 Identities=14% Similarity=0.049 Sum_probs=17.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHHH
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~ 79 (82)
++.+.=+|++++++...++++-
T Consensus 15 p~~T~eiA~~~gls~~~aR~yL 36 (62)
T PF04703_consen 15 PLKTREIADALGLSIYQARYYL 36 (62)
T ss_dssp -EEHHHHHHHHTS-HHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHH
Confidence 5788899999999999888753
No 156
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=25.63 E-value=1.1e+02 Score=15.59 Aligned_cols=22 Identities=18% Similarity=0.148 Sum_probs=18.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHHH
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~ 79 (82)
+.+.+-+|+.++++..+|++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~ 36 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHL 36 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
Confidence 4889999999999999887754
No 157
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.37 E-value=1.1e+02 Score=15.50 Aligned_cols=20 Identities=15% Similarity=0.114 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCHHHHHHHHh
Q 039148 61 TDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 61 ~~vLa~af~~d~~~i~kl~~ 80 (82)
..=+|+.++++..++++...
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 44578889999999987643
No 158
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=25.26 E-value=80 Score=27.39 Aligned_cols=24 Identities=17% Similarity=0.255 Sum_probs=21.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
||+|+.||+..+++++.|++++.+
T Consensus 492 gfsd~~ia~~~~~~~~~v~~~r~~ 515 (1068)
T PRK12815 492 GFSDALLAELTGVTEEEVRALRKK 515 (1068)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHH
Confidence 499999999999999999999864
No 159
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=25.05 E-value=97 Score=18.19 Aligned_cols=20 Identities=20% Similarity=0.310 Sum_probs=16.5
Q ss_pred HHHHHHHhCCCHHHHHHHHh
Q 039148 61 TDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 61 ~~vLa~af~~d~~~i~kl~~ 80 (82)
-+.||++++++...++++-+
T Consensus 47 ~~~lAk~~G~t~~~l~~~~~ 66 (75)
T TIGR02675 47 LQALAKAMGVTRGELRKMLS 66 (75)
T ss_pred HHHHHHHhCCCHHHHHHHHH
Confidence 35799999999998888754
No 160
>PF07734 FBA_1: F-box associated; InterPro: IPR006527 This domain occurs in a diverse superfamily of genes in plants. Most examples are found C-terminal to an F-box (IPR001810 from INTERPRO), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes []. Some members have two copies of this domain.
Probab=24.99 E-value=1e+02 Score=20.08 Aligned_cols=28 Identities=21% Similarity=0.339 Sum_probs=21.0
Q ss_pred EEccCceeEEEecCCcceE-EEEeeecCC
Q 039148 15 VFLVGLVHFKCNVGYGNVV-AIVAFSSQN 42 (82)
Q Consensus 15 vfP~G~~H~~~N~G~~~av-~i~~~~s~n 42 (82)
|+=.|.+||.-.....+.. .|.+||-.+
T Consensus 2 V~vnG~~hW~~~~~~~~~~~~IlsFDl~~ 30 (164)
T PF07734_consen 2 VFVNGALHWLAYDENNDEKDFILSFDLST 30 (164)
T ss_pred EEECCEEEeeEEecCCCCceEEEEEeccc
Confidence 4557999999888765543 889999654
No 161
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=24.69 E-value=1.1e+02 Score=15.35 Aligned_cols=21 Identities=10% Similarity=0.202 Sum_probs=17.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 039148 58 AIVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl 78 (82)
++...-|++.++++..++.+.
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~ 34 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRD 34 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHH
Confidence 478888999999999887654
No 162
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=24.68 E-value=74 Score=17.67 Aligned_cols=15 Identities=40% Similarity=0.417 Sum_probs=13.0
Q ss_pred eeEEEeecCCcEEEE
Q 039148 2 RLIIMVLKKGDVFVF 16 (82)
Q Consensus 2 ~~~~~~l~~GDv~vf 16 (82)
|+++=+|++||.+.+
T Consensus 7 rV~sG~l~~gd~v~~ 21 (74)
T PF03144_consen 7 RVYSGTLKKGDKVRV 21 (74)
T ss_dssp EEEESEEETTEEEEE
T ss_pred EEEEeEEcCCCEEEE
Confidence 688899999998876
No 163
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=24.54 E-value=64 Score=20.78 Aligned_cols=18 Identities=39% Similarity=0.468 Sum_probs=10.2
Q ss_pred HHHHhCCCHHHHHHHHhc
Q 039148 64 LAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 64 La~af~~d~~~i~kl~~~ 81 (82)
|+++||.+++.--.||+.
T Consensus 58 L~k~fGtspefWlNlQ~~ 75 (104)
T COG3093 58 LAKVFGTSPEFWLNLQNA 75 (104)
T ss_pred HHHHhCCCHHHHHHHHHH
Confidence 556666666655555543
No 164
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This is entry represents an essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) []. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology [].; PDB: 2K2E_A 2Q4Q_B 2AB1_A 2FVT_A 2CYJ_A 1IHN_B 2GM2_A 3CPK_A 2FI9_A.
Probab=24.29 E-value=69 Score=19.92 Aligned_cols=27 Identities=15% Similarity=0.234 Sum_probs=18.2
Q ss_pred eecCCcEEEEccCceeEEEecCCcceEE
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYGNVVA 34 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~~av~ 34 (82)
.-..||++++|.|++ |..+.+...-+.
T Consensus 14 ~~~~~~iii~p~~~~-~~w~~~~~~~l~ 40 (110)
T PF04430_consen 14 KEYEGSIIIFPDGVI-RDWKVKSPHDLT 40 (110)
T ss_dssp EEESSEEEEETTSEE-EEEHHSSTTCEE
T ss_pred EEEccCEEEECCCcc-cCcCCCCcccCC
Confidence 446899999999996 444555444333
No 165
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=24.04 E-value=79 Score=17.60 Aligned_cols=21 Identities=10% Similarity=0.308 Sum_probs=18.1
Q ss_pred CcHHHHHHHhCCCHHHHHHHH
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~ 79 (82)
++.+.||...|++..++.++-
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l 49 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRIL 49 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 889999999999998777653
No 166
>cd00468 HIT_like HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups.
Probab=23.83 E-value=1.5e+02 Score=16.67 Aligned_cols=49 Identities=14% Similarity=0.236 Sum_probs=32.7
Q ss_pred CcceEEEEeeecCCCcceeec----cccccCCCCCcHHHHHHHhCCCHHHHHHHHh
Q 039148 29 YGNVVAIVAFSSQNLGVVTIA----NTAFGSNPAIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 29 ~~~av~i~~~~s~npg~~~~~----~~~F~~~p~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
++..+++.-.....||-..+- ..-|.. ++++.+.+.+.+-.+..++|++
T Consensus 4 ~~~~~a~~~~~p~~~gh~lIipk~H~~~~~~---l~~~~~~~l~~~~~~~~~~l~~ 56 (86)
T cd00468 4 DEHSFAFVNLKPAAPGHVLVCPKRHVETLPD---LDEALLADLVITAQRVAAELEK 56 (86)
T ss_pred cCcEEEEECCCCCCCCcEEEeCchhhCChhH---CCHHHHHHHHHHHHHHHHHHHH
Confidence 345566666667778876543 123332 8898888888887778887764
No 167
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=23.76 E-value=1e+02 Score=14.71 Aligned_cols=21 Identities=14% Similarity=0.265 Sum_probs=12.6
Q ss_pred CcHHHHHHHhC-CCHHHHHHHH
Q 039148 59 IVTDMLAKAFQ-AEKKIVKQLQ 79 (82)
Q Consensus 59 ~~~~vLa~af~-~d~~~i~kl~ 79 (82)
+|+|++.+.|. ++...+.+++
T Consensus 1 lP~~ll~~I~~~l~~~d~~~~~ 22 (41)
T smart00256 1 LPDEILEEILSKLPPKDLLRLR 22 (41)
T ss_pred CCHHHHHHHHHcCCHHHHHHHH
Confidence 46777777764 6665554443
No 168
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=23.72 E-value=1.2e+02 Score=15.54 Aligned_cols=23 Identities=13% Similarity=0.252 Sum_probs=19.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
++..+-||+..+++..++.++..
T Consensus 15 gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 15 GLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHC
Confidence 47788899999999999988753
No 169
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=23.58 E-value=90 Score=26.99 Aligned_cols=24 Identities=17% Similarity=0.282 Sum_probs=20.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
||+|..||+..+++++.|+++|.+
T Consensus 492 g~~d~~~a~~~~~~~~~~~~~~~~ 515 (1066)
T PRK05294 492 GFSDARIAKLLGVTEDEVRKLRKA 515 (1066)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHH
Confidence 488999999999999999998864
No 170
>PF14173 ComGG: ComG operon protein 7
Probab=23.52 E-value=1.8e+02 Score=17.62 Aligned_cols=25 Identities=16% Similarity=0.339 Sum_probs=18.3
Q ss_pred cEEEEccCceeEEEecCCcceEEEE
Q 039148 12 DVFVFLVGLVHFKCNVGYGNVVAIV 36 (82)
Q Consensus 12 Dv~vfP~G~~H~~~N~G~~~av~i~ 36 (82)
-.+.||.|-+.+++..-++..+.++
T Consensus 42 ~~~~y~~G~Vsy~~~~~~~~~~~v~ 66 (95)
T PF14173_consen 42 GSFQYPDGTVSYQITKEDEDVITVT 66 (95)
T ss_pred eEEEecCCEEEEEEEeccceEEEEE
Confidence 4688999999998888774343333
No 171
>COG2094 Mpg 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=23.48 E-value=1.5e+02 Score=21.23 Aligned_cols=61 Identities=20% Similarity=0.122 Sum_probs=34.5
Q ss_pred CcEEEEccCc--------eeEEEecCCcc-----eEEEEeeec---CCCcceeec---cccccCCCCCcHHHHHHHhCCC
Q 039148 11 GDVFVFLVGL--------VHFKCNVGYGN-----VVAIVAFSS---QNLGVVTIA---NTAFGSNPAIVTDMLAKAFQAE 71 (82)
Q Consensus 11 GDv~vfP~G~--------~H~~~N~G~~~-----av~i~~~~s---~npg~~~~~---~~~F~~~p~~~~~vLa~af~~d 71 (82)
-++|.-|.|- +||+.|.-+.+ ||+|=+.-- .++=.+.-. .-...+.|+ -|.+|++++
T Consensus 64 ~~aMf~~~G~~YvY~~~G~h~~lNvv~~~eG~p~aVLIRAieP~eg~~~m~~rR~~~~~~~l~nGPg----kLc~ALgI~ 139 (200)
T COG2094 64 NRAMFGPPGHAYVYRIYGMHYCLNVVTGPEGIPAAVLIRAIEPEEGIEPMRQRRGVRVLRLLTNGPG----KLCKALGIT 139 (200)
T ss_pred cHhhccCCceEEEEEEeccEEEEEEEecCCCCcceEEEEeeccccccchhhhccCccccchhccCch----HHHHHhCCC
Confidence 3556666665 78999996655 776666542 222111111 112333333 799999998
Q ss_pred HHHH
Q 039148 72 KKIV 75 (82)
Q Consensus 72 ~~~i 75 (82)
.+..
T Consensus 140 ~~~~ 143 (200)
T COG2094 140 REDN 143 (200)
T ss_pred HHHc
Confidence 7653
No 172
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=23.42 E-value=45 Score=20.07 Aligned_cols=23 Identities=30% Similarity=0.596 Sum_probs=12.4
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEE
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAI 35 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i 35 (82)
|+++.||.++| .|+.+.-..+.+
T Consensus 17 ~~F~vGD~LvF-------~y~~~~h~V~~V 39 (85)
T PF02298_consen 17 KTFRVGDTLVF-------NYDSGQHSVVEV 39 (85)
T ss_dssp S-BETTEEEEE-------E--TTTB-EEEE
T ss_pred CcEeCCCEEEE-------EecCCCCeEEec
Confidence 67899999864 556554444443
No 173
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=23.34 E-value=70 Score=22.30 Aligned_cols=25 Identities=20% Similarity=0.312 Sum_probs=20.4
Q ss_pred ccCCCCCcHHHHHHHhCCCHHHHHH
Q 039148 53 FGSNPAIVTDMLAKAFQAEKKIVKQ 77 (82)
Q Consensus 53 F~~~p~~~~~vLa~af~~d~~~i~k 77 (82)
+.++=.++.--||+++|+|+.++..
T Consensus 36 ~~gdIEI~~t~iAka~gVdRrvV~~ 60 (167)
T COG2150 36 YCGDIEIPITKIAKATGVDRRVVYA 60 (167)
T ss_pred eeCcEEechHHHHHHhCcchHhHHH
Confidence 6666678899999999999987653
No 174
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=23.27 E-value=77 Score=19.32 Aligned_cols=23 Identities=22% Similarity=0.291 Sum_probs=16.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
.+.++-||+..+++..+++++-.
T Consensus 27 ~l~de~la~~~~l~~~~vRkiL~ 49 (105)
T PF02002_consen 27 ELTDEDLAKKLGLKPKEVRKILY 49 (105)
T ss_dssp -B-HHHHHHTT-S-HHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHH
Confidence 48999999999999999988743
No 175
>PRK09857 putative transposase; Provisional
Probab=23.21 E-value=96 Score=22.85 Aligned_cols=30 Identities=10% Similarity=0.055 Sum_probs=23.2
Q ss_pred eccccccCCCCCcHHHHHHHhCCCHHHHHHHH
Q 039148 48 IANTAFGSNPAIVTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 48 ~~~~~F~~~p~~~~~vLa~af~~d~~~i~kl~ 79 (82)
++..+... |++.+.+++..|++.+.+++|.
T Consensus 262 ia~~ml~~--g~~~~~I~~~TgLs~eel~~~~ 291 (292)
T PRK09857 262 IAKIMLES--GVPLADIMRFTGLSEEELAAAS 291 (292)
T ss_pred HHHHHHHc--CCCHHHHHHHhCCCHHHHHHhc
Confidence 34444443 4999999999999999999874
No 176
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=23.20 E-value=1.4e+02 Score=16.27 Aligned_cols=23 Identities=13% Similarity=0.283 Sum_probs=17.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
+++-+-+|+..+++...+.++-+
T Consensus 14 gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 14 GLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHC
Confidence 37788899999999998888753
No 177
>PLN02735 carbamoyl-phosphate synthase
Probab=23.16 E-value=92 Score=27.27 Aligned_cols=24 Identities=17% Similarity=0.148 Sum_probs=21.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
||+|..||+..+++++.|+++|.+
T Consensus 512 g~~d~~ia~~~~~~~~~v~~~r~~ 535 (1102)
T PLN02735 512 GFSDKQIAFATKSTEKEVRSKRLS 535 (1102)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHH
Confidence 489999999999999999999864
No 178
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=23.11 E-value=42 Score=26.35 Aligned_cols=20 Identities=25% Similarity=0.290 Sum_probs=18.3
Q ss_pred eecCCcEEEEccCceeEEEe
Q 039148 7 VLKKGDVFVFLVGLVHFKCN 26 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N 26 (82)
.|++||.+..-+|.-||.|-
T Consensus 335 sL~p~d~i~~tr~~~~wlyg 354 (414)
T KOG1314|consen 335 SLPPGDGIKATRGFNHWLYG 354 (414)
T ss_pred ccCCCcceeeeeeeecccch
Confidence 47899999999999999985
No 179
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.98 E-value=1.1e+02 Score=16.78 Aligned_cols=19 Identities=11% Similarity=0.162 Sum_probs=15.1
Q ss_pred HHHHHhCCCHHHHHHHHhc
Q 039148 63 MLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 63 vLa~af~~d~~~i~kl~~~ 81 (82)
=+|+.++++.++++.....
T Consensus 5 eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 5 EVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHCcCHHHHHHHHHh
Confidence 4788999999999876543
No 180
>KOG4736 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.97 E-value=2.4e+02 Score=21.49 Aligned_cols=49 Identities=10% Similarity=0.213 Sum_probs=36.1
Q ss_pred cceEEEEeeecCCCcceeeccccccCCCCCcHH--HHHHHhCCCHHHHHHH
Q 039148 30 GNVVAIVAFSSQNLGVVTIANTAFGSNPAIVTD--MLAKAFQAEKKIVKQL 78 (82)
Q Consensus 30 ~~av~i~~~~s~npg~~~~~~~~F~~~p~~~~~--vLa~af~~d~~~i~kl 78 (82)
..++.+..-|++.-|+..++..||...+.+++. ++.++-..|...=++-
T Consensus 189 ~~~isvlv~n~~~~GTv~itGDLf~~~~dlde~d~i~~~e~s~d~~~kr~~ 239 (302)
T KOG4736|consen 189 QHDISVLVHNVDLYGTVAITGDLFPREEDLDEKDDIMSQEGSEDNAAKRQS 239 (302)
T ss_pred CcceEEEEEeecccceEEEEeecccCCccccchhhhhhhccCCchhhhhhh
Confidence 456777788888899999999999998888777 6655555555443433
No 181
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=22.86 E-value=1.2e+02 Score=18.07 Aligned_cols=28 Identities=11% Similarity=0.153 Sum_probs=23.2
Q ss_pred ccccCCCCCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 51 TAFGSNPAIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 51 ~~F~~~p~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
++|-- ++.+=|++.++.+..+|.+++++
T Consensus 48 ~vYi~---~s~eel~~~L~~s~~tv~~~~ke 75 (76)
T PF06970_consen 48 NVYII---FSIEELMELLNCSKSTVIKAKKE 75 (76)
T ss_pred CEEEE---eeHHHHHHHHCCCHHHHHHHHHc
Confidence 35544 88899999999999999998875
No 182
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=22.54 E-value=1.4e+02 Score=20.82 Aligned_cols=28 Identities=25% Similarity=0.281 Sum_probs=21.4
Q ss_pred cccccC-CCCCcHHHHHHHhCCCHHHHHH
Q 039148 50 NTAFGS-NPAIVTDMLAKAFQAEKKIVKQ 77 (82)
Q Consensus 50 ~~~F~~-~p~~~~~vLa~af~~d~~~i~k 77 (82)
.-+|.+ +||++.+-|++.++++.+.+++
T Consensus 11 A~LF~sg~pgls~~~La~~l~~~~~~v~~ 39 (188)
T PRK00135 11 ALLFVSGEEGLSLEQLAEILELEPTEVQQ 39 (188)
T ss_pred HHHHHcCCCCCCHHHHHHHHCCCHHHHHH
Confidence 346775 4679999999999999866544
No 183
>TIGR01221 rmlC dTDP-4-dehydrorhamnose 3,5-epimerase. This enzyme participates in the biosynthesis of dTDP-L-rhamnose, often as a precursor to LPS O-antigen
Probab=22.29 E-value=2.7e+02 Score=19.10 Aligned_cols=41 Identities=7% Similarity=-0.048 Sum_probs=28.0
Q ss_pred EEEeecC--CcEEEEccCceeEEEecCCcceEEEEeeecC-CCcc
Q 039148 4 IIMVLKK--GDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQ-NLGV 45 (82)
Q Consensus 4 ~~~~l~~--GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~-npg~ 45 (82)
..-.|.. +..+.+|+|++|=.+..++. +++.-.-+.. +|+.
T Consensus 96 ~~~~L~~~~~~~l~IP~G~aHGF~~L~d~-a~v~Y~~~~~y~p~~ 139 (176)
T TIGR01221 96 VGVLLSAENKRQLWIPEGFAHGFVVLSDE-AEFLYKCTDYYAPEY 139 (176)
T ss_pred EEEEECCCCCCEEEeCCcceeEEEEcCCC-eEEEEeCCCCcCccc
Confidence 3445544 66999999999999999866 5554444432 5554
No 184
>TIGR01784 T_den_put_tspse conserved hypothetical protein (putative transposase or invertase). Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The strongest similarities are usually within rather than between species. PSI-BLAST shows similarity to proteins designated as possible transposases, DNA invertases (resolvases), and recombinases. In the oral pathogenic spirochete Treponema denticola, full-length members are often found near transporters or other membrane proteins. This family includes members of the putative transposase family pfam04754.
Probab=21.88 E-value=93 Score=21.51 Aligned_cols=29 Identities=10% Similarity=0.173 Sum_probs=22.2
Q ss_pred eccccccCCCCCcHHHHHHHhCCCHHHHHHH
Q 039148 48 IANTAFGSNPAIVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 48 ~~~~~F~~~p~~~~~vLa~af~~d~~~i~kl 78 (82)
++..+.+. +++.+.+++.++++.+.|+++
T Consensus 242 ~a~~ll~~--g~~~~~i~~~~~Ls~eei~~~ 270 (270)
T TIGR01784 242 TAKKLLKN--GLTLEQVAEATGLSVEELEEI 270 (270)
T ss_pred HHHHHHHc--CCCHHHHHHHHCcCHHHHhhC
Confidence 44456654 599999999999999888763
No 185
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=21.73 E-value=1e+02 Score=21.96 Aligned_cols=20 Identities=5% Similarity=0.069 Sum_probs=17.5
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 039148 58 AIVTDMLAKAFQAEKKIVKQ 77 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~k 77 (82)
.+...-|++.|++++++||+
T Consensus 21 ~v~v~eLa~~~~VS~~TIRR 40 (252)
T PRK10681 21 KLHLKDAAALLGVSEMTIRR 40 (252)
T ss_pred CCcHHHHHHHhCCCHHHHHH
Confidence 47788899999999999976
No 186
>PF00962 A_deaminase: Adenosine/AMP deaminase immunodeficiency disease (SCID); InterPro: IPR001365 Adenosine deaminase (3.5.4.4 from EC) catalyzes the hydrolytic deamination of adenosine into inosine and AMP deaminase (3.5.4.6 from EC) catalyzes the hydrolytic deamination of AMP into IMP. It has been shown [] that these two enzymes share three regions of sequence similarities; these regions are centred on residues which are proposed to play an important role in the catalytic mechanism of these two enzymes.; GO: 0019239 deaminase activity, 0009168 purine ribonucleoside monophosphate biosynthetic process; PDB: 3LGG_B 3LGD_B 2AMX_B 3EWD_A 2QVN_A 2PGF_A 2PGR_A 3EWC_A 1W1I_G 1O5R_A ....
Probab=21.64 E-value=66 Score=23.25 Aligned_cols=35 Identities=26% Similarity=0.479 Sum_probs=20.1
Q ss_pred eeecCCCcceeeccccccCCCCCcHH--HHHHHhCCCHHHHHHHHh
Q 039148 37 AFSSQNLGVVTIANTAFGSNPAIVTD--MLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 37 ~~~s~npg~~~~~~~~F~~~p~~~~~--vLa~af~~d~~~i~kl~~ 80 (82)
+++|.||+ +|+++ +..| ++++.++++.+++.+|..
T Consensus 276 ~i~TDd~~-------~~~~~--l~~ey~~~~~~~~l~~~~l~~l~~ 312 (331)
T PF00962_consen 276 SINTDDPG-------VFGTT--LSDEYYLAAEAFGLSLADLKQLAR 312 (331)
T ss_dssp EE--BSHH-------HHT-S--HHHHHHHHHHHHT--HHHHHHHHH
T ss_pred eccCCCcc-------ccCCC--cHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45555554 56654 6666 566789999998888753
No 187
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=21.47 E-value=63 Score=18.90 Aligned_cols=13 Identities=31% Similarity=0.248 Sum_probs=7.5
Q ss_pred EeecCCcEEEEcc
Q 039148 6 MVLKKGDVFVFLV 18 (82)
Q Consensus 6 ~~l~~GDv~vfP~ 18 (82)
+.|++||++.|.-
T Consensus 47 ~Kl~~GD~V~~~~ 59 (65)
T PF13275_consen 47 KKLRPGDVVEIDG 59 (65)
T ss_dssp ----SSEEEEETT
T ss_pred CcCCCCCEEEECC
Confidence 5789999998843
No 188
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=21.43 E-value=1.3e+02 Score=15.42 Aligned_cols=21 Identities=14% Similarity=0.238 Sum_probs=16.8
Q ss_pred CC-cHHHHHHHhCCCHHHHHHH
Q 039148 58 AI-VTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 58 ~~-~~~vLa~af~~d~~~i~kl 78 (82)
.+ +..-|++.|+++..++++.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~ 40 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREA 40 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHH
Confidence 35 5778999999999887763
No 189
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=21.42 E-value=1.5e+02 Score=18.15 Aligned_cols=23 Identities=4% Similarity=0.049 Sum_probs=20.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
+.+..-+|+.++++..+|.++++
T Consensus 50 G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 37788899999999999998875
No 190
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=21.18 E-value=1.6e+02 Score=16.01 Aligned_cols=42 Identities=19% Similarity=0.192 Sum_probs=29.5
Q ss_pred EeecCCcEEEEccCceeEEEecCCcceEEEEeeecCCCcceeeccc
Q 039148 6 MVLKKGDVFVFLVGLVHFKCNVGYGNVVAIVAFSSQNLGVVTIANT 51 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~H~~~N~G~~~av~i~~~~s~npg~~~~~~~ 51 (82)
....+||.+-+= =-.-|.|..+|.-+..-|.=.+|...++.+
T Consensus 6 ~~~~~Gd~v~Yt----i~v~N~g~~~a~~v~v~D~lP~g~~~v~~S 47 (53)
T TIGR01451 6 TVATIGDTITYT----ITVTNNGNVPATNVVVTDILPSGTTFVSNS 47 (53)
T ss_pred cccCCCCEEEEE----EEEEECCCCceEeEEEEEcCCCCCEEEeCc
Confidence 345667766431 134588999999899888888888777654
No 191
>smart00753 PAM PCI/PINT associated module.
Probab=21.00 E-value=1.2e+02 Score=17.50 Aligned_cols=20 Identities=30% Similarity=0.213 Sum_probs=17.0
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 039148 59 IVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl 78 (82)
++-+-|++.|+++.+.++++
T Consensus 25 i~~~~i~~~~~l~~~~vE~~ 44 (88)
T smart00753 25 ISLSDLAKLLGLSVPEVEKL 44 (88)
T ss_pred eeHHHHHHHhCcCHHHHHHH
Confidence 88899999999998877654
No 192
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=21.00 E-value=1.2e+02 Score=17.50 Aligned_cols=20 Identities=30% Similarity=0.213 Sum_probs=17.0
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 039148 59 IVTDMLAKAFQAEKKIVKQL 78 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl 78 (82)
++-+-|++.|+++.+.++++
T Consensus 25 i~~~~i~~~~~l~~~~vE~~ 44 (88)
T smart00088 25 ISLSDLAKLLGLSVPEVEKL 44 (88)
T ss_pred eeHHHHHHHhCcCHHHHHHH
Confidence 88899999999998877654
No 193
>PLN02177 glycerol-3-phosphate acyltransferase
Probab=20.85 E-value=46 Score=26.56 Aligned_cols=16 Identities=25% Similarity=0.482 Sum_probs=13.2
Q ss_pred EeecCCcEEEEccCce
Q 039148 6 MVLKKGDVFVFLVGLV 21 (82)
Q Consensus 6 ~~l~~GDv~vfP~G~~ 21 (82)
+.+++||+++||.|..
T Consensus 361 ~lL~~g~lvIFPEGTr 376 (497)
T PLN02177 361 RLLEEGDLVICPEGTT 376 (497)
T ss_pred HHHhcCCEEECcCcCC
Confidence 3467899999999965
No 194
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=20.58 E-value=78 Score=22.63 Aligned_cols=19 Identities=16% Similarity=0.387 Sum_probs=16.6
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 039148 59 IVTDMLAKAFQAEKKIVKQ 77 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~k 77 (82)
+.-+=|++.|++++++||+
T Consensus 20 v~v~eLa~~~~VS~~TIRR 38 (253)
T COG1349 20 VSVEELAELFGVSEMTIRR 38 (253)
T ss_pred EEHHHHHHHhCCCHHHHHH
Confidence 5667799999999999986
No 195
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit. In several thermophilic species (Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Aquifex aeolicus), the large subunit appears split, at different points, into two separate genes.
Probab=20.54 E-value=1.1e+02 Score=26.42 Aligned_cols=24 Identities=13% Similarity=0.249 Sum_probs=20.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHhc
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQNT 81 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~~ 81 (82)
||+|+.||+..+++++.|+++|.+
T Consensus 491 g~~d~~~a~~~~~~~~~~~~~~~~ 514 (1050)
T TIGR01369 491 GFSDAQIARLIGVTEAEVRKLRKE 514 (1050)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHH
Confidence 488999999999999999998864
No 196
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=20.49 E-value=1.6e+02 Score=15.77 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=14.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHHh
Q 039148 58 AIVTDMLAKAFQAEKKIVKQLQN 80 (82)
Q Consensus 58 ~~~~~vLa~af~~d~~~i~kl~~ 80 (82)
++...-||+..|++..++.++..
T Consensus 10 ~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 10 GITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp T--HHHHHHHHT--HHHHHHHHT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHh
Confidence 36677788888888888887754
No 197
>KOG3995 consensus 3-hydroxyanthranilate oxygenase HAAO [Amino acid transport and metabolism]
Probab=20.33 E-value=70 Score=23.57 Aligned_cols=24 Identities=17% Similarity=0.404 Sum_probs=18.4
Q ss_pred eecCCcEEEEccCceeEEEecCCc
Q 039148 7 VLKKGDVFVFLVGLVHFKCNVGYG 30 (82)
Q Consensus 7 ~l~~GDv~vfP~G~~H~~~N~G~~ 30 (82)
.+++||++.+|.-+-|--.--.++
T Consensus 78 vI~qGe~flLParVpHSPqRFant 101 (279)
T KOG3995|consen 78 VIRQGEIFLLPARVPHSPQRFANT 101 (279)
T ss_pred EEecCcEEEeccCCCCChhhhccc
Confidence 578999999999998865544443
No 198
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=20.27 E-value=40 Score=22.88 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=11.7
Q ss_pred EEeecCCcEEEEccCc
Q 039148 5 IMVLKKGDVFVFLVGL 20 (82)
Q Consensus 5 ~~~l~~GDv~vfP~G~ 20 (82)
.+.|++||++.+.+|-
T Consensus 49 ~~~L~~GDiI~l~~g~ 64 (230)
T PF00122_consen 49 SSELVPGDIIILKAGD 64 (230)
T ss_dssp GGGT-TTSEEEEETTE
T ss_pred Hhhccceeeeeccccc
Confidence 4568899999887765
No 199
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=20.09 E-value=69 Score=18.35 Aligned_cols=13 Identities=38% Similarity=0.307 Sum_probs=8.3
Q ss_pred eecCCcEEEEccC
Q 039148 7 VLKKGDVFVFLVG 19 (82)
Q Consensus 7 ~l~~GDv~vfP~G 19 (82)
.|++||++-++.-
T Consensus 28 ~L~~Gdvi~l~~~ 40 (77)
T PF01052_consen 28 NLKVGDVIPLDKP 40 (77)
T ss_dssp C--TT-EEEECCE
T ss_pred cCCCCCEEEeCCC
Confidence 5789999998875
No 200
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=20.05 E-value=1.1e+02 Score=15.81 Aligned_cols=21 Identities=10% Similarity=0.064 Sum_probs=17.1
Q ss_pred CcHHHHHHHhCCCHHHHHHHH
Q 039148 59 IVTDMLAKAFQAEKKIVKQLQ 79 (82)
Q Consensus 59 ~~~~vLa~af~~d~~~i~kl~ 79 (82)
.+-.-+|+-++++..+|+++=
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~ 48 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIF 48 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 366778999999999998764
Done!