Query psy17228
Match_columns 99
No_of_seqs 121 out of 1048
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 16:36:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17228.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17228hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01715 IPPT: IPP transferase 99.9 1.8E-22 3.9E-27 153.7 4.8 75 16-98 40-125 (253)
2 PRK14729 miaA tRNA delta(2)-is 99.8 1.9E-21 4.2E-26 151.9 6.4 75 16-98 76-161 (300)
3 COG0324 MiaA tRNA delta(2)-iso 99.8 1.2E-20 2.7E-25 148.1 7.0 75 17-98 77-161 (308)
4 TIGR00174 miaA tRNA isopenteny 99.8 3.1E-20 6.7E-25 144.3 6.7 75 16-98 72-157 (287)
5 PLN02748 tRNA dimethylallyltra 99.8 6.7E-20 1.5E-24 150.4 7.0 75 17-98 96-192 (468)
6 PLN02840 tRNA dimethylallyltra 99.8 3.6E-19 7.9E-24 144.6 6.1 74 16-98 94-183 (421)
7 PRK00091 miaA tRNA delta(2)-is 99.7 5.4E-18 1.2E-22 132.6 7.4 75 16-98 77-162 (307)
8 PLN02165 adenylate isopentenyl 99.0 5.1E-10 1.1E-14 89.1 5.3 39 15-53 116-154 (334)
9 KOG1384|consensus 98.8 9.4E-09 2E-13 82.2 4.5 35 17-51 81-115 (348)
10 COG2069 CdhD CO dehydrogenase/ 93.2 0.085 1.9E-06 42.7 2.9 25 18-42 184-208 (403)
11 cd04235 AAK_CK AAK_CK: Carbama 78.4 1.9 4.1E-05 34.3 2.5 21 23-43 172-192 (308)
12 PRK13775 formimidoylglutamase; 74.9 5.9 0.00013 31.2 4.5 36 17-52 108-143 (328)
13 PF03464 eRF1_2: eRF1 domain 2 74.2 5.3 0.00011 27.3 3.6 39 14-52 53-93 (133)
14 COG4359 Uncharacterized conser 74.0 5.5 0.00012 30.4 3.9 22 32-53 88-111 (220)
15 PRK13776 formimidoylglutamase; 73.9 6.2 0.00013 31.0 4.4 34 19-52 104-137 (318)
16 TIGR01229 rocF_arginase argina 73.3 4.5 9.8E-05 31.3 3.4 33 19-51 70-102 (300)
17 TIGR01227 hutG formimidoylglut 72.8 6.6 0.00014 30.5 4.2 35 18-52 97-131 (307)
18 PRK13773 formimidoylglutamase; 72.5 7.2 0.00016 30.7 4.4 35 18-52 105-139 (324)
19 PRK13774 formimidoylglutamase; 72.5 7.5 0.00016 30.4 4.5 36 17-52 105-140 (311)
20 cd02070 corrinoid_protein_B12- 72.0 4.4 9.5E-05 29.5 2.9 25 19-43 148-175 (201)
21 PRK13772 formimidoylglutamase; 72.0 5 0.00011 31.4 3.4 33 17-49 101-133 (314)
22 TIGR01230 agmatinase agmatinas 71.8 5.2 0.00011 30.6 3.4 36 17-52 78-113 (275)
23 TIGR01768 GGGP-family geranylg 71.5 2.5 5.4E-05 32.2 1.5 34 9-42 4-37 (223)
24 cd02067 B12-binding B12 bindin 71.4 5.3 0.00012 26.2 3.0 25 19-43 65-91 (119)
25 PF00491 Arginase: Arginase fa 70.4 6.3 0.00014 29.7 3.6 36 17-52 65-100 (277)
26 PF01884 PcrB: PcrB family; I 69.7 4.5 9.8E-05 31.0 2.6 38 2-42 1-42 (230)
27 PRK02190 agmatinase; Provision 69.3 9.1 0.0002 29.7 4.3 36 17-52 95-130 (301)
28 PF02310 B12-binding: B12 bind 67.7 13 0.00028 23.9 4.3 37 14-50 61-100 (121)
29 cd02065 B12-binding_like B12 b 66.3 10 0.00022 24.5 3.5 24 20-43 65-90 (125)
30 PRK01722 formimidoylglutamase; 66.1 12 0.00026 29.2 4.4 34 18-51 103-136 (320)
31 PF09970 DUF2204: Nucleotidyl 65.4 7.7 0.00017 28.2 3.0 27 19-45 3-29 (181)
32 PRK12454 carbamate kinase-like 64.2 6.3 0.00014 31.5 2.5 22 22-43 175-196 (313)
33 cd02868 PseudoU_synth_hTruB2_l 64.2 4.7 0.0001 30.7 1.8 16 38-53 171-186 (226)
34 PF00994 MoCF_biosynth: Probab 63.7 9.7 0.00021 26.0 3.1 24 20-43 45-68 (144)
35 PRK04169 geranylgeranylglycery 63.4 4.5 9.8E-05 30.9 1.6 38 2-42 3-42 (232)
36 COG0528 PyrH Uridylate kinase 60.7 7.1 0.00015 30.3 2.2 27 13-43 110-136 (238)
37 TIGR01769 GGGP geranylgeranylg 59.4 14 0.0003 27.7 3.5 31 9-41 3-33 (205)
38 cd02068 radical_SAM_B12_BD B12 58.9 13 0.00027 24.7 3.0 28 16-43 50-78 (127)
39 cd02069 methionine_synthase_B1 58.5 12 0.00025 27.9 3.0 27 17-43 152-179 (213)
40 TIGR02137 HSK-PSP phosphoserin 57.2 19 0.00042 26.3 3.9 35 20-54 72-106 (203)
41 PRK14556 pyrH uridylate kinase 56.5 10 0.00022 29.3 2.5 16 27-42 131-146 (249)
42 cd02071 MM_CoA_mut_B12_BD meth 56.4 18 0.00038 24.2 3.4 27 17-43 63-91 (122)
43 cd00758 MoCF_BD MoCF_BD: molyb 56.1 12 0.00025 25.4 2.5 23 21-43 48-70 (133)
44 TIGR00640 acid_CoA_mut_C methy 54.7 20 0.00044 24.7 3.5 23 19-41 68-92 (132)
45 KOG1221|consensus 52.6 11 0.00024 31.8 2.2 27 26-53 7-33 (467)
46 PRK08202 purine nucleoside pho 50.6 18 0.00039 27.8 3.0 12 34-45 23-34 (272)
47 PRK12353 putative amino acid k 49.9 14 0.0003 29.2 2.3 24 22-45 175-198 (314)
48 smart00852 MoCF_biosynth Proba 49.8 20 0.00042 24.1 2.8 22 22-43 48-69 (135)
49 PRK09552 mtnX 2-hydroxy-3-keto 49.7 26 0.00056 25.2 3.6 33 20-52 78-111 (219)
50 cd02072 Glm_B12_BD B12 binding 47.9 26 0.00057 24.4 3.2 22 21-42 67-90 (128)
51 TIGR00177 molyb_syn molybdenum 47.0 22 0.00047 24.5 2.7 23 21-43 56-78 (144)
52 PF09818 ABC_ATPase: Predicted 47.0 29 0.00062 29.3 3.8 34 12-48 369-405 (448)
53 TIGR02370 pyl_corrinoid methyl 46.8 22 0.00048 25.9 2.8 25 19-43 150-177 (197)
54 cd00885 cinA Competence-damage 46.3 21 0.00046 25.5 2.7 22 22-43 49-70 (170)
55 PLN02615 arginase 46.1 42 0.00091 26.8 4.5 35 17-51 131-166 (338)
56 TIGR01488 HAD-SF-IB Haloacid D 44.7 37 0.00079 22.9 3.6 34 19-52 76-110 (177)
57 PF00941 FAD_binding_5: FAD bi 44.7 18 0.00039 25.8 2.0 28 17-47 10-37 (171)
58 COG0149 TpiA Triosephosphate i 44.1 33 0.00072 26.7 3.5 27 16-42 180-211 (251)
59 smart00804 TAP_C C-terminal do 43.5 15 0.00033 22.6 1.3 25 11-35 34-58 (63)
60 cd01078 NAD_bind_H4MPT_DH NADP 42.7 38 0.00081 24.0 3.5 35 17-51 7-47 (194)
61 PRK12354 carbamate kinase; Rev 42.5 23 0.00049 28.3 2.5 22 22-43 165-186 (307)
62 cd00209 DHFR Dihydrofolate red 42.3 34 0.00073 23.9 3.1 31 20-50 79-109 (158)
63 PRK02261 methylaspartate mutas 42.0 40 0.00087 23.3 3.4 24 19-42 69-94 (137)
64 PF08030 NAD_binding_6: Ferric 41.6 12 0.00025 25.3 0.6 19 33-51 3-26 (156)
65 PF12710 HAD: haloacid dehalog 41.1 39 0.00085 23.0 3.3 36 19-54 92-128 (192)
66 COG4752 Uncharacterized protei 41.1 31 0.00067 25.6 2.8 32 9-42 82-113 (190)
67 TIGR01501 MthylAspMutase methy 41.0 40 0.00087 23.6 3.3 22 21-42 69-92 (134)
68 COG4962 CpaF Flp pilus assembl 40.7 34 0.00074 28.0 3.3 36 19-54 160-195 (355)
69 PRK01215 competence damage-ind 40.0 34 0.00074 26.4 3.1 24 20-43 51-74 (264)
70 cd00886 MogA_MoaB MogA_MoaB fa 39.4 31 0.00067 23.9 2.6 22 22-43 50-73 (152)
71 PRK13900 type IV secretion sys 39.4 35 0.00076 27.1 3.1 33 20-52 148-184 (332)
72 COG0010 SpeB Arginase/agmatina 38.8 41 0.00089 26.2 3.4 36 16-51 86-121 (305)
73 PRK00115 hemE uroporphyrinogen 38.6 63 0.0014 25.3 4.4 34 17-50 222-258 (346)
74 PRK12686 carbamate kinase; Rev 38.6 28 0.0006 27.8 2.4 21 22-42 173-193 (312)
75 TIGR03333 salvage_mtnX 2-hydro 38.5 45 0.00098 23.9 3.4 33 20-52 74-107 (214)
76 PRK10078 ribose 1,5-bisphospho 38.5 55 0.0012 23.0 3.8 27 25-52 82-108 (186)
77 PLN02662 cinnamyl-alcohol dehy 38.4 19 0.00042 26.8 1.4 19 31-49 3-21 (322)
78 TIGR01125 MiaB-like tRNA modif 38.2 37 0.0008 27.5 3.1 24 19-43 53-76 (430)
79 PRK14558 pyrH uridylate kinase 37.3 37 0.0008 25.0 2.8 23 19-41 105-127 (231)
80 TIGR00746 arcC carbamate kinas 37.2 14 0.00031 29.3 0.6 24 20-43 170-193 (310)
81 KOG3985|consensus 37.1 11 0.00024 29.7 -0.1 15 37-51 14-28 (283)
82 COG1954 GlpP Glycerol-3-phosph 36.8 29 0.00063 25.9 2.1 19 22-40 133-151 (181)
83 PF03297 Ribosomal_S25: S25 ri 36.7 24 0.00051 24.0 1.5 26 19-44 74-99 (105)
84 TIGR01464 hemE uroporphyrinoge 36.4 82 0.0018 24.4 4.7 34 17-50 216-252 (338)
85 PLN02989 cinnamyl-alcohol dehy 36.4 21 0.00046 26.8 1.4 20 31-50 4-23 (325)
86 PF04263 TPK_catalytic: Thiami 36.0 47 0.001 22.7 3.0 34 19-52 71-105 (123)
87 COG3962 Acetolactate synthase 35.0 32 0.00069 29.8 2.3 38 19-56 217-260 (617)
88 cd05398 NT_ClassII-CCAase Nucl 34.9 48 0.001 22.9 2.9 30 20-52 3-33 (139)
89 COG1537 PelA Predicted RNA-bin 34.5 72 0.0016 26.2 4.2 35 15-52 177-211 (352)
90 PRK13851 type IV secretion sys 34.3 44 0.00095 26.8 2.9 33 19-51 149-185 (344)
91 COG0005 Pnp Purine nucleoside 34.2 14 0.00031 28.9 0.2 12 35-46 19-30 (262)
92 PF00175 NAD_binding_1: Oxidor 33.8 21 0.00046 22.3 0.9 8 36-43 1-8 (109)
93 PLN00198 anthocyanidin reducta 33.8 26 0.00056 26.6 1.5 21 31-51 8-28 (338)
94 PRK08564 5'-methylthioadenosin 33.7 13 0.00029 28.7 -0.1 10 36-45 11-20 (267)
95 PRK15181 Vi polysaccharide bio 33.6 23 0.0005 27.2 1.2 22 30-51 13-34 (348)
96 TIGR01544 HAD-SF-IE haloacid d 32.9 74 0.0016 24.9 3.9 34 20-53 125-159 (277)
97 PLN02650 dihydroflavonol-4-red 32.4 27 0.00058 26.7 1.4 22 30-51 3-24 (351)
98 COG1646 Predicted phosphate-bi 32.3 24 0.00052 27.5 1.1 24 19-42 28-51 (240)
99 TIGR02622 CDP_4_6_dhtase CDP-g 32.3 25 0.00054 26.9 1.2 14 31-44 3-16 (349)
100 TIGR02782 TrbB_P P-type conjug 31.9 53 0.0011 25.5 3.0 34 19-52 119-156 (299)
101 PLN02572 UDP-sulfoquinovose sy 31.3 26 0.00057 28.5 1.2 21 31-51 46-66 (442)
102 cd01130 VirB11-like_ATPase Typ 31.3 59 0.0013 22.9 3.0 33 18-50 11-47 (186)
103 PRK13833 conjugal transfer pro 31.2 56 0.0012 26.0 3.1 33 20-52 132-168 (323)
104 TIGR02667 moaB_proteo molybden 31.1 48 0.001 23.5 2.5 22 22-43 52-75 (163)
105 cd02812 PcrB_like PcrB_like pr 31.0 42 0.00091 25.4 2.2 18 25-42 17-35 (219)
106 PLN02653 GDP-mannose 4,6-dehyd 30.9 24 0.00052 26.8 0.9 21 31-51 5-25 (340)
107 PF03943 TAP_C: TAP C-terminal 30.9 8.5 0.00018 22.6 -1.2 25 11-35 22-46 (51)
108 PRK13946 shikimate kinase; Pro 30.8 62 0.0013 22.8 3.0 31 13-44 61-91 (184)
109 cd04254 AAK_UMPK-PyrH-Ec UMP k 30.8 47 0.001 24.5 2.5 21 22-42 110-130 (231)
110 TIGR00381 cdhD CO dehydrogenas 30.4 50 0.0011 27.4 2.7 24 18-41 173-196 (389)
111 cd01886 EF-G Elongation factor 30.2 62 0.0014 24.7 3.1 42 11-52 219-263 (270)
112 COG1735 Php Predicted metal-de 30.1 14 0.00031 29.8 -0.4 16 35-50 89-104 (316)
113 cd04261 AAK_AKii-LysC-BS AAK_A 30.1 1E+02 0.0022 22.8 4.2 32 19-50 18-50 (239)
114 cd00311 TIM Triosephosphate is 30.1 77 0.0017 24.2 3.6 25 19-43 179-209 (242)
115 TIGR03676 aRF1/eRF1 peptide ch 29.7 92 0.002 25.5 4.1 35 16-50 188-226 (403)
116 PF00186 DHFR_1: Dihydrofolate 29.4 55 0.0012 23.3 2.5 30 20-49 79-108 (161)
117 PRK14822 nucleoside-triphospha 29.2 24 0.00052 26.2 0.7 34 17-51 47-80 (200)
118 PRK07823 5'-methylthioadenosin 29.1 20 0.00044 27.8 0.3 10 36-45 9-18 (264)
119 TIGR01697 PNPH-PUNA-XAPA inosi 29.1 20 0.00044 27.0 0.2 10 36-45 3-12 (248)
120 PLN02583 cinnamoyl-CoA reducta 29.0 30 0.00066 26.0 1.2 21 31-51 5-25 (297)
121 cd05637 SIS_PGI_PMI_2 The memb 29.0 57 0.0012 22.4 2.5 21 22-45 4-24 (132)
122 PF01370 Epimerase: NAD depend 28.9 27 0.00058 24.4 0.8 17 36-52 2-18 (236)
123 PRK00042 tpiA triosephosphate 28.8 92 0.002 23.9 3.8 26 19-44 183-214 (250)
124 PRK05835 fructose-bisphosphate 28.8 68 0.0015 25.6 3.2 19 24-42 195-214 (307)
125 PRK09417 mogA molybdenum cofac 28.6 52 0.0011 24.3 2.4 22 22-43 55-78 (193)
126 PRK00120 dITP/XTP pyrophosphat 28.5 29 0.00062 25.7 1.0 33 17-49 45-77 (196)
127 PF03018 Dirigent: Dirigent-li 28.4 23 0.00051 24.8 0.4 16 36-53 106-121 (144)
128 PRK14821 putative deoxyribonuc 28.3 44 0.00094 24.4 1.9 34 17-51 42-75 (184)
129 TIGR00042 non-canonical purine 28.3 30 0.00064 25.3 1.0 33 17-49 42-74 (184)
130 PF01113 DapB_N: Dihydrodipico 28.2 58 0.0013 21.7 2.4 26 19-45 78-103 (124)
131 PRK05057 aroK shikimate kinase 28.2 96 0.0021 21.7 3.6 31 13-43 55-85 (172)
132 TIGR01491 HAD-SF-IB-PSPlk HAD- 27.7 1E+02 0.0023 21.1 3.7 34 19-52 83-117 (201)
133 PRK13894 conjugal transfer ATP 27.7 68 0.0015 25.3 3.0 33 20-52 136-172 (319)
134 cd04168 TetM_like Tet(M)-like 27.7 75 0.0016 23.6 3.1 42 11-52 186-230 (237)
135 COG2704 DcuB Anaerobic C4-dica 27.6 50 0.0011 27.7 2.3 64 36-99 25-89 (436)
136 TIGR03702 lip_kinase_YegS lipi 27.6 80 0.0017 24.0 3.3 35 18-53 38-73 (293)
137 cd03813 GT1_like_3 This family 27.6 36 0.00078 27.5 1.5 23 30-52 6-28 (475)
138 PRK15016 isochorismate synthas 27.6 74 0.0016 26.2 3.3 28 15-42 51-79 (391)
139 cd07044 CofD_YvcK Family of Co 27.6 38 0.00082 26.9 1.5 18 34-53 1-18 (309)
140 TIGR00761 argB acetylglutamate 27.5 1.4E+02 0.0031 21.8 4.5 35 19-53 16-50 (231)
141 cd07995 TPK Thiamine pyrophosp 27.3 73 0.0016 23.2 2.9 34 19-52 77-111 (208)
142 TIGR01472 gmd GDP-mannose 4,6- 26.8 30 0.00064 26.4 0.8 17 34-50 2-18 (343)
143 TIGR01579 MiaB-like-C MiaB-lik 26.8 79 0.0017 25.3 3.3 24 19-42 50-74 (414)
144 PLN02954 phosphoserine phospha 26.7 1E+02 0.0022 21.8 3.5 35 19-53 87-122 (224)
145 PF13458 Peripla_BP_6: Peripla 26.6 1.1E+02 0.0024 22.5 3.9 44 7-50 43-87 (343)
146 PF00437 T2SE: Type II/IV secr 26.5 43 0.00093 24.8 1.6 35 19-53 114-152 (270)
147 COG0549 ArcC Carbamate kinase 26.4 58 0.0013 26.3 2.4 22 22-43 174-195 (312)
148 PRK08931 5'-methylthioadenosin 26.4 22 0.00047 28.1 -0.0 9 36-44 7-15 (289)
149 COG0521 MoaB Molybdopterin bio 26.4 59 0.0013 23.9 2.3 21 23-43 58-79 (169)
150 PF00696 AA_kinase: Amino acid 26.2 1.7E+02 0.0036 21.0 4.7 35 19-53 20-54 (242)
151 cd00717 URO-D Uroporphyrinogen 26.2 1.4E+02 0.0031 23.0 4.5 35 16-50 212-249 (335)
152 PLN02896 cinnamyl-alcohol dehy 26.1 37 0.0008 26.0 1.2 23 30-52 8-30 (353)
153 TIGR03199 pucC xanthine dehydr 26.1 1E+02 0.0022 23.4 3.6 27 18-47 4-30 (264)
154 PF00270 DEAD: DEAD/DEAH box h 26.1 71 0.0015 21.1 2.5 19 23-42 6-24 (169)
155 PRK13337 putative lipid kinase 26.1 80 0.0017 24.1 3.1 35 18-53 43-78 (304)
156 TIGR01490 HAD-SF-IB-hyp1 HAD-s 26.1 1.3E+02 0.0029 20.8 4.0 34 19-52 90-124 (202)
157 cd07186 CofD_like LPPG:FO 2-ph 26.0 43 0.00093 26.8 1.6 17 35-53 2-18 (303)
158 TIGR03589 PseB UDP-N-acetylglu 26.0 37 0.00079 26.0 1.2 21 31-51 3-23 (324)
159 PRK07315 fructose-bisphosphate 26.0 54 0.0012 25.7 2.1 22 24-45 192-215 (293)
160 PRK08309 short chain dehydroge 25.8 38 0.00082 24.3 1.2 17 35-52 3-19 (177)
161 PF06506 PrpR_N: Propionate ca 25.8 1.4E+02 0.0031 20.9 4.2 35 18-53 111-145 (176)
162 PF08599 Nbs1_C: DNA damage re 25.7 42 0.00091 21.1 1.2 15 31-45 15-29 (65)
163 PRK05717 oxidoreductase; Valid 25.6 38 0.00083 24.4 1.2 23 30-52 8-30 (255)
164 PRK03670 competence damage-ind 25.6 73 0.0016 24.4 2.8 22 22-43 50-72 (252)
165 PTZ00333 triosephosphate isome 25.6 76 0.0017 24.4 2.9 13 32-44 206-218 (255)
166 TIGR00338 serB phosphoserine p 25.5 1.2E+02 0.0025 21.4 3.7 34 19-52 88-122 (219)
167 cd04246 AAK_AK-DapG-like AAK_A 25.5 1.4E+02 0.003 22.0 4.2 32 20-51 19-51 (239)
168 PLN02240 UDP-glucose 4-epimera 25.4 39 0.00084 25.5 1.2 20 32-51 5-24 (352)
169 PLN02214 cinnamoyl-CoA reducta 25.4 41 0.00088 25.9 1.3 21 31-51 9-29 (342)
170 PF11997 DUF3492: Domain of un 25.4 39 0.00085 26.0 1.2 23 30-52 7-29 (268)
171 PRK06806 fructose-bisphosphate 25.3 59 0.0013 25.3 2.2 25 23-47 190-215 (281)
172 KOG3148|consensus 25.1 84 0.0018 24.3 3.0 25 19-43 116-140 (273)
173 COG2331 Uncharacterized protei 24.9 20 0.00044 23.5 -0.4 15 32-46 48-62 (82)
174 PLN02206 UDP-glucuronate decar 24.9 38 0.00083 27.6 1.2 22 30-51 117-138 (442)
175 PF08672 APC2: Anaphase promot 24.9 89 0.0019 18.9 2.5 29 12-41 29-57 (60)
176 PLN02695 GDP-D-mannose-3',5'-e 24.7 40 0.00086 26.4 1.2 22 30-51 19-40 (370)
177 PLN02686 cinnamoyl-CoA reducta 24.6 45 0.00098 26.1 1.5 23 30-52 51-73 (367)
178 COG2185 Sbm Methylmalonyl-CoA 24.6 1.1E+02 0.0023 22.0 3.2 23 18-40 77-101 (143)
179 cd00537 MTHFR Methylenetetrahy 24.6 78 0.0017 23.8 2.7 38 17-55 171-216 (274)
180 COG0560 SerB Phosphoserine pho 24.5 1.1E+02 0.0025 22.4 3.6 34 20-53 81-115 (212)
181 PRK14567 triosephosphate isome 24.5 1.1E+02 0.0023 23.8 3.5 24 19-42 182-211 (253)
182 cd07187 YvcK_like family of mo 24.5 47 0.001 26.4 1.5 17 35-53 2-18 (308)
183 PF10432 bact-PGI_C: Bacterial 24.4 67 0.0015 22.6 2.2 25 18-45 5-29 (155)
184 PF06995 Phage_P2_GpU: Phage P 24.4 73 0.0016 21.3 2.3 33 12-44 50-84 (121)
185 PRK09136 5'-methylthioadenosin 24.3 27 0.00059 26.6 0.2 10 36-45 3-12 (245)
186 PLN02778 3,5-epimerase/4-reduc 24.3 41 0.00089 25.5 1.2 19 33-51 10-28 (298)
187 PRK13606 LPPG:FO 2-phospho-L-l 24.2 43 0.00093 26.8 1.3 19 33-53 2-20 (303)
188 TIGR03471 HpnJ hopanoid biosyn 24.2 76 0.0016 25.9 2.8 33 16-48 79-115 (472)
189 PRK13582 thrH phosphoserine ph 24.2 1.7E+02 0.0036 20.3 4.2 34 20-53 72-105 (205)
190 COG1687 AzlD Predicted branche 24.1 47 0.001 22.8 1.3 21 25-45 79-99 (106)
191 cd03052 GST_N_GDAP1 GST_N fami 24.1 34 0.00075 20.6 0.6 17 25-41 43-60 (73)
192 CHL00202 argB acetylglutamate 24.0 1.3E+02 0.0027 23.2 3.8 34 20-53 43-76 (284)
193 PRK11150 rfaD ADP-L-glycero-D- 24.0 40 0.00088 25.0 1.1 16 35-50 2-17 (308)
194 KOG1430|consensus 24.0 62 0.0013 26.4 2.2 22 31-52 3-24 (361)
195 COG1564 THI80 Thiamine pyropho 23.9 82 0.0018 23.9 2.7 35 19-53 78-113 (212)
196 PRK00131 aroK shikimate kinase 23.9 1.4E+02 0.0031 19.8 3.7 31 14-44 56-86 (175)
197 smart00463 SMR Small MutS-rela 23.9 69 0.0015 19.5 2.0 30 10-39 3-39 (80)
198 TIGR03407 urea_ABC_UrtA urea A 23.8 62 0.0013 24.9 2.1 40 7-46 42-81 (359)
199 TIGR01463 mtaA_cmuA methyltran 23.8 1.5E+02 0.0033 22.8 4.3 35 16-50 217-253 (340)
200 cd04724 Tryptophan_synthase_al 23.6 67 0.0014 24.1 2.2 22 19-40 173-194 (242)
201 PF15569 Imm21: Immunity prote 23.6 76 0.0017 21.2 2.2 24 15-39 11-34 (91)
202 PRK08264 short chain dehydroge 23.5 46 0.00099 23.5 1.2 21 31-51 5-25 (238)
203 TIGR01859 fruc_bis_ald_ fructo 23.5 54 0.0012 25.5 1.7 24 24-47 191-215 (282)
204 PRK12938 acetyacetyl-CoA reduc 23.5 45 0.00098 23.7 1.2 22 31-52 2-23 (246)
205 COG1134 TagH ABC-type polysacc 23.3 1.9E+02 0.004 22.7 4.6 38 14-51 179-216 (249)
206 PRK04011 peptide chain release 23.2 1.5E+02 0.0032 24.4 4.2 35 16-50 196-234 (411)
207 cd06344 PBP1_ABC_ligand_bindin 23.1 64 0.0014 24.2 2.0 36 8-43 41-76 (332)
208 PF06351 Allene_ox_cyc: Allene 23.0 22 0.00047 26.3 -0.5 12 34-45 103-114 (176)
209 PRK14565 triosephosphate isome 23.0 96 0.0021 23.8 2.9 27 18-44 173-200 (237)
210 PF12775 AAA_7: P-loop contain 22.9 74 0.0016 24.4 2.3 33 20-52 21-57 (272)
211 PF01933 UPF0052: Uncharacteri 22.9 58 0.0013 25.7 1.8 18 34-53 1-18 (300)
212 PF02798 GST_N: Glutathione S- 22.8 63 0.0014 19.4 1.6 19 23-41 41-60 (76)
213 TIGR03263 guanyl_kin guanylate 22.8 67 0.0014 22.0 1.9 29 22-50 81-112 (180)
214 PF08841 DDR: Diol dehydratase 22.8 38 0.00083 27.4 0.8 33 13-45 252-289 (332)
215 COG0127 Xanthosine triphosphat 22.8 58 0.0013 24.4 1.7 59 15-75 45-109 (194)
216 TIGR03819 heli_sec_ATPase heli 22.8 96 0.0021 24.7 3.0 32 19-50 165-200 (340)
217 PF01116 F_bP_aldolase: Fructo 22.7 50 0.0011 25.8 1.4 31 23-53 194-230 (287)
218 cd04255 AAK_UMPK-MosAB AAK_UMP 22.7 58 0.0013 25.0 1.7 19 24-42 127-145 (262)
219 PRK14557 pyrH uridylate kinase 22.6 75 0.0016 24.2 2.3 17 26-42 119-135 (247)
220 TIGR02788 VirB11 P-type DNA tr 22.6 92 0.002 24.1 2.8 30 21-50 133-166 (308)
221 PRK07432 5'-methylthioadenosin 22.5 29 0.00063 27.4 0.0 15 36-50 7-21 (290)
222 PF02219 MTHFR: Methylenetetra 22.3 1E+02 0.0022 23.6 3.0 39 16-55 182-228 (287)
223 TIGR02026 BchE magnesium-proto 22.3 94 0.002 25.7 3.0 27 16-42 74-101 (497)
224 PF10743 Phage_Cox: Regulatory 22.3 78 0.0017 21.0 2.0 16 22-37 26-41 (87)
225 COG0543 UbiB 2-polyprenylpheno 22.3 68 0.0015 24.1 2.0 20 34-53 110-130 (252)
226 cd06356 PBP1_Amide_Urea_BP_lik 22.2 72 0.0016 24.1 2.1 38 8-45 42-79 (334)
227 KOG1324|consensus 22.2 64 0.0014 24.3 1.8 20 33-52 111-130 (190)
228 COG0262 FolA Dihydrofolate red 22.2 1.4E+02 0.0029 21.2 3.4 33 20-52 82-115 (167)
229 cd04252 AAK_NAGK-fArgBP AAK_NA 22.1 2.1E+02 0.0045 21.4 4.6 35 20-54 16-50 (248)
230 PRK13055 putative lipid kinase 22.1 1.2E+02 0.0025 23.7 3.3 34 19-53 46-80 (334)
231 KOG3974|consensus 22.1 86 0.0019 25.2 2.6 36 11-47 111-146 (306)
232 cd02572 PseudoU_synth_hDyskeri 22.0 40 0.00086 24.7 0.7 17 37-53 130-146 (182)
233 PRK06923 isochorismate synthas 22.0 1.1E+02 0.0024 25.2 3.3 25 16-40 49-74 (399)
234 PRK10769 folA dihydrofolate re 21.8 1.4E+02 0.003 21.2 3.4 28 20-48 77-104 (159)
235 TIGR00725 conserved hypothetic 21.8 1.5E+02 0.0033 20.9 3.7 37 14-51 13-49 (159)
236 PRK03673 hypothetical protein; 21.7 89 0.0019 25.7 2.7 24 20-43 49-72 (396)
237 PRK09334 30S ribosomal protein 21.6 1.4E+02 0.003 19.7 3.1 27 18-44 55-81 (86)
238 TIGR02075 pyrH_bact uridylate 21.6 89 0.0019 23.1 2.5 20 22-41 111-130 (233)
239 PLN02427 UDP-apiose/xylose syn 21.5 47 0.001 25.8 1.0 16 34-49 16-31 (386)
240 TIGR02082 metH 5-methyltetrahy 21.4 93 0.002 29.2 3.0 26 18-43 797-823 (1178)
241 TIGR01489 DKMTPPase-SF 2,3-dik 21.4 1.9E+02 0.0041 19.4 4.0 33 20-52 76-109 (188)
242 PRK08945 putative oxoacyl-(acy 21.3 53 0.0012 23.4 1.2 21 31-51 11-31 (247)
243 TIGR01826 CofD_related conserv 21.1 62 0.0014 25.8 1.6 18 34-53 1-18 (310)
244 PRK07276 DNA polymerase III su 21.0 1.1E+02 0.0024 24.0 3.0 28 18-45 7-37 (290)
245 PLN02725 GDP-4-keto-6-deoxyman 20.9 29 0.00063 25.5 -0.3 16 36-51 1-16 (306)
246 PRK12935 acetoacetyl-CoA reduc 20.8 55 0.0012 23.2 1.2 21 31-51 5-25 (247)
247 PRK11914 diacylglycerol kinase 20.8 1.9E+02 0.0042 21.9 4.3 35 18-53 50-85 (306)
248 PRK09135 pteridine reductase; 20.7 56 0.0012 22.9 1.2 22 31-52 5-26 (249)
249 PLN02561 triosephosphate isome 20.7 1.4E+02 0.0031 23.0 3.5 13 32-44 203-215 (253)
250 TIGR00089 RNA modification enz 20.6 1.3E+02 0.0028 24.2 3.4 26 18-43 52-79 (429)
251 COG0451 WcaG Nucleoside-diphos 20.6 45 0.00097 24.4 0.7 16 35-50 3-18 (314)
252 cd01917 ACS_2 Acetyl-CoA synth 20.5 1.3E+02 0.0028 24.0 3.3 30 18-47 140-169 (287)
253 PRK14825 putative deoxyribonuc 20.5 63 0.0014 23.9 1.5 34 17-51 43-78 (199)
254 PLN02986 cinnamyl-alcohol dehy 20.5 83 0.0018 23.5 2.2 22 31-52 4-25 (322)
255 PF01872 RibD_C: RibD C-termin 20.5 2E+02 0.0044 20.2 4.1 31 20-50 122-152 (200)
256 PF07005 DUF1537: Protein of u 20.4 83 0.0018 22.7 2.1 33 19-52 44-76 (223)
257 KOG0867|consensus 20.3 26 0.00057 25.9 -0.6 19 25-44 45-63 (226)
258 cd06183 cyt_b5_reduct_like Cyt 20.3 67 0.0015 22.8 1.6 22 32-53 105-127 (234)
259 PRK04302 triosephosphate isome 20.3 1.4E+02 0.003 21.9 3.2 24 19-42 158-182 (223)
260 PRK08125 bifunctional UDP-gluc 20.3 58 0.0012 27.8 1.4 21 30-50 313-333 (660)
261 cd03465 URO-D_like The URO-D _ 20.2 2.8E+02 0.006 21.0 5.0 36 15-50 204-241 (330)
262 PF14399 Transpep_BrtH: NlpC/p 20.0 89 0.0019 23.5 2.2 28 18-46 74-101 (317)
263 COG0391 Uncharacterized conser 20.0 50 0.0011 26.6 0.9 21 31-53 7-27 (323)
264 PRK07774 short chain dehydroge 20.0 60 0.0013 23.0 1.3 22 31-52 5-26 (250)
265 PRK07998 gatY putative fructos 20.0 80 0.0017 24.8 2.0 30 23-52 189-223 (283)
No 1
>PF01715 IPPT: IPP transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) [].; GO: 0005524 ATP binding, 0008033 tRNA processing; PDB: 2ZXU_A 3FOZ_A 2ZM5_B 3D3Q_A 3EXA_B 2QGN_A 3A8T_A 3EPK_B 3EPH_A 3EPJ_A ....
Probab=99.86 E-value=1.8e-22 Score=153.73 Aligned_cols=75 Identities=35% Similarity=0.432 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccCCCCCCCcc-----------cchHhHHHHHhhcchhhchhhh
Q psy17228 16 WTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNIND-----------QGEFTLYDMDKIRNLEHGRDVL 84 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~~~~~~~~~-----------~~~~~l~~~l~~~d~e~~~~~p 84 (99)
-|+++|.++|++|+++|++||||||||||++||++|+. +.|+.++. .|...+|+.|..+| |
T Consensus 40 ~f~~~a~~~i~~i~~rgk~PIlvGGTglYi~all~g~~-~~p~~~~~~r~~~~~~~~~~~~~~l~~~L~~~D-------P 111 (253)
T PF01715_consen 40 DFQRDAREAIEDILARGKIPILVGGTGLYIQALLNGLA-DIPEVDPELRAELRAELEEEGNEELYEELKEVD-------P 111 (253)
T ss_dssp HHHHHHHHHHHHHHHTT-EEEEEES-HHHHHHHHCTS---TSSSHHHHHHHHHHHHHHSCHHHHHHHHHHC--------H
T ss_pred HHHHHHHHHHHHHHhcCCeEEEECChHHHHHHHHhChh-hhccccHHHHHHHHHHHHhccHHHHHHHHHhhC-------c
Confidence 46689999999999999999999999999999999986 22333222 36778999999999 9
Q ss_pred HHhhccCCCCCCCC
Q psy17228 85 ESLWKLDMNYSYRI 98 (99)
Q Consensus 85 ~~A~rI~pnD~~RI 98 (99)
++|++|||||++||
T Consensus 112 ~~A~~i~~nd~~Ri 125 (253)
T PF01715_consen 112 EAAAKIHPNDRRRI 125 (253)
T ss_dssp HHHCTS-TT-HHHH
T ss_pred HhhhcCCCCcHHHH
Confidence 99999999999997
No 2
>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional
Probab=99.84 E-value=1.9e-21 Score=151.91 Aligned_cols=75 Identities=24% Similarity=0.347 Sum_probs=64.1
Q ss_pred HHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccCCCCCCCcc-----------cchHhHHHHHhhcchhhchhhh
Q psy17228 16 WTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNIND-----------QGEFTLYDMDKIRNLEHGRDVL 84 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~~~~~~~~~-----------~~~~~l~~~l~~~d~e~~~~~p 84 (99)
.|+++|.++|++|+++|++||||||||||++||++|+.. .|+.++. .|...+|++|..+| |
T Consensus 76 ~f~~~a~~~i~~i~~~gk~PilvGGTglYi~all~gl~~-~p~~~~~~r~~~~~~~~~~g~~~l~~~L~~~D-------P 147 (300)
T PRK14729 76 IFYKEALKIIKELRQQKKIPIFVGGSAFYFKHLKYGLPS-TPPVSSKIRIYVNNLFTLKGKSYLLEELKRVD-------F 147 (300)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEeCchHHHHHHHcCCCC-CCCCCHHHHHHHHHHHHhcCHHHHHHHHHhcC-------H
Confidence 467999999999999999999999999999999999863 2333321 35667899999999 9
Q ss_pred HHhhccCCCCCCCC
Q psy17228 85 ESLWKLDMNYSYRI 98 (99)
Q Consensus 85 ~~A~rI~pnD~~RI 98 (99)
++|++|||||++||
T Consensus 148 ~~A~~i~pnd~~Ri 161 (300)
T PRK14729 148 IRYESINKNDIYRI 161 (300)
T ss_pred HHHhhCCcCCHHHH
Confidence 99999999999997
No 3
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=99.82 E-value=1.2e-20 Score=148.10 Aligned_cols=75 Identities=33% Similarity=0.374 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhccc-CCCCCCCc---------ccchHhHHHHHhhcchhhchhhhHH
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTIL-LDNKTNIN---------DQGEFTLYDMDKIRNLEHGRDVLES 86 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~-~~~~~~~~---------~~~~~~l~~~l~~~d~e~~~~~p~~ 86 (99)
|.++|...|++|.++||+|||||||||||+||++|++ +|..+... ..|...||++|...| |++
T Consensus 77 f~~~a~~~i~~i~~rgk~pIlVGGTglY~~aL~~g~~~~p~~~~~~r~~~~~~~~~~g~~~L~~~L~~~D-------p~~ 149 (308)
T COG0324 77 FQRDALAAIDDILARGKLPILVGGTGLYLKALLEGLSLLPEADPEVRRRLEAELAELGNDALHAELKKID-------PEA 149 (308)
T ss_pred HHHHHHHHHHHHHhCCCCcEEEccHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHhcCHHHHHHHHHhhC-------HHH
Confidence 6789999999999999999999999999999999987 33222111 235678899999999 999
Q ss_pred hhccCCCCCCCC
Q psy17228 87 LWKLDMNYSYRI 98 (99)
Q Consensus 87 A~rI~pnD~~RI 98 (99)
|++|||||++|+
T Consensus 150 a~~i~pnD~~Ri 161 (308)
T COG0324 150 AAKIHPNDPQRI 161 (308)
T ss_pred HHhcCCCchhHH
Confidence 999999999997
No 4
>TIGR00174 miaA tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.
Probab=99.81 E-value=3.1e-20 Score=144.33 Aligned_cols=75 Identities=29% Similarity=0.336 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccCCCCCCCc-----------ccchHhHHHHHhhcchhhchhhh
Q psy17228 16 WTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNIN-----------DQGEFTLYDMDKIRNLEHGRDVL 84 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~~~~~~~~-----------~~~~~~l~~~l~~~d~e~~~~~p 84 (99)
-|..+|.++|++++++|++|||||||||||+||++|+.. .|+.++ ..|.+.+|++|..+| |
T Consensus 72 ~f~~~a~~~i~~~~~~g~~pi~vGGTg~Yi~all~g~~~-~p~~~~~~r~~l~~~~~~~g~~~l~~~L~~~D-------P 143 (287)
T TIGR00174 72 DFQTLALNAIADITARGKIPLLVGGTGLYLKALLEGLSP-TPSADKLIREQLEILAEEQGWDFLYNELKKVD-------P 143 (287)
T ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCcHHHHHHHHcCCCC-CCCCCHHHHHHHHHHHHHcCHHHHHHHHHhcC-------H
Confidence 356899999999999999999999999999999999862 233322 135677899999999 9
Q ss_pred HHhhccCCCCCCCC
Q psy17228 85 ESLWKLDMNYSYRI 98 (99)
Q Consensus 85 ~~A~rI~pnD~~RI 98 (99)
++|++|||||++||
T Consensus 144 ~~a~~i~~nd~~Ri 157 (287)
T TIGR00174 144 VAAAKIHPNDTRRV 157 (287)
T ss_pred HHHHhcCCccHHHH
Confidence 99999999999997
No 5
>PLN02748 tRNA dimethylallyltransferase
Probab=99.80 E-value=6.7e-20 Score=150.36 Aligned_cols=75 Identities=32% Similarity=0.476 Sum_probs=61.7
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccCCC-CCCC--------c-------------ccchHhHHHHHhh
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILLDN-KTNI--------N-------------DQGEFTLYDMDKI 74 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~~~-~~~~--------~-------------~~~~~~l~~~l~~ 74 (99)
|.++|..+|++|+++|++|||||||||||+||++|+.++. |+.. + ..+...+|++|..
T Consensus 96 F~~~A~~~I~~I~~rgk~PIlVGGTglYi~aLl~g~~~~~~p~~~~~~~~~~~~~~r~~l~~~~~~~~~g~~~l~~~L~~ 175 (468)
T PLN02748 96 FRDHAVPLIEEILSRNGLPVIVGGTNYYIQALVSPFLLDDMAEETEDCTFVVASVLDEHMDVESGLGNDDEDHGYELLKE 175 (468)
T ss_pred HHHHHHHHHHHHHhcCCCeEEEcChHHHHHHHHcCcccccCCccccccccccCHHHHHHHHHHHHHHhcCHHHHHHHHHh
Confidence 5689999999999999999999999999999999986421 1111 0 1244568888999
Q ss_pred cchhhchhhhHHhhccCCCCCCCC
Q psy17228 75 RNLEHGRDVLESLWKLDMNYSYRI 98 (99)
Q Consensus 75 ~d~e~~~~~p~~A~rI~pnD~~RI 98 (99)
+| |++|++|||||++||
T Consensus 176 vD-------P~~A~rihpnD~rRI 192 (468)
T PLN02748 176 LD-------PVAANRIHPNNHRKI 192 (468)
T ss_pred hC-------HHHHhhcCCccHHHH
Confidence 99 999999999999997
No 6
>PLN02840 tRNA dimethylallyltransferase
Probab=99.77 E-value=3.6e-19 Score=144.57 Aligned_cols=74 Identities=20% Similarity=0.248 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccCCCCCCCccc---------------chHhHHHHH-hhcchhh
Q psy17228 16 WTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNINDQ---------------GEFTLYDMD-KIRNLEH 79 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~~~~~~~~~~---------------~~~~l~~~l-~~~d~e~ 79 (99)
-|+++|.++|++|+++|++|||||||||||+||++|+.. .|+.++.. +...++++| +..|
T Consensus 94 ~F~~~A~~~I~~i~~rgkiPIvVGGTGlYl~aLl~G~~~-~p~~~~~~r~~l~~~l~~~~~~~g~~~l~~~Ll~~~D--- 169 (421)
T PLN02840 94 AFFDDARRATQDILNRGRVPIVAGGTGLYLRWYIYGKPD-VPKSSPEITSEVWSELVDFQKNGDWDAAVELVVNAGD--- 169 (421)
T ss_pred HHHHHHHHHHHHHHhcCCCEEEEcCccHHHHHHhcCCCC-CCCCCHHHHHHHHHHHHHhccccCHHHHHHHHHhccC---
Confidence 467899999999999999999999999999999999862 23322221 134455553 3456
Q ss_pred chhhhHHhhccCCCCCCCC
Q psy17228 80 GRDVLESLWKLDMNYSYRI 98 (99)
Q Consensus 80 ~~~~p~~A~rI~pnD~~RI 98 (99)
| +|++|||||++||
T Consensus 170 ----P-~A~~i~pnD~~Ri 183 (421)
T PLN02840 170 ----P-KARSLPRNDWYRL 183 (421)
T ss_pred ----c-HHHhcCCCcHHHH
Confidence 8 9999999999997
No 7
>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
Probab=99.74 E-value=5.4e-18 Score=132.57 Aligned_cols=75 Identities=29% Similarity=0.275 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccCCCCCCCcc-----------cchHhHHHHHhhcchhhchhhh
Q psy17228 16 WTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNIND-----------QGEFTLYDMDKIRNLEHGRDVL 84 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~~~~~~~~~-----------~~~~~l~~~l~~~d~e~~~~~p 84 (99)
-|.++|.+.|++++++|++||||||||||++||++|+. ..|+.++. .|...+|+.|..+| |
T Consensus 77 ~f~~~a~~~i~~i~~~gk~pIlvGGt~~Y~~al~~g~~-~~p~~~~~~r~~l~~~~~~~g~~~l~~~L~~~D-------p 148 (307)
T PRK00091 77 DFQRDALAAIADILARGKLPILVGGTGLYIKALLEGLS-PLPPADPELRAELEALAAEEGWEALHAELAEID-------P 148 (307)
T ss_pred HHHHHHHHHHHHHHhCCCCEEEECcHHHHHHHhccCCC-CCCCCCHHHHHHHHHHHHhcCHHHHHHHHHhcC-------H
Confidence 57789999999999999999999999999999999976 33444332 35677899999999 9
Q ss_pred HHhhccCCCCCCCC
Q psy17228 85 ESLWKLDMNYSYRI 98 (99)
Q Consensus 85 ~~A~rI~pnD~~RI 98 (99)
++|++|||||++||
T Consensus 149 ~~a~~i~~~d~~Ri 162 (307)
T PRK00091 149 EAAARIHPNDPQRI 162 (307)
T ss_pred HHHhhcCCCCCchh
Confidence 99999999999998
No 8
>PLN02165 adenylate isopentenyltransferase
Probab=99.00 E-value=5.1e-10 Score=89.12 Aligned_cols=39 Identities=33% Similarity=0.525 Sum_probs=36.4
Q ss_pred hHHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhccc
Q psy17228 15 KWTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 15 ~~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~ 53 (99)
..|.++|..+|++|+++|++||+||||||||+||++|+.
T Consensus 116 ~~F~~~a~~~I~~i~~~~~~PI~vGGTglYi~aLl~g~~ 154 (334)
T PLN02165 116 SEFRSLASLSISEITSRQKLPIVAGGSNSFIHALLADRF 154 (334)
T ss_pred HHHHHHHHHHHHHHHHCCCcEEEECChHHHHHHHHcCCC
Confidence 567889999999999999999999999999999999964
No 9
>KOG1384|consensus
Probab=98.75 E-value=9.4e-09 Score=82.15 Aligned_cols=35 Identities=37% Similarity=0.633 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhc
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g 51 (99)
|..+|...|++|++||++|||||||++|++||+.+
T Consensus 81 F~~~a~~aie~I~~rgk~PIv~GGs~~yi~al~~~ 115 (348)
T KOG1384|consen 81 FEDDASRAIEEIHSRGKLPIVVGGSNSYLQALLSK 115 (348)
T ss_pred HHHHHHHHHHHHHhCCCCCEEeCCchhhHHHHhhc
Confidence 66899999999999999999999999999999999
No 10
>COG2069 CdhD CO dehydrogenase/acetyl-CoA synthase delta subunit (corrinoid Fe-S protein) [Energy production and conversion]
Probab=93.16 E-value=0.085 Score=42.73 Aligned_cols=25 Identities=40% Similarity=0.732 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccH
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTg 42 (99)
.++|.+.++++++.=++||++||||
T Consensus 184 ~~EAak~lEdvLqAVdvPiiiGGSG 208 (403)
T COG2069 184 AKEAAKTLEDVLQAVDVPIIIGGSG 208 (403)
T ss_pred HHHHHHHHHHHHHhcCcCEEecCCC
Confidence 5789999999999999999999998
No 11
>cd04235 AAK_CK AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an essential precursor of arginine and pyrimidine bases, in the presence of ATP, bicarbonate, and ammonia. CK is a homodimer of 33 kDa subunits and is a member of the Amino Acid Kinase Superfamily (AAK).
Probab=78.40 E-value=1.9 Score=34.32 Aligned_cols=21 Identities=19% Similarity=0.396 Sum_probs=17.8
Q ss_pred HHHHHHHhcCCceEEEcccHH
Q psy17228 23 TKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 23 ~~i~~i~~~~~~pilVGGTgl 43 (99)
+.|+.++++|.+||++||+|-
T Consensus 172 ~~I~~Ll~~g~IpI~~GggGi 192 (308)
T cd04235 172 EAIKTLVDNGVIVIAAGGGGI 192 (308)
T ss_pred HHHHHHHHCCCEEEEECCCcc
Confidence 567788899999999999753
No 12
>PRK13775 formimidoylglutamase; Provisional
Probab=74.91 E-value=5.9 Score=31.22 Aligned_cols=36 Identities=17% Similarity=0.179 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
+.+...+.+.++.++|++||+.||-.----+.+.|+
T Consensus 108 ~~~~l~~~v~~~~~~g~~PivlGGdHsit~g~~~g~ 143 (328)
T PRK13775 108 LQNSLSKAIKRMCDLNLKPIVLGGGHETAYGHYLGL 143 (328)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEcCcHHHHHHHHHHH
Confidence 345667778889999999999999866555555553
No 13
>PF03464 eRF1_2: eRF1 domain 2; InterPro: IPR005141 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination ; PDB: 3AGK_A 2VGN_A 2VGM_A 3J16_A 3IZQ 3IR9_A 3OBW_A 3MCA_B 2QI2_A 3E1Y_D ....
Probab=74.22 E-value=5.3 Score=27.29 Aligned_cols=39 Identities=13% Similarity=0.158 Sum_probs=27.0
Q ss_pred chHHHHHHHHHHHH--HHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 14 TKWTIKLTKTKIDD--ILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 14 ~~~~~~~a~~~i~~--i~~~~~~pilVGGTglYi~all~g~ 52 (99)
+.||.+-+..+.+. .-...--+||+||.|++-+-+.+-+
T Consensus 53 ~~f~~~i~~~l~~~f~~~~~~~~~iIiaGPGf~k~~f~~~l 93 (133)
T PF03464_consen 53 EKFFKEIAEALKKYFLVNFDDVKCIIIAGPGFTKEEFYKYL 93 (133)
T ss_dssp HHHHHHHHHHHHHHCCCHTTTCSEEEEEESTTHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhhccccccEEEEECCHHHHHHHHHHH
Confidence 45666555555554 3345667999999999988887664
No 14
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=74.01 E-value=5.5 Score=30.42 Aligned_cols=22 Identities=32% Similarity=0.599 Sum_probs=16.9
Q ss_pred CCceEEE--cccHHHHHHHHhccc
Q psy17228 32 NKVPIIV--GGTNYYIESLLWTIL 53 (99)
Q Consensus 32 ~~~pilV--GGTglYi~all~g~~ 53 (99)
+.+|++| ||+-+||++|++|+.
T Consensus 88 ~di~fiVvSsGm~~fI~~lfe~iv 111 (220)
T COG4359 88 HDIPFIVVSSGMDPFIYPLFEGIV 111 (220)
T ss_pred cCCCEEEEeCCCchHHHHHHHhhc
Confidence 3344443 999999999999975
No 15
>PRK13776 formimidoylglutamase; Provisional
Probab=73.92 E-value=6.2 Score=31.01 Aligned_cols=34 Identities=21% Similarity=0.348 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
+...+.+.++.++|++||++||-.----+.+.|+
T Consensus 104 ~~i~~~v~~i~~~g~~Pi~lGGdHsit~g~~~a~ 137 (318)
T PRK13776 104 SRYAQRVHDLLDRGHLPIGLGGGHEIAWASFQGL 137 (318)
T ss_pred HHHHHHHHHHHhCCCeEEEEcCchHHHHHhHHHH
Confidence 4556677778899999999999866554555443
No 16
>TIGR01229 rocF_arginase arginase. This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase).
Probab=73.32 E-value=4.5 Score=31.33 Aligned_cols=33 Identities=12% Similarity=0.362 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHHHHHHHhc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglYi~all~g 51 (99)
+...+.+.++.++|++||+.||-.----+.+.|
T Consensus 70 ~~i~~~v~~~~~~g~~pi~lGGdHsi~~~~~~a 102 (300)
T TIGR01229 70 EQLAPKVYEVFEEGRFPLVLGGDHSIAIGTISG 102 (300)
T ss_pred HHHHHHHHHHHhCCCeeEEEcCcchhhhhhHHH
Confidence 455777888899999999999986544444444
No 17
>TIGR01227 hutG formimidoylglutamase. Formiminoglutamase, the fourth enzyme of histidine degradation, is similar to arginases and agmatinases. It is often encoded near other enzymes of the histidine degredation pathway: histidine ammonia-lyase, urocanate hydratase, and imidazolonepropionase.
Probab=72.76 E-value=6.6 Score=30.51 Aligned_cols=35 Identities=17% Similarity=0.311 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
.+...+.+.+++++|+.||+.||-..---+.+.++
T Consensus 97 ~~~i~~~v~~~~~~g~~Pi~lGGdHsit~~~~~al 131 (307)
T TIGR01227 97 QHEIAQTAAALLADHRVPVILGGGHSIAYATFAAL 131 (307)
T ss_pred HHHHHHHHHHHHhcCCeEEEECCcchhHHHHHHHH
Confidence 45667777889999999999999976554555553
No 18
>PRK13773 formimidoylglutamase; Provisional
Probab=72.52 E-value=7.2 Score=30.67 Aligned_cols=35 Identities=11% Similarity=0.256 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
.+...+.+.++.++|++||+.||-.----+.+.|+
T Consensus 105 ~~~i~~~v~~~~~~g~~PivLGGdHsit~g~~~a~ 139 (324)
T PRK13773 105 QERLGDAVSALLDAGHLPVVLGGGHETAFGSYLGV 139 (324)
T ss_pred HHHHHHHHHHHHHCCCeeEEECCchHHHHHhHHHH
Confidence 45566778888999999999999966555555553
No 19
>PRK13774 formimidoylglutamase; Provisional
Probab=72.50 E-value=7.5 Score=30.39 Aligned_cols=36 Identities=11% Similarity=0.089 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
+.+...+.+.++.++|++||+.||-.----..+.|+
T Consensus 105 ~~~~i~~~v~~i~~~g~~pivlGGdHsit~g~~~a~ 140 (311)
T PRK13774 105 TQKEFAMLAAKSIANHRQTFLLGGGHDIAYAQYLAT 140 (311)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEcCchHHHHHHHHHH
Confidence 345667778889999999999999866544555543
No 20
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=72.04 E-value=4.4 Score=29.50 Aligned_cols=25 Identities=28% Similarity=0.410 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHhcC---CceEEEcccHH
Q psy17228 19 KLTKTKIDDILQRN---KVPIIVGGTNY 43 (99)
Q Consensus 19 ~~a~~~i~~i~~~~---~~pilVGGTgl 43 (99)
..+.+.++.+.+.+ +++|+|||..+
T Consensus 148 ~~~~~~i~~lr~~~~~~~~~i~vGG~~~ 175 (201)
T cd02070 148 GGMKEVIEALKEAGLRDKVKVMVGGAPV 175 (201)
T ss_pred HHHHHHHHHHHHCCCCcCCeEEEECCcC
Confidence 45677777777776 68999999875
No 21
>PRK13772 formimidoylglutamase; Provisional
Probab=71.97 E-value=5 Score=31.41 Aligned_cols=33 Identities=12% Similarity=0.219 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHH
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLL 49 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all 49 (99)
..+...+.+.++.++|+.||+.||-.----+.+
T Consensus 101 ~~~~i~~~v~~~~~~g~~PivlGGdHsit~g~~ 133 (314)
T PRK13772 101 AQAALAEVVAEVLAAGARPLVLGGGHEVAWGTW 133 (314)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEcCchHHHHhhH
Confidence 445667788889999999999999855433333
No 22
>TIGR01230 agmatinase agmatinase. Note: a history of early misannotation of members of this family is detailed in PUBMED:10931887.
Probab=71.83 E-value=5.2 Score=30.58 Aligned_cols=36 Identities=14% Similarity=0.410 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
+.+...+.+.++.++|++||++||-..=--+++.++
T Consensus 78 ~~~~i~~~v~~~~~~~~~pi~lGGdHsis~~~i~al 113 (275)
T TIGR01230 78 MFEKIQEHAEEFLEEGKFPVAIGGEHSITLPVIRAM 113 (275)
T ss_pred HHHHHHHHHHHHHhcCCeEEEecCcchhhHHHHHHH
Confidence 445566677788899999999999865444454443
No 23
>TIGR01768 GGGP-family geranylgeranylglyceryl phosphate synthase family protein. This model represents a family of sequences including geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea. The clade of bacterial sequences may have the same function or a closely related function. This model supercedes TIGR00265, which has been retired.
Probab=71.52 E-value=2.5 Score=32.23 Aligned_cols=34 Identities=12% Similarity=0.146 Sum_probs=27.0
Q ss_pred hhcccchHHHHHHHHHHHHHHhcCCceEEEcccH
Q psy17228 9 LKLTKTKWTIKLTKTKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 9 ~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGGTg 42 (99)
.+||-++.....+.+.++.+.+.|.--|+||||-
T Consensus 4 ~liDPdK~~~~~~~~~~~~~~~~gtdai~vGGS~ 37 (223)
T TIGR01768 4 TLIDPDKTNPSEADEIAKAAAESGTDAILIGGSQ 37 (223)
T ss_pred eeECCCCCCccccHHHHHHHHhcCCCEEEEcCCC
Confidence 3566666655567778888888999999999997
No 24
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=71.40 E-value=5.3 Score=26.20 Aligned_cols=25 Identities=28% Similarity=0.626 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHhcC--CceEEEcccHH
Q psy17228 19 KLTKTKIDDILQRN--KVPIIVGGTNY 43 (99)
Q Consensus 19 ~~a~~~i~~i~~~~--~~pilVGGTgl 43 (99)
..+.++++.+.+.+ +++|++||..+
T Consensus 65 ~~~~~~i~~l~~~~~~~~~i~vGG~~~ 91 (119)
T cd02067 65 TLMKEVIEELKEAGLDDIPVLVGGAIV 91 (119)
T ss_pred HHHHHHHHHHHHcCCCCCeEEEECCCC
Confidence 56677777777775 58999999864
No 25
>PF00491 Arginase: Arginase family; InterPro: IPR006035 The ureohydrolase superfamily includes arginase (3.5.3.1 from EC), agmatinase (3.5.3.11 from EC), formiminoglutamase (3.5.3.8 from EC) and proclavaminate amidinohydrolase (3.5.3.22 from EC) []. These enzymes share a 3-layer alpha-beta-alpha structure [, , ], and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways. Arginase, which catalyses the conversion of arginine to urea and ornithine, is one of the five members of the urea cycle enzymes that convert ammonia to urea as the principal product of nitrogen excretion []. There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia. Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals. Formiminoglutamase catalyses the fourth step in histidine degradation, acting to hydrolyse N-formimidoyl-L-glutamate to L-glutamate and formamide. Proclavaminate amidinohydrolase is involved in clavulanic acid biosynthesis. Clavulanic acid acts as an inhibitor of a wide range of beta-lactamase enzymes that are used by various microorganisms to resist beta-lactam antibiotics. As a result, this enzyme improves the effectiveness of beta-lactamase antibiotics [].; GO: 0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines, 0046872 metal ion binding; PDB: 4DZ4_A 3SL0_A 3MMR_A 3SL1_A 2EF5_D 2EIV_K 2EF4_A 3NIO_F 3THH_A 1WVA_A ....
Probab=70.40 E-value=6.3 Score=29.69 Aligned_cols=36 Identities=14% Similarity=0.345 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
..+...+.+.++.++|..||+.||-..---+++.++
T Consensus 65 ~~~~l~~~v~~~~~~g~~pi~lGGdhsis~~~~~~l 100 (277)
T PF00491_consen 65 VFERLAEAVAEVLEAGAFPIVLGGDHSISYGTIAAL 100 (277)
T ss_dssp HHHHHHHHHHHHHHTTEEEEEEESSGGGHHHHHHHH
T ss_pred HHHHHHHHHHHhhcCCCEEEecCCCchhHHHhHHHH
Confidence 466778888889999999999999887666666664
No 26
>PF01884 PcrB: PcrB family; InterPro: IPR008205 This entry represents geranylgeranylglyceryl phosphate (GGGP) synthase, which is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. This entry also matches putative glycerol-1-phosphate prenyltransferases that may catalyse the transfer of a prenyl moiety to sn-glycerol-1-phosphate (G1P) []. Some of the prokaryotic proteins in this family are related to pcrB. The Staphylococcus aureus chromosomal gene pcrA encodes a protein with significant similarity (40% identity) to two Escherichia coli helicases: the helicase II encoded by the uvrD gene and the Rep helicase. PcrB gene seems to belong to an operon containing at least one other gene, pcrBA, downstream from pcrB []. The PcrB proteins often contain an FMN binding site although the function of these proteins is still unknown.; GO: 0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups; PDB: 1VIZ_A 2F6X_B 2F6U_B 3VKD_A 3VKA_A 3VK5_B 3VKC_B 3VKB_B.
Probab=69.73 E-value=4.5 Score=31.01 Aligned_cols=38 Identities=24% Similarity=0.425 Sum_probs=22.4
Q ss_pred hhhhhhh----hhcccchHHHHHHHHHHHHHHhcCCceEEEcccH
Q psy17228 2 YRKKQWR----LKLTKTKWTIKLTKTKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 2 ~~~~~~~----~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGGTg 42 (99)
|-.+.|| .+||-++--..++. +.+.+.|.--|+||||-
T Consensus 1 ~~~~~~~~~h~~liDPdK~~~~~~~---~~~~~~gtDai~VGGS~ 42 (230)
T PF01884_consen 1 YDIREWRKLHATLIDPDKPNPEEAL---EAACESGTDAIIVGGSD 42 (230)
T ss_dssp SGGGG----EEEEE-TTSS-HHHHH---HHHHCTT-SEEEEE-ST
T ss_pred CcccccccceEEEECCCCCCcHHHH---HHHHhcCCCEEEECCCC
Confidence 3456777 67777775555444 44478899999999997
No 27
>PRK02190 agmatinase; Provisional
Probab=69.28 E-value=9.1 Score=29.66 Aligned_cols=36 Identities=19% Similarity=0.277 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
+.+...+.++++.++|+.||+.||-..---+.+.++
T Consensus 95 ~~~~i~~~v~~~~~~g~~pi~lGGdHsit~~~~~a~ 130 (301)
T PRK02190 95 FPEALEAHAEKILAAGKRMLTLGGDHFITLPLLRAH 130 (301)
T ss_pred HHHHHHHHHHHHHhCCCeEEEECCcchhhHHHHHHH
Confidence 345666778888999999999999876655555553
No 28
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=67.72 E-value=13 Score=23.94 Aligned_cols=37 Identities=30% Similarity=0.402 Sum_probs=25.1
Q ss_pred chHHHHHHHHHHHHHHhcC-CceEEEcccH--HHHHHHHh
Q psy17228 14 TKWTIKLTKTKIDDILQRN-KVPIIVGGTN--YYIESLLW 50 (99)
Q Consensus 14 ~~~~~~~a~~~i~~i~~~~-~~pilVGGTg--lYi~all~ 50 (99)
..|....+.++++.+.+.+ +++|++||.. +.-+.+++
T Consensus 61 ~~~~~~~~~~l~~~~k~~~p~~~iv~GG~~~t~~~~~~l~ 100 (121)
T PF02310_consen 61 MTPNLPEAKRLARAIKERNPNIPIVVGGPHATADPEEILR 100 (121)
T ss_dssp SSTHHHHHHHHHHHHHTTCTTSEEEEEESSSGHHHHHHHH
T ss_pred CcCcHHHHHHHHHHHHhcCCCCEEEEECCchhcChHHHhc
Confidence 4556667788888866653 6899999965 44455443
No 29
>cd02065 B12-binding_like B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.
Probab=66.28 E-value=10 Score=24.48 Aligned_cols=24 Identities=21% Similarity=0.434 Sum_probs=16.0
Q ss_pred HHHHHHHHHHhcC--CceEEEcccHH
Q psy17228 20 LTKTKIDDILQRN--KVPIIVGGTNY 43 (99)
Q Consensus 20 ~a~~~i~~i~~~~--~~pilVGGTgl 43 (99)
.+.+.+..+.++. +++|+|||.+.
T Consensus 65 ~~~~~~~~~~~~~p~~~~ivvGG~~~ 90 (125)
T cd02065 65 EAMKLVIEALKELGIDIPVVVGGAHP 90 (125)
T ss_pred HHHHHHHHHHHhcCCCCeEEEeCCcC
Confidence 4455555555554 69999999654
No 30
>PRK01722 formimidoylglutamase; Provisional
Probab=66.14 E-value=12 Score=29.19 Aligned_cols=34 Identities=15% Similarity=0.140 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhc
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g 51 (99)
.+...+.+.++.++|+.||+.||-..=--+.+.+
T Consensus 103 ~~~i~~~v~~~~~~g~~pi~lGGdHsit~~~~~a 136 (320)
T PRK01722 103 QQALADTVGHCLRPNMRTIVLGGGHEIAFGSFAG 136 (320)
T ss_pred HHHHHHHHHHHHhCCCeeEEEcCchHHHHHHHHH
Confidence 3555677778888999999999986544444444
No 31
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=65.38 E-value=7.7 Score=28.23 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHHH
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYYI 45 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglYi 45 (99)
++..++++.+.++|-.++||||+-+-+
T Consensus 3 ~~l~~~~~~L~~~gv~~~ivGG~av~l 29 (181)
T PF09970_consen 3 EALKEILEELNKRGVEYVIVGGAAVNL 29 (181)
T ss_pred HHHHHHHHHHHHcCCeEEEECHHHHHH
Confidence 456667777777777799999997654
No 32
>PRK12454 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed
Probab=64.20 E-value=6.3 Score=31.50 Aligned_cols=22 Identities=18% Similarity=0.294 Sum_probs=18.7
Q ss_pred HHHHHHHHhcCCceEEEcccHH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTgl 43 (99)
.+.|+.+++.|.+||++||.|.
T Consensus 175 ~~aI~~LLe~G~IvI~~GgGGi 196 (313)
T PRK12454 175 IEVIKALVENGFIVIASGGGGI 196 (313)
T ss_pred HHHHHHHHHCCCEEEEeCCCcc
Confidence 5678889999999999999754
No 33
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=64.20 E-value=4.7 Score=30.66 Aligned_cols=16 Identities=25% Similarity=0.414 Sum_probs=13.9
Q ss_pred EcccHHHHHHHHhccc
Q psy17228 38 VGGTNYYIESLLWTIL 53 (99)
Q Consensus 38 VGGTglYi~all~g~~ 53 (99)
..|||.||+||.+.+-
T Consensus 171 skGT~~YIRsL~~Dig 186 (226)
T cd02868 171 INETQEYLRKLIHEIG 186 (226)
T ss_pred ECCCHHHHHHHHHHHH
Confidence 4799999999999863
No 34
>PF00994 MoCF_biosynth: Probable molybdopterin binding domain; InterPro: IPR001453 Eukaryotic and prokaryotic molybdoenzymes require a molybdopterin cofactor (MoCF) for their activity. The biosynthesis of this cofactor involves a complex multistep enzymatic pathway. One of the eukaryotic proteins involved in this pathway is the Drosophila protein cinnamon [] which is highly similar to gephyrin, a rat microtubule-associated protein which was thought to anchor the glycine receptor to subsynaptic microtubules. Cinnamon and gephyrin are evolutionary related, in their N-terminal half, to the Escherichia coli MoCF biosynthesis proteins mog/chlG and moaB/chlA2 and, in their C-terminal half, to E. coli moeA/chlE.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 3TCR_B 1O8O_B 1O8Q_G 1EAV_D 1O8N_C 1UUX_A 1UUY_A 2G2C_A 2G4R_C 3K6A_F ....
Probab=63.75 E-value=9.7 Score=25.96 Aligned_cols=24 Identities=29% Similarity=0.397 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhcCCceEEEcccHH
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
.-.+.+.+..++..+.|.+||||.
T Consensus 45 ~i~~~l~~~~~~~D~VittGG~g~ 68 (144)
T PF00994_consen 45 AIKEALRRALDRADLVITTGGTGP 68 (144)
T ss_dssp HHHHHHHHHHHTTSEEEEESSSSS
T ss_pred HHHHHHHhhhccCCEEEEcCCcCc
Confidence 444555777778899999999984
No 35
>PRK04169 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed
Probab=63.38 E-value=4.5 Score=30.89 Aligned_cols=38 Identities=26% Similarity=0.289 Sum_probs=27.1
Q ss_pred hhhhhhh--hhcccchHHHHHHHHHHHHHHhcCCceEEEcccH
Q psy17228 2 YRKKQWR--LKLTKTKWTIKLTKTKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 2 ~~~~~~~--~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGGTg 42 (99)
+..+.|+ .+||-++....++. +.+...|.--|+||||-
T Consensus 3 ~~~~~~~h~~liDP~k~~~~~~~---~~~~~~gtdai~vGGS~ 42 (232)
T PRK04169 3 IDWKGWLHVTLLDPDKPLPDEAL---EAICESGTDAIIVGGSD 42 (232)
T ss_pred ccccCceEEEEECCCCCCCHHHH---HHHHhcCCCEEEEcCCC
Confidence 3455565 47777776665544 56777899999999997
No 36
>COG0528 PyrH Uridylate kinase [Nucleotide transport and metabolism]
Probab=60.73 E-value=7.1 Score=30.28 Aligned_cols=27 Identities=19% Similarity=0.362 Sum_probs=21.4
Q ss_pred cchHHHHHHHHHHHHHHhcCCceEEEcccHH
Q psy17228 13 KTKWTIKLTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 13 ~~~~~~~~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
.+++..+.|.+.+ ++|+++|+.||||-
T Consensus 110 ~e~~~~~~A~~~l----~~grVvIf~gGtg~ 136 (238)
T COG0528 110 AEPYSRREAIRHL----EKGRVVIFGGGTGN 136 (238)
T ss_pred cCccCHHHHHHHH----HcCCEEEEeCCCCC
Confidence 6778777776654 48999999998874
No 37
>TIGR01769 GGGP geranylgeranylglyceryl phosphate synthase. This model represents geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea. The active enzyme is reported to be a homopentamer in Methanobacterium thermoautotrophicum but is reported to be a homodimer in Thermoplasma acidophilum.
Probab=59.35 E-value=14 Score=27.69 Aligned_cols=31 Identities=16% Similarity=0.181 Sum_probs=25.2
Q ss_pred hhcccchHHHHHHHHHHHHHHhcCCceEEEccc
Q psy17228 9 LKLTKTKWTIKLTKTKIDDILQRNKVPIIVGGT 41 (99)
Q Consensus 9 ~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGGT 41 (99)
.+||-++. ++..+++..+.+.|.--|+||||
T Consensus 3 ~~iDP~k~--e~~~~ia~~v~~~gtDaI~VGGS 33 (205)
T TIGR01769 3 TLIDPEKS--DEIEKIAKNAKDAGTDAIMVGGS 33 (205)
T ss_pred cccCCCcH--HHHHHHHHHHHhcCCCEEEEcCc
Confidence 35666666 67777888888899999999999
No 38
>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Probab=58.91 E-value=13 Score=24.71 Aligned_cols=28 Identities=18% Similarity=0.073 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHhcC-CceEEEcccHH
Q psy17228 16 WTIKLTKTKIDDILQRN-KVPIIVGGTNY 43 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~-~~pilVGGTgl 43 (99)
+....+.++++.+.+++ ..+|++||...
T Consensus 50 ~~~~~~~~~~~~ik~~~p~~~iv~GG~~~ 78 (127)
T cd02068 50 SAIYEALELAKIAKEVLPNVIVVVGGPHA 78 (127)
T ss_pred ccHHHHHHHHHHHHHHCCCCEEEECCcch
Confidence 33346666777776655 59999999763
No 39
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=58.52 E-value=12 Score=27.91 Aligned_cols=27 Identities=19% Similarity=0.529 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHhcC-CceEEEcccHH
Q psy17228 17 TIKLTKTKIDDILQRN-KVPIIVGGTNY 43 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~-~~pilVGGTgl 43 (99)
....+.+.++.+.+.+ +++|+|||.++
T Consensus 152 ~~~~~~~~i~~L~~~~~~~~i~vGG~~~ 179 (213)
T cd02069 152 SLDEMVEVAEEMNRRGIKIPLLIGGAAT 179 (213)
T ss_pred cHHHHHHHHHHHHhcCCCCeEEEEChhc
Confidence 3456777788887765 79999999754
No 40
>TIGR02137 HSK-PSP phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein. This enzyme is a member of the haloacid dehalogenase (HAD) superfamily, specifically part of subfamily IB by virtue of the presence of an alpha helical domain in between motifs I and II of the HAD domain . The closest homologs to this family are monofunctional phosphoserine phosphatases (TIGR00338).
Probab=57.19 E-value=19 Score=26.28 Aligned_cols=35 Identities=14% Similarity=0.099 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccC
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILL 54 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~ 54 (99)
.+.+.|+.+.+++++-|+.||...|++.+++.+-+
T Consensus 72 ga~ell~~lk~~~~~~IVS~~~~~~~~~il~~lgi 106 (203)
T TIGR02137 72 GAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGF 106 (203)
T ss_pred cHHHHHHHHHhCCeEEEEeCChHHHHHHHHHHcCC
Confidence 57778888888888899999999999999887644
No 41
>PRK14556 pyrH uridylate kinase; Provisional
Probab=56.46 E-value=10 Score=29.31 Aligned_cols=16 Identities=38% Similarity=0.628 Sum_probs=12.9
Q ss_pred HHHhcCCceEEEcccH
Q psy17228 27 DILQRNKVPIIVGGTN 42 (99)
Q Consensus 27 ~i~~~~~~pilVGGTg 42 (99)
+.+++|+++|++||||
T Consensus 131 ~~l~~g~vvi~~gg~G 146 (249)
T PRK14556 131 QELAKGRVLIFAGGTG 146 (249)
T ss_pred HHHhCCCEEEEECCCC
Confidence 3456899999999985
No 42
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=56.42 E-value=18 Score=24.20 Aligned_cols=27 Identities=15% Similarity=0.197 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHhcC--CceEEEcccHH
Q psy17228 17 TIKLTKTKIDDILQRN--KVPIIVGGTNY 43 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~--~~pilVGGTgl 43 (99)
....+.+.++.+.+.+ +++|++||+..
T Consensus 63 ~~~~~~~~~~~L~~~~~~~i~i~~GG~~~ 91 (122)
T cd02071 63 HMTLFPEVIELLRELGAGDILVVGGGIIP 91 (122)
T ss_pred hHHHHHHHHHHHHhcCCCCCEEEEECCCC
Confidence 3456777788777763 68999999864
No 43
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=56.12 E-value=12 Score=25.43 Aligned_cols=23 Identities=13% Similarity=0.297 Sum_probs=17.2
Q ss_pred HHHHHHHHHhcCCceEEEcccHH
Q psy17228 21 TKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 21 a~~~i~~i~~~~~~pilVGGTgl 43 (99)
..+.+++..++..+.|.+||||.
T Consensus 48 i~~~i~~~~~~~DlvittGG~g~ 70 (133)
T cd00758 48 IRAALIEASREADLVLTTGGTGV 70 (133)
T ss_pred HHHHHHHHHhcCCEEEECCCCCC
Confidence 34556666667889999999984
No 44
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=54.70 E-value=20 Score=24.74 Aligned_cols=23 Identities=17% Similarity=0.369 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHhcC--CceEEEccc
Q psy17228 19 KLTKTKIDDILQRN--KVPIIVGGT 41 (99)
Q Consensus 19 ~~a~~~i~~i~~~~--~~pilVGGT 41 (99)
..+.+.++.+.++| .++|+|||.
T Consensus 68 ~~~~~~~~~L~~~g~~~i~vivGG~ 92 (132)
T TIGR00640 68 TLVPALRKELDKLGRPDILVVVGGV 92 (132)
T ss_pred HHHHHHHHHHHhcCCCCCEEEEeCC
Confidence 34566666666665 588999983
No 45
>KOG1221|consensus
Probab=52.58 E-value=11 Score=31.84 Aligned_cols=27 Identities=22% Similarity=0.377 Sum_probs=22.7
Q ss_pred HHHHhcCCceEEEcccHHHHHHHHhccc
Q psy17228 26 DDILQRNKVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 26 ~~i~~~~~~pilVGGTglYi~all~g~~ 53 (99)
.+.+ +||.-+|+|||||--+.|++.+.
T Consensus 7 ~~f~-~~k~i~vTG~tGFlgKVliEklL 33 (467)
T KOG1221|consen 7 VQFY-KNKTIFVTGATGFLGKVLIEKLL 33 (467)
T ss_pred HHHh-CCCeEEEEcccchhHHHHHHHHH
Confidence 3444 68999999999999999999964
No 46
>PRK08202 purine nucleoside phosphorylase; Provisional
Probab=50.55 E-value=18 Score=27.82 Aligned_cols=12 Identities=8% Similarity=-0.103 Sum_probs=9.4
Q ss_pred ceEEEcccHHHH
Q psy17228 34 VPIIVGGTNYYI 45 (99)
Q Consensus 34 ~pilVGGTglYi 45 (99)
..-|+||||||=
T Consensus 23 ~i~iI~GsGl~~ 34 (272)
T PRK08202 23 EIGLILGSGLGA 34 (272)
T ss_pred CEEEEeCCchhH
Confidence 446789999994
No 47
>PRK12353 putative amino acid kinase; Reviewed
Probab=49.94 E-value=14 Score=29.16 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=19.6
Q ss_pred HHHHHHHHhcCCceEEEcccHHHH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTNYYI 45 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTglYi 45 (99)
.+.|+.+++.|.+||+.||+|.-+
T Consensus 175 ~~~i~~lL~~g~IpV~~g~gg~Pi 198 (314)
T PRK12353 175 IEAIKTLVDAGQVVIAAGGGGIPV 198 (314)
T ss_pred HHHHHHHHHCCCEEEEcCCCCCCE
Confidence 578888999999999999965433
No 48
>smart00852 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=49.85 E-value=20 Score=24.13 Aligned_cols=22 Identities=32% Similarity=0.517 Sum_probs=15.8
Q ss_pred HHHHHHHHhcCCceEEEcccHH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTgl 43 (99)
.+.+++..++..+.|.+||||.
T Consensus 48 ~~~l~~~~~~~dliittGG~g~ 69 (135)
T smart00852 48 KEALREALERADLVITTGGTGP 69 (135)
T ss_pred HHHHHHHHhCCCEEEEcCCCCC
Confidence 3445555566789999999983
No 49
>PRK09552 mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase; Reviewed
Probab=49.72 E-value=26 Score=25.24 Aligned_cols=33 Identities=15% Similarity=0.318 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhcC-CceEEEcccHHHHHHHHhcc
Q psy17228 20 LTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~ 52 (99)
-+.+.++.+.++| ++-|+.||...|+++++..+
T Consensus 78 G~~e~l~~l~~~g~~~~IvS~~~~~~i~~il~~~ 111 (219)
T PRK09552 78 GFHEFVQFVKENNIPFYVVSGGMDFFVYPLLQGL 111 (219)
T ss_pred CHHHHHHHHHHcCCeEEEECCCcHHHHHHHHHHh
Confidence 5667888887777 45566699999999999875
No 50
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=47.91 E-value=26 Score=24.45 Aligned_cols=22 Identities=18% Similarity=0.217 Sum_probs=14.7
Q ss_pred HHHHHHHHHhcC--CceEEEcccH
Q psy17228 21 TKTKIDDILQRN--KVPIIVGGTN 42 (99)
Q Consensus 21 a~~~i~~i~~~~--~~pilVGGTg 42 (99)
..+.++.+.++| .+||+|||.-
T Consensus 67 ~~~~~~~l~~~gl~~v~vivGG~~ 90 (128)
T cd02072 67 CKGLREKCDEAGLKDILLYVGGNL 90 (128)
T ss_pred HHHHHHHHHHCCCCCCeEEEECCC
Confidence 344555555554 6999999973
No 51
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=47.02 E-value=22 Score=24.48 Aligned_cols=23 Identities=17% Similarity=0.352 Sum_probs=17.1
Q ss_pred HHHHHHHHHhcCCceEEEcccHH
Q psy17228 21 TKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 21 a~~~i~~i~~~~~~pilVGGTgl 43 (99)
-.+.+++..++..+.|++||||.
T Consensus 56 i~~~l~~~~~~~DliIttGG~g~ 78 (144)
T TIGR00177 56 IREILRKAVDEADVVLTTGGTGV 78 (144)
T ss_pred HHHHHHHHHhCCCEEEECCCCCC
Confidence 34445666667899999999997
No 52
>PF09818 ABC_ATPase: Predicted ATPase of the ABC class; InterPro: IPR019195 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry consists of various predicted ABC transporter class ATPases.
Probab=46.95 E-value=29 Score=29.30 Aligned_cols=34 Identities=18% Similarity=0.305 Sum_probs=19.9
Q ss_pred ccchHHH--HHHHHHHHHHHhcC-CceEEEcccHHHHHHH
Q psy17228 12 TKTKWTI--KLTKTKIDDILQRN-KVPIIVGGTNYYIESL 48 (99)
Q Consensus 12 ~~~~~~~--~~a~~~i~~i~~~~-~~pilVGGTglYi~al 48 (99)
+++|.+. ..+....+ ..| .+.+|+||+|-|+..-
T Consensus 369 ~kEPITPfidrvr~l~~---~~GvStIlV~Ggsgdy~~vA 405 (448)
T PF09818_consen 369 EKEPITPFIDRVRSLYE---KLGVSTILVVGGSGDYFDVA 405 (448)
T ss_pred CCCCcchHHHHHHHHHH---HcCceEEEEeccchhhHhhC
Confidence 5555543 33433333 235 4566679999999854
No 53
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=46.80 E-value=22 Score=25.89 Aligned_cols=25 Identities=24% Similarity=0.292 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHhcC---CceEEEcccHH
Q psy17228 19 KLTKTKIDDILQRN---KVPIIVGGTNY 43 (99)
Q Consensus 19 ~~a~~~i~~i~~~~---~~pilVGGTgl 43 (99)
..+.+.++.+.+.| +++|+|||.-+
T Consensus 150 ~~~~~~i~~l~~~~~~~~v~i~vGG~~~ 177 (197)
T TIGR02370 150 YGQKDINDKLKEEGYRDSVKFMVGGAPV 177 (197)
T ss_pred HHHHHHHHHHHHcCCCCCCEEEEEChhc
Confidence 34566777777764 58999999775
No 54
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=46.32 E-value=21 Score=25.54 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=16.8
Q ss_pred HHHHHHHHhcCCceEEEcccHH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTgl 43 (99)
.+.++++.++..+.|++||+|.
T Consensus 49 ~~~l~~~~~~~dlVIttGG~G~ 70 (170)
T cd00885 49 AEALRRASERADLVITTGGLGP 70 (170)
T ss_pred HHHHHHHHhCCCEEEECCCCCC
Confidence 4555666667889999999996
No 55
>PLN02615 arginase
Probab=46.07 E-value=42 Score=26.78 Aligned_cols=35 Identities=9% Similarity=0.302 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHhc-CCceEEEcccHHHHHHHHhc
Q psy17228 17 TIKLTKTKIDDILQR-NKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~-~~~pilVGGTglYi~all~g 51 (99)
+.+...+.+..+.++ +++||+.||-..---+++.+
T Consensus 131 ~~~~i~~~v~~ll~~~~~~Pi~LGGDHsit~~~ira 166 (338)
T PLN02615 131 LMNVISESVKLVMEEEPLRPLVLGGDHSISYPVVRA 166 (338)
T ss_pred HHHHHHHHHHHHHhcCCCceEEECcchHhhHHHHHH
Confidence 455677777888885 67999999986654444443
No 56
>TIGR01488 HAD-SF-IB Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like. Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences.
Probab=44.73 E-value=37 Score=22.94 Aligned_cols=34 Identities=18% Similarity=0.368 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~ 52 (99)
..+.+.++.+.++| ++.|+.||...|++.++..+
T Consensus 76 ~g~~~~l~~l~~~g~~~~ivS~~~~~~i~~~~~~~ 110 (177)
T TIGR01488 76 PGARELISWLKERGIDTVIVSGGFDFFVEPVAEKL 110 (177)
T ss_pred cCHHHHHHHHHHCCCEEEEECCCcHHHHHHHHHHc
Confidence 46788888888887 56677799999999998754
No 57
>PF00941 FAD_binding_5: FAD binding domain in molybdopterin dehydrogenase; InterPro: IPR002346 Oxidoreductases, that also bind molybdopterin, have essentially no similarity outside this common domain. They include aldehyde oxidase (1.2.3.1 from EC), that converts an aldehyde and water to an acid and hydrogen peroxide, and xanthine dehydrogenase (1.1.1.204 from EC), that converts xanthine to urate. These enzymes require molybdopterin and FAD as cofactors and have and two 2FE-2S clusters. Another enzyme that contains this domain is the Pseudomonas thermocarboxydovorans carbon monoxide oxygenase.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2E1Q_C 2CKJ_A 3EUB_K 3NS1_K 3NVV_B 1FO4_B 3AM9_A 3AX7_B 3BDJ_A 3ETR_B ....
Probab=44.68 E-value=18 Score=25.75 Aligned_cols=28 Identities=14% Similarity=0.303 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHH
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIES 47 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~a 47 (99)
+.++|.++++ ..++..++.|||.+...-
T Consensus 10 sl~ea~~ll~---~~~~a~~vaGgT~l~~~~ 37 (171)
T PF00941_consen 10 SLEEALELLA---KGPDARIVAGGTDLGVQM 37 (171)
T ss_dssp SHHHHHHHHH---HGTTEEEESS-TTHHHHH
T ss_pred CHHHHHHHHh---cCCCCEEEeCCCccchhc
Confidence 3456666666 578889999999998653
No 58
>COG0149 TpiA Triosephosphate isomerase [Carbohydrate transport and metabolism]
Probab=44.12 E-value=33 Score=26.72 Aligned_cols=27 Identities=26% Similarity=0.340 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHhc-----CCceEEEcccH
Q psy17228 16 WTIKLTKTKIDDILQR-----NKVPIIVGGTN 42 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~-----~~~pilVGGTg 42 (99)
-..+.....|+..... .++||++|||=
T Consensus 180 ~~a~~v~~~Ir~~~~~~~~~~~~v~IlYGGSV 211 (251)
T COG0149 180 ADAEEVHAFIRAVLAELFGAEEKVRILYGGSV 211 (251)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCeEEEEeCCc
Confidence 3445666677777766 59999999983
No 59
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=43.48 E-value=15 Score=22.63 Aligned_cols=25 Identities=12% Similarity=0.452 Sum_probs=23.2
Q ss_pred cccchHHHHHHHHHHHHHHhcCCce
Q psy17228 11 LTKTKWTIKLTKTKIDDILQRNKVP 35 (99)
Q Consensus 11 ~~~~~~~~~~a~~~i~~i~~~~~~p 35 (99)
|+..-|....|.....++.++|++|
T Consensus 34 Le~~~Wd~~~Al~~F~~lk~~~~IP 58 (63)
T smart00804 34 LEDNNWDYERALKNFTELKSEGSIP 58 (63)
T ss_pred HHHcCCCHHHHHHHHHHHHhcCCCC
Confidence 6788999999999999999999998
No 60
>cd01078 NAD_bind_H4MPT_DH NADP binding domain of methylene tetrahydromethanopterin dehydrogenase. Methylene Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP binding domain. NADP-dependent H4MPT DH catalyzes the dehydrogenation of methylene- H4MPT and methylene-tetrahydrofolate (H4F) with NADP+ as cofactor. H4F and H4MPT are both cofactors that carry the one-carbon units between the formyl and methyl oxidation level. H4F and H4MPT are structurally analogous to each other with respect to the pterin moiety, but each has distinct side chain. H4MPT is present only in anaerobic methanogenic archaea and aerobic methylotrophic proteobacteria. H4MPT seems to have evolved independently from H4F and functions as a distinct carrier in C1 metabolism. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclo
Probab=42.72 E-value=38 Score=23.96 Aligned_cols=35 Identities=17% Similarity=0.203 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHh------cCCceEEEcccHHHHHHHHhc
Q psy17228 17 TIKLTKTKIDDILQ------RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 17 ~~~~a~~~i~~i~~------~~~~pilVGGTglYi~all~g 51 (99)
+...+.+.+...+. +++..+|+||||.==+++..-
T Consensus 7 ta~aav~~~~~~l~~~~~~l~~~~vlVlGgtG~iG~~~a~~ 47 (194)
T cd01078 7 TAAAAVAAAGKALELMGKDLKGKTAVVLGGTGPVGQRAAVL 47 (194)
T ss_pred HHHHHHHHHHHHHHHhCcCCCCCEEEEECCCCHHHHHHHHH
Confidence 34444445554442 567888999987654444443
No 61
>PRK12354 carbamate kinase; Reviewed
Probab=42.51 E-value=23 Score=28.27 Aligned_cols=22 Identities=23% Similarity=0.344 Sum_probs=17.8
Q ss_pred HHHHHHHHhcCCceEEEcccHH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTgl 43 (99)
.+.|+.++++|.+||.+||-|-
T Consensus 165 ~~~I~~Ll~~g~ivIa~GGGGI 186 (307)
T PRK12354 165 IRPIRWLLEKGHLVICAGGGGI 186 (307)
T ss_pred HHHHHHHHHCCCEEEEeCCCcc
Confidence 6788899999998888877664
No 62
>cd00209 DHFR Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy. 5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis.
Probab=42.30 E-value=34 Score=23.86 Aligned_cols=31 Identities=13% Similarity=0.278 Sum_probs=21.3
Q ss_pred HHHHHHHHHHhcCCceEEEcccHHHHHHHHh
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNYYIESLLW 50 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTglYi~all~ 50 (99)
+..++++.+.+.++...|+||..+|-..+-.
T Consensus 79 ~~~~~v~~lk~~~~~I~v~GG~~l~~~~l~~ 109 (158)
T cd00209 79 SLEEALELAENTVEEIFVIGGAEIYKQALPY 109 (158)
T ss_pred CHHHHHHHHhcCCCeEEEECcHHHHHHHHhh
Confidence 6777788777455555567998888665543
No 63
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=41.96 E-value=40 Score=23.33 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHhcC--CceEEEcccH
Q psy17228 19 KLTKTKIDDILQRN--KVPIIVGGTN 42 (99)
Q Consensus 19 ~~a~~~i~~i~~~~--~~pilVGGTg 42 (99)
..+.+.++.+.+.+ .++|+|||+-
T Consensus 69 ~~~~~~~~~L~~~~~~~~~i~vGG~~ 94 (137)
T PRK02261 69 IDCRGLREKCIEAGLGDILLYVGGNL 94 (137)
T ss_pred HHHHHHHHHHHhcCCCCCeEEEECCC
Confidence 35566666666552 5899999985
No 64
>PF08030 NAD_binding_6: Ferric reductase NAD binding domain; InterPro: IPR013121 This entry contains ferric reductase NAD binding proteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3A1F_A.
Probab=41.59 E-value=12 Score=25.26 Aligned_cols=19 Identities=26% Similarity=0.543 Sum_probs=12.8
Q ss_pred CceEEEcccHH-----HHHHHHhc
Q psy17228 33 KVPIIVGGTNY-----YIESLLWT 51 (99)
Q Consensus 33 ~~pilVGGTgl-----Yi~all~g 51 (99)
++.+|+||||. ++..|+..
T Consensus 3 ~vvlvAGG~GIt~~l~~l~~l~~~ 26 (156)
T PF08030_consen 3 NVVLVAGGSGITPILPILRDLLQR 26 (156)
T ss_dssp EEEEEEEGGGHHHHHHHHHHHHHH
T ss_pred EEEEEecCcCHHHHHHHHHHHHHh
Confidence 46789999996 44444444
No 65
>PF12710 HAD: haloacid dehalogenase-like hydrolase; PDB: 3P96_A 3N28_A 3FVV_A 1RKU_A 1RKV_A 1Y8A_A 2FEA_B 3KD3_B.
Probab=41.12 E-value=39 Score=22.99 Aligned_cols=36 Identities=19% Similarity=0.226 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhcccC
Q psy17228 19 KLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTILL 54 (99)
Q Consensus 19 ~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~~~ 54 (99)
.++.+.|+.+.++| ++-|+.||.-.|+++++..+.+
T Consensus 92 ~~~~e~i~~~~~~~~~v~IvS~~~~~~i~~~~~~~~i 128 (192)
T PF12710_consen 92 PDAMELIRELKDNGIKVVIVSGSPDEIIEPIAERLGI 128 (192)
T ss_dssp TTHHHHHHHHHHTTSEEEEEEEEEHHHHHHHHHHTTS
T ss_pred hhHHHHHHHHHHCCCEEEEECCCcHHHHHHHHHHcCC
Confidence 45558888877776 5555669999999999875443
No 66
>COG4752 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.10 E-value=31 Score=25.60 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=25.5
Q ss_pred hhcccchHHHHHHHHHHHHHHhcCCceEEEcccH
Q psy17228 9 LKLTKTKWTIKLTKTKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 9 ~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGGTg 42 (99)
++|.+-.++..++.+-|+.+ +|..|+|||-|.
T Consensus 82 ~~lv~l~~~le~ViEdIEk~--eG~rPLi~~TsA 113 (190)
T COG4752 82 VQLVRLAYTLEEVIEDIEKE--EGRRPLIVGTSA 113 (190)
T ss_pred HHHHhHHHHHHHHHHHHHhh--cCCCceEEeccc
Confidence 56677778888888888876 799999998764
No 67
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=40.97 E-value=40 Score=23.61 Aligned_cols=22 Identities=18% Similarity=0.166 Sum_probs=14.2
Q ss_pred HHHHHHHHHhcC--CceEEEcccH
Q psy17228 21 TKTKIDDILQRN--KVPIIVGGTN 42 (99)
Q Consensus 21 a~~~i~~i~~~~--~~pilVGGTg 42 (99)
..+.++.+.++| .++|+|||+.
T Consensus 69 ~~~~~~~l~~~gl~~~~vivGG~~ 92 (134)
T TIGR01501 69 CKGLRQKCDEAGLEGILLYVGGNL 92 (134)
T ss_pred HHHHHHHHHHCCCCCCEEEecCCc
Confidence 334455555565 5789999974
No 68
>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]
Probab=40.68 E-value=34 Score=28.03 Aligned_cols=36 Identities=17% Similarity=0.063 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccC
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILL 54 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~ 54 (99)
.++.+.+..+.+....-+|+||||--=.+|++-++.
T Consensus 160 ~~~a~~L~~av~~r~NILisGGTGSGKTTlLNal~~ 195 (355)
T COG4962 160 RRAAKFLRRAVGIRCNILISGGTGSGKTTLLNALSG 195 (355)
T ss_pred HHHHHHHHHHHhhceeEEEeCCCCCCHHHHHHHHHh
Confidence 567777777877777889999999988888888753
No 69
>PRK01215 competence damage-inducible protein A; Provisional
Probab=40.02 E-value=34 Score=26.38 Aligned_cols=24 Identities=17% Similarity=0.270 Sum_probs=18.9
Q ss_pred HHHHHHHHHHhcCCceEEEcccHH
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
+-.+.++++.++..+.|++||+|.
T Consensus 51 ~I~~~l~~a~~~~DlVIttGG~g~ 74 (264)
T PRK01215 51 EIVSAFREAIDRADVVVSTGGLGP 74 (264)
T ss_pred HHHHHHHHHhcCCCEEEEeCCCcC
Confidence 345666777778899999999996
No 70
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=39.42 E-value=31 Score=23.92 Aligned_cols=22 Identities=14% Similarity=0.253 Sum_probs=16.0
Q ss_pred HHHHHHHHh--cCCceEEEcccHH
Q psy17228 22 KTKIDDILQ--RNKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~~--~~~~pilVGGTgl 43 (99)
.+.+++..+ +..+.|.+||||.
T Consensus 50 ~~~l~~~~~~~~~DlVittGG~s~ 73 (152)
T cd00886 50 REALIEWADEDGVDLILTTGGTGL 73 (152)
T ss_pred HHHHHHHHhcCCCCEEEECCCcCC
Confidence 344555555 6789999999985
No 71
>PRK13900 type IV secretion system ATPase VirB11; Provisional
Probab=39.38 E-value=35 Score=27.05 Aligned_cols=33 Identities=27% Similarity=0.349 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhcCCceEEEcccH----HHHHHHHhcc
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTN----YYIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTg----lYi~all~g~ 52 (99)
+....+..+...++.-+|+|||| -.++||+.-+
T Consensus 148 ~~~~~L~~~v~~~~nili~G~tgSGKTTll~aL~~~i 184 (332)
T PRK13900 148 KIKEFLEHAVISKKNIIISGGTSTGKTTFTNAALREI 184 (332)
T ss_pred HHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHhhC
Confidence 44567777888899999999998 4778887644
No 72
>COG0010 SpeB Arginase/agmatinase/formimionoglutamate hydrolase, arginase family [Amino acid transport and metabolism]
Probab=38.79 E-value=41 Score=26.20 Aligned_cols=36 Identities=14% Similarity=0.323 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhc
Q psy17228 16 WTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g 51 (99)
-++....+.+.++..+++.||+.||=..=--+.+.|
T Consensus 86 ~~~~~~~~~~~~~~~~~~~pi~lGGDHsit~~~~~a 121 (305)
T COG0010 86 DAVDAIEEAVAELLSAGAFPIVLGGDHSITLGTVRA 121 (305)
T ss_pred HHHHHHHHHHHHHHhcCCeeEEECCcchhhHHHHHH
Confidence 344556666677888899999999965544444444
No 73
>PRK00115 hemE uroporphyrinogen decarboxylase; Validated
Probab=38.59 E-value=63 Score=25.28 Aligned_cols=34 Identities=18% Similarity=0.351 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHhcC-CceEE--EcccHHHHHHHHh
Q psy17228 17 TIKLTKTKIDDILQRN-KVPII--VGGTNYYIESLLW 50 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~-~~pil--VGGTglYi~all~ 50 (99)
..--..++++.+.+.+ ..||+ ||||+-+++.+.+
T Consensus 222 ~~P~~k~i~~~i~~~~~~~~ilh~cg~~~~~~~~~~~ 258 (346)
T PRK00115 222 VLPYMKRIVAELKREHPDVPVILFGKGAGELLEAMAE 258 (346)
T ss_pred HHHHHHHHHHHHHHhCCCCCEEEEcCCcHHHHHHHHh
Confidence 3344567777777775 55655 8999999888766
No 74
>PRK12686 carbamate kinase; Reviewed
Probab=38.58 E-value=28 Score=27.80 Aligned_cols=21 Identities=19% Similarity=0.431 Sum_probs=18.0
Q ss_pred HHHHHHHHhcCCceEEEcccH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTg 42 (99)
.+.|+.++++|-+||.+||-|
T Consensus 173 ~~~I~~Ll~~G~IpI~~Gggg 193 (312)
T PRK12686 173 HDTIRTLVDGGNIVIACGGGG 193 (312)
T ss_pred HHHHHHHHHCCCEEEEeCCCC
Confidence 468899999999999998855
No 75
>TIGR03333 salvage_mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase. Members of this family are the methionine salvage enzyme MnxX, a member of the HAD-superfamily hydrolases, subfamily IB (see TIGR01488). Members are found in Bacillus subtilis and related species, paired with MtnW (TIGR03332). In most species that recycle methionine from methylthioadenosine, the single protein MtnC replaces the MtnW/MtnX pair. In B. subtilis, mtnX was first known as ykrX.
Probab=38.51 E-value=45 Score=23.92 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhcC-CceEEEcccHHHHHHHHhcc
Q psy17228 20 LTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~ 52 (99)
.+.+.++.+.++| ++-|+.||.-.|++.++..+
T Consensus 74 g~~e~l~~l~~~g~~~~IvS~~~~~~i~~il~~~ 107 (214)
T TIGR03333 74 GFREFVAFINEHGIPFYVISGGMDFFVYPLLEGI 107 (214)
T ss_pred cHHHHHHHHHHCCCeEEEECCCcHHHHHHHHHhh
Confidence 5667888887766 45566689999999998875
No 76
>PRK10078 ribose 1,5-bisphosphokinase; Provisional
Probab=38.49 E-value=55 Score=22.99 Aligned_cols=27 Identities=19% Similarity=0.125 Sum_probs=18.8
Q ss_pred HHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 25 IDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 25 i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
+++.++.|+. ||++|++-+++.+...+
T Consensus 82 ~~~~l~~g~~-VI~~G~~~~~~~~~~~~ 108 (186)
T PRK10078 82 IDLWLHAGFD-VLVNGSRAHLPQARARY 108 (186)
T ss_pred HHHHHhCCCE-EEEeChHHHHHHHHHHc
Confidence 4556667764 77799998877776543
No 77
>PLN02662 cinnamyl-alcohol dehydrogenase family protein
Probab=38.43 E-value=19 Score=26.78 Aligned_cols=19 Identities=26% Similarity=0.450 Sum_probs=13.0
Q ss_pred cCCceEEEcccHHHHHHHH
Q psy17228 31 RNKVPIIVGGTNYYIESLL 49 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all 49 (99)
+++.-+|+|||||==..|+
T Consensus 3 ~~~~ilVtGatGfIG~~l~ 21 (322)
T PLN02662 3 EGKVVCVTGASGYIASWLV 21 (322)
T ss_pred CCCEEEEECChHHHHHHHH
Confidence 4677889999987533333
No 78
>TIGR01125 MiaB-like tRNA modifying enzyme YliG, TIGR01125. This clade spans alpha and gamma proteobacteria, cyano bacteria, deinococcus, porphyromonas, aquifex, helicobacter, campylobacter, thermotoga, chlamydia, streptococcus coelicolor and clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes.
Probab=38.24 E-value=37 Score=27.45 Aligned_cols=24 Identities=17% Similarity=0.230 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHH
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
+.+.+++.++.++| .+|||||-+.
T Consensus 53 ~~~~~~i~~~~~~~-~~vvvgGc~a 76 (430)
T TIGR01125 53 QESIDTIGELADAG-KKVIVTGCLV 76 (430)
T ss_pred HHHHHHHHHHHhcC-CCEEEECCcc
Confidence 56788888887665 5899999854
No 79
>PRK14558 pyrH uridylate kinase; Provisional
Probab=37.34 E-value=37 Score=25.05 Aligned_cols=23 Identities=22% Similarity=0.384 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHhcCCceEEEccc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGT 41 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGT 41 (99)
....+.+..+++.|.+||+.|++
T Consensus 105 ~~~~~~i~~ll~~g~vpV~~G~~ 127 (231)
T PRK14558 105 PINYDDIELYFRAGYIVIFAGGT 127 (231)
T ss_pred hhhHHHHHHHHHCCCEEEEECCC
Confidence 33467788888999999999964
No 80
>TIGR00746 arcC carbamate kinase. The seed alignment for this model includes experimentally confirmed examples from a set of phylogenetically distinct species. In a neighbor-joining tree constructed from an alignment of candidate carbamate kinases and several acetylglutamate kinases, the latter group forms a clear outgroup which roots the tree of carbamate kinase-like proteins. This analysis suggests that in E. coli, the ArcC paralog YqeA may be a second isozyme, while the paralog YahI branches as an outlier and is less likely to be an authentic carbamate kinase. The homolog from Mycoplasma pneumoniae likewise branches outside the set containing known carbamate kinases and also scores below the trusted cutoff.
Probab=37.18 E-value=14 Score=29.26 Aligned_cols=24 Identities=17% Similarity=0.349 Sum_probs=18.2
Q ss_pred HHHHHHHHHHhcCCceEEEcccHH
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
-..+.|+.+++.|.+.|.+||.|.
T Consensus 170 v~~~~I~~LL~~G~iVI~~ggggi 193 (310)
T TIGR00746 170 VEAETIKTLVENGVIVISSGGGGV 193 (310)
T ss_pred ccHHHHHHHHHCCCEEEeCCCCCc
Confidence 345688889999987777777763
No 81
>KOG3985|consensus
Probab=37.12 E-value=11 Score=29.67 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=11.3
Q ss_pred EEcccHHHHHHHHhc
Q psy17228 37 IVGGTNYYIESLLWT 51 (99)
Q Consensus 37 lVGGTglYi~all~g 51 (99)
|.||||||=--++++
T Consensus 14 IIGGsGl~dp~ile~ 28 (283)
T KOG3985|consen 14 IIGGSGLYDPDILED 28 (283)
T ss_pred EeccCCCCCchhhhc
Confidence 569999996666664
No 82
>COG1954 GlpP Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]
Probab=36.76 E-value=29 Score=25.93 Aligned_cols=19 Identities=37% Similarity=0.793 Sum_probs=16.6
Q ss_pred HHHHHHHHhcCCceEEEcc
Q psy17228 22 KTKIDDILQRNKVPIIVGG 40 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGG 40 (99)
=++|.++.++-+.|||.||
T Consensus 133 Pkvi~~i~~~t~~piIAGG 151 (181)
T COG1954 133 PKVIKEITEKTHIPIIAGG 151 (181)
T ss_pred HHHHHHHHHhcCCCEEecc
Confidence 3678889999999999998
No 83
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=36.68 E-value=24 Score=24.02 Aligned_cols=26 Identities=4% Similarity=0.124 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHH
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYY 44 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglY 44 (99)
..|+.+|+++.++|.+-.|+++++..
T Consensus 74 SlAr~~Lr~L~~kG~Ik~V~k~~~~~ 99 (105)
T PF03297_consen 74 SLARKALRELESKGLIKPVSKHHRQR 99 (105)
T ss_dssp HHHHHHHHHHHHCCSSEEEECCTTCE
T ss_pred HHHHHHHHHHHHCCCEEEEeccCCeE
Confidence 58999999999999999999987754
No 84
>TIGR01464 hemE uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products.
Probab=36.45 E-value=82 Score=24.39 Aligned_cols=34 Identities=26% Similarity=0.437 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHhc-CCceEE--EcccHHHHHHHHh
Q psy17228 17 TIKLTKTKIDDILQR-NKVPII--VGGTNYYIESLLW 50 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~-~~~pil--VGGTglYi~all~ 50 (99)
..--.+++++.+.+. |..||+ ||||.-+++.+.+
T Consensus 216 ~~p~~k~i~~~i~~~~~~~~ilh~cg~~~~~~~~~~~ 252 (338)
T TIGR01464 216 VLPYLKKIIEEVKARLPNVPVILFAKGAGHLLEELAE 252 (338)
T ss_pred HHHHHHHHHHHHHHhCCCCCEEEEeCCcHHHHHHHHh
Confidence 344456777777766 555666 8999988887776
No 85
>PLN02989 cinnamyl-alcohol dehydrogenase family protein
Probab=36.37 E-value=21 Score=26.75 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=14.8
Q ss_pred cCCceEEEcccHHHHHHHHh
Q psy17228 31 RNKVPIIVGGTNYYIESLLW 50 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~ 50 (99)
+|+..+|+||||+==.+|+.
T Consensus 4 ~~k~vlVtG~~G~IG~~l~~ 23 (325)
T PLN02989 4 GGKVVCVTGASGYIASWIVK 23 (325)
T ss_pred CCCEEEEECCchHHHHHHHH
Confidence 57889999999985444444
No 86
>PF04263 TPK_catalytic: Thiamin pyrophosphokinase, catalytic domain; InterPro: IPR007371 Thiamin pyrophosphokinase (TPK, 2.7.6.2 from EC) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [].; GO: 0004788 thiamine diphosphokinase activity, 0005524 ATP binding, 0009229 thiamine diphosphate biosynthetic process; PDB: 2F17_B 1IG3_B 3S4Y_B 2OMK_B 1IG0_A 3MEL_B 3CQ9_A 3LM8_B 3K94_B 3L8M_B ....
Probab=36.02 E-value=47 Score=22.70 Aligned_cols=34 Identities=12% Similarity=0.160 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhcCCceEE-EcccHHHHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRNKVPII-VGGTNYYIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pil-VGGTglYi~all~g~ 52 (99)
.|...+++.+.+.+...|+ .||+|==+...+..+
T Consensus 71 TD~e~Al~~~~~~~~~~i~v~Ga~GgR~DH~lanl 105 (123)
T PF04263_consen 71 TDLEKALEYAIEQGPDEIIVLGALGGRFDHTLANL 105 (123)
T ss_dssp -HHHHHHHHHHHTTTSEEEEES-SSSSHHHHHHHH
T ss_pred CHHHHHHHHHHHCCCCEEEEEecCCCcHHHHHHHH
Confidence 4777888888777766655 699997777766654
No 87
>COG3962 Acetolactate synthase [Amino acid transport and metabolism]
Probab=35.03 E-value=32 Score=29.83 Aligned_cols=38 Identities=18% Similarity=0.139 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHH------HHHHHhcccCCC
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYY------IESLLWTILLDN 56 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglY------i~all~g~~~~~ 56 (99)
++...++.-|.+..++.||+||--+| +.++.+.-.+|.
T Consensus 217 ~eL~~A~~lik~ak~PlIvaGGGv~YS~A~~~L~af~E~~~iPv 260 (617)
T COG3962 217 RELADAAALIKSAKKPLIVAGGGVLYSGAREALRAFAETHGIPV 260 (617)
T ss_pred HHHHHHHHHHHhcCCCEEEecCceeechHHHHHHHHHHhcCCce
Confidence 45566666677778888888998888 445666544443
No 88
>cd05398 NT_ClassII-CCAase Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal io
Probab=34.91 E-value=48 Score=22.88 Aligned_cols=30 Identities=17% Similarity=0.220 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhc-CCceEEEcccHHHHHHHHhcc
Q psy17228 20 LTKTKIDDILQR-NKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~-~~~pilVGGTglYi~all~g~ 52 (99)
.+..+++.+.+. |....|||| +++=++-|.
T Consensus 3 ~~~~il~~l~~~~g~~~ylVGG---~VRD~Llg~ 33 (139)
T cd05398 3 ELLKLLRELKKALGYEAYLVGG---AVRDLLLGR 33 (139)
T ss_pred HHHHHHHHHHhccCceEEEECC---hHHHHHcCC
Confidence 466778888887 899999999 566555554
No 89
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=34.54 E-value=72 Score=26.15 Aligned_cols=35 Identities=20% Similarity=0.214 Sum_probs=24.1
Q ss_pred hHHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 15 KWTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 15 ~~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
.||-. ..+.+.+.. +.-.|||.|.|||-+.+..=+
T Consensus 177 k~~~~-i~~~~~~~~--~~~~iIvaGPGF~k~~~~~~~ 211 (352)
T COG1537 177 KFFDE-IAKALKEYA--NLDIIIVAGPGFAKEDFYDFL 211 (352)
T ss_pred HHHHH-HHHHHHHhh--CCCeEEEeCCchHHHHHHHHH
Confidence 44443 334444443 677999999999999887653
No 90
>PRK13851 type IV secretion system protein VirB11; Provisional
Probab=34.28 E-value=44 Score=26.79 Aligned_cols=33 Identities=9% Similarity=0.057 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhcCCceEEEcccH----HHHHHHHhc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTN----YYIESLLWT 51 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTg----lYi~all~g 51 (99)
.+....+..+.+.++.-+|+|||| -.++||+.-
T Consensus 149 ~~~~~~l~~~v~~~~nilI~G~tGSGKTTll~aLl~~ 185 (344)
T PRK13851 149 GDLEAFLHACVVGRLTMLLCGPTGSGKTTMSKTLISA 185 (344)
T ss_pred HHHHHHHHHHHHcCCeEEEECCCCccHHHHHHHHHcc
Confidence 345677888888999999999987 477787754
No 91
>COG0005 Pnp Purine nucleoside phosphorylase [Nucleotide transport and metabolism]
Probab=34.22 E-value=14 Score=28.88 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=9.2
Q ss_pred eEEEcccHHHHH
Q psy17228 35 PIIVGGTNYYIE 46 (99)
Q Consensus 35 pilVGGTglYi~ 46 (99)
-=|+||||||-=
T Consensus 19 igiIgGSGl~~l 30 (262)
T COG0005 19 IGIIGGSGLYDL 30 (262)
T ss_pred EEEEeccccccc
Confidence 346799999963
No 92
>PF00175 NAD_binding_1: Oxidoreductase NAD-binding domain ; InterPro: IPR001433 Bacterial ferredoxin-NADP+ reductase may be bound to the thylakoid membrane or anchored to the thylakoid-bound phycobilisomes. Chloroplast ferredoxin-NADP+ reductase (1.18.1.2 from EC) may play a key role in regulating the relative amounts of cyclic and non-cyclic electron flow to meet the demands of the plant for ATP and reducing power. It is involved in the final step in the linear photosynthetic electron transport chain and has also been implicated in cyclic electron flow around photosystem I where its role would be to return electrons from ferredoxin to the cytochrome B-F complex. This domain is present in a variety of proteins that include, bacterial flavohemoprotein, mammalian NADH-cytochrome b5 reductase, eukaryotic NADPH-cytochrome P450 reductase, nitrate reductase from plants, nitric-oxide synthase, bacterial vanillate demethylase, as well as others.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1UMK_A 1CNE_A 2CND_A 1CNF_A 4FK8_A 4F7D_A 2XNJ_B 1FDR_A 1JB9_A 3LVB_A ....
Probab=33.83 E-value=21 Score=22.31 Aligned_cols=8 Identities=50% Similarity=0.929 Sum_probs=6.7
Q ss_pred EEEcccHH
Q psy17228 36 IIVGGTNY 43 (99)
Q Consensus 36 ilVGGTgl 43 (99)
+|.||||.
T Consensus 1 lIagGtGI 8 (109)
T PF00175_consen 1 LIAGGTGI 8 (109)
T ss_dssp EEEEGGGG
T ss_pred CeecceeH
Confidence 58899996
No 93
>PLN00198 anthocyanidin reductase; Provisional
Probab=33.82 E-value=26 Score=26.59 Aligned_cols=21 Identities=24% Similarity=0.460 Sum_probs=14.8
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
+++..+|+|||||==.+|+..
T Consensus 8 ~~~~vlItG~~GfIG~~l~~~ 28 (338)
T PLN00198 8 GKKTACVIGGTGFLASLLIKL 28 (338)
T ss_pred CCCeEEEECCchHHHHHHHHH
Confidence 467789999999755555443
No 94
>PRK08564 5'-methylthioadenosine phosphorylase II; Reviewed
Probab=33.69 E-value=13 Score=28.75 Aligned_cols=10 Identities=40% Similarity=0.723 Sum_probs=8.1
Q ss_pred EEEcccHHHH
Q psy17228 36 IIVGGTNYYI 45 (99)
Q Consensus 36 ilVGGTglYi 45 (99)
=|+||||||-
T Consensus 11 giIgGSGl~~ 20 (267)
T PRK08564 11 GIIGGSGLYD 20 (267)
T ss_pred EEEecCCCCC
Confidence 4789999975
No 95
>PRK15181 Vi polysaccharide biosynthesis protein TviC; Provisional
Probab=33.56 E-value=23 Score=27.24 Aligned_cols=22 Identities=23% Similarity=0.128 Sum_probs=15.3
Q ss_pred hcCCceEEEcccHHHHHHHHhc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g 51 (99)
-+++..+|+|||||==..|+.-
T Consensus 13 ~~~~~vlVtGatGfiG~~lv~~ 34 (348)
T PRK15181 13 LAPKRWLITGVAGFIGSGLLEE 34 (348)
T ss_pred ccCCEEEEECCccHHHHHHHHH
Confidence 3567789999999854444444
No 96
>TIGR01544 HAD-SF-IE haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.
Probab=32.92 E-value=74 Score=24.95 Aligned_cols=34 Identities=21% Similarity=0.166 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhcC-CceEEEcccHHHHHHHHhccc
Q psy17228 20 LTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 20 ~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~~ 53 (99)
-+.+.++.+.++| .+-|+.||.+.+++.++..+.
T Consensus 125 G~~efl~~L~~~GIpv~IvS~G~~~~Ie~vL~~lg 159 (277)
T TIGR01544 125 GYENFFDKLQQHSIPVFIFSAGIGNVLEEVLRQAG 159 (277)
T ss_pred CHHHHHHHHHHCCCcEEEEeCCcHHHHHHHHHHcC
Confidence 3566777787776 556666999999999999643
No 97
>PLN02650 dihydroflavonol-4-reductase
Probab=32.39 E-value=27 Score=26.73 Aligned_cols=22 Identities=9% Similarity=0.218 Sum_probs=15.5
Q ss_pred hcCCceEEEcccHHHHHHHHhc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g 51 (99)
++++..+|+|||||==.+|+.-
T Consensus 3 ~~~k~iLVTGatGfIGs~l~~~ 24 (351)
T PLN02650 3 SQKETVCVTGASGFIGSWLVMR 24 (351)
T ss_pred CCCCEEEEeCCcHHHHHHHHHH
Confidence 3567788999999855555543
No 98
>COG1646 Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]
Probab=32.33 E-value=24 Score=27.45 Aligned_cols=24 Identities=13% Similarity=0.313 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhcCCceEEEcccH
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTg 42 (99)
..+.++.+.+...|.=.|+||||=
T Consensus 28 ~~~~ei~~~~~~~GTDaImIGGS~ 51 (240)
T COG1646 28 EEADEIAEAAAEAGTDAIMIGGSD 51 (240)
T ss_pred cccHHHHHHHHHcCCCEEEECCcc
Confidence 677888888888999999999984
No 99
>TIGR02622 CDP_4_6_dhtase CDP-glucose 4,6-dehydratase. Members of this protein family are CDP-glucose 4,6-dehydratase from a variety of Gram-negative and Gram-positive bacteria. Members typically are encoded next to a gene that encodes a glucose-1-phosphate cytidylyltransferase, which produces the substrate, CDP-D-glucose, used by this enzyme to produce CDP-4-keto-6-deoxyglucose.
Probab=32.30 E-value=25 Score=26.93 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=11.4
Q ss_pred cCCceEEEcccHHH
Q psy17228 31 RNKVPIIVGGTNYY 44 (99)
Q Consensus 31 ~~~~pilVGGTglY 44 (99)
.|+..+|+||||+=
T Consensus 3 ~~k~ilItGatG~I 16 (349)
T TIGR02622 3 QGKKVLVTGHTGFK 16 (349)
T ss_pred CCCEEEEECCCChh
Confidence 46788999999973
No 100
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.
Probab=31.92 E-value=53 Score=25.54 Aligned_cols=34 Identities=24% Similarity=0.345 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHH----HHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNY----YIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTgl----Yi~all~g~ 52 (99)
.+..+.+..+.+.++.-+|+|+||- .++||+.-+
T Consensus 119 ~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~al~~~i 156 (299)
T TIGR02782 119 AAQRDVLREAVLARKNILVVGGTGSGKTTLANALLAEI 156 (299)
T ss_pred HHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHh
Confidence 3455667777777888899998874 777777543
No 101
>PLN02572 UDP-sulfoquinovose synthase
Probab=31.32 E-value=26 Score=28.47 Aligned_cols=21 Identities=19% Similarity=0.344 Sum_probs=15.6
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
+++..+|+|||||==.+|+.-
T Consensus 46 ~~k~VLVTGatGfIGs~Lv~~ 66 (442)
T PLN02572 46 KKKKVMVIGGDGYCGWATALH 66 (442)
T ss_pred cCCEEEEECCCcHHHHHHHHH
Confidence 467789999999865555554
No 102
>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.
Probab=31.30 E-value=59 Score=22.92 Aligned_cols=33 Identities=24% Similarity=0.237 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHH----HHHHHHh
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNY----YIESLLW 50 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTgl----Yi~all~ 50 (99)
-.+..+.+..+.+.|..-+|+|.||- .+++|+.
T Consensus 11 ~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll~aL~~ 47 (186)
T cd01130 11 SPLQAAYLWLAVEARKNILISGGTGSGKTTLLNALLA 47 (186)
T ss_pred CHHHHHHHHHHHhCCCEEEEECCCCCCHHHHHHHHHh
Confidence 35667788888889999999996664 5677764
No 103
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=31.17 E-value=56 Score=26.02 Aligned_cols=33 Identities=18% Similarity=0.253 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhcCCceEEEcccHH----HHHHHHhcc
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNY----YIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTgl----Yi~all~g~ 52 (99)
...+.+..+...++.-+|+||||- .++||+.-+
T Consensus 132 ~~~~~L~~~v~~~~nilI~G~tGSGKTTll~aL~~~i 168 (323)
T PRK13833 132 AQASVIRSAIDSRLNIVISGGTGSGKTTLANAVIAEI 168 (323)
T ss_pred HHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHH
Confidence 344667777777888899999884 788888754
No 104
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.
Probab=31.07 E-value=48 Score=23.48 Aligned_cols=22 Identities=23% Similarity=0.557 Sum_probs=15.0
Q ss_pred HHHHHHHH--hcCCceEEEcccHH
Q psy17228 22 KTKIDDIL--QRNKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~--~~~~~pilVGGTgl 43 (99)
.+.+++.. ++..+.|++||||.
T Consensus 52 ~~~l~~~~~~~~~DlVIttGGtg~ 75 (163)
T TIGR02667 52 RAQVSAWIADPDVQVILITGGTGF 75 (163)
T ss_pred HHHHHHHHhcCCCCEEEECCCcCC
Confidence 34455553 24688899999985
No 105
>cd02812 PcrB_like PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown.
Probab=30.97 E-value=42 Score=25.41 Aligned_cols=18 Identities=28% Similarity=0.593 Sum_probs=13.6
Q ss_pred HHHHHh-cCCceEEEcccH
Q psy17228 25 IDDILQ-RNKVPIIVGGTN 42 (99)
Q Consensus 25 i~~i~~-~~~~pilVGGTg 42 (99)
++.+.. .|.-.|+||||-
T Consensus 17 ~~~~~~~~gtdai~vGGS~ 35 (219)
T cd02812 17 IAKLAEESGTDAIMVGGSD 35 (219)
T ss_pred HHHHHHhcCCCEEEECCcc
Confidence 444444 889999999997
No 106
>PLN02653 GDP-mannose 4,6-dehydratase
Probab=30.95 E-value=24 Score=26.80 Aligned_cols=21 Identities=29% Similarity=0.060 Sum_probs=14.5
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
.++..+|+|||||==.+|+.-
T Consensus 5 ~~~~vlVTGatGfiG~~l~~~ 25 (340)
T PLN02653 5 PRKVALITGITGQDGSYLTEF 25 (340)
T ss_pred CCCEEEEECCCCccHHHHHHH
Confidence 367789999998755554443
No 107
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=30.89 E-value=8.5 Score=22.65 Aligned_cols=25 Identities=16% Similarity=0.546 Sum_probs=19.8
Q ss_pred cccchHHHHHHHHHHHHHHhcCCce
Q psy17228 11 LTKTKWTIKLTKTKIDDILQRNKVP 35 (99)
Q Consensus 11 ~~~~~~~~~~a~~~i~~i~~~~~~p 35 (99)
|+...|....|.....++.+.|++|
T Consensus 22 L~~n~Wd~~~A~~~F~~l~~~~~IP 46 (51)
T PF03943_consen 22 LEENNWDYERALQNFEELKAQGKIP 46 (51)
T ss_dssp HHHTTT-CCHHHHHHHHCCCTT-S-
T ss_pred HHHcCCCHHHHHHHHHHHHHcCCCC
Confidence 6778899999999999999999988
No 108
>PRK13946 shikimate kinase; Provisional
Probab=30.84 E-value=62 Score=22.80 Aligned_cols=31 Identities=13% Similarity=0.222 Sum_probs=20.0
Q ss_pred cchHHHHHHHHHHHHHHhcCCceEEEcccHHH
Q psy17228 13 KTKWTIKLTKTKIDDILQRNKVPIIVGGTNYY 44 (99)
Q Consensus 13 ~~~~~~~~a~~~i~~i~~~~~~pilVGGTglY 44 (99)
.+.||...-.+++..+...+.. ||+||.|-|
T Consensus 61 ge~~~~~~e~~~l~~l~~~~~~-Vi~~ggg~~ 91 (184)
T PRK13946 61 GEPEFRDLERRVIARLLKGGPL-VLATGGGAF 91 (184)
T ss_pred CHHHHHHHHHHHHHHHHhcCCe-EEECCCCCc
Confidence 4566766667888888877655 555544433
No 109
>cd04254 AAK_UMPK-PyrH-Ec UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinase of E. coli (Ec) is known to function as a homohexamer, with GTP and UTP being allosteric effectors. Like other related enzymes (carbamate kinase, aspartokinase, and N-acetylglutamate kinase) the E. coli and most bacterial and chloroplast UMPKs (this CD) have a conserved, N-terminal, lysine residue proposed to function in the catalysis of the phosphoryl group transfer, whereas most archaeal UMPKs appear to lack this residue and the Pyrococcus furiosus structure has an additional Mg ion bound to the ATP molecule which is proposed to function as the catalysis instead. Members of this CD be
Probab=30.81 E-value=47 Score=24.52 Aligned_cols=21 Identities=29% Similarity=0.515 Sum_probs=17.3
Q ss_pred HHHHHHHHhcCCceEEEcccH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTg 42 (99)
.+.+...+++|.+||+.|+.|
T Consensus 110 ~~~l~~~l~~g~ipV~~g~~G 130 (231)
T cd04254 110 RRRAIRHLEKGRVVIFAGGTG 130 (231)
T ss_pred HHHHHHHHHCCCEEEEECCcC
Confidence 367788888999999998865
No 110
>TIGR00381 cdhD CO dehydrogenase/acetyl-CoA synthase, delta subunit. This is the small subunit of a heterodimer which catalyzes the reaction CO + H2O + Acceptor = CO2 + Reduced acceptor and is involved in the synthesis of acetyl-CoA from CO2 and H2.
Probab=30.43 E-value=50 Score=27.38 Aligned_cols=24 Identities=33% Similarity=0.652 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHhcCCceEEEccc
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGT 41 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGT 41 (99)
.+.+.+.++.+.+.-++|++++||
T Consensus 173 ~~e~a~~vk~V~~av~vPLIL~gs 196 (389)
T TIGR00381 173 PSEAAKVLEDVLQAVDVPIVIGGS 196 (389)
T ss_pred HHHHHHHHHHHHHhCCCCEEEeCC
Confidence 346788888888889999999999
No 111
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=30.17 E-value=62 Score=24.68 Aligned_cols=42 Identities=26% Similarity=0.272 Sum_probs=25.6
Q ss_pred cccchHHHHHHHHHHHHHHhcC-CceEEEcc--cHHHHHHHHhcc
Q psy17228 11 LTKTKWTIKLTKTKIDDILQRN-KVPIIVGG--TNYYIESLLWTI 52 (99)
Q Consensus 11 ~~~~~~~~~~a~~~i~~i~~~~-~~pilVGG--TglYi~all~g~ 52 (99)
|+..+....+..+.+.....+| -+||+||- ++.=++.|++.+
T Consensus 219 l~~~~~~~~el~~~l~~~~~~~~~~PV~~gSa~~~~Gi~~lld~i 263 (270)
T cd01886 219 LEGEEITEEEIKAAIRKGTIANKIVPVLCGSAFKNKGVQPLLDAV 263 (270)
T ss_pred hCCCCCCHHHHHHHHHHHHHcCcEEEEEeCcCCCCcCHHHHHHHH
Confidence 3444555566666666665565 56888875 344446666664
No 112
>COG1735 Php Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]
Probab=30.12 E-value=14 Score=29.76 Aligned_cols=16 Identities=25% Similarity=0.276 Sum_probs=12.8
Q ss_pred eEEEcccHHHHHHHHh
Q psy17228 35 PIIVGGTNYYIESLLW 50 (99)
Q Consensus 35 pilVGGTglYi~all~ 50 (99)
.=||+|||||..+...
T Consensus 89 lnIV~~TGfy~~~~~p 104 (316)
T COG1735 89 LNIVAATGFYKAAFHP 104 (316)
T ss_pred CcEEEeccccccccch
Confidence 3479999999987765
No 113
>cd04261 AAK_AKii-LysC-BS AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine, and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase isoenzyme type, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In this organism and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regulated by the concerted action of lysine and
Probab=30.09 E-value=1e+02 Score=22.75 Aligned_cols=32 Identities=13% Similarity=0.158 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhcCCceE-EEcccHHHHHHHHh
Q psy17228 19 KLTKTKIDDILQRNKVPI-IVGGTNYYIESLLW 50 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pi-lVGGTglYi~all~ 50 (99)
+...+.|..+...|.-|| |+||-|-..+.++.
T Consensus 18 ~~~~~~i~~l~~~g~~~vvV~sg~g~~~~~l~~ 50 (239)
T cd04261 18 KRVAERIKKRKKKGNQVVVVVSAMGGTTDELIE 50 (239)
T ss_pred HHHHHHHHHHHHcCCCEEEEECCCCchhHHHHH
Confidence 345555666666775555 46876777777765
No 114
>cd00311 TIM Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually homodimeric, but in some organisms tetrameric, is ubiqitous and conserved in function across eukaryotes, bacteria and archaea.
Probab=30.07 E-value=77 Score=24.17 Aligned_cols=25 Identities=28% Similarity=0.417 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHhc------CCceEEEcccHH
Q psy17228 19 KLTKTKIDDILQR------NKVPIIVGGTNY 43 (99)
Q Consensus 19 ~~a~~~i~~i~~~------~~~pilVGGTgl 43 (99)
.++...|.+..++ .+++||.|||=-
T Consensus 179 ~ev~~~ir~~l~~~~~~~~~~~~IlYGGSV~ 209 (242)
T cd00311 179 QEVHAFIRKLLAELYGEVAEKVRILYGGSVN 209 (242)
T ss_pred HHHHHHHHHHHHHhcccccCceeEEECCCCC
Confidence 4455555555543 479999999843
No 115
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=29.69 E-value=92 Score=25.55 Aligned_cols=35 Identities=14% Similarity=0.071 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHhc----CCceEEEcccHHHHHHHHh
Q psy17228 16 WTIKLTKTKIDDILQR----NKVPIIVGGTNYYIESLLW 50 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~----~~~pilVGGTglYi~all~ 50 (99)
-|.+.+.+.+.+++.+ +--.||+||.|+.-+.+.+
T Consensus 188 ~f~~~Vae~~~~~f~~~~~~~v~~lILaGpg~~K~~f~~ 226 (403)
T TIGR03676 188 EFYKRVGEAANEAFLPLKDKKLKGILIGGPGPTKEEFAE 226 (403)
T ss_pred HHHHHHHHHHHHHHhhcccccccEEEEeCCHHHHHHHhh
Confidence 3455555555555432 3468999999999888877
No 116
>PF00186 DHFR_1: Dihydrofolate reductase; InterPro: IPR001796 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself [].; GO: 0004146 dihydrofolate reductase activity, 0006545 glycine biosynthetic process, 0009165 nucleotide biosynthetic process, 0055114 oxidation-reduction process; PDB: 1ZDR_B 3SA2_B 3JWK_B 3E0B_A 3S9U_B 3FL9_H 3FL8_F 2QK8_A 3JW3_A 3SA1_B ....
Probab=29.42 E-value=55 Score=23.33 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhcCCceEEEcccHHHHHHHH
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNYYIESLL 49 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTglYi~all 49 (99)
...++++-+....+...|+||.+.|=.+|-
T Consensus 79 s~~~al~~~~~~~~~i~ViGG~~iy~~~l~ 108 (161)
T PF00186_consen 79 SLEEALELAKDKDEEIFVIGGAEIYEQFLP 108 (161)
T ss_dssp SHHHHHHHHTTSESEEEEEE-HHHHHHHHH
T ss_pred CHHHHHHHhhccCCcEEEECCHHHHHHHHH
Confidence 334445422222367888899999988775
No 117
>PRK14822 nucleoside-triphosphatase; Provisional
Probab=29.19 E-value=24 Score=26.19 Aligned_cols=34 Identities=12% Similarity=0.107 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhc
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g 51 (99)
|...|......+.+.-..|+|+==||||++|| .|
T Consensus 47 ~~enA~~KA~~~~~~~~~pviaDDSGL~v~AL-~G 80 (200)
T PRK14822 47 FEENAILKAEAAAKALNKPVIADDSGLEVDAL-NG 80 (200)
T ss_pred HHHHHHHHHHHHHHHHCCCEEEeccEEEEccc-CC
Confidence 55566666666666656799999999999998 45
No 118
>PRK07823 5'-methylthioadenosine phosphorylase; Validated
Probab=29.10 E-value=20 Score=27.80 Aligned_cols=10 Identities=30% Similarity=0.929 Sum_probs=8.2
Q ss_pred EEEcccHHHH
Q psy17228 36 IIVGGTNYYI 45 (99)
Q Consensus 36 ilVGGTglYi 45 (99)
=|+||||||-
T Consensus 9 gII~GSGl~~ 18 (264)
T PRK07823 9 GVIGGSGFYS 18 (264)
T ss_pred EEEeccccch
Confidence 4779999985
No 119
>TIGR01697 PNPH-PUNA-XAPA inosine guanosine and xanthosine phosphorylase family. Sequences from Clostridium and Thermotoga fall between these last two clades and are uncharacterized with respect to substrate range and operon.
Probab=29.05 E-value=20 Score=26.98 Aligned_cols=10 Identities=20% Similarity=0.188 Sum_probs=8.5
Q ss_pred EEEcccHHHH
Q psy17228 36 IIVGGTNYYI 45 (99)
Q Consensus 36 ilVGGTglYi 45 (99)
-|+||||+|=
T Consensus 3 ~ii~gsg~~~ 12 (248)
T TIGR01697 3 AIILGSGLGA 12 (248)
T ss_pred EEEeeCCcch
Confidence 4789999995
No 120
>PLN02583 cinnamoyl-CoA reductase
Probab=29.04 E-value=30 Score=25.97 Aligned_cols=21 Identities=14% Similarity=0.071 Sum_probs=15.3
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
.++..+|+||||+==.+++.-
T Consensus 5 ~~k~vlVTGatG~IG~~lv~~ 25 (297)
T PLN02583 5 SSKSVCVMDASGYVGFWLVKR 25 (297)
T ss_pred CCCEEEEECCCCHHHHHHHHH
Confidence 467788899998766665554
No 121
>cd05637 SIS_PGI_PMI_2 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the second SIS domain.
Probab=28.95 E-value=57 Score=22.36 Aligned_cols=21 Identities=33% Similarity=0.578 Sum_probs=14.2
Q ss_pred HHHHHHHHhcCCceEEEcccHHHH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTNYYI 45 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTglYi 45 (99)
+.+-..+ .|.+|||.|.| +|.
T Consensus 4 k~LA~~l--~g~~Pvi~g~~-~~~ 24 (132)
T cd05637 4 KELALEL--AGRIPIIYGST-LYE 24 (132)
T ss_pred HHHHHHh--cCCCCEEEecc-chH
Confidence 3344444 47999999998 554
No 122
>PF01370 Epimerase: NAD dependent epimerase/dehydratase family; InterPro: IPR001509 This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions []. It contains the NAD(P)- binding domain (IPR016040 from INTERPRO) which is a commonly found domain with a core Rossmann-type fold. One of the best studied of these proteins is UDP-galactose 4-epimerase which catalyses the conversion of UDP-galactose to UDP-glucose during galactose metabolism [, ].; GO: 0003824 catalytic activity, 0050662 coenzyme binding, 0044237 cellular metabolic process; PDB: 2NNL_D 3C1T_B 3BXX_C 2IOD_C 2X4G_A 2Q1W_B 3SLG_B 1R66_A 1R6D_A 1KEU_B ....
Probab=28.87 E-value=27 Score=24.41 Aligned_cols=17 Identities=24% Similarity=0.491 Sum_probs=13.4
Q ss_pred EEEcccHHHHHHHHhcc
Q psy17228 36 IIVGGTNYYIESLLWTI 52 (99)
Q Consensus 36 ilVGGTglYi~all~g~ 52 (99)
+|+|||||==.+|+.-+
T Consensus 2 lI~GatG~iG~~l~~~l 18 (236)
T PF01370_consen 2 LITGATGFIGSALVRQL 18 (236)
T ss_dssp EEETTTSHHHHHHHHHH
T ss_pred EEEccCCHHHHHHHHHH
Confidence 68899999777777664
No 123
>PRK00042 tpiA triosephosphate isomerase; Provisional
Probab=28.82 E-value=92 Score=23.90 Aligned_cols=26 Identities=27% Similarity=0.333 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHh------cCCceEEEcccHHH
Q psy17228 19 KLTKTKIDDILQ------RNKVPIIVGGTNYY 44 (99)
Q Consensus 19 ~~a~~~i~~i~~------~~~~pilVGGTglY 44 (99)
+++...|++..+ ..+++||.|||=-=
T Consensus 183 ~~v~~~Ir~~l~~~~~~~~~~~~IlYGGSV~~ 214 (250)
T PRK00042 183 QEVHAFIRAVLAELYGEVAEKVRILYGGSVKP 214 (250)
T ss_pred HHHHHHHHHHHHHhcccccCCceEEEcCCCCH
Confidence 445555655554 24689999998543
No 124
>PRK05835 fructose-bisphosphate aldolase; Provisional
Probab=28.77 E-value=68 Score=25.59 Aligned_cols=19 Identities=11% Similarity=0.656 Sum_probs=12.0
Q ss_pred HHHHHHhcCCceEEE-cccH
Q psy17228 24 KIDDILQRNKVPIIV-GGTN 42 (99)
Q Consensus 24 ~i~~i~~~~~~pilV-GGTg 42 (99)
.+++|.+.=.+|++- ||||
T Consensus 195 ~L~~I~~~~~iPLVLHGgSG 214 (307)
T PRK05835 195 RLQEVKRLTNIPLVLHGASA 214 (307)
T ss_pred HHHHHHHHhCCCEEEeCCCC
Confidence 445555554566554 9999
No 125
>PRK09417 mogA molybdenum cofactor biosynthesis protein MogA; Provisional
Probab=28.60 E-value=52 Score=24.30 Aligned_cols=22 Identities=14% Similarity=0.326 Sum_probs=15.2
Q ss_pred HHHHHHHHh--cCCceEEEcccHH
Q psy17228 22 KTKIDDILQ--RNKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~~--~~~~pilVGGTgl 43 (99)
.+.+.++.. .-.+.|.+||||+
T Consensus 55 ~~aL~~a~~~~~~DlIITTGGtg~ 78 (193)
T PRK09417 55 EQTLIELVDEMGCDLVLTTGGTGP 78 (193)
T ss_pred HHHHHHHhhcCCCCEEEECCCCCC
Confidence 345555554 4588888899996
No 126
>PRK00120 dITP/XTP pyrophosphatase; Reviewed
Probab=28.55 E-value=29 Score=25.68 Aligned_cols=33 Identities=9% Similarity=0.178 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHH
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLL 49 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all 49 (99)
|..-|......+.+.-+.|+|+==|||||+||=
T Consensus 45 ~~enA~~KA~~~~~~~~~pviaDDSGL~i~aL~ 77 (196)
T PRK00120 45 FVENALIKARHAAKATGLPALADDSGLCVDALG 77 (196)
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEcCEEEEcccC
Confidence 555666666666655566999999999999983
No 127
>PF03018 Dirigent: Dirigent-like protein; InterPro: IPR004265 This family contains a number of proteins which are induced during disease response in plants.
Probab=28.37 E-value=23 Score=24.85 Aligned_cols=16 Identities=25% Similarity=0.439 Sum_probs=12.0
Q ss_pred EEEcccHHHHHHHHhccc
Q psy17228 36 IIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 36 ilVGGTglYi~all~g~~ 53 (99)
-||||||-| +.-.|+.
T Consensus 106 ~VVGGTG~F--r~ArG~~ 121 (144)
T PF03018_consen 106 AVVGGTGEF--RMARGYA 121 (144)
T ss_pred eEecCCCeE--cceEEEE
Confidence 489999988 5557753
No 128
>PRK14821 putative deoxyribonucleotide triphosphate pyrophosphatase; Provisional
Probab=28.34 E-value=44 Score=24.43 Aligned_cols=34 Identities=18% Similarity=0.248 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhc
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g 51 (99)
|...|......+.+.-..|+|+==||||++|| .|
T Consensus 42 ~~enA~~KA~~~~~~~~~pvlaDDSGL~v~aL-~g 75 (184)
T PRK14821 42 LEEVAAFGAKWVYNKLNRPVIVEDSGLFIEAL-NG 75 (184)
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEcCEEeehhh-CC
Confidence 55666666666666656799999999999998 44
No 129
>TIGR00042 non-canonical purine NTP pyrophosphatase, rdgB/HAM1 family. Saccharomyces cerevisiae HAM1 protects against the mutagenic effects of the base analog 6-N-hydroxylaminopurine, which can be a natural product of monooxygenase activity on adenine. Methanococcus jannaschii MJ0226 and E. coli RdgB are also characterized as pyrophosphatases active against non-standard purines NTPs. E. coli RdgB appears to act by intercepting non-canonical deoxyribonucleotide triphosphates from replication precursor pools.
Probab=28.28 E-value=30 Score=25.32 Aligned_cols=33 Identities=12% Similarity=0.164 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHhcCCceEEEcccHHHHHHHH
Q psy17228 17 TIKLTKTKIDDILQRNKVPIIVGGTNYYIESLL 49 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~~~pilVGGTglYi~all 49 (99)
|...|......+.+.-..|+|+==||||++||=
T Consensus 42 ~~enA~~KA~~~~~~~~~pvlaDDSGL~v~AL~ 74 (184)
T TIGR00042 42 FEENALLKAKHAAKILNKPVIAEDSGLFVDALN 74 (184)
T ss_pred HHHHHHHHHHHHHHHhCCCeEEcccEEEEhhcC
Confidence 455566555555555567999999999999984
No 130
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=28.25 E-value=58 Score=21.73 Aligned_cols=26 Identities=19% Similarity=0.428 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHHH
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYYI 45 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglYi 45 (99)
..+...++.+.+ .++|+|+|=||+.-
T Consensus 78 ~~~~~~~~~~~~-~g~~~ViGTTG~~~ 103 (124)
T PF01113_consen 78 DAVYDNLEYALK-HGVPLVIGTTGFSD 103 (124)
T ss_dssp HHHHHHHHHHHH-HT-EEEEE-SSSHH
T ss_pred HHhHHHHHHHHh-CCCCEEEECCCCCH
Confidence 344555555554 48899999999963
No 131
>PRK05057 aroK shikimate kinase I; Reviewed
Probab=28.18 E-value=96 Score=21.73 Aligned_cols=31 Identities=10% Similarity=0.204 Sum_probs=21.4
Q ss_pred cchHHHHHHHHHHHHHHhcCCceEEEcccHH
Q psy17228 13 KTKWTIKLTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 13 ~~~~~~~~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
.+..|.....+.++++...+..+|-+||.-.
T Consensus 55 g~~~fr~~e~~~l~~l~~~~~~vi~~ggg~v 85 (172)
T PRK05057 55 GEEGFRDREEKVINELTEKQGIVLATGGGSV 85 (172)
T ss_pred CHHHHHHHHHHHHHHHHhCCCEEEEcCCchh
Confidence 3444555567788888777777787887644
No 132
>TIGR01491 HAD-SF-IB-PSPlk HAD-superfamily, subfamily-IB PSPase-like hydrolase, archaeal. This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this alignment are all from archaeal species. The phylogenetically closest group of sequences to these are phosphoserine phosphatases (TIGR00338). There are no known archaeal phosphoserine phosphatases, and no archaea fall within TIGR00338. It is likely, then, that This model represents the archaeal branch of the PSPase equivalog.
Probab=27.71 E-value=1e+02 Score=21.06 Aligned_cols=34 Identities=12% Similarity=0.222 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~ 52 (99)
..+.+.++.+.++| ++-|+.||...+++.++..+
T Consensus 83 ~g~~e~l~~l~~~g~~~~IvS~~~~~~~~~~l~~~ 117 (201)
T TIGR01491 83 DYAEELVRWLKEKGLKTAIVSGGIMCLAKKVAEKL 117 (201)
T ss_pred ccHHHHHHHHHHCCCEEEEEeCCcHHHHHHHHHHh
Confidence 36788899998887 55666688889999987643
No 133
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=27.71 E-value=68 Score=25.32 Aligned_cols=33 Identities=12% Similarity=0.351 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhcCCceEEEcccH----HHHHHHHhcc
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTN----YYIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTg----lYi~all~g~ 52 (99)
...+.+..+...++.-+|+|||| -+++||+..+
T Consensus 136 ~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~aL~~~~ 172 (319)
T PRK13894 136 AQREAIIAAVRAHRNILVIGGTGSGKTTLVNAIINEM 172 (319)
T ss_pred HHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHhh
Confidence 34466777777888899999988 4677888653
No 134
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=27.66 E-value=75 Score=23.64 Aligned_cols=42 Identities=19% Similarity=0.179 Sum_probs=25.4
Q ss_pred cccchHHHHHHHHHHHHHHhcC-CceEEEcc--cHHHHHHHHhcc
Q psy17228 11 LTKTKWTIKLTKTKIDDILQRN-KVPIIVGG--TNYYIESLLWTI 52 (99)
Q Consensus 11 ~~~~~~~~~~a~~~i~~i~~~~-~~pilVGG--TglYi~all~g~ 52 (99)
|+.++....+..+.+.....+| -+||+||- ++.=++.|+..+
T Consensus 186 l~~~~~~~~el~~~l~~~~~~~~~~Pv~~gsa~~~~Gv~~ll~~~ 230 (237)
T cd04168 186 LEGGPIEELELDNELSARIAKRKVFPVYHGSALKGIGIEELLEGI 230 (237)
T ss_pred hCCCCCCHHHHHHHHHHHHHhCCeEEEEEccccCCcCHHHHHHHH
Confidence 4555666666666666666555 56888874 333345666554
No 135
>COG2704 DcuB Anaerobic C4-dicarboxylate transporter [General function prediction only]
Probab=27.62 E-value=50 Score=27.71 Aligned_cols=64 Identities=11% Similarity=-0.019 Sum_probs=34.5
Q ss_pred EEEcccHHHHHHHHhcccCCCCCCCcccchHhHHHHHhhcchhhchhh-hHHhhccCCCCCCCCC
Q psy17228 36 IIVGGTNYYIESLLWTILLDNKTNINDQGEFTLYDMDKIRNLEHGRDV-LESLWKLDMNYSYRIE 99 (99)
Q Consensus 36 ilVGGTglYi~all~g~~~~~~~~~~~~~~~~l~~~l~~~d~e~~~~~-p~~A~rI~pnD~~RI~ 99 (99)
=++||-|+-+.++..|+....||.+.-.=.-..-.-.......-+.|+ -+-|+||-..|++||+
T Consensus 25 G~~GGlGv~il~f~f~~~P~~~PidViliImAVv~aaaamQaaGGLD~mvqiAEkiLRknPK~iT 89 (436)
T COG2704 25 GVAGGLGVLILVFIFGLKPGKPPIDVILIIMAVVAAAAAMQAAGGLDYMVQIAEKILRKNPKYIT 89 (436)
T ss_pred eecccccHHHHhhhhcCCCCCCChhhHHHHHHHHHHHHHHHHccChhHHHHHHHHHHHhCCCeEE
Confidence 367999999999999977333554442100000000000011123333 4678888888888763
No 136
>TIGR03702 lip_kinase_YegS lipid kinase YegS. Members of this protein family are designated YegS, an apparent lipid kinase family in the Proteobacteria. Bakali, et al. report phosphatidylglycerol kinase activity for the member from Escherichia coli, but refrain from calling that activity synonymous with its biological role. Note that a broader, subfamily-type model (TIGR00147), includes this family but also multiple paralogs in some species and varied functions.
Probab=27.62 E-value=80 Score=23.99 Aligned_cols=35 Identities=11% Similarity=0.116 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhccc
Q psy17228 18 IKLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~~ 53 (99)
..+|.++..++.+.+ ...|+|||=|. +..+++|+.
T Consensus 38 ~~~a~~~a~~~~~~~~d~vv~~GGDGT-i~ev~ngl~ 73 (293)
T TIGR03702 38 KGDAQRYVAEALALGVSTVIAGGGDGT-LREVATALA 73 (293)
T ss_pred CCCHHHHHHHHHHcCCCEEEEEcCChH-HHHHHHHHH
Confidence 346777777665544 67888999997 555667763
No 137
>cd03813 GT1_like_3 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=27.62 E-value=36 Score=27.53 Aligned_cols=23 Identities=17% Similarity=0.453 Sum_probs=21.3
Q ss_pred hcCCceEEEcccHHHHHHHHhcc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g~ 52 (99)
-+|.-|.++||...+++.|+.|+
T Consensus 6 ~egtyp~~~ggvs~w~~~~i~~~ 28 (475)
T cd03813 6 LEGTYPYVRGGVSSWVHQLITGL 28 (475)
T ss_pred EecCCCCcCCchhHHHHHHHhhC
Confidence 46889999999999999999996
No 138
>PRK15016 isochorismate synthase EntC; Provisional
Probab=27.61 E-value=74 Score=26.19 Aligned_cols=28 Identities=18% Similarity=0.176 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHHHHHhcC-CceEEEcccH
Q psy17228 15 KWTIKLTKTKIDDILQRN-KVPIIVGGTN 42 (99)
Q Consensus 15 ~~~~~~a~~~i~~i~~~~-~~pilVGGTg 42 (99)
.=|.+.+...+++..+.| ..|||||--.
T Consensus 51 ~~~~~~~~~~~~~a~~~g~~~p~~vGaiP 79 (391)
T PRK15016 51 SPFQQKLAALFADAKAQGIKNPVMVGAIP 79 (391)
T ss_pred hhHHHHHHHHHHHHHHcCCCCCeEEEECC
Confidence 346778888888898898 8999999533
No 139
>cd07044 CofD_YvcK Family of CofD-like proteins and proteins related to YvcK. CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway. Both families appear to have a conserved phosphate binding site, but ha
Probab=27.55 E-value=38 Score=26.95 Aligned_cols=18 Identities=33% Similarity=0.379 Sum_probs=14.3
Q ss_pred ceEEEcccHHHHHHHHhccc
Q psy17228 34 VPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 34 ~pilVGGTglYi~all~g~~ 53 (99)
+.+|-||||++ .|+.|+.
T Consensus 1 iv~igGGtGl~--~ll~gLk 18 (309)
T cd07044 1 VVVFGGGTGLP--VLLRGLK 18 (309)
T ss_pred CEEEeccccHH--HHHHHHH
Confidence 35788999998 7888864
No 140
>TIGR00761 argB acetylglutamate kinase. This model describes N-acetylglutamate kinases (ArgB) of many prokaryotes and the N-acetylglutamate kinase domains of multifunctional proteins from yeasts. This enzyme is the second step in the "acetylated" ornithine biosynthesis pathway. A related group of enzymes representing the first step of the pathway contain a homologous domain and are excluded from this model.
Probab=27.47 E-value=1.4e+02 Score=21.76 Aligned_cols=35 Identities=23% Similarity=0.175 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHHHHHHHhccc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~ 53 (99)
..+.+.|..+.+.|..+|||=|.|-+++.++..+.
T Consensus 16 ~~~~~~i~~l~~~g~~~VlVhggg~~~~~~~~~~~ 50 (231)
T TIGR00761 16 EAFASDIAFLRAVGIKPVIVHGGGPEINELLEALG 50 (231)
T ss_pred HHHHHHHHHHHHcCCCEEEEcCCcHHHHHHHHHcC
Confidence 34445556666788778999888888988876543
No 141
>cd07995 TPK Thiamine pyrophosphokinase. Thiamine pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions, and thiamine deficiency is associated with potentially fatal human diseases. The structure of thiamine pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
Probab=27.30 E-value=73 Score=23.16 Aligned_cols=34 Identities=18% Similarity=0.198 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHhcCC-ceEEEcccHHHHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRNK-VPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~-~pilVGGTglYi~all~g~ 52 (99)
.|...+++.+.+++. .-+|+|+||==++..+..+
T Consensus 77 TD~e~Al~~~~~~~~~~i~i~Ga~GgR~DH~lani 111 (208)
T cd07995 77 TDFEKALKLALERGADEIVILGATGGRLDHTLANL 111 (208)
T ss_pred CHHHHHHHHHHHcCCCEEEEEccCCCcHHHHHHHH
Confidence 477888888888875 4556699998777776664
No 142
>TIGR01472 gmd GDP-mannose 4,6-dehydratase. Excluded from this model are members of the clade that score poorly because of highly dervied (phylogenetically long-branch) sequences, e.g. Aneurinibacillus thermoaerophilus Gmd, described as a bifunctional GDP-mannose 4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase (PUBMED:11096116).
Probab=26.79 E-value=30 Score=26.38 Aligned_cols=17 Identities=24% Similarity=0.061 Sum_probs=11.4
Q ss_pred ceEEEcccHHHHHHHHh
Q psy17228 34 VPIIVGGTNYYIESLLW 50 (99)
Q Consensus 34 ~pilVGGTglYi~all~ 50 (99)
..+|+|||||==.+|+.
T Consensus 2 ~vlVTGatGfIG~~l~~ 18 (343)
T TIGR01472 2 IALITGITGQDGSYLAE 18 (343)
T ss_pred eEEEEcCCCcHHHHHHH
Confidence 46888999975444443
No 143
>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme. This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium.
Probab=26.77 E-value=79 Score=25.31 Aligned_cols=24 Identities=25% Similarity=0.314 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHhcC-CceEEEcccH
Q psy17228 19 KLTKTKIDDILQRN-KVPIIVGGTN 42 (99)
Q Consensus 19 ~~a~~~i~~i~~~~-~~pilVGGTg 42 (99)
+.+.+++..+.+++ +.+|+|||-.
T Consensus 50 ~~~~~~i~~~k~~~p~~~vvvgGc~ 74 (414)
T TIGR01579 50 SKARRAIRRARRQNPTAKIIVTGCY 74 (414)
T ss_pred HHHHHHHHHHHhhCCCcEEEEECCc
Confidence 45778888887665 5789999964
No 144
>PLN02954 phosphoserine phosphatase
Probab=26.65 E-value=1e+02 Score=21.80 Aligned_cols=35 Identities=14% Similarity=0.146 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhcCC-ceEEEcccHHHHHHHHhccc
Q psy17228 19 KLTKTKIDDILQRNK-VPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~-~pilVGGTglYi~all~g~~ 53 (99)
..+.+.++.+.++|. +-|+.||...+++.++..+.
T Consensus 87 pg~~e~l~~l~~~g~~~~IvS~~~~~~i~~~l~~~g 122 (224)
T PLN02954 87 PGIPELVKKLRARGTDVYLVSGGFRQMIAPVAAILG 122 (224)
T ss_pred ccHHHHHHHHHHCCCEEEEECCCcHHHHHHHHHHhC
Confidence 366778888877774 55777999999999887653
No 145
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=26.64 E-value=1.1e+02 Score=22.54 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=31.6
Q ss_pred hhhhcccchHHHHHHHHHHHHHHhcCCceEEEcc-cHHHHHHHHh
Q psy17228 7 WRLKLTKTKWTIKLTKTKIDDILQRNKVPIIVGG-TNYYIESLLW 50 (99)
Q Consensus 7 ~~~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGG-TglYi~all~ 50 (99)
.++...++......+.+.++++..+.++.+|+|+ +.-...++..
T Consensus 43 i~l~~~D~~~~~~~a~~~~~~l~~~~~v~~vvg~~~s~~~~~~~~ 87 (343)
T PF13458_consen 43 IELVVYDDGGDPAQAVQAARKLIDDDGVDAVVGPLSSAQAEAVAP 87 (343)
T ss_dssp EEEEEEE-TT-HHHHHHHHHHHHHTSTESEEEESSSHHHHHHHHH
T ss_pred ceeeeccCCCChHHHHHHHHHhhhhcCcEEEEecCCcHHHHHHHH
Confidence 4455667788888999999999998899999997 4454555443
No 146
>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]. These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....
Probab=26.50 E-value=43 Score=24.84 Aligned_cols=35 Identities=17% Similarity=0.143 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhcCCceEEEcccH----HHHHHHHhccc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTN----YYIESLLWTIL 53 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTg----lYi~all~g~~ 53 (99)
....+.+....+.+..-+|+|+|| -.++|++..+.
T Consensus 114 ~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~ 152 (270)
T PF00437_consen 114 EEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIP 152 (270)
T ss_dssp HHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCH
T ss_pred HHHHHHHhhccccceEEEEECCCccccchHHHHHhhhcc
Confidence 556666777767789999999888 46677776543
No 147
>COG0549 ArcC Carbamate kinase [Amino acid transport and metabolism]
Probab=26.43 E-value=58 Score=26.28 Aligned_cols=22 Identities=27% Similarity=0.445 Sum_probs=18.2
Q ss_pred HHHHHHHHhcCCceEEEcccHH
Q psy17228 22 KTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGTgl 43 (99)
.+.|+.+.++|.++|.+||-|-
T Consensus 174 ~~~Ik~L~~~g~vVI~~GGGGI 195 (312)
T COG0549 174 AEAIKALLESGHVVIAAGGGGI 195 (312)
T ss_pred HHHHHHHHhCCCEEEEeCCCCc
Confidence 3568889999999999998764
No 148
>PRK08931 5'-methylthioadenosine phosphorylase; Provisional
Probab=26.41 E-value=22 Score=28.08 Aligned_cols=9 Identities=44% Similarity=0.903 Sum_probs=7.9
Q ss_pred EEEcccHHH
Q psy17228 36 IIVGGTNYY 44 (99)
Q Consensus 36 ilVGGTglY 44 (99)
=|+||||||
T Consensus 7 gIIgGSGl~ 15 (289)
T PRK08931 7 GIIGGSGVY 15 (289)
T ss_pred EEEecCCcC
Confidence 478999999
No 149
>COG0521 MoaB Molybdopterin biosynthesis enzymes [Coenzyme metabolism]
Probab=26.40 E-value=59 Score=23.88 Aligned_cols=21 Identities=19% Similarity=0.449 Sum_probs=13.2
Q ss_pred HHHHHHHhcC-CceEEEcccHH
Q psy17228 23 TKIDDILQRN-KVPIIVGGTNY 43 (99)
Q Consensus 23 ~~i~~i~~~~-~~pilVGGTgl 43 (99)
..+.+...+. .+.|..||||+
T Consensus 58 ~~l~~~~~~~~DvvlttGGTG~ 79 (169)
T COG0521 58 ATLIALIDEDVDVVLTTGGTGI 79 (169)
T ss_pred HHHHHHhcCCCCEEEEcCCccC
Confidence 3344444443 67777899997
No 150
>PF00696 AA_kinase: Amino acid kinase family Match to Glutamate-5-kinases, C-terminal end of the alignment Match to Aspartate kinases; InterPro: IPR001048 This entry contains proteins with various specificities and includes the aspartate, glutamate and uridylate kinase families. In prokaryotes and plants the synthesis of the essential amino acids lysine and threonine is predominantly regulated by feed-back inhibition of aspartate kinase (AK) and dihydrodipicolinate synthase (DHPS). In Escherichia coli, thrA, metLM, and lysC encode aspartokinase isozymes that show feedback inhibition by threonine, methionine, and lysine, respectively []. The lysine-sensitive isoenzyme of aspartate kinase from spinach leaves has a subunit composition of 4 large and 4 small subunits []. In plants although the control of carbon fixation and nitrogen assimilation has been studied in detail, relatively little is known about the regulation of carbon and nitrogen flow into amino acids. The metabolic regulation of expression of an Arabidopsis thaliana aspartate kinase/homoserine dehydrogenase (AK/HSD) gene, which encodes two linked key enzymes in the biosynthetic pathway of aspartate family amino acids has been studied []. The conversion of aspartate into either the storage amino acid asparagine or aspartate family amino acids may be subject to a coordinated, reciprocal metabolic control, and this biochemical branch point is a part of a larger, coordinated regulatory mechanism of nitrogen and carbon storage and utilization.; GO: 0008652 cellular amino acid biosynthetic process; PDB: 2X2W_B 2WXB_B 1B7B_C 2J4L_F 2J4K_E 2J4J_F 2OGX_B 3QUO_A 3D40_A 3D41_A ....
Probab=26.20 E-value=1.7e+02 Score=21.03 Aligned_cols=35 Identities=17% Similarity=0.123 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHHHHHHHhccc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~ 53 (99)
....+.|..+.+.|..+|||=|.|-+.+.++.-..
T Consensus 20 ~~~~~~i~~l~~~g~~vvvV~g~g~~~~~~~~~~~ 54 (242)
T PF00696_consen 20 RELADDIALLSQLGIKVVVVHGGGSFTDELLEKYG 54 (242)
T ss_dssp HHHHHHHHHHHHTTSEEEEEESSHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHhCCCeEEEEECChhhcCchHHhcc
Confidence 34445555566778888999888889999988643
No 151
>cd00717 URO-D Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction is located at the branching point of the tetrapyrrole biosynthetic pathway, leading to the biosynthesis of heme, chlorophyll or bacteriochlorophyll. URO-D deficiency is responsible for the human genetic diseases familial porphyria cutanea tarda (fPCT) and hepatoerythropoietic porphyria (HEP).
Probab=26.18 E-value=1.4e+02 Score=22.97 Aligned_cols=35 Identities=26% Similarity=0.435 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHhcC-CceEE--EcccHHHHHHHHh
Q psy17228 16 WTIKLTKTKIDDILQRN-KVPII--VGGTNYYIESLLW 50 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~-~~pil--VGGTglYi~all~ 50 (99)
|..--..++++.+.+.+ ..||+ ||||.-.++.+.+
T Consensus 212 f~~P~~k~i~~~i~~~~~~~~ilh~cg~~~~~~~~~~~ 249 (335)
T cd00717 212 FVLPYLKRIIEEVKKRLPGVPVILFAKGAGGLLEDLAQ 249 (335)
T ss_pred HHHHHHHHHHHHHHHhCCCCCEEEEcCCCHHHHHHHHh
Confidence 33445567777887764 44555 8999977777766
No 152
>PLN02896 cinnamyl-alcohol dehydrogenase
Probab=26.14 E-value=37 Score=26.01 Aligned_cols=23 Identities=17% Similarity=0.164 Sum_probs=16.9
Q ss_pred hcCCceEEEcccHHHHHHHHhcc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g~ 52 (99)
.++...+|+|||||-=.+|+.-+
T Consensus 8 ~~~~~vLVtG~~GfIG~~l~~~L 30 (353)
T PLN02896 8 SATGTYCVTGATGYIGSWLVKLL 30 (353)
T ss_pred cCCCEEEEECCCcHHHHHHHHHH
Confidence 45677899999998766666543
No 153
>TIGR03199 pucC xanthine dehydrogenase C subunit. This gene has been characterized in B. subtilis as the FAD binding-subunit of xanthine dehydrogenase (pucC), acting in conjunction with pucD, the molybdopterin-binding subunit and pucE, the FeS-binding subunit.
Probab=26.14 E-value=1e+02 Score=23.35 Aligned_cols=27 Identities=7% Similarity=0.128 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHHHHH
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYYIES 47 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglYi~a 47 (99)
..+|.+++.+ .+..-|+.|||.+++.-
T Consensus 4 l~ea~~ll~~---~~~a~ivaGgT~l~~~~ 30 (264)
T TIGR03199 4 LDEAWSLLEK---APDSTFVSGSTLLQLQW 30 (264)
T ss_pred HHHHHHHHHh---CCCCEEEEccChHHHHH
Confidence 3455555554 24567899999998864
No 154
>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....
Probab=26.14 E-value=71 Score=21.12 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=13.4
Q ss_pred HHHHHHHhcCCceEEEcccH
Q psy17228 23 TKIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 23 ~~i~~i~~~~~~pilVGGTg 42 (99)
++++.+. +|+--+++|+||
T Consensus 6 ~~~~~i~-~~~~~li~aptG 24 (169)
T PF00270_consen 6 EAIEAII-SGKNVLISAPTG 24 (169)
T ss_dssp HHHHHHH-TTSEEEEECSTT
T ss_pred HHHHHHH-cCCCEEEECCCC
Confidence 3455555 577788999988
No 155
>PRK13337 putative lipid kinase; Reviewed
Probab=26.12 E-value=80 Score=24.11 Aligned_cols=35 Identities=14% Similarity=0.213 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhccc
Q psy17228 18 IKLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~~ 53 (99)
..++.+++.++.+++ ...|++||=|. +..+++|+.
T Consensus 43 ~~~a~~~a~~~~~~~~d~vvv~GGDGT-l~~vv~gl~ 78 (304)
T PRK13337 43 PGDATLAAERAVERKFDLVIAAGGDGT-LNEVVNGIA 78 (304)
T ss_pred CCCHHHHHHHHHhcCCCEEEEEcCCCH-HHHHHHHHh
Confidence 356777777766554 68888899998 666677753
No 156
>TIGR01490 HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrolase, TIGR01490. A subset of these sequences, including the Caulobacter crescentus CicA protein, cluster together and may represent a separate equivalog.
Probab=26.10 E-value=1.3e+02 Score=20.75 Aligned_cols=34 Identities=6% Similarity=0.065 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~ 52 (99)
..+.+.++.+.++| ++-|+.||...|++.+++-+
T Consensus 90 ~~~~~~l~~l~~~g~~v~ivS~s~~~~v~~~~~~l 124 (202)
T TIGR01490 90 PEARDLIRWHKAEGHTIVLVSASLTILVKPLARIL 124 (202)
T ss_pred HHHHHHHHHHHHCCCEEEEEeCCcHHHHHHHHHHc
Confidence 46788888888887 56666688899999988743
No 157
>cd07186 CofD_like LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis. CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis.
Probab=26.00 E-value=43 Score=26.75 Aligned_cols=17 Identities=29% Similarity=0.376 Sum_probs=14.5
Q ss_pred eEEEcccHHHHHHHHhccc
Q psy17228 35 PIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 35 pilVGGTglYi~all~g~~ 53 (99)
.+|.||||++ .++.|+.
T Consensus 2 v~lgGGtG~~--~lL~GL~ 18 (303)
T cd07186 2 VVLSGGTGGA--KLLRGLK 18 (303)
T ss_pred EEEeCCccHH--HHHHHHH
Confidence 5789999999 8888874
No 158
>TIGR03589 PseB UDP-N-acetylglucosamine 4,6-dehydratase. This enzyme catalyzes the first step in the biosynthesis of pseudaminic acid, the conversion of UDP-N-acetylglucosamine to UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences are members of the broader pfam01073 (3-beta hydroxysteroid dehydrogenase/isomerase family) family.
Probab=25.98 E-value=37 Score=25.99 Aligned_cols=21 Identities=29% Similarity=0.460 Sum_probs=14.8
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
.|+..+|+||||+==.+|+..
T Consensus 3 ~~k~vLVTGatG~IG~~l~~~ 23 (324)
T TIGR03589 3 NNKSILITGGTGSFGKAFISR 23 (324)
T ss_pred CCCEEEEeCCCCHHHHHHHHH
Confidence 367788999999855555443
No 159
>PRK07315 fructose-bisphosphate aldolase; Provisional
Probab=25.95 E-value=54 Score=25.66 Aligned_cols=22 Identities=18% Similarity=0.456 Sum_probs=13.7
Q ss_pred HHHHHHhcC-CceEEE-cccHHHH
Q psy17228 24 KIDDILQRN-KVPIIV-GGTNYYI 45 (99)
Q Consensus 24 ~i~~i~~~~-~~pilV-GGTglYi 45 (99)
.+++|.+.- .+|++. ||||.=.
T Consensus 192 ~L~~i~~~~~~iPlVlhGGSGi~~ 215 (293)
T PRK07315 192 HLEKLTEAVPGFPIVLHGGSGIPD 215 (293)
T ss_pred HHHHHHHhccCCCEEEECCCCCCH
Confidence 456666654 366655 9988643
No 160
>PRK08309 short chain dehydrogenase; Provisional
Probab=25.84 E-value=38 Score=24.28 Aligned_cols=17 Identities=18% Similarity=0.536 Sum_probs=12.4
Q ss_pred eEEEcccHHHHHHHHhcc
Q psy17228 35 PIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 35 pilVGGTglYi~all~g~ 52 (99)
.+|+||||| +.++...+
T Consensus 3 vlVtGGtG~-gg~la~~L 19 (177)
T PRK08309 3 ALVIGGTGM-LKRVSLWL 19 (177)
T ss_pred EEEECcCHH-HHHHHHHH
Confidence 578899985 56677654
No 161
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=25.82 E-value=1.4e+02 Score=20.94 Aligned_cols=35 Identities=17% Similarity=0.111 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhccc
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~ 53 (99)
..++...|.++.+.| .=+||||+..+=-|--.|+.
T Consensus 111 ~~e~~~~i~~~~~~G-~~viVGg~~~~~~A~~~gl~ 145 (176)
T PF06506_consen 111 EEEIEAAIKQAKAEG-VDVIVGGGVVCRLARKLGLP 145 (176)
T ss_dssp HHHHHHHHHHHHHTT---EEEESHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHHcC-CcEEECCHHHHHHHHHcCCc
Confidence 468899999998877 88899998887666666653
No 162
>PF08599 Nbs1_C: DNA damage repair protein Nbs1; InterPro: IPR013908 This C-terminal region of the DNA damage repair protein Nbs1 has been identified to be necessary for the binding of Mre11 and Tel1 [].
Probab=25.68 E-value=42 Score=21.15 Aligned_cols=15 Identities=27% Similarity=0.631 Sum_probs=12.3
Q ss_pred cCCceEEEcccHHHH
Q psy17228 31 RNKVPIIVGGTNYYI 45 (99)
Q Consensus 31 ~~~~pilVGGTglYi 45 (99)
.|++|=|.|||-|-.
T Consensus 15 a~~lP~IIGGSDLi~ 29 (65)
T PF08599_consen 15 AGGLPHIIGGSDLIA 29 (65)
T ss_pred CCCCCeeecchhhhh
Confidence 578999999998753
No 163
>PRK05717 oxidoreductase; Validated
Probab=25.65 E-value=38 Score=24.36 Aligned_cols=23 Identities=9% Similarity=0.117 Sum_probs=16.9
Q ss_pred hcCCceEEEcccHHHHHHHHhcc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g~ 52 (99)
-.|++.+|+||||.==.++..-+
T Consensus 8 ~~~k~vlItG~sg~IG~~~a~~l 30 (255)
T PRK05717 8 HNGRVALVTGAARGIGLGIAAWL 30 (255)
T ss_pred cCCCEEEEeCCcchHHHHHHHHH
Confidence 35789999999987666555543
No 164
>PRK03670 competence damage-inducible protein A; Provisional
Probab=25.63 E-value=73 Score=24.44 Aligned_cols=22 Identities=36% Similarity=0.522 Sum_probs=15.2
Q ss_pred HHHHHHHHhc-CCceEEEcccHH
Q psy17228 22 KTKIDDILQR-NKVPIIVGGTNY 43 (99)
Q Consensus 22 ~~~i~~i~~~-~~~pilVGGTgl 43 (99)
.+.++++.++ ..+.|++||+|.
T Consensus 50 ~~~l~~a~~~~~DlVIttGGlGp 72 (252)
T PRK03670 50 KSVVLEILSRKPEVLVISGGLGP 72 (252)
T ss_pred HHHHHHHhhCCCCEEEECCCccC
Confidence 3445555554 488999999984
No 165
>PTZ00333 triosephosphate isomerase; Provisional
Probab=25.61 E-value=76 Score=24.44 Aligned_cols=13 Identities=31% Similarity=0.383 Sum_probs=10.2
Q ss_pred CCceEEEcccHHH
Q psy17228 32 NKVPIIVGGTNYY 44 (99)
Q Consensus 32 ~~~pilVGGTglY 44 (99)
.+++||.|||=-=
T Consensus 206 ~~~~ILYGGSV~~ 218 (255)
T PTZ00333 206 EATRIIYGGSVNE 218 (255)
T ss_pred ccceEEEcCCCCH
Confidence 4689999998543
No 166
>TIGR00338 serB phosphoserine phosphatase SerB. Phosphoserine phosphatase catalyzes the reaction 3-phospho-serine + H2O = L-serine + phosphate. It catalyzes the last of three steps in the biosynthesis of serine from D-3-phosphoglycerate. Note that this enzyme acts on free phosphoserine, not on phosphoserine residues of phosphoproteins.
Probab=25.54 E-value=1.2e+02 Score=21.41 Aligned_cols=34 Identities=18% Similarity=0.362 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~ 52 (99)
..+.+.++.+.++| ++-|+.||...+++.++..+
T Consensus 88 ~g~~~~l~~l~~~g~~~~IvS~~~~~~~~~~l~~~ 122 (219)
T TIGR00338 88 EGAEELVKTLKEKGYKVAVISGGFDLFAEHVKDKL 122 (219)
T ss_pred CCHHHHHHHHHHCCCEEEEECCCcHHHHHHHHHHc
Confidence 36777888888876 56677799999999988754
No 167
>cd04246 AAK_AK-DapG-like AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species, as well as, the catalytic AK domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related isoenzymes. In Bacillus subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. The role of the AKI isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulati
Probab=25.51 E-value=1.4e+02 Score=21.99 Aligned_cols=32 Identities=9% Similarity=0.142 Sum_probs=20.3
Q ss_pred HHHHHHHHHHhcCCceEE-EcccHHHHHHHHhc
Q psy17228 20 LTKTKIDDILQRNKVPII-VGGTNYYIESLLWT 51 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pil-VGGTglYi~all~g 51 (99)
...+.|..+...|..||| |||-|-..+.++.-
T Consensus 19 ~~~~~i~~l~~~g~~~viV~sg~g~~~~~ll~~ 51 (239)
T cd04246 19 RVAERIKKAVKKGYQVVVVVSAMGGTTDELIGL 51 (239)
T ss_pred HHHHHHHHHHHcCCCEEEEECCCCchHHHHHHH
Confidence 444555566666655555 68777777877764
No 168
>PLN02240 UDP-glucose 4-epimerase
Probab=25.38 E-value=39 Score=25.53 Aligned_cols=20 Identities=15% Similarity=0.385 Sum_probs=14.1
Q ss_pred CCceEEEcccHHHHHHHHhc
Q psy17228 32 NKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 32 ~~~pilVGGTglYi~all~g 51 (99)
++..+|+||||+==.+|+.-
T Consensus 5 ~~~vlItGatG~iG~~l~~~ 24 (352)
T PLN02240 5 GRTILVTGGAGYIGSHTVLQ 24 (352)
T ss_pred CCEEEEECCCChHHHHHHHH
Confidence 56788999999655555444
No 169
>PLN02214 cinnamoyl-CoA reductase
Probab=25.38 E-value=41 Score=25.94 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=15.4
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
+++..+|+|||||==.+|+.-
T Consensus 9 ~~~~vlVTGatGfIG~~l~~~ 29 (342)
T PLN02214 9 AGKTVCVTGAGGYIASWIVKI 29 (342)
T ss_pred CCCEEEEECCCcHHHHHHHHH
Confidence 467789999998866665554
No 170
>PF11997 DUF3492: Domain of unknown function (DUF3492); InterPro: IPR022622 This domain is functionally uncharacterised and is found in bacteria, archaea and eukaryotes. It is typically between 259 to 282 amino acids in length. This region is found N-terminal PF00534 from PFAM. There are two conserved sequence motifs: GGVS and EHGIY.
Probab=25.37 E-value=39 Score=25.98 Aligned_cols=23 Identities=17% Similarity=0.504 Sum_probs=21.3
Q ss_pred hcCCceEEEcccHHHHHHHHhcc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g~ 52 (99)
-+|.-|.+.||-+-.++.|++|+
T Consensus 7 ~EGtYPyv~GGVSsW~~~LI~gl 29 (268)
T PF11997_consen 7 TEGTYPYVRGGVSSWVHQLIRGL 29 (268)
T ss_pred ecCcCCCCCCchhHHHHHHHhcC
Confidence 46889999999999999999996
No 171
>PRK06806 fructose-bisphosphate aldolase; Provisional
Probab=25.33 E-value=59 Score=25.32 Aligned_cols=25 Identities=20% Similarity=0.531 Sum_probs=15.3
Q ss_pred HHHHHHHhcCCceEEE-cccHHHHHH
Q psy17228 23 TKIDDILQRNKVPIIV-GGTNYYIES 47 (99)
Q Consensus 23 ~~i~~i~~~~~~pilV-GGTglYi~a 47 (99)
+.+++|.+.-.+|++. ||||.=.+-
T Consensus 190 ~~L~~i~~~~~iPlV~hG~SGI~~e~ 215 (281)
T PRK06806 190 DRLQEINDVVHIPLVLHGGSGISPED 215 (281)
T ss_pred HHHHHHHHhcCCCEEEECCCCCCHHH
Confidence 3455665555677665 988865443
No 172
>KOG3148|consensus
Probab=25.15 E-value=84 Score=24.30 Aligned_cols=25 Identities=16% Similarity=0.181 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHH
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
.++.+.=+.|.+.|.+-++|||-|-
T Consensus 116 aec~~fe~kikeaggidlfvggigp 140 (273)
T KOG3148|consen 116 AECDAFERKIKEAGGIDLFVGGIGP 140 (273)
T ss_pred HHHHHHHHHHHhcCCeEEEeeccCC
Confidence 4566666778889999999999874
No 173
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.94 E-value=20 Score=23.49 Aligned_cols=15 Identities=33% Similarity=0.793 Sum_probs=12.7
Q ss_pred CCceEEEcccHHHHH
Q psy17228 32 NKVPIIVGGTNYYIE 46 (99)
Q Consensus 32 ~~~pilVGGTglYi~ 46 (99)
+.+-|+-=|||||+.
T Consensus 48 ~~vgi~fKGSGfYvt 62 (82)
T COG2331 48 NAVGIVFKGSGFYVT 62 (82)
T ss_pred ccceEEEecceEEEe
Confidence 567788899999986
No 174
>PLN02206 UDP-glucuronate decarboxylase
Probab=24.92 E-value=38 Score=27.63 Aligned_cols=22 Identities=14% Similarity=0.290 Sum_probs=15.4
Q ss_pred hcCCceEEEcccHHHHHHHHhc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g 51 (99)
.+++..+|+|||||==..|+.-
T Consensus 117 ~~~~kILVTGatGfIGs~Lv~~ 138 (442)
T PLN02206 117 RKGLRVVVTGGAGFVGSHLVDR 138 (442)
T ss_pred cCCCEEEEECcccHHHHHHHHH
Confidence 3556678889999865555554
No 175
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=24.86 E-value=89 Score=18.92 Aligned_cols=29 Identities=14% Similarity=0.286 Sum_probs=20.0
Q ss_pred ccchHHHHHHHHHHHHHHhcCCceEEEccc
Q psy17228 12 TKTKWTIKLTKTKIDDILQRNKVPIIVGGT 41 (99)
Q Consensus 12 ~~~~~~~~~a~~~i~~i~~~~~~pilVGGT 41 (99)
+..+|..++....++...++|++-+. ||+
T Consensus 29 ~~~~~s~~eL~~fL~~lv~e~~L~~~-~G~ 57 (60)
T PF08672_consen 29 GGYDISLEELQEFLDRLVEEGKLECS-GGS 57 (60)
T ss_dssp --TT--HHHHHHHHHHHHHTTSEE---TTE
T ss_pred CCCCCCHHHHHHHHHHHHHCCcEEec-CCE
Confidence 44678889999999999999988776 774
No 176
>PLN02695 GDP-D-mannose-3',5'-epimerase
Probab=24.74 E-value=40 Score=26.45 Aligned_cols=22 Identities=9% Similarity=0.114 Sum_probs=15.0
Q ss_pred hcCCceEEEcccHHHHHHHHhc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g 51 (99)
..++..+|+|||||==.+|+.-
T Consensus 19 ~~~~~IlVtGgtGfIG~~l~~~ 40 (370)
T PLN02695 19 SEKLRICITGAGGFIASHIARR 40 (370)
T ss_pred CCCCEEEEECCccHHHHHHHHH
Confidence 4567788899999854444433
No 177
>PLN02686 cinnamoyl-CoA reductase
Probab=24.64 E-value=45 Score=26.10 Aligned_cols=23 Identities=9% Similarity=0.286 Sum_probs=16.5
Q ss_pred hcCCceEEEcccHHHHHHHHhcc
Q psy17228 30 QRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~g~ 52 (99)
..++..+|+|||||==.+|+.-+
T Consensus 51 ~~~k~VLVTGatGfIG~~lv~~L 73 (367)
T PLN02686 51 AEARLVCVTGGVSFLGLAIVDRL 73 (367)
T ss_pred CCCCEEEEECCchHHHHHHHHHH
Confidence 45778899999998656655543
No 178
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=24.64 E-value=1.1e+02 Score=22.01 Aligned_cols=23 Identities=17% Similarity=0.505 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHhcC--CceEEEcc
Q psy17228 18 IKLTKTKIDDILQRN--KVPIIVGG 40 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~--~~pilVGG 40 (99)
..++..+++.+.++| .+.++|||
T Consensus 77 ~~l~~~lve~lre~G~~~i~v~~GG 101 (143)
T COG2185 77 LTLVPGLVEALREAGVEDILVVVGG 101 (143)
T ss_pred HHHHHHHHHHHHHhCCcceEEeecC
Confidence 356777788888887 45556676
No 179
>cd00537 MTHFR Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease.
Probab=24.58 E-value=78 Score=23.84 Aligned_cols=38 Identities=18% Similarity=0.142 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHhcC-CceEEEc-------ccHHHHHHHHhcccCC
Q psy17228 17 TIKLTKTKIDDILQRN-KVPIIVG-------GTNYYIESLLWTILLD 55 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~~-~~pilVG-------GTglYi~all~g~~~~ 55 (99)
..+.+.+.++.+.+.| .+||++| ++-.|+...+ |..+|
T Consensus 171 d~~~~~~~~~~~~~~gi~vPIi~GI~p~~s~~~l~~~~~~~-Gv~vP 216 (274)
T cd00537 171 DNDAFLRFVDRCRAAGITVPIIPGIMPLTSYKQAKRFAKLC-GVEIP 216 (274)
T ss_pred cHHHHHHHHHHHHHcCCCCCEEeeccccCCHHHHHHHHHhh-CCCCC
Confidence 3477888888888888 8999998 4455666666 76643
No 180
>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=24.54 E-value=1.1e+02 Score=22.45 Aligned_cols=34 Identities=21% Similarity=0.286 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhcC-CceEEEcccHHHHHHHHhccc
Q psy17228 20 LTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 20 ~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~~ 53 (99)
.|.+.++.+.++| ++.||.||-.+|++-+-+.+-
T Consensus 81 ga~elv~~lk~~G~~v~iiSgg~~~lv~~ia~~lg 115 (212)
T COG0560 81 GAEELVAALKAAGAKVVIISGGFTFLVEPIAERLG 115 (212)
T ss_pred cHHHHHHHHHHCCCEEEEEcCChHHHHHHHHHHhC
Confidence 4888999999997 566666888889998887654
No 181
>PRK14567 triosephosphate isomerase; Provisional
Probab=24.50 E-value=1.1e+02 Score=23.80 Aligned_cols=24 Identities=25% Similarity=0.425 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHh------cCCceEEEcccH
Q psy17228 19 KLTKTKIDDILQ------RNKVPIIVGGTN 42 (99)
Q Consensus 19 ~~a~~~i~~i~~------~~~~pilVGGTg 42 (99)
+++...|++..+ ..+++|+.|||-
T Consensus 182 ~~~~~~IR~~l~~~~~~~a~~v~IlYGGSV 211 (253)
T PRK14567 182 QETHQFIRSLLAKVDERLAKNIKIVYGGSL 211 (253)
T ss_pred HHHHHHHHHHHHhhcccccccceEEEcCcC
Confidence 444445554443 247899999986
No 182
>cd07187 YvcK_like family of mostly uncharacterized proteins similar to B.subtilis YvcK. One member of this protein family, YvcK from Bacillus subtilis, has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and the pentose phosphate pathway. In general, this family of mostly uncharacterized proteins is related to the CofD-like protein family. CofD has been characterized as a 2-phospho-L-lactate transferase involved in F420 biosynthesis. This family appears to have the same conserved phosphate binding site as the other family in this hierarchy, but a different substrate binding site.
Probab=24.46 E-value=47 Score=26.40 Aligned_cols=17 Identities=29% Similarity=0.331 Sum_probs=13.9
Q ss_pred eEEEcccHHHHHHHHhccc
Q psy17228 35 PIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 35 pilVGGTglYi~all~g~~ 53 (99)
.+|-||||+. .++.|+.
T Consensus 2 V~igGGtGl~--~ll~gLk 18 (308)
T cd07187 2 VAFGGGTGLS--TLLRGLK 18 (308)
T ss_pred EEEeccccHH--HHHHHHH
Confidence 5788999998 7888864
No 183
>PF10432 bact-PGI_C: Bacterial phospho-glucose isomerase C-terminal region; InterPro: IPR019490 Phosphoglucose isomerase (PGI) catalyses the interconversion of phosphoglucose and phosphofructose, and is a component of many sugar metabolic pathways. In some archaea and bacteria PGI activity occurs via a bifunctional enzyme that also exhibits phosphomannose isomerase (PMI) activity. Though not closely related to eukaryotic PGIs, the bifunctional enzyme is similar enough that the sequence includes the cluster of threonines and serines that forms the sugar phosphate-binding site in conventional PGI. This entry represents the C-terminal half of the bifunctional PGI/PMI enzyme, which contains many of the active catalytic site residues. The enzyme is thought to use the same catalytic mechanisms for both glucose ring-opening and isomerisation for the interconversion of glucose 6-phosphate to fructose 6-phosphate [].; GO: 0004347 glucose-6-phosphate isomerase activity, 0004476 mannose-6-phosphate isomerase activity; PDB: 1TZB_A 1X9H_A 1TZC_B 1X9I_A 1WIW_A.
Probab=24.43 E-value=67 Score=22.62 Aligned_cols=25 Identities=20% Similarity=0.482 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHHH
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYYI 45 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglYi 45 (99)
...|..+-..+ .|++|||.|+ ++|-
T Consensus 5 ~n~Ak~LA~~L--~~~~Pvi~~~-~~~~ 29 (155)
T PF10432_consen 5 VNPAKRLALEL--AGRIPVIYGS-PLYA 29 (155)
T ss_dssp HHHHHHHHHHH--TTSEEEEEEC-GCGC
T ss_pred cCHHHHHHHHH--cCCCcEEEEC-ccch
Confidence 34555555555 4588888888 5553
No 184
>PF06995 Phage_P2_GpU: Phage P2 GpU; InterPro: IPR009734 This family consists of several bacterial and phage proteins of around 130 residues in length which seem to be related to the bacteriophage P2 GpU protein (O64315 from SWISSPROT) which is thought to be involved in tail assembly [].
Probab=24.43 E-value=73 Score=21.30 Aligned_cols=33 Identities=9% Similarity=-0.072 Sum_probs=24.7
Q ss_pred ccchHH--HHHHHHHHHHHHhcCCceEEEcccHHH
Q psy17228 12 TKTKWT--IKLTKTKIDDILQRNKVPIIVGGTNYY 44 (99)
Q Consensus 12 ~~~~~~--~~~a~~~i~~i~~~~~~pilVGGTglY 44 (99)
...+.+ .....+.+..+..+|++-.+|-|+|.|
T Consensus 50 ~l~~~~~~~~~~l~~Lr~~~~~g~p~~Lv~G~G~~ 84 (121)
T PF06995_consen 50 VLFPEFGGGRKELDKLRAMAESGEPLPLVIGSGKV 84 (121)
T ss_pred EEehHHCCCHHHHHHHHHHHHcCCceEEEECCCce
Confidence 334444 256677888888999999999999976
No 185
>PRK09136 5'-methylthioadenosine phosphorylase; Validated
Probab=24.33 E-value=27 Score=26.61 Aligned_cols=10 Identities=40% Similarity=0.620 Sum_probs=8.2
Q ss_pred EEEcccHHHH
Q psy17228 36 IIVGGTNYYI 45 (99)
Q Consensus 36 ilVGGTglYi 45 (99)
-|+||||||=
T Consensus 3 giI~Gsgl~~ 12 (245)
T PRK09136 3 AIIGGTGLTQ 12 (245)
T ss_pred EEEeccccch
Confidence 3789999985
No 186
>PLN02778 3,5-epimerase/4-reductase
Probab=24.33 E-value=41 Score=25.54 Aligned_cols=19 Identities=21% Similarity=-0.045 Sum_probs=12.8
Q ss_pred CceEEEcccHHHHHHHHhc
Q psy17228 33 KVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 33 ~~pilVGGTglYi~all~g 51 (99)
+..+|+|||||==.+|+.-
T Consensus 10 ~kiLVtG~tGfiG~~l~~~ 28 (298)
T PLN02778 10 LKFLIYGKTGWIGGLLGKL 28 (298)
T ss_pred CeEEEECCCCHHHHHHHHH
Confidence 3467889999865554443
No 187
>PRK13606 LPPG:FO 2-phospho-L-lactate transferase; Provisional
Probab=24.23 E-value=43 Score=26.77 Aligned_cols=19 Identities=26% Similarity=0.436 Sum_probs=15.8
Q ss_pred CceEEEcccHHHHHHHHhccc
Q psy17228 33 KVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 33 ~~pilVGGTglYi~all~g~~ 53 (99)
++.+|-||||+. .|+.|+.
T Consensus 2 ~iv~lgGGtG~~--~lL~GL~ 20 (303)
T PRK13606 2 MITVLSGGTGTA--KLLRGLK 20 (303)
T ss_pred eEEEEeCccCHH--HHHHHHH
Confidence 467889999998 7888875
No 188
>TIGR03471 HpnJ hopanoid biosynthesis associated radical SAM protein HpnJ. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift.
Probab=24.20 E-value=76 Score=25.89 Aligned_cols=33 Identities=12% Similarity=0.075 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHhcC-CceEEEcccH---HHHHHH
Q psy17228 16 WTIKLTKTKIDDILQRN-KVPIIVGGTN---YYIESL 48 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~-~~pilVGGTg---lYi~al 48 (99)
.....+.++++.+.+++ .++||+||.+ ++=++|
T Consensus 79 ~~~~~~~~ia~~iK~~~p~~~vv~GG~h~t~~pe~~l 115 (472)
T TIGR03471 79 PSFPSDVKTAEALKEQNPATKIGFVGAHVAVLPEKTL 115 (472)
T ss_pred cchHHHHHHHHHHHHhCCCCEEEEECCCcccCHHHHH
Confidence 33456777777777664 7899999964 444444
No 189
>PRK13582 thrH phosphoserine phosphatase; Provisional
Probab=24.17 E-value=1.7e+02 Score=20.30 Aligned_cols=34 Identities=15% Similarity=0.065 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhcCCceEEEcccHHHHHHHHhccc
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~ 53 (99)
.+.+.++.+.++.++-|+.||...+++.++..+.
T Consensus 72 g~~e~L~~L~~~~~~~IvS~~~~~~~~~~l~~~g 105 (205)
T PRK13582 72 GAVEFLDWLRERFQVVILSDTFYEFAGPLMRQLG 105 (205)
T ss_pred CHHHHHHHHHhcCCEEEEeCCcHHHHHHHHHHcC
Confidence 4667888887776667788999999999877643
No 190
>COG1687 AzlD Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]
Probab=24.12 E-value=47 Score=22.82 Aligned_cols=21 Identities=24% Similarity=0.292 Sum_probs=16.7
Q ss_pred HHHHHhcCCceEEEcccHHHH
Q psy17228 25 IDDILQRNKVPIIVGGTNYYI 45 (99)
Q Consensus 25 i~~i~~~~~~pilVGGTglYi 45 (99)
.-..++++-..=|.+||++|.
T Consensus 79 ~Lh~wkkn~~LSI~~GT~~Ym 99 (106)
T COG1687 79 ALHLWKKNMLLSIALGTILYM 99 (106)
T ss_pred HHHHHhcceeEEeccccchhh
Confidence 345667788888999999996
No 191
>cd03052 GST_N_GDAP1 GST_N family, Ganglioside-induced differentiation-associated protein 1 (GDAP1) subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal TRX-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates.
Probab=24.10 E-value=34 Score=20.58 Aligned_cols=17 Identities=18% Similarity=0.509 Sum_probs=12.6
Q ss_pred HHHHHhcCCceEEE-ccc
Q psy17228 25 IDDILQRNKVPIIV-GGT 41 (99)
Q Consensus 25 i~~i~~~~~~pilV-GGT 41 (99)
..++.-.|++|+++ ||+
T Consensus 43 ~~~inP~g~vP~L~~~g~ 60 (73)
T cd03052 43 FMRLNPTGEVPVLIHGDN 60 (73)
T ss_pred HHHhCcCCCCCEEEECCE
Confidence 45677789999988 444
No 192
>CHL00202 argB acetylglutamate kinase; Provisional
Probab=24.00 E-value=1.3e+02 Score=23.18 Aligned_cols=34 Identities=15% Similarity=-0.102 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhcCCceEEEcccHHHHHHHHhccc
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~ 53 (99)
...+-|..+.+.|..||||=|.|-+++..+..+-
T Consensus 43 ~~~~di~~l~~~g~~~VlVHGgg~~i~~~~~~~g 76 (284)
T CHL00202 43 DIIKDILFLSCIGLKIVVVHGGGPEINFWLKQLN 76 (284)
T ss_pred HHHHHHHHHHHCCCcEEEEeCCcHHHHHHHHHCC
Confidence 3445566677789999999999999998886543
No 193
>PRK11150 rfaD ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional
Probab=23.98 E-value=40 Score=25.03 Aligned_cols=16 Identities=19% Similarity=0.434 Sum_probs=10.5
Q ss_pred eEEEcccHHHHHHHHh
Q psy17228 35 PIIVGGTNYYIESLLW 50 (99)
Q Consensus 35 pilVGGTglYi~all~ 50 (99)
.+|+|||||==..|+.
T Consensus 2 ilVtGa~GfiG~~l~~ 17 (308)
T PRK11150 2 IIVTGGAGFIGSNIVK 17 (308)
T ss_pred EEEecCCcHHHHHHHH
Confidence 4788999975444433
No 194
>KOG1430|consensus
Probab=23.97 E-value=62 Score=26.40 Aligned_cols=22 Identities=14% Similarity=0.428 Sum_probs=17.8
Q ss_pred cCCceEEEcccHHHHHHHHhcc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g~ 52 (99)
++..-+|+||+||-=+.|+.-+
T Consensus 3 ~~~~vlVtGG~GflG~hlv~~L 24 (361)
T KOG1430|consen 3 KKLSVLVTGGSGFLGQHLVQAL 24 (361)
T ss_pred cCCEEEEECCccHHHHHHHHHH
Confidence 4567789999999988887754
No 195
>COG1564 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism]
Probab=23.94 E-value=82 Score=23.87 Aligned_cols=35 Identities=17% Similarity=0.275 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhcCC-ceEEEcccHHHHHHHHhccc
Q psy17228 19 KLTKTKIDDILQRNK-VPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~-~pilVGGTglYi~all~g~~ 53 (99)
.|...+++.+.++|. ..+++||+|==++.++..+.
T Consensus 78 TD~elAl~~a~e~g~d~i~i~Ga~GGR~DH~l~nl~ 113 (212)
T COG1564 78 TDLELALDEALERGADEIVILGALGGRLDHALANLF 113 (212)
T ss_pred chHHHHHHHHHHcCCCEEEEEecCCChHHHHHHHHH
Confidence 588889999999997 78888999988888887753
No 196
>PRK00131 aroK shikimate kinase; Reviewed
Probab=23.94 E-value=1.4e+02 Score=19.81 Aligned_cols=31 Identities=19% Similarity=0.294 Sum_probs=21.1
Q ss_pred chHHHHHHHHHHHHHHhcCCceEEEcccHHH
Q psy17228 14 TKWTIKLTKTKIDDILQRNKVPIIVGGTNYY 44 (99)
Q Consensus 14 ~~~~~~~a~~~i~~i~~~~~~pilVGGTglY 44 (99)
..+|.....+.+.++.......|.+||+-.+
T Consensus 56 ~~~~~~~~~~~~~~l~~~~~~vi~~g~~~~~ 86 (175)
T PRK00131 56 EAAFRELEEEVLAELLARHNLVISTGGGAVL 86 (175)
T ss_pred HHHHHHHHHHHHHHHHhcCCCEEEeCCCEee
Confidence 3556666667888888766666666776544
No 197
>smart00463 SMR Small MutS-related domain.
Probab=23.87 E-value=69 Score=19.53 Aligned_cols=30 Identities=23% Similarity=0.263 Sum_probs=18.6
Q ss_pred hcccchHHHHHHHHHHHH----HHhcCC---ceEEEc
Q psy17228 10 KLTKTKWTIKLTKTKIDD----ILQRNK---VPIIVG 39 (99)
Q Consensus 10 ~~~~~~~~~~~a~~~i~~----i~~~~~---~pilVG 39 (99)
.||.|-.+..+|...++. +.+.+. +-||+|
T Consensus 3 ~lDLHG~~~~eA~~~l~~~l~~~~~~~~~~~~~II~G 39 (80)
T smart00463 3 SLDLHGLTVEEALTALDKFLNNARLKGLEQKLVIITG 39 (80)
T ss_pred eEEcCCCCHHHHHHHHHHHHHHHHHcCCCceEEEEEc
Confidence 467788888777665554 445553 455555
No 198
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=23.84 E-value=62 Score=24.88 Aligned_cols=40 Identities=10% Similarity=0.027 Sum_probs=31.9
Q ss_pred hhhhcccchHHHHHHHHHHHHHHhcCCceEEEcccHHHHH
Q psy17228 7 WRLKLTKTKWTIKLTKTKIDDILQRNKVPIIVGGTNYYIE 46 (99)
Q Consensus 7 ~~~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGGTglYi~ 46 (99)
.++...++......|....+++..++++.+|+|+.+-...
T Consensus 42 i~l~~~Dd~~~p~~a~~~a~~Lv~~~~V~~iiG~~~S~~~ 81 (359)
T TIGR03407 42 IEPVVEDGASDWPTFAEKARKLITQDKVAAVFGCWTSASR 81 (359)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHHhhCCCcEEEcCCcHHHH
Confidence 4455567777778899999999999999999998766653
No 199
>TIGR01463 mtaA_cmuA methyltransferase, MtaA/CmuA family. This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein.
Probab=23.79 E-value=1.5e+02 Score=22.81 Aligned_cols=35 Identities=11% Similarity=0.151 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHhcCCceEE--EcccHHHHHHHHh
Q psy17228 16 WTIKLTKTKIDDILQRNKVPII--VGGTNYYIESLLW 50 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~~~pil--VGGTglYi~all~ 50 (99)
|...-..++++.+.+.|..|++ ||++.-.+..+.+
T Consensus 217 ~~~p~~k~i~~~i~~~g~~~ilH~CG~~~~~~~~l~~ 253 (340)
T TIGR01463 217 FGLPYQKRLFAYIKEIGGITVLHICGFTQPILRDIAN 253 (340)
T ss_pred HHHHHHHHHHHHHHhcCCceEEEECCCchhhHHHHHH
Confidence 3444556777788777877777 8999877777765
No 200
>cd04724 Tryptophan_synthase_alpha Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both strongly stimulated by the formation of the complex. The alpha subunit catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Indole is then channeled to the active site of the beta subunit, a PLP-dependent enzyme that catalyzes a replacement reaction to convert L-serine into L-tryptophan.
Probab=23.63 E-value=67 Score=24.07 Aligned_cols=22 Identities=32% Similarity=0.309 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHhcCCceEEEcc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGG 40 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGG 40 (99)
....+.++.+.+..++||+|||
T Consensus 173 ~~~~~~i~~lr~~~~~pI~vgg 194 (242)
T cd04724 173 DDLKELIKRIRKYTDLPIAVGF 194 (242)
T ss_pred hhHHHHHHHHHhcCCCcEEEEc
Confidence 4566777777777789999976
No 201
>PF15569 Imm21: Immunity protein 21
Probab=23.62 E-value=76 Score=21.16 Aligned_cols=24 Identities=17% Similarity=0.343 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHHHHHhcCCceEEEc
Q psy17228 15 KWTIKLTKTKIDDILQRNKVPIIVG 39 (99)
Q Consensus 15 ~~~~~~a~~~i~~i~~~~~~pilVG 39 (99)
-|-.++|.++|+-+ +..++|||=|
T Consensus 11 A~~~~dal~ii~~~-~~~~i~ILGG 34 (91)
T PF15569_consen 11 AYPFQDALKIINIC-EEKNIPILGG 34 (91)
T ss_pred ecCHHHHHHHHHHH-HhcCceEEcc
Confidence 46778999999865 4567777644
No 202
>PRK08264 short chain dehydrogenase; Validated
Probab=23.53 E-value=46 Score=23.49 Aligned_cols=21 Identities=14% Similarity=0.216 Sum_probs=14.8
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
.++..+|+||||.==.++..-
T Consensus 5 ~~~~vlItGgsg~iG~~la~~ 25 (238)
T PRK08264 5 KGKVVLVTGANRGIGRAFVEQ 25 (238)
T ss_pred CCCEEEEECCCchHHHHHHHH
Confidence 467889999998655555443
No 203
>TIGR01859 fruc_bis_ald_ fructose-1,6-bisphosphate aldolase, class II, various bacterial and amitochondriate protist. This model represents of one of several subtypes of the class II fructose-1,6-bisphosphate aldolase, an enzyme of glycolysis. The subtypes are split into several models to allow separation of a family of tagatose bisphosphate aldolases. This form is found in Gram-positive bacteria, a variety of Gram-negative, and in amitochondriate protists. The class II enzymes share homology with tagatose bisphosphate aldolase but not with class I aldolase.
Probab=23.53 E-value=54 Score=25.47 Aligned_cols=24 Identities=17% Similarity=0.502 Sum_probs=14.6
Q ss_pred HHHHHHhcCCceEEE-cccHHHHHH
Q psy17228 24 KIDDILQRNKVPIIV-GGTNYYIES 47 (99)
Q Consensus 24 ~i~~i~~~~~~pilV-GGTglYi~a 47 (99)
.+++|.+.-.+|++. ||||.=.+-
T Consensus 191 ~L~~i~~~~~iPlv~hGgSGi~~e~ 215 (282)
T TIGR01859 191 RLKEIKELTNIPLVLHGASGIPEEQ 215 (282)
T ss_pred HHHHHHHHhCCCEEEECCCCCCHHH
Confidence 445555554577665 988875433
No 204
>PRK12938 acetyacetyl-CoA reductase; Provisional
Probab=23.46 E-value=45 Score=23.66 Aligned_cols=22 Identities=14% Similarity=0.246 Sum_probs=16.1
Q ss_pred cCCceEEEcccHHHHHHHHhcc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g~ 52 (99)
.+++.+|+||||.==.++..-+
T Consensus 2 ~~k~~lVtG~s~giG~~~a~~l 23 (246)
T PRK12938 2 SQRIAYVTGGMGGIGTSICQRL 23 (246)
T ss_pred CCCEEEEECCCChHHHHHHHHH
Confidence 3688999999987666665543
No 205
>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=23.35 E-value=1.9e+02 Score=22.67 Aligned_cols=38 Identities=11% Similarity=0.087 Sum_probs=35.4
Q ss_pred chHHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhc
Q psy17228 14 TKWTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 14 ~~~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g 51 (99)
+..|++-|.+.+++..+++++-|+|.=+.=.++.+++-
T Consensus 179 D~~F~~K~~~rl~e~~~~~~tiv~VSHd~~~I~~~Cd~ 216 (249)
T COG1134 179 DAAFQEKCLERLNELVEKNKTIVLVSHDLGAIKQYCDR 216 (249)
T ss_pred CHHHHHHHHHHHHHHHHcCCEEEEEECCHHHHHHhcCe
Confidence 56799999999999999999999999999999999987
No 206
>PRK04011 peptide chain release factor 1; Provisional
Probab=23.20 E-value=1.5e+02 Score=24.40 Aligned_cols=35 Identities=20% Similarity=0.154 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHh----cCCceEEEcccHHHHHHHHh
Q psy17228 16 WTIKLTKTKIDDILQ----RNKVPIIVGGTNYYIESLLW 50 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~----~~~~pilVGGTglYi~all~ 50 (99)
-|.+.+.+.+.+++. .+--.||+||.|+.-+.+.+
T Consensus 196 ~f~k~Vae~~~~~f~~~~~~~v~~IvlaGpg~~K~~f~~ 234 (411)
T PRK04011 196 EFYKRVGEKANEAFLPLLEGKLKGILIGGPGPTKEEFLE 234 (411)
T ss_pred HHHHHHHHHHHHHHhhhccccccEEEEECChhHHHHHhh
Confidence 344555555555543 34567899999999888877
No 207
>cd06344 PBP1_ABC_ligand_binding_like_9 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine/isoleucine/valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=23.06 E-value=64 Score=24.23 Aligned_cols=36 Identities=11% Similarity=0.221 Sum_probs=28.3
Q ss_pred hhhcccchHHHHHHHHHHHHHHhcCCceEEEcccHH
Q psy17228 8 RLKLTKTKWTIKLTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 8 ~~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
++-..++......+....+++..+.++.+|+|+++.
T Consensus 41 elv~~D~~~~p~~a~~~a~~li~~~~v~aiiG~~~s 76 (332)
T cd06344 41 KVVIANDGNDPEIAKKVADELVKDPEILGVVGHYSS 76 (332)
T ss_pred EEEEECCCCChHHHHHHHHHHhcccCceEEEcCCCc
Confidence 444566667778888899999988899999998754
No 208
>PF06351 Allene_ox_cyc: Allene oxide cyclase; InterPro: IPR009410 This family consists of several plant specific allene oxide cyclase proteins (5.3.99.6 from EC). The allene oxide cyclase (AOC)-catalysed step in jasmonate (JA) biosynthesis is important in the wound response of tomato [].; GO: 0016853 isomerase activity, 0009507 chloroplast; PDB: 2GIN_A 2DIO_B 2BRJ_B 2Q4I_B 1Z8K_A 1ZVC_A.
Probab=23.01 E-value=22 Score=26.33 Aligned_cols=12 Identities=25% Similarity=0.465 Sum_probs=9.4
Q ss_pred ceEEEcccHHHH
Q psy17228 34 VPIIVGGTNYYI 45 (99)
Q Consensus 34 ~pilVGGTglYi 45 (99)
..-|+||||.|-
T Consensus 103 yLAVTGGtGiF~ 114 (176)
T PF06351_consen 103 YLAVTGGTGIFE 114 (176)
T ss_dssp EEEEEEEEETTT
T ss_pred eEEEeccCceee
Confidence 356899999983
No 209
>PRK14565 triosephosphate isomerase; Provisional
Probab=22.97 E-value=96 Score=23.76 Aligned_cols=27 Identities=22% Similarity=0.186 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHh-cCCceEEEcccHHH
Q psy17228 18 IKLTKTKIDDILQ-RNKVPIIVGGTNYY 44 (99)
Q Consensus 18 ~~~a~~~i~~i~~-~~~~pilVGGTglY 44 (99)
..++.+.+..|.+ ..+++|+.|||---
T Consensus 173 ~e~i~~~~~~Ir~~~~~~~IlYGGSV~~ 200 (237)
T PRK14565 173 NDAIAEAFEIIRSYDSKSHIIYGGSVNQ 200 (237)
T ss_pred HHHHHHHHHHHHHhCCCceEEEcCccCH
Confidence 3455555555543 25789999998543
No 210
>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=22.90 E-value=74 Score=24.39 Aligned_cols=33 Identities=18% Similarity=0.303 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhcCCceEEEcccH----HHHHHHHhcc
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTN----YYIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTg----lYi~all~g~ 52 (99)
.....++.+.++++..+|||-|| ..++..+..+
T Consensus 21 r~~~ll~~l~~~~~pvLl~G~~GtGKT~li~~~l~~l 57 (272)
T PF12775_consen 21 RYSYLLDLLLSNGRPVLLVGPSGTGKTSLIQNFLSSL 57 (272)
T ss_dssp HHHHHHHHHHHCTEEEEEESSTTSSHHHHHHHHHHCS
T ss_pred HHHHHHHHHHHcCCcEEEECCCCCchhHHHHhhhccC
Confidence 34567888889999999999666 6777777654
No 211
>PF01933 UPF0052: Uncharacterised protein family UPF0052; InterPro: IPR002882 This entry contains LPPG:Fo 2-phospho-L-lactate transferase (CofD) and related sequences of unknown function belong to unidentified protein family UPF0052. CofD catalyses the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterised so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) [] but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. ; PDB: 2HZB_A 2O2Z_C 3CGW_A 3C3E_D 3C3D_D 2PPV_A 2P0Y_A 2Q7X_B.
Probab=22.86 E-value=58 Score=25.66 Aligned_cols=18 Identities=28% Similarity=0.449 Sum_probs=13.9
Q ss_pred ceEEEcccHHHHHHHHhccc
Q psy17228 34 VPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 34 ~pilVGGTglYi~all~g~~ 53 (99)
+.+|.||||+. .|+.|+.
T Consensus 1 Ivvl~GGtG~~--~ll~gL~ 18 (300)
T PF01933_consen 1 IVVLGGGTGLS--KLLRGLK 18 (300)
T ss_dssp EEEEE-SCHHH--HHHHHHT
T ss_pred CEEEeCcccHH--HHHHHHH
Confidence 35789999998 8899975
No 212
>PF02798 GST_N: Glutathione S-transferase, N-terminal domain; InterPro: IPR004045 In eukaryotes, glutathione S-transferases (GSTs) participate in the detoxification of reactive electrophillic compounds by catalysing their conjugation to glutathione. The GST domain is also found in S-crystallins from squid, and proteins with no known GST activity, such as eukaryotic elongation factors 1-gamma and the HSP26 family of stress-related proteins, which include auxin-regulated proteins in plants and stringent starvation proteins in Escherichia coli. The major lens polypeptide of Cephalopoda is also a GST [, , , ]. Bacterial GSTs of known function often have a specific, growth-supporting role in biodegradative metabolism: epoxide ring opening and tetrachlorohydroquinone reductive dehalogenation are two examples of the reactions catalysed by these bacterial GSTs. Some regulatory proteins, like the stringent starvation proteins, also belong to the GST family [, ]. GST seems to be absent from Archaea in which gamma-glutamylcysteine substitute to glutathione as major thiol. Soluble GSTs activate glutathione (GSH) to GS-. In many GSTs, this is accomplished by a Tyr at H-bonding distance from the sulphur of GSH. These enzymes catalyse nucleophilic attack by reduced glutathione (GSH) on nonpolar compounds that contain an electrophillic carbon, nitrogen, or sulphur atom []. Glutathione S-transferases form homodimers, but in eukaryotes can also form heterodimers of the A1 and A2 or YC1 and YC2 subunits. The homodimeric enzymes display a conserved structural fold, with each monomer composed of two distinct domains []. The N-terminal domain forms a thioredoxin-like fold that binds the glutathione moiety, while the C-terminal domain contains several hydrophobic alpha-helices that specifically bind hydrophobic substrates. This entry represents the N-terminal domain of GST.; GO: 0005515 protein binding; PDB: 2VCT_H 2WJU_B 4ACS_A 1BYE_D 1AXD_B 2VCV_P 1TDI_A 1JLV_D 1Y6E_A 1U88_B ....
Probab=22.81 E-value=63 Score=19.45 Aligned_cols=19 Identities=26% Similarity=0.326 Sum_probs=13.9
Q ss_pred HHHHHHHhc-CCceEEEccc
Q psy17228 23 TKIDDILQR-NKVPIIVGGT 41 (99)
Q Consensus 23 ~~i~~i~~~-~~~pilVGGT 41 (99)
+....+... |++|+++.|.
T Consensus 41 ~e~~~~~p~~g~vP~l~~~~ 60 (76)
T PF02798_consen 41 PEFLAINPMFGKVPALEDGD 60 (76)
T ss_dssp HHHHHHTTTSSSSSEEEETT
T ss_pred hhhhhcccccceeeEEEECC
Confidence 344556667 9999999883
No 213
>TIGR03263 guanyl_kin guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.
Probab=22.81 E-value=67 Score=21.98 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=23.5
Q ss_pred HHHHHHHHhcCCceEE---EcccHHHHHHHHh
Q psy17228 22 KTKIDDILQRNKVPII---VGGTNYYIESLLW 50 (99)
Q Consensus 22 ~~~i~~i~~~~~~pil---VGGTglYi~all~ 50 (99)
...|+++++.|+++|+ ++|...+.+++..
T Consensus 81 ~~~i~~~~~~g~~vi~d~~~~~~~~~~~~~~~ 112 (180)
T TIGR03263 81 KSPVEEALAAGKDVLLEIDVQGARQVKKKFPD 112 (180)
T ss_pred HHHHHHHHHCCCeEEEECCHHHHHHHHHhCCC
Confidence 5668888999999998 6888888888754
No 214
>PF08841 DDR: Diol dehydratase reactivase ATPase-like domain; InterPro: IPR009191 Diol dehydratase (propanediol dehydratase) and glycerol dehydratase undergo concomitant, irreversible inactivation by glycerol during catalysis [, ]. This inactivation is mechanism-based and involves cleavage of the Co-C bond of the cobalamin cofactor, coenzyme B12 (AdoCbl), forming 5 -deoxyadenosine and a modified coenzyme []. Irreversible inactivation of the enzyme results from tight binding to the modified, inactive cobalamin [, ]. The glycerol-inactivated enzyme undergoes rapid reactivation in the presence of free AdoCbl, ATP, and Mg 2+ (or Mn 2+ ) []. Reactivation is mediated by a complex of two proteins: a large subunit (DdrA/PduG) and a small subunit (DdrB/PduH, IPR009192 from INTERPRO) [, ]. The two subunits of the reactivating factor for glycerol dehydratase have been shown to form a tight complex that serves to reactivate the glycerol-inactivated holoenzyme, as well as O2-inactivated holoenzyme in vitro []. It is believed that this reactivating factor replaces an enzyme-bound, adenine-lacking inactive cobalamin with a free, adenine-containing active cobalamin []. PduG and PduH, part of the propanediol utilization pdu operon, are believed to have a similar function in the reactivation of propanediol dehydratase. PduG was also proposed, on the basis of genetic tests, to be a cobalamin adenosyltransferase involved in the conversion of inactive cobalamin (B12) to AdoCbl []. However, this function has since been shown to belong to another protein, PduO (IPR009221 from INTERPRO, IPR012228 from INTERPRO) []. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO for more details on the propanediol utilization pathway and pdu operon, as well as on the glycerol breakdown pathway.; PDB: 1NBW_C 2D0P_C 2D0O_C.
Probab=22.79 E-value=38 Score=27.43 Aligned_cols=33 Identities=15% Similarity=0.292 Sum_probs=23.2
Q ss_pred cchHHHHHHHHHHHHHHhcCCc-----eEEEcccHHHH
Q psy17228 13 KTKWTIKLTKTKIDDILQRNKV-----PIIVGGTNYYI 45 (99)
Q Consensus 13 ~~~~~~~~a~~~i~~i~~~~~~-----pilVGGTglYi 45 (99)
+++-|+..|.+++..+.-.|++ .++||||.|=|
T Consensus 252 K~kVFVtNa~RaL~~vsPtgniR~i~fVVlVGGSALDF 289 (332)
T PF08841_consen 252 KEKVFVTNALRALKQVSPTGNIRDIPFVVLVGGSALDF 289 (332)
T ss_dssp HHHHHHHHHHHHHCCCSTTSSCCC--EEEEESGGGGSS
T ss_pred hhhhhHHHHHHHHHhcCCCCCcccCceEEEecCchhhh
Confidence 4556777888887777655533 68889998744
No 215
>COG0127 Xanthosine triphosphate pyrophosphatase [Nucleotide transport and metabolism]
Probab=22.76 E-value=58 Score=24.39 Aligned_cols=59 Identities=10% Similarity=0.019 Sum_probs=39.7
Q ss_pred hHHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccC------CCCCCCcccchHhHHHHHhhc
Q psy17228 15 KWTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILL------DNKTNINDQGEFTLYDMDKIR 75 (99)
Q Consensus 15 ~~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~------~~~~~~~~~~~~~l~~~l~~~ 75 (99)
.-|.+.|....+.+...-..|+||==|||.++|| +|+-- ... .+...+...+.+.|...
T Consensus 45 ~tf~enA~~Ka~~~a~~~g~pviaDDSGL~v~aL-~G~PGvYSar~~~~-~~d~~~~~klL~~l~~~ 109 (194)
T COG0127 45 LTFEENALLKARAAAKATGLPVIADDSGLCVDAL-NGFPGVYSARFAGE-ADDTIGNEKLLKLLEGV 109 (194)
T ss_pred hHHHHHHHHHHHHHHhhcCCcEEEecCceEEecc-CCCCcceeehhccc-CchhhhHHHHHHHhcCC
Confidence 3466778888888877889999999999999998 55321 101 12344566666666543
No 216
>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase. Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.
Probab=22.75 E-value=96 Score=24.68 Aligned_cols=32 Identities=22% Similarity=0.236 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHH----HHHHHHh
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNY----YIESLLW 50 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTgl----Yi~all~ 50 (99)
.+..+.+..+.+.++.-+|+|+||. .+++|+.
T Consensus 165 ~~~~~~L~~~v~~~~~ili~G~tGsGKTTll~al~~ 200 (340)
T TIGR03819 165 PGVARLLRAIVAARLAFLISGGTGSGKTTLLSALLA 200 (340)
T ss_pred HHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHc
Confidence 4566778888888889999998875 6666654
No 217
>PF01116 F_bP_aldolase: Fructose-bisphosphate aldolase class-II; InterPro: IPR000771 Fructose-bisphosphate aldolase [, ] is a glycolytic enzyme that catalyses the reversible aldol cleavage or condensation of fructose-1,6-bisphosphate into dihydroxyacetone-phosphate and glyceraldehyde 3-phosphate. There are two classes of fructose-bisphosphate aldolases with different catalytic mechanisms. Class-II aldolases [], mainly found in prokaryotes and fungi, are homodimeric enzymes, which require a divalent metal ion, generally zinc, for their activity. This family also includes the Escherichia coli galactitol operon protein, gatY, which catalyses the transformation of tagatose 1,6-bisphosphate into glycerone phosphate and D-glyceraldehyde 3-phosphate; and E. coli N-acetyl galactosamine operon protein, agaY, which catalyses the same reaction. There are two histidine residues in the first half of the sequence of these enzymes that have been shown to be involved in binding a zinc ion [].; GO: 0008270 zinc ion binding, 0016832 aldehyde-lyase activity, 0005975 carbohydrate metabolic process; PDB: 3Q94_A 1RVG_B 1RV8_C 3C4U_A 3C56_B 3C52_A 2FJK_A 3N9R_P 3N9S_A 1GVF_B ....
Probab=22.68 E-value=50 Score=25.84 Aligned_cols=31 Identities=16% Similarity=0.437 Sum_probs=19.5
Q ss_pred HHHHHHHhcC-CceEEE-cccHH----HHHHHHhccc
Q psy17228 23 TKIDDILQRN-KVPIIV-GGTNY----YIESLLWTIL 53 (99)
Q Consensus 23 ~~i~~i~~~~-~~pilV-GGTgl----Yi~all~g~~ 53 (99)
+.+++|.+.- .+|++. ||||+ +-+++-.|+.
T Consensus 194 ~~L~~I~~~~~~iPLVlHGgSG~~~e~~~~ai~~Gi~ 230 (287)
T PF01116_consen 194 DRLKEIREAVPDIPLVLHGGSGLPDEQIRKAIKNGIS 230 (287)
T ss_dssp HHHHHHHHHHHTSEEEESSCTTS-HHHHHHHHHTTEE
T ss_pred HHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHcCce
Confidence 3445555554 677666 99996 5556666654
No 218
>cd04255 AAK_UMPK-MosAB AAK_UMPK-MosAB: This CD includes the alpha and beta subunits of the Mo storage protein (MosA and MosB) which are related to uridine monophosphate kinase (UMPK) enzymes that catalyze the phosphorylation of UMP by ATP, yielding UDP, and playing a key role in pyrimidine nucleotide biosynthesis. The Mo storage protein from the nitrogen-fixing bacterium, Azotobacter vinelandii, is characterized as an alpha4-beta4 octamer containing a polynuclear molybdenum-oxide cluster which is ATP-dependent to bind Mo and pH-dependent to release Mo. These and related bacterial sequences in this CD are members of the Amino Acid Kinase Superfamily (AAK).
Probab=22.67 E-value=58 Score=24.97 Aligned_cols=19 Identities=21% Similarity=0.504 Sum_probs=16.2
Q ss_pred HHHHHHhcCCceEEEcccH
Q psy17228 24 KIDDILQRNKVPIIVGGTN 42 (99)
Q Consensus 24 ~i~~i~~~~~~pilVGGTg 42 (99)
.+..+++.|.+||+.|+++
T Consensus 127 ~l~~lL~~g~vPVi~g~~~ 145 (262)
T cd04255 127 QLPTFLKAGRAPVISGMPP 145 (262)
T ss_pred HHHHHHHCCCeEEEeCCcC
Confidence 4778889999999999954
No 219
>PRK14557 pyrH uridylate kinase; Provisional
Probab=22.62 E-value=75 Score=24.17 Aligned_cols=17 Identities=24% Similarity=0.313 Sum_probs=12.6
Q ss_pred HHHHhcCCceEEEcccH
Q psy17228 26 DDILQRNKVPIIVGGTN 42 (99)
Q Consensus 26 ~~i~~~~~~pilVGGTg 42 (99)
.+.+++|.+||+.||+|
T Consensus 119 ~~~l~~g~VvV~~G~~g 135 (247)
T PRK14557 119 VHHLDNGYIVIFGGGNG 135 (247)
T ss_pred HHHHhCCCEEEEECCcC
Confidence 33467889999999755
No 220
>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11. The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.
Probab=22.61 E-value=92 Score=24.06 Aligned_cols=30 Identities=30% Similarity=0.347 Sum_probs=22.8
Q ss_pred HHHHHHHHHhcCCceEEEcccH----HHHHHHHh
Q psy17228 21 TKTKIDDILQRNKVPIIVGGTN----YYIESLLW 50 (99)
Q Consensus 21 a~~~i~~i~~~~~~pilVGGTg----lYi~all~ 50 (99)
..+.++.+...|..-+|+|+|| ..+++|+.
T Consensus 133 ~~~~l~~~v~~~~~ili~G~tGsGKTTll~al~~ 166 (308)
T TIGR02788 133 IKEFLRLAIASRKNIIISGGTGSGKTTFLKSLVD 166 (308)
T ss_pred HHHHHHHHhhCCCEEEEECCCCCCHHHHHHHHHc
Confidence 4556777888899999999888 45666664
No 221
>PRK07432 5'-methylthioadenosine phosphorylase; Provisional
Probab=22.48 E-value=29 Score=27.40 Aligned_cols=15 Identities=33% Similarity=0.466 Sum_probs=10.3
Q ss_pred EEEcccHHHHHHHHh
Q psy17228 36 IIVGGTNYYIESLLW 50 (99)
Q Consensus 36 ilVGGTglYi~all~ 50 (99)
=|+||||+|==+.+.
T Consensus 7 gIIgGSGl~~l~~l~ 21 (290)
T PRK07432 7 GIIGGSGLYKMEALK 21 (290)
T ss_pred EEEecCccCChhhcC
Confidence 478999999533343
No 222
>PF02219 MTHFR: Methylenetetrahydrofolate reductase; InterPro: IPR003171 This family includes the 5,10-methylenetetrahydrofolate reductase 1.7.99.5 from EC from bacteria and methylenetetrahydrofolate reductase 1.5.1.20 from EC from eukaryotes. The structure for this domain is known [] to be a TIM barrel.; GO: 0004489 methylenetetrahydrofolate reductase (NADPH) activity, 0006555 methionine metabolic process, 0055114 oxidation-reduction process; PDB: 3IJD_B 1B5T_B 3FSU_C 1ZPT_C 2FMO_B 3FST_C 2FMN_C 1ZP3_A 1ZP4_B 1ZRQ_B ....
Probab=22.32 E-value=1e+02 Score=23.57 Aligned_cols=39 Identities=18% Similarity=0.350 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHhcC-CceEEEc-------ccHHHHHHHHhcccCC
Q psy17228 16 WTIKLTKTKIDDILQRN-KVPIIVG-------GTNYYIESLLWTILLD 55 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~-~~pilVG-------GTglYi~all~g~~~~ 55 (99)
|....+.+.++.+.+.| .+||++| ++-.|+..+. |..+|
T Consensus 182 fd~~~~~~~~~~~~~~g~~~pIi~GI~p~~s~~~~~~~~~~~-Gv~iP 228 (287)
T PF02219_consen 182 FDAEAFERFLDRLREAGIDVPIIPGIMPLTSAKSARFLAKLC-GVDIP 228 (287)
T ss_dssp SSHHHHHHHHHHHHHTTHTSEEEEEEE-HCCHHHHHHHHHHH-T-EEE
T ss_pred CCHHHHHHHHHHHHHcCCCCcEEEEEeccCCHHHHHHHHhcc-CccCC
Confidence 33466777888888777 6999998 6677887776 77653
No 223
>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase. This model respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This model identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologs of this gene are not found in plants which rely solely on the aerobic cyclase.
Probab=22.30 E-value=94 Score=25.74 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHhc-CCceEEEcccH
Q psy17228 16 WTIKLTKTKIDDILQR-NKVPIIVGGTN 42 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~-~~~pilVGGTg 42 (99)
+....|.++++.+.++ ..++||+||..
T Consensus 74 ~~~~~a~~~~~~~k~~~P~~~iV~GG~h 101 (497)
T TIGR02026 74 PAIYIACETLKFARERLPNAIIVLGGIH 101 (497)
T ss_pred ccHHHHHHHHHHHHHHCCCCEEEEcCCC
Confidence 4445666777666554 48999999964
No 224
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=22.28 E-value=78 Score=21.03 Aligned_cols=16 Identities=19% Similarity=0.627 Sum_probs=13.5
Q ss_pred HHHHHHHHhcCCceEE
Q psy17228 22 KTKIDDILQRNKVPII 37 (99)
Q Consensus 22 ~~~i~~i~~~~~~pil 37 (99)
..++..+.++||+|++
T Consensus 26 ~sAVr~Mi~~gKLP~i 41 (87)
T PF10743_consen 26 PSAVRKMIKAGKLPVI 41 (87)
T ss_pred HHHHHHHHHcCCCCeE
Confidence 4577888899999997
No 225
>COG0543 UbiB 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion]
Probab=22.25 E-value=68 Score=24.09 Aligned_cols=20 Identities=25% Similarity=0.338 Sum_probs=16.6
Q ss_pred ceEEEcccHH-HHHHHHhccc
Q psy17228 34 VPIIVGGTNY-YIESLLWTIL 53 (99)
Q Consensus 34 ~pilVGGTgl-Yi~all~g~~ 53 (99)
+.+|.||||+ .+.+++..+.
T Consensus 110 vlliagGtG~aPl~~i~~~~~ 130 (252)
T COG0543 110 VLLIAGGTGIAPLYAIAKELK 130 (252)
T ss_pred EEEEecccCHhHHHHHHHHHH
Confidence 7788899999 8888888754
No 226
>cd06356 PBP1_Amide_Urea_BP_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
Probab=22.20 E-value=72 Score=24.14 Aligned_cols=38 Identities=16% Similarity=0.110 Sum_probs=29.3
Q ss_pred hhhcccchHHHHHHHHHHHHHHhcCCceEEEcccHHHH
Q psy17228 8 RLKLTKTKWTIKLTKTKIDDILQRNKVPIIVGGTNYYI 45 (99)
Q Consensus 8 ~~~~~~~~~~~~~a~~~i~~i~~~~~~pilVGGTglYi 45 (99)
+|-..++......+..+.+++..+.++.+|+|+++.-.
T Consensus 42 ~lv~~D~~~~p~~a~~~~~~Li~~~~V~aiiG~~~s~~ 79 (334)
T cd06356 42 ELVDYDTQSDNERYQQYAQRLALQDKVDVVWGGISSAS 79 (334)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHhCCCCEEEeCcchHH
Confidence 34445666667888899999998999999999876643
No 227
>KOG1324|consensus
Probab=22.19 E-value=64 Score=24.33 Aligned_cols=20 Identities=25% Similarity=0.481 Sum_probs=16.4
Q ss_pred CceEEEcccHHHHHHHHhcc
Q psy17228 33 KVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 33 ~~pilVGGTglYi~all~g~ 52 (99)
....|+||+..|=+||-.++
T Consensus 111 e~vfvIGG~~vy~~al~~p~ 130 (190)
T KOG1324|consen 111 EMVFVIGGSEVYSEALNSPR 130 (190)
T ss_pred eEEEEEcCHHHHHHHHcCcC
Confidence 45789999999999987653
No 228
>COG0262 FolA Dihydrofolate reductase [Coenzyme metabolism]
Probab=22.16 E-value=1.4e+02 Score=21.25 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhc-CCceEEEcccHHHHHHHHhcc
Q psy17228 20 LTKTKIDDILQR-NKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~-~~~pilVGGTglYi~all~g~ 52 (99)
...+++...... ++-..|+||.-+|=..|=+|+
T Consensus 82 s~~~al~~~~~~~~~~i~IiGG~~l~~~~l~~~l 115 (167)
T COG0262 82 SIEEALLLLLKEEGEDIFIIGGGELYRQFLPAGL 115 (167)
T ss_pred CHHHHHHHHhhcCCCeEEEEcCHHHHHHHhcccc
Confidence 445556655554 677899999999988777664
No 229
>cd04252 AAK_NAGK-fArgBP AAK_NAGK-fArgBP: N-Acetyl-L-glutamate kinase (NAGK) of the fungal arginine-biosynthetic pathway (fArgBP). The nuclear-encoded, mitochondrial polyprotein precursor with an N-terminal NAGK (ArgB) domain (this CD), a central DUF619 domain, and a C-terminal reductase domain (ArgC, N-Acetylglutamate Phosphate Reductase, NAGPR). The precursor is cleaved in the mitochondria into two distinct enzymes (NAGK-DUF619 and NAGPR). Native molecular weights of these proteins indicate that the kinase is an octamer whereas the reductase is a dimer. This CD also includes some gamma-proteobacteria (Xanthomonas and Xylella) NAG kinases with an N-terminal NAGK (ArgB) domain (this CD) and a C-terminal DUF619 domain. The DUF619 domain is described as a putative distant homolog of the acetyltransferase, ArgA, predicted to function in NAG synthase association in fungi. Eukaryotic sequences have an N-terminal mitochondrial transit peptide. Members of this NAG kinase domain CD belong to th
Probab=22.14 E-value=2.1e+02 Score=21.43 Aligned_cols=35 Identities=14% Similarity=0.098 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhcCCceEEEcccHHHHHHHHhcccC
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNYYIESLLWTILL 54 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTglYi~all~g~~~ 54 (99)
.+...|..+.+.|..||||=|.|-+++.++..+-+
T Consensus 16 ~~~~di~~l~~~g~~~VlVHGgg~~i~~~~~~~gi 50 (248)
T cd04252 16 ELAASLSFLQHVGLYPIVVHGAGPQLNEELEAAGV 50 (248)
T ss_pred HHHHHHHHHHHCCCcEEEEeCCCHHHHHHHHHcCC
Confidence 34445556777788889999999999999986543
No 230
>PRK13055 putative lipid kinase; Reviewed
Probab=22.07 E-value=1.2e+02 Score=23.75 Aligned_cols=34 Identities=18% Similarity=0.243 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhccc
Q psy17228 19 KLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 19 ~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~~ 53 (99)
.++.+++.++.+.+ ...|++||=|. ++.+++|+.
T Consensus 46 ~~a~~~~~~~~~~~~d~vvv~GGDGT-l~evvngl~ 80 (334)
T PRK13055 46 NSAKNEAKRAAEAGFDLIIAAGGDGT-INEVVNGIA 80 (334)
T ss_pred ccHHHHHHHHhhcCCCEEEEECCCCH-HHHHHHHHh
Confidence 36666776666554 67888999998 566667764
No 231
>KOG3974|consensus
Probab=22.06 E-value=86 Score=25.18 Aligned_cols=36 Identities=11% Similarity=0.287 Sum_probs=29.5
Q ss_pred cccchHHHHHHHHHHHHHHhcCCceEEEcccHHHHHH
Q psy17228 11 LTKTKWTIKLTKTKIDDILQRNKVPIIVGGTNYYIES 47 (99)
Q Consensus 11 ~~~~~~~~~~a~~~i~~i~~~~~~pilVGGTglYi~a 47 (99)
|--++|..+...++++-+. ..++|+++-|-|+++=+
T Consensus 111 LGRdp~~~k~i~~iley~~-~~dvP~VIDaDGL~Lv~ 146 (306)
T KOG3974|consen 111 LGRDPAILKEIAKILEYLR-GKDVPLVIDADGLWLVE 146 (306)
T ss_pred CCCCHHHHHHHHHHHHHHh-cCCCcEEEcCCceEehh
Confidence 4557899999999998765 45999999999999743
No 232
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=22.04 E-value=40 Score=24.68 Aligned_cols=17 Identities=24% Similarity=0.223 Sum_probs=14.5
Q ss_pred EEcccHHHHHHHHhccc
Q psy17228 37 IVGGTNYYIESLLWTIL 53 (99)
Q Consensus 37 lVGGTglYi~all~g~~ 53 (99)
+.-.+|.||++|..++.
T Consensus 130 v~cs~GTYIRsL~~dlg 146 (182)
T cd02572 130 VSCEAGTYIRTLCVHIG 146 (182)
T ss_pred EEECCCcCHHHHHHHHH
Confidence 55689999999999864
No 233
>PRK06923 isochorismate synthase DhbC; Validated
Probab=22.01 E-value=1.1e+02 Score=25.24 Aligned_cols=25 Identities=20% Similarity=0.242 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHhcC-CceEEEcc
Q psy17228 16 WTIKLTKTKIDDILQRN-KVPIIVGG 40 (99)
Q Consensus 16 ~~~~~a~~~i~~i~~~~-~~pilVGG 40 (99)
=|.+.+...+++....| ..|||||-
T Consensus 49 ~l~~~~~~~~~~a~~~g~~~p~~vGa 74 (399)
T PRK06923 49 SFPERVQAVLRNAKQAGNPNPIVVGA 74 (399)
T ss_pred hHHHHHHHHHHHHHHcCCCCCeEEEE
Confidence 35567777888888888 89999994
No 234
>PRK10769 folA dihydrofolate reductase; Provisional
Probab=21.84 E-value=1.4e+02 Score=21.24 Aligned_cols=28 Identities=14% Similarity=0.224 Sum_probs=17.7
Q ss_pred HHHHHHHHHHhcCCceEEEcccHHHHHHH
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNYYIESL 48 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTglYi~al 48 (99)
...++++.+ +.++--.|+||.++|=++|
T Consensus 77 ~l~~~l~~~-~~~~~I~viGG~~iy~~~l 104 (159)
T PRK10769 77 SVDEALAAA-GDVPEIMVIGGGRVYEQFL 104 (159)
T ss_pred CHHHHHHHh-cCCCCEEEECcHHHHHHHH
Confidence 445555533 2334456779999998766
No 235
>TIGR00725 conserved hypothetical protein, DprA/Smf-related, family 1. This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this model show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of PFAM model pfam03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE.
Probab=21.84 E-value=1.5e+02 Score=20.87 Aligned_cols=37 Identities=11% Similarity=0.112 Sum_probs=26.1
Q ss_pred chHHHHHHHHHHHHHHhcCCceEEEcccHHHHHHHHhc
Q psy17228 14 TKWTIKLTKTKIDDILQRNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 14 ~~~~~~~a~~~i~~i~~~~~~pilVGGTglYi~all~g 51 (99)
.+.+.+.|.++-+.+.++| ..|+.||..==..++-+|
T Consensus 13 ~~~~~~~A~~lg~~La~~g-~~lv~Gg~~GlM~a~a~g 49 (159)
T TIGR00725 13 SEELYEIAYRLGKELAKKG-HILINGGRTGVMEAVSKG 49 (159)
T ss_pred ChHHHHHHHHHHHHHHHCC-CEEEcCCchhHHHHHHHH
Confidence 5688889999999887776 567777755445555544
No 236
>PRK03673 hypothetical protein; Provisional
Probab=21.69 E-value=89 Score=25.66 Aligned_cols=24 Identities=21% Similarity=0.192 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhcCCceEEEcccHH
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNY 43 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTgl 43 (99)
.-.+.+++..++..+.|++||+|-
T Consensus 49 ~i~~~l~~a~~~~DlVI~tGGlGp 72 (396)
T PRK03673 49 ALVAILRERSQHADVLIVNGGLGP 72 (396)
T ss_pred HHHHHHHHHhccCCEEEEcCCCCC
Confidence 445566667778899999999984
No 237
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=21.61 E-value=1.4e+02 Score=19.66 Aligned_cols=27 Identities=11% Similarity=0.171 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHH
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYY 44 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglY 44 (99)
...|+.+++++.++|-+-.+++++..-
T Consensus 55 ~SlAr~~Lr~L~~kG~Ik~V~~~~~q~ 81 (86)
T PRK09334 55 ISVAKKVLRELEKRGVLVLYSKNRRTP 81 (86)
T ss_pred HHHHHHHHHHHHHCCCEEEEecCCCeE
Confidence 468999999999999997788887643
No 238
>TIGR02075 pyrH_bact uridylate kinase. This protein, also called UMP kinase, converts UMP to UDP by adding a phosphate from ATP. It is the first step in pyrimidine biosynthesis. GTP is an allosteric activator. In a large fraction of all bacterial genomes, the gene tends to be located immediately downstream of elongation factor Ts and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function and found in the archaea and in spirochetes, is described by a separate model, TIGR02076.
Probab=21.57 E-value=89 Score=23.12 Aligned_cols=20 Identities=40% Similarity=0.546 Sum_probs=15.8
Q ss_pred HHHHHHHHhcCCceEEEccc
Q psy17228 22 KTKIDDILQRNKVPIIVGGT 41 (99)
Q Consensus 22 ~~~i~~i~~~~~~pilVGGT 41 (99)
.+.+++++++|.+||+.|+.
T Consensus 111 ~~~i~~ll~~g~VpV~~g~~ 130 (233)
T TIGR02075 111 RRKAIKHLEKGKVVIFSGGT 130 (233)
T ss_pred HHHHHHHHHCCCEEEEECCC
Confidence 36667788899999998774
No 239
>PLN02427 UDP-apiose/xylose synthase
Probab=21.54 E-value=47 Score=25.83 Aligned_cols=16 Identities=13% Similarity=0.225 Sum_probs=10.7
Q ss_pred ceEEEcccHHHHHHHH
Q psy17228 34 VPIIVGGTNYYIESLL 49 (99)
Q Consensus 34 ~pilVGGTglYi~all 49 (99)
..+|+|||||==..|+
T Consensus 16 ~VlVTGgtGfIGs~lv 31 (386)
T PLN02427 16 TICMIGAGGFIGSHLC 31 (386)
T ss_pred EEEEECCcchHHHHHH
Confidence 3688899998433333
No 240
>TIGR02082 metH 5-methyltetrahydrofolate--homocysteine methyltransferase. S-methyltransferase (MetE, EC 2.1.1.14, the cobalamin-independent methionine synthase) and betaine-homocysteine methyltransferase.
Probab=21.38 E-value=93 Score=29.23 Aligned_cols=26 Identities=19% Similarity=0.553 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHhcC-CceEEEcccHH
Q psy17228 18 IKLTKTKIDDILQRN-KVPIIVGGTNY 43 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~-~~pilVGGTgl 43 (99)
.....+.++.+.++| ++||+|||..+
T Consensus 797 ~~~m~~vi~~L~~~g~~v~v~vGGa~~ 823 (1178)
T TIGR02082 797 LDEMKEVAEEMNRRGITIPLLIGGAAT 823 (1178)
T ss_pred HHHHHHHHHHHHhcCCCceEEEecccc
Confidence 456677888888887 79999999765
No 241
>TIGR01489 DKMTPPase-SF 2,3-diketo-5-methylthio-1-phosphopentane phosphatase. Note that SP|P53981 from S. cerevisiae, a member of this family, is annotated as a "probable membrane protein" due to a predicted transmembrane helix. The region in question contains the second of the three conserved HAD superfamily catalytic motifs and thus, considering the fold of the HAD catalytic domain, is unlikely to be a transmembrane region in fact.
Probab=21.36 E-value=1.9e+02 Score=19.41 Aligned_cols=33 Identities=24% Similarity=0.327 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhcC-CceEEEcccHHHHHHHHhcc
Q psy17228 20 LTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 20 ~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~ 52 (99)
.+.+.++.+.++| ++-|+.+|+..+++.++..+
T Consensus 76 g~~~ll~~l~~~g~~~~i~S~~~~~~~~~~l~~~ 109 (188)
T TIGR01489 76 GFKEFIAFIKEHGIDFIVISDGNDFFIDPVLEGI 109 (188)
T ss_pred cHHHHHHHHHHcCCcEEEEeCCcHHHHHHHHHHc
Confidence 4677888887776 45566688899999988754
No 242
>PRK08945 putative oxoacyl-(acyl carrier protein) reductase; Provisional
Probab=21.33 E-value=53 Score=23.42 Aligned_cols=21 Identities=10% Similarity=0.208 Sum_probs=15.6
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
+++..+|+||||.==.++..-
T Consensus 11 ~~k~vlItG~~g~iG~~la~~ 31 (247)
T PRK08945 11 KDRIILVTGAGDGIGREAALT 31 (247)
T ss_pred CCCEEEEeCCCchHHHHHHHH
Confidence 688999999999655555543
No 243
>TIGR01826 CofD_related conserved hypothetical protein, cofD-related. This model represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (TIGR01819), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis. Both this family and TIGR01819 are within the scope of the pfam model pfam01933.
Probab=21.07 E-value=62 Score=25.81 Aligned_cols=18 Identities=39% Similarity=0.385 Sum_probs=14.0
Q ss_pred ceEEEcccHHHHHHHHhccc
Q psy17228 34 VPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 34 ~pilVGGTglYi~all~g~~ 53 (99)
+.+|-||||+. .++.|+.
T Consensus 1 vV~igGGtGl~--~ll~gLk 18 (310)
T TIGR01826 1 VVAIGGGTGLS--VLLRGLK 18 (310)
T ss_pred CEEEeCcchHH--HHHHHHH
Confidence 35788999998 7778863
No 244
>PRK07276 DNA polymerase III subunit delta'; Validated
Probab=21.01 E-value=1.1e+02 Score=23.96 Aligned_cols=28 Identities=11% Similarity=0.254 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhcCCce---EEEcccHHHH
Q psy17228 18 IKLTKTKIDDILQRNKVP---IIVGGTNYYI 45 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~p---ilVGGTglYi 45 (99)
+..+.+.+..+.++|++| +++||+|-..
T Consensus 7 q~~~~~~L~~~~~~~rl~hAyLf~G~~G~~~ 37 (290)
T PRK07276 7 QPKVFQRFQTILEQDRLNHAYLFSGDFASFE 37 (290)
T ss_pred HHHHHHHHHHHHHcCCcceeeeeeCCccHHH
Confidence 456778888888999887 8999998643
No 245
>PLN02725 GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase
Probab=20.95 E-value=29 Score=25.47 Aligned_cols=16 Identities=6% Similarity=0.177 Sum_probs=9.1
Q ss_pred EEEcccHHHHHHHHhc
Q psy17228 36 IIVGGTNYYIESLLWT 51 (99)
Q Consensus 36 ilVGGTglYi~all~g 51 (99)
+|+|||||==..|+.-
T Consensus 1 lItGa~GfiG~~l~~~ 16 (306)
T PLN02725 1 FVAGHRGLVGSAIVRK 16 (306)
T ss_pred CcccCCCcccHHHHHH
Confidence 4678887744444433
No 246
>PRK12935 acetoacetyl-CoA reductase; Provisional
Probab=20.84 E-value=55 Score=23.21 Aligned_cols=21 Identities=24% Similarity=0.349 Sum_probs=16.4
Q ss_pred cCCceEEEcccHHHHHHHHhc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g 51 (99)
+++..+|+||||.==.++..-
T Consensus 5 ~~~~~lItG~s~~iG~~la~~ 25 (247)
T PRK12935 5 NGKVAIVTGGAKGIGKAITVA 25 (247)
T ss_pred CCCEEEEECCCCHHHHHHHHH
Confidence 478899999999876666654
No 247
>PRK11914 diacylglycerol kinase; Reviewed
Probab=20.80 E-value=1.9e+02 Score=21.91 Aligned_cols=35 Identities=14% Similarity=0.247 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhcC-CceEEEcccHHHHHHHHhccc
Q psy17228 18 IKLTKTKIDDILQRN-KVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~-~~pilVGGTglYi~all~g~~ 53 (99)
..++.++++++.+++ ...|++||=|..= .+++++.
T Consensus 50 ~~~~~~~a~~~~~~~~d~vvv~GGDGTi~-evv~~l~ 85 (306)
T PRK11914 50 AHDARHLVAAALAKGTDALVVVGGDGVIS-NALQVLA 85 (306)
T ss_pred HHHHHHHHHHHHhcCCCEEEEECCchHHH-HHhHHhc
Confidence 467888888877665 6788999999854 4556754
No 248
>PRK09135 pteridine reductase; Provisional
Probab=20.75 E-value=56 Score=22.94 Aligned_cols=22 Identities=27% Similarity=0.406 Sum_probs=16.6
Q ss_pred cCCceEEEcccHHHHHHHHhcc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g~ 52 (99)
.++..+|+||||+==.++..-+
T Consensus 5 ~~~~vlItGa~g~iG~~l~~~l 26 (249)
T PRK09135 5 SAKVALITGGARRIGAAIARTL 26 (249)
T ss_pred CCCEEEEeCCCchHHHHHHHHH
Confidence 4577899999998777766554
No 249
>PLN02561 triosephosphate isomerase
Probab=20.66 E-value=1.4e+02 Score=22.98 Aligned_cols=13 Identities=31% Similarity=0.319 Sum_probs=10.2
Q ss_pred CCceEEEcccHHH
Q psy17228 32 NKVPIIVGGTNYY 44 (99)
Q Consensus 32 ~~~pilVGGTglY 44 (99)
..+||+.|||=--
T Consensus 203 ~~i~ILYGGSV~~ 215 (253)
T PLN02561 203 ATTRIIYGGSVTG 215 (253)
T ss_pred ccceEEEeCCcCH
Confidence 4689999998544
No 250
>TIGR00089 RNA modification enzyme, MiaB family. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.
Probab=20.62 E-value=1.3e+02 Score=24.21 Aligned_cols=26 Identities=15% Similarity=0.305 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHhcCCc--eEEEcccHH
Q psy17228 18 IKLTKTKIDDILQRNKV--PIIVGGTNY 43 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~--pilVGGTgl 43 (99)
.+.+.+++..+.++++- +|||||-.-
T Consensus 52 ~~~~~~~i~~~~~~~~~~~~vvvgGc~a 79 (429)
T TIGR00089 52 EQKVRSRLGELAKLKKKNAKIVVAGCLA 79 (429)
T ss_pred HHHHHHHHHHHHHhCcCCCEEEEECccc
Confidence 35778888888776642 799999753
No 251
>COG0451 WcaG Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]
Probab=20.61 E-value=45 Score=24.36 Aligned_cols=16 Identities=19% Similarity=0.395 Sum_probs=10.2
Q ss_pred eEEEcccHHHHHHHHh
Q psy17228 35 PIIVGGTNYYIESLLW 50 (99)
Q Consensus 35 pilVGGTglYi~all~ 50 (99)
.+|+|||||==.+|+.
T Consensus 3 ILVtG~tGfiG~~l~~ 18 (314)
T COG0451 3 ILVTGGAGFIGSHLVE 18 (314)
T ss_pred EEEEcCcccHHHHHHH
Confidence 4677999985444443
No 252
>cd01917 ACS_2 Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA. ACS forms a heterotetramer with carbon monoxide dehydrogenase (CODH) consisting of two ACS and two CODH subunits. CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP). ACS has three structural domains, an N-terminal rossman fold domain with a helical region at its N-terminus which interacts with CODH, and two alpha + beta fold domains. A Ni-Fe-S center referred to as the A-cluster is located in the C-terminal domain. A large cavity exists between the three domains which may bind CoA.
Probab=20.49 E-value=1.3e+02 Score=24.04 Aligned_cols=30 Identities=17% Similarity=0.162 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHHHHH
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYYIES 47 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglYi~a 47 (99)
.+++.++++++.+||-+.+++|.-+.|+..
T Consensus 140 ~e~~~~I~~e~q~r~~lv~l~G~i~~q~~E 169 (287)
T cd01917 140 SKALKKIVDDLMGRGFMLFLCDEIVEQLLE 169 (287)
T ss_pred hHHHHHHHHHHHHCCcEEEEecHHHHHHHH
Confidence 478999999999999999999987777653
No 253
>PRK14825 putative deoxyribonucleotide triphosphate pyrophosphatase; Provisional
Probab=20.48 E-value=63 Score=23.93 Aligned_cols=34 Identities=21% Similarity=0.231 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHhc-C-CceEEEcccHHHHHHHHhc
Q psy17228 17 TIKLTKTKIDDILQR-N-KVPIIVGGTNYYIESLLWT 51 (99)
Q Consensus 17 ~~~~a~~~i~~i~~~-~-~~pilVGGTglYi~all~g 51 (99)
|...|......+.+. + ..|+|+==|||||+|| .|
T Consensus 43 f~enA~~KA~~~~~~~~~~~pvlaDDSGL~vdAL-~G 78 (199)
T PRK14825 43 FKENSLLKAKALFEILNNKQPVFSEDSGLCIEAL-NL 78 (199)
T ss_pred HHHHHHHHHHHHHHHHCCCCcEEEecCeEEEhhh-CC
Confidence 555666555555543 2 4799999999999998 45
No 254
>PLN02986 cinnamyl-alcohol dehydrogenase family protein
Probab=20.47 E-value=83 Score=23.55 Aligned_cols=22 Identities=14% Similarity=0.295 Sum_probs=17.7
Q ss_pred cCCceEEEcccHHHHHHHHhcc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g~ 52 (99)
.|+..+|+|||||-=.+++.-+
T Consensus 4 ~~~~vlVTGatG~iG~~l~~~L 25 (322)
T PLN02986 4 GGKLVCVTGASGYIASWIVKLL 25 (322)
T ss_pred CCCEEEEECCCcHHHHHHHHHH
Confidence 5788899999999877777653
No 255
>PF01872 RibD_C: RibD C-terminal domain; InterPro: IPR002734 This domain is found in the C terminus of the bifunctional deaminase-reductase of Escherichia coli, Bacillus subtilis and other bacteria in combination with IPR002125 from INTERPRO that catalyses the second and third steps in the biosynthesis of riboflavin, i.e., the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (deaminase) and the subsequent reduction of the ribosyl side chain (reductase) []. The domain is also present in some HTP reductases from archaea and fungi.; GO: 0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity, 0009231 riboflavin biosynthetic process, 0055114 oxidation-reduction process; PDB: 3KY8_B 3KGY_B 2GD9_B 3JTW_B 2XW7_B 2D5N_B 2B3Z_A 3EX8_B 2AZN_A 2P4G_A ....
Probab=20.47 E-value=2e+02 Score=20.20 Aligned_cols=31 Identities=19% Similarity=0.196 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhcCCceEEEcccHHHHHHHHh
Q psy17228 20 LTKTKIDDILQRNKVPIIVGGTNYYIESLLW 50 (99)
Q Consensus 20 ~a~~~i~~i~~~~~~pilVGGTglYi~all~ 50 (99)
+..++++.+.++|-..|+|-|.|--..+++.
T Consensus 122 dl~~~l~~L~~~g~~~i~v~GG~~l~~~~l~ 152 (200)
T PF01872_consen 122 DLEEALRRLKERGGKDILVEGGGSLNGSFLR 152 (200)
T ss_dssp HHHHHHHHHHHTTTSEEEEEEHHHHHHHHHH
T ss_pred CHHHHHHHHHhcCCCEEEEechHHHHHHHHh
Confidence 4778888888898788887444444555554
No 256
>PF07005 DUF1537: Protein of unknown function, DUF1537; InterPro: IPR010737 This entry represents a conserved region found in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. This entry includes YgbK from Escherichia coli, which is dependent upon FlhDC, the master regulator of the flagellar genes. The ygbK gene appears to be regulated by sigmaF [].; PDB: 3DQQ_B 1YZY_B.
Probab=20.38 E-value=83 Score=22.72 Aligned_cols=33 Identities=12% Similarity=0.198 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHhcCCceEEEcccHHHHHHHHhcc
Q psy17228 19 KLTKTKIDDILQRNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 19 ~~a~~~i~~i~~~~~~pilVGGTglYi~all~g~ 52 (99)
+|...+.+.+.+.+...++||++|| ..+|..-+
T Consensus 44 ~DL~~ia~a~~~~~~~~l~vGsagl-a~aL~~~~ 76 (223)
T PF07005_consen 44 EDLDAIAEALLELGRRVLWVGSAGL-AAALARAL 76 (223)
T ss_dssp HHHHHHHHHCTT-S---EEEESCHH-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCceEEecchHH-HHHHHhhh
Confidence 4555566666555656688888885 56666654
No 257
>KOG0867|consensus
Probab=20.34 E-value=26 Score=25.90 Aligned_cols=19 Identities=21% Similarity=0.261 Sum_probs=14.9
Q ss_pred HHHHHhcCCceEEEcccHHH
Q psy17228 25 IDDILQRNKVPIIVGGTNYY 44 (99)
Q Consensus 25 i~~i~~~~~~pilVGGTglY 44 (99)
.-.+.-.|++|.+++| |++
T Consensus 45 fl~~nP~~kVP~l~d~-~~~ 63 (226)
T KOG0867|consen 45 FLKLNPLGKVPALEDG-GLT 63 (226)
T ss_pred HHhcCcCCCCCeEecC-CeE
Confidence 3357778999999999 654
No 258
>cd06183 cyt_b5_reduct_like Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound differently than in canonical Rossmann fold proteins. Nitrate reductases, flavoproteins similar to pyridine nucleotide cytochrome reductases, catalyze the reduction of nitrate to nitrite. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron, and FAD/NADH.
Probab=20.30 E-value=67 Score=22.79 Aligned_cols=22 Identities=32% Similarity=0.539 Sum_probs=17.0
Q ss_pred CCceEEEcccHH-HHHHHHhccc
Q psy17228 32 NKVPIIVGGTNY-YIESLLWTIL 53 (99)
Q Consensus 32 ~~~pilVGGTgl-Yi~all~g~~ 53 (99)
..+.+|.||||. -+-+++..+.
T Consensus 105 ~~~vliagGtGiaP~~~~l~~~~ 127 (234)
T cd06183 105 KHIGMIAGGTGITPMLQLIRAIL 127 (234)
T ss_pred cEEEEEcCCcchhHHHHHHHHHH
Confidence 456778899999 7788877753
No 259
>PRK04302 triosephosphate isomerase; Provisional
Probab=20.25 E-value=1.4e+02 Score=21.90 Aligned_cols=24 Identities=8% Similarity=0.329 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHh-cCCceEEEcccH
Q psy17228 19 KLTKTKIDDILQ-RNKVPIIVGGTN 42 (99)
Q Consensus 19 ~~a~~~i~~i~~-~~~~pilVGGTg 42 (99)
....+.++.+.+ ..++||++||+=
T Consensus 158 ~~i~~~~~~ir~~~~~~pvi~GggI 182 (223)
T PRK04302 158 EVVEDAVEAVKKVNPDVKVLCGAGI 182 (223)
T ss_pred HHHHHHHHHHHhccCCCEEEEECCC
Confidence 344555555544 247899999843
No 260
>PRK08125 bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase; Validated
Probab=20.25 E-value=58 Score=27.80 Aligned_cols=21 Identities=19% Similarity=0.234 Sum_probs=14.9
Q ss_pred hcCCceEEEcccHHHHHHHHh
Q psy17228 30 QRNKVPIIVGGTNYYIESLLW 50 (99)
Q Consensus 30 ~~~~~pilVGGTglYi~all~ 50 (99)
.+++..+|+|||||==..|+.
T Consensus 313 ~~~~~VLVTGatGFIGs~Lv~ 333 (660)
T PRK08125 313 KRRTRVLILGVNGFIGNHLTE 333 (660)
T ss_pred hcCCEEEEECCCchHHHHHHH
Confidence 467778999999986444443
No 261
>cd03465 URO-D_like The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane.
Probab=20.21 E-value=2.8e+02 Score=20.96 Aligned_cols=36 Identities=19% Similarity=0.159 Sum_probs=27.0
Q ss_pred hHHHHHHHHHHHHHHhcCCceEE--EcccHHHHHHHHh
Q psy17228 15 KWTIKLTKTKIDDILQRNKVPII--VGGTNYYIESLLW 50 (99)
Q Consensus 15 ~~~~~~a~~~i~~i~~~~~~pil--VGGTglYi~all~ 50 (99)
.|...-..++++.+.+.|...++ ||.++-.++.+.+
T Consensus 204 e~~~p~~k~i~~~i~~~g~~~~lH~cG~~~~~~~~l~~ 241 (330)
T cd03465 204 EFSLPYLKKVFDAIKALGGPVIHHNCGDTAPILELMAD 241 (330)
T ss_pred HHhhHHHHHHHHHHHHcCCceEEEECCCchhHHHHHHH
Confidence 45556667888888887776666 8888888888876
No 262
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=20.03 E-value=89 Score=23.50 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHhcCCceEEEcccHHHHH
Q psy17228 18 IKLTKTKIDDILQRNKVPIIVGGTNYYIE 46 (99)
Q Consensus 18 ~~~a~~~i~~i~~~~~~pilVGGTglYi~ 46 (99)
..++.+.|.+.+.+| .||+|+.-.+|+.
T Consensus 74 ~~~~~~~l~~~l~~g-~pv~~~~D~~~lp 101 (317)
T PF14399_consen 74 PDEAWEELKEALDAG-RPVIVWVDMYYLP 101 (317)
T ss_pred HHHHHHHHHHHHhCC-CceEEEeccccCC
Confidence 467788888888777 5777778777764
No 263
>COG0391 Uncharacterized conserved protein [Function unknown]
Probab=20.01 E-value=50 Score=26.63 Aligned_cols=21 Identities=33% Similarity=0.423 Sum_probs=16.5
Q ss_pred cCCceEEEcccHHHHHHHHhccc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWTIL 53 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g~~ 53 (99)
.-++-+|-||||+. -++.|+.
T Consensus 7 ~~kvvvlgGGtGl~--~lL~gLk 27 (323)
T COG0391 7 KPKVVVLGGGTGLP--KLLSGLK 27 (323)
T ss_pred CceEEEEcCCCCHH--HHHHHHH
Confidence 34778888999998 6777764
No 264
>PRK07774 short chain dehydrogenase; Provisional
Probab=20.01 E-value=60 Score=22.99 Aligned_cols=22 Identities=18% Similarity=0.237 Sum_probs=15.8
Q ss_pred cCCceEEEcccHHHHHHHHhcc
Q psy17228 31 RNKVPIIVGGTNYYIESLLWTI 52 (99)
Q Consensus 31 ~~~~pilVGGTglYi~all~g~ 52 (99)
.++.-+|+||||+==.++...+
T Consensus 5 ~~k~vlItGasg~iG~~la~~l 26 (250)
T PRK07774 5 DDKVAIVTGAAGGIGQAYAEAL 26 (250)
T ss_pred CCCEEEEECCCchHHHHHHHHH
Confidence 4677899999987656665543
No 265
>PRK07998 gatY putative fructose-1,6-bisphosphate aldolase; Reviewed
Probab=20.00 E-value=80 Score=24.82 Aligned_cols=30 Identities=17% Similarity=0.401 Sum_probs=17.8
Q ss_pred HHHHHHHhcCCceEEE-cccHHHH----HHHHhcc
Q psy17228 23 TKIDDILQRNKVPIIV-GGTNYYI----ESLLWTI 52 (99)
Q Consensus 23 ~~i~~i~~~~~~pilV-GGTglYi----~all~g~ 52 (99)
+.+++|.+.-.+|++. ||||.=- +|+-.|+
T Consensus 189 ~~l~~I~~~~~vPLVlHGgSG~~~e~~~~ai~~Gi 223 (283)
T PRK07998 189 PLLKRIAEVSPVPLVIHGGSGIPPEILRSFVNYKV 223 (283)
T ss_pred HHHHHHHhhCCCCEEEeCCCCCCHHHHHHHHHcCC
Confidence 4555666565666555 9999743 3444554
Done!