Query 023914
Match_columns 275
No_of_seqs 361 out of 2185
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:34:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023914.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023914hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2816 NPY1 NTP pyrophosphohy 100.0 5E-46 1.1E-50 335.3 11.3 171 70-245 76-249 (279)
2 PRK00241 nudC NADH pyrophospha 100.0 7.7E-42 1.7E-46 309.5 18.6 189 71-267 66-255 (256)
3 KOG3084 NADH pyrophosphatase I 100.0 1.2E-39 2.5E-44 295.3 5.6 242 1-269 67-335 (345)
4 cd04511 Nudix_Hydrolase_4 Memb 99.9 2.9E-27 6.3E-32 192.4 12.4 128 129-256 1-128 (130)
5 COG1051 ADP-ribose pyrophospha 99.9 1.6E-21 3.5E-26 162.7 12.9 115 133-247 2-122 (145)
6 cd04681 Nudix_Hydrolase_22 Mem 99.8 1.4E-20 3E-25 152.1 12.7 120 143-265 3-130 (130)
7 PLN02325 nudix hydrolase 99.8 1.8E-20 4E-25 155.8 12.8 112 135-246 3-124 (144)
8 cd03430 GDPMH GDP-mannose glyc 99.8 3.5E-20 7.5E-25 154.0 12.4 115 139-253 10-138 (144)
9 cd03429 NADH_pyrophosphatase N 99.8 1.8E-20 3.9E-25 153.1 10.2 122 143-265 2-129 (131)
10 cd04679 Nudix_Hydrolase_20 Mem 99.8 8.1E-20 1.8E-24 147.0 12.9 107 140-246 1-114 (125)
11 cd03675 Nudix_Hydrolase_2 Cont 99.8 8.7E-20 1.9E-24 148.3 12.8 123 143-269 2-132 (134)
12 cd04684 Nudix_Hydrolase_25 Con 99.8 7.2E-20 1.6E-24 146.6 11.4 113 143-256 2-125 (128)
13 PRK15434 GDP-mannose mannosyl 99.8 1.2E-19 2.6E-24 153.6 12.8 116 139-254 15-144 (159)
14 cd03427 MTH1 MutT homolog-1 (M 99.8 3.4E-19 7.5E-24 145.2 13.2 124 142-269 2-129 (137)
15 cd04673 Nudix_Hydrolase_15 Mem 99.8 1.6E-19 3.4E-24 143.7 10.9 108 143-250 2-117 (122)
16 cd04691 Nudix_Hydrolase_32 Mem 99.8 2.9E-19 6.3E-24 143.0 12.4 102 144-246 3-107 (117)
17 cd04696 Nudix_Hydrolase_37 Mem 99.8 3E-19 6.6E-24 143.8 12.2 108 140-249 1-116 (125)
18 cd04683 Nudix_Hydrolase_24 Mem 99.8 3.3E-19 7.1E-24 142.2 12.0 105 143-247 2-114 (120)
19 cd04669 Nudix_Hydrolase_11 Mem 99.8 5.4E-19 1.2E-23 142.2 12.6 105 144-251 4-118 (121)
20 cd04671 Nudix_Hydrolase_13 Mem 99.8 5.1E-19 1.1E-23 143.3 12.2 102 143-245 3-108 (123)
21 cd04678 Nudix_Hydrolase_19 Mem 99.8 7E-19 1.5E-23 142.1 12.6 108 140-247 1-117 (129)
22 cd04700 DR1025_like DR1025 fro 99.8 6.5E-19 1.4E-23 145.8 12.0 112 135-246 7-124 (142)
23 PRK15472 nucleoside triphospha 99.8 9.1E-19 2E-23 144.1 12.3 110 141-250 4-128 (141)
24 cd04687 Nudix_Hydrolase_28 Mem 99.8 1.1E-18 2.3E-23 141.2 12.4 108 142-250 2-124 (128)
25 cd04680 Nudix_Hydrolase_21 Mem 99.8 9.9E-19 2.2E-23 138.9 11.7 98 146-246 6-107 (120)
26 cd04672 Nudix_Hydrolase_14 Mem 99.8 1.1E-18 2.4E-23 140.3 12.0 104 140-246 1-111 (123)
27 cd03673 Ap6A_hydrolase Diadeno 99.8 1.2E-18 2.6E-23 140.1 10.3 104 152-259 16-127 (131)
28 cd03674 Nudix_Hydrolase_1 Memb 99.8 3.2E-18 6.9E-23 140.8 12.1 104 143-249 5-125 (138)
29 cd04682 Nudix_Hydrolase_23 Mem 99.8 1.9E-18 4.1E-23 138.7 9.8 108 143-250 3-117 (122)
30 PRK09438 nudB dihydroneopterin 99.8 2.2E-18 4.8E-23 142.9 9.9 125 137-267 4-145 (148)
31 cd04690 Nudix_Hydrolase_31 Mem 99.8 4.1E-18 8.8E-23 135.3 10.9 103 143-249 3-112 (118)
32 cd03424 ADPRase_NUDT5 ADP-ribo 99.8 6.8E-18 1.5E-22 137.7 11.9 124 140-266 2-135 (137)
33 cd04688 Nudix_Hydrolase_29 Mem 99.8 1.1E-17 2.3E-22 134.8 12.1 105 144-251 4-122 (126)
34 PRK10546 pyrimidine (deoxy)nuc 99.7 2.3E-17 5.1E-22 134.0 13.6 121 142-267 5-128 (135)
35 cd04677 Nudix_Hydrolase_18 Mem 99.7 1.6E-17 3.6E-22 134.1 12.2 104 140-246 6-121 (132)
36 cd04664 Nudix_Hydrolase_7 Memb 99.7 5.8E-18 1.3E-22 136.9 9.4 114 141-256 2-126 (129)
37 cd04689 Nudix_Hydrolase_30 Mem 99.7 1.2E-17 2.6E-22 134.3 10.3 102 142-246 2-113 (125)
38 PRK05379 bifunctional nicotina 99.7 2E-17 4.2E-22 155.8 13.1 111 136-246 198-321 (340)
39 PRK10776 nucleoside triphospha 99.7 8.3E-17 1.8E-21 128.8 14.3 106 143-249 7-115 (129)
40 cd04670 Nudix_Hydrolase_12 Mem 99.7 2.1E-17 4.5E-22 133.3 10.7 103 144-247 6-113 (127)
41 cd04676 Nudix_Hydrolase_17 Mem 99.7 5.7E-17 1.2E-21 129.4 13.1 104 141-247 2-117 (129)
42 cd03671 Ap4A_hydrolase_plant_l 99.7 4.1E-17 8.8E-22 135.5 12.5 101 145-247 8-131 (147)
43 cd04674 Nudix_Hydrolase_16 Mem 99.7 9.2E-17 2E-21 129.7 14.1 105 139-245 2-111 (118)
44 cd03672 Dcp2p mRNA decapping e 99.7 2.4E-17 5.1E-22 137.4 10.8 125 142-269 2-142 (145)
45 cd04699 Nudix_Hydrolase_39 Mem 99.7 2.4E-17 5.3E-22 132.1 10.2 104 142-245 2-112 (129)
46 cd04667 Nudix_Hydrolase_10 Mem 99.7 4.1E-17 8.8E-22 129.1 10.9 96 145-246 4-100 (112)
47 cd04695 Nudix_Hydrolase_36 Mem 99.7 3.7E-17 8.1E-22 133.0 10.0 116 147-264 9-130 (131)
48 cd03425 MutT_pyrophosphohydrol 99.7 2.5E-16 5.5E-21 124.4 12.9 107 142-249 3-112 (124)
49 cd03428 Ap4A_hydrolase_human_l 99.7 7.2E-17 1.6E-21 130.2 9.7 102 153-259 18-126 (130)
50 cd04693 Nudix_Hydrolase_34 Mem 99.7 6.5E-17 1.4E-21 130.5 8.9 103 143-246 3-112 (127)
51 cd04697 Nudix_Hydrolase_38 Mem 99.7 9.9E-17 2.2E-21 129.8 9.6 102 144-246 4-111 (126)
52 cd03426 CoAse Coenzyme A pyrop 99.7 9.9E-17 2.1E-21 135.0 9.5 105 143-247 4-118 (157)
53 TIGR00586 mutt mutator mutT pr 99.7 5.6E-16 1.2E-20 124.3 13.1 109 142-253 6-117 (128)
54 cd04661 MRP_L46 Mitochondrial 99.7 1.7E-16 3.8E-21 129.7 9.5 95 150-246 11-119 (132)
55 PRK11762 nudE adenosine nucleo 99.7 7.8E-16 1.7E-20 133.0 14.0 130 139-268 46-184 (185)
56 PRK00714 RNA pyrophosphohydrol 99.7 3.7E-16 8.1E-21 131.6 11.6 103 142-246 9-134 (156)
57 PRK15393 NUDIX hydrolase YfcD; 99.7 4.7E-16 1E-20 134.0 10.6 121 144-269 41-169 (180)
58 cd04666 Nudix_Hydrolase_9 Memb 99.7 6.3E-16 1.4E-20 125.1 10.4 91 152-245 15-113 (122)
59 cd04686 Nudix_Hydrolase_27 Mem 99.7 7.1E-16 1.5E-20 125.8 10.2 101 143-246 2-118 (131)
60 cd04665 Nudix_Hydrolase_8 Memb 99.6 3.4E-15 7.4E-20 120.5 12.4 98 144-245 3-103 (118)
61 cd02885 IPP_Isomerase Isopente 99.6 6.8E-16 1.5E-20 130.8 8.7 105 142-246 31-147 (165)
62 PF00293 NUDIX: NUDIX domain; 99.6 7.4E-16 1.6E-20 123.5 8.4 106 141-246 2-118 (134)
63 cd04692 Nudix_Hydrolase_33 Mem 99.6 1.2E-15 2.5E-20 126.3 9.4 101 145-245 7-125 (144)
64 cd02883 Nudix_Hydrolase Nudix 99.6 6.1E-15 1.3E-19 115.2 11.7 102 144-246 3-111 (123)
65 cd04694 Nudix_Hydrolase_35 Mem 99.6 8.1E-15 1.8E-19 122.0 10.6 103 143-245 3-129 (143)
66 cd04685 Nudix_Hydrolase_26 Mem 99.6 1E-14 2.2E-19 119.9 9.7 103 145-247 5-123 (133)
67 PRK03759 isopentenyl-diphospha 99.6 7.7E-15 1.7E-19 126.7 8.9 105 141-246 34-151 (184)
68 PRK08999 hypothetical protein; 99.6 3.1E-14 6.6E-19 131.9 12.9 107 142-249 7-116 (312)
69 PRK10729 nudF ADP-ribose pyrop 99.6 5.3E-14 1.1E-18 123.6 12.9 109 137-245 46-169 (202)
70 TIGR02150 IPP_isom_1 isopenten 99.5 2.2E-14 4.8E-19 121.0 7.5 100 144-246 31-141 (158)
71 TIGR00052 nudix-type nucleosid 99.5 6.1E-14 1.3E-18 121.6 9.7 109 137-245 41-163 (185)
72 PRK10707 putative NUDIX hydrol 99.5 2.2E-13 4.7E-18 118.6 11.4 105 142-246 32-145 (190)
73 TIGR02705 nudix_YtkD nucleosid 99.5 2.7E-13 5.8E-18 114.5 11.3 98 143-246 26-126 (156)
74 cd03670 ADPRase_NUDT9 ADP-ribo 99.5 4.5E-13 9.9E-18 116.1 12.9 99 153-256 50-178 (186)
75 cd04662 Nudix_Hydrolase_5 Memb 99.5 3.8E-13 8.2E-18 109.7 11.4 90 152-241 15-126 (126)
76 cd03676 Nudix_hydrolase_3 Memb 99.4 4.6E-13 1E-17 114.9 10.0 107 152-258 48-173 (180)
77 PRK15009 GDP-mannose pyrophosp 99.4 3.3E-12 7.2E-17 111.3 12.1 109 137-246 42-165 (191)
78 cd04663 Nudix_Hydrolase_6 Memb 99.3 1.1E-11 2.5E-16 101.1 11.6 91 153-247 15-116 (126)
79 PLN02709 nudix hydrolase 99.3 4.8E-12 1E-16 112.4 9.9 95 152-246 51-154 (222)
80 COG0494 MutT NTP pyrophosphohy 99.2 1.3E-10 2.7E-15 92.5 11.8 104 143-248 13-135 (161)
81 PLN03143 nudix hydrolase; Prov 99.2 1.5E-10 3.3E-15 106.7 11.0 109 137-245 125-263 (291)
82 PLN02552 isopentenyl-diphospha 99.2 1.4E-10 3.1E-15 104.7 10.3 102 145-246 61-202 (247)
83 cd03431 DNA_Glycosylase_C DNA 99.1 8.3E-10 1.8E-14 86.7 11.4 102 143-253 5-109 (118)
84 PLN02791 Nudix hydrolase homol 99.0 9.6E-10 2.1E-14 112.6 9.5 104 142-245 33-156 (770)
85 KOG2839 Diadenosine and diphos 98.9 7.1E-10 1.5E-14 91.4 4.3 92 152-245 24-123 (145)
86 KOG3041 Nucleoside diphosphate 98.9 1.1E-08 2.3E-13 88.4 9.5 107 140-246 74-193 (225)
87 PF14803 Nudix_N_2: Nudix N-te 98.8 1.3E-09 2.7E-14 68.9 1.3 34 105-138 1-34 (34)
88 KOG3069 Peroxisomal NUDIX hydr 98.8 1.9E-08 4E-13 89.1 7.5 115 132-246 34-162 (246)
89 PF09297 zf-NADH-PPase: NADH p 98.7 5.6E-09 1.2E-13 65.2 1.6 32 102-137 1-32 (32)
90 PF14815 NUDIX_4: NUDIX domain 98.7 9.6E-08 2.1E-12 75.7 7.7 105 144-254 1-108 (114)
91 KOG0648 Predicted NUDIX hydrol 98.4 1.8E-07 3.9E-12 85.8 2.9 109 141-249 115-233 (295)
92 COG1443 Idi Isopentenyldiphosp 98.2 1.5E-06 3.3E-11 74.0 5.1 101 145-246 38-152 (185)
93 PLN02839 nudix hydrolase 98.1 1.4E-05 3.1E-10 75.7 9.7 94 152-245 218-325 (372)
94 COG4119 Predicted NTP pyrophos 98.1 4.7E-06 1E-10 67.6 4.9 80 165-245 35-133 (161)
95 smart00661 RPOL9 RNA polymeras 97.4 0.00025 5.3E-09 48.5 4.6 39 105-145 1-39 (52)
96 COG1998 RPS31 Ribosomal protei 97.3 0.00014 2.9E-09 49.4 1.9 35 101-139 16-50 (51)
97 KOG4195 Transient receptor pot 97.2 0.0021 4.5E-08 57.0 8.7 39 153-194 140-178 (275)
98 PRK00432 30S ribosomal protein 97.1 0.00028 6E-09 48.5 2.2 32 102-138 18-49 (50)
99 COG4112 Predicted phosphoester 97.1 0.0028 6.1E-08 53.7 8.5 102 145-246 65-186 (203)
100 KOG2937 Decapping enzyme compl 96.9 0.00018 3.9E-09 66.9 -1.0 108 133-244 74-189 (348)
101 PRK10880 adenine DNA glycosyla 96.6 0.015 3.3E-07 55.3 9.6 101 144-255 234-337 (350)
102 PF13240 zinc_ribbon_2: zinc-r 96.1 0.0028 6E-08 36.5 1.1 22 106-135 1-22 (23)
103 PF13869 NUDIX_2: Nucleotide h 95.9 0.026 5.7E-07 49.0 6.8 61 145-209 49-117 (188)
104 PF13248 zf-ribbon_3: zinc-rib 95.2 0.01 2.2E-07 35.1 1.1 24 104-135 2-25 (26)
105 PF02150 RNA_POL_M_15KD: RNA p 95.0 0.0062 1.3E-07 38.7 -0.0 30 104-136 1-30 (35)
106 PF07754 DUF1610: Domain of un 94.5 0.031 6.7E-07 32.5 1.9 24 107-134 1-24 (24)
107 PF10571 UPF0547: Uncharacteri 94.5 0.025 5.5E-07 33.5 1.6 24 105-136 1-24 (26)
108 PF12773 DZR: Double zinc ribb 93.4 0.048 1E-06 36.8 1.6 33 102-139 10-42 (50)
109 KOG0142 Isopentenyl pyrophosph 93.2 0.066 1.4E-06 47.0 2.7 99 146-246 58-182 (225)
110 PRK13910 DNA glycosylase MutY; 93.2 0.59 1.3E-05 43.5 9.0 84 144-255 189-274 (289)
111 PF09296 NUDIX-like: NADH pyro 93.1 0.038 8.3E-07 41.8 1.0 32 69-100 66-98 (98)
112 PRK00420 hypothetical protein; 92.7 0.11 2.3E-06 41.7 2.9 32 99-135 18-49 (112)
113 PF06677 Auto_anti-p27: Sjogre 92.6 0.12 2.6E-06 34.0 2.5 34 95-133 8-41 (41)
114 COG1594 RPB9 DNA-directed RNA 92.5 0.079 1.7E-06 42.5 2.0 35 104-140 2-36 (113)
115 KOG1689 mRNA cleavage factor I 92.3 0.19 4.2E-06 43.0 4.2 39 152-194 84-122 (221)
116 KOG4432 Uncharacterized NUDIX 92.0 0.39 8.4E-06 44.7 6.0 59 168-226 81-143 (405)
117 TIGR00686 phnA alkylphosphonat 91.9 0.1 2.2E-06 41.3 1.8 51 105-160 3-63 (109)
118 PHA00626 hypothetical protein 91.8 0.13 2.8E-06 36.0 2.1 34 105-138 1-35 (59)
119 PF07282 OrfB_Zn_ribbon: Putat 91.2 0.16 3.5E-06 36.5 2.3 30 103-136 27-56 (69)
120 COG1645 Uncharacterized Zn-fin 91.2 0.11 2.5E-06 42.5 1.5 24 105-134 29-52 (131)
121 KOG4548 Mitochondrial ribosoma 91.1 0.82 1.8E-05 41.5 7.0 93 153-246 140-246 (263)
122 PRK00398 rpoP DNA-directed RNA 91.1 0.2 4.3E-06 33.4 2.4 27 106-136 5-31 (46)
123 PF06044 DRP: Dam-replacing fa 90.5 0.11 2.3E-06 47.0 0.8 43 93-136 19-63 (254)
124 TIGR01384 TFS_arch transcripti 90.1 0.21 4.5E-06 39.0 2.1 29 105-139 1-29 (104)
125 PF08274 PhnA_Zn_Ribbon: PhnA 90.0 0.14 3.1E-06 31.3 0.9 26 105-135 3-28 (30)
126 PRK00464 nrdR transcriptional 89.8 0.22 4.8E-06 42.1 2.2 31 106-136 2-38 (154)
127 PF13453 zf-TFIIB: Transcripti 89.7 0.24 5.1E-06 32.2 1.8 31 106-138 1-31 (41)
128 PRK10220 hypothetical protein; 89.5 0.3 6.5E-06 38.8 2.6 32 104-140 3-34 (111)
129 TIGR02098 MJ0042_CXXC MJ0042 f 89.1 0.26 5.7E-06 31.3 1.7 32 106-137 4-36 (38)
130 PF03119 DNA_ligase_ZBD: NAD-d 88.9 0.17 3.6E-06 30.5 0.6 22 106-131 1-22 (28)
131 PF09538 FYDLN_acid: Protein o 88.2 0.29 6.3E-06 38.9 1.7 32 103-139 8-39 (108)
132 PF09862 DUF2089: Protein of u 88.0 0.31 6.8E-06 39.1 1.8 21 107-135 1-21 (113)
133 COG1997 RPL43A Ribosomal prote 87.8 0.35 7.7E-06 36.9 1.8 39 94-136 25-63 (89)
134 TIGR00244 transcriptional regu 87.8 0.49 1.1E-05 39.6 2.8 47 105-151 1-55 (147)
135 COG0353 RecR Recombinational D 87.5 0.43 9.4E-06 41.8 2.5 95 86-194 36-132 (198)
136 PRK13844 recombination protein 87.4 0.36 7.8E-06 42.5 2.0 96 85-194 38-135 (200)
137 COG1327 Predicted transcriptio 87.3 0.52 1.1E-05 39.6 2.7 45 105-149 1-53 (156)
138 PF07295 DUF1451: Protein of u 87.3 0.28 6E-06 41.1 1.2 32 105-140 113-144 (146)
139 PF13717 zinc_ribbon_4: zinc-r 86.9 0.47 1E-05 30.1 1.8 32 106-137 4-36 (36)
140 COG4640 Predicted membrane pro 86.7 0.34 7.4E-06 46.5 1.5 26 104-137 1-26 (465)
141 COG3677 Transposase and inacti 86.6 0.89 1.9E-05 37.2 3.8 46 91-136 17-63 (129)
142 smart00659 RPOLCX RNA polymera 86.5 0.46 1E-05 31.6 1.6 25 106-135 4-28 (44)
143 COG1571 Predicted DNA-binding 86.4 0.25 5.5E-06 48.0 0.5 37 95-136 341-377 (421)
144 PRK11032 hypothetical protein; 86.2 0.33 7.2E-06 41.3 1.1 32 105-140 125-156 (160)
145 COG1996 RPC10 DNA-directed RNA 85.9 0.35 7.6E-06 33.0 0.9 29 106-138 8-36 (49)
146 PF08271 TF_Zn_Ribbon: TFIIB z 85.9 0.49 1.1E-05 31.0 1.6 28 106-136 2-29 (43)
147 PF13719 zinc_ribbon_5: zinc-r 85.6 0.47 1E-05 30.3 1.3 31 106-136 4-35 (37)
148 PF03604 DNA_RNApol_7kD: DNA d 85.5 0.42 9.1E-06 29.7 1.0 25 106-135 2-26 (32)
149 PF12760 Zn_Tnp_IS1595: Transp 85.4 1.2 2.7E-05 29.6 3.4 39 92-134 7-45 (46)
150 PF09889 DUF2116: Uncharacteri 85.3 0.17 3.8E-06 35.9 -0.9 27 103-137 2-29 (59)
151 KOG2906 RNA polymerase III sub 85.2 0.55 1.2E-05 36.6 1.7 30 105-136 2-31 (105)
152 COG1096 Predicted RNA-binding 85.1 0.49 1.1E-05 41.1 1.6 29 104-138 149-177 (188)
153 TIGR00615 recR recombination p 84.9 0.58 1.3E-05 41.0 2.0 94 87-194 36-131 (195)
154 COG2888 Predicted Zn-ribbon RN 84.7 0.46 9.9E-06 33.7 1.0 26 104-133 9-34 (61)
155 PRK14559 putative protein seri 84.7 0.54 1.2E-05 48.4 1.9 35 102-136 13-51 (645)
156 COG2824 PhnA Uncharacterized Z 84.6 0.81 1.8E-05 36.2 2.5 52 104-160 3-65 (112)
157 TIGR01206 lysW lysine biosynth 84.4 0.73 1.6E-05 32.1 1.9 30 106-137 4-33 (54)
158 PRK14890 putative Zn-ribbon RN 84.3 0.55 1.2E-05 33.3 1.2 27 105-135 8-34 (59)
159 PRK12286 rpmF 50S ribosomal pr 84.1 0.67 1.5E-05 32.6 1.7 23 103-134 26-48 (57)
160 smart00834 CxxC_CXXC_SSSS Puta 83.9 0.56 1.2E-05 29.9 1.1 28 106-134 7-34 (41)
161 TIGR01084 mutY A/G-specific ad 83.8 2.4 5.2E-05 39.1 5.7 24 149-172 236-260 (275)
162 TIGR02300 FYDLN_acid conserved 83.8 0.74 1.6E-05 37.6 2.0 31 103-138 8-38 (129)
163 COG1779 C4-type Zn-finger prot 83.7 2.5 5.5E-05 37.1 5.4 87 104-195 14-124 (201)
164 PF09723 Zn-ribbon_8: Zinc rib 83.7 0.52 1.1E-05 30.9 0.9 28 106-134 7-34 (42)
165 COG5349 Uncharacterized protei 83.5 0.96 2.1E-05 36.6 2.5 30 104-136 21-50 (126)
166 PF12773 DZR: Double zinc ribb 83.5 0.78 1.7E-05 30.7 1.8 25 101-133 26-50 (50)
167 PRK00076 recR recombination pr 83.4 0.73 1.6E-05 40.5 2.0 94 86-193 35-130 (196)
168 COG1194 MutY A/G-specific DNA 82.7 3.6 7.7E-05 39.1 6.4 92 143-253 238-331 (342)
169 PF08792 A2L_zn_ribbon: A2L zi 82.6 0.94 2E-05 28.3 1.7 30 103-136 2-31 (33)
170 PF14205 Cys_rich_KTR: Cystein 82.5 1.3 2.9E-05 30.8 2.5 33 105-137 5-39 (55)
171 PRK11827 hypothetical protein; 82.4 1 2.3E-05 32.0 2.1 34 101-139 5-38 (60)
172 TIGR03655 anti_R_Lar restricti 82.4 1.3 2.7E-05 30.5 2.5 31 105-135 2-35 (53)
173 KOG4432 Uncharacterized NUDIX 82.4 3.6 7.8E-05 38.4 6.1 79 168-246 286-375 (405)
174 PF14353 CpXC: CpXC protein 81.8 2.1 4.6E-05 34.4 4.1 50 106-158 3-67 (128)
175 TIGR01031 rpmF_bact ribosomal 81.7 0.87 1.9E-05 31.8 1.4 22 104-134 26-47 (55)
176 PF01599 Ribosomal_S27: Riboso 81.7 0.73 1.6E-05 31.2 1.0 29 102-134 16-46 (47)
177 COG1656 Uncharacterized conser 81.1 0.82 1.8E-05 39.0 1.4 39 100-138 92-142 (165)
178 PF13824 zf-Mss51: Zinc-finger 78.7 1.4 3E-05 30.8 1.7 26 106-138 1-26 (55)
179 PF14354 Lar_restr_allev: Rest 78.4 1.7 3.8E-05 30.2 2.2 31 104-134 3-37 (61)
180 COG4260 Membrane protease subu 77.5 1 2.3E-05 41.7 1.0 31 102-135 313-343 (345)
181 PF10083 DUF2321: Uncharacteri 77.3 0.31 6.7E-06 41.1 -2.3 23 102-135 26-48 (158)
182 PRK05978 hypothetical protein; 77.3 1.6 3.5E-05 36.7 2.0 37 100-139 29-65 (148)
183 KOG3507 DNA-directed RNA polym 77.2 1.2 2.7E-05 31.4 1.1 25 106-135 22-46 (62)
184 PHA02942 putative transposase; 77.2 1.8 3.9E-05 41.7 2.6 30 103-137 324-353 (383)
185 PRK14890 putative Zn-ribbon RN 76.8 2.2 4.8E-05 30.2 2.2 33 103-135 24-57 (59)
186 COG2888 Predicted Zn-ribbon RN 76.8 1.8 3.9E-05 30.7 1.8 32 104-135 27-59 (61)
187 PRK09710 lar restriction allev 76.6 1.8 4E-05 31.1 1.8 32 103-135 5-36 (64)
188 PF01927 Mut7-C: Mut7-C RNAse 76.2 1.8 3.8E-05 36.0 1.9 35 104-138 91-136 (147)
189 PF01783 Ribosomal_L32p: Ribos 76.1 1.3 2.8E-05 30.9 0.9 21 104-133 26-46 (56)
190 PF12677 DUF3797: Domain of un 75.7 2.2 4.8E-05 29.0 1.9 41 94-135 3-47 (49)
191 PF04216 FdhE: Protein involve 74.4 1.2 2.6E-05 41.1 0.6 33 104-136 172-207 (290)
192 KOG3799 Rab3 effector RIM1 and 74.4 1.2 2.5E-05 36.9 0.4 29 102-134 87-115 (169)
193 cd04476 RPA1_DBD_C RPA1_DBD_C: 74.3 4.4 9.5E-05 34.0 3.9 42 104-150 34-76 (166)
194 PF06827 zf-FPG_IleRS: Zinc fi 74.0 1.9 4.2E-05 25.9 1.2 27 106-134 3-29 (30)
195 PF01780 Ribosomal_L37ae: Ribo 73.9 1.1 2.3E-05 34.5 0.1 36 96-135 27-62 (90)
196 KOG4313 Thiamine pyrophosphoki 73.9 6.5 0.00014 35.8 5.0 90 153-243 149-254 (306)
197 PRK10445 endonuclease VIII; Pr 73.5 2 4.2E-05 39.3 1.7 29 103-133 234-262 (263)
198 PRK14892 putative transcriptio 73.5 2.6 5.7E-05 33.0 2.2 33 103-136 20-52 (99)
199 smart00778 Prim_Zn_Ribbon Zinc 73.3 3.9 8.5E-05 26.2 2.6 32 103-134 2-33 (37)
200 KOG2907 RNA polymerase I trans 73.2 1.2 2.6E-05 35.6 0.2 32 103-138 6-37 (116)
201 TIGR02605 CxxC_CxxC_SSSS putat 73.2 2.1 4.6E-05 28.9 1.4 29 106-135 7-35 (52)
202 TIGR03831 YgiT_finger YgiT-typ 72.9 2.4 5.1E-05 27.5 1.6 14 125-138 31-44 (46)
203 PF14446 Prok-RING_1: Prokaryo 72.8 2.6 5.5E-05 29.4 1.7 28 104-137 5-32 (54)
204 PF08273 Prim_Zn_Ribbon: Zinc- 71.9 2.6 5.7E-05 27.5 1.5 30 104-133 3-33 (40)
205 COG0675 Transposase and inacti 71.5 2.6 5.6E-05 38.4 2.0 31 99-138 304-334 (364)
206 PF04981 NMD3: NMD3 family ; 71.4 24 0.00053 31.5 8.2 25 107-138 1-25 (236)
207 PTZ00255 60S ribosomal protein 71.2 5.4 0.00012 30.7 3.3 37 95-135 27-63 (90)
208 PF12647 RNHCP: RNHCP domain; 71.1 9.1 0.0002 29.6 4.6 54 105-160 5-70 (92)
209 PRK14714 DNA polymerase II lar 71.0 2.2 4.9E-05 46.7 1.7 19 56-74 595-613 (1337)
210 PF08772 NOB1_Zn_bind: Nin one 69.9 1.9 4.1E-05 31.9 0.6 15 102-116 22-36 (73)
211 PF01485 IBR: IBR domain; Int 69.5 2.9 6.3E-05 28.8 1.5 31 101-135 15-49 (64)
212 PRK14559 putative protein seri 69.2 2.7 5.8E-05 43.4 1.7 12 179-190 130-141 (645)
213 PRK13945 formamidopyrimidine-D 68.9 3 6.5E-05 38.5 1.8 28 104-133 254-281 (282)
214 PRK03976 rpl37ae 50S ribosomal 68.6 3.2 6.8E-05 32.0 1.6 37 95-135 27-63 (90)
215 COG4031 Predicted metal-bindin 68.4 17 0.00036 31.9 6.1 20 106-135 2-21 (227)
216 PF11781 RRN7: RNA polymerase 68.4 2.8 6.1E-05 26.6 1.1 31 100-135 3-34 (36)
217 TIGR00577 fpg formamidopyrimid 68.4 3 6.5E-05 38.3 1.7 28 104-133 245-272 (272)
218 TIGR01562 FdhE formate dehydro 68.2 3.6 7.9E-05 38.6 2.2 35 103-137 183-221 (305)
219 PRK14810 formamidopyrimidine-D 68.1 3.1 6.7E-05 38.2 1.7 31 102-134 242-272 (272)
220 PF09986 DUF2225: Uncharacteri 67.8 3.3 7.1E-05 36.7 1.8 15 125-139 47-61 (214)
221 PRK01103 formamidopyrimidine/5 67.8 3.3 7.1E-05 38.0 1.8 29 104-134 245-273 (274)
222 PRK12380 hydrogenase nickel in 67.4 2.2 4.8E-05 34.0 0.6 28 102-135 68-95 (113)
223 PRK12495 hypothetical protein; 67.1 3.8 8.1E-05 36.6 2.0 33 100-138 38-70 (226)
224 TIGR00280 L37a ribosomal prote 67.0 6.7 0.00015 30.3 3.1 38 94-135 25-62 (91)
225 PRK14811 formamidopyrimidine-D 66.6 3.5 7.6E-05 37.8 1.8 31 103-135 234-264 (269)
226 PF09855 DUF2082: Nucleic-acid 66.2 4.7 0.0001 29.0 2.0 9 106-114 2-10 (64)
227 smart00647 IBR In Between Ring 65.8 6.9 0.00015 26.9 2.8 33 101-135 15-49 (64)
228 COG1326 Uncharacterized archae 65.6 5.8 0.00012 34.8 2.8 34 103-136 5-40 (201)
229 smart00531 TFIIE Transcription 65.5 2.3 5E-05 35.3 0.3 35 104-138 99-135 (147)
230 PRK03681 hypA hydrogenase nick 65.3 2.7 5.9E-05 33.5 0.7 30 101-135 67-96 (114)
231 PF11023 DUF2614: Protein of u 65.3 3.3 7.2E-05 33.1 1.1 29 106-140 71-99 (114)
232 PF08646 Rep_fac-A_C: Replicat 65.1 9.7 0.00021 31.2 4.0 43 104-151 18-63 (146)
233 PF01873 eIF-5_eIF-2B: Domain 65.0 4.1 9E-05 33.2 1.7 41 95-136 84-124 (125)
234 PRK09678 DNA-binding transcrip 64.4 5.5 0.00012 29.4 2.1 32 105-136 2-39 (72)
235 PRK15103 paraquat-inducible me 64.3 5.5 0.00012 39.0 2.7 34 105-140 11-44 (419)
236 KOG1710 MYND Zn-finger and ank 64.3 1.9 4E-05 40.3 -0.5 44 84-137 299-342 (396)
237 PRK04023 DNA polymerase II lar 64.1 4 8.6E-05 43.9 1.8 13 102-114 624-636 (1121)
238 TIGR00155 pqiA_fam integral me 64.1 5.9 0.00013 38.5 2.9 33 106-140 15-47 (403)
239 PF03811 Zn_Tnp_IS1: InsA N-te 63.9 6.9 0.00015 24.9 2.2 29 104-132 5-35 (36)
240 PF04606 Ogr_Delta: Ogr/Delta- 63.7 5 0.00011 26.8 1.7 31 106-136 1-37 (47)
241 PRK09521 exosome complex RNA-b 63.6 4.6 0.0001 34.9 1.9 30 104-138 149-178 (189)
242 COG4306 Uncharacterized protei 63.6 1.9 4.1E-05 35.2 -0.5 20 105-135 29-48 (160)
243 TIGR00100 hypA hydrogenase nic 63.1 3.1 6.8E-05 33.2 0.7 28 102-135 68-95 (115)
244 PRK03988 translation initiatio 63.0 5.4 0.00012 33.1 2.1 44 93-137 91-134 (138)
245 PF09526 DUF2387: Probable met 62.6 4.7 0.0001 29.6 1.5 36 106-141 10-45 (71)
246 PRK13130 H/ACA RNA-protein com 62.6 3.5 7.6E-05 28.9 0.8 26 102-137 3-28 (56)
247 COG3364 Zn-ribbon containing p 62.6 2.8 6.1E-05 33.0 0.3 29 106-138 4-32 (112)
248 PRK04179 rpl37e 50S ribosomal 62.5 3.9 8.4E-05 29.3 1.0 25 103-134 16-40 (62)
249 PF01396 zf-C4_Topoisom: Topoi 61.9 8.3 0.00018 24.8 2.4 31 105-137 2-35 (39)
250 COG3058 FdhE Uncharacterized p 61.1 3.7 8.1E-05 37.9 0.9 16 104-119 185-200 (308)
251 PRK00423 tfb transcription ini 60.9 5.7 0.00012 37.1 2.1 32 102-136 9-40 (310)
252 PRK08402 replication factor A; 60.5 11 0.00024 36.1 4.0 49 103-156 211-260 (355)
253 PRK04023 DNA polymerase II lar 60.5 7.9 0.00017 41.7 3.2 40 99-138 633-675 (1121)
254 PRK12366 replication factor A; 60.4 10 0.00022 39.1 4.0 41 104-151 532-572 (637)
255 PRK03564 formate dehydrogenase 60.4 15 0.00032 34.6 4.7 35 103-137 186-223 (309)
256 COG3809 Uncharacterized protei 60.4 5.1 0.00011 30.1 1.3 27 105-133 2-28 (88)
257 PF10058 DUF2296: Predicted in 60.2 6.8 0.00015 27.2 1.9 31 105-135 23-53 (54)
258 PRK00564 hypA hydrogenase nick 60.1 4 8.7E-05 32.7 0.8 27 104-135 71-97 (117)
259 PRK08665 ribonucleotide-diphos 59.9 5.3 0.00011 42.0 1.8 25 105-135 725-749 (752)
260 PF09538 FYDLN_acid: Protein o 59.8 4.2 9.2E-05 32.3 0.9 23 122-144 5-28 (108)
261 PRK14873 primosome assembly pr 59.5 6.2 0.00013 40.9 2.2 24 153-177 473-497 (665)
262 smart00653 eIF2B_5 domain pres 59.1 7 0.00015 31.1 2.0 40 94-134 70-109 (110)
263 COG0266 Nei Formamidopyrimidin 58.7 5.9 0.00013 36.6 1.7 33 100-134 241-273 (273)
264 smart00401 ZnF_GATA zinc finge 58.6 8 0.00017 26.5 2.0 33 104-136 3-35 (52)
265 COG2051 RPS27A Ribosomal prote 57.9 6.4 0.00014 28.6 1.4 24 125-148 18-43 (67)
266 PRK01110 rpmF 50S ribosomal pr 57.7 5.8 0.00013 28.1 1.2 21 104-134 27-47 (60)
267 TIGR00340 zpr1_rel ZPR1-relate 57.5 8.2 0.00018 32.9 2.3 30 107-137 1-39 (163)
268 TIGR00311 aIF-2beta translatio 57.4 7.5 0.00016 32.0 2.0 42 94-136 87-128 (133)
269 PRK02935 hypothetical protein; 57.4 7.6 0.00016 30.8 1.9 29 105-139 71-99 (110)
270 COG0333 RpmF Ribosomal protein 57.3 7.1 0.00015 27.5 1.6 22 104-134 27-48 (57)
271 TIGR02443 conserved hypothetic 57.2 8.1 0.00018 27.4 1.8 35 106-140 11-45 (59)
272 PRK07218 replication factor A; 57.0 15 0.00033 36.0 4.4 47 96-153 289-335 (423)
273 TIGR00595 priA primosomal prot 55.5 7.4 0.00016 38.9 2.0 24 107-134 225-248 (505)
274 KOG0402 60S ribosomal protein 55.1 10 0.00022 28.8 2.1 36 96-135 28-63 (92)
275 TIGR00373 conserved hypothetic 54.3 3.9 8.4E-05 34.6 -0.2 30 103-135 108-137 (158)
276 PF03833 PolC_DP2: DNA polymer 54.2 4.2 9.1E-05 42.9 0.0 11 104-114 655-665 (900)
277 PF01155 HypA: Hydrogenase exp 54.2 2.8 6.1E-05 33.3 -1.0 26 105-136 71-96 (113)
278 PRK14714 DNA polymerase II lar 54.0 9.6 0.00021 42.0 2.6 15 38-52 606-620 (1337)
279 COG2126 RPL37A Ribosomal prote 54.0 5.9 0.00013 28.0 0.7 29 102-137 14-42 (61)
280 PF03487 IL13: Interleukin-13; 53.7 12 0.00027 24.4 2.1 26 168-193 11-36 (43)
281 PRK06266 transcription initiat 53.6 4.2 9E-05 35.1 -0.1 30 104-136 117-146 (178)
282 COG4888 Uncharacterized Zn rib 52.7 8 0.00017 30.4 1.3 32 105-136 23-56 (104)
283 PF11672 DUF3268: Protein of u 52.6 11 0.00025 29.6 2.2 29 105-133 3-38 (102)
284 KOG2767 Translation initiation 52.5 5.7 0.00012 37.8 0.6 45 96-140 88-132 (400)
285 TIGR03830 CxxCG_CxxCG_HTH puta 51.9 9.7 0.00021 30.1 1.8 14 125-138 30-43 (127)
286 PRK11788 tetratricopeptide rep 51.6 11 0.00024 35.0 2.3 32 101-140 351-382 (389)
287 COG1439 Predicted nucleic acid 51.6 7.2 0.00016 33.7 1.0 11 104-114 153-163 (177)
288 cd01121 Sms Sms (bacterial rad 51.6 9.7 0.00021 36.6 2.0 21 106-134 2-22 (372)
289 PF01907 Ribosomal_L37e: Ribos 51.4 4 8.7E-05 28.5 -0.4 27 102-135 13-39 (55)
290 PRK12336 translation initiatio 51.2 10 0.00022 33.4 1.9 42 94-136 88-129 (201)
291 COG1592 Rubrerythrin [Energy p 50.5 9.7 0.00021 32.6 1.6 23 106-135 136-158 (166)
292 PRK11823 DNA repair protein Ra 49.9 9.9 0.00021 37.4 1.8 22 105-134 8-29 (446)
293 TIGR01053 LSD1 zinc finger dom 49.8 14 0.00029 22.8 1.8 27 106-136 3-29 (31)
294 PF09845 DUF2072: Zn-ribbon co 49.2 8.3 0.00018 31.7 1.0 29 106-138 3-31 (131)
295 TIGR00310 ZPR1_znf ZPR1 zinc f 49.2 9.3 0.0002 33.4 1.4 31 107-137 3-41 (192)
296 COG2835 Uncharacterized conser 49.1 13 0.00028 26.5 1.8 29 105-138 9-37 (60)
297 COG1499 NMD3 NMD protein affec 49.1 14 0.0003 35.4 2.7 30 103-139 5-34 (355)
298 COG3791 Uncharacterized conser 48.7 20 0.00043 29.2 3.2 13 105-117 70-82 (133)
299 smart00709 Zpr1 Duplicated dom 48.4 11 0.00024 32.0 1.7 30 106-136 2-39 (160)
300 TIGR00416 sms DNA repair prote 48.1 11 0.00024 37.2 1.8 22 105-134 8-29 (454)
301 COG3877 Uncharacterized protei 47.9 11 0.00024 30.0 1.4 26 104-137 6-31 (122)
302 PF04216 FdhE: Protein involve 47.9 3.2 6.9E-05 38.3 -1.9 26 102-135 195-220 (290)
303 PF09332 Mcm10: Mcm10 replicat 47.7 6.2 0.00013 37.6 0.0 32 104-139 285-316 (344)
304 TIGR00155 pqiA_fam integral me 47.6 13 0.00028 36.2 2.2 29 105-140 216-244 (403)
305 COG1545 Predicted nucleic-acid 47.5 9.2 0.0002 31.6 1.0 24 104-135 29-52 (140)
306 PRK13264 3-hydroxyanthranilate 46.8 9.1 0.0002 33.1 0.9 35 106-140 122-171 (177)
307 PTZ00073 60S ribosomal protein 46.7 11 0.00023 29.1 1.1 26 102-134 14-39 (91)
308 PRK03824 hypA hydrogenase nick 46.6 8.5 0.00019 31.6 0.7 12 104-115 70-81 (135)
309 PRK08351 DNA-directed RNA poly 46.5 9.9 0.00021 27.2 0.9 36 105-150 4-39 (61)
310 PF14690 zf-ISL3: zinc-finger 46.4 18 0.00038 23.5 2.1 10 105-114 3-12 (47)
311 PF07191 zinc-ribbons_6: zinc- 45.7 11 0.00024 27.7 1.0 23 106-134 3-25 (70)
312 TIGR00354 polC DNA polymerase, 45.4 9.6 0.00021 40.9 1.0 23 104-136 625-647 (1095)
313 PRK08332 ribonucleotide-diphos 44.9 13 0.00028 42.6 1.9 27 103-135 1703-1735(1740)
314 PF05191 ADK_lid: Adenylate ki 44.7 6.6 0.00014 24.9 -0.2 32 106-139 3-34 (36)
315 CHL00174 accD acetyl-CoA carbo 43.9 7.5 0.00016 36.3 -0.0 27 105-134 39-65 (296)
316 KOG0909 Peptide:N-glycanase [P 43.9 20 0.00044 35.2 2.9 45 95-139 145-208 (500)
317 smart00532 LIGANc Ligase N fam 43.8 14 0.0003 36.4 1.8 27 103-133 398-426 (441)
318 COG3024 Uncharacterized protei 43.8 12 0.00025 27.0 0.9 29 104-135 7-36 (65)
319 PF03966 Trm112p: Trm112p-like 43.8 14 0.0003 26.5 1.3 12 125-136 52-63 (68)
320 PF05876 Terminase_GpA: Phage 43.6 16 0.00035 37.0 2.3 51 88-138 184-241 (557)
321 PF13408 Zn_ribbon_recom: Reco 43.6 13 0.00029 25.0 1.2 15 103-117 4-18 (58)
322 PF03367 zf-ZPR1: ZPR1 zinc-fi 43.5 9.4 0.0002 32.4 0.5 32 106-137 3-41 (161)
323 PRK00415 rps27e 30S ribosomal 43.5 15 0.00032 26.1 1.4 25 107-134 14-38 (59)
324 COG0272 Lig NAD-dependent DNA 43.1 14 0.00031 38.1 1.8 28 103-134 403-433 (667)
325 COG0777 AccD Acetyl-CoA carbox 43.0 8.5 0.00018 35.6 0.2 27 105-134 29-55 (294)
326 PRK05654 acetyl-CoA carboxylas 42.9 8.1 0.00017 36.0 -0.0 16 100-115 42-57 (292)
327 PRK00762 hypA hydrogenase nick 42.6 11 0.00024 30.5 0.8 34 100-135 66-101 (124)
328 PRK05580 primosome assembly pr 42.1 16 0.00034 38.0 2.0 26 106-135 392-417 (679)
329 TIGR01562 FdhE formate dehydro 41.9 11 0.00025 35.3 0.8 26 102-135 208-233 (305)
330 KOG4537 Zn-ribbon-containing p 41.8 9.1 0.0002 32.4 0.1 36 90-135 31-66 (178)
331 TIGR00515 accD acetyl-CoA carb 41.7 8.7 0.00019 35.7 0.0 14 101-114 42-55 (285)
332 COG1198 PriA Primosomal protei 41.3 16 0.00035 38.3 1.9 25 107-135 447-471 (730)
333 KOG3940 Uncharacterized conser 41.2 10 0.00023 35.5 0.5 25 104-134 322-346 (351)
334 PF03884 DUF329: Domain of unk 41.2 11 0.00024 26.5 0.5 25 106-133 4-29 (57)
335 PRK06386 replication factor A; 40.8 40 0.00086 32.4 4.3 43 103-156 235-277 (358)
336 smart00064 FYVE Protein presen 40.8 18 0.00039 25.5 1.6 32 99-136 3-36 (68)
337 PRK12722 transcriptional activ 40.7 33 0.00073 29.9 3.5 42 91-134 117-162 (187)
338 PF04810 zf-Sec23_Sec24: Sec23 40.6 16 0.00035 23.5 1.1 31 106-136 4-34 (40)
339 PRK07217 replication factor A; 40.5 47 0.001 31.3 4.7 48 100-158 184-233 (311)
340 COG2995 PqiA Uncharacterized p 40.1 20 0.00043 34.8 2.2 34 103-138 17-50 (418)
341 PRK12496 hypothetical protein; 39.8 18 0.0004 30.7 1.7 27 106-138 129-155 (164)
342 PF01363 FYVE: FYVE zinc finge 39.6 18 0.00038 25.6 1.4 30 102-137 7-36 (69)
343 PF14319 Zn_Tnp_IS91: Transpos 39.5 16 0.00035 29.0 1.2 27 105-135 43-69 (111)
344 PRK14973 DNA topoisomerase I; 38.7 18 0.00038 39.1 1.7 36 105-140 636-671 (936)
345 PF15616 TerY-C: TerY-C metal 38.6 16 0.00036 30.0 1.2 32 104-137 77-116 (131)
346 KOG1842 FYVE finger-containing 38.6 7.6 0.00017 38.1 -0.9 35 95-135 169-205 (505)
347 PRK08173 DNA topoisomerase III 38.5 18 0.0004 38.6 1.8 28 105-138 625-652 (862)
348 COG4469 CoiA Competence protei 38.4 15 0.00033 34.8 1.1 13 105-117 26-38 (342)
349 cd00202 ZnF_GATA Zinc finger D 38.4 13 0.00029 25.6 0.5 31 106-136 1-31 (54)
350 COG2093 DNA-directed RNA polym 38.2 20 0.00044 25.7 1.4 41 103-151 3-43 (64)
351 KOG2463 Predicted RNA-binding 38.2 38 0.00081 32.2 3.6 56 105-171 243-301 (376)
352 TIGR02300 FYDLN_acid conserved 38.2 14 0.00031 30.2 0.7 23 122-144 5-28 (129)
353 PRK07956 ligA NAD-dependent DN 37.4 20 0.00044 37.2 1.9 23 104-130 404-426 (665)
354 COG2023 RPR2 RNase P subunit R 36.6 22 0.00048 28.1 1.6 32 105-136 57-92 (105)
355 COG2260 Predicted Zn-ribbon RN 36.1 21 0.00045 25.3 1.2 14 106-119 19-32 (59)
356 COG1579 Zn-ribbon protein, pos 36.1 11 0.00023 34.2 -0.3 36 103-138 196-233 (239)
357 PF03833 PolC_DP2: DNA polymer 36.0 12 0.00026 39.6 0.0 19 99-117 662-680 (900)
358 PF14255 Cys_rich_CPXG: Cystei 35.8 19 0.0004 24.9 0.9 29 106-134 2-32 (52)
359 PRK00418 DNA gyrase inhibitor; 35.5 24 0.00051 25.3 1.4 28 104-134 6-34 (62)
360 PRK11088 rrmA 23S rRNA methylt 35.2 56 0.0012 29.4 4.3 20 106-131 4-23 (272)
361 PF09779 Ima1_N: Ima1 N-termin 35.1 29 0.00063 28.3 2.1 29 107-138 3-32 (131)
362 COG0375 HybF Zn finger protein 35.0 21 0.00045 28.7 1.2 27 105-137 71-97 (115)
363 PF13005 zf-IS66: zinc-finger 34.5 18 0.0004 23.6 0.7 14 104-117 2-15 (47)
364 PF10122 Mu-like_Com: Mu-like 33.7 20 0.00044 24.6 0.8 31 105-137 5-35 (51)
365 COG0846 SIR2 NAD-dependent pro 33.2 29 0.00063 31.6 2.0 30 174-204 161-190 (250)
366 TIGR02820 formald_GSH S-(hydro 33.2 16 0.00035 31.7 0.3 28 170-197 134-162 (182)
367 COG1655 Uncharacterized protei 33.1 17 0.00037 32.8 0.5 17 101-117 16-32 (267)
368 PHA02998 RNA polymerase subuni 32.8 37 0.0008 29.5 2.4 36 103-138 142-183 (195)
369 KOG2463 Predicted RNA-binding 32.7 17 0.00038 34.4 0.5 13 104-116 257-269 (376)
370 COG4111 Uncharacterized conser 32.3 1.4E+02 0.003 27.6 6.1 97 144-247 28-135 (322)
371 PF12172 DUF35_N: Rubredoxin-l 31.7 32 0.0007 21.4 1.5 12 127-138 12-23 (37)
372 PF14206 Cys_rich_CPCC: Cystei 31.7 32 0.0007 25.7 1.7 29 106-137 3-31 (78)
373 PF06906 DUF1272: Protein of u 31.6 14 0.0003 26.0 -0.3 14 127-140 42-55 (57)
374 COG4530 Uncharacterized protei 31.4 26 0.00056 28.1 1.2 22 123-144 6-28 (129)
375 cd00350 rubredoxin_like Rubred 31.3 26 0.00057 21.4 1.0 23 106-134 3-25 (33)
376 PRK06393 rpoE DNA-directed RNA 31.2 46 0.00099 24.0 2.3 39 103-151 4-42 (64)
377 PF01667 Ribosomal_S27e: Ribos 31.0 28 0.00062 24.3 1.2 26 107-135 10-35 (55)
378 PRK00504 rpmG 50S ribosomal pr 31.0 22 0.00047 24.4 0.6 14 104-117 34-47 (50)
379 TIGR00575 dnlj DNA ligase, NAD 30.7 29 0.00062 36.0 1.7 26 104-133 392-419 (652)
380 COG1601 GCD7 Translation initi 30.7 16 0.00034 30.9 -0.2 41 95-136 96-136 (151)
381 PLN00209 ribosomal protein S27 30.4 34 0.00074 26.1 1.6 25 107-134 39-63 (86)
382 COG4307 Uncharacterized protei 30.4 17 0.00038 33.5 0.1 25 104-136 3-27 (349)
383 PRK06260 threonine synthase; V 30.2 27 0.00059 33.6 1.4 24 105-134 4-27 (397)
384 COG1066 Sms Predicted ATP-depe 29.5 29 0.00063 34.1 1.4 21 105-133 8-28 (456)
385 COG4068 Uncharacterized protei 29.3 29 0.00064 24.6 1.1 24 103-134 7-31 (64)
386 TIGR02827 RNR_anaer_Bdell anae 29.3 29 0.00063 35.5 1.5 26 101-134 529-554 (586)
387 PF06750 DiS_P_DiS: Bacterial 29.3 38 0.00083 25.9 1.8 37 100-136 29-68 (92)
388 PF02132 RecR: RecR protein; 29.2 30 0.00066 22.3 1.1 24 92-115 5-28 (41)
389 PTZ00083 40S ribosomal protein 29.0 38 0.00082 25.8 1.7 25 107-134 38-62 (85)
390 TIGR00595 priA primosomal prot 28.9 29 0.00063 34.7 1.4 24 103-135 239-262 (505)
391 PRK06556 vitamin B12-dependent 28.8 32 0.00069 37.3 1.7 32 98-135 918-949 (953)
392 TIGR03826 YvyF flagellar opero 28.7 19 0.00041 29.8 0.0 25 103-134 2-26 (137)
393 cd00729 rubredoxin_SM Rubredox 28.7 34 0.00074 21.2 1.2 23 106-134 4-26 (34)
394 PRK12860 transcriptional activ 28.5 73 0.0016 27.9 3.6 41 91-133 117-161 (189)
395 COG1885 Uncharacterized protei 28.5 27 0.00059 27.6 0.9 22 178-200 82-103 (115)
396 PRK06450 threonine synthase; V 28.4 30 0.00064 32.7 1.3 22 106-134 5-26 (338)
397 PRK08271 anaerobic ribonucleos 28.4 35 0.00075 35.2 1.8 27 101-135 563-589 (623)
398 PF02318 FYVE_2: FYVE-type zin 28.3 39 0.00085 26.9 1.8 28 103-135 53-80 (118)
399 PF04135 Nop10p: Nucleolar RNA 28.3 32 0.0007 23.8 1.1 14 106-119 19-32 (53)
400 COG1867 TRM1 N2,N2-dimethylgua 28.2 32 0.00068 33.3 1.4 37 93-134 229-265 (380)
401 PRK03564 formate dehydrogenase 28.0 39 0.00084 31.8 2.0 25 102-134 210-234 (309)
402 PF14369 zf-RING_3: zinc-finge 28.0 36 0.00077 21.4 1.2 26 106-134 4-29 (35)
403 KOG2691 RNA polymerase II subu 28.0 33 0.00071 27.3 1.2 13 127-139 5-17 (113)
404 PF00320 GATA: GATA zinc finge 27.7 10 0.00022 23.8 -1.3 28 107-134 1-28 (36)
405 PF06689 zf-C4_ClpX: ClpX C4-t 27.6 12 0.00026 24.3 -1.1 28 105-133 2-31 (41)
406 PRK07220 DNA topoisomerase I; 27.6 42 0.00091 35.3 2.3 35 104-138 635-669 (740)
407 COG1405 SUA7 Transcription ini 27.3 37 0.00079 31.6 1.6 29 105-136 2-30 (285)
408 PRK15103 paraquat-inducible me 27.0 49 0.0011 32.4 2.5 30 103-140 220-249 (419)
409 TIGR03829 YokU_near_AblA uncha 26.9 30 0.00066 26.6 0.9 34 125-163 34-67 (89)
410 PF01921 tRNA-synt_1f: tRNA sy 26.9 17 0.00036 35.0 -0.7 38 100-137 170-210 (360)
411 PF00628 PHD: PHD-finger; Int 26.8 47 0.001 21.8 1.7 24 106-136 1-24 (51)
412 PF04828 GFA: Glutathione-depe 26.7 15 0.00032 26.9 -0.9 15 102-116 46-60 (92)
413 PF10005 DUF2248: Uncharacteri 26.7 53 0.0012 31.3 2.6 28 106-141 1-28 (343)
414 PF05129 Elf1: Transcription e 26.5 36 0.00078 25.5 1.2 33 104-136 22-56 (81)
415 cd00065 FYVE FYVE domain; Zinc 26.5 47 0.001 22.3 1.7 26 105-136 3-28 (57)
416 PRK03922 hypothetical protein; 26.3 34 0.00073 27.3 1.0 22 178-200 82-103 (113)
417 PRK07111 anaerobic ribonucleos 26.0 37 0.00079 35.8 1.5 25 101-134 677-701 (735)
418 COG1198 PriA Primosomal protei 26.0 34 0.00074 35.9 1.3 24 103-135 461-484 (730)
419 PRK08579 anaerobic ribonucleos 25.6 41 0.00088 34.8 1.8 26 101-134 565-590 (625)
420 PF07649 C1_3: C1-like domain; 25.5 46 0.001 19.7 1.3 25 105-136 1-25 (30)
421 COG1379 PHP family phosphoeste 25.5 20 0.00044 34.1 -0.4 27 105-134 247-273 (403)
422 PRK08270 anaerobic ribonucleos 25.2 40 0.00086 35.0 1.6 26 101-135 623-648 (656)
423 PRK14715 DNA polymerase II lar 25.2 33 0.00072 38.3 1.1 20 104-133 674-693 (1627)
424 KOG0720 Molecular chaperone (D 25.2 22 0.00047 35.2 -0.3 35 102-136 325-359 (490)
425 PRK05580 primosome assembly pr 25.1 39 0.00084 35.1 1.5 23 104-135 408-430 (679)
426 smart00504 Ubox Modified RING 25.1 60 0.0013 22.0 2.1 22 95-116 26-47 (63)
427 TIGR03844 cysteate_syn cysteat 24.9 36 0.00078 33.0 1.2 22 105-133 3-24 (398)
428 PF15025 DUF4524: Domain of un 24.9 62 0.0014 27.2 2.4 82 58-157 40-121 (148)
429 KOG1814 Predicted E3 ubiquitin 24.8 51 0.0011 32.3 2.1 34 99-136 362-396 (445)
430 TIGR02159 PA_CoA_Oxy4 phenylac 24.2 27 0.00057 29.2 0.1 31 104-134 105-138 (146)
431 PRK14704 anaerobic ribonucleos 24.1 42 0.0009 34.6 1.5 25 101-134 556-580 (618)
432 PRK00595 rpmG 50S ribosomal pr 24.0 34 0.00073 23.6 0.6 14 104-117 37-50 (53)
433 PRK01343 zinc-binding protein; 23.9 48 0.001 23.3 1.4 25 103-134 8-33 (57)
434 PRK09263 anaerobic ribonucleos 23.9 49 0.0011 34.7 2.0 31 101-135 638-668 (711)
435 PRK07591 threonine synthase; V 23.7 43 0.00093 32.6 1.5 22 105-133 19-40 (421)
436 PF06943 zf-LSD1: LSD1 zinc fi 23.5 67 0.0014 18.8 1.7 24 107-134 1-24 (25)
437 PF05280 FlhC: Flagellar trans 23.5 46 0.00099 28.7 1.4 41 91-133 117-161 (175)
438 cd01411 SIR2H SIR2H: Uncharact 23.2 47 0.001 29.5 1.5 11 125-135 117-127 (225)
439 PF14149 YhfH: YhfH-like prote 22.9 10 0.00022 24.4 -2.0 14 104-117 13-26 (37)
440 KOG3092 Casein kinase II, beta 22.9 1.2E+02 0.0027 26.8 3.9 48 93-140 94-148 (216)
441 PF09505 Dimeth_Pyl: Dimethyla 22.8 45 0.00098 31.8 1.3 24 174-197 408-431 (466)
442 COG4643 Uncharacterized protei 22.7 65 0.0014 30.8 2.3 43 91-133 19-61 (366)
443 TIGR01023 rpmG_bact ribosomal 22.6 38 0.00083 23.5 0.6 14 104-117 38-51 (54)
444 PF13821 DUF4187: Domain of un 22.6 55 0.0012 22.7 1.4 35 92-131 14-49 (55)
445 KOG3970 Predicted E3 ubiquitin 22.3 1E+02 0.0022 28.0 3.3 49 95-143 38-111 (299)
446 PRK14873 primosome assembly pr 22.2 50 0.0011 34.4 1.6 27 106-136 394-420 (665)
447 COG0267 RpmG Ribosomal protein 22.0 36 0.00079 23.3 0.4 14 104-117 34-47 (50)
448 PF09082 DUF1922: Domain of un 22.0 37 0.0008 24.8 0.5 15 179-193 41-57 (68)
449 COG2995 PqiA Uncharacterized p 22.0 47 0.001 32.3 1.3 14 104-117 38-51 (418)
450 COG4416 Com Mu-like prophage p 21.6 20 0.00044 25.0 -0.9 32 104-137 4-35 (60)
451 KOG2879 Predicted E3 ubiquitin 21.5 59 0.0013 30.2 1.8 25 92-116 212-251 (298)
452 COG4332 Uncharacterized protei 21.4 55 0.0012 28.5 1.5 32 104-135 17-58 (203)
453 PHA02031 putative DnaG-like pr 21.2 26 0.00057 32.2 -0.5 46 90-137 8-54 (266)
454 TIGR02487 NrdD anaerobic ribon 20.9 59 0.0013 33.2 1.9 27 101-135 521-547 (579)
455 TIGR00269 conserved hypothetic 20.8 51 0.0011 25.6 1.1 21 103-133 79-99 (104)
456 COG5595 Zn-ribbon-containing, 20.6 63 0.0014 28.6 1.7 31 103-134 217-247 (256)
457 TIGR00375 conserved hypothetic 20.2 42 0.0009 32.5 0.6 28 104-135 240-267 (374)
458 PF14901 Jiv90: Cleavage induc 20.2 24 0.00052 27.4 -0.9 35 102-136 3-37 (94)
459 PF04475 DUF555: Protein of un 20.1 53 0.0011 25.8 1.0 20 178-198 80-99 (102)
No 1
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=100.00 E-value=5e-46 Score=335.33 Aligned_cols=171 Identities=23% Similarity=0.338 Sum_probs=164.5
Q ss_pred ecceeeccccccc-CCCCCccHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEE
Q 023914 70 RASRVCATRSESN-QDATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLI 148 (275)
Q Consensus 70 ~~~~~~~~r~~~~-~~~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI 148 (275)
.+++++++|+++. +|+.++.++++|++|++|+++|+|||+||++|... +++++++|++||..+||+++|+|++++
T Consensus 76 ~~~~~~~lR~l~~~~~~~~~~~~~~a~~l~~w~~~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fPR~dP~vIv~v 151 (279)
T COG2816 76 EPFELVDLRSLLTELDEGLFGLAARAVQLLEWYRSHRFCGRCGTKTYPR----EGGWARVCPKCGHEHFPRIDPCVIVAV 151 (279)
T ss_pred CccceeeHHHHhccCCHHHHHHHHHHHHHHHHHhhCcCCCCCCCcCccc----cCceeeeCCCCCCccCCCCCCeEEEEE
Confidence 6788999999987 89999999999999999999999999999999988 899999999999999999999999999
Q ss_pred eeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCCEEEEEEEEEEcCCCCC
Q 023914 149 EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKLKRPHFS 228 (275)
Q Consensus 149 ~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~f~a~~~~~e~~ 228 (275)
.+++++||.++.+++ +|+|++.+||||+|||+|+|++||++||+|++|++++|+++|+||+++++|++|.+++.++++.
T Consensus 152 ~~~~~ilLa~~~~h~-~g~yS~LAGFVE~GETlE~AV~REv~EE~Gi~V~~vrY~~SQPWPfP~SLMigf~aey~sgeI~ 230 (279)
T COG2816 152 IRGDEILLARHPRHF-PGMYSLLAGFVEPGETLEQAVAREVFEEVGIKVKNVRYVGSQPWPFPHSLMLGFMAEYDSGEIT 230 (279)
T ss_pred ecCCceeecCCCCCC-CcceeeeeecccCCccHHHHHHHHHHHhhCeEEeeeeEEeccCCCCchhhhhhheeeecccccc
Confidence 999999999999887 8999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CC-CCceeEEEecCCC-CC
Q 023914 229 PG-PESSECRLFALDE-IP 245 (275)
Q Consensus 229 ~~-~E~~d~~W~~~de-L~ 245 (275)
++ .|++|++||+.+| ++
T Consensus 231 ~d~~Eleda~WFs~~evl~ 249 (279)
T COG2816 231 PDEGELEDARWFSRDEVLP 249 (279)
T ss_pred CCcchhhhccccCHhHHhh
Confidence 87 7999999999999 54
No 2
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=100.00 E-value=7.7e-42 Score=309.46 Aligned_cols=189 Identities=20% Similarity=0.288 Sum_probs=173.2
Q ss_pred cceeecccccccCCCCCccHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEee
Q 023914 71 ASRVCATRSESNQDATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEH 150 (275)
Q Consensus 71 ~~~~~~~r~~~~~~~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~ 150 (275)
++++.+||++..+++.+++++++|++|.+|+++++|||+||+++... ++++++.|++||+.+||++.++|+++|.+
T Consensus 66 ~~~~~~lr~~~~~~~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~yp~~~paViv~V~~ 141 (256)
T PRK00241 66 GHEMGSLRQLLDLDDGLFQLLGRAVQLAEFYRSHRFCGYCGHPMHPS----KTEWAMLCPHCRERYYPRIAPCIIVAVRR 141 (256)
T ss_pred cccchhhhhhccCCHHHHHHHHHHHHHHHHhhcCccccccCCCCeec----CCceeEECCCCCCEECCCCCCEEEEEEEe
Confidence 56778999987789999999999999999999999999999999776 67899999999999999999999999999
Q ss_pred CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCCEEEEEEEEEEcCCCCCCC
Q 023914 151 DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKLKRPHFSPG 230 (275)
Q Consensus 151 ~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~f~a~~~~~e~~~~ 230 (275)
+++|||+||...+ .|.|++|||++|+|||+++||+||++||||+++..++++++++|++++.+|++|.++..++++..+
T Consensus 142 ~~~iLL~rr~~~~-~g~wslPgG~vE~GEs~eeAa~REv~EEtGl~v~~~~~~~s~~~~~p~~lm~~f~a~~~~~~~~~~ 220 (256)
T PRK00241 142 GDEILLARHPRHR-NGVYTVLAGFVEVGETLEQCVAREVMEESGIKVKNLRYVGSQPWPFPHSLMLGFHADYDSGEIVFD 220 (256)
T ss_pred CCEEEEEEccCCC-CCcEeCcccCCCCCCCHHHHhhhhhhhccCceeeeeEEEEeEeecCCCeEEEEEEEEecCCcccCC
Confidence 9999999998877 799999999999999999999999999999999999999999999999999999999987776665
Q ss_pred -CCceeEEEecCCCCCCCCCCCcHHHHHHHHHHHHHhh
Q 023914 231 -PESSECRLFALDEIPFDSLAFSSISVTLQLVRFYFEH 267 (275)
Q Consensus 231 -~E~~d~~W~~~deL~~~~l~~~s~~~al~li~~~l~~ 267 (275)
+|+.+++||+++|++. + ++..+++.++|++|++.
T Consensus 221 ~~Ei~~a~W~~~del~~--l-p~~~sia~~li~~~~~~ 255 (256)
T PRK00241 221 PKEIADAQWFRYDELPL--L-PPSGTIARRLIEDTVAL 255 (256)
T ss_pred cccEEEEEEECHHHCcc--c-CCchHHHHHHHHHHHHh
Confidence 7889999999999984 3 45667899999999874
No 3
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=100.00 E-value=1.2e-39 Score=295.26 Aligned_cols=242 Identities=31% Similarity=0.420 Sum_probs=186.9
Q ss_pred Ccchhhhcccccch-hhceeecccCCccceeeEEeecCCCCccccccccccccccccccccccccccceeecceeecccc
Q 023914 1 MLKSVQILGSSSGF-LSLILKKSHNSCYGLSFVAVSTNPLPYSTARRHEIVSKTDSLVSPAFLTRRTRCFRASRVCATRS 79 (275)
Q Consensus 1 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~ 79 (275)
|++|.|+.+|.||+ ++++.++.++.+ +.|++-++.+ -+ .+.-...++. .|.+.|+..-
T Consensus 67 ~~~a~~~~~~~sg~~~~~~~~~~~~e~-~v~~~~~~~~-------------e~---~l~~~~~g~~--~F~~~r~~~~-- 125 (345)
T KOG3084|consen 67 MLDAVRIPGWESGLVISQDLTKDRKES-SVSYIGSSLN-------------ES---QLTSSLGGRI--SFVPLRMSMS-- 125 (345)
T ss_pred chhheecccccccceeeehhccCcccc-cceecccchh-------------hh---hhcccCCCce--eeccchhhcc--
Confidence 78999999999999 778867777664 4443332222 11 1111111111 7877777543
Q ss_pred cccCCCCCc-cHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecC--CCC--CccccCCcEEEEEEE-eeC-C
Q 023914 80 ESNQDATSS-HPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICT--VCG--KIAYQNPKMVVGCLI-EHD-K 152 (275)
Q Consensus 80 ~~~~~~~~~-~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~--~Cg--~~~y~~p~~~V~viI-~~~-~ 152 (275)
+.++.++. ++.+.|+++++|+++++|||.||+++... ++|.+..|. .|. ...||+.+++|++++ +++ .
T Consensus 126 -~~~~~~d~~~~~a~ars~l~W~skykFCp~CG~~tkp~----e~g~k~~Cs~~~C~~~n~~yPr~dPvVIm~li~~d~~ 200 (345)
T KOG3084|consen 126 -LPGSDEDARSLTAVARSLLDWVSKYKFCPGCGSPTKPE----EAGTKLQCSDETCPSCNVIYPRTDPVVIMLLIDHDGK 200 (345)
T ss_pred -CCCChhhhhcHHHHHHHHHHHHHHhccCcccCCCcccc----cCCccceeecccCCcCCeeccCCCCeEEEEEEcCCCC
Confidence 44555555 89999999999999999999999999887 677788888 688 899999888887655 444 5
Q ss_pred eEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeC-CCCEEEEEEEEEEcC-CCCCCC
Q 023914 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP-RIGQIYIIFLAKLKR-PHFSPG 230 (275)
Q Consensus 153 ~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~-~~~~~~~~f~a~~~~-~e~~~~ 230 (275)
++||.|+.+.+ +|+|+++|||+|+|||+||||+||++||+|++|+.+.|+.+|+|| .+.++|+++.+-... +++..+
T Consensus 201 ~~LL~R~~r~~-~gl~t~lAGFlEpGES~eeav~REtwEEtGi~V~~I~~~asQPWP~~p~SLMIgc~ala~~~~~I~vd 279 (345)
T KOG3084|consen 201 HALLGRQKRYP-PGLWTCLAGFLEPGESIEEAVRRETWEETGIEVEVISYVASQPWPLMPQSLMIGCLALAKLNGKISVD 279 (345)
T ss_pred EeeeecccCCC-CchhhhhhccCCccccHHHHHHHHHHHHhCceeeeEeeeecCCCCCCchHHHHHHHHHHhhCCccccC
Confidence 67777766665 899999999999999999999999999999999999999999999 888899887666544 555554
Q ss_pred --CCceeEEEecCCCCCC---------------CCCCCcHHHHHHHHHHHHHhhcc
Q 023914 231 --PESSECRLFALDEIPF---------------DSLAFSSISVTLQLVRFYFEHMT 269 (275)
Q Consensus 231 --~E~~d~~W~~~deL~~---------------~~l~~~s~~~al~li~~~l~~~~ 269 (275)
.|.+|++||+.+|+.. .-+.+++..+|++||.+|+....
T Consensus 280 ~dlEleDaqwF~r~ev~~aL~~kg~~Rv~~~~a~i~~P~~~aIA~qLI~~~~~~~~ 335 (345)
T KOG3084|consen 280 KDLELEDAQWFDREEVKSALTTKGLVRVQIEKALILIPPPFAIAHQLILHWVGFVP 335 (345)
T ss_pred cchhhhhcccccHHHHHHHHHhcCCccccccCcceecCChhHHHHHHHHHHHccch
Confidence 4999999999988521 12457889999999999997643
No 4
>cd04511 Nudix_Hydrolase_4 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specifici
Probab=99.95 E-value=2.9e-27 Score=192.43 Aligned_cols=128 Identities=53% Similarity=1.031 Sum_probs=116.1
Q ss_pred cCCCCCccccCCcEEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe
Q 023914 129 CTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI 208 (275)
Q Consensus 129 C~~Cg~~~y~~p~~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~ 208 (275)
|+.||+++|++|.++|++++.++++|||++|...+..|.|++|||++|.||++++|++||++||||+++....+++.++.
T Consensus 1 c~~~~~~~~~~~~~~v~~ii~~~~~vLL~kr~~~~~~g~w~lPgG~ve~gE~~~~a~~REl~EEtGl~~~~~~~~~~~~~ 80 (130)
T cd04511 1 CPDCGYIHYQNPKIIVGCVPEWEGKVLLCRRAIEPRHGFWTLPAGFMENGETTEQGALRETWEEAGARVEIDGLYAVYSV 80 (130)
T ss_pred CCCCccccCCCCcEEEEEEEecCCEEEEEEecCCCCCCeEECCcccccCCCCHHHHHHHHHHHHhCCEEEeeeEEEEEec
Confidence 99999999999999999998888999999998777779999999999999999999999999999999988888888888
Q ss_pred CCCCEEEEEEEEEEcCCCCCCCCCceeEEEecCCCCCCCCCCCcHHHH
Q 023914 209 PRIGQIYIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISV 256 (275)
Q Consensus 209 ~~~~~~~~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s~~~ 256 (275)
+..+..+++|.+++.++.+..+.|..+++|+++++|+...+++++.+.
T Consensus 81 ~~~~~~~~~f~~~~~~~~~~~~~e~~~~~~~~~~~l~~~~l~~~~~~~ 128 (130)
T cd04511 81 PHISQVYMFYRARLLDLDFAPGPESLEVRLFTEEEIPWDELAFPTVRR 128 (130)
T ss_pred CCceEEEEEEEEEEcCCcccCCcchhceEEECHHHCCchhcccccccc
Confidence 877788999999998776666788889999999999987888887654
No 5
>COG1051 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]
Probab=99.87 E-value=1.6e-21 Score=162.67 Aligned_cols=115 Identities=36% Similarity=0.579 Sum_probs=98.0
Q ss_pred CCccccCCcEEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC-
Q 023914 133 GKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI- 211 (275)
Q Consensus 133 g~~~y~~p~~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~- 211 (275)
....|++|.++|.+++..+++|||+||...|..|.|++|||+||.|||+++||+||++||||++++.++++++++.+..
T Consensus 2 ~~~~~~~p~~~v~~~i~~~~~iLLvrR~~~p~~g~WalPGG~ve~GEt~eeaa~REl~EETgL~~~~~~~~~v~~~~~rd 81 (145)
T COG1051 2 LAMGYRTPLVAVGALIVRNGRILLVRRANEPGAGYWALPGGFVEIGETLEEAARRELKEETGLRVRVLELLAVFDDPGRD 81 (145)
T ss_pred ccccCCCcceeeeEEEEeCCEEEEEEecCCCCCCcEeCCCccCCCCCCHHHHHHHHHHHHhCCcccceeEEEEecCCCCC
Confidence 3467889999999999998999999999999899999999999999999999999999999999999999999987653
Q ss_pred ---CEEEEEEEEEEcCCCCCCC--CCceeEEEecCCCCCCC
Q 023914 212 ---GQIYIIFLAKLKRPHFSPG--PESSECRLFALDEIPFD 247 (275)
Q Consensus 212 ---~~~~~~f~a~~~~~e~~~~--~E~~d~~W~~~deL~~~ 247 (275)
++..+.|++....++.... ++..++.||+.++++..
T Consensus 82 ~r~~~v~~~~~~~~~~g~~~~~~~~d~~~~~~~~~~~l~~~ 122 (145)
T COG1051 82 PRGHHVSFLFFAAEPEGELLAGDGDDAAEVGWFPLDELPEL 122 (145)
T ss_pred CceeEEEEEEEEEecCCCcccCChhhHhhcceecHhHcccc
Confidence 3455566666655544433 47888999999999964
No 6
>cd04681 Nudix_Hydrolase_22 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.85 E-value=1.4e-20 Score=152.10 Aligned_cols=120 Identities=27% Similarity=0.457 Sum_probs=92.9
Q ss_pred EEEE-EEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe--CCC----CEEE
Q 023914 143 VVGC-LIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI--PRI----GQIY 215 (275)
Q Consensus 143 ~V~v-iI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~--~~~----~~~~ 215 (275)
+|.+ +++.++++||++|...+.+|.|.+|||++|.|||+++||.||++||||+++....+++.... +.. +...
T Consensus 3 av~~~i~~~~~~vLL~~r~~~~~~~~w~~PgG~ve~gEs~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (130)
T cd04681 3 AVGVLILNEDGELLVVRRAREPGKGTLDLPGGFVDPGESAEEALIREIREETGLKVTELSYLFSLPNTYPYGGMEYDTLD 82 (130)
T ss_pred eEEEEEEcCCCcEEEEEecCCCCCCcEeCCceeecCCCCHHHHHHHHHHHHhCCcccceeEEEeecceeeeCCceeEEEE
Confidence 3444 44567899999998776678999999999999999999999999999999988887776532 211 1233
Q ss_pred EEEEEEEcCCCCCCC-CCceeEEEecCCCCCCCCCCCcHHHHHHHHHHHHH
Q 023914 216 IIFLAKLKRPHFSPG-PESSECRLFALDEIPFDSLAFSSISVTLQLVRFYF 265 (275)
Q Consensus 216 ~~f~a~~~~~e~~~~-~E~~d~~W~~~deL~~~~l~~~s~~~al~li~~~l 265 (275)
++|.+.+.++....+ +|+.+++|+++++++...+.+++.+.+++ +|+
T Consensus 83 ~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~~~~~~~---~~~ 130 (130)
T cd04681 83 LFFVCQVDDKPIVKAPDDVAELKWVVPQDIELENFAFPSIRQAVE---RWL 130 (130)
T ss_pred EEEEEEeCCCCCcCChHHhheeEEecHHHCCcccCCcHHHHHHHH---hhC
Confidence 467788765544333 78899999999999866788888887776 663
No 7
>PLN02325 nudix hydrolase
Probab=99.84 E-value=1.8e-20 Score=155.82 Aligned_cols=112 Identities=21% Similarity=0.265 Sum_probs=89.5
Q ss_pred ccccCCcEEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCC----
Q 023914 135 IAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPR---- 210 (275)
Q Consensus 135 ~~y~~p~~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~---- 210 (275)
..|+.|.++|.+++.++++|||+||...+..|.|.+|||++|.|||+++||+||++||||+++...++++..+..+
T Consensus 3 ~~~~~p~~~v~~vi~~~~~vLL~rr~~~~~~g~W~lPGG~ve~gEs~~~aa~REv~EEtGl~v~~~~~l~~~~~~~~~~~ 82 (144)
T PLN02325 3 TGEPIPRVAVVVFLLKGNSVLLGRRRSSIGDSTFALPGGHLEFGESFEECAAREVKEETGLEIEKIELLTVTNNVFLEEP 82 (144)
T ss_pred CCCCCCeEEEEEEEEcCCEEEEEEecCCCCCCeEECCceeCCCCCCHHHHHHHHHHHHHCCCCcceEEEEEecceeecCC
Confidence 4578899999999988899999999876667899999999999999999999999999999999888887654321
Q ss_pred --CCEEEEEEEEEEcCCCCC---CC-CCceeEEEecCCCCCC
Q 023914 211 --IGQIYIIFLAKLKRPHFS---PG-PESSECRLFALDEIPF 246 (275)
Q Consensus 211 --~~~~~~~f~a~~~~~e~~---~~-~E~~d~~W~~~deL~~ 246 (275)
.+...++|.+...++... .+ +|..+++||++++|+.
T Consensus 83 ~~~~~i~~~f~~~~~~~~~~~~~~e~~e~~~~~W~~~d~Lp~ 124 (144)
T PLN02325 83 KPSHYVTVFMRAVLADPSQVPQNLEPEKCYGWDWYEWDNLPE 124 (144)
T ss_pred CCcEEEEEEEEEEECCCCCCCCcCCchhcCceEEEChHHCCh
Confidence 123445677776554321 12 4567899999999994
No 8
>cd03430 GDPMH GDP-mannose glycosyl hydrolase (AKA GDP-mannose mannosyl hydrolase (GDPMH)) is a member of the Nudix hydrolase superfamily. This class of enzymes is unique from other members of the superfamily in two aspects. First, it contains a modified Nudix signature sequence. The slight changes to the conserved sequence motif, GX5EX7REUXEEXGU, where U = I, L or V), are believed to contribute to the removal of all magnesium binding sites but one, retaining only the metal site that coordinates the pyrophosphate of the substrate. Secondly, it is not a pyrophosphatase that substitutes at a phosphorus; instead, it hydrolyzes nucleotide sugars such as GDP-mannose to GDP and mannose, cleaving the phosphoglycosyl bond by substituting at a carbon position. GDP-mannose provides mannosyl components for cell wall synthesis and is required for the synthesis of other glycosyl donors (such as GDP-fucose and colitose) for the cell wall. The importance of GDP-sugar hydrolase activities is thus close
Probab=99.83 E-value=3.5e-20 Score=154.01 Aligned_cols=115 Identities=21% Similarity=0.346 Sum_probs=88.7
Q ss_pred CCcEEEEEEEee-CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccc--eeeEEEEe-------
Q 023914 139 NPKMVVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ--SPFAQLDI------- 208 (275)
Q Consensus 139 ~p~~~V~viI~~-~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~--~~~~~~~~------- 208 (275)
.|.++|.++|.+ +++|||+||...|.+|.|.+|||++|.|||+++|++||++||||+++... ++++....
T Consensus 10 ~p~v~v~~vI~~~~g~vLl~~R~~~p~~g~w~lPGG~ve~gEs~~~aa~RE~~EE~Gl~v~~~~~~~l~~~~~~~~~~~~ 89 (144)
T cd03430 10 TPLVSIDLIVENEDGQYLLGKRTNRPAQGYWFVPGGRIRKNETLTEAFERIAKDELGLEFLISDAELLGVFEHFYDDNFF 89 (144)
T ss_pred CCeEEEEEEEEeCCCeEEEEEccCCCCCCcEECCCceecCCCCHHHHHHHHHHHHHCCCcccccceEEEEEEEEeccccc
Confidence 456677777754 58999999987777899999999999999999999999999999998766 66665431
Q ss_pred -CC--CCEEEEEEEEEEcCCCCC-CCCCceeEEEecCCCCCCCCCCCcH
Q 023914 209 -PR--IGQIYIIFLAKLKRPHFS-PGPESSECRLFALDEIPFDSLAFSS 253 (275)
Q Consensus 209 -~~--~~~~~~~f~a~~~~~e~~-~~~E~~d~~W~~~deL~~~~l~~~s 253 (275)
+. .+...++|.+....+++. .++|..+++|+++++++......|.
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~ 138 (144)
T cd03430 90 GDDFSTHYVVLGYVLKLSSNELLLPDEQHSEYQWLTSDELLADDDVHPN 138 (144)
T ss_pred cCCCccEEEEEEEEEEEcCCcccCCchhccEeEEecHHHHhcCCCcCHH
Confidence 11 134567788887766543 4578999999999999865433333
No 9
>cd03429 NADH_pyrophosphatase NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity. Members of this family are also recognized by the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. A block of 8 conserved amino acids downstream of the nudix motif is thought to give NADH pyrophosphatase its specificity for NADH. NADH pyrophosphatase forms a dimer.
Probab=99.83 E-value=1.8e-20 Score=153.06 Aligned_cols=122 Identities=25% Similarity=0.300 Sum_probs=98.2
Q ss_pred EEEEEEee-CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCCEEEEEEEEE
Q 023914 143 VVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAK 221 (275)
Q Consensus 143 ~V~viI~~-~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~f~a~ 221 (275)
+|.+.+.+ ++++||++|+..+ .|.|++|||+++.|||+++||+||++||||+++..+.+++...+...+..+++|.+.
T Consensus 2 ~v~i~l~~~~~~vLL~~r~~~~-~~~w~lPgG~ie~gEt~~~aA~REl~EEtGl~~~~~~~l~~~~~~~~~~~~~~f~~~ 80 (131)
T cd03429 2 AVIVLVIDGGDRILLARQPRFP-PGMYSLLAGFVEPGESLEEAVRREVKEEVGIRVKNIRYVGSQPWPFPSSLMLGFTAE 80 (131)
T ss_pred eEEEEEEeCCCEEEEEEecCCC-CCcCcCCcccccCCCCHHHHHhhhhhhccCceeeeeEEEeecCCCCCceEEEEEEEE
Confidence 44444544 4899999998765 789999999999999999999999999999999988888887776667788889999
Q ss_pred EcCCCCCCC-CCceeEEEecCCCCCCC----CCCCcHHHHHHHHHHHHH
Q 023914 222 LKRPHFSPG-PESSECRLFALDEIPFD----SLAFSSISVTLQLVRFYF 265 (275)
Q Consensus 222 ~~~~e~~~~-~E~~d~~W~~~deL~~~----~l~~~s~~~al~li~~~l 265 (275)
...+++..+ +|+.+++|++++++... .-.++..+.+..+++.|+
T Consensus 81 ~~~~~~~~~~~E~~~~~w~~~~el~~~~~~~~~~~~~~~~~~~~~~~~~ 129 (131)
T cd03429 81 ADSGEIVVDDDELEDARWFSRDEVRAAGEGLPELPPPGSIARQLIEAWL 129 (131)
T ss_pred EcCCcccCCchhhhccEeecHHHHhhcccCCccCCCcchHHHHHHHHHh
Confidence 876665544 78889999999997642 223455666777777776
No 10
>cd04679 Nudix_Hydrolase_20 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.83 E-value=8.1e-20 Score=146.99 Aligned_cols=107 Identities=26% Similarity=0.367 Sum_probs=85.1
Q ss_pred CcEEEEEEE-eeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeC----CCCEE
Q 023914 140 PKMVVGCLI-EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP----RIGQI 214 (275)
Q Consensus 140 p~~~V~viI-~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~----~~~~~ 214 (275)
|++.|.+++ +.+++|||++|...+..|.|.+|||++|+|||+++||+||++||||+++...++++..... ..+..
T Consensus 1 ~~~~~~~~i~~~~~~vLL~~r~~~~~~~~w~lPgG~ve~gEt~~eaa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~ 80 (125)
T cd04679 1 PRVGCGAAILRDDGKLLLVKRLRAPEAGHWGIPGGKVDWMEAVEDAVVREIEEETGLSIHSTRLLCVVDHIIEEPPQHWV 80 (125)
T ss_pred CceEEEEEEECCCCEEEEEEecCCCCCCeEeCCeeeccCCCCHHHHHHHHHHHHHCCCcccceEEEEEeecccCCCCeEE
Confidence 445566555 4568999999987666799999999999999999999999999999999888887765532 23456
Q ss_pred EEEEEEEEcCCCCC--CCCCceeEEEecCCCCCC
Q 023914 215 YIIFLAKLKRPHFS--PGPESSECRLFALDEIPF 246 (275)
Q Consensus 215 ~~~f~a~~~~~e~~--~~~E~~d~~W~~~deL~~ 246 (275)
.++|.+....+... ..+|..+++|+++++++.
T Consensus 81 ~~~f~~~~~~~~~~~~~~~E~~~~~W~~~~~l~~ 114 (125)
T cd04679 81 APVYLAENFSGEPRLMEPDKLLELGWFALDALPQ 114 (125)
T ss_pred EEEEEEeecCCccccCCCccccEEEEeCHHHCCc
Confidence 67788887665432 236889999999999984
No 11
>cd03675 Nudix_Hydrolase_2 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability,
Probab=99.83 E-value=8.7e-20 Score=148.34 Aligned_cols=123 Identities=24% Similarity=0.263 Sum_probs=94.6
Q ss_pred EEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC----CEEEEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI----GQIYIIF 218 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~----~~~~~~f 218 (275)
+|++++.+++++||++|... .++.|.+|||++|+|||+++||.||++||||+++....+++.+.+..+ ....++|
T Consensus 2 ~v~~ii~~~~~vLlv~r~~~-~~~~w~~PgG~ve~gEs~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~f 80 (134)
T cd03675 2 TVAAVVERDGRFLLVEEETD-GGLVFNQPAGHLEPGESLIEAAVRETLEETGWHVEPTALLGIYQWTAPDSDTTYLRFAF 80 (134)
T ss_pred eEEEEEEECCEEEEEEEccC-CCceEECCCccCCCCCCHHHHHHHHHHHHHCcccccceEEEEEEeecCCCCeeEEEEEE
Confidence 56778888999999999876 478999999999999999999999999999999988887776654322 2345678
Q ss_pred EEEEcCCCC--CCCCCceeEEEecCCCCCCCC--CCCcHHHHHHHHHHHHHhhcc
Q 023914 219 LAKLKRPHF--SPGPESSECRLFALDEIPFDS--LAFSSISVTLQLVRFYFEHMT 269 (275)
Q Consensus 219 ~a~~~~~e~--~~~~E~~d~~W~~~deL~~~~--l~~~s~~~al~li~~~l~~~~ 269 (275)
.+.+..+.. ..++|+.++.|++.++++... +..+... +.|.+|+..++
T Consensus 81 ~~~~~~~~~~~~~~~e~~~~~w~~~~el~~~~~~~~~~~~~---~~i~~~l~~~~ 132 (134)
T cd03675 81 AAELLEHLPDQPLDSGIVRAHWLTLEEILALAARLRSPLVL---RCIEDYLAGRR 132 (134)
T ss_pred EEEECCCCCCCCCCCCceeeEEEeHHHHHhhhhhhcCchHH---HHHHHHHhcCc
Confidence 888776543 334788899999999998643 3344444 44558887643
No 12
>cd04684 Nudix_Hydrolase_25 Contains a crystal structure of the Nudix hydrolase from Enterococcus faecalis, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability
Probab=99.82 E-value=7.2e-20 Score=146.61 Aligned_cols=113 Identities=27% Similarity=0.375 Sum_probs=88.6
Q ss_pred EEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe----CC----CCEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----PR----IGQI 214 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~----~~----~~~~ 214 (275)
++.+++.++++|||++|...+.+|.|.+|||++|.||++++||+||++||||+++....+++...+ +. .+..
T Consensus 2 ~~~~ii~~~~~vLl~~~~~~~~~~~w~lPgG~ve~gE~~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (128)
T cd04684 2 GAYAVIPRDGKLLLIQKNGGPYEGRWDLPGGGIEPGESPEEALHREVLEETGLTVEIGRRLGSASRYFYSPDGDYDAHHL 81 (128)
T ss_pred eeEEEEEeCCEEEEEEccCCCCCCeEECCCcccCCCCCHHHHHHHHHHHHhCcEeecceeeeEEEEEEECCCCCeeccEE
Confidence 456667777999999999776679999999999999999999999999999999988887776543 21 1456
Q ss_pred EEEEEEEEcCCCC---CCCCCceeEEEecCCCCCCCCCCCcHHHH
Q 023914 215 YIIFLAKLKRPHF---SPGPESSECRLFALDEIPFDSLAFSSISV 256 (275)
Q Consensus 215 ~~~f~a~~~~~e~---~~~~E~~d~~W~~~deL~~~~l~~~s~~~ 256 (275)
.++|.+....+.. ..++|..+++|++++++..... .|....
T Consensus 82 ~~~f~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~~~-~~~~~~ 125 (128)
T cd04684 82 CVFYDARVVGGALPVQEPGEDSHGAAWLPLDEAIERLL-SPLVLW 125 (128)
T ss_pred EEEEEEEEecCccccCCCCCCceeeEEECHHHhhccCC-CHHHHH
Confidence 6788888876653 3447788999999999986433 344443
No 13
>PRK15434 GDP-mannose mannosyl hydrolase NudD; Provisional
Probab=99.82 E-value=1.2e-19 Score=153.64 Aligned_cols=116 Identities=16% Similarity=0.247 Sum_probs=87.4
Q ss_pred CCcEEEEEEEee-CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccc--cceeeEEEE--eC----
Q 023914 139 NPKMVVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVE--VQSPFAQLD--IP---- 209 (275)
Q Consensus 139 ~p~~~V~viI~~-~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~--~~~~~~~~~--~~---- 209 (275)
.|.++|.++|.+ +++|||+||...+..|.|++|||+||+|||+++||+||++||||+++. ..++++.+. +.
T Consensus 15 ~~~~~v~~vI~~~~g~VLL~kR~~~~~~g~W~lPGG~VE~GEt~~~Aa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~ 94 (159)
T PRK15434 15 TPLISLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFS 94 (159)
T ss_pred CceEEEEEEEECCCCEEEEEEccCCCCCCcEECCceecCCCCCHHHHHHHHHHHHHCCccccccceEEEEEEeecccccC
Confidence 345677777765 589999999876667999999999999999999999999999999874 335555322 11
Q ss_pred ----CCCEEEEEEEEEEcCCCCCCC-CCceeEEEecCCCCCCCCCCCcHH
Q 023914 210 ----RIGQIYIIFLAKLKRPHFSPG-PESSECRLFALDEIPFDSLAFSSI 254 (275)
Q Consensus 210 ----~~~~~~~~f~a~~~~~e~~~~-~E~~d~~W~~~deL~~~~l~~~s~ 254 (275)
..+.++++|.+....+++... +|..+++|+++++++......+..
T Consensus 95 ~~~~~~~~i~~~f~~~~~~g~~~~~~~E~~~~~W~~~~el~~~~~~~~~~ 144 (159)
T PRK15434 95 GTDFTTHYVVLGFRLRVAEEDLLLPDEQHDDYRWLTPDALLASDNVHANS 144 (159)
T ss_pred CCccceEEEEEEEEEEecCCcccCChHHeeEEEEEeHHHhhhccccCHHH
Confidence 113456678888877766654 689999999999998644434443
No 14
>cd03427 MTH1 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved nudix motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a m
Probab=99.81 E-value=3.4e-19 Score=145.19 Aligned_cols=124 Identities=26% Similarity=0.347 Sum_probs=95.2
Q ss_pred EEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC----CEEEEE
Q 023914 142 MVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI----GQIYII 217 (275)
Q Consensus 142 ~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~----~~~~~~ 217 (275)
++..+++.+++++||++|...+..|.|.+|||++|.||++++||+||++||||+++...++++.+.+..+ ...++.
T Consensus 2 ~~~~~~i~~~~~vLL~~r~~~~~~~~w~~PgG~ve~gEs~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (137)
T cd03427 2 LTTLCFIKDPDKVLLLNRKKGPGWGGWNGPGGKVEPGETPEECAIRELKEETGLTIDNLKLVGIIKFPFPGEEERYGVFV 81 (137)
T ss_pred eEEEEEEEECCEEEEEEecCCCCCCeEeCCceeCCCCCCHHHHHHHHHHHhhCeEeecceEEEEEEEEcCCCCcEEEEEE
Confidence 3455667777999999998766678999999999999999999999999999999998888887765433 345567
Q ss_pred EEEEEcCCCCCCCCCceeEEEecCCCCCCCCCCCcHHHHHHHHHHHHHhhcc
Q 023914 218 FLAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLVRFYFEHMT 269 (275)
Q Consensus 218 f~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s~~~al~li~~~l~~~~ 269 (275)
|.+....++....+|..+++|+++++++...+. +.....+. .+++.+.
T Consensus 82 f~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~-~~~~~~l~---~~~~~~~ 129 (137)
T cd03427 82 FLATEFEGEPLKESEEGILDWFDIDDLPLLPMW-PGDREWLP---LMLEKNL 129 (137)
T ss_pred EEECCcccccCCCCccccceEEcHhhcccccCC-CCcHHHHH---HHhCCCe
Confidence 777766665554566678999999999865554 44444444 7776443
No 15
>cd04673 Nudix_Hydrolase_15 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.81 E-value=1.6e-19 Score=143.70 Aligned_cols=108 Identities=30% Similarity=0.513 Sum_probs=85.6
Q ss_pred EEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCC--------CCEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPR--------IGQI 214 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~--------~~~~ 214 (275)
+|.+++.+++++||++|...+..+.|.+|||++++|||+++||+||++||||+++....+++...+.. .+..
T Consensus 2 ~v~~ii~~~~~vLl~~r~~~~~~~~w~~PgG~ie~gE~~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (122)
T cd04673 2 AVGAVVFRGGRVLLVRRANPPDAGLWSFPGGKVELGETLEQAALRELLEETGLEAEVGRLLTVVDVIERDAAGRVEFHYV 81 (122)
T ss_pred cEEEEEEECCEEEEEEEcCCCCCCeEECCCcccCCCCCHHHHHHHHHHHhhCcEeeeceeEEEEEEeeccCCCccceEEE
Confidence 45556666789999999876667899999999999999999999999999999988777776554321 1245
Q ss_pred EEEEEEEEcCCCCCCCCCceeEEEecCCCCCCCCCC
Q 023914 215 YIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSLA 250 (275)
Q Consensus 215 ~~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l~ 250 (275)
++.|.+....++....+|..+++|++++++....+.
T Consensus 82 ~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~~~~~ 117 (122)
T cd04673 82 LIDFLCRYLGGEPVAGDDALDARWVPLDELAALSLT 117 (122)
T ss_pred EEEEEEEeCCCcccCCcccceeEEECHHHHhhCcCC
Confidence 567888877666655688899999999999865443
No 16
>cd04691 Nudix_Hydrolase_32 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.81 E-value=2.9e-19 Score=142.96 Aligned_cols=102 Identities=25% Similarity=0.340 Sum_probs=80.9
Q ss_pred EEEEEeeCCeEEEEEeccCC--CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC-CEEEEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI-GQIYIIFLA 220 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p--~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~-~~~~~~f~a 220 (275)
|++++.++++|||+||...+ .+|.|++|||++|+||++++||+||++||||+++....++..+..+.. ...+++|.+
T Consensus 3 v~~vi~~~~~vLL~rR~~~~~~~~g~w~lPgG~ve~gE~~~~aa~REl~EEtGl~~~~~~~l~~~~~~~~~~~~~~~~~~ 82 (117)
T cd04691 3 VVGVLFSDDKVLLERRSLTKNADPGKLNIPGGHIEAGESQEEALLREVQEELGVDPLSYTYLCSLYHPTSELQLLHYYVV 82 (117)
T ss_pred EEEEEEECCEEEEEEeCCCCCCCCCeEECcceeecCCCCHHHHHHHHHHHHHCCCcccceEEEEEeccCCCeEEEEEEEE
Confidence 33344456999999997653 579999999999999999999999999999999877777776655443 345567777
Q ss_pred EEcCCCCCCCCCceeEEEecCCCCCC
Q 023914 221 KLKRPHFSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 221 ~~~~~e~~~~~E~~d~~W~~~deL~~ 246 (275)
....+.+.. +|..+++|+++++++.
T Consensus 83 ~~~~~~~~~-~E~~~~~W~~~~~l~~ 107 (117)
T cd04691 83 TFWQGEIPA-QEAAEVHWMTANDIVL 107 (117)
T ss_pred EEecCCCCc-ccccccEEcCHHHcch
Confidence 776665443 7888999999999984
No 17
>cd04696 Nudix_Hydrolase_37 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.81 E-value=3e-19 Score=143.79 Aligned_cols=108 Identities=27% Similarity=0.324 Sum_probs=83.5
Q ss_pred CcEEEEEEEee-CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeC-------CC
Q 023914 140 PKMVVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP-------RI 211 (275)
Q Consensus 140 p~~~V~viI~~-~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~-------~~ 211 (275)
|.++|.+++.+ +++|||+||.. .+|.|++|||+++.|||+++||.||++||||+++...+++....+. ..
T Consensus 1 p~~~v~~~i~~~~~~iLL~r~~~--~~~~w~lPGG~ve~gEs~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~ 78 (125)
T cd04696 1 PLVTVGALIYAPDGRILLVRTTK--WRGLWGVPGGKVEWGETLEEALKREFREETGLKLRDIKFAMVQEAIFSEEFHKPA 78 (125)
T ss_pred CccEEEEEEECCCCCEEEEEccC--CCCcEeCCceeccCCCCHHHHHHHHHHHHhCCcccccceEEEEEEeccCCCCCcc
Confidence 34566666654 78999998764 3689999999999999999999999999999999877766543221 12
Q ss_pred CEEEEEEEEEEcCCCCCCCCCceeEEEecCCCCCCCCC
Q 023914 212 GQIYIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSL 249 (275)
Q Consensus 212 ~~~~~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l 249 (275)
+.+++.|.+....+++..++|..+++|++++++...++
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~ 116 (125)
T cd04696 79 HFVLFDFFARTDGTEVTPNEEIVEWEWVTPEEALDYPL 116 (125)
T ss_pred EEEEEEEEEEecCCcccCCcccceeEEECHHHHhcCCC
Confidence 34556788887665666678899999999999985543
No 18
>cd04683 Nudix_Hydrolase_24 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.81 E-value=3.3e-19 Score=142.16 Aligned_cols=105 Identities=29% Similarity=0.388 Sum_probs=81.8
Q ss_pred EEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccc--cceeeEEEEeCC---CCEEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVE--VQSPFAQLDIPR---IGQIYI 216 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~--~~~~~~~~~~~~---~~~~~~ 216 (275)
+|.+++.++++|||+||...+ .+|.|++|||++++|||+++||+||++||||+++. .+.+++.+.... .+.+++
T Consensus 2 ~v~~vi~~~~~vLL~~r~~~~~~~~~w~lPgG~ve~gE~~~~aa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~~~~~ 81 (120)
T cd04683 2 AVYVLLRRDDEVLLQRRANTGYMDGQWALPAGHLEKGEDAVTAAVREAREEIGVTLDPEDLRLAHTMHRRTEDIESRIGL 81 (120)
T ss_pred cEEEEEEECCEEEEEEccCCCCCCCeEeCCccccCCCCCHHHHHHHHHHHHHCCccChhheEEEEEEEecCCCCceEEEE
Confidence 566777888999999987653 37899999999999999999999999999999987 556666554332 245566
Q ss_pred EEEEEEcCCCCC--CCCCceeEEEecCCCCCCC
Q 023914 217 IFLAKLKRPHFS--PGPESSECRLFALDEIPFD 247 (275)
Q Consensus 217 ~f~a~~~~~e~~--~~~E~~d~~W~~~deL~~~ 247 (275)
+|.+....+... ..+|..+++|+++++++..
T Consensus 82 ~f~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~ 114 (120)
T cd04683 82 FFTVRRWSGEPRNCEPDKCAELRWFPLDALPDD 114 (120)
T ss_pred EEEEEeecCccccCCCCcEeeEEEEchHHCcch
Confidence 777776555432 2367889999999999853
No 19
>cd04669 Nudix_Hydrolase_11 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.80 E-value=5.4e-19 Score=142.21 Aligned_cols=105 Identities=26% Similarity=0.299 Sum_probs=81.6
Q ss_pred EEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCCEEEEEEEEEEc
Q 023914 144 VGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKLK 223 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~f~a~~~ 223 (275)
++++++++++|||++|.... .+.|++|||++|.|||+++||+||++||||+++....+++.+..+ +...++|.+...
T Consensus 4 ~~ii~~~~~~vLL~~r~~~~-~~~w~lPGG~ve~gEs~~~a~~REl~EEtGl~~~~~~~~~~~~~~--~~~~~~f~~~~~ 80 (121)
T cd04669 4 SIVIINDQGEILLIRRIKPG-KTYYVFPGGGIEEGETPEEAAKREALEELGLDVRVEEIFLIVNQN--GRTEHYFLARVI 80 (121)
T ss_pred EEEEEeCCCEEEEEEEecCC-CCcEECCceeccCCCCHHHHHHHHHHHhhCeeEeeeeEEEEEeeC--CcEEEEEEEEEE
Confidence 34455555899999987543 688999999999999999999999999999999887877776653 445678888877
Q ss_pred CCCCCC----------CCCceeEEEecCCCCCCCCCCC
Q 023914 224 RPHFSP----------GPESSECRLFALDEIPFDSLAF 251 (275)
Q Consensus 224 ~~e~~~----------~~E~~d~~W~~~deL~~~~l~~ 251 (275)
++++.. +++..+++|+++++++..++.+
T Consensus 81 ~g~~~~~~~~e~~~~~~~~~~~~~Wv~~~el~~l~~~p 118 (121)
T cd04669 81 SGKLGLGVGEEFERQSDDNQYHPVWVDLDQLETIPLRP 118 (121)
T ss_pred CCeecCCCchhhcccCCCCceEEEEEEHHHcccCCCCC
Confidence 665332 2334578999999999765543
No 20
>cd04671 Nudix_Hydrolase_13 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.80 E-value=5.1e-19 Score=143.26 Aligned_cols=102 Identities=25% Similarity=0.403 Sum_probs=82.8
Q ss_pred EEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCCEEEEEEEEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKL 222 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~f~a~~ 222 (275)
+.+++++.+++|||++|...+..+.|.+|||++|.||++++||.||++||||+++...+++.....+ .+..+++|.++.
T Consensus 3 ~~~vv~~~~~~vLl~~r~~~~~~~~w~lPgG~ve~gEt~~~aa~REl~EEtG~~~~~~~~~~~~~~~-~~~~~~~f~a~~ 81 (123)
T cd04671 3 VAAVILNNQGEVLLIQEAKRSCRGKWYLPAGRMEPGETIEEAVKREVKEETGLDCEPTTLLSVEEQG-GSWFRFVFTGNI 81 (123)
T ss_pred EEEEEEcCCCEEEEEEecCCCCCCeEECceeecCCCCCHHHHHHHHHHHHHCCeeecceEEEEEccC-CeEEEEEEEEEE
Confidence 3445556689999999987666789999999999999999999999999999999888877765433 456677888988
Q ss_pred cCCCCCC----CCCceeEEEecCCCCC
Q 023914 223 KRPHFSP----GPESSECRLFALDEIP 245 (275)
Q Consensus 223 ~~~e~~~----~~E~~d~~W~~~deL~ 245 (275)
.++++.. ++|+.+++|++.++++
T Consensus 82 ~~g~~~~~~~~~~e~~~~~W~~~~el~ 108 (123)
T cd04671 82 TGGDLKTEKEADSESLQARWYSNKDLP 108 (123)
T ss_pred eCCeEccCCCCCcceEEEEEECHHHCC
Confidence 7765332 3567799999999996
No 21
>cd04678 Nudix_Hydrolase_19 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.80 E-value=7e-19 Score=142.13 Aligned_cols=108 Identities=29% Similarity=0.396 Sum_probs=85.1
Q ss_pred CcEEEEEEEee-CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe----CCCCEE
Q 023914 140 PKMVVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----PRIGQI 214 (275)
Q Consensus 140 p~~~V~viI~~-~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~----~~~~~~ 214 (275)
|.++|.+++.+ ++++||++|...+..|.|.+|||+++.|||+++|++||++||||+++...++++.... ...+..
T Consensus 1 p~~~v~~ii~~~~~~iLl~~r~~~~~~~~w~~PGG~ve~gEt~~~Aa~REl~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
T cd04678 1 PRVGVGVFVLNPKGKVLLGKRKGSHGAGTWALPGGHLEFGESFEECAAREVLEETGLHIENVQFLTVTNDVFEEEGKHYV 80 (129)
T ss_pred CceEEEEEEECCCCeEEEEeccCCCCCCeEECCcccccCCCCHHHHHHHHHHHHhCCcccceEEEEEEeEEeCCCCcEEE
Confidence 45677776655 5899999998765679999999999999999999999999999999988777765432 223456
Q ss_pred EEEEEEEEcCCCCCC----CCCceeEEEecCCCCCCC
Q 023914 215 YIIFLAKLKRPHFSP----GPESSECRLFALDEIPFD 247 (275)
Q Consensus 215 ~~~f~a~~~~~e~~~----~~E~~d~~W~~~deL~~~ 247 (275)
.++|.+....++... .+|..+++|+++++++..
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~ 117 (129)
T cd04678 81 TIFVKAEVDDGEAEPNKMEPEKCEGWEWFDWEELPSV 117 (129)
T ss_pred EEEEEEEeCCCCcccCCCCCceeCceEEeCHHHCCCc
Confidence 677888877654322 257788999999999954
No 22
>cd04700 DR1025_like DR1025 from Deinococcus radiodurans, a member of the Nudix hydrolase superfamily, show nucleoside triphosphatase and dinucleoside polyphosphate pyrophosphatase activities. Like other enzymes belonging to this superfamily, it requires a divalent cation, in this case Mg2+, for its activity. It also contains a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. In general, substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is us
Probab=99.80 E-value=6.5e-19 Score=145.85 Aligned_cols=112 Identities=22% Similarity=0.304 Sum_probs=88.6
Q ss_pred ccccCCcEEEEEEEe-eCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCC-
Q 023914 135 IAYQNPKMVVGCLIE-HDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG- 212 (275)
Q Consensus 135 ~~y~~p~~~V~viI~-~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~- 212 (275)
-+||....+|++++. .++++||++|...+.+|.|++|||++++|||+++||+||++||||+++...++++.+.+..+.
T Consensus 7 ~~~~~~~~av~~vv~~~~~~vLL~~r~~~~~~~~w~lPgG~ve~gEt~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~ 86 (142)
T cd04700 7 HHVEVEARAAGAVILNERNDVLLVQEKGGPKKGLWHIPSGAVEDGEFPQDAAVREACEETGLRVRPVKFLGTYLGRFDDG 86 (142)
T ss_pred cCcceeeeeEEEEEEeCCCcEEEEEEcCCCCCCeEECCceecCCCCCHHHHHHHHHHHhhCceeeccEEEEEEEEEcCCC
Confidence 467777788876665 477999999876666799999999999999999999999999999999888887766533222
Q ss_pred --EEEEEEEEEEcCCCC--CCCCCceeEEEecCCCCCC
Q 023914 213 --QIYIIFLAKLKRPHF--SPGPESSECRLFALDEIPF 246 (275)
Q Consensus 213 --~~~~~f~a~~~~~e~--~~~~E~~d~~W~~~deL~~ 246 (275)
...++|.+....... ...+|+.+++||+++++..
T Consensus 87 ~~~~~~~f~~~~~~~~~~~~~~~E~~~~~w~~~~el~~ 124 (142)
T cd04700 87 VLVLRHVWLAEPEGQTLAPKFTDEIAEASFFSREDVAQ 124 (142)
T ss_pred cEEEEEEEEEEecCCccccCCCCCEEEEEEECHHHhhh
Confidence 334678888765432 3347899999999999884
No 23
>PRK15472 nucleoside triphosphatase NudI; Provisional
Probab=99.79 E-value=9.1e-19 Score=144.11 Aligned_cols=110 Identities=24% Similarity=0.284 Sum_probs=79.3
Q ss_pred cEEEEEEEeeCCeEEEEEeccCC--CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeE--------EEEeCC
Q 023914 141 KMVVGCLIEHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFA--------QLDIPR 210 (275)
Q Consensus 141 ~~~V~viI~~~~~iLL~rr~~~p--~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~--------~~~~~~ 210 (275)
..++++++.++++|||+||+..+ .+|.|++|||++|+|||+++||.||++||||+++....... ...++.
T Consensus 4 r~~~~~ii~~~~~vLl~~R~~~~~~~~g~W~lPgG~ve~gEs~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~ 83 (141)
T PRK15472 4 RTIVCPLIQNDGAYLLCKMADDRGVFPGQWALSGGGVEPGERIEEALRREIREELGEQLLLTEITPWTFRDDIRTKTYAD 83 (141)
T ss_pred eeEEEEEEecCCEEEEEEecccCCCCCCceeCCcccCCCCCCHHHHHHHHHHHHHCCceeeeeeccccccccceeEEecC
Confidence 45667777788999999987542 46999999999999999999999999999999874332110 111222
Q ss_pred CC--EE---EEEEEEEEcCCCCCCCCCceeEEEecCCCCCCCCCC
Q 023914 211 IG--QI---YIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSLA 250 (275)
Q Consensus 211 ~~--~~---~~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l~ 250 (275)
.. .. +++|.+....+++.+++|..+++|++++|++...+.
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~l~~~ 128 (141)
T PRK15472 84 GRKEEIYMIYLIFDCVSANRDVKINEEFQDYAWVKPEDLVHYDLN 128 (141)
T ss_pred CCceeEEEEEEEEEeecCCCcccCChhhheEEEccHHHhcccccc
Confidence 21 22 233445545555666789999999999999965443
No 24
>cd04687 Nudix_Hydrolase_28 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.79 E-value=1.1e-18 Score=141.16 Aligned_cols=108 Identities=27% Similarity=0.294 Sum_probs=82.1
Q ss_pred EEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe----------CCC
Q 023914 142 MVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----------PRI 211 (275)
Q Consensus 142 ~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~----------~~~ 211 (275)
+.+.+++.++++|||++|.... .+.|.+|||++|.|||+++||.||++||||+++...+++....+ ...
T Consensus 2 ~~a~~iv~~~~~vLl~~r~~~~-~~~~~lPGG~ve~gEt~~~aa~RE~~EEtGl~v~~~~~~~~~~~~~~~~~~~~~~~~ 80 (128)
T cd04687 2 NSAKAVIIKNDKILLIKHHDDG-GVWYILPGGGQEPGETLEDAAHRECKEEIGIDVEIGPLLFVREYIGHNPTSELPGHF 80 (128)
T ss_pred cEEEEEEEECCEEEEEEEEcCC-CCeEECCCcccCCCCCHHHHHHHHHHHHHCCccccCcEEEEEEEeccCccccCCCce
Confidence 4556666778999999997543 57899999999999999999999999999999877665544332 123
Q ss_pred CEEEEEEEEEEcCCCC-----CCCCCceeEEEecCCCCCCCCCC
Q 023914 212 GQIYIIFLAKLKRPHF-----SPGPESSECRLFALDEIPFDSLA 250 (275)
Q Consensus 212 ~~~~~~f~a~~~~~e~-----~~~~E~~d~~W~~~deL~~~~l~ 250 (275)
+..+++|.+....+.. .+++|..+++|+++++++...+.
T Consensus 81 ~~i~~~f~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~l~~~~~~ 124 (128)
T cd04687 81 HQVELMFECKIKSGTPAKTPSKPDPNQIGVEWLKLKELGDIPLY 124 (128)
T ss_pred eEEEEEEEEEECCCCcccccCCCCCCEEeeEEEcHHHhCccccc
Confidence 4566788888876542 23445568999999999865543
No 25
>cd04680 Nudix_Hydrolase_21 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.79 E-value=9.9e-19 Score=138.85 Aligned_cols=98 Identities=30% Similarity=0.401 Sum_probs=80.3
Q ss_pred EEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccc-cceeeEEEEeCC--CCEEEEEEEEEE
Q 023914 146 CLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVE-VQSPFAQLDIPR--IGQIYIIFLAKL 222 (275)
Q Consensus 146 viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~-~~~~~~~~~~~~--~~~~~~~f~a~~ 222 (275)
++++.++++||++|+.. +.|.+|||++++|||+++||+||++||||+.+. ....++.+.... ....+++|.+..
T Consensus 6 ~i~~~~~~vLL~~r~~~---~~w~~PgG~ve~gEt~~~aa~REl~EEtG~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~ 82 (120)
T cd04680 6 VVTDADGRVLLVRHTYG---PGWYLPGGGLERGETFAEAARRELLEELGIRLAVVAELLGVYYHSASGSWDHVIVFRARA 82 (120)
T ss_pred EEECCCCeEEEEEECCC---CcEeCCCCcCCCCCCHHHHHHHHHHHHHCCccccccceEEEEecCCCCCceEEEEEEecc
Confidence 34456789999998743 489999999999999999999999999999998 888888766543 346677888888
Q ss_pred cCCC-CCCCCCceeEEEecCCCCCC
Q 023914 223 KRPH-FSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 223 ~~~e-~~~~~E~~d~~W~~~deL~~ 246 (275)
..++ ...++|..+++|+++++++.
T Consensus 83 ~~~~~~~~~~E~~~~~w~~~~~l~~ 107 (120)
T cd04680 83 DTQPVIRPSHEISEARFFPPDALPE 107 (120)
T ss_pred cCCCccCCcccEEEEEEECHHHCcc
Confidence 7665 33458889999999999995
No 26
>cd04672 Nudix_Hydrolase_14 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.79 E-value=1.1e-18 Score=140.28 Aligned_cols=104 Identities=38% Similarity=0.568 Sum_probs=83.0
Q ss_pred CcEEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeC---C---C-C
Q 023914 140 PKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP---R---I-G 212 (275)
Q Consensus 140 p~~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~---~---~-~ 212 (275)
|.+.|.+++.+++++||++|+. .|.|.+|||++++|||+++||+||++||||+++....+++..... . . +
T Consensus 1 p~~~v~~~i~~~~~vLL~~~~~---~~~w~~PGG~ve~gEs~~~aa~REl~EEtG~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (123)
T cd04672 1 PKVDVRAAIFKDGKILLVREKS---DGLWSLPGGWADVGLSPAENVVKEVKEETGLDVKVRKLAAVDDRNKHHPPPQPYQ 77 (123)
T ss_pred CcceEEEEEEECCEEEEEEEcC---CCcEeCCccccCCCCCHHHHHHHHHHHHhCCeeeEeEEEEEeccccccCCCCceE
Confidence 4566777777779999999874 689999999999999999999999999999998776766654321 1 1 2
Q ss_pred EEEEEEEEEEcCCCCCCCCCceeEEEecCCCCCC
Q 023914 213 QIYIIFLAKLKRPHFSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 213 ~~~~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~ 246 (275)
...++|.+....+.+...+|..+++|+++++++.
T Consensus 78 ~~~~~f~~~~~~~~~~~~~E~~~~~W~~~~el~~ 111 (123)
T cd04672 78 VYKLFFLCEILGGEFKPNIETSEVGFFALDDLPP 111 (123)
T ss_pred EEEEEEEEEecCCcccCCCceeeeEEECHHHCcc
Confidence 3456788887766666668889999999999984
No 27
>cd03673 Ap6A_hydrolase Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most preferred substrate, hydrolyzes to produce two ATP molecules, which is a novel hydrolysis mode for Ap6A. These results indicate that Ap6A hydrolase is a diadenosine polyphosphate hydrolase. It requires the presence of a divalent cation, such as Mn2+, Mg2+, Zn2+, and Co2+, for activity. Members of the Nudix superfamily are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site.
Probab=99.78 E-value=1.2e-18 Score=140.06 Aligned_cols=104 Identities=28% Similarity=0.371 Sum_probs=84.0
Q ss_pred CeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC------CEEEEEEEEEEcCC
Q 023914 152 KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI------GQIYIIFLAKLKRP 225 (275)
Q Consensus 152 ~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~------~~~~~~f~a~~~~~ 225 (275)
++|||++|.. .+.|.+|||++++|||+++||.||++||||+++.....++.+.++.+ ...+++|.+....+
T Consensus 16 ~~vLl~~~~~---~~~w~~PgG~v~~gEs~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (131)
T cd03673 16 IEVLLIHRPR---GDDWSLPKGKLEPGETPPEAAVREVEEETGIRAEVGDPLGTIRYWFSSSGKRVHKTVHWWLMRALGG 92 (131)
T ss_pred eEEEEEEcCC---CCcccCCCCccCCCCCHHHHHHHHHhhhhCCceEecceEEEEEEeccCCCCCcceEEEEEEEEEcCC
Confidence 8999999874 37899999999999999999999999999999988888776655332 35566788877666
Q ss_pred CCC--CCCCceeEEEecCCCCCCCCCCCcHHHHHHH
Q 023914 226 HFS--PGPESSECRLFALDEIPFDSLAFSSISVTLQ 259 (275)
Q Consensus 226 e~~--~~~E~~d~~W~~~deL~~~~l~~~s~~~al~ 259 (275)
+.. .++|..+++|++++++.. .+.++..+.++.
T Consensus 93 ~~~~~~~~E~~~~~W~~~~el~~-~~~~~~~~~~l~ 127 (131)
T cd03673 93 EFTPQPDEEVDEVRWLPPDEARD-RLSYPNDRELLR 127 (131)
T ss_pred CcccCCCCcEEEEEEcCHHHHHH-HcCCHhHHHHHH
Confidence 655 458889999999999985 355777776665
No 28
>cd03674 Nudix_Hydrolase_1 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamil
Probab=99.77 E-value=3.2e-18 Score=140.75 Aligned_cols=104 Identities=28% Similarity=0.398 Sum_probs=76.8
Q ss_pred EEEEEEeeC-CeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeE------EEE---eCC--
Q 023914 143 VVGCLIEHD-KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFA------QLD---IPR-- 210 (275)
Q Consensus 143 ~V~viI~~~-~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~------~~~---~~~-- 210 (275)
+.+++++++ ++|||++|+. .|.|.+|||++|+||++++||.||++||||+++......+ ... .+.
T Consensus 5 ~~~~v~~~~~~~vLLv~r~~---~~~w~lPgG~ve~gE~~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (138)
T cd03674 5 ASAFVVNPDRGKVLLTHHRK---LGSWLQPGGHIDPDESLLEAALRELREETGIELLGLRPLSVLVDLDVHPIDGHPKRG 81 (138)
T ss_pred EEEEEEeCCCCeEEEEEEcC---CCcEECCceecCCCCCHHHHHHHHHHHHHCCCcccceeccccccceeEeecCCCCCC
Confidence 334444555 8999999874 5889999999999999999999999999999886665432 111 111
Q ss_pred ---CCEEEEEEEEEEcCCCCC--CCCCceeEEEecCCCCCCCCC
Q 023914 211 ---IGQIYIIFLAKLKRPHFS--PGPESSECRLFALDEIPFDSL 249 (275)
Q Consensus 211 ---~~~~~~~f~a~~~~~e~~--~~~E~~d~~W~~~deL~~~~l 249 (275)
...+.++|.+....++.. .++|..+++|++++++....+
T Consensus 82 ~~~~~~~~~~y~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~ 125 (138)
T cd03674 82 VPGHLHLDLRFLAVAPADDVAPPKSDESDAVRWFPLDELASLEL 125 (138)
T ss_pred CCCcEEEEEEEEEEccCccccCCCCCcccccEEEcHHHhhhccC
Confidence 123446788887666544 457889999999999975444
No 29
>cd04682 Nudix_Hydrolase_23 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.77 E-value=1.9e-18 Score=138.71 Aligned_cols=108 Identities=27% Similarity=0.302 Sum_probs=81.8
Q ss_pred EEEEEEeeCCeEEEEEeccCC---CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccce--eeEEEEeCCCCEEEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEP---SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQS--PFAQLDIPRIGQIYII 217 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p---~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~--~~~~~~~~~~~~~~~~ 217 (275)
++++++.++++|||++|...| .+|.|++|||+++.||++++||.||++||||+++.... +...+..+.....+++
T Consensus 3 v~~~~~~~~g~vLl~~r~~~~~~~~~g~w~~PgG~ve~gE~~~~aa~RE~~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~~ 82 (122)
T cd04682 3 VALALLIGDGRLLLQLRDDKPGIPYPGHWDLPGGHREGGETPLECVLRELLEEIGLTLPESRIPWFRVYPSASPPGTEHV 82 (122)
T ss_pred eEEEEEEcCCEEEEEEccCCCCCCCCCcEeCCCccccCCCCHHHHHHHHHHHHhCCcccccccceeEecccCCCCceEEE
Confidence 344455566999999998653 46999999999999999999999999999999986433 3333333344567778
Q ss_pred EEEEEcCCC--CCCCCCceeEEEecCCCCCCCCCC
Q 023914 218 FLAKLKRPH--FSPGPESSECRLFALDEIPFDSLA 250 (275)
Q Consensus 218 f~a~~~~~e--~~~~~E~~d~~W~~~deL~~~~l~ 250 (275)
|.+...... ....+|+.+++|++++++......
T Consensus 83 f~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~~ 117 (122)
T cd04682 83 FVVPLTAREDAILFGDEGQALRLMTVEEFLAHEDA 117 (122)
T ss_pred EEEEEecCCCccccCchhheeecccHHHHhhcccc
Confidence 888877653 234588999999999998765443
No 30
>PRK09438 nudB dihydroneopterin triphosphate pyrophosphatase; Provisional
Probab=99.76 E-value=2.2e-18 Score=142.91 Aligned_cols=125 Identities=21% Similarity=0.189 Sum_probs=86.8
Q ss_pred ccCCcEEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCcc--ccceeeEE-----EE--
Q 023914 137 YQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADV--EVQSPFAQ-----LD-- 207 (275)
Q Consensus 137 y~~p~~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v--~~~~~~~~-----~~-- 207 (275)
|..+..+++++++.+++|||++|... +|.|++|||++|.|||+++||+||++||||+++ ....+++. +.
T Consensus 4 ~~~~~~v~~vi~~~~~~vLl~~r~~~--~~~W~lPgG~ve~gEs~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~ 81 (148)
T PRK09438 4 YKRPVSVLVVIYTPDLGVLMLQRADD--PDFWQSVTGSLEEGETPAQTAIREVKEETGIDVLAEQLTLIDCQRSIEYEIF 81 (148)
T ss_pred ccCceEEEEEEEeCCCeEEEEEecCC--CCcEeCCcccCCCCCCHHHHHHHHHHHHhCcCccccceeecccccccccccc
Confidence 44444555556667889999988643 578999999999999999999999999999998 44333221 00
Q ss_pred ------eC--CCCEEEEEEEEEEcCCCCCCCCCceeEEEecCCCCCCCCCCCcHHHHHHHHHHHHHhh
Q 023914 208 ------IP--RIGQIYIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLVRFYFEH 267 (275)
Q Consensus 208 ------~~--~~~~~~~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s~~~al~li~~~l~~ 267 (275)
++ ..+...++|.+....+.....+|..+++|++++++.... ..++.+.+++ .+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~E~~~~~W~~~~e~~~~~-~~~~~~~~l~---~~~~~ 145 (148)
T PRK09438 82 PHWRHRYAPGVTRNTEHWFCLALPHERPVVLTEHLAYQWLDAREAAALT-KSWSNAEAIE---QLVIR 145 (148)
T ss_pred hhhhhccccccCCceeEEEEEecCCCCccccCcccceeeCCHHHHHHHh-cChhHHHHHH---HHHHH
Confidence 01 113456778887655432223588999999999998543 3566666555 55543
No 31
>cd04690 Nudix_Hydrolase_31 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.76 E-value=4.1e-18 Score=135.26 Aligned_cols=103 Identities=24% Similarity=0.385 Sum_probs=81.3
Q ss_pred EEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCcccc--ceeeEEEEeCC---C--CEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEV--QSPFAQLDIPR---I--GQIY 215 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~--~~~~~~~~~~~---~--~~~~ 215 (275)
+++++++.++++||+||+ ..+.|.+|||++++||++++||+||++||||+++.. ++.++.+..+. . ....
T Consensus 3 ~~~~v~~~~~~vLl~~r~---~~~~w~~PgG~ve~~Es~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (118)
T cd04690 3 AAALILVRDGRVLLVRKR---GTDVFYLPGGKIEAGETPLQALIRELSEELGLDLDPDSLEYLGTFRAPAANEPGVDVRA 79 (118)
T ss_pred EEEEEEecCCeEEEEEEC---CCCcEECCCCccCCCCCHHHHHHHHHHHHHCCccChhheEEEEEEecccccCCCcEEEE
Confidence 455566777899999987 357899999999999999999999999999999877 77777665431 1 3456
Q ss_pred EEEEEEEcCCCCCCCCCceeEEEecCCCCCCCCC
Q 023914 216 IIFLAKLKRPHFSPGPESSECRLFALDEIPFDSL 249 (275)
Q Consensus 216 ~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l 249 (275)
++|.+.... .+...+|..+++|+++++++...+
T Consensus 80 ~~f~~~~~~-~~~~~~e~~~~~W~~~~e~~~~~~ 112 (118)
T cd04690 80 TVYVAELTG-EPVPAAEIEEIRWVDYDDPADDRL 112 (118)
T ss_pred EEEEEcccC-CcCCCchhhccEEecHHHcccccc
Confidence 778887655 455567889999999999875444
No 32
>cd03424 ADPRase_NUDT5 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue Nudix motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the Nudix motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirem
Probab=99.76 E-value=6.8e-18 Score=137.69 Aligned_cols=124 Identities=24% Similarity=0.238 Sum_probs=91.6
Q ss_pred CcEEEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeC--CCCEEEE
Q 023914 140 PKMVVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP--RIGQIYI 216 (275)
Q Consensus 140 p~~~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~--~~~~~~~ 216 (275)
+..+++++++.++++||++|.+.+ .++.|++|||++|.||++++||+||++||||+.+..+.+++.+... .....+.
T Consensus 2 ~~~v~v~~~~~~~~iLl~~~~~~~~~~~~w~~PgG~ve~gEs~~~aa~RE~~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~ 81 (137)
T cd03424 2 PDAVAVLPYDDDGKVVLVRQYRPPVGGWLLELPAGLIDPGEDPEEAARRELEEETGYEAGDLEKLGSFYPSPGFSDERIH 81 (137)
T ss_pred CCEEEEEEEcCCCeEEEEEeeecCCCCEEEEeCCccCCCCCCHHHHHHHHHHHHHCCCccceEEEeeEecCCcccCccEE
Confidence 445566666777999999887655 3578999999999999999999999999999999877777765432 2234566
Q ss_pred EEEEEEcCCC--CCC-CCCceeEEEecCCCCCC----CCCCCcHHHHHHHHHHHHHh
Q 023914 217 IFLAKLKRPH--FSP-GPESSECRLFALDEIPF----DSLAFSSISVTLQLVRFYFE 266 (275)
Q Consensus 217 ~f~a~~~~~e--~~~-~~E~~d~~W~~~deL~~----~~l~~~s~~~al~li~~~l~ 266 (275)
+|.+...... ... ++|..+++|++++++.. ..+..+....++. .|++
T Consensus 82 ~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~~~~~~~~~~~~~~~~~~---~~~~ 135 (137)
T cd03424 82 LFLAEDLSPGEEGLLDEGEDIEVVLVPLDEALELLADGEIIDDATLIALL---LWLA 135 (137)
T ss_pred EEEEEcccccccCCCCCCCeeEEEEecHHHHHHHHHcCCCcccHHHHHHH---HHHH
Confidence 7888876654 223 47889999999999864 2344455555444 5654
No 33
>cd04688 Nudix_Hydrolase_29 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.75 E-value=1.1e-17 Score=134.77 Aligned_cols=105 Identities=25% Similarity=0.277 Sum_probs=82.4
Q ss_pred EEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe----CC--CCEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----PR--IGQIYII 217 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~----~~--~~~~~~~ 217 (275)
|.+++.++++|||+|+.. .+.|.+|||++|.||++++||.||++||||+++...++++.... .. .+...++
T Consensus 4 v~~vi~~~~~vLl~~~~~---~~~w~lPgG~ve~gEs~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (126)
T cd04688 4 AAAIIIHNGKLLVQKNPD---ETFYRPPGGGIEFGESSEEALIREFKEELGLKIEITRLLGVVENIFTYNGKPGHEIEFY 80 (126)
T ss_pred EEEEEEECCEEEEEEeCC---CCeEECCCccccCCCCHHHHHHHHHHHHhCCceecceeeEEEEEeeccCCcccEEEEEE
Confidence 445555677999999874 57899999999999999999999999999999988887776432 11 2345678
Q ss_pred EEEEEcCCCCC--------CCCCceeEEEecCCCCCCCCCCC
Q 023914 218 FLAKLKRPHFS--------PGPESSECRLFALDEIPFDSLAF 251 (275)
Q Consensus 218 f~a~~~~~e~~--------~~~E~~d~~W~~~deL~~~~l~~ 251 (275)
|.+...++... .++|..+++|++++++...++.+
T Consensus 81 f~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~~~~p 122 (126)
T cd04688 81 YLVTLLDESLYQQDIEILEEEGEKIVFRWIPIDELKEIKLYP 122 (126)
T ss_pred EEEEeCCCcccccccceeccCCCEEEEEEeeHHHcccCccCC
Confidence 88988776543 23688899999999999766544
No 34
>PRK10546 pyrimidine (deoxy)nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=99.75 E-value=2.3e-17 Score=134.03 Aligned_cols=121 Identities=26% Similarity=0.260 Sum_probs=88.7
Q ss_pred EEEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCC--EEEEEE
Q 023914 142 MVVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIF 218 (275)
Q Consensus 142 ~~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~--~~~~~f 218 (275)
.++.+++.++++|||++|.... .+|+|++|||++|.||++++|+.||++||||+++....+++...+.+.+ ..+++|
T Consensus 5 ~~~~~ii~~~~~vLL~~R~~~~~~~g~w~~PgG~ve~gE~~~~a~~RE~~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (135)
T PRK10546 5 DVVAAIIERDGKILLAQRPAHSDQAGLWEFAGGKVEPGESQPQALIRELREELGIEATVGEYVASHQREVSGRRIHLHAW 84 (135)
T ss_pred EEEEEEEecCCEEEEEEccCCCCCCCcEECCcccCCCCCCHHHHHHHHHHHHHCCccccceeEEEEEEecCCcEEEEEEE
Confidence 3455666788999999987543 4799999999999999999999999999999998877777666554433 345567
Q ss_pred EEEEcCCCCCCCCCceeEEEecCCCCCCCCCCCcHHHHHHHHHHHHHhh
Q 023914 219 LAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLVRFYFEH 267 (275)
Q Consensus 219 ~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s~~~al~li~~~l~~ 267 (275)
.+....+++. ..|..+++|+++++++...+. +..+..++ .|++.
T Consensus 85 ~~~~~~~~~~-~~e~~~~~W~~~~el~~~~~~-~~~~~~l~---~~~~~ 128 (135)
T PRK10546 85 HVPDFHGELQ-AHEHQALVWCTPEEALRYPLA-PADIPLLE---AFMAL 128 (135)
T ss_pred EEEEecCccc-ccccceeEEcCHHHcccCCCC-cCcHHHHH---HHHHh
Confidence 6665544432 246678999999999865443 44444444 66654
No 35
>cd04677 Nudix_Hydrolase_18 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.75 E-value=1.6e-17 Score=134.10 Aligned_cols=104 Identities=31% Similarity=0.435 Sum_probs=75.0
Q ss_pred CcEEEEEEE-eeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEE----eC--CCC
Q 023914 140 PKMVVGCLI-EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD----IP--RIG 212 (275)
Q Consensus 140 p~~~V~viI-~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~----~~--~~~ 212 (275)
+.+++.+++ +.++++||++|.. .|.|.+|||+|++|||+++||.||++||||+++.....++.+. +. ...
T Consensus 6 ~~~~~~~~v~~~~~~vLL~~r~~---~~~w~~PgG~v~~gEt~~~aa~REl~EE~Gi~~~~~~~~~~~~~~~~~~~~~~~ 82 (132)
T cd04677 6 ILVGAGVILLNEQGEVLLQKRSD---TGDWGLPGGAMELGESLEETARRELKEETGLEVEELELLGVYSGKEFYVKPNGD 82 (132)
T ss_pred cccceEEEEEeCCCCEEEEEecC---CCcEECCeeecCCCCCHHHHHHHHHHHHhCCeeeeeEEEEEecCCceeecCCCC
Confidence 344555444 5568999999874 3789999999999999999999999999999998877765432 11 111
Q ss_pred ----EEEEEEEEEEcCCCCC-CCCCceeEEEecCCCCCC
Q 023914 213 ----QIYIIFLAKLKRPHFS-PGPESSECRLFALDEIPF 246 (275)
Q Consensus 213 ----~~~~~f~a~~~~~e~~-~~~E~~d~~W~~~deL~~ 246 (275)
..+++|.+....+.+. ..+|..+++|+++++++.
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~e~~~ 121 (132)
T cd04677 83 DEQYIVTLYYVTKVFGGKLVPDGDETLELKFFSLDELPE 121 (132)
T ss_pred cEEEEEEEEEEEeccCCcccCCCCceeeEEEEChhHCcc
Confidence 2234444544444433 447888999999999984
No 36
>cd04664 Nudix_Hydrolase_7 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate s
Probab=99.75 E-value=5.8e-18 Score=136.86 Aligned_cols=114 Identities=23% Similarity=0.168 Sum_probs=85.2
Q ss_pred cEEEEEEEee--CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEE------eCC--
Q 023914 141 KMVVGCLIEH--DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD------IPR-- 210 (275)
Q Consensus 141 ~~~V~viI~~--~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~------~~~-- 210 (275)
+.+.+++.+. ++++||+||... .+|.|.+|||+++.||++++||.||++||||+.+....++.... +..
T Consensus 2 ~~~~v~~~~~~~~~~vLL~~r~~~-~~~~w~~PgG~ve~~Es~~~aa~RE~~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~ 80 (129)
T cd04664 2 RSVLVVPYRLTGEGRVLLLRRSDK-YAGFWQSVTGGIEDGESPAEAARREVAEETGLDPERLTLLDRGASIAFVEFTDNG 80 (129)
T ss_pred cEEEEEEEEeCCCCEEEEEEeCCC-CCCcccccCcccCCCCCHHHHHHHHHHHHHCCChhheEEEeecccccccccCCCc
Confidence 3455555566 799999999876 57999999999999999999999999999999986666555332 222
Q ss_pred CCEEEEEEEEEEcCCC-CCCCCCceeEEEecCCCCCCCCCCCcHHHH
Q 023914 211 IGQIYIIFLAKLKRPH-FSPGPESSECRLFALDEIPFDSLAFSSISV 256 (275)
Q Consensus 211 ~~~~~~~f~a~~~~~e-~~~~~E~~d~~W~~~deL~~~~l~~~s~~~ 256 (275)
.+...++|.+...... ...++|..++.|++++++... +.+++.+.
T Consensus 81 ~~~~~~~f~~~~~~~~~~~~~~E~~~~~W~~~~e~~~~-~~~~~~~~ 126 (129)
T cd04664 81 RVWTEHPFAFHLPSDAVVTLDWEHDAFEWVPPEEAAAL-LLWESNRR 126 (129)
T ss_pred eEEEEeEEEEEcCCCCcccCCccccccEecCHHHHHHH-HcChhhhh
Confidence 1245677888876654 344578889999999998742 34555444
No 37
>cd04689 Nudix_Hydrolase_30 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate sp
Probab=99.74 E-value=1.2e-17 Score=134.33 Aligned_cols=102 Identities=18% Similarity=0.223 Sum_probs=78.8
Q ss_pred EEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe--CC----CCEEE
Q 023914 142 MVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI--PR----IGQIY 215 (275)
Q Consensus 142 ~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~--~~----~~~~~ 215 (275)
..|.+++.+++++||+++. ..+.|.+|||++|+|||+++||.||++||||+++...++++.... .. .+..+
T Consensus 2 ~~~~~vi~~~~~vLlv~~~---~~~~~~lPGG~ve~gEt~~~aa~REl~EEtGl~~~~~~~l~~~~~~~~~~~~~~~~~~ 78 (125)
T cd04689 2 LRARAIVRAGNKVLLARVI---GQPHYFLPGGHVEPGETAENALRRELQEELGVAVSDGRFLGAIENQWHEKGVRTHEIN 78 (125)
T ss_pred eEEEEEEEeCCEEEEEEec---CCCCEECCCCcCCCCCCHHHHHHHHHHHHhCceeeccEEEEEEeeeeccCCceEEEEE
Confidence 3456666788999999986 357899999999999999999999999999999988887775542 11 12455
Q ss_pred EEEEEEEcCCC----CCCCCCceeEEEecCCCCCC
Q 023914 216 IIFLAKLKRPH----FSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 216 ~~f~a~~~~~e----~~~~~E~~d~~W~~~deL~~ 246 (275)
++|.+....+. ...++|+.+++|++++++..
T Consensus 79 ~~f~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~ 113 (125)
T cd04689 79 HIFAVESSWLASDGPPQADEDHLSFSWVPVSDLSL 113 (125)
T ss_pred EEEEEEcccccccCCccCccceEEEEEccHHHccc
Confidence 67887765432 22346788999999999873
No 38
>PRK05379 bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional
Probab=99.74 E-value=2e-17 Score=155.81 Aligned_cols=111 Identities=25% Similarity=0.434 Sum_probs=88.2
Q ss_pred cccCCcEEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeE------EEEeC
Q 023914 136 AYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFA------QLDIP 209 (275)
Q Consensus 136 ~y~~p~~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~------~~~~~ 209 (275)
-||.+.++|.+++.++++|||++|...|..|.|.+|||++|+|||+++||+||++||||+++....+.+ .++.+
T Consensus 198 ~~~~~~vtv~avv~~~g~VLLvrR~~~p~~g~W~lPGG~ve~gEt~~~Aa~REl~EETGl~v~~~~l~~~~~~~~~f~~p 277 (340)
T PRK05379 198 PYPPTFVTVDAVVVQSGHVLLVRRRAEPGKGLWALPGGFLEQDETLLDACLRELREETGLKLPEPVLRGSIRDQQVFDHP 277 (340)
T ss_pred CCCCcceEEEEEEEECCEEEEEEecCCCCCCeEECCcccCCCCCCHHHHHHHHHHHHHCCcccccccceeeeeeEEEcCC
Confidence 366677888888888999999999987778999999999999999999999999999999986554332 22233
Q ss_pred C----CCEEEEEEEEEEcCCC---CCCCCCceeEEEecCCCCCC
Q 023914 210 R----IGQIYIIFLAKLKRPH---FSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 210 ~----~~~~~~~f~a~~~~~e---~~~~~E~~d~~W~~~deL~~ 246 (275)
. .+...++|.+....++ +..++|..+++|++.+++..
T Consensus 278 ~r~~~~~~i~~~f~~~~~~~~~~~~~~~de~~~~~W~~~~el~~ 321 (340)
T PRK05379 278 GRSLRGRTITHAFLFEFPAGELPRVKGGDDADKARWVPLAELLA 321 (340)
T ss_pred CCCCCCcEEEEEEEEEecCCccCccCCCCceeeEEEEEHHHhhh
Confidence 2 2456677888776543 34568889999999999985
No 39
>PRK10776 nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=99.73 E-value=8.3e-17 Score=128.78 Aligned_cols=106 Identities=23% Similarity=0.342 Sum_probs=78.9
Q ss_pred EEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCC--EEEEEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIFL 219 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~--~~~~~f~ 219 (275)
+++++++.++++||.||+..+ ..|+|++|||++++||++++|+.||++||+|+++....+++...+.+++ ..+.+|.
T Consensus 7 ~~~ii~~~~~~vll~rR~~~~~~~g~w~~PgG~~~~gE~~~~a~~Re~~EE~gl~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (129)
T PRK10776 7 AVGIIRNPNNEIFITRRAADAHMAGKWEFPGGKIEAGETPEQALIRELQEEVGITVQHATLFEKLEYEFPDRHITLWFWL 86 (129)
T ss_pred EEEEEECCCCEEEEEEecCCCCCCCeEECCceecCCCCCHHHHHHHHHHHHHCCceecceEEEEEEeeCCCcEEEEEEEE
Confidence 344444556799999998765 3799999999999999999999999999999998777766665554443 3345566
Q ss_pred EEEcCCCCCCCCCceeEEEecCCCCCCCCC
Q 023914 220 AKLKRPHFSPGPESSECRLFALDEIPFDSL 249 (275)
Q Consensus 220 a~~~~~e~~~~~E~~d~~W~~~deL~~~~l 249 (275)
+....+.. ...|..+++|++.++++...+
T Consensus 87 ~~~~~~~~-~~~e~~~~~W~~~~~l~~~~~ 115 (129)
T PRK10776 87 VESWEGEP-WGKEGQPGRWVSQVALNADEF 115 (129)
T ss_pred EEEECCcc-CCccCCccEEecHHHCccCCC
Confidence 65543332 235677889999999996443
No 40
>cd04670 Nudix_Hydrolase_12 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.73 E-value=2.1e-17 Score=133.31 Aligned_cols=103 Identities=23% Similarity=0.390 Sum_probs=74.7
Q ss_pred EEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeC-C-CCEEEEEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP-R-IGQIYIIFLAK 221 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~-~-~~~~~~~f~a~ 221 (275)
++++++.+++|||++|+.. .+|.|.+|||++|.|||+++||.||++||||+++....+++...+. . .....+.|.+.
T Consensus 6 ~~~v~~~~~~vLl~~r~~~-~~~~w~~PGG~ve~gEt~~~aa~RE~~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (127)
T cd04670 6 GGLVLNEKNEVLVVQERNK-TPNGWKLPGGLVDPGEDIFDGAVREVLEETGIDTEFVSVVGFRHAHPGAFGKSDLYFICR 84 (127)
T ss_pred EEEEEcCCCeEEEEEccCC-CCCcEECCCccCCCCCCHHHHHHHHHHHHHCCCcceeEEEEEEecCCCCcCceeEEEEEE
Confidence 3445566789999998755 4789999999999999999999999999999999877766644321 1 11222334555
Q ss_pred EcC--CCCCC-CCCceeEEEecCCCCCCC
Q 023914 222 LKR--PHFSP-GPESSECRLFALDEIPFD 247 (275)
Q Consensus 222 ~~~--~e~~~-~~E~~d~~W~~~deL~~~ 247 (275)
+.. .++.. .+|..+++|++++++...
T Consensus 85 ~~~~~~~~~~~~~E~~~~~w~~~~el~~~ 113 (127)
T cd04670 85 LKPLSFDINFDTSEIAAAKWMPLEEYISQ 113 (127)
T ss_pred EccCcCcCCCChhhhheeEEEcHHHHhcc
Confidence 432 22333 367888999999999753
No 41
>cd04676 Nudix_Hydrolase_17 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.73 E-value=5.7e-17 Score=129.38 Aligned_cols=104 Identities=31% Similarity=0.433 Sum_probs=77.9
Q ss_pred cEEEEEEE-eeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEE-------eCCC-
Q 023914 141 KMVVGCLI-EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD-------IPRI- 211 (275)
Q Consensus 141 ~~~V~viI-~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~-------~~~~- 211 (275)
.++|.+++ ++++++||++|.. .|.|.+|||+++.||++++||.||++||||+++...++++.+. ++..
T Consensus 2 ~~~v~~ii~~~~~~vLl~~r~~---~~~w~lPgG~v~~~E~~~~aa~REl~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~~ 78 (129)
T cd04676 2 LPGVTAVVRDDEGRVLLIRRSD---NGLWALPGGAVEPGESPADTAVREVREETGLDVEVTGLVGIYTGPVHVVTYPNGD 78 (129)
T ss_pred cceEEEEEECCCCeEEEEEecC---CCcEECCeeccCCCCCHHHHHHHHHHHHhCceeEeeEEEEEeecccceeecCCCC
Confidence 34555555 5558999999874 4899999999999999999999999999999987766643321 2221
Q ss_pred --CEEEEEEEEEEcCCCC-CCCCCceeEEEecCCCCCCC
Q 023914 212 --GQIYIIFLAKLKRPHF-SPGPESSECRLFALDEIPFD 247 (275)
Q Consensus 212 --~~~~~~f~a~~~~~e~-~~~~E~~d~~W~~~deL~~~ 247 (275)
+...+.|.+...++.. ...+|..+++|++++++...
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~~w~~~~el~~~ 117 (129)
T cd04676 79 VRQYLDITFRCRVVGGELRVGDDESLDVAWFDPDGLPPL 117 (129)
T ss_pred cEEEEEEEEEEEeeCCeecCCCCceeEEEEEChhhCccc
Confidence 3344667777666544 34578889999999999954
No 42
>cd03671 Ap4A_hydrolase_plant_like Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one group (represented by this subfamily) and fungi/animals/archaea enzymes fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for the inhibition of such invasive bacteria. Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A hydrolase is structurally
Probab=99.73 E-value=4.1e-17 Score=135.53 Aligned_cols=101 Identities=31% Similarity=0.487 Sum_probs=76.4
Q ss_pred EEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEE------EeC---------
Q 023914 145 GCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQL------DIP--------- 209 (275)
Q Consensus 145 ~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~------~~~--------- 209 (275)
+++++.++++||++|...+ +.|++|+|++|+||++.+||.||++||||+++...++++.. ..+
T Consensus 8 ~ii~~~~~~vLL~~r~~~~--~~W~~PgG~~e~gE~~~~aA~REv~EEtGl~~~~~~~l~~~~~~~~y~~~~~~~~~~~~ 85 (147)
T cd03671 8 VVLFNEDGKVFVGRRIDTP--GAWQFPQGGIDEGEDPEQAALRELEEETGLDPDSVEIIAEIPDWLRYDLPPELKLKIWG 85 (147)
T ss_pred EEEEeCCCEEEEEEEcCCC--CCEECCcCCCCCCcCHHHHHHHHHHHHHCCCcCceEEEEEcCCeeEeeChhhhhccccC
Confidence 3444667899999998765 89999999999999999999999999999998777776643 111
Q ss_pred --CCCEEEEEEEEEEcC--CCC--CC--CCCceeEEEecCCCCCCC
Q 023914 210 --RIGQIYIIFLAKLKR--PHF--SP--GPESSECRLFALDEIPFD 247 (275)
Q Consensus 210 --~~~~~~~~f~a~~~~--~e~--~~--~~E~~d~~W~~~deL~~~ 247 (275)
..+...+.|.+.+.. .++ .. ++|..+++|+++++++..
T Consensus 86 ~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~E~~~~~W~~~~el~~~ 131 (147)
T cd03671 86 GRYRGQEQKWFLFRFTGDDSEIDLNAPEHPEFDEWRWVPLEELPDL 131 (147)
T ss_pred CcCCCEEEEEEEEEecCCCccccCCCCCCCCEeeEEeCCHHHHHHh
Confidence 113344556666654 333 22 368999999999999953
No 43
>cd04674 Nudix_Hydrolase_16 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.73 E-value=9.2e-17 Score=129.69 Aligned_cols=105 Identities=28% Similarity=0.414 Sum_probs=78.5
Q ss_pred CCcEEEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCcccc--ceeeEEEEeCCCCEEEE
Q 023914 139 NPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEV--QSPFAQLDIPRIGQIYI 216 (275)
Q Consensus 139 ~p~~~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~--~~~~~~~~~~~~~~~~~ 216 (275)
||.+++++++..++++||++|...+..|.|.+|||++|+||++++||+||++||+|+++.. +..+..+..+....+++
T Consensus 2 ~p~~~av~vl~~~~~~lL~~r~~~~~~~~w~lPgG~ve~~E~~~~aa~REl~EE~g~~~~~~~l~~~~~~~~~~~~~~~~ 81 (118)
T cd04674 2 NPLPVVVALLPVDDGLLVIRRGIEPGRGKLALPGGFIELGETWQDAVARELLEETGVAVDPADIRLFDVRSAPDGTLLVF 81 (118)
T ss_pred CCcEEEEEEEEECCCEEEEEeecCCCCCeEECCceecCCCCCHHHHHHHHHHHHHCCcccccEEEEEEEEecCCCeEEEE
Confidence 6777777777666678888888776679999999999999999999999999999998863 45556666676667777
Q ss_pred EEEEEEcCCCC-C--CCCCceeEEEecCCCCC
Q 023914 217 IFLAKLKRPHF-S--PGPESSECRLFALDEIP 245 (275)
Q Consensus 217 ~f~a~~~~~e~-~--~~~E~~d~~W~~~deL~ 245 (275)
+|.+....+.. . .+.|..+ |+.....+
T Consensus 82 ~~~~~~~~~~~~~~~~~~E~~~--~~~~~~~~ 111 (118)
T cd04674 82 GLLPERRAADLPPFEPTDETTE--RAVVTAPS 111 (118)
T ss_pred EEEeccccccCCCCCCCcceee--EEEccCCc
Confidence 78777665553 2 2355555 44444444
No 44
>cd03672 Dcp2p mRNA decapping enzyme 2 (Dcp2p), the catalytic subunit, and Dcp1p are the two components of the decapping enzyme complex. Decapping is a key step in both general and nonsense-mediated 5'-3' mRNA-decay pathways. Dcp2p contains an all-alpha helical N-terminal domain and a C-terminal domain which has the Nudix fold. While decapping is not dependent on the N-terminus of Dcp2p, it does affect its efficiency. Dcp1p binds the N-terminal domain of Dcp2p stimulating the decapping activity of Dcp2p. Decapping permits the degradation of the transcript and is a site of numerous control inputs. It is responsible for nonsense-mediated decay as well as AU-rich element (ARE)-mediated decay. In addition, it may also play a role in the levels of mRNA. Enzymes belonging to the Nudix superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V).
Probab=99.73 E-value=2.4e-17 Score=137.39 Aligned_cols=125 Identities=19% Similarity=0.229 Sum_probs=80.5
Q ss_pred EEEEEEEee--CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEE-eCCCCEEEEEE
Q 023914 142 MVVGCLIEH--DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD-IPRIGQIYIIF 218 (275)
Q Consensus 142 ~~V~viI~~--~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~-~~~~~~~~~~f 218 (275)
+++++++.+ +++|||+||.. .+.|++|||++|+|||+++||+||++||||+++........+. ....+..+..|
T Consensus 2 p~~gaii~~~~~~~vLLvr~~~---~~~W~lPGG~ve~gEs~~~AA~REl~EETGl~v~~~~~~~~~~~~~~~~~~~~~f 78 (145)
T cd03672 2 PVYGAIILNEDLDKVLLVKGWK---SKSWSFPKGKINKDEDDHDCAIREVYEETGFDISKYIDKDDYIELIIRGQNVKLY 78 (145)
T ss_pred CeeEEEEEeCCCCEEEEEEecC---CCCEECCCccCCCCcCHHHHHHHHHHHhhCccceeccccceeeecccCCcEEEEE
Confidence 344444443 36999999863 3589999999999999999999999999999986532211221 11223344455
Q ss_pred EEEEcCCC----CCCCCCceeEEEecCCCCCCCCCCC---------cHHHHHHHHHHHHHhhcc
Q 023914 219 LAKLKRPH----FSPGPESSECRLFALDEIPFDSLAF---------SSISVTLQLVRFYFEHMT 269 (275)
Q Consensus 219 ~a~~~~~e----~~~~~E~~d~~W~~~deL~~~~l~~---------~s~~~al~li~~~l~~~~ 269 (275)
.+....+. ....+|+.+++|+++++++...... --....+.-|.+|+.+++
T Consensus 79 ~~~~~~~~~~~~~~~~~E~~~~~Wv~~~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (145)
T cd03672 79 IVPGVPEDTPFEPKTRKEISKIEWFDIKDLPTKKNKKIPGLNSNKFFMVIPFIKPLKKWINRQK 142 (145)
T ss_pred EEecCCCCcccCcCChhhhheEEEeeHHHhhhhhhhccccccccceEEEhHHHHHHHHHHHHhh
Confidence 55433221 2234789999999999988532111 112333445558988765
No 45
>cd04699 Nudix_Hydrolase_39 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.73 E-value=2.4e-17 Score=132.09 Aligned_cols=104 Identities=28% Similarity=0.441 Sum_probs=77.9
Q ss_pred EEEEEEEeeC-CeEEEEEeccCC--CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEE-EEeCCC---CEE
Q 023914 142 MVVGCLIEHD-KKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQ-LDIPRI---GQI 214 (275)
Q Consensus 142 ~~V~viI~~~-~~iLL~rr~~~p--~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~-~~~~~~---~~~ 214 (275)
++|.++|.++ +++||++|...+ .+|+|++|||++++||++++||.||++||||+++....++.. ...... ...
T Consensus 2 ~~v~~vv~~~~~~iLl~kr~~~~~~~~g~w~~PgG~ve~gEs~~~aa~RE~~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~ 81 (129)
T cd04699 2 VAVAALIVKDVGRILILKRSKDERTAPGKWELPGGKVEEGETFEEALKREVYEETGLTVTPFLRYPSTVTHEDSGVYNVI 81 (129)
T ss_pred ceEEEEEECCCCcEEEEEecCCCCCCCCcCcCCccCccCCCCHHHHHHHHHHHhhCcEEEeeeeeeEEEEEcCCCEEEEE
Confidence 3455555444 899999998765 378999999999999999999999999999999877776432 222222 344
Q ss_pred EEEEEEEEcCCCCCCCCCceeEEEecCCCCC
Q 023914 215 YIIFLAKLKRPHFSPGPESSECRLFALDEIP 245 (275)
Q Consensus 215 ~~~f~a~~~~~e~~~~~E~~d~~W~~~deL~ 245 (275)
++.|.+....+....++|..+++|++++++.
T Consensus 82 ~~~~~~~~~~~~~~~~~e~~~~~w~~~~el~ 112 (129)
T cd04699 82 YLVFVCEALSGAVKLSDEHEEYAWVTLEELA 112 (129)
T ss_pred EEEEEeeecCCcccCChhheEEEEecHHHhh
Confidence 5667766554433445788899999999986
No 46
>cd04667 Nudix_Hydrolase_10 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.72 E-value=4.1e-17 Score=129.07 Aligned_cols=96 Identities=24% Similarity=0.336 Sum_probs=77.7
Q ss_pred EEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCCEEEEEEEEEEcC
Q 023914 145 GCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKLKR 224 (275)
Q Consensus 145 ~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~f~a~~~~ 224 (275)
++|+.+++++||++|. .|.|++|||++++||++++||.||++||||+++..+..++.+.. .....++|.+.+..
T Consensus 4 ~~i~~~~~~vLlv~r~----~~~w~~PgG~ve~gE~~~~aa~REl~EEtGl~~~~~~~~~~~~~--~~~~~~~f~~~~~~ 77 (112)
T cd04667 4 TVICRRGGRVLLVRKS----GSRWALPGGKIEPGETPLQAARRELQEETGLQGLDLLYLFHVDG--GSTRHHVFVASVPP 77 (112)
T ss_pred EEEEecCCEEEEEEcC----CCcEeCCCCcCCCCCCHHHHHHHHHHHHhCCcccceEEEEEEeC--CCEEEEEEEEEcCC
Confidence 3445667899999986 38899999999999999999999999999999887777766543 34556678887765
Q ss_pred CC-CCCCCCceeEEEecCCCCCC
Q 023914 225 PH-FSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 225 ~e-~~~~~E~~d~~W~~~deL~~ 246 (275)
+. ..+.+|..+++|++++++..
T Consensus 78 ~~~~~~~~e~~~~~W~~~~el~~ 100 (112)
T cd04667 78 SAQPKPSNEIADCRWLSLDALGD 100 (112)
T ss_pred cCCCCCchheeEEEEecHHHhhh
Confidence 53 33557888999999999984
No 47
>cd04695 Nudix_Hydrolase_36 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.71 E-value=3.7e-17 Score=132.99 Aligned_cols=116 Identities=22% Similarity=0.215 Sum_probs=84.5
Q ss_pred EEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceee---E-EEEeCCC-CEEEEEEEEE
Q 023914 147 LIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPF---A-QLDIPRI-GQIYIIFLAK 221 (275)
Q Consensus 147 iI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~---~-~~~~~~~-~~~~~~f~a~ 221 (275)
.+..++++||++|... .+|.|.+|||++|+|||+++||.||++||||+++..+... . .+..+.. ......|.+.
T Consensus 9 ~~~~~~~vLl~~r~~~-~~g~w~~PgG~ve~gEs~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~ 87 (131)
T cd04695 9 SLDKETKVLLLKRVKT-LGGFWCHVAGGVEAGETAWQAALRELKEETGISLPELYNADYLEQFYEANDNRILMAPVFVGF 87 (131)
T ss_pred EcCCCCEEEEEEecCC-CCCcEECCcccccCCCCHHHHHHHHHHHHhCCCccccccccceeeEeecCCceEEEEEEEEEE
Confidence 3356789999999865 4799999999999999999999999999999998655321 1 1222221 1234467777
Q ss_pred EcCCC-CCCCCCceeEEEecCCCCCCCCCCCcHHHHHHHHHHHH
Q 023914 222 LKRPH-FSPGPESSECRLFALDEIPFDSLAFSSISVTLQLVRFY 264 (275)
Q Consensus 222 ~~~~e-~~~~~E~~d~~W~~~deL~~~~l~~~s~~~al~li~~~ 264 (275)
...+. ...++|..+++|++++++... ...+..+.++..+..|
T Consensus 88 ~~~~~~~~~~~E~~~~~W~~~~e~~~~-~~~~~~~~~~~~~~~~ 130 (131)
T cd04695 88 VPPHQEVVLNHEHTEYRWCSFAEALEL-APFPGQRALYDHVWRY 130 (131)
T ss_pred ecCCCccccCchhcccEecCHHHHHHh-cCChhHHHHHHHHHhh
Confidence 65443 445578999999999999853 4567777777766665
No 48
>cd03425 MutT_pyrophosphohydrolase The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi). This enzyme requires two divalent cations for activity; one coordinates the phosphoryl groups of the NTP/dNTP substrate, and the other coordinates to the enzyme. It also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as metal binding and catalytic site. MutT pyrophosphohydrolase is important in preventing errors in DNA replication by hydrolyzing mutagenic nucleotides such as 8-oxo-dGTP (a product of oxidative damage), which can mispair with template adenine during DNA replication, to guanine nucleotides.
Probab=99.70 E-value=2.5e-16 Score=124.36 Aligned_cols=107 Identities=27% Similarity=0.368 Sum_probs=83.1
Q ss_pred EEEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC--CEEEEEE
Q 023914 142 MVVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIF 218 (275)
Q Consensus 142 ~~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~--~~~~~~f 218 (275)
+++++++++++++||++|...+ .+|+|++|+|+++.||+++++|.||++||+|+++...++++...+.++ +..+.+|
T Consensus 3 ~~~~~i~~~~~~~Ll~~r~~~~~~~g~w~~p~G~~~~~e~~~~~a~Re~~EE~g~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (124)
T cd03425 3 VVAAIIIDDDGRILIAQRPAGKHLGGLWEFPGGKVEPGETPEQALVRELREELGIEVEVGELLATVEHDYPDKRVTLHVF 82 (124)
T ss_pred EEEEEEECCCCEEEEEEeCCCCCCCCeEeCCCcccCCCCCHHHHHHHHHHHhhCcEEeccceEEEEEeeCCCCeEEEEEE
Confidence 3444444556999999998665 589999999999999999999999999999999887777776665443 4566777
Q ss_pred EEEEcCCCCCCCCCceeEEEecCCCCCCCCC
Q 023914 219 LAKLKRPHFSPGPESSECRLFALDEIPFDSL 249 (275)
Q Consensus 219 ~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l 249 (275)
.+....+... ..|..++.|++++++....+
T Consensus 83 ~~~~~~~~~~-~~e~~~~~W~~~~el~~~~~ 112 (124)
T cd03425 83 LVELWSGEPQ-LLEHQELRWVPPEELDDLDF 112 (124)
T ss_pred EEeeeCCCcc-cccCceEEEeeHHHcccCCC
Confidence 7776554332 35678899999999985433
No 49
>cd03428 Ap4A_hydrolase_human_like Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one subfamily and fungi/animals/archaea enzymes, represented by this subfamily, fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for inhibition of such invasive bacteria. Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val) that functions as a metal binding and
Probab=99.70 E-value=7.2e-17 Score=130.17 Aligned_cols=102 Identities=26% Similarity=0.357 Sum_probs=79.0
Q ss_pred eEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeE----EEEeC--CCCEEEEEEEEEEcC-C
Q 023914 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFA----QLDIP--RIGQIYIIFLAKLKR-P 225 (275)
Q Consensus 153 ~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~----~~~~~--~~~~~~~~f~a~~~~-~ 225 (275)
++||++|+. +.|.+|||++++|||+++||.||++||||+++....+++ .+.+. ..+...++|.+.+.. .
T Consensus 18 ~vLl~~~~~----~~w~~PgG~ve~gEs~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~ 93 (130)
T cd03428 18 EYLLLQASY----GHWDFPKGHVEPGEDDLEAALRETEEETGITAEQLFIVLGFKETLNYQVRGKLKTVTYFLAELRPDV 93 (130)
T ss_pred eEEEEEccC----CcCcCCcCCCCCCCCHHHHHHHHHHHHHCCChhhhhhhccceeEEEccccCcceEEEEEEEEeCCCC
Confidence 699999883 889999999999999999999999999999988776642 22222 234666778888873 3
Q ss_pred CCCCCCCceeEEEecCCCCCCCCCCCcHHHHHHH
Q 023914 226 HFSPGPESSECRLFALDEIPFDSLAFSSISVTLQ 259 (275)
Q Consensus 226 e~~~~~E~~d~~W~~~deL~~~~l~~~s~~~al~ 259 (275)
.+..++|..+++|++++++.. .+.++..+.+++
T Consensus 94 ~~~~~~E~~~~~W~~~~e~~~-~~~~~~~~~~~~ 126 (130)
T cd03428 94 EVKLSEEHQDYRWLPYEEALK-LLTYEDLKAVLD 126 (130)
T ss_pred ccccccceeeEEeecHHHHHH-HcCchhHHHHHH
Confidence 445557899999999999985 345677666555
No 50
>cd04693 Nudix_Hydrolase_34 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.70 E-value=6.5e-17 Score=130.51 Aligned_cols=103 Identities=25% Similarity=0.354 Sum_probs=74.8
Q ss_pred EEEEEEeeCCeEEEEEeccCC--CCCceeee-eEEeeCCCCHHHHHHHHHHHHhCCcccc--ceeeEEEEeCC-CCEEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEV--QSPFAQLDIPR-IGQIYI 216 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p--~~g~w~lP-gG~vE~GEs~eeAa~REl~EEtGl~v~~--~~~~~~~~~~~-~~~~~~ 216 (275)
+.+++++.+++|||++|+... .+|.|++| ||++++||++ +||+||++||||+++.. ...+..+.... ....++
T Consensus 3 v~v~~~~~~g~vLl~~R~~~~~~~pg~w~~p~GG~ve~gE~~-~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~ 81 (127)
T cd04693 3 VHVCIFNSKGELLLQKRSPNKDGWPGMWDLSVGGHVQAGETS-TAAEREVKEELGLELDFSELRPLFRYFFEAEGFDDYY 81 (127)
T ss_pred EEEEEEeCCCeEEEEEccCCCCCCCCcccccCCCcCCCCCCH-HHHHHHHHHHhCCCcChhhcEEEEEEEeecCCeEEEE
Confidence 344556778899999988543 46899998 8999999999 99999999999999764 33445544433 333444
Q ss_pred EEEEEEcCCCCCCC-CCceeEEEecCCCCCC
Q 023914 217 IFLAKLKRPHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 217 ~f~a~~~~~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
.|.+....+...++ +|..+++|++++++..
T Consensus 82 ~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~ 112 (127)
T cd04693 82 LFYADVEIGKLILQKEEVDEVKFVSKDEIDG 112 (127)
T ss_pred EEEecCcccccccCHHHhhhEEEeCHHHHHH
Confidence 45554444444444 7889999999999763
No 51
>cd04697 Nudix_Hydrolase_38 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.69 E-value=9.9e-17 Score=129.76 Aligned_cols=102 Identities=21% Similarity=0.216 Sum_probs=79.4
Q ss_pred EEEEEeeCCeEEEEEeccCC--CCCceee-eeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC--CEEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEP--SYGLWTL-PAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIF 218 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p--~~g~w~l-PgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~--~~~~~~f 218 (275)
.+++++.+++|||++|...+ .+|+|++ |||++++||++++||+||++||||+++..+..++.+.+... ....++|
T Consensus 4 ~v~i~~~~~~iLl~~R~~~~~~~~g~w~~~~GG~ve~gE~~~~aa~REl~EEtGl~~~~l~~~~~~~~~~~~~~~~~~~f 83 (126)
T cd04697 4 YIFVFNSEGKLCVHKRTLTKDWCPGYWDIAFGGVVQAGESYLQNAQRELEEELGIDGVQLTPLGLFYYDTDGNRVWGKVF 83 (126)
T ss_pred EEEEEcCCCeEEEEECCCCCCCCCCcccCcCCcccCCCCCHHHHHHHHHHHHHCCCccccEEeeEEEecCCCceEEEEEE
Confidence 34556778999999987543 3799999 59999999999999999999999999987777777665443 3444567
Q ss_pred EEEEcCCCCCCC-CCceeEEEecCCCCCC
Q 023914 219 LAKLKRPHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 219 ~a~~~~~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
.+... +++..+ +|..+++|++++++..
T Consensus 84 ~~~~~-~~~~~~~~E~~~~~w~~~~el~~ 111 (126)
T cd04697 84 SCVYD-GPLKLQEEEVEEITWLSINEILQ 111 (126)
T ss_pred EEEEC-CCCCCCHhHhhheEEcCHHHHHH
Confidence 77764 344443 7888999999999864
No 52
>cd03426 CoAse Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative stress. CoAse has a conserved Nudix fold and requires a single divalent cation for catalysis. In addition to a signature Nudix motif G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val, CoAse contains an additional motif upstream called the NuCoA motif (LLTXT(SA)X3RX3GX3FPGG) which is postulated to be involved in CoA recognition. CoA plays a central role in lipid metabolism. It is involved in the initial steps of fatty acid sythesis in the cytosol, in the oxidation of fatty acids and the citric acid cycle in the mitochondria, and in the oxidation of long-chain fatty acids in peroxisomes. CoA has the important role of activating fatty acids for further modification into key biological signalling molecules.
Probab=99.69 E-value=9.9e-17 Score=134.99 Aligned_cols=105 Identities=22% Similarity=0.230 Sum_probs=79.9
Q ss_pred EEEEEEe-eC--CeEEEEEeccCC--CCCceeeeeEEeeCC-CCHHHHHHHHHHHHhCCccccceeeEEEEe--CCCCEE
Q 023914 143 VVGCLIE-HD--KKILLCKRKIEP--SYGLWTLPAGYMEIG-ESAAEGAIRETWEEARADVEVQSPFAQLDI--PRIGQI 214 (275)
Q Consensus 143 ~V~viI~-~~--~~iLL~rr~~~p--~~g~w~lPgG~vE~G-Es~eeAa~REl~EEtGl~v~~~~~~~~~~~--~~~~~~ 214 (275)
+|.+++. .+ ++|||+||.... .+|.|++|||++|+| |++++||+||++||||+++....+++.... ...+..
T Consensus 4 av~v~l~~~~~~~~vLL~~R~~~~~~~~g~w~lPGG~ve~gdEs~~eaa~REl~EEtGl~~~~~~~l~~~~~~~~~~~~~ 83 (157)
T cd03426 4 AVLVLLVEREGELRVLLTKRASHLRSHPGQVAFPGGKVDPGDEDPVATALREAEEEIGLPPDSVEVLGRLPPYYTRSGFV 83 (157)
T ss_pred EEEEEEEeCCCceEEEEEEcccccccCCCcEECCCCCcCCCcCCHHHHHHHHHHHHhCCCccceEEEEECCCccccCCCE
Confidence 4444443 33 699999998753 479999999999999 999999999999999999988888776542 222344
Q ss_pred EEEEEEEEcCC-CCCCC-CCceeEEEecCCCCCCC
Q 023914 215 YIIFLAKLKRP-HFSPG-PESSECRLFALDEIPFD 247 (275)
Q Consensus 215 ~~~f~a~~~~~-e~~~~-~E~~d~~W~~~deL~~~ 247 (275)
+..|.+..... ++.++ +|..+++|++++++...
T Consensus 84 v~~~~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~ 118 (157)
T cd03426 84 VTPVVGLVPPPLPLVLNPDEVAEVFEVPLSFLLDP 118 (157)
T ss_pred EEEEEEEECCCCCCCCCHHHhheeEEEcHHHHhCc
Confidence 55677766553 34444 68899999999999864
No 53
>TIGR00586 mutt mutator mutT protein. All proteins in this family for which functions are known are involved in repairing oxidative damage to dGTP (they are 8-oxo-dGTPases). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.69 E-value=5.6e-16 Score=124.33 Aligned_cols=109 Identities=16% Similarity=0.097 Sum_probs=80.2
Q ss_pred EEEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC--CEEEEEE
Q 023914 142 MVVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIF 218 (275)
Q Consensus 142 ~~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~--~~~~~~f 218 (275)
.++++++++++++||.+|...+ ..|+|++|||.++.||++++|+.||+.||+|+++....+++.....+. ...+.+|
T Consensus 6 ~~~~ii~~~~~~vLl~~R~~~~~~~g~w~~Pgg~ve~ge~~~~~~~RE~~EE~g~~~~~~~~~~~~~h~~~~~~~~~~~~ 85 (128)
T TIGR00586 6 IAVGIIRNENGEIIITRRADGHMFAKLLEFPGGKEEGGETPEQAVVRELEEEIGIPQHFSEFEKLEYEFYPRHITLWFWL 85 (128)
T ss_pred EEEEEEECCCCEEEEEEEeCCCCCCCeEECCCcccCCCCCHHHHHHHHHHHHHCCcceeeeEEEEEEEECCCcEEEEEEE
Confidence 3444445666799999997654 479999999999999999999999999999999877666665544333 3455667
Q ss_pred EEEEcCCCCCCCCCceeEEEecCCCCCCCCCCCcH
Q 023914 219 LAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSS 253 (275)
Q Consensus 219 ~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s 253 (275)
.+...++... ..+..+++|++.++++. +++|.
T Consensus 86 ~~~~~~~~~~-~~~~~~~~W~~~~~l~~--~~~p~ 117 (128)
T TIGR00586 86 LERWEGGPPG-KEGQPEEWWVLVGLLAD--DFFPA 117 (128)
T ss_pred EEEEcCCCcC-cccccccEEeCHHHCCc--cCCCC
Confidence 6766544322 34566789999999995 44544
No 54
>cd04661 MRP_L46 Mitochondrial ribosomal protein L46 (MRP L46) is a component of the large subunit (39S) of the mammalian mitochondrial ribosome and a member of the Nudix hydrolase superfamily. MRPs are thought to be involved in the maintenance of the mitochondrial DNA. In general, members of the Nudix superfamily require a divalent cation, such as Mg2+ or Mn2+, for activity and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. MRP L46 appears to contain a modified nudix motif.
Probab=99.68 E-value=1.7e-16 Score=129.75 Aligned_cols=95 Identities=23% Similarity=0.382 Sum_probs=74.7
Q ss_pred eCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceee-----EEEEe--CC-------CCEEE
Q 023914 150 HDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPF-----AQLDI--PR-------IGQIY 215 (275)
Q Consensus 150 ~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~-----~~~~~--~~-------~~~~~ 215 (275)
+++++||+++... ..|.|+||+|++|+|||+++||.||++||||+++.. ..+ +.+.+ +. .+...
T Consensus 11 ~~~~~Llvk~~~~-~~g~W~fPgG~ve~gEt~~eaa~REl~EEtGl~v~~-~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (132)
T cd04661 11 DDTLVLLVQQKVG-SQNHWILPQGKREEGETLRQTAERTLKELCGNNLKA-KFYGNAPVGFYKYKYPKAVRNEGIVGAKV 88 (132)
T ss_pred cCcEEEEEEeecC-CCCeeECCcccccCCCCHHHHHHHHHHHhhCCCceE-EEEEecCcEEEEEecCcccccccCcccEE
Confidence 4678999998754 368999999999999999999999999999998754 222 22222 21 12456
Q ss_pred EEEEEEEcCCCCCCCCCceeEEEecCCCCCC
Q 023914 216 IIFLAKLKRPHFSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 216 ~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~ 246 (275)
++|.+...++++...+|+.+++|++++|++.
T Consensus 89 ~~f~~~~~~g~~~~~~e~~~~~W~~~~el~~ 119 (132)
T cd04661 89 FFFKARYMSGQFELSQNQVDFKWLAKEELQK 119 (132)
T ss_pred EEEEEEEecCccccCCCcceeEecCHHHHHh
Confidence 7889998888777678899999999999984
No 55
>PRK11762 nudE adenosine nucleotide hydrolase NudE; Provisional
Probab=99.68 E-value=7.8e-16 Score=132.99 Aligned_cols=130 Identities=21% Similarity=0.216 Sum_probs=91.4
Q ss_pred CCcEEEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeC--CCCEEE
Q 023914 139 NPKMVVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP--RIGQIY 215 (275)
Q Consensus 139 ~p~~~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~--~~~~~~ 215 (275)
++..++++.+.+++++||+|+.+.+ ..+.|++|||.+|+||++++||+||++||||+++..+.+++.+... .....+
T Consensus 46 ~~~~v~v~~~~~~~~vlLvrq~r~~~~~~~~elPaG~ve~gE~~~~aA~REl~EEtG~~~~~l~~l~~~~~~~~~~~~~~ 125 (185)
T PRK11762 46 GRGAVMIVPILDDDTLLLIREYAAGTERYELGFPKGLIDPGETPLEAANRELKEEVGFGARQLTFLKELSLAPSYFSSKM 125 (185)
T ss_pred CCCEEEEEEEeCCCEEEEEEeecCCCCCcEEEccceeCCCCCCHHHHHHHHHHHHHCCCCcceEEEEEEecCCCccCcEE
Confidence 3334444445677899999997665 3677999999999999999999999999999999999988876532 224566
Q ss_pred EEEEEEEcCCC-CC-CCCCceeEEEecCCCCCC----CCCCCcHHHHHHHHHHHHHhhc
Q 023914 216 IIFLAKLKRPH-FS-PGPESSECRLFALDEIPF----DSLAFSSISVTLQLVRFYFEHM 268 (275)
Q Consensus 216 ~~f~a~~~~~e-~~-~~~E~~d~~W~~~deL~~----~~l~~~s~~~al~li~~~l~~~ 268 (275)
+.|.+....+. .. .+.|..++.|++.+++.. ..+.....-.++.+...|++++
T Consensus 126 ~~f~a~~~~~~~~~~~e~E~i~~~~~~~~e~~~~~~~g~i~d~~ti~al~~~~~~l~~~ 184 (185)
T PRK11762 126 NIVLAEDLYPERLEGDEPEPLEVVRWPLADLDELLARPDFSEARSVAALFLAREWLKQQ 184 (185)
T ss_pred EEEEEEccccccCCCCCCceeEEEEEcHHHHHHHHHcCCCCcHHHHHHHHHHHHHHhcc
Confidence 67777754332 12 225666889999998753 3344333444555666676653
No 56
>PRK00714 RNA pyrophosphohydrolase; Reviewed
Probab=99.68 E-value=3.7e-16 Score=131.58 Aligned_cols=103 Identities=22% Similarity=0.239 Sum_probs=76.6
Q ss_pred EEEE-EEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEE----eCC------
Q 023914 142 MVVG-CLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD----IPR------ 210 (275)
Q Consensus 142 ~~V~-viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~----~~~------ 210 (275)
++|. ++++.+++|||+||... ++.|++|||++++||++++||.||++||||+++...++++... +.+
T Consensus 9 ~~v~~~i~~~~g~vLL~~r~~~--~~~w~~P~G~~~~gE~~~~aa~REl~EEtG~~~~~~~~~~~~~~~~~y~~~~~~~~ 86 (156)
T PRK00714 9 PNVGIILLNRQGQVFWGRRIGQ--GHSWQFPQGGIDPGETPEQAMYRELYEEVGLRPEDVEILAETRDWLRYDLPKRLVR 86 (156)
T ss_pred CeEEEEEEecCCEEEEEEEcCC--CCeEECCcccCCCCcCHHHHHHHHHHHHhCCCccceEEEEEcCCeEEecCcHHHhh
Confidence 3443 44566889999999853 4889999999999999999999999999999988777766531 111
Q ss_pred ------CCEEEEEEEEEEcCC--CCCC----CCCceeEEEecCCCCCC
Q 023914 211 ------IGQIYIIFLAKLKRP--HFSP----GPESSECRLFALDEIPF 246 (275)
Q Consensus 211 ------~~~~~~~f~a~~~~~--e~~~----~~E~~d~~W~~~deL~~ 246 (275)
.+...++|.+....+ ++.. ++|..+++|++++|++.
T Consensus 87 ~~~~~~~~~~~~~fl~~~~~~~~~~~l~~~~~~E~~~~~W~~~del~~ 134 (156)
T PRK00714 87 RSKGVYRGQKQKWFLLRLTGDDSEINLNTTSHPEFDAWRWVSYWYPLD 134 (156)
T ss_pred ccCCcccCcEEEEEEEEecCCCccccCCCCCCCCeeeeEeCCHHHHHH
Confidence 122456777776432 2222 26889999999999984
No 57
>PRK15393 NUDIX hydrolase YfcD; Provisional
Probab=99.66 E-value=4.7e-16 Score=133.99 Aligned_cols=121 Identities=19% Similarity=0.137 Sum_probs=83.1
Q ss_pred EEEEEeeCCeEEEEEeccCC--CCCce-eeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCC--EEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEP--SYGLW-TLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIF 218 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p--~~g~w-~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~--~~~~~f 218 (275)
.+++++.+++|||++|...+ .+|.| .+|||++++|||+++||+||++||||+.+....+++.+.+.... ...++|
T Consensus 41 ~v~v~~~~g~iLL~~R~~~~~~~pg~~~~~pGG~ve~GEs~~eAA~REL~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~f 120 (180)
T PRK15393 41 YIVVHDGMGKILVQRRTETKDFLPGMLDATAGGVVQAGEQLLESARREAEEELGIAGVPFAEHGQFYFEDENCRVWGALF 120 (180)
T ss_pred EEEEECCCCeEEEEEeCCCCCCCCCcccccCCCcCCCCCCHHHHHHHHHHHHHCCCCccceeceeEEecCCCceEEEEEE
Confidence 33445667899999987543 25666 57899999999999999999999999997776666655443332 233456
Q ss_pred EEEEcCCCCCCC-CCceeEEEecCCCCCCC--CCCCcHHHHHHHHHHHHHhhcc
Q 023914 219 LAKLKRPHFSPG-PESSECRLFALDEIPFD--SLAFSSISVTLQLVRFYFEHMT 269 (275)
Q Consensus 219 ~a~~~~~e~~~~-~E~~d~~W~~~deL~~~--~l~~~s~~~al~li~~~l~~~~ 269 (275)
.+.. .+....+ +|..+++|+++++++.. .+.+.. . ..+..|+.+..
T Consensus 121 ~~~~-~~~~~~~~~E~~~~~W~~~~el~~~~~~~~~~~-~---~~l~~~l~~~~ 169 (180)
T PRK15393 121 SCVS-HGPFALQEEEVSEVCWMTPEEITARCDEFTPDS-L---KALALWLTRNA 169 (180)
T ss_pred EEEe-CCCCCCChHHeeEEEECCHHHHhhhhhhcCccH-H---HHHHHHHHhhc
Confidence 6654 3444433 78899999999999854 233322 2 33446766543
No 58
>cd04666 Nudix_Hydrolase_9 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate s
Probab=99.66 E-value=6.3e-16 Score=125.11 Aligned_cols=91 Identities=25% Similarity=0.408 Sum_probs=71.6
Q ss_pred CeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccc-eeeEEEEeCCC------CEEEEEEEEEEcC
Q 023914 152 KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ-SPFAQLDIPRI------GQIYIIFLAKLKR 224 (275)
Q Consensus 152 ~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~-~~~~~~~~~~~------~~~~~~f~a~~~~ 224 (275)
+++||++|.. .+.|.+|||++|.|||+++||+||++||||+++... ++++.+.+..+ +...++|.+....
T Consensus 15 ~~vLLv~~~~---~~~w~~PgG~ve~~E~~~~aa~RE~~EEtG~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~f~~~~~~ 91 (122)
T cd04666 15 VEVLLVTSRR---TGRWIVPKGGPEKDESPAEAAAREAWEEAGVRGKIGKRPLGRFEYRKRSKNRPPRCEVAVFPLEVTE 91 (122)
T ss_pred eEEEEEEecC---CCeEECCCCCcCCCCCHHHHHHHHHHHHhCCcccccceEEEEEEeeecCCCCCceEEEEEEEEEEec
Confidence 6899999873 488999999999999999999999999999998777 88887765432 3445667777654
Q ss_pred CCCC-CCCCceeEEEecCCCCC
Q 023914 225 PHFS-PGPESSECRLFALDEIP 245 (275)
Q Consensus 225 ~e~~-~~~E~~d~~W~~~deL~ 245 (275)
.... ++.+..+++|++++++.
T Consensus 92 ~~~~~~~~e~~~~~W~~~~ea~ 113 (122)
T cd04666 92 ELDEWPEMHQRKRKWFSPEEAA 113 (122)
T ss_pred cccCCcccCceEEEEecHHHHH
Confidence 4322 34567789999999975
No 59
>cd04686 Nudix_Hydrolase_27 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.65 E-value=7.1e-16 Score=125.76 Aligned_cols=101 Identities=28% Similarity=0.297 Sum_probs=72.9
Q ss_pred EEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCcc-ccceeeEEEE----eCCC-----C
Q 023914 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADV-EVQSPFAQLD----IPRI-----G 212 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v-~~~~~~~~~~----~~~~-----~ 212 (275)
+|.+||.++++|||+++.. .+.|.+|||++|+||++++||+||++||||+++ .....++.+. +..+ +
T Consensus 2 ~~~~ii~~~~~vLLv~~~~---~~~w~lPgG~ve~gEt~~~aa~REl~EEtGl~~~~~~~~l~~~~~~~~~~~~~~~~~~ 78 (131)
T cd04686 2 AVRAIILQGDKILLLYTKR---YGDYKFPGGGVEKGEDHIEGLIRELQEETGATNIRVIEKFGTYTERRPWRKPDADIFH 78 (131)
T ss_pred cEEEEEEECCEEEEEEEcC---CCcEECccccCCCCCCHHHHHHHHHHHHHCCcccccceEEEEEEeeccccCCCCceeE
Confidence 3566777789999999874 368999999999999999999999999999987 4555555442 1111 2
Q ss_pred EEEEEEEEEEcCCC--CCCC-CCc---eeEEEecCCCCCC
Q 023914 213 QIYIIFLAKLKRPH--FSPG-PES---SECRLFALDEIPF 246 (275)
Q Consensus 213 ~~~~~f~a~~~~~e--~~~~-~E~---~d~~W~~~deL~~ 246 (275)
...++|.+.+.... ...+ .|. .+++|++++++..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~W~~~~ea~~ 118 (131)
T cd04686 79 MISYYYLCEVDAELGAQQLEDYEAELGMKPIWINIHEAIE 118 (131)
T ss_pred EEEEEEEEEEcCCcCCcccchhhHhcCCCcEEecHHHHHH
Confidence 34567888876543 2222 222 3589999999874
No 60
>cd04665 Nudix_Hydrolase_8 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate s
Probab=99.64 E-value=3.4e-15 Score=120.48 Aligned_cols=98 Identities=24% Similarity=0.311 Sum_probs=80.8
Q ss_pred EEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC--CEEEEEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIFLAK 221 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~--~~~~~~f~a~ 221 (275)
|.+++.+++++||+++. .+.|++|||++|+||++++||+||++||+|+++....+++.+..+.. .....+|.+.
T Consensus 3 v~vi~~~~~~vLl~~~~----~~~w~lPgG~ve~gE~~~~aa~REl~EE~G~~~~~~~~l~~~~~~~~~~~~~~~~y~a~ 78 (118)
T cd04665 3 VLVICFYDDGLLLVRHK----DRGWEFPGGHVEPGETIEEAARREVWEETGAELGSLTLVGYYQVDLFESGFETLVYPAV 78 (118)
T ss_pred EEEEEEECCEEEEEEeC----CCEEECCccccCCCCCHHHHHHHHHHHHHCCccCceEEEEEEEecCCCCcEEEEEEEEE
Confidence 45566678999999986 46799999999999999999999999999999999999888776543 4566778888
Q ss_pred EcCCC-CCCCCCceeEEEecCCCCC
Q 023914 222 LKRPH-FSPGPESSECRLFALDEIP 245 (275)
Q Consensus 222 ~~~~e-~~~~~E~~d~~W~~~deL~ 245 (275)
..... ..++.|+....|++.+...
T Consensus 79 ~~~~~~~~~~~E~~~~~~~~~~~~~ 103 (118)
T cd04665 79 SAQLEEKASYLETDGPVLFKNEPEE 103 (118)
T ss_pred EEecccccccccccCcEEeccCCcc
Confidence 77665 4467899999999977653
No 61
>cd02885 IPP_Isomerase Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mamm
Probab=99.64 E-value=6.8e-16 Score=130.81 Aligned_cols=105 Identities=22% Similarity=0.288 Sum_probs=77.2
Q ss_pred EEEEE-EEeeCCeEEEEEeccCC--CCCceeee-eEEeeCCCCHHHHHHHHHHHHhCCccccceee-EEEEe--CC----
Q 023914 142 MVVGC-LIEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQSPF-AQLDI--PR---- 210 (275)
Q Consensus 142 ~~V~v-iI~~~~~iLL~rr~~~p--~~g~w~lP-gG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~-~~~~~--~~---- 210 (275)
.+|.+ +++.+++|||++|+... .+|.|++| ||++|+|||+++||+||++||||+.+....++ +...+ +.
T Consensus 31 ~~v~v~i~~~~~~iLl~kR~~~~~~~Pg~w~~~~gG~ie~GEt~~eaa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~ 110 (165)
T cd02885 31 RAFSVFLFNSKGRLLLQRRALSKYTFPGLWTNTCCSHPLPGEGVKDAAQRRLREELGITGDLLELVLPRFRYRAPDDGGL 110 (165)
T ss_pred eEEEEEEEcCCCcEEEEeccCCCccCCCcccccccCCCCCCCCHHHHHHHHHHHHhCCCccchhhccceEEEEEEcCCCc
Confidence 34444 45667899999998643 47999997 89999999999999999999999998776664 43322 11
Q ss_pred -CCEEEEEEEEEEcCCCCCCCCCceeEEEecCCCCCC
Q 023914 211 -IGQIYIIFLAKLKRPHFSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 211 -~~~~~~~f~a~~~~~e~~~~~E~~d~~W~~~deL~~ 246 (275)
.+...++|.+....+.....+|..+++|++++++..
T Consensus 111 ~~~~i~~~f~~~~~~~~~~~~~Ev~~~~w~~~~el~~ 147 (165)
T cd02885 111 VEHEIDHVFFARADVTLIPNPDEVSEYRWVSLEDLKE 147 (165)
T ss_pred eeeEEEEEEEEEeCCCCCCCccceeEEEEECHHHHHH
Confidence 123446677776544333347889999999999874
No 62
>PF00293 NUDIX: NUDIX domain; InterPro: IPR000086 The generic name 'NUDIX hydrolases' (NUcleoside DIphosphate linked to some other moiety X) has been coined for this domain family []. The family can be divided into a number of subgroups, of which MutT anti- mutagenic activity represents only one type; most of the rest hydrolyse diverse nucleoside diphosphate derivatives (including ADP-ribose, GDP- mannose, TDP-glucose, NADH, UDP-sugars, dNTP and NTP).; GO: 0016787 hydrolase activity; PDB: 3FJY_A 3MGM_A 2XSQ_A 3COU_A 2O5F_A 1Q27_A 3F6A_A 3E57_B 3SON_B 2GT4_C ....
Probab=99.64 E-value=7.4e-16 Score=123.50 Aligned_cols=106 Identities=38% Similarity=0.523 Sum_probs=80.4
Q ss_pred cEEEEEEEee-CCeEEEEEeccCC--CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe--CCC---C
Q 023914 141 KMVVGCLIEH-DKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI--PRI---G 212 (275)
Q Consensus 141 ~~~V~viI~~-~~~iLL~rr~~~p--~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~--~~~---~ 212 (275)
..+|.+++.+ ++++||++|...+ .++.|.+|||++++|||+++||+||+.||||+++..........+ +.. +
T Consensus 2 ~~~v~~ii~~~~~~vLl~~r~~~~~~~~~~~~~pgG~i~~~E~~~~aa~REl~EE~g~~~~~~~~~~~~~~~~~~~~~~~ 81 (134)
T PF00293_consen 2 RRAVGVIIFNEDGKVLLIKRSRSPITFPGYWELPGGGIEPGESPEEAARRELKEETGLDVSPLELLGLFSYPSPSGDPEG 81 (134)
T ss_dssp EEEEEEEEEETTTEEEEEEESTTSSSSTTEEESSEEEECTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEETTTESSE
T ss_pred CCEEEEEEEeCCcEEEEEEecCCCCCCCCeEecceeeEEcCCchhhhHHhhhhhcccceecccccceeeeecccCCCccc
Confidence 3456655544 4599999999875 478999999999999999999999999999999866666554443 222 2
Q ss_pred EEEEEEEEEEcCCC--CCCC-CCceeEEEecCCCCCC
Q 023914 213 QIYIIFLAKLKRPH--FSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 213 ~~~~~f~a~~~~~e--~~~~-~E~~d~~W~~~deL~~ 246 (275)
...++|.+....+. ...+ +|..++.|++++++..
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~ 118 (134)
T PF00293_consen 82 EIVIFFIAELPSEQSEIQPQDEEISEVKWVPPDELLE 118 (134)
T ss_dssp EEEEEEEEEEEEEESECHTTTTTEEEEEEEEHHHHHH
T ss_pred EEEEEEEEEEeCCccccCCCCccEEEEEEEEHHHhhh
Confidence 56666777765543 2233 5999999999999874
No 63
>cd04692 Nudix_Hydrolase_33 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.63 E-value=1.2e-15 Score=126.26 Aligned_cols=101 Identities=32% Similarity=0.422 Sum_probs=74.3
Q ss_pred EEEEeeC---CeEEEEEeccC--CCCCceee-eeEEeeCCCCHHHHHHHHHHHHhCCccc--cceeeEEEEeCC------
Q 023914 145 GCLIEHD---KKILLCKRKIE--PSYGLWTL-PAGYMEIGESAAEGAIRETWEEARADVE--VQSPFAQLDIPR------ 210 (275)
Q Consensus 145 ~viI~~~---~~iLL~rr~~~--p~~g~w~l-PgG~vE~GEs~eeAa~REl~EEtGl~v~--~~~~~~~~~~~~------ 210 (275)
+.+++.+ +++|+++|+.. ..+|.|++ |||++++|||+++||+||++||||+++. .+.+++.+....
T Consensus 7 ~~v~~~~~~~~~vLl~~R~~~~~~~pg~W~~~~gG~ve~gEt~~~aa~REl~EEtGl~~~~~~l~~~~~~~~~~~~~~~~ 86 (144)
T cd04692 7 CWIITKDEGKGYVLLQKRSANKKTYPGLWDISSAGHILAGETPLEDGIRELEEELGLDVSADDLIPLGTFKIEYDHIGKL 86 (144)
T ss_pred EEEEEccCCCCEEEEEecCCCCCCCCCccccccCcccCCCCCHHHHHHHHHHHHhCCCCChHHeEEeeEEEEeccccCCC
Confidence 3444555 89999999864 24799999 5999999999999999999999999864 445555543321
Q ss_pred -CCEEEEEEEEEEcC--CCCCCC-CCceeEEEecCCCCC
Q 023914 211 -IGQIYIIFLAKLKR--PHFSPG-PESSECRLFALDEIP 245 (275)
Q Consensus 211 -~~~~~~~f~a~~~~--~e~~~~-~E~~d~~W~~~deL~ 245 (275)
.....++|.+.... +.+.++ +|..+++|++++++.
T Consensus 87 ~~~~~~~~f~~~~~~~~~~~~~~~~E~~~~~W~~~~el~ 125 (144)
T cd04692 87 IDREFHHVYLYELKVPLEEFTLQKEEVAGVVLIPLDEFA 125 (144)
T ss_pred ccceEEEEEEEeccCChhhcCCChhHhheEEEECHHHHH
Confidence 12355677777654 334444 788999999999875
No 64
>cd02883 Nudix_Hydrolase Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzy
Probab=99.62 E-value=6.1e-15 Score=115.24 Aligned_cols=102 Identities=38% Similarity=0.583 Sum_probs=79.4
Q ss_pred EEEEE-eeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCC----CCEEEEEE
Q 023914 144 VGCLI-EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPR----IGQIYIIF 218 (275)
Q Consensus 144 V~viI-~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~----~~~~~~~f 218 (275)
+.+++ +.++++||++|... ..|+|.+|+|+++.||++.++|.||+.||+|+.+........+.... ....+++|
T Consensus 3 ~~~i~~~~~~~ill~kr~~~-~~~~~~~p~G~~~~~e~~~~~a~RE~~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (123)
T cd02883 3 VGAVILDEDGRVLLVRRADS-PGGLWELPGGGVEPGETLEEAAIREVREETGLDVDVLRLLGVYEVESPDEGEHAVVFVF 81 (123)
T ss_pred eEEEEECCCCCEEEEEEcCC-CCCeEeCCcccccCCCCHHHHHHHHHHHhhCccceeeeEEEEEEeeccCCCceEEEEEE
Confidence 44555 44489999999865 47999999999999999999999999999999986555555444322 35667788
Q ss_pred EEEEcCCCC--CCCCCceeEEEecCCCCCC
Q 023914 219 LAKLKRPHF--SPGPESSECRLFALDEIPF 246 (275)
Q Consensus 219 ~a~~~~~e~--~~~~E~~d~~W~~~deL~~ 246 (275)
.+....++. ...+|..+.+|++++++..
T Consensus 82 ~~~~~~~~~~~~~~~e~~~~~w~~~~~l~~ 111 (123)
T cd02883 82 LARLVGGEPTLLPPDEISEVRWVTLDELPA 111 (123)
T ss_pred EEEeCCCCcCCCCCCccceEEEEcHHHCcc
Confidence 888776654 3347778899999999985
No 65
>cd04694 Nudix_Hydrolase_35 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.59 E-value=8.1e-15 Score=121.99 Aligned_cols=103 Identities=24% Similarity=0.346 Sum_probs=72.3
Q ss_pred EEEEE-EeeCCeEEEEEeccCC--CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccc----eeeEEEE--eCC---
Q 023914 143 VVGCL-IEHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ----SPFAQLD--IPR--- 210 (275)
Q Consensus 143 ~V~vi-I~~~~~iLL~rr~~~p--~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~----~~~~~~~--~~~--- 210 (275)
+|.++ ++.++++||+||...+ .+|.|++|||++++||++++||+||++||+|+.+... ++++... ++.
T Consensus 3 ~v~viv~~~~~~vLl~rr~~~~~~~~g~w~~PgG~v~~~E~~~~aa~RE~~EE~gi~~~~~~~~~~~l~~~~~~~~~~~~ 82 (143)
T cd04694 3 GVAVLLQSSDQKLLLTRRASSLRIFPNVWVPPGGHVELGENLLEAGLRELNEETGLTLDPIDKSWQVLGLWESVYPPLLS 82 (143)
T ss_pred EEEEEEEcCCCEEEEEEECCCCCCCCCeEECcccccCCCCCHHHHHHHHHHHHHCCCccccccceeEEeeeccccccccC
Confidence 44444 5678899999998653 4799999999999999999999999999999988654 4555432 221
Q ss_pred -----CCEEEEEEEEEEcCC------CCCCC-CCceeEEEecCCCCC
Q 023914 211 -----IGQIYIIFLAKLKRP------HFSPG-PESSECRLFALDEIP 245 (275)
Q Consensus 211 -----~~~~~~~f~a~~~~~------e~~~~-~E~~d~~W~~~deL~ 245 (275)
.+...++|.+....+ ++.++ +|+.+++|++++++.
T Consensus 83 ~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~Ev~~~~Wv~~~~a~ 129 (143)
T cd04694 83 RGLPKRHHIVVYILVKSSETHQQLQARLQPDPNEVSAAAWLDKSLAK 129 (143)
T ss_pred CCcccceeEEEEEEEEeccccccccccccCChhhccceEeeCHHHHH
Confidence 122333333333221 22343 799999999998865
No 66
>cd04685 Nudix_Hydrolase_26 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.58 E-value=1e-14 Score=119.85 Aligned_cols=103 Identities=26% Similarity=0.312 Sum_probs=74.9
Q ss_pred EEEEeeCCeEEEEEeccCC--CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCcc-ccceeeEEE----EeC--CCCEEE
Q 023914 145 GCLIEHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADV-EVQSPFAQL----DIP--RIGQIY 215 (275)
Q Consensus 145 ~viI~~~~~iLL~rr~~~p--~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v-~~~~~~~~~----~~~--~~~~~~ 215 (275)
+++++.+++|||+++.... ..+.|.+|||+++.||++++|+.||++||||+++ .....+... .+. ..+...
T Consensus 5 ~~i~~~~g~vLl~r~~~~~~~~~~~w~~PgG~ve~gE~~~~a~~Re~~EE~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~ 84 (133)
T cd04685 5 VVLLDPDDRVLLLRGDDPDSPGPDWWFTPGGGVEPGESPEQAARRELREETGITVADLGPPVWRRDAAFTFLGVDGRQEE 84 (133)
T ss_pred EEEEcCCCeEEEEEEeCCCCCCCCEEECCcCCCCCCCCHHHHHHHHHHHHHCCccccccceEEEEEEEEEecCccceeeE
Confidence 4556678999999987542 4689999999999999999999999999999998 545444322 222 223455
Q ss_pred EEEEEEEcCCCCCC----C---CCceeEEEecCCCCCCC
Q 023914 216 IIFLAKLKRPHFSP----G---PESSECRLFALDEIPFD 247 (275)
Q Consensus 216 ~~f~a~~~~~e~~~----~---~E~~d~~W~~~deL~~~ 247 (275)
++|.++...+++.. . .+..+++|+++++|...
T Consensus 85 ~~f~~~~~~~~~~~~~~~~~E~~~~~~~~W~~~~el~~~ 123 (133)
T cd04685 85 RFFLARTPRTEPSPAGWTALERRSILGWRWWTRAELAAT 123 (133)
T ss_pred EEEEEEcCCccccCCCCChhhhhhcccccCCCHHHHhhC
Confidence 77888876543221 1 23457899999999865
No 67
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=99.57 E-value=7.7e-15 Score=126.69 Aligned_cols=105 Identities=19% Similarity=0.389 Sum_probs=75.7
Q ss_pred cEEEEEE-EeeCCeEEEEEeccCC--CCCceeee-eEEeeCCCCHHHHHHHHHHHHhCCccccce-eeEEEEe----CCC
Q 023914 141 KMVVGCL-IEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQS-PFAQLDI----PRI 211 (275)
Q Consensus 141 ~~~V~vi-I~~~~~iLL~rr~~~p--~~g~w~lP-gG~vE~GEs~eeAa~REl~EEtGl~v~~~~-~~~~~~~----~~~ 211 (275)
..+|.++ ++.+++|||+||+... .+|.|.+| ||++++|||+++||+||++||||+++.... +++.+.+ +..
T Consensus 34 h~av~v~i~~~~g~vLL~rR~~~~~~~PG~w~~~~gG~ve~GEt~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~ 113 (184)
T PRK03759 34 HLAFSCYLFDADGRLLVTRRALSKKTWPGVWTNSCCGHPQPGESLEDAVIRRCREELGVEITDLELVLPDFRYRATDPNG 113 (184)
T ss_pred eeEEEEEEEcCCCeEEEEEccCCCCCCCCcccccccCCCCCCCCHHHHHHHHHHHHhCCCccccccccceEEEEEecCCC
Confidence 3444444 4557899999986432 36889887 899999999999999999999999986443 2333321 111
Q ss_pred ---CEEEEEEEEEEcCCCCCCC-CCceeEEEecCCCCCC
Q 023914 212 ---GQIYIIFLAKLKRPHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 212 ---~~~~~~f~a~~~~~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
+..+++|.+... +++.++ +|..+++|++++++..
T Consensus 114 ~~~~~~~~vf~~~~~-~~~~~~~~Ev~~~~W~~~~el~~ 151 (184)
T PRK03759 114 IVENEVCPVFAARVT-SALQPNPDEVMDYQWVDPADLLR 151 (184)
T ss_pred ceeeEEEEEEEEEEC-CCCCCChhHeeeEEEECHHHHHH
Confidence 235567888776 345554 7889999999999864
No 68
>PRK08999 hypothetical protein; Provisional
Probab=99.56 E-value=3.1e-14 Score=131.94 Aligned_cols=107 Identities=23% Similarity=0.303 Sum_probs=79.4
Q ss_pred EEEEEEEeeCCeEEEEEeccC-CCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC--CEEEEEE
Q 023914 142 MVVGCLIEHDKKILLCKRKIE-PSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIF 218 (275)
Q Consensus 142 ~~V~viI~~~~~iLL~rr~~~-p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~--~~~~~~f 218 (275)
.+++++++.++++||.||... ...|+|++|||++|.||++++|+.||++||+|+++.....+....+.++ ...+.+|
T Consensus 7 ~~~~vi~~~~~~vLL~kR~~~~~~~g~w~~PgG~ve~gE~~~~aa~RE~~EE~Gl~~~~~~~l~~~~h~~~~~~~~i~~y 86 (312)
T PRK08999 7 VAAGVIRDADGRILLARRPEGKHQGGLWEFPGGKVEPGETVEQALARELQEELGIEVTAARPLITVRHDYPDKRVRLDVR 86 (312)
T ss_pred EEEEEEECCCCeEEEEEecCCCCCCCeEECCccCCCCCCCHHHHHHHHHHHHhCCceecceeEEEEEEEcCCCeEEEEEE
Confidence 344444456689999998754 3579999999999999999999999999999999877766666554443 3455667
Q ss_pred EEEEcCCCCCCCCCceeEEEecCCCCCCCCC
Q 023914 219 LAKLKRPHFSPGPESSECRLFALDEIPFDSL 249 (275)
Q Consensus 219 ~a~~~~~e~~~~~E~~d~~W~~~deL~~~~l 249 (275)
.+....+.. ...|..+++|+++++++...+
T Consensus 87 ~~~~~~~~~-~~~e~~~~~Wv~~~el~~~~~ 116 (312)
T PRK08999 87 RVTAWQGEP-HGREGQPLAWVAPDELAVYPF 116 (312)
T ss_pred EEEEecCcc-cCccCCccEEecHHHcccCCC
Confidence 666544432 235667889999999995433
No 69
>PRK10729 nudF ADP-ribose pyrophosphatase NudF; Provisional
Probab=99.55 E-value=5.3e-14 Score=123.57 Aligned_cols=109 Identities=18% Similarity=0.159 Sum_probs=81.4
Q ss_pred ccCCcEEEEEEEee-CCeEEEEEeccCCC------CCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe-
Q 023914 137 YQNPKMVVGCLIEH-DKKILLCKRKIEPS------YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI- 208 (275)
Q Consensus 137 y~~p~~~V~viI~~-~~~iLL~rr~~~p~------~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~- 208 (275)
+.++..++++.++. +++|||+++.+.+- +-.|++|+|.+|+||++++||+||+.||||+.+..+.++..+..
T Consensus 46 v~~~~~V~il~~~~~~~~vlLvrQyR~~~~~~~~~~~~lE~PAG~vd~gE~p~~aA~REL~EETGy~a~~~~~l~~~~~s 125 (202)
T PRK10729 46 FERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVGRTKPVLSYLAS 125 (202)
T ss_pred EEcCCeEEEEEEECCCCEEEEEEeeecccccCCCCCeEEEccceEcCCCCCHHHHHHHHHHHHhCceeeEEEEEEEEEcC
Confidence 45566666555554 57999999988763 14699999999999999999999999999999988887765532
Q ss_pred C-CCCEEEEEEEEEEcCC---C--CCC-CCCceeEEEecCCCCC
Q 023914 209 P-RIGQIYIIFLAKLKRP---H--FSP-GPESSECRLFALDEIP 245 (275)
Q Consensus 209 ~-~~~~~~~~f~a~~~~~---e--~~~-~~E~~d~~W~~~deL~ 245 (275)
| ..+..++.|+++.... . ... .+|..++.|++.+++.
T Consensus 126 pg~~~e~~~~fla~~~~~~~~~~~~~~de~E~i~v~~~~~~e~~ 169 (202)
T PRK10729 126 PGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAY 169 (202)
T ss_pred CCcCceEEEEEEEEEcchhcccCCCCCCCCCceEEEEEcHHHHH
Confidence 2 3456778888885221 1 122 2566679999999975
No 70
>TIGR02150 IPP_isom_1 isopentenyl-diphosphate delta-isomerase, type 1. This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate.
Probab=99.52 E-value=2.2e-14 Score=120.95 Aligned_cols=100 Identities=23% Similarity=0.306 Sum_probs=72.8
Q ss_pred EEEEEeeCCeEEEEEeccCC--CCCceeee-eEEeeCCCCHHHHHHHHHHHHhCCccccce--eeEEEE----eCCC-CE
Q 023914 144 VGCLIEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQS--PFAQLD----IPRI-GQ 213 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p--~~g~w~lP-gG~vE~GEs~eeAa~REl~EEtGl~v~~~~--~~~~~~----~~~~-~~ 213 (275)
.+++++.+++|||+||+... .+|.|++| ||+++.|| .+||+||++||||+++...+ .+.... .+.. ..
T Consensus 31 ~v~v~~~~g~vLl~kR~~~k~~~PG~W~~~~gG~v~~GE--~eaa~REl~EE~Gl~~~~~~l~~~~~~~~~~~~~~g~~~ 108 (158)
T TIGR02150 31 SVFLFNEEGQLLLQRRALSKITWPGVWTNSCCSHPLPGE--LEAAIRRLREELGIPADDVPLTVLPRFSYRARDAWGEHE 108 (158)
T ss_pred EEEEEcCCCeEEEEeccCCCcCCCCCccccccCCCCccc--HHHHHHHHHHHHCCCccccceEEcceEEEEEecCCCcEE
Confidence 34445667899999998642 47999998 89999999 49999999999999987654 233222 1212 34
Q ss_pred EEEEEEEEEcCCCCCCC-CCceeEEEecCCCCCC
Q 023914 214 IYIIFLAKLKRPHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 214 ~~~~f~a~~~~~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
...+|.+.... ++.++ +|+.+++|++++|++.
T Consensus 109 ~~~~f~~~~~~-~~~~~~~Ev~~~~W~~~~el~~ 141 (158)
T TIGR02150 109 LCPVFFARAPV-PLNPNPEEVAEYRWVSLEELKE 141 (158)
T ss_pred EEEEEEEecCC-cccCChhHeeeEEEeCHHHHHH
Confidence 55677777654 45555 6999999999999874
No 71
>TIGR00052 nudix-type nucleoside diphosphatase, YffH/AdpP family.
Probab=99.51 E-value=6.1e-14 Score=121.56 Aligned_cols=109 Identities=20% Similarity=0.240 Sum_probs=80.6
Q ss_pred ccCCcEEEEEEEe-eCCeEEEEEeccCC------CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeC
Q 023914 137 YQNPKMVVGCLIE-HDKKILLCKRKIEP------SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP 209 (275)
Q Consensus 137 y~~p~~~V~viI~-~~~~iLL~rr~~~p------~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~ 209 (275)
+.++..+++++++ +++++||+++.+.+ .+..|++|||++|+||++++||+||++||||+.+..+..++.+...
T Consensus 41 v~~~~~v~vl~~~~~~~~vlLvrq~R~~~~~~~~~~~~lelPaG~ve~gE~~~~aA~REl~EEtG~~~~~~~~~~~~~~~ 120 (185)
T TIGR00052 41 YDRGNAAAVLLYDPKKDTVVLIEQFRIAAYVNGEEPWLLELSAGMVEKGESPEDVARREAIEEAGYQVKNLRKLLSFYSS 120 (185)
T ss_pred EEcCCeEEEEEEECCCCEEEEEECceeeeeecCCcceEEEECcEecCCCCCHHHHHHHHccccccceecceEEEEEEEcC
Confidence 3455555555454 45799999987654 2467999999999999999999999999999999888887765432
Q ss_pred --CCCEEEEEEEEEEcCCC---C--CCCCCceeEEEecCCCCC
Q 023914 210 --RIGQIYIIFLAKLKRPH---F--SPGPESSECRLFALDEIP 245 (275)
Q Consensus 210 --~~~~~~~~f~a~~~~~e---~--~~~~E~~d~~W~~~deL~ 245 (275)
..+..++.|+++...+. . ..++|..+..|++++++.
T Consensus 121 ~g~~~~~~~~f~a~~~~~~~~~~~~~~~~E~ie~~~~~~~e~~ 163 (185)
T TIGR00052 121 PGGVTELIHLFIAEVDDNQAAGIGGGADEEEIEVLHLVFSQAL 163 (185)
T ss_pred CCCCcEEEEEEEEEEchhhcCCCCCCCCccceEEEEeCHHHHH
Confidence 23467788999875432 1 123555678999999875
No 72
>PRK10707 putative NUDIX hydrolase; Provisional
Probab=99.49 E-value=2.2e-13 Score=118.63 Aligned_cols=105 Identities=18% Similarity=0.184 Sum_probs=75.8
Q ss_pred EEEEE-EEee-CCeEEEEEeccCC--CCCceeeeeEEeeCC-CCHHHHHHHHHHHHhCCccccceeeEEEEe--CCCCEE
Q 023914 142 MVVGC-LIEH-DKKILLCKRKIEP--SYGLWTLPAGYMEIG-ESAAEGAIRETWEEARADVEVQSPFAQLDI--PRIGQI 214 (275)
Q Consensus 142 ~~V~v-iI~~-~~~iLL~rr~~~p--~~g~w~lPgG~vE~G-Es~eeAa~REl~EEtGl~v~~~~~~~~~~~--~~~~~~ 214 (275)
.+|++ ++.+ ++++||.+|+... ..|.|+||||++|+| |++++||+||++||||+.+..+.+++.... +..+..
T Consensus 32 aavvl~l~~~~~~~vLl~~R~~~~r~~~G~~~~PGG~~e~~de~~~~tA~REl~EEtGl~~~~~~~lg~l~~~~~~~~~~ 111 (190)
T PRK10707 32 AAVLIPIVRRPQPTLLLTQRSIHLRKHAGQVAFPGGAVDPTDASLIATALREAQEEVAIPPSAVEVIGVLPPVDSSTGYQ 111 (190)
T ss_pred eEEEEEEEECCCCEEEEEEeCCcccCCCCcEEcCCcccCCCcccHHHHHHHHHHHHHCCCccceEEEEEeeeeeccCCcE
Confidence 44433 4333 4589999977543 368999999999975 689999999999999999999998887652 333444
Q ss_pred EEEEEEEEcCC-CCCCC-CCceeEEEecCCCCCC
Q 023914 215 YIIFLAKLKRP-HFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 215 ~~~f~a~~~~~-e~~~~-~E~~d~~W~~~deL~~ 246 (275)
...|.+.+... ...++ +|..++.|++++++..
T Consensus 112 ~~~~v~~~~~~~~~~~d~~Ev~~v~~vpl~e~~~ 145 (190)
T PRK10707 112 VTPVVGIIPPDLPYRANEDEVAAVFEMPLAEALH 145 (190)
T ss_pred EEEEEEEECCCCCCCCChhhhheEEEEeHHHHhC
Confidence 44454444332 33444 7888999999999764
No 73
>TIGR02705 nudix_YtkD nucleoside triphosphatase YtkD. The functional assignment to the proteins of this family is contentious. Reference challenges the findings of reference, both in interpretation and in enzyme assay results. This protein belongs to the nudix family and shares some sequence identity with E. coli MutT but appears not to be functionally interchangeable with it.
Probab=99.49 E-value=2.7e-13 Score=114.49 Aligned_cols=98 Identities=26% Similarity=0.280 Sum_probs=74.8
Q ss_pred EEEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCC--CCEEEEEEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPR--IGQIYIIFLA 220 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~--~~~~~~~f~a 220 (275)
.|.++...++++||+++.. ..|++|||++|+||++++||.||++||||+.+..+++++.+.... .......|.|
T Consensus 26 ~V~ii~~~~~~~LL~~~~~----~~~elPgG~vE~gEt~~eaA~REl~EETG~~~~~~~~lg~~~~~~~~~~~~~~vf~A 101 (156)
T TIGR02705 26 HVLVIPRYKDQWLLTEHKR----RGLEFPGGKVEPGETSKEAAIREVMEETGAIVKELHYIGQYEVEGESTDFVKDVYFA 101 (156)
T ss_pred EEEEEEEECCEEEEEEEcC----CcEECCceecCCCCCHHHHHHHHHHHHhCcEeeeeEEEEEEEecCCCcEEEEEEEEE
Confidence 3444445566999998763 349999999999999999999999999999999999999876533 3466788999
Q ss_pred EEcCCCCCCCCCceeEE-EecCCCCCC
Q 023914 221 KLKRPHFSPGPESSECR-LFALDEIPF 246 (275)
Q Consensus 221 ~~~~~e~~~~~E~~d~~-W~~~deL~~ 246 (275)
+....+ ..+|..+.. ++++++++.
T Consensus 102 ~~~~~~--~~~e~~E~~~~~~~~~~~~ 126 (156)
T TIGR02705 102 EVSALE--SKDDYLETKGPVLLQEIPD 126 (156)
T ss_pred EEeccc--cCCCceeeEeEEEHHHHHH
Confidence 987443 225545555 688888753
No 74
>cd03670 ADPRase_NUDT9 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the Nudix hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue Nudix motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the Nudix motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer.
Probab=99.49 E-value=4.5e-13 Score=116.12 Aligned_cols=99 Identities=20% Similarity=0.237 Sum_probs=68.6
Q ss_pred eEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccc----------------eeeEEE----EeCCC-
Q 023914 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ----------------SPFAQL----DIPRI- 211 (275)
Q Consensus 153 ~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~----------------~~~~~~----~~~~~- 211 (275)
++|+++|+ ..|.|.+|||++|+||++++|++||++||||+.+..+ ..+.++ ..|..
T Consensus 50 ~vLl~~r~---~~g~walPGG~v~~~E~~~~aa~Rel~EEt~l~l~~~~~~~~~l~~l~~~~~~~~~~vy~~~~~dpr~t 126 (186)
T cd03670 50 QFVAIKRP---DSGEWAIPGGMVDPGEKISATLKREFGEEALNSLQKSDEEKEEIKKLVELFSKDGVEVYKGYVDDPRNT 126 (186)
T ss_pred EEEEEEeC---CCCcCcCCeeeccCCCCHHHHHHHHHHHHHcccccccchhhhhhcchhhhhcccccEEEeccccCCCCC
Confidence 78888886 3689999999999999999999999999997653221 012222 12221
Q ss_pred ---CEEEEEEEEEEcCC------CCCCCCCceeEEEecCCCCCCCCCCCcHHHH
Q 023914 212 ---GQIYIIFLAKLKRP------HFSPGPESSECRLFALDEIPFDSLAFSSISV 256 (275)
Q Consensus 212 ---~~~~~~f~a~~~~~------e~~~~~E~~d~~W~~~deL~~~~l~~~s~~~ 256 (275)
....+.|......+ .+...+|..+++||++++++ ++.+++..+
T Consensus 127 d~~w~~Tva~~f~~~~~~~~~~~~~~a~dda~~a~W~~v~~l~--~L~~dH~~I 178 (186)
T cd03670 127 DNAWMETVAVNFHDEDGNDVENLPLEAGDDAGSVRWQDIDSKL--PLYANHSQF 178 (186)
T ss_pred CcceEEEEEEEEEecCcccccccccCCCCchheeEEEEccccc--ccccCHHHH
Confidence 22445555544322 23345788999999999998 677777544
No 75
>cd04662 Nudix_Hydrolase_5 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate s
Probab=99.48 E-value=3.8e-13 Score=109.71 Aligned_cols=90 Identities=21% Similarity=0.200 Sum_probs=62.0
Q ss_pred CeEEEEEeccC----CCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccc-eeeEEEEeCC---------------C
Q 023914 152 KKILLCKRKIE----PSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ-SPFAQLDIPR---------------I 211 (275)
Q Consensus 152 ~~iLL~rr~~~----p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~-~~~~~~~~~~---------------~ 211 (275)
.+|||++|... +..+.|++|||+++.||++++||+||++||||+++... ..+..+..+. .
T Consensus 15 ~~vlL~~~~~~~~~~~~~~~W~lPgG~ie~~E~~~~aA~REl~EEtGl~~~~~~~~l~~~~~~~~~~v~~fl~~~~~d~~ 94 (126)
T cd04662 15 IEVLLVHPGGPFWANKDLGAWSIPKGEYTEGEDPLLAAKREFSEETGFCVDGPFIDLGSLKQSGGKVVHAWAVEADLDIT 94 (126)
T ss_pred EEEEEEEccCccccCCCCCEEECCcccCCCCcCHHHHHHHHHHHHhCCcceeeEEeEEEEECCCCeEEEEEEEEecCChh
Confidence 36999987432 34688999999999999999999999999999987411 1122222111 1
Q ss_pred CEEEEEEEEEEcCCCCCC--CCCceeEEEecC
Q 023914 212 GQIYIIFLAKLKRPHFSP--GPESSECRLFAL 241 (275)
Q Consensus 212 ~~~~~~f~a~~~~~e~~~--~~E~~d~~W~~~ 241 (275)
....++|.+....++... .+|..+++||+.
T Consensus 95 ~~~~~~f~~~~~~~~~~~~~~~e~~~~~w~~~ 126 (126)
T cd04662 95 DIKSNTFEMEWPKGSGKMRKFPEVDRAGWFDI 126 (126)
T ss_pred HeEEEEEEEEccCCCCccccCCccceeEeecC
Confidence 233455666655544433 488889999973
No 76
>cd03676 Nudix_hydrolase_3 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate spe
Probab=99.45 E-value=4.6e-13 Score=114.92 Aligned_cols=107 Identities=22% Similarity=0.253 Sum_probs=75.2
Q ss_pred CeEEEEEeccCC--CCCcee-eeeEEeeCCCCHHHHHHHHHHHHhCCccccc---eeeEEEE--e--CC---CCEEEEEE
Q 023914 152 KKILLCKRKIEP--SYGLWT-LPAGYMEIGESAAEGAIRETWEEARADVEVQ---SPFAQLD--I--PR---IGQIYIIF 218 (275)
Q Consensus 152 ~~iLL~rr~~~p--~~g~w~-lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~---~~~~~~~--~--~~---~~~~~~~f 218 (275)
++++++||+... .+|+|+ +|||+++.||++++||+||++||||+++... .+++... . .. .+...++|
T Consensus 48 ~~l~lqrRs~~K~~~Pg~wd~~~~G~v~~gE~~~~aA~REl~EE~Gl~~~~~~~l~~~g~~~~~~~~~~~~~~~e~~~~f 127 (180)
T cd03676 48 LRIWIPRRSPTKATWPGMLDNLVAGGLGHGEGPEETLVKECDEEAGLPEDLVRQLKPVGVVSYLREGEAGGLQPEVEYVY 127 (180)
T ss_pred eEEEEEeccCCCCCCCCceeeecccCCCCCCCHHHHHHHHHHHHhCCCHHHHhhceeccEEEEEEEcCCCcEeeeEEEEE
Confidence 799999998764 489995 8999999999999999999999999998653 3333221 1 11 12455667
Q ss_pred EEEEcCCC-CCCC-CCceeEEEecCCCCCC----CCCCCcHHHHHH
Q 023914 219 LAKLKRPH-FSPG-PESSECRLFALDEIPF----DSLAFSSISVTL 258 (275)
Q Consensus 219 ~a~~~~~e-~~~~-~E~~d~~W~~~deL~~----~~l~~~s~~~al 258 (275)
.+.+.... +.++ +|..++.|++++|+.. .++.+.....++
T Consensus 128 ~~~~~~~~~~~~~~~Ev~~~~~~~~~el~~~l~~g~~~~~~~lv~~ 173 (180)
T cd03676 128 DLELPPDFIPAPQDGEVESFRLLTIDEVLRALKEGEFKPNCALVTL 173 (180)
T ss_pred EEEcCCCCeeCCCCCcEeEEEEECHHHHHHHHHcCCCCcccHhHHH
Confidence 77654332 3344 7899999999999753 345444433333
No 77
>PRK15009 GDP-mannose pyrophosphatase NudK; Provisional
Probab=99.40 E-value=3.3e-12 Score=111.29 Aligned_cols=109 Identities=17% Similarity=0.134 Sum_probs=78.9
Q ss_pred ccCCcEEEEEEEee-CCeEEEEEeccCC-------CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEE-
Q 023914 137 YQNPKMVVGCLIEH-DKKILLCKRKIEP-------SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD- 207 (275)
Q Consensus 137 y~~p~~~V~viI~~-~~~iLL~rr~~~p-------~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~- 207 (275)
+.++..+++++++. +++++|+++.+.+ .+-.|++|||.+|+| ++++||+||+.||||+.+..+.+++.+.
T Consensus 42 v~~~~~v~Vl~~~~~~~~vvLvrQyR~~v~~~~~~~~~~lElPAG~vd~~-~p~~aA~REL~EETGy~a~~~~~l~~~~~ 120 (191)
T PRK15009 42 YDRGNGATILLYNAKKKTVVLIRQFRVATWVNGNESGQLIETCAGLLDND-EPEVCIRKEAIEETGYEVGEVRKLFELYM 120 (191)
T ss_pred EEECCEEEEEEEECCCCEEEEEEcccccccccCCCCceEEEEeccccCCC-CHHHHHHHHHHHhhCCccceEEEeeEEEc
Confidence 34455554444444 6799999999876 234599999999976 6999999999999999998888877652
Q ss_pred eC-CCCEEEEEEEEEEcCC-CC----CCCCCceeEEEecCCCCCC
Q 023914 208 IP-RIGQIYIIFLAKLKRP-HF----SPGPESSECRLFALDEIPF 246 (275)
Q Consensus 208 ~~-~~~~~~~~f~a~~~~~-e~----~~~~E~~d~~W~~~deL~~ 246 (275)
.| ..+..++.|+|+.... .. ..++|..++.|++.+++..
T Consensus 121 spG~s~e~~~lf~a~~~~~~~~~~~~~de~E~iev~~~~~~e~~~ 165 (191)
T PRK15009 121 SPGGVTELIHFFIAEYSDSQRANAGGGVEDEDIEVLELPFSQALE 165 (191)
T ss_pred CCcccCcEEEEEEEEECchhcccCCCCCCCceEEEEEEcHHHHHH
Confidence 22 2346777888886421 11 1236667899999999753
No 78
>cd04663 Nudix_Hydrolase_6 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V) which functions as metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are
Probab=99.35 E-value=1.1e-11 Score=101.11 Aligned_cols=91 Identities=15% Similarity=0.194 Sum_probs=57.6
Q ss_pred eEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCcccccee-eEEEEeC--CCCEEEEEEEEEEcCC--C-
Q 023914 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSP-FAQLDIP--RIGQIYIIFLAKLKRP--H- 226 (275)
Q Consensus 153 ~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~-~~~~~~~--~~~~~~~~f~a~~~~~--e- 226 (275)
++|+.|.. .+.|.+|||.+++||++++||+||++||||+++..... .+..+.. ..+..++.+.+..... +
T Consensus 15 ~ll~~r~~----~~~~~lPgG~ve~~E~~~~aa~Rel~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 90 (126)
T cd04663 15 ELLVFEHP----LAGFQIVKGTVEPGETPEAAALRELQEESGLPSFLSDYILHVWERRFYQKRHFWHLTLCEVDQDLPDS 90 (126)
T ss_pred EEEEEEcC----CCcEECCCccCCCCCCHHHHHHHHHHHHHCCeeeeeeecceeeeCCEeeccEEEEEEEEEecCCCccc
Confidence 67777654 24599999999999999999999999999999732222 2222211 1334444444544211 1
Q ss_pred ---CCCCCCcee--EEEecCCCCCCC
Q 023914 227 ---FSPGPESSE--CRLFALDEIPFD 247 (275)
Q Consensus 227 ---~~~~~E~~d--~~W~~~deL~~~ 247 (275)
....+|... +.|+++++++..
T Consensus 91 ~~~~~~~~E~~~i~~~Wv~l~~~~~~ 116 (126)
T cd04663 91 WVHFVQDDGGHEFRFFWVDLASCLDE 116 (126)
T ss_pred ccCcccCCCCceEEEEEEcccccccc
Confidence 112234444 459999999753
No 79
>PLN02709 nudix hydrolase
Probab=99.34 E-value=4.8e-12 Score=112.36 Aligned_cols=95 Identities=21% Similarity=0.210 Sum_probs=73.0
Q ss_pred CeEEEEEeccC--CCCCceeeeeEEeeCC-CCHHHHHHHHHHHHhCCccccceeeEEEE--eCCCCEEEEEEEEEEcC--
Q 023914 152 KKILLCKRKIE--PSYGLWTLPAGYMEIG-ESAAEGAIRETWEEARADVEVQSPFAQLD--IPRIGQIYIIFLAKLKR-- 224 (275)
Q Consensus 152 ~~iLL~rr~~~--p~~g~w~lPgG~vE~G-Es~eeAa~REl~EEtGl~v~~~~~~~~~~--~~~~~~~~~~f~a~~~~-- 224 (275)
.+|||.+|+.. +..|.|+||||++|+| +++.+||+||++||+|+....++.++..+ .+..+....-|.+.+..
T Consensus 51 ~~vLl~~Rs~~l~~h~GqiafPGG~~e~~D~~~~~tAlRE~~EEiGl~~~~v~vlg~L~~~~t~sg~~V~P~V~~~~~~~ 130 (222)
T PLN02709 51 LRVILTKRSSTLSSHPGEVALPGGKRDEEDKDDIATALREAREEIGLDPSLVTIISVLEPFVNKKGMSVAPVIGFLHDKK 130 (222)
T ss_pred eEEEEEEcCCCCCCCCCCccCCCcccCCCCCCHHHHHHHHHHHHHCCCchheEEeeecCCeECCCCCEEEEEEEEecCCC
Confidence 38999999876 3589999999999997 57899999999999999998888887654 22234445556665543
Q ss_pred -CCCCCC-CCceeEEEecCCCCCC
Q 023914 225 -PHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 225 -~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
..+.++ +|.+++.|++++++..
T Consensus 131 ~~~~~~np~EV~~vf~vPL~~ll~ 154 (222)
T PLN02709 131 AFKPLPNPAEVEEIFDVPLEMFLK 154 (222)
T ss_pred CccccCChhhhheeEEecHHHHhC
Confidence 123345 7999999999998754
No 80
>COG0494 MutT NTP pyrophosphohydrolases including oxidative damage repair enzymes [DNA replication, recombination, and repair / General function prediction only]
Probab=99.24 E-value=1.3e-10 Score=92.46 Aligned_cols=104 Identities=27% Similarity=0.387 Sum_probs=68.0
Q ss_pred EEEEEEeeC--CeEEEEEeccCCCCCceeeeeEEeeCCCCHHH-HHHHHHHHHhCCccc--cceeeEEEEeCCCC-----
Q 023914 143 VVGCLIEHD--KKILLCKRKIEPSYGLWTLPAGYMEIGESAAE-GAIRETWEEARADVE--VQSPFAQLDIPRIG----- 212 (275)
Q Consensus 143 ~V~viI~~~--~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~ee-Aa~REl~EEtGl~v~--~~~~~~~~~~~~~~----- 212 (275)
++.+++..+ .++|+.+|.... +.|.+|||.+|.||+.++ ||+||++||||+.+. ....++.+......
T Consensus 13 ~~~~~~~~~~~~~vl~~~~~~~~--~~~~~PgG~ve~~e~~~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~ 90 (161)
T COG0494 13 AVAVLVGRDGPGEVLLAQRRDDG--GLWELPGGKVEPGEELPEEAAARELEEETGLRVKDERLELLGEFPPSPGDGSSVG 90 (161)
T ss_pred eEEEEEecCCCCEEeEEEccccC--CceecCCcccCCCCchHHHHHHHHHHHHhCCeeeeecceeeeeccCcccCccccc
Confidence 333434333 789999888543 689999999999999888 999999999999988 56665555432221
Q ss_pred -EEE-EEEEEEEc---CCCCCC----CCCceeEEEecCCCCCCCC
Q 023914 213 -QIY-IIFLAKLK---RPHFSP----GPESSECRLFALDEIPFDS 248 (275)
Q Consensus 213 -~~~-~~f~a~~~---~~e~~~----~~E~~d~~W~~~deL~~~~ 248 (275)
... ..+..... ...... ..|..+..|++.+++....
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~ 135 (161)
T COG0494 91 GREHRVFFVAEVDDSLAVAIEGLSAPSEELEDLEWVPLDELAALV 135 (161)
T ss_pred ceEEEEEEeeeccccccccccccCCCcchhhceeeeeHHHccccc
Confidence 111 12222211 111111 1467889999999987543
No 81
>PLN03143 nudix hydrolase; Provisional
Probab=99.18 E-value=1.5e-10 Score=106.72 Aligned_cols=109 Identities=17% Similarity=0.191 Sum_probs=69.5
Q ss_pred ccCCc-EEEEEEEeeCCe--EEEEEeccCCC-CCceeeeeEEeeC-CCCHHHHHHHHHHHHhCCcccc--ceee------
Q 023914 137 YQNPK-MVVGCLIEHDKK--ILLCKRKIEPS-YGLWTLPAGYMEI-GESAAEGAIRETWEEARADVEV--QSPF------ 203 (275)
Q Consensus 137 y~~p~-~~V~viI~~~~~--iLL~rr~~~p~-~g~w~lPgG~vE~-GEs~eeAa~REl~EEtGl~v~~--~~~~------ 203 (275)
+.++. ++|.++++.+++ ++|++|.+.|. .-.|++|||.+|+ ||++++||+||++||||+.+.. ...+
T Consensus 125 ~~rg~aVaVL~~l~~~ge~~VlLVrQ~R~pvg~~~lE~PAG~lD~~~edp~~aA~REL~EETG~~~~a~~lv~L~~~~~~ 204 (291)
T PLN03143 125 FARGPAVAVLILLESEGETYAVLTEQVRVPVGKFVLELPAGMLDDDKGDFVGTAVREVEEETGIKLKLEDMVDLTAFLDP 204 (291)
T ss_pred EEcCCeEEEEEEEeCCCCEEEEEEEeEecCCCcEEEEecccccCCCCCCHHHHHHHHHHHHHCCccccceEEEeeecccc
Confidence 44443 344444454444 99999998663 4579999999997 4899999999999999998643 2222
Q ss_pred ----EEEEeCCC-CEEEEEEEEEEcCC---------C---CCCCCCceeEEEecCCCCC
Q 023914 204 ----AQLDIPRI-GQIYIIFLAKLKRP---------H---FSPGPESSECRLFALDEIP 245 (275)
Q Consensus 204 ----~~~~~~~~-~~~~~~f~a~~~~~---------e---~~~~~E~~d~~W~~~deL~ 245 (275)
..++.+.. ...+..|.+..... . ....+|..++.|++.+++-
T Consensus 205 ~~g~~v~pspG~~dE~i~Lfla~~~v~~~~l~~l~~~~~~l~degE~Iev~~vpl~eiw 263 (291)
T PLN03143 205 STGCRMFPSPGGCDEEISLFLYRGHVDKETIRQLQGKETGLRDHGELIKVHVVPYRELW 263 (291)
T ss_pred CcCceEEecCCccCCeEEEEEEccccchhhhcccccccCCCCCCCcEEEEEEEEHHHHH
Confidence 22233221 23444555443211 1 1123566789999999965
No 82
>PLN02552 isopentenyl-diphosphate delta-isomerase
Probab=99.17 E-value=1.4e-10 Score=104.71 Aligned_cols=102 Identities=15% Similarity=0.183 Sum_probs=68.0
Q ss_pred EEEEeeCCeEEEEEeccCC--CCCceeee-eEEeeCCCC-----------------HHHHHHHHHHHHhCCcccc-----
Q 023914 145 GCLIEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGES-----------------AAEGAIRETWEEARADVEV----- 199 (275)
Q Consensus 145 ~viI~~~~~iLL~rr~~~p--~~g~w~lP-gG~vE~GEs-----------------~eeAa~REl~EEtGl~v~~----- 199 (275)
+.|.+.++++||+||+... .+|+|+.. +|++..||+ ..+||+||++||+||.+..
T Consensus 61 v~i~n~~g~lLLQkRs~~K~~~Pg~Wd~s~~GHp~~ge~~~e~~~e~~~~~~~~~~~~eAA~REL~EElGI~~~~~~~~~ 140 (247)
T PLN02552 61 VFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLYGQDPNEVDRESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQ 140 (247)
T ss_pred EEEEcCCCeEEEEEecCCCCCCCcceecccCCccccccccccccccccccccchhhHHHHHHhHHHHHhCCCcccccccc
Confidence 3445677899999998754 58999766 455544422 6789999999999998643
Q ss_pred ceeeEEEEeCC---------C----CEEEEEEEEE-EcCCCCCCC-CCceeEEEecCCCCCC
Q 023914 200 QSPFAQLDIPR---------I----GQIYIIFLAK-LKRPHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 200 ~~~~~~~~~~~---------~----~~~~~~f~a~-~~~~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
+.+++.+.+.. . +...++|... ...+++.++ +|+.+++|+++++++.
T Consensus 141 l~~~~~~~y~~~~~~~~~~~~~~~E~e~~~v~~~~~~~~~~l~lq~eEV~~~~wvs~~el~~ 202 (247)
T PLN02552 141 FTFLTRLHYKAADDVTHGPDGKWGEHELDYLLFIRPVRDVKVNPNPDEVADVKYVNREELKE 202 (247)
T ss_pred ceeeeEEEEecccccccccCCCccceEEEEEEEEEecCCCcccCCHHHhheEEEEeHHHHHH
Confidence 45555433211 1 2222333333 223456666 8999999999999874
No 83
>cd03431 DNA_Glycosylase_C DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important for the repair of various genotoxic lesions. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity. They are also recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V). However, DNA glycosylase does not seem to contain this signature motif. DNA glycosylase consists of 2 domains: the N-terminal domain contains the catalytic properties of the enzyme and the C-terminal domain affects substrate (oxoG) binding and enzymatic turnover. The C-terminal domain is highly similar to MutT, based on secondary structure and topology, despite low sequence identity. MutT sanitizes the nucleotide precursor pool by hydrolyzing oxo-dGTP to
Probab=99.12 E-value=8.3e-10 Score=86.70 Aligned_cols=102 Identities=22% Similarity=0.302 Sum_probs=73.3
Q ss_pred EEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCC--EEEEEEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIFL 219 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~--~~~~~f~ 219 (275)
.+++++.+++++||.||.... .+|+|+||+|.++.+|+.+++..||+.||.++ ....++.....+.+ ..+.+|.
T Consensus 5 ~~~~ii~~~~~~ll~kR~~~gl~~glwefP~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~H~fth~~~~~~~~~ 81 (118)
T cd03431 5 IAVVVIRNDGRVLLEKRPEKGLLAGLWEFPSVEWEEEADGEEALLSALKKALRL---SLEPLGTVKHTFTHFRLTLHVYL 81 (118)
T ss_pred EEEEEEecCCeEEEEECCCCCCCCcceeCCCccccCCcCHHHHHHHHHHHHhCc---ccccceeEEEecCCeEEEEEEEE
Confidence 445556667899999997654 58999999999999999999999999999765 22234444444433 4566787
Q ss_pred EEEcCCCCCCCCCceeEEEecCCCCCCCCCCCcH
Q 023914 220 AKLKRPHFSPGPESSECRLFALDEIPFDSLAFSS 253 (275)
Q Consensus 220 a~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s 253 (275)
+....+. .+..+.+|++.++++. ++++.
T Consensus 82 ~~~~~~~----~~~~~~~W~~~eel~~--~~~p~ 109 (118)
T cd03431 82 ARLEGDL----LAPDEGRWVPLEELDE--YALPT 109 (118)
T ss_pred EEEeCCC----cCccccEEccHHHHhh--CCCCH
Confidence 7765542 2446789999999984 44444
No 84
>PLN02791 Nudix hydrolase homolog
Probab=99.02 E-value=9.6e-10 Score=112.65 Aligned_cols=104 Identities=20% Similarity=0.239 Sum_probs=74.3
Q ss_pred EEEEEEE-ee-CCeEEEEEeccCC--CCCceee-eeEEeeCCCCHHHHHHHHHHHHhCCccc--cceeeEEEEe----CC
Q 023914 142 MVVGCLI-EH-DKKILLCKRKIEP--SYGLWTL-PAGYMEIGESAAEGAIRETWEEARADVE--VQSPFAQLDI----PR 210 (275)
Q Consensus 142 ~~V~viI-~~-~~~iLL~rr~~~p--~~g~w~l-PgG~vE~GEs~eeAa~REl~EEtGl~v~--~~~~~~~~~~----~~ 210 (275)
.++.+++ +. ++++||+||+... .+|.|++ +||+++.||+.++|++||+.||+||.+. .+.+++.+.. ..
T Consensus 33 rAvhVwIfn~~~gelLLQkRS~~K~~~PG~WDiS~gGHv~aGEs~~eAA~REL~EELGI~l~~~~l~~l~~~~~~~~~~~ 112 (770)
T PLN02791 33 RAVHVWIYSESTQELLLQRRADCKDSWPGQWDISSAGHISAGDTSLLSAQRELEEELGIILPKDAFELLFVFLQECVIND 112 (770)
T ss_pred EEEEEEEEECCCCeEEEEEecCCCCCCCCcccCcCCCCCCCCCCHHHHHHHHHHHHhCCCCChhheeeeeeEEEEeeccC
Confidence 4454444 43 5899999998654 4899999 6999999999999999999999999863 3444444311 11
Q ss_pred ----CCEEEEEEEEEEcCC----CCCCC-CCceeEEEecCCCCC
Q 023914 211 ----IGQIYIIFLAKLKRP----HFSPG-PESSECRLFALDEIP 245 (275)
Q Consensus 211 ----~~~~~~~f~a~~~~~----e~~~~-~E~~d~~W~~~deL~ 245 (275)
.+....+|.+..... ++.++ +|+.+++|++.+|+.
T Consensus 113 g~~~e~E~~~VYlv~~~~~~p~~~~~lq~eEV~~v~wvsl~El~ 156 (770)
T PLN02791 113 GKFINNEYNDVYLVTTLDPIPLEAFTLQESEVSAVKYMSIEEYK 156 (770)
T ss_pred CCcceeeEEEEEEEEECCCCCcccCCCChhhhheeEEEcHHHHH
Confidence 124455676654332 34555 899999999999975
No 85
>KOG2839 consensus Diadenosine and diphosphoinositol polyphosphate phosphohydrolase [Signal transduction mechanisms]
Probab=98.94 E-value=7.1e-10 Score=91.42 Aligned_cols=92 Identities=26% Similarity=0.355 Sum_probs=63.6
Q ss_pred CeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEE-eCCCC-EE----EEEEEEEEcCC
Q 023914 152 KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD-IPRIG-QI----YIIFLAKLKRP 225 (275)
Q Consensus 152 ~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~-~~~~~-~~----~~~f~a~~~~~ 225 (275)
-+|||+..+..+ ..|.+|+|++|+||+..+||.||++||.|+.....+.++.+. +.... .. +++.++....-
T Consensus 24 ieVLlvsSs~~~--~~wi~PKGGwE~dE~~~eAA~REt~EEAGv~G~l~~~~~g~~~~~~~~~~~~~k~~~~~l~v~e~l 101 (145)
T KOG2839|consen 24 IEVLLVSSSKKP--HRWIVPKGGWEPDESVEEAALRETWEEAGVKGKLGRLLGGFEDFLSKKHRTKPKGVMYVLAVTEEL 101 (145)
T ss_pred eEEEEEecCCCC--CCccCCCCCCCCCCCHHHHHHHHHHHHhCceeeeeccccchhhccChhhcccccceeehhhhhhhc
Confidence 389999987643 569999999999999999999999999999988888655443 22211 11 11122222222
Q ss_pred CCCCC--CCceeEEEecCCCCC
Q 023914 226 HFSPG--PESSECRLFALDEIP 245 (275)
Q Consensus 226 e~~~~--~E~~d~~W~~~deL~ 245 (275)
+..++ .|..+.+|+.++|.-
T Consensus 102 e~wp~~~~~~r~r~W~~ledA~ 123 (145)
T KOG2839|consen 102 EDWPESEHEFREREWLKLEDAI 123 (145)
T ss_pred ccChhhhcccceeEEeeHHHHH
Confidence 23333 457789999999854
No 86
>KOG3041 consensus Nucleoside diphosphate-sugar hydrolase of the MutT (NUDIX) family [Replication, recombination and repair]
Probab=98.88 E-value=1.1e-08 Score=88.41 Aligned_cols=107 Identities=23% Similarity=0.186 Sum_probs=72.6
Q ss_pred CcEEEEEEEeeCC--eEEEEEeccCCCCC-ceeeeeEEeeCCCCHHHHHHHHHHHHhCCcccccee-eEEEE---eCCCC
Q 023914 140 PKMVVGCLIEHDK--KILLCKRKIEPSYG-LWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSP-FAQLD---IPRIG 212 (275)
Q Consensus 140 p~~~V~viI~~~~--~iLL~rr~~~p~~g-~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~-~~~~~---~~~~~ 212 (275)
+.+++.+++..++ .++|+++.+.|-++ -.++|+|-+|.||+.++||+||++||||+.-+.... ...+. +.+-+
T Consensus 74 dgVaIl~il~~dG~~~ivL~kQfRpP~Gk~ciElPAGLiD~ge~~~~aAiREl~EEtGy~gkv~~~s~~~f~DPGltn~~ 153 (225)
T KOG3041|consen 74 DGVAILAILESDGKPYIVLVKQFRPPTGKICIELPAGLIDDGEDFEGAAIRELEEETGYKGKVDMVSPTVFLDPGLTNCN 153 (225)
T ss_pred CeEEEEEEEecCCcEEEEEEEeecCCCCcEEEEcccccccCCCchHHHHHHHHHHHhCccceeeeccccEEcCCCCCCCc
Confidence 3456666666655 68999999888433 388999999999999999999999999998433221 11222 22334
Q ss_pred EEEEEEEEEEcCCC-CC----C-CCCceeEEEecCCCCCC
Q 023914 213 QIYIIFLAKLKRPH-FS----P-GPESSECRLFALDEIPF 246 (275)
Q Consensus 213 ~~~~~f~a~~~~~e-~~----~-~~E~~d~~W~~~deL~~ 246 (275)
..++.+..+....+ .+ + +.|..++.-++..+|..
T Consensus 154 ~~iv~v~idg~~pEnqrp~q~ledgEfIev~~i~~~~L~~ 193 (225)
T KOG3041|consen 154 LCIVVVDIDGDVPENQRPVQQLEDGEFIEVFLIPLSELWR 193 (225)
T ss_pred eEEEEEEecCCCccccCccccCCCCceEEEEEeeHHHHHH
Confidence 56666666654433 11 2 37778888888877653
No 87
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=98.82 E-value=1.3e-09 Score=68.93 Aligned_cols=34 Identities=41% Similarity=1.094 Sum_probs=22.5
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
+|||.||++++...++||+..|.+|++||+++|.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~IhY~ 34 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFIHYQ 34 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEEE--
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCEEeC
Confidence 6999999999999999999999999999999983
No 88
>KOG3069 consensus Peroxisomal NUDIX hydrolase [Replication, recombination and repair]
Probab=98.77 E-value=1.9e-08 Score=89.14 Aligned_cols=115 Identities=23% Similarity=0.195 Sum_probs=79.2
Q ss_pred CCCccccCCcEEEEEEEeeC----CeEEEEEeccCC--CCCceeeeeEEeeCC-CCHHHHHHHHHHHHhCCccccceeeE
Q 023914 132 CGKIAYQNPKMVVGCLIEHD----KKILLCKRKIEP--SYGLWTLPAGYMEIG-ESAAEGAIRETWEEARADVEVQSPFA 204 (275)
Q Consensus 132 Cg~~~y~~p~~~V~viI~~~----~~iLL~rr~~~p--~~g~w~lPgG~vE~G-Es~eeAa~REl~EEtGl~v~~~~~~~ 204 (275)
|....++++..+|.+.+..+ .++||.||.+.- ..|.-+||||.+|+. ++-+++|.||.+||.|++...+.+++
T Consensus 34 ~~~~~~~~~~~aVlI~L~~~~~~~l~vLltkRSr~LrshsGev~fPGG~~d~~D~s~~~tAlREt~EEIGl~~~~~~~~g 113 (246)
T KOG3069|consen 34 SETHDFPNRKAAVLIPLVQVGSGELSVLLTKRSRTLRSHSGEVCFPGGRRDPHDKSDIQTALRETEEEIGLDPELVDVLG 113 (246)
T ss_pred cccccCCCCCccEEEEEEEcCCCceEEEEEeccccccccCCceeCCCCcCCccccchHHHHHHHHHHHhCCCHHHhhhhh
Confidence 44455577777766555332 489999998653 378999999999964 67888999999999999987777666
Q ss_pred EEE---eCCC--CEEEEEEEEEEcC-CCCCCC-CCceeEEEecCCCCCC
Q 023914 205 QLD---IPRI--GQIYIIFLAKLKR-PHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 205 ~~~---~~~~--~~~~~~f~a~~~~-~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
..+ .+.. -.-+++|.....- ....++ +|..++.|++++++-.
T Consensus 114 ~l~~~~~r~~~~v~p~v~~l~~~~~l~~~~ln~gEv~~~F~VPL~~ll~ 162 (246)
T KOG3069|consen 114 ALPPFVLRSGWSVFPVVGFLSDKKILPSLRLNSGEVESAFWVPLTDLLL 162 (246)
T ss_pred hccceeeccCcccceeEEEEecccccccccCCchheeeeeeeeHHHHhh
Confidence 443 1111 1223445444321 223444 8999999999999764
No 89
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=98.70 E-value=5.6e-09 Score=65.16 Aligned_cols=32 Identities=31% Similarity=0.643 Sum_probs=22.7
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
++++|||+||+++... ++++.++|++||..+|
T Consensus 1 ~~~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~~y 32 (32)
T PF09297_consen 1 RNHRFCGRCGAPTKPA----PGGWARRCPSCGHEHY 32 (32)
T ss_dssp HTTSB-TTT--BEEE-----SSSS-EEESSSS-EE-
T ss_pred CCCcccCcCCccccCC----CCcCEeECCCCcCEeC
Confidence 4789999999999888 7899999999999887
No 90
>PF14815 NUDIX_4: NUDIX domain; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A.
Probab=98.65 E-value=9.6e-08 Score=75.72 Aligned_cols=105 Identities=17% Similarity=0.191 Sum_probs=65.1
Q ss_pred EEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCC--EEEEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIFLA 220 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~--~~~~~f~a 220 (275)
|.+++++++++||.||.... .+|+|+||.-.++ +++..+.+.+.+.+..|+.+.....++.+...+.| ..+.+|.+
T Consensus 1 ~~~i~~~~~~~Ll~kRp~~gll~GLwefP~~e~~-~~~~~~~l~~~~~~~~~~~~~~~~~~~~v~H~fSH~~~~~~~~~~ 79 (114)
T PF14815_consen 1 VLLIIRSQGRVLLEKRPEKGLLAGLWEFPLIESD-EEDDEEELEEWLEEQLGLSIRSVEPLGTVKHVFSHRRWTIHVYEV 79 (114)
T ss_dssp EEEEEETTSEEEEEE--SSSTTTT-EE--EEE-S-SS-CHHHHHHHTCCSSS-EEEE-S-SEEEEEE-SSEEEEEEEEEE
T ss_pred CEEEEEeCCEEEEEECCCCChhhcCcccCEeCcc-CCCCHHHHHHHHHHHcCCChhhheecCcEEEEccceEEEEEEEEE
Confidence 45678899999999999754 5899999997776 44446666666777888888777777877766665 45567888
Q ss_pred EEcCCCCCCCCCceeEEEecCCCCCCCCCCCcHH
Q 023914 221 KLKRPHFSPGPESSECRLFALDEIPFDSLAFSSI 254 (275)
Q Consensus 221 ~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s~ 254 (275)
.+...... +..+.+|++.+++. .+++|..
T Consensus 80 ~~~~~~~~---~~~~~~W~~~~~l~--~~~~p~~ 108 (114)
T PF14815_consen 80 EVSADPPA---EPEEGQWVSLEELD--QYPLPTP 108 (114)
T ss_dssp EEE-SS-------TTEEEEEGGGGG--GS---HH
T ss_pred EecCCCCC---CCCCcEEEEHHHHh--hCCCCHH
Confidence 87765322 34678999999998 5666653
No 91
>KOG0648 consensus Predicted NUDIX hydrolase FGF-2 and related proteins [Signal transduction mechanisms]
Probab=98.38 E-value=1.8e-07 Score=85.81 Aligned_cols=109 Identities=25% Similarity=0.351 Sum_probs=73.6
Q ss_pred cEEEEEEE-eeCCeEEEEEeccCC--CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEE---EEeCCC-CE
Q 023914 141 KMVVGCLI-EHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQ---LDIPRI-GQ 213 (275)
Q Consensus 141 ~~~V~viI-~~~~~iLL~rr~~~p--~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~---~~~~~~-~~ 213 (275)
.+.|++.| +.+++||+++..... ..|.|-+|+|.|++||++-++++||++||||++......+.. ..-.+. ..
T Consensus 115 ~vgvg~~V~n~~~eVlVv~e~d~~~~~~~~wK~ptG~v~~~e~i~~gavrEvkeetgid~ef~eVla~r~~H~~~~~~~k 194 (295)
T KOG0648|consen 115 RVGVGAFVLNKKKEVLVVQEKDGAVKIRGGWKLPTGRVEEGEDIWHGAVREVKEETGIDTEFVEVLAFRRAHNATFGLIK 194 (295)
T ss_pred heeeeeeEecCCceeEEEEecccceeecccccccceEecccccchhhhhhhhHHHhCcchhhhhHHHHHhhhcchhhccc
Confidence 45565555 455699999865443 478999999999999999999999999999997654443331 111111 12
Q ss_pred EEEEEEEEEcCC--CCCC-CCCceeEEEecCCCCCCCCC
Q 023914 214 IYIIFLAKLKRP--HFSP-GPESSECRLFALDEIPFDSL 249 (275)
Q Consensus 214 ~~~~f~a~~~~~--e~~~-~~E~~d~~W~~~deL~~~~l 249 (275)
.-++|.+.+... ++.. +.|+..+.|++.++......
T Consensus 195 sd~f~~c~L~p~s~~i~~~~~ei~~~~Wmp~~e~v~qp~ 233 (295)
T KOG0648|consen 195 SDMFFTCELRPRSLDITKCKREIEAAAWMPIEEYVSQPL 233 (295)
T ss_pred ccceeEEEeeccccccchhHHHHHHHhcccHHHhhcccc
Confidence 334566665432 2333 36788889999998765443
No 92
>COG1443 Idi Isopentenyldiphosphate isomerase [Lipid metabolism]
Probab=98.23 E-value=1.5e-06 Score=73.97 Aligned_cols=101 Identities=19% Similarity=0.271 Sum_probs=73.1
Q ss_pred EEEEeeCCeEEEEEeccCC--CCCceeee-eEEeeCCCCHHHHHHHHHHHHhCCccccc---eeeEEEEe--CC-----C
Q 023914 145 GCLIEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQ---SPFAQLDI--PR-----I 211 (275)
Q Consensus 145 ~viI~~~~~iLL~rr~~~p--~~g~w~lP-gG~vE~GEs~eeAa~REl~EEtGl~v~~~---~~~~~~~~--~~-----~ 211 (275)
..+.+.+|++||.||+... ++|.|.-- +|+=-+||+.++|++|-+.+|+||++... +++..+.+ +. .
T Consensus 38 ~~lFne~g~LLltrRA~~K~twP~vWTNSvCsHP~~~es~~~A~~rRl~~ELGie~~~~d~~~il~rf~YrA~~~~~~~E 117 (185)
T COG1443 38 SFLFNERGQLLLTRRALSKKTWPGVWTNSVCSHPLPGESNEDAARRRLAYELGIEPDQYDKLEILPRFRYRAADPDGIVE 117 (185)
T ss_pred eeEECCCCceeeehhhhhcccCcccccccccCCCcCCCchHHHHHHHHHHHhCCCCcccCccccccceEEeccCCCCcce
Confidence 3455778999999998654 47888765 78878999999999999999999998632 22222222 11 1
Q ss_pred CEEEEEEEEEEcCCCCCCC-CCceeEEEecCCCCCC
Q 023914 212 GQIYIIFLAKLKRPHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 212 ~~~~~~f~a~~~~~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
+.+..++.++... .+.++ +|..+++|++++++-.
T Consensus 118 ~Eic~V~~~~~~~-~~~~npdEV~~~~wv~~e~l~~ 152 (185)
T COG1443 118 NEICPVLAARLDS-ALDPNPDEVMDYRWVSPEDLKE 152 (185)
T ss_pred eeeeeEEEEeecC-CCCCChHHhhheeccCHHHHHH
Confidence 2444566666655 45554 8999999999999764
No 93
>PLN02839 nudix hydrolase
Probab=98.12 E-value=1.4e-05 Score=75.65 Aligned_cols=94 Identities=17% Similarity=0.184 Sum_probs=66.8
Q ss_pred CeEEEEEeccCC--CCCceeee-eEEeeCCCCHHHHHHHHHHHHhCCccc---cceeeEEEEeC--C----CCEEEEEEE
Q 023914 152 KKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVE---VQSPFAQLDIP--R----IGQIYIIFL 219 (275)
Q Consensus 152 ~~iLL~rr~~~p--~~g~w~lP-gG~vE~GEs~eeAa~REl~EEtGl~v~---~~~~~~~~~~~--~----~~~~~~~f~ 219 (275)
.++.+.||+..+ .+|+|+.- ||.+..||++.++++||.+||.||... .....|...+- . .....++|-
T Consensus 218 ~~lWV~RRS~tK~t~PGmLDn~VAGGi~aGesp~etliREa~EEAgLp~~l~~~~~~~G~VsY~~~~~~g~~~evly~YD 297 (372)
T PLN02839 218 KFLWIGKRSLSKSTYPGMLDHLVAGGLPHGISCGENLVKECEEEAGISKAIADRAIAVGAVSYMDIDQYCFKRDVLFCYD 297 (372)
T ss_pred eEEEeeccCCCCCCCCChhhhccccCccCCCCHHHHHHHHHHHHcCCCHHHHhcceEeEEEEEEEEcCCccccCEEEEee
Confidence 468888888654 48999866 899999999999999999999999743 34444544321 1 112233466
Q ss_pred EEEcCCC-CCC-CCCceeEEEecCCCCC
Q 023914 220 AKLKRPH-FSP-GPESSECRLFALDEIP 245 (275)
Q Consensus 220 a~~~~~e-~~~-~~E~~d~~W~~~deL~ 245 (275)
.++..+- +.+ ++|++++.+++.+|+.
T Consensus 298 LeLP~df~P~~qDGEVe~F~Lm~v~EV~ 325 (372)
T PLN02839 298 LELPQDFVPKNQDGEVESFKLIPVAQVA 325 (372)
T ss_pred eecCCccccCCCccceeEEEEecHHHHH
Confidence 6655442 233 4899999999999975
No 94
>COG4119 Predicted NTP pyrophosphohydrolase [DNA replication, recombination, and repair / General function prediction only]
Probab=98.09 E-value=4.7e-06 Score=67.61 Aligned_cols=80 Identities=25% Similarity=0.295 Sum_probs=53.7
Q ss_pred CCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccc-eeeEEEEeCCCCEEEE----------------EEEEEEcCC--
Q 023914 165 YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ-SPFAQLDIPRIGQIYI----------------IFLAKLKRP-- 225 (275)
Q Consensus 165 ~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~-~~~~~~~~~~~~~~~~----------------~f~a~~~~~-- 225 (275)
.|-|++|.|....||.++.||+||.-||+||.++-. ..++...-+. +.+.. .|..++...
T Consensus 35 ~GAWSIPKGey~~gEdp~~AArREf~EE~Gi~vdGP~~~lG~~kQ~G-GKvVta~~veae~Dva~~rSntFe~eWPprSG 113 (161)
T COG4119 35 DGAWSIPKGEYTGGEDPWLAARREFSEEIGICVDGPRIDLGSLKQSG-GKVVTAFGVEAELDVADARSNTFELEWPPRSG 113 (161)
T ss_pred CCcccccccccCCCcCHHHHHHHHhhhhhceeecCchhhhhhhccCC-CcEEEEEeeeeeeehhhhhcceeeeecCCCCC
Confidence 688999999999999999999999999999988432 2234333222 22222 233333221
Q ss_pred CCCCCCCceeEEEecCCCCC
Q 023914 226 HFSPGPESSECRLFALDEIP 245 (275)
Q Consensus 226 e~~~~~E~~d~~W~~~deL~ 245 (275)
..+.-.|.+.+.||++.+..
T Consensus 114 ~M~~FPEVDRagWF~l~eAr 133 (161)
T COG4119 114 KMRKFPEVDRAGWFPLAEAR 133 (161)
T ss_pred ccccCcccccccceecHHHH
Confidence 12223788889999998865
No 95
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=97.44 E-value=0.00025 Score=48.48 Aligned_cols=39 Identities=33% Similarity=0.585 Sum_probs=29.0
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEE
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVG 145 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~ 145 (275)
+|||.||..+.... ++...+.+|+.||+..+.++..+..
T Consensus 1 ~FCp~Cg~~l~~~~--~~~~~~~vC~~Cg~~~~~~~~~~~~ 39 (52)
T smart00661 1 KFCPKCGNMLIPKE--GKEKRRFVCRKCGYEEPIEQKYVYK 39 (52)
T ss_pred CCCCCCCCcccccc--CCCCCEEECCcCCCeEECCCcEEEE
Confidence 59999999875552 1223478999999999988874443
No 96
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=97.30 E-value=0.00014 Score=49.40 Aligned_cols=35 Identities=29% Similarity=0.562 Sum_probs=27.9
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
.+.++|||+||..+-+. +.+.|+.|..||...|.+
T Consensus 16 ~rk~~~CPrCG~gvfmA----~H~dR~~CGkCgyTe~~~ 50 (51)
T COG1998 16 KRKNRFCPRCGPGVFMA----DHKDRWACGKCGYTEFKK 50 (51)
T ss_pred EEccccCCCCCCcchhh----hcCceeEeccccceEeec
Confidence 46789999999876666 345699999999988864
No 97
>KOG4195 consensus Transient receptor potential-related channel 7 [Inorganic ion transport and metabolism]
Probab=97.20 E-value=0.0021 Score=56.97 Aligned_cols=39 Identities=33% Similarity=0.547 Sum_probs=34.2
Q ss_pred eEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhC
Q 023914 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEAR 194 (275)
Q Consensus 153 ~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtG 194 (275)
+++.++|. ..|.|.+|||.||+||.+-.+++||+.||.=
T Consensus 140 e~vavkr~---d~~~WAiPGGmvdpGE~vs~tLkRef~eEa~ 178 (275)
T KOG4195|consen 140 EFVAVKRP---DNGEWAIPGGMVDPGEKVSATLKREFGEEAM 178 (275)
T ss_pred EEEEEecC---CCCcccCCCCcCCchhhhhHHHHHHHHHHHH
Confidence 56677776 5789999999999999999999999999964
No 98
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=97.15 E-value=0.00028 Score=48.47 Aligned_cols=32 Identities=31% Similarity=0.588 Sum_probs=24.6
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
+.++|||.||+. -+. ....+..|..||+..|.
T Consensus 18 ~~~~fCP~Cg~~-~m~----~~~~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 18 RKNKFCPRCGSG-FMA----EHLDRWHCGKCGYTEFK 49 (50)
T ss_pred EccCcCcCCCcc-hhe----ccCCcEECCCcCCEEec
Confidence 467899999996 333 23468899999999885
No 99
>COG4112 Predicted phosphoesterase (MutT family) [General function prediction only]
Probab=97.13 E-value=0.0028 Score=53.67 Aligned_cols=102 Identities=20% Similarity=0.226 Sum_probs=69.4
Q ss_pred EEEEeeCCeEEEEEeccCCC----CCceeee-eEEeeCCC--C-HHH----HHHHHHHHHhCCc---cccceeeEEEEeC
Q 023914 145 GCLIEHDKKILLCKRKIEPS----YGLWTLP-AGYMEIGE--S-AAE----GAIRETWEEARAD---VEVQSPFAQLDIP 209 (275)
Q Consensus 145 ~viI~~~~~iLL~rr~~~p~----~g~w~lP-gG~vE~GE--s-~ee----Aa~REl~EEtGl~---v~~~~~~~~~~~~ 209 (275)
.|++.++++||+-.|-.... .+.+++- ||++..++ + .++ .+.||+.||+++. ...+.++|.....
T Consensus 65 Yvvi~~edevliyeRltgggE~RLHn~~SlG~GGHmn~~~GA~s~~evLk~n~~REleEEv~vseqd~q~~e~lGlINdd 144 (203)
T COG4112 65 YVVIMDEDEVLIYERLTGGGEKRLHNLYSLGIGGHMNEGDGATSREEVLKGNLERELEEEVDVSEQDLQELEFLGLINDD 144 (203)
T ss_pred EEEEecCCEEEEEEeccCcchhhhccccccccccccccCCCcccHHHHHccchHHHHHHHhCcCHHHhhhheeeeeecCC
Confidence 34677888999999976542 5678876 89998654 3 333 2679999999998 4566777766433
Q ss_pred CC---C-EEEEEEEEEEcCCCCCCC-CCceeEEEecCCCCCC
Q 023914 210 RI---G-QIYIIFLAKLKRPHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 210 ~~---~-~~~~~f~a~~~~~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
.. . ++-+.|..+....++... .+..++.|+..++|..
T Consensus 145 ~neVgkVHiG~lf~~~~k~ndvevKEkd~~~~kwik~~ele~ 186 (203)
T COG4112 145 TNEVGKVHIGALFLGRGKFNDVEVKEKDLFEWKWIKLEELEK 186 (203)
T ss_pred CcccceEEEEEEEEeeccccceeeeecceeeeeeeeHHHHHH
Confidence 22 1 223456666655555443 5667899999999873
No 100
>KOG2937 consensus Decapping enzyme complex, predicted pyrophosphatase DCP2 [RNA processing and modification]
Probab=96.87 E-value=0.00018 Score=66.94 Aligned_cols=108 Identities=24% Similarity=0.266 Sum_probs=74.0
Q ss_pred CCccccCCcEEEEEEEeeC--CeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccc--eeeEEEEe
Q 023914 133 GKIAYQNPKMVVGCLIEHD--KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ--SPFAQLDI 208 (275)
Q Consensus 133 g~~~y~~p~~~V~viI~~~--~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~--~~~~~~~~ 208 (275)
.+.-|..+.|+.++++.+. .++||++.-. ...|.+|-|++..+|+..+++.|||.||+|.++... ...+ .+.
T Consensus 74 ~f~~yk~~iPv~ga~ild~~~sr~llv~g~q---a~sw~fprgK~~kdesd~~caiReV~eetgfD~skql~~~e~-Ie~ 149 (348)
T KOG2937|consen 74 DFAPYKARIPVRGAIILDEKRSRCLLVKGWQ---ASSWSFPRGKISKDESDSDCAIREVTEETGFDYSKQLQDNEG-IET 149 (348)
T ss_pred hhccccCCCCCchHhhhhhhhhhhheeecee---cccccccCccccccchhhhcchhcccchhhcCHHHHhccccC-ccc
Confidence 3556777888887777543 5899988653 344999999999999999999999999999987432 1111 222
Q ss_pred CCCCEEEEEEEEEEcCCC----CCCCCCceeEEEecCCCC
Q 023914 209 PRIGQIYIIFLAKLKRPH----FSPGPESSECRLFALDEI 244 (275)
Q Consensus 209 ~~~~~~~~~f~a~~~~~e----~~~~~E~~d~~W~~~deL 244 (275)
...+.....|.......+ +..-.|+..+.|+..+++
T Consensus 150 nI~dq~~~~fIi~gvs~d~~f~~~v~~eis~ihW~~l~~l 189 (348)
T KOG2937|consen 150 NIRDQLVRLFIINGVSEDTNFNPRVRKEISKIHWHYLDHL 189 (348)
T ss_pred chhhceeeeeeeccceeeeecchhhhccccceeeeehhhh
Confidence 223334433444222222 233478889999999998
No 101
>PRK10880 adenine DNA glycosylase; Provisional
Probab=96.56 E-value=0.015 Score=55.30 Aligned_cols=101 Identities=12% Similarity=0.097 Sum_probs=56.9
Q ss_pred EEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCC--EEEEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIFLA 220 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~--~~~~~f~a 220 (275)
..+++.+++++||.+|.... .+|+|+||.. + + ++ ..++..|+.|+.......++.....+.| ..+..|.+
T Consensus 234 ~~~~~~~~~~~~l~~r~~~gl~~gl~~fP~~--~---~-~~-~~~~~~~~~~~~~~~~~~~~~~~H~fTH~~~~~~~~~~ 306 (350)
T PRK10880 234 YFLLLQHGDEVWLEQRPPSGLWGGLFCFPQF--A---D-EE-ELRQWLAQRGIAADNLTQLTAFRHTFSHFHLDIVPMWL 306 (350)
T ss_pred EEEEEEECCEEEEEECCccChhhccccCCCC--c---c-hh-hHHHHHHhcCCchhhhcccCceEEEEeeEEEEEEEEEE
Confidence 33455678899999998654 5899999962 2 1 12 2355667888753222223333333333 33445555
Q ss_pred EEcCCCCCCCCCceeEEEecCCCCCCCCCCCcHHH
Q 023914 221 KLKRPHFSPGPESSECRLFALDEIPFDSLAFSSIS 255 (275)
Q Consensus 221 ~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s~~ 255 (275)
.......... ..+..|++++++. .+++|+..
T Consensus 307 ~~~~~~~~~~--~~~~~w~~~~~~~--~~~~p~~~ 337 (350)
T PRK10880 307 PVSSFTGCMD--EGNGLWYNLAQPP--SVGLAAPV 337 (350)
T ss_pred EccccccccC--CcCCeEechHHhc--ccCCcHHH
Confidence 5432211111 1234699999999 56677643
No 102
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.07 E-value=0.0028 Score=36.50 Aligned_cols=22 Identities=27% Similarity=0.936 Sum_probs=17.2
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
|||+||+++... ...|+.||..
T Consensus 1 ~Cp~CG~~~~~~--------~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD--------AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc--------CcchhhhCCc
Confidence 799999997432 4679999964
No 103
>PF13869 NUDIX_2: Nucleotide hydrolase; PDB: 3MDG_B 2J8Q_B 3Q2S_A 3P5T_D 3BAP_A 2CL3_A 3P6Y_A 3Q2T_B 3BHO_A 3N9U_A ....
Probab=95.90 E-value=0.026 Score=49.05 Aligned_cols=61 Identities=25% Similarity=0.316 Sum_probs=39.8
Q ss_pred EEEEeeCC--eEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCcc------ccceeeEEEEeC
Q 023914 145 GCLIEHDK--KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADV------EVQSPFAQLDIP 209 (275)
Q Consensus 145 ~viI~~~~--~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v------~~~~~~~~~~~~ 209 (275)
++++...+ .|||.|.. ...|.+|||.+.+||+.++...|.+.|-.|..- ...+.++.+-.|
T Consensus 49 Vllvh~h~~PHvLLLq~~----~~~fkLPGg~l~~gE~e~~gLkrkL~~~l~~~~~~~~~w~vge~l~~WwRp 117 (188)
T PF13869_consen 49 VLLVHEHGHPHVLLLQIG----NTFFKLPGGRLRPGEDEIEGLKRKLTEKLSPEDGVDPDWEVGECLGTWWRP 117 (188)
T ss_dssp EEEEEETTEEEEEEEEET----TTEEE-SEEE--TT--HHHHHHHHHHHHHB-SSSS----EEEEEEEEEEES
T ss_pred EEEEecCCCcEEEEEecc----CccccCCccEeCCCCChhHHHHHHHHHHcCCCcCCCCCcEecCEEEEEeCC
Confidence 33444443 68988865 348999999999999999999999999999752 334566666444
No 104
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=95.16 E-value=0.01 Score=35.08 Aligned_cols=24 Identities=29% Similarity=0.718 Sum_probs=17.9
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.++||.||+.+.. ..+.|+.||..
T Consensus 2 ~~~Cp~Cg~~~~~--------~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDP--------DAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCc--------ccccChhhCCC
Confidence 3799999996422 35789999964
No 105
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=95.04 E-value=0.0062 Score=38.67 Aligned_cols=30 Identities=30% Similarity=0.616 Sum_probs=19.5
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.+|||.||.-|..... ..... .|..|++..
T Consensus 1 m~FCp~C~nlL~p~~~--~~~~~-~C~~C~Y~~ 30 (35)
T PF02150_consen 1 MRFCPECGNLLYPKED--KEKRV-ACRTCGYEE 30 (35)
T ss_dssp --BETTTTSBEEEEEE--TTTTE-EESSSS-EE
T ss_pred CeeCCCCCccceEcCC--CccCc-CCCCCCCcc
Confidence 3799999999977632 22233 799999764
No 106
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=94.48 E-value=0.031 Score=32.51 Aligned_cols=24 Identities=29% Similarity=0.671 Sum_probs=19.8
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCC
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
|..||..+... +......||+||+
T Consensus 1 C~sC~~~i~~r----~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPR----EQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCc----ccCceEeCCCCCC
Confidence 78899998766 4478899999995
No 107
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.47 E-value=0.025 Score=33.49 Aligned_cols=24 Identities=25% Similarity=0.621 Sum_probs=18.6
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
+.||.||+..... .+.|+.||+..
T Consensus 1 K~CP~C~~~V~~~--------~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES--------AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh--------cCcCCCCCCCC
Confidence 5799999996333 57899999864
No 108
>PF12773 DZR: Double zinc ribbon
Probab=93.39 E-value=0.048 Score=36.80 Aligned_cols=33 Identities=27% Similarity=0.610 Sum_probs=24.4
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
...+||+.||.++.. .......|+.||....++
T Consensus 10 ~~~~fC~~CG~~l~~-----~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPP-----PDQSKKICPNCGAENPPN 42 (50)
T ss_pred ccccCChhhcCChhh-----ccCCCCCCcCCcCCCcCC
Confidence 347899999999872 234567899999875544
No 109
>KOG0142 consensus Isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=93.25 E-value=0.066 Score=46.95 Aligned_cols=99 Identities=26% Similarity=0.309 Sum_probs=61.6
Q ss_pred EEEeeCCeEEEEEeccCC--CCCceee---------eeEEee-CCCCHHHHHHHHHHHHhCCcccc-----ceeeEEEEe
Q 023914 146 CLIEHDKKILLCKRKIEP--SYGLWTL---------PAGYME-IGESAAEGAIRETWEEARADVEV-----QSPFAQLDI 208 (275)
Q Consensus 146 viI~~~~~iLL~rr~~~p--~~g~w~l---------PgG~vE-~GEs~eeAa~REl~EEtGl~v~~-----~~~~~~~~~ 208 (275)
.+.+.++++||++|+... .++.|.- |+.--+ .+..+..||.|-+.-|+||..+. +.+++...+
T Consensus 58 FlFns~~~lLlQqRS~~KitFP~~~TNtccSHPL~~~~el~~~d~lGVr~AAqRkL~~ELGIp~e~v~pee~~~ltrihY 137 (225)
T KOG0142|consen 58 FLFNSKNELLLQQRSDEKITFPGLWTNTCCSHPLYNPGELEENDALGVRRAAQRKLKAELGIPLEEVPPEEFNFLTRIHY 137 (225)
T ss_pred EEecCcchHHHhhhccccccccchhhhhhhcCcCCChhhhccCchHHHHHHHHHHHHHhhCCCccccCHHHcccceeeee
Confidence 345678999999998653 3455532 222111 23357889999999999997643 445655443
Q ss_pred CCC--------CEEEEEEEEEEcCCCCCCC-CCceeEEEecCCCCCC
Q 023914 209 PRI--------GQIYIIFLAKLKRPHFSPG-PESSECRLFALDEIPF 246 (275)
Q Consensus 209 ~~~--------~~~~~~f~a~~~~~e~~~~-~E~~d~~W~~~deL~~ 246 (275)
..+ ..-|+.|... +-.+.++ +|..+++|++.+||..
T Consensus 138 kA~sdg~wGEhEiDYiL~~~~--~~~~nPnpnEv~e~ryvs~eelke 182 (225)
T KOG0142|consen 138 KAPSDGIWGEHEIDYILFLVK--DVTLNPNPNEVSEIRYVSREELKE 182 (225)
T ss_pred ecCCCCCcccceeeEEEEEec--cCCCCCChhhhhHhheecHHHHHH
Confidence 221 1333434333 2235565 8999999999999763
No 110
>PRK13910 DNA glycosylase MutY; Provisional
Probab=93.18 E-value=0.59 Score=43.46 Aligned_cols=84 Identities=15% Similarity=0.235 Sum_probs=46.1
Q ss_pred EEEEEeeCCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCC--CEEEEEEEEE
Q 023914 144 VGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIFLAK 221 (275)
Q Consensus 144 V~viI~~~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~--~~~~~~f~a~ 221 (275)
..+++.+++++||.||...-.+|+|+||.. +. +.+.... .++.....+. ...+.+|.+.
T Consensus 189 ~~~~~~~~~~~ll~kr~~~l~~gl~~fP~~--~~--------------~~~~~~~---~~~~~~H~fTH~~~~~~~~~~~ 249 (289)
T PRK13910 189 YLGVVIQNNQIALEKIEQKLYLGMHHFPNL--KE--------------NLEYKLP---FLGAIKHSHTKFKLNLNLYLAA 249 (289)
T ss_pred EEEEEEECCEEEEEECCCchhcccccCCCC--hh--------------hhccccc---ccCceEEEEEeEEEEEEEEEEE
Confidence 344455678999999854335899999962 21 0111111 1222222222 2344556555
Q ss_pred EcCCCCCCCCCceeEEEecCCCCCCCCCCCcHHH
Q 023914 222 LKRPHFSPGPESSECRLFALDEIPFDSLAFSSIS 255 (275)
Q Consensus 222 ~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s~~ 255 (275)
.... ..+.+|++.+++. .+++|+..
T Consensus 250 ~~~~-------~~~~~w~~~~~~~--~~~~p~~~ 274 (289)
T PRK13910 250 IKDL-------KNPIRFYSLKDLE--TLPISSMT 274 (289)
T ss_pred eccC-------CccceEecHHHhh--hcCCcHHH
Confidence 4311 1345899999998 56666643
No 111
>PF09296 NUDIX-like: NADH pyrophosphatase-like rudimentary NUDIX domain; InterPro: IPR015375 This entry represents the N-terminal domain found in NADH pyrophosphatase. Nitrate reductase inactivator (NRI) protein shares 51.1-68.3% of its amino acid sequence with three types of the nucleotide pyrophosphatase-like protein from Arabidopsis thaliana.; GO: 0016787 hydrolase activity; PDB: 1VK6_A 2GB5_A.
Probab=93.15 E-value=0.038 Score=41.85 Aligned_cols=32 Identities=6% Similarity=-0.119 Sum_probs=22.3
Q ss_pred eecceeecccccc-cCCCCCccHHHHHHHHHhh
Q 023914 69 FRASRVCATRSES-NQDATSSHPSSAAVHSAGN 100 (275)
Q Consensus 69 ~~~~~~~~~r~~~-~~~~~~~~~~~~a~~l~~w 100 (275)
-.++++++||+++ .+++.+++++++|+||.+|
T Consensus 66 ~~~~~~~~LR~~~~~l~~~~~~l~a~A~~ll~W 98 (98)
T PF09296_consen 66 PEGFEFVDLRQLGGQLPEEDAGLAARARQLLDW 98 (98)
T ss_dssp -----EE-GGGGT-TS-HHHHHHHHHHHHHHH-
T ss_pred cccccchhHHHHHHcCCHHHHHHHHHHHHHhcC
Confidence 3566778999887 5899999999999999999
No 112
>PRK00420 hypothetical protein; Validated
Probab=92.67 E-value=0.11 Score=41.72 Aligned_cols=32 Identities=25% Similarity=0.514 Sum_probs=23.8
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
+|..-...||.||.++... .. -..+||.||..
T Consensus 18 Ga~ml~~~CP~Cg~pLf~l----k~-g~~~Cp~Cg~~ 49 (112)
T PRK00420 18 GAKMLSKHCPVCGLPLFEL----KD-GEVVCPVHGKV 49 (112)
T ss_pred HHHHccCCCCCCCCcceec----CC-CceECCCCCCe
Confidence 5666779999999998652 12 25799999963
No 113
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=92.55 E-value=0.12 Score=34.01 Aligned_cols=34 Identities=21% Similarity=0.499 Sum_probs=26.4
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
.-|..|..-..+||.||.++-.. .++ ...|+.|+
T Consensus 8 ~LL~G~~ML~~~Cp~C~~PL~~~----k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 8 YLLQGWTMLDEHCPDCGTPLMRD----KDG-KIYCVSCG 41 (41)
T ss_pred HHHHhHhHhcCccCCCCCeeEEe----cCC-CEECCCCC
Confidence 45778999999999999998653 222 47899996
No 114
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=92.52 E-value=0.079 Score=42.47 Aligned_cols=35 Identities=23% Similarity=0.521 Sum_probs=26.5
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
.+|||.||+-|..... +.+....|..||...=-..
T Consensus 2 m~FCp~Cgsll~p~~~--~~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 2 MRFCPKCGSLLYPKKD--DEGGKLVCRKCGYEEEASN 36 (113)
T ss_pred ccccCCccCeeEEeEc--CCCcEEECCCCCcchhccc
Confidence 5899999999987643 2345899999997765443
No 115
>KOG1689 consensus mRNA cleavage factor I subunit [RNA processing and modification]
Probab=92.33 E-value=0.19 Score=43.00 Aligned_cols=39 Identities=28% Similarity=0.395 Sum_probs=34.3
Q ss_pred CeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHHHHHHhC
Q 023914 152 KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEAR 194 (275)
Q Consensus 152 ~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~REl~EEtG 194 (275)
-.|||.+-. .-.+.+|||..++||+-.+.+.|-+-|-+|
T Consensus 84 PHvLLLQig----~tf~KLPGG~L~pGE~e~~Gl~r~l~~~Lg 122 (221)
T KOG1689|consen 84 PHVLLLQIG----NTFFKLPGGRLRPGEDEADGLKRLLTESLG 122 (221)
T ss_pred CeEEEEeeC----CEEEecCCCccCCCcchhHHHHHHHHHHhc
Confidence 578887743 457999999999999999999999999999
No 116
>KOG4432 consensus Uncharacterized NUDIX family hydrolase [General function prediction only]
Probab=91.98 E-value=0.39 Score=44.68 Aligned_cols=59 Identities=20% Similarity=0.197 Sum_probs=47.4
Q ss_pred eeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEe----CCCCEEEEEEEEEEcCCC
Q 023914 168 WTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----PRIGQIYIIFLAKLKRPH 226 (275)
Q Consensus 168 w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~----~~~~~~~~~f~a~~~~~e 226 (275)
.++-||-|+..-|+.|-|..|+.||.|.++..-.++.++++ ...++.++.|+|++.+..
T Consensus 81 ielc~g~idke~s~~eia~eev~eecgy~v~~d~l~hv~~~~~g~~~s~sa~~l~y~ei~es~ 143 (405)
T KOG4432|consen 81 IELCAGLIDKELSPREIASEEVAEECGYRVDPDDLIHVITFVVGAHQSGSAQHLYYAEIDESM 143 (405)
T ss_pred eeeeccccccccCHHHHhHHHHHHHhCCcCChhHceEEEEEEeccccCccchheeeeecchhh
Confidence 56779999999999999999999999999977766665554 234577888999987653
No 117
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=91.85 E-value=0.1 Score=41.33 Aligned_cols=51 Identities=20% Similarity=0.328 Sum_probs=33.5
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCCcE----------EEEEEEeeCCeEEEEEec
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKM----------VVGCLIEHDKKILLCKRK 160 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~----------~V~viI~~~~~iLL~rr~ 160 (275)
.-||+|++..... ++.-..||.|+++.-+.-.. +.+.++.++|.|.|++--
T Consensus 3 p~CP~C~seytY~-----dg~~~iCpeC~~EW~~~~~~~~~~~~~~kDsnG~~L~dGDsV~liKDL 63 (109)
T TIGR00686 3 PPCPKCNSEYTYH-----DGTQLICPSCLYEWNENEVNDDDDELIVKDCNGNLLANGDSVILIKDL 63 (109)
T ss_pred CcCCcCCCcceEe-----cCCeeECccccccccccccccccCCceEEcCCCCCccCCCEEEEEeec
Confidence 5699999998665 45569999999887654211 111222345677777754
No 118
>PHA00626 hypothetical protein
Probab=91.80 E-value=0.13 Score=35.98 Aligned_cols=34 Identities=18% Similarity=0.289 Sum_probs=21.4
Q ss_pred CCCcCCCCCCcccccC-CCccceeecCCCCCcccc
Q 023914 105 SFCQWCGGQTKHEVPH-GEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~-~~~~~~~~C~~Cg~~~y~ 138 (275)
..||.||+......-. .....+..|++||+.+-.
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 3799999975443110 011356899999986643
No 119
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=91.23 E-value=0.16 Score=36.46 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=24.2
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
+.+.||.||...... ..+....|+.||+..
T Consensus 27 TSq~C~~CG~~~~~~----~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKR----RSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccc----cccceEEcCCCCCEE
Confidence 678999999998763 345678999999873
No 120
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=91.16 E-value=0.11 Score=42.54 Aligned_cols=24 Identities=29% Similarity=0.780 Sum_probs=19.4
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.+||.||.|+-.. +| .-+||.||+
T Consensus 29 ~hCp~Cg~PLF~K----dG--~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRK----DG--EVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceee----CC--eEECCCCCc
Confidence 6899999998664 33 369999997
No 121
>KOG4548 consensus Mitochondrial ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=91.13 E-value=0.82 Score=41.49 Aligned_cols=93 Identities=17% Similarity=0.198 Sum_probs=61.2
Q ss_pred eEEEEEeccCCCCCceeeeeEEe-eCCCCHHHHHHHHHHHHhCCccccc----eeeEEEEeCCC---------CEEEEEE
Q 023914 153 KILLCKRKIEPSYGLWTLPAGYM-EIGESAAEGAIRETWEEARADVEVQ----SPFAQLDIPRI---------GQIYIIF 218 (275)
Q Consensus 153 ~iLL~rr~~~p~~g~w~lPgG~v-E~GEs~eeAa~REl~EEtGl~v~~~----~~~~~~~~~~~---------~~~~~~f 218 (275)
=+||+++..+ ..+.|.||-+-. +.++++...|.|++++-.|=..... ..++...+..+ +...++|
T Consensus 140 LyLLV~~k~g-~~s~w~fP~~~~s~~~~~lr~~ae~~Lk~~~ge~~~t~fvgnaP~g~~~~q~pr~~~~e~~~~sk~ff~ 218 (263)
T KOG4548|consen 140 LYLLVKRKFG-KSSVWIFPNRQFSSSEKTLRGHAERDLKVLSGENKSTWFVGNAPFGHTPLQSPREMTTEEPVSSKVFFF 218 (263)
T ss_pred EEEEEeeccC-ccceeeCCCcccCCccchHHHHHHHHHHHHhcchhhhheeccCccccccccCcccccccccccceeEEe
Confidence 3778876544 357899999988 9999999999999999988544221 12332111111 2334556
Q ss_pred EEEEcCCCCCCCCCceeEEEecCCCCCC
Q 023914 219 LAKLKRPHFSPGPESSECRLFALDEIPF 246 (275)
Q Consensus 219 ~a~~~~~e~~~~~E~~d~~W~~~deL~~ 246 (275)
.+.+..+...-.....|..|++.+||..
T Consensus 219 k~~lv~~~~~kn~n~edfvWvTkdel~e 246 (263)
T KOG4548|consen 219 KASLVANSNQKNQNKEDFVWVTKDELGE 246 (263)
T ss_pred eeeeccccchhcccccceEEechHHHhh
Confidence 6666655433334456799999999984
No 122
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.11 E-value=0.2 Score=33.40 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=20.2
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
-|+.||+.+... +......|+.||...
T Consensus 5 ~C~~CG~~~~~~----~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELD----EYGTGVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEEC----CCCCceECCCCCCeE
Confidence 599999998665 233368999999744
No 123
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=90.48 E-value=0.11 Score=46.96 Aligned_cols=43 Identities=16% Similarity=0.253 Sum_probs=18.2
Q ss_pred HHHHH-HhhhhcCCCCcCCCCC-CcccccCCCccceeecCCCCCcc
Q 023914 93 AAVHS-AGNVLKISFCQWCGGQ-TKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 93 ~a~~l-~~w~~~~~fC~~CG~~-~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.|+-| -.|...+.|||.||+. +... .....---..|+.|+..+
T Consensus 19 ~aRVltE~Wv~~n~yCP~Cg~~~L~~f-~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 19 IARVLTEDWVAENMYCPNCGSKPLSKF-ENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp HHHHHHHHHHHHH---TTT--SS-EE---------EEE-TTT--EE
T ss_pred hhHHHHHHHHHHCCcCCCCCChhHhhc-cCCCccceeECCCCchHH
Confidence 33333 3699999999999999 4333 221122236899998644
No 124
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=90.06 E-value=0.21 Score=38.97 Aligned_cols=29 Identities=24% Similarity=0.583 Sum_probs=22.3
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
+|||.||..|... +....|+.|++.....
T Consensus 1 ~fC~~Cg~~l~~~------~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 1 KFCPKCGSLMTPK------NGVYVCPSCGYEKEKK 29 (104)
T ss_pred CCCcccCcccccC------CCeEECcCCCCccccc
Confidence 5999999999543 2368999999876543
No 125
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=90.04 E-value=0.14 Score=31.32 Aligned_cols=26 Identities=27% Similarity=0.673 Sum_probs=14.3
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.-||.||+..... ++...+|+.|++.
T Consensus 3 p~Cp~C~se~~y~-----D~~~~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTYE-----DGELLVCPECGHE 28 (30)
T ss_dssp ---TTT-----EE------SSSEEETTTTEE
T ss_pred CCCCCCCCcceec-----cCCEEeCCccccc
Confidence 4699999998774 5677999999975
No 126
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.85 E-value=0.22 Score=42.10 Aligned_cols=31 Identities=29% Similarity=0.657 Sum_probs=18.7
Q ss_pred CCcCCCCCCccc-----ccCCC-ccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHE-----VPHGE-EKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~-----~~~~~-~~~~~~C~~Cg~~~ 136 (275)
-||.||++-... +.+|. -..++.|++||+..
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 599999975222 11111 11348999999654
No 127
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=89.72 E-value=0.24 Score=32.25 Aligned_cols=31 Identities=23% Similarity=0.542 Sum_probs=23.7
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
.||+|+..|..... .+-....|++|+-..+.
T Consensus 1 ~CP~C~~~l~~~~~--~~~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 1 KCPRCGTELEPVRL--GDVEIDVCPSCGGIWFD 31 (41)
T ss_pred CcCCCCcccceEEE--CCEEEEECCCCCeEEcc
Confidence 59999999877755 34567789999966553
No 128
>PRK10220 hypothetical protein; Provisional
Probab=89.50 E-value=0.3 Score=38.75 Aligned_cols=32 Identities=19% Similarity=0.411 Sum_probs=25.6
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
..-||+|++..... ++....|+.|+++.-+.-
T Consensus 3 lP~CP~C~seytY~-----d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 3 LPHCPKCNSEYTYE-----DNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCcCCCCCCcceEc-----CCCeEECCcccCcCCccc
Confidence 46799999998665 456699999999887754
No 129
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=89.15 E-value=0.26 Score=31.26 Aligned_cols=32 Identities=22% Similarity=0.468 Sum_probs=21.1
Q ss_pred CCcCCCCCCccccc-CCCccceeecCCCCCccc
Q 023914 106 FCQWCGGQTKHEVP-HGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 106 fC~~CG~~~~~~~~-~~~~~~~~~C~~Cg~~~y 137 (275)
-||+||+....... .++.+....|+.||...+
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 49999997644310 112344689999998765
No 130
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=88.94 E-value=0.17 Score=30.45 Aligned_cols=22 Identities=27% Similarity=0.594 Sum_probs=12.4
Q ss_pred CCcCCCCCCcccccCCCccceeecCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTV 131 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~ 131 (275)
+||.||+++... +++...+|++
T Consensus 1 ~CP~C~s~l~~~----~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSKLVRE----EGEVDIRCPN 22 (28)
T ss_dssp B-TTT--BEEE-----CCTTCEEE--
T ss_pred CcCCCCCEeEcC----CCCEeEECCC
Confidence 699999999865 5566778864
No 131
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=88.22 E-value=0.29 Score=38.94 Aligned_cols=32 Identities=22% Similarity=0.420 Sum_probs=21.3
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
+-+-||.||++.--- .+.-.+||.||..+-+.
T Consensus 8 tKR~Cp~CG~kFYDL-----nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL-----NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccC-----CCCCccCCCCCCccCcc
Confidence 347889998886433 23345788888776554
No 132
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=87.98 E-value=0.31 Score=39.08 Aligned_cols=21 Identities=38% Similarity=0.912 Sum_probs=17.9
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
||.||+++... +..|++|+..
T Consensus 1 CPvCg~~l~vt--------~l~C~~C~t~ 21 (113)
T PF09862_consen 1 CPVCGGELVVT--------RLKCPSCGTE 21 (113)
T ss_pred CCCCCCceEEE--------EEEcCCCCCE
Confidence 99999998765 6899999854
No 133
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=87.76 E-value=0.35 Score=36.87 Aligned_cols=39 Identities=18% Similarity=0.296 Sum_probs=27.2
Q ss_pred HHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 94 AVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
-..+..=.+.---||.||.+...+ .+--.+.|..||+..
T Consensus 25 v~~ie~~~~~~~~Cp~C~~~~VkR----~a~GIW~C~kCg~~f 63 (89)
T COG1997 25 VKEIEAQQRAKHVCPFCGRTTVKR----IATGIWKCRKCGAKF 63 (89)
T ss_pred HHHHHHHHhcCCcCCCCCCcceee----eccCeEEcCCCCCee
Confidence 344444455566799999997666 334468999999753
No 134
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=87.76 E-value=0.49 Score=39.64 Aligned_cols=47 Identities=17% Similarity=0.465 Sum_probs=26.4
Q ss_pred CCCcCCCCCCcccccC--CCcc----ceeecCCCCCc--cccCCcEEEEEEEeeC
Q 023914 105 SFCQWCGGQTKHEVPH--GEEK----MRAICTVCGKI--AYQNPKMVVGCLIEHD 151 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~--~~~~----~~~~C~~Cg~~--~y~~p~~~V~viI~~~ 151 (275)
+.||.||+.-...... .++| .|+.|.+||.. .|-+.-..-..++-++
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~ViKkd 55 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQD 55 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccccEEEcCC
Confidence 3699999975433211 1222 56899999954 4555444433344433
No 135
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=87.54 E-value=0.43 Score=41.76 Aligned_cols=95 Identities=20% Similarity=0.333 Sum_probs=64.9
Q ss_pred CCccHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeCCeEEEEEeccCCCC
Q 023914 86 TSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSY 165 (275)
Q Consensus 86 ~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~iLL~rr~~~p~~ 165 (275)
.+..+-.-|.+|.+-..+.++|+.||.-++.. .|.-|....- +-.++++|..-.-++...+... ..
T Consensus 36 ~~~~~~~la~al~~a~~~i~~C~~C~~~te~d----------~C~ICsd~~R---d~~~icVVe~p~Dv~a~E~~~~-f~ 101 (198)
T COG0353 36 DREDVERLAKALLEAKENIKHCSVCGNLTESD----------PCDICSDESR---DKSQLCVVEEPKDVLALEKTGE-FR 101 (198)
T ss_pred CHHHHHHHHHHHHHHHhcCccccccCCcCCCC----------cCcCcCCccc---CCceEEEEcchHHHHHHHHhcc-cC
Confidence 33444556777888899999999999886332 5777764433 3335666665555555554433 47
Q ss_pred CceeeeeEEeeC--CCCHHHHHHHHHHHHhC
Q 023914 166 GLWTLPAGYMEI--GESAAEGAIRETWEEAR 194 (275)
Q Consensus 166 g~w~lPgG~vE~--GEs~eeAa~REl~EEtG 194 (275)
|.|.+.+|.+.+ |-.+++--.+++.+-..
T Consensus 102 G~YhVL~G~lspl~gigpe~l~i~~L~~Rl~ 132 (198)
T COG0353 102 GLYHVLGGLLSPLDGIGPEDLNIDELLQRLA 132 (198)
T ss_pred eeEEEecCccCcccCCCcccccHHHHHHHHh
Confidence 999999999985 66777777777777655
No 136
>PRK13844 recombination protein RecR; Provisional
Probab=87.44 E-value=0.36 Score=42.51 Aligned_cols=96 Identities=15% Similarity=0.230 Sum_probs=65.2
Q ss_pred CCCccHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeCCeEEEEEeccCCC
Q 023914 85 ATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPS 164 (275)
Q Consensus 85 ~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~iLL~rr~~~p~ 164 (275)
.++..+-.-|.++.+-..+.++|+.||.-++.. .|+-|....- +-..++||..-.-++-+.+... .
T Consensus 38 ~~~~~~~~la~~i~~~~~~i~~C~~C~~lte~~----------~C~IC~d~~R---d~~~iCVVE~~~Dv~aiE~t~~-y 103 (200)
T PRK13844 38 KSPETAIAIANSLLDATANIKKCVYCQALTEDD----------VCNICSNTNR---DDTKLCIIESMLDMIAIEEAGI-Y 103 (200)
T ss_pred CCHHHHHHHHHHHHHHHHhCCcCCCCCCCCCCC----------CCCCCCCCCC---CCCEEEEECCHHHHHHHHhhCc-c
Confidence 334444566777888889999999999886332 4777764433 3344556665555555555433 4
Q ss_pred CCceeeeeEEeeC--CCCHHHHHHHHHHHHhC
Q 023914 165 YGLWTLPAGYMEI--GESAAEGAIRETWEEAR 194 (275)
Q Consensus 165 ~g~w~lPgG~vE~--GEs~eeAa~REl~EEtG 194 (275)
.|.|.+.+|.+.+ |..+++--..++.+-..
T Consensus 104 ~G~YhVL~G~ispl~gi~p~~l~i~~L~~Ri~ 135 (200)
T PRK13844 104 RGKYFVLNGRISPLDGIGPSELKLDILQQIIA 135 (200)
T ss_pred ceEEEEccCccCccCCCChhhcCHHHHHHHHh
Confidence 8999999999984 77888877777776653
No 137
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=87.30 E-value=0.52 Score=39.60 Aligned_cols=45 Identities=18% Similarity=0.479 Sum_probs=25.4
Q ss_pred CCCcCCCCCCccccc---CCCc---cceeecCCCCCcc--ccCCcEEEEEEEe
Q 023914 105 SFCQWCGGQTKHEVP---HGEE---KMRAICTVCGKIA--YQNPKMVVGCLIE 149 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~---~~~~---~~~~~C~~Cg~~~--y~~p~~~V~viI~ 149 (275)
++||.||+.-..... ..++ ..|+.|++||..+ |-+.-..-.++|-
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~~VvK 53 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRPLIVVK 53 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeeccceEEC
Confidence 479999988544321 1111 2578999999644 4443333333443
No 138
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=87.28 E-value=0.28 Score=41.12 Aligned_cols=32 Identities=19% Similarity=0.531 Sum_probs=26.4
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
-.|-.||+.+.... .+....||.||...|.|-
T Consensus 113 l~C~~Cg~~~~~~~----~~~l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 113 LVCENCGHEVELTH----PERLPPCPKCGHTEFTRQ 144 (146)
T ss_pred EecccCCCEEEecC----CCcCCCCCCCCCCeeeeC
Confidence 57999999998873 446789999999999764
No 139
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.92 E-value=0.47 Score=30.14 Aligned_cols=32 Identities=16% Similarity=0.468 Sum_probs=22.0
Q ss_pred CCcCCCCCCccccc-CCCccceeecCCCCCccc
Q 023914 106 FCQWCGGQTKHEVP-HGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 106 fC~~CG~~~~~~~~-~~~~~~~~~C~~Cg~~~y 137 (275)
-||.|++....... ....+....|+.|+++.+
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 49999998654310 124566789999998754
No 140
>COG4640 Predicted membrane protein [Function unknown]
Probab=86.71 E-value=0.34 Score=46.55 Aligned_cols=26 Identities=38% Similarity=0.864 Sum_probs=17.3
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
++|||.||+.-. ++ ...|+.||...-
T Consensus 1 M~fC~kcG~qk~------Ed--~~qC~qCG~~~t 26 (465)
T COG4640 1 MKFCPKCGSQKA------ED--DVQCTQCGHKFT 26 (465)
T ss_pred CCcccccccccc------cc--cccccccCCcCC
Confidence 489999995521 11 234999997543
No 141
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.59 E-value=0.89 Score=37.24 Aligned_cols=46 Identities=15% Similarity=0.247 Sum_probs=30.9
Q ss_pred HHHHHHHHhhhhcCCCCcCCCCCCcccc-cCCCccceeecCCCCCcc
Q 023914 91 SSAAVHSAGNVLKISFCQWCGGQTKHEV-PHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 91 ~~~a~~l~~w~~~~~fC~~CG~~~~~~~-~~~~~~~~~~C~~Cg~~~ 136 (275)
..-|..-..++....+||.|++...... ....+..+..|++|++..
T Consensus 17 ~~~~~~~~~~~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf 63 (129)
T COG3677 17 LADAAYAIRMQITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTF 63 (129)
T ss_pred HHHHHHHHhhhcccCcCCCCCccceeeECCccccccccccCCcCcce
Confidence 3344445568888999999999982221 112235678999999654
No 142
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.49 E-value=0.46 Score=31.65 Aligned_cols=25 Identities=28% Similarity=0.611 Sum_probs=19.2
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
-|+.||...... .+....|+.||..
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCce
Confidence 399999997665 3455799999964
No 143
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=86.38 E-value=0.25 Score=47.99 Aligned_cols=37 Identities=30% Similarity=0.548 Sum_probs=28.7
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
..|..|...+.-||.||+.|+.. |.. .+.|++||...
T Consensus 341 ~~l~~~~~~~p~Cp~Cg~~m~S~---G~~--g~rC~kCg~~~ 377 (421)
T COG1571 341 LKLARYERVNPVCPRCGGRMKSA---GRN--GFRCKKCGTRA 377 (421)
T ss_pred EEeeeeEEcCCCCCccCCchhhc---CCC--CcccccccccC
Confidence 34556888889999999999876 222 68999999654
No 144
>PRK11032 hypothetical protein; Provisional
Probab=86.19 E-value=0.33 Score=41.27 Aligned_cols=32 Identities=19% Similarity=0.501 Sum_probs=26.7
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
.-|-.||..+... ..+....|+.||...|.|.
T Consensus 125 LvC~~Cg~~~~~~----~p~~i~pCp~C~~~~F~R~ 156 (160)
T PRK11032 125 LVCEKCHHHLAFY----TPEVLPLCPKCGHDQFQRR 156 (160)
T ss_pred EEecCCCCEEEec----CCCcCCCCCCCCCCeeeeC
Confidence 5699999999887 3457789999999999763
No 145
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=85.93 E-value=0.35 Score=33.03 Aligned_cols=29 Identities=24% Similarity=0.583 Sum_probs=21.6
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
-|.+||+..+.. .....-.|+.||+...-
T Consensus 8 ~C~~Cg~~~~~~----~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 8 KCARCGREVELD----QETRGIRCPYCGSRILV 36 (49)
T ss_pred EhhhcCCeeehh----hccCceeCCCCCcEEEE
Confidence 399999998543 34556789999986654
No 146
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=85.92 E-value=0.49 Score=31.00 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=17.8
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.||.||+..... . ...--.+|+.||.+.
T Consensus 2 ~Cp~Cg~~~~~~-D--~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVF-D--PERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEE-E--TTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEE-c--CCCCeEECCCCCCEe
Confidence 699999986222 1 122345999999764
No 147
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.60 E-value=0.47 Score=30.27 Aligned_cols=31 Identities=16% Similarity=0.362 Sum_probs=21.7
Q ss_pred CCcCCCCCCccccc-CCCccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHEVP-HGEEKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~-~~~~~~~~~C~~Cg~~~ 136 (275)
-||.|++....... -+.++.+..|+.|+.+.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 49999999754411 01356688999999865
No 148
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=85.48 E-value=0.42 Score=29.70 Aligned_cols=25 Identities=24% Similarity=0.605 Sum_probs=17.3
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
-|+.||+..... .+..-.|+.||+.
T Consensus 2 ~C~~Cg~~~~~~-----~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELK-----PGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BS-----TSSTSSBSSSS-S
T ss_pred CCCcCCCeeEcC-----CCCcEECCcCCCe
Confidence 389999998754 2345689999964
No 149
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=85.40 E-value=1.2 Score=29.55 Aligned_cols=39 Identities=18% Similarity=0.313 Sum_probs=26.6
Q ss_pred HHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 92 SAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 92 ~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
-..+.-..|-.. ..||+||+.-... . ....++.|.+|++
T Consensus 7 ~~~l~~~RW~~g-~~CP~Cg~~~~~~-~--~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 7 REYLEEIRWPDG-FVCPHCGSTKHYR-L--KTRGRYRCKACRK 45 (46)
T ss_pred HHHHHHhcCCCC-CCCCCCCCeeeEE-e--CCCCeEECCCCCC
Confidence 345566678777 4499999973333 2 2356789999975
No 150
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=85.34 E-value=0.17 Score=35.86 Aligned_cols=27 Identities=19% Similarity=0.518 Sum_probs=19.5
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecC-CCCCccc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICT-VCGKIAY 137 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~~~y 137 (275)
.|++|+.||++.... ...|. .|+..+.
T Consensus 2 ~HkHC~~CG~~Ip~~--------~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPD--------ESFCSPKCREEYR 29 (59)
T ss_pred CCCcCCcCCCcCCcc--------hhhhCHHHHHHHH
Confidence 589999999996432 46885 7876543
No 151
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=85.19 E-value=0.55 Score=36.60 Aligned_cols=30 Identities=33% Similarity=0.602 Sum_probs=22.3
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.|||.||.-+... .|+.-.+..|..|++++
T Consensus 2 ~FCP~Cgn~Live--~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCPTCGNMLIVE--SGESCNRFSCRTCPYVF 31 (105)
T ss_pred cccCCCCCEEEEe--cCCeEeeEEcCCCCcee
Confidence 6999999998665 22334788999998643
No 152
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=85.12 E-value=0.49 Score=41.11 Aligned_cols=29 Identities=17% Similarity=0.412 Sum_probs=23.1
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
+-.|++||++|... +....||.||++.-.
T Consensus 149 ~A~CsrC~~~L~~~------~~~l~Cp~Cg~tEkR 177 (188)
T COG1096 149 YARCSRCRAPLVKK------GNMLKCPNCGNTEKR 177 (188)
T ss_pred EEEccCCCcceEEc------CcEEECCCCCCEEee
Confidence 46899999999764 467899999987543
No 153
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.93 E-value=0.58 Score=41.04 Aligned_cols=94 Identities=17% Similarity=0.310 Sum_probs=63.8
Q ss_pred CccHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeCCeEEEEEeccCCCCC
Q 023914 87 SSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYG 166 (275)
Q Consensus 87 ~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~iLL~rr~~~p~~g 166 (275)
......-|.++.+-..+.++|+.||.-++. -.|+-|....- +...++||..-.-++-..+... ..|
T Consensus 36 ~~~~~~la~ai~~~~~~i~~C~~C~~lse~----------~~C~IC~d~~R---d~~~iCVVE~~~Dv~aiE~~~~-y~G 101 (195)
T TIGR00615 36 PSEVLRLAQALLEAKENLRTCSVCGAISDQ----------EVCNICSDERR---DNSVICVVEDPKDVFALEKTKE-FRG 101 (195)
T ss_pred HHHHHHHHHHHHHHHHcCCcCCCCCCCCCC----------CcCCCCCCCCC---CCCEEEEECCHHHHHHHHhhCc-cce
Confidence 334455667778888899999999977532 24777765433 3345566665555555555533 489
Q ss_pred ceeeeeEEeeC--CCCHHHHHHHHHHHHhC
Q 023914 167 LWTLPAGYMEI--GESAAEGAIRETWEEAR 194 (275)
Q Consensus 167 ~w~lPgG~vE~--GEs~eeAa~REl~EEtG 194 (275)
.|.+.+|.+.| |..+++--..++.+-..
T Consensus 102 ~YhVL~G~iSPldgigp~~l~i~~L~~Ri~ 131 (195)
T TIGR00615 102 RYHVLGGHISPLDGIGPEDLTIAALLKRLQ 131 (195)
T ss_pred EEEEccCccCccCCCChhhcCHHHHHHHHh
Confidence 99999999985 67777777777766653
No 154
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.71 E-value=0.46 Score=33.70 Aligned_cols=26 Identities=27% Similarity=0.667 Sum_probs=15.1
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
...|-.||..+... +....+.||+||
T Consensus 9 ~~~CtSCg~~i~p~----e~~v~F~CPnCG 34 (61)
T COG2888 9 PPVCTSCGREIAPG----ETAVKFPCPNCG 34 (61)
T ss_pred CceeccCCCEeccC----CceeEeeCCCCC
Confidence 34566666665443 455566666666
No 155
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=84.70 E-value=0.54 Score=48.37 Aligned_cols=35 Identities=31% Similarity=0.577 Sum_probs=18.6
Q ss_pred hcCCCCcCCCCCCcc-cccC---CCccceeecCCCCCcc
Q 023914 102 LKISFCQWCGGQTKH-EVPH---GEEKMRAICTVCGKIA 136 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~-~~~~---~~~~~~~~C~~Cg~~~ 136 (275)
...+||+.||.++.. .++. .-....+.|+.||...
T Consensus 13 ~~akFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 13 NNNRFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CCCccccccCCCCCCCcCCCCCCCCCcccccccccCCcc
Confidence 346777777777642 1110 0112346788887643
No 156
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=84.62 E-value=0.81 Score=36.19 Aligned_cols=52 Identities=21% Similarity=0.365 Sum_probs=35.2
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcE-----------EEEEEEeeCCeEEEEEec
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKM-----------VVGCLIEHDKKILLCKRK 160 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~-----------~V~viI~~~~~iLL~rr~ 160 (275)
..-||+|.+..... + +....|+.|++..-++-.. +.+.++.+++.|.|++--
T Consensus 3 lp~cp~c~sEytYe----d-~~~~~cpec~~ew~~~~~~~~~~~~~~v~DsnGn~L~dGDsV~lIKDL 65 (112)
T COG2824 3 LPPCPKCNSEYTYE----D-GGQLICPECAHEWNENEAAEEADEALIVKDSNGNLLADGDSVTLIKDL 65 (112)
T ss_pred CCCCCccCCceEEe----c-CceEeCchhccccccccccccccCceEEEcCCCcEeccCCeEEEEEee
Confidence 46799999998775 3 4489999999888755321 122333456777777754
No 157
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=84.41 E-value=0.73 Score=32.12 Aligned_cols=30 Identities=33% Similarity=0.562 Sum_probs=22.3
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
-||.||+.+...-. ..+....|+.||....
T Consensus 4 ~CP~CG~~iev~~~--~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 4 ECPDCGAEIELENP--ELGELVICDECGAELE 33 (54)
T ss_pred CCCCCCCEEecCCC--ccCCEEeCCCCCCEEE
Confidence 69999999766422 3366789999997654
No 158
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.29 E-value=0.55 Score=33.27 Aligned_cols=27 Identities=26% Similarity=0.739 Sum_probs=15.8
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..|..||..+... +...++.||+||..
T Consensus 8 ~~CtSCg~~i~~~----~~~~~F~CPnCG~~ 34 (59)
T PRK14890 8 PKCTSCGIEIAPR----EKAVKFLCPNCGEV 34 (59)
T ss_pred ccccCCCCcccCC----CccCEeeCCCCCCe
Confidence 3566666665443 33456666666654
No 159
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=84.12 E-value=0.67 Score=32.62 Aligned_cols=23 Identities=26% Similarity=0.696 Sum_probs=17.9
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
....||.||+..... ..|+.||+
T Consensus 26 ~l~~C~~CG~~~~~H---------~vC~~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKLPH---------RVCPSCGY 48 (57)
T ss_pred cceECCCCCCccCCe---------EECCCCCc
Confidence 346899999996443 68999993
No 160
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=83.93 E-value=0.56 Score=29.94 Aligned_cols=28 Identities=25% Similarity=0.464 Sum_probs=20.0
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.|+.||+..+......+ +....|+.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 69999998765533222 45678999997
No 161
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=83.78 E-value=2.4 Score=39.07 Aligned_cols=24 Identities=29% Similarity=0.423 Sum_probs=19.4
Q ss_pred eeCCeEEEEEeccCC-CCCceeeee
Q 023914 149 EHDKKILLCKRKIEP-SYGLWTLPA 172 (275)
Q Consensus 149 ~~~~~iLL~rr~~~p-~~g~w~lPg 172 (275)
..++++||.+|.... .+|+|+||.
T Consensus 236 ~~~~~~~~~~r~~~~~~~gl~~~p~ 260 (275)
T TIGR01084 236 NYDGEVLLEQRPEKGLWGGLYCFPQ 260 (275)
T ss_pred eCCCeEEEEeCCCCchhhccccCCC
Confidence 457899999997654 489999996
No 162
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=83.76 E-value=0.74 Score=37.60 Aligned_cols=31 Identities=13% Similarity=0.144 Sum_probs=22.2
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
+.+-||.||++.--. .+...+||.||..+-+
T Consensus 8 tKr~Cp~cg~kFYDL-----nk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSKFYDL-----NRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCcccccc-----CCCCccCCCcCCccCc
Confidence 457899999996443 3455789999988533
No 163
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=83.72 E-value=2.5 Score=37.08 Aligned_cols=87 Identities=21% Similarity=0.332 Sum_probs=50.7
Q ss_pred CCCCcCCCCCCcccccC----CCcc---ceeecCCCCCcccc-------CCcEEEEEEEe--eCCeEEEEEeccCCCCCc
Q 023914 104 ISFCQWCGGQTKHEVPH----GEEK---MRAICTVCGKIAYQ-------NPKMVVGCLIE--HDKKILLCKRKIEPSYGL 167 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~----~~~~---~~~~C~~Cg~~~y~-------~p~~~V~viI~--~~~~iLL~rr~~~p~~g~ 167 (275)
.--||-||+.+...... .-+. .-.+|.+||+.+.. .|.- +.+-++ ++-+.+++|.. .|.
T Consensus 14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~eP~r-~~lkve~~edL~~~V~RS~----s~~ 88 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEEREPRR-YTLKVESEEDLSARVVRSK----SAT 88 (201)
T ss_pred eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeecccCCCeE-EEEEeCCHHHhhhheeecC----Ccc
Confidence 45799999976544211 0111 24689999987653 3322 222232 23467777755 455
Q ss_pred eeee--eEEeeCCC------CHHHHHHHHHHHHhCC
Q 023914 168 WTLP--AGYMEIGE------SAAEGAIRETWEEARA 195 (275)
Q Consensus 168 w~lP--gG~vE~GE------s~eeAa~REl~EEtGl 195 (275)
-.+| |=.+++|. |-.|.+.+-+.|++..
T Consensus 89 I~IPELg~~iePG~~s~G~ITtIEGvL~rv~e~l~~ 124 (201)
T COG1779 89 IYIPELGLEIEPGPASEGFITTIEGVLERVYEVLET 124 (201)
T ss_pred EEcccCceEeccccccCceEehHHHHHHHHHHHHHH
Confidence 6666 44455554 4467777778887775
No 164
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=83.65 E-value=0.52 Score=30.88 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=21.6
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.|..||+..+...+..+ .....|+.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 49999988777655544 56789999997
No 165
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.54 E-value=0.96 Score=36.63 Aligned_cols=30 Identities=27% Similarity=0.473 Sum_probs=20.6
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.--||+||.---.+ +=-+.+..|.+||..+
T Consensus 21 ~grCP~CGeGrLF~---gFLK~~p~C~aCG~dy 50 (126)
T COG5349 21 RGRCPRCGEGRLFR---GFLKVVPACEACGLDY 50 (126)
T ss_pred cCCCCCCCCchhhh---hhcccCchhhhccccc
Confidence 35799999873222 2235678999999765
No 166
>PF12773 DZR: Double zinc ribbon
Probab=83.53 E-value=0.78 Score=30.73 Aligned_cols=25 Identities=24% Similarity=0.623 Sum_probs=18.7
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
.....+|+.||+.+.. ...+|+.||
T Consensus 26 ~~~~~~C~~Cg~~~~~--------~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPP--------NAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcC--------CcCccCccc
Confidence 3456899999998533 357899997
No 167
>PRK00076 recR recombination protein RecR; Reviewed
Probab=83.43 E-value=0.73 Score=40.46 Aligned_cols=94 Identities=22% Similarity=0.349 Sum_probs=63.9
Q ss_pred CCccHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeCCeEEEEEeccCCCC
Q 023914 86 TSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSY 165 (275)
Q Consensus 86 ~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~iLL~rr~~~p~~ 165 (275)
.+.....-|.++.+-..+.++|+.||.-++. -.|+-|....- +...++||..-..++-..+... ..
T Consensus 35 ~~~~~~~la~~i~~~~~~i~~C~~C~~lse~----------~~C~IC~d~~R---d~~~icVVE~~~Dv~aiE~s~~-y~ 100 (196)
T PRK00076 35 DREDVLRLAQALEEAKEKIKHCSVCGNLTEQ----------DPCEICSDPRR---DQSLICVVESPADVLAIERTGE-YR 100 (196)
T ss_pred CHHHHHHHHHHHHHHHHcCCcCCCCCCcCCC----------CcCCCCCCCCC---CCCEEEEECCHHHHHHHHhhCc-Cc
Confidence 3444456677788888899999999988633 25777764433 3445566666555665555533 47
Q ss_pred CceeeeeEEeeC--CCCHHHHHHHHHHHHh
Q 023914 166 GLWTLPAGYMEI--GESAAEGAIRETWEEA 193 (275)
Q Consensus 166 g~w~lPgG~vE~--GEs~eeAa~REl~EEt 193 (275)
|.|.+.+|.+.+ |-.+++--..++.+-.
T Consensus 101 G~YhVL~G~ispl~gi~p~~l~i~~L~~ri 130 (196)
T PRK00076 101 GLYHVLGGLLSPLDGIGPEDLNIDELLERL 130 (196)
T ss_pred eEEEEecCCcCCCCCCCccccCHHHHHHHH
Confidence 999999999985 6666666666666666
No 168
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=82.70 E-value=3.6 Score=39.14 Aligned_cols=92 Identities=17% Similarity=0.192 Sum_probs=52.2
Q ss_pred EEEEEEeeCCeEEEEEeccCC-CCCceeeeeEEeeCCCCHHHHHHHHHHHHhCCccccceeeEEEEeCCCCEEEEE-EEE
Q 023914 143 VVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYII-FLA 220 (275)
Q Consensus 143 ~V~viI~~~~~iLL~rr~~~p-~~g~w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~~~~~~~~~~~~~~-f~a 220 (275)
.+.+++..+++++|.+|...+ ..|+|++|....+. .. .+...+.|+.. +.++.+...+.+..... |.+
T Consensus 238 ~~~~~~~~~~~~~l~kr~~~gl~~gl~~fP~~e~~~--~~-----~~~~~~~~~~~---~~~~~~~H~fth~~l~i~~~a 307 (342)
T COG1194 238 AAFLILNRDGEVLLEKRPEKGLLGGLWCFPQFEDEA--DL-----LDWLAADGLAA---EPLGAFRHTFTHFRLTIELRA 307 (342)
T ss_pred eeEEEEccCcchhhhhCcccCceecccccccccccc--hh-----hhHhhhccccc---ccccceeeeeeEEEEEEEEEe
Confidence 445556778899999988765 48999999854433 22 22223334433 33444444444332222 333
Q ss_pred EEcCCCCCCCCCceeEEEecCCCCCCCCCCCcH
Q 023914 221 KLKRPHFSPGPESSECRLFALDEIPFDSLAFSS 253 (275)
Q Consensus 221 ~~~~~e~~~~~E~~d~~W~~~deL~~~~l~~~s 253 (275)
.... .+. +..|++.+++.. ++++.
T Consensus 308 ~~~~------~~~-~~~w~~~~~~~~--~~l~~ 331 (342)
T COG1194 308 SASL------VLS-DGRWYNLSDLES--IGLPA 331 (342)
T ss_pred eccc------CCC-Cceecccccccc--ccccH
Confidence 3222 222 789999999984 44444
No 169
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=82.55 E-value=0.94 Score=28.30 Aligned_cols=30 Identities=27% Similarity=0.649 Sum_probs=22.5
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
+.+-|+.||+..... ......+|..||.++
T Consensus 2 ~~~~C~~C~~~~i~~----~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVN----KEDDYEVCIFCGSSF 31 (33)
T ss_pred CceEcCCCCCCeEEE----ecCCeEEcccCCcEe
Confidence 346799999998773 233468999999764
No 170
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=82.47 E-value=1.3 Score=30.81 Aligned_cols=33 Identities=18% Similarity=0.579 Sum_probs=21.6
Q ss_pred CCCcCCCCCCcccccCCC--ccceeecCCCCCccc
Q 023914 105 SFCQWCGGQTKHEVPHGE--EKMRAICTVCGKIAY 137 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~--~~~~~~C~~Cg~~~y 137 (275)
-+||.||.++....-+.. .....+|+.|..+.-
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~Etl 39 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETL 39 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEE
Confidence 589999999855432211 124568999987643
No 171
>PRK11827 hypothetical protein; Provisional
Probab=82.42 E-value=1 Score=32.04 Aligned_cols=34 Identities=29% Similarity=0.568 Sum_probs=24.4
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
....--||.|.+++... .+....+|..|+ ..||-
T Consensus 5 LLeILaCP~ckg~L~~~----~~~~~Lic~~~~-laYPI 38 (60)
T PRK11827 5 LLEIIACPVCNGKLWYN----QEKQELICKLDN-LAFPL 38 (60)
T ss_pred HHhheECCCCCCcCeEc----CCCCeEECCccC-eeccc
Confidence 33446799999999765 345568999997 55653
No 172
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=82.39 E-value=1.3 Score=30.46 Aligned_cols=31 Identities=23% Similarity=0.448 Sum_probs=18.4
Q ss_pred CCCcCCCCCCcccc---cCCCccceeecCCCCCc
Q 023914 105 SFCQWCGGQTKHEV---PHGEEKMRAICTVCGKI 135 (275)
Q Consensus 105 ~fC~~CG~~~~~~~---~~~~~~~~~~C~~Cg~~ 135 (275)
+=||.||+.-.... ...+......|..||..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 45999999876321 11112223369999865
No 173
>KOG4432 consensus Uncharacterized NUDIX family hydrolase [General function prediction only]
Probab=82.37 E-value=3.6 Score=38.45 Aligned_cols=79 Identities=23% Similarity=0.201 Sum_probs=50.1
Q ss_pred eeeeeEEeeCCCCHHHHHHHHHHHHhCCccc--cceeeEEEEe--CCCCEEEEEEEEEEcCCC-------CCCCCCceeE
Q 023914 168 WTLPAGYMEIGESAAEGAIRETWEEARADVE--VQSPFAQLDI--PRIGQIYIIFLAKLKRPH-------FSPGPESSEC 236 (275)
Q Consensus 168 w~lPgG~vE~GEs~eeAa~REl~EEtGl~v~--~~~~~~~~~~--~~~~~~~~~f~a~~~~~e-------~~~~~E~~d~ 236 (275)
.++-+|.|+..-+.++-+.||..||.|.++. .++.+..+-- ...+....-|++++.+.+ ....+|..+.
T Consensus 286 lELcag~Vd~p~s~~e~a~~e~veecGYdlp~~~~k~va~y~sGVG~SG~~QTmfy~eVTdA~rsgpGgg~~ee~E~IEv 365 (405)
T KOG4432|consen 286 LELCAGRVDDPFSDPEKAARESVEECGYDLPEDSFKLVAKYISGVGQSGDTQTMFYVEVTDARRSGPGGGEKEEDEDIEV 365 (405)
T ss_pred eeeecccCCCCcccHHHHHHHHHHHhCCCCCHHHHhhhheeecccCCcCCeeEEEEEEeehhhccCCCCCcccccceeeE
Confidence 5677888888889999999999999999873 3444444321 111122222556655432 2223566777
Q ss_pred EEecCCCCCC
Q 023914 237 RLFALDEIPF 246 (275)
Q Consensus 237 ~W~~~deL~~ 246 (275)
.-+++++++.
T Consensus 366 v~lsle~a~~ 375 (405)
T KOG4432|consen 366 VRLSLEDAPS 375 (405)
T ss_pred EEechhhhhH
Confidence 7788888764
No 174
>PF14353 CpXC: CpXC protein
Probab=81.84 E-value=2.1 Score=34.43 Aligned_cols=50 Identities=20% Similarity=0.383 Sum_probs=29.4
Q ss_pred CCcCCCCCCccccc---C------------CCccceeecCCCCCccccCCcEEEEEEEeeCCeEEEEE
Q 023914 106 FCQWCGGQTKHEVP---H------------GEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCK 158 (275)
Q Consensus 106 fC~~CG~~~~~~~~---~------------~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~iLL~r 158 (275)
-||.||++...... . ...-....||+||......... ..++.+.++++.-
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~---lY~D~~~~~~i~~ 67 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPL---LYHDPEKKFMIYY 67 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCE---EEEcCCCCEEEEE
Confidence 59999998753311 0 0112468999999887654322 2345555555543
No 175
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=81.67 E-value=0.87 Score=31.78 Aligned_cols=22 Identities=27% Similarity=0.768 Sum_probs=17.1
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
...||.||+..... .+|+.||+
T Consensus 26 l~~C~~cG~~~~~H---------~vc~~cG~ 47 (55)
T TIGR01031 26 LVVCPNCGEFKLPH---------RVCPSCGY 47 (55)
T ss_pred ceECCCCCCcccCe---------eECCccCe
Confidence 46799999985443 68999993
No 176
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=81.67 E-value=0.73 Score=31.20 Aligned_cols=29 Identities=31% Similarity=0.510 Sum_probs=20.9
Q ss_pred hcCCCCc--CCCCCCcccccCCCccceeecCCCCC
Q 023914 102 LKISFCQ--WCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 102 ~~~~fC~--~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
+..+.|| .||...-+. +-..|..|..||.
T Consensus 16 r~rk~CP~~~CG~GvFMA----~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 16 RLRKECPSPRCGAGVFMA----EHKDRHYCGKCGY 46 (47)
T ss_dssp ESSEE-TSTTTTSSSEEE----E-SSEEEETTTSS
T ss_pred EhhhcCCCcccCCceEee----ecCCCccCCCccc
Confidence 4578999 999987555 3346899999985
No 177
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=81.11 E-value=0.82 Score=38.98 Aligned_cols=39 Identities=23% Similarity=0.471 Sum_probs=25.3
Q ss_pred hhhc-CCCCcCCCCCCcccccC-----------CCccceeecCCCCCcccc
Q 023914 100 NVLK-ISFCQWCGGQTKHEVPH-----------GEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 100 w~~~-~~fC~~CG~~~~~~~~~-----------~~~~~~~~C~~Cg~~~y~ 138 (275)
|... +.-||.|++++....-+ .....-..|+.||.++|+
T Consensus 92 ~~~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 92 RLFPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred hcccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence 4444 78899999998654110 001113569999999886
No 178
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=78.69 E-value=1.4 Score=30.82 Aligned_cols=26 Identities=19% Similarity=0.445 Sum_probs=19.8
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
+||.|++... +.....|+.||...|-
T Consensus 1 ~Cpv~~~~~~-------~~v~~~Cp~cGipthc 26 (55)
T PF13824_consen 1 LCPVCKKDLP-------AHVNFECPDCGIPTHC 26 (55)
T ss_pred CCCCCccccc-------cccCCcCCCCCCcCcc
Confidence 6999998751 3456899999987763
No 179
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=78.39 E-value=1.7 Score=30.24 Aligned_cols=31 Identities=23% Similarity=0.450 Sum_probs=19.5
Q ss_pred CCCCcCCCCCCcccccCCCc--c--ceeecCCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEE--K--MRAICTVCGK 134 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~--~--~~~~C~~Cg~ 134 (275)
.+=||.||++.......... + ....|..||.
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 45699999886554321111 1 4567999987
No 180
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=77.46 E-value=1 Score=41.66 Aligned_cols=31 Identities=29% Similarity=0.695 Sum_probs=22.4
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.+.+||+.||-.+.... +.+....||.||..
T Consensus 313 ~k~nfc~ncG~~~t~~~---~ng~a~fcp~cgq~ 343 (345)
T COG4260 313 AKLNFCLNCGCGTTADF---DNGKAKFCPECGQG 343 (345)
T ss_pred cccccccccCcccccCC---ccchhhhChhhcCC
Confidence 35679999995544432 56778999999853
No 181
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=77.27 E-value=0.31 Score=41.11 Aligned_cols=23 Identities=35% Similarity=0.819 Sum_probs=17.9
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.+..||.+||+++.. .|++|+..
T Consensus 26 ~~~~fC~kCG~~tI~-----------~Cp~C~~~ 48 (158)
T PF10083_consen 26 LREKFCSKCGAKTIT-----------SCPNCSTP 48 (158)
T ss_pred HHHHHHHHhhHHHHH-----------HCcCCCCC
Confidence 456899999999744 48899854
No 182
>PRK05978 hypothetical protein; Provisional
Probab=77.26 E-value=1.6 Score=36.66 Aligned_cols=37 Identities=19% Similarity=0.180 Sum_probs=25.0
Q ss_pred hhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 100 NVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
|.--..-||+||+.--.+ +--+.+..|+.||..+...
T Consensus 29 ~rGl~grCP~CG~G~LF~---g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 29 WRGFRGRCPACGEGKLFR---AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HHHHcCcCCCCCCCcccc---cccccCCCccccCCccccC
Confidence 444467899999984332 2245678999999766543
No 183
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=77.19 E-value=1.2 Score=31.43 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=20.7
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
-|+-||++.... .+...+|..||+.
T Consensus 22 iCgdC~~en~lk-----~~D~irCReCG~R 46 (62)
T KOG3507|consen 22 ICGDCGQENTLK-----RGDVIRCRECGYR 46 (62)
T ss_pred Eecccccccccc-----CCCcEehhhcchH
Confidence 599999998776 4567899999974
No 184
>PHA02942 putative transposase; Provisional
Probab=77.17 E-value=1.8 Score=41.73 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=21.9
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
+.+.||.||+.... .......|+.||+..-
T Consensus 324 TSq~Cs~CG~~~~~-----l~~r~f~C~~CG~~~d 353 (383)
T PHA02942 324 SSVSCPKCGHKMVE-----IAHRYFHCPSCGYEND 353 (383)
T ss_pred CCccCCCCCCccCc-----CCCCEEECCCCCCEeC
Confidence 56889999998642 1234589999998653
No 185
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=76.77 E-value=2.2 Score=30.23 Aligned_cols=33 Identities=18% Similarity=0.331 Sum_probs=19.7
Q ss_pred cCCCCcCCCCCCcccccC-CCccceeecCCCCCc
Q 023914 103 KISFCQWCGGQTKHEVPH-GEEKMRAICTVCGKI 135 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~-~~~~~~~~C~~Cg~~ 135 (275)
..-.||.||+.+..+..- ...+....|++||+.
T Consensus 24 ~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCeeEeechhHHhcCCceECCCCCCc
Confidence 345799998874433210 123355788888874
No 186
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=76.75 E-value=1.8 Score=30.70 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=18.2
Q ss_pred CCCCcCCCCCCcccccC-CCccceeecCCCCCc
Q 023914 104 ISFCQWCGGQTKHEVPH-GEEKMRAICTVCGKI 135 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~-~~~~~~~~C~~Cg~~ 135 (275)
.-.||.||..+..+..- ..-+...+|++||+.
T Consensus 27 ~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 27 KFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred EeeCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence 34688888665443110 123355778888864
No 187
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=76.61 E-value=1.8 Score=31.15 Aligned_cols=32 Identities=22% Similarity=0.461 Sum_probs=23.0
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..+=||.||......... .+-.+..|..|+..
T Consensus 5 ~lKPCPFCG~~~~~v~~~-~g~~~v~C~~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAI-SGYYRAKCNGCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEec-CceEEEEcCCCCcC
Confidence 457799999997665432 34456899999864
No 188
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=76.15 E-value=1.8 Score=36.00 Aligned_cols=35 Identities=26% Similarity=0.441 Sum_probs=24.8
Q ss_pred CCCCcCCCCCCcccccCC-----------CccceeecCCCCCcccc
Q 023914 104 ISFCQWCGGQTKHEVPHG-----------EEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~-----------~~~~~~~C~~Cg~~~y~ 138 (275)
+.-|+.|++++.....+. ....-+.|+.||+++|+
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 789999999986552210 01135799999999886
No 189
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=76.14 E-value=1.3 Score=30.93 Aligned_cols=21 Identities=29% Similarity=0.822 Sum_probs=15.8
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
...||.||.....+ ..|++||
T Consensus 26 l~~c~~cg~~~~~H---------~vc~~cG 46 (56)
T PF01783_consen 26 LVKCPNCGEPKLPH---------RVCPSCG 46 (56)
T ss_dssp EEESSSSSSEESTT---------SBCTTTB
T ss_pred eeeeccCCCEeccc---------EeeCCCC
Confidence 46799999764332 6899998
No 190
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=75.73 E-value=2.2 Score=29.02 Aligned_cols=41 Identities=22% Similarity=0.365 Sum_probs=23.6
Q ss_pred HHHHHhhhhcCCCCcCCCCCCccc----ccCCCccceeecCCCCCc
Q 023914 94 AVHSAGNVLKISFCQWCGGQTKHE----VPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~----~~~~~~~~~~~C~~Cg~~ 135 (275)
|+..+.-...+-+||.||..-.-. ....++-.++.| .||+.
T Consensus 3 ~~~~~~L~~kY~~Cp~CGN~~vGngEG~liV~edtfkRtC-kCGfn 47 (49)
T PF12677_consen 3 AWKTLKLSNKYCKCPKCGNDKVGNGEGTLIVEEDTFKRTC-KCGFN 47 (49)
T ss_pred hhhhcchhhhhccCcccCCcEeecCcceEEEeccceeeee-ccccc
Confidence 344455566688999999764322 000133456777 57763
No 191
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=74.44 E-value=1.2 Score=41.10 Aligned_cols=33 Identities=27% Similarity=0.571 Sum_probs=15.7
Q ss_pred CCCCcCCCCCCcccccCCC---ccceeecCCCCCcc
Q 023914 104 ISFCQWCGGQTKHEVPHGE---EKMRAICTVCGKIA 136 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~---~~~~~~C~~Cg~~~ 136 (275)
..|||.||++-......++ |....+|.-|+...
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEW 207 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EE
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCee
Confidence 3699999999655544433 33456888888654
No 192
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.41 E-value=1.2 Score=36.89 Aligned_cols=29 Identities=31% Similarity=0.826 Sum_probs=20.4
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
-..+||.+||++...+ ..+.+++|.-|..
T Consensus 87 Cq~r~CARCGGrv~lr----sNKv~wvcnlc~k 115 (169)
T KOG3799|consen 87 CQTRFCARCGGRVSLR----SNKVMWVCNLCRK 115 (169)
T ss_pred hhhhHHHhcCCeeeec----cCceEEeccCCcH
Confidence 3457888888887666 4567778877753
No 193
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=74.26 E-value=4.4 Score=34.01 Aligned_cols=42 Identities=14% Similarity=0.296 Sum_probs=29.2
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcc-ccCCcEEEEEEEee
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA-YQNPKMVVGCLIEH 150 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~-y~~p~~~V~viI~~ 150 (275)
+.-||.|.+++... +.....|+.|+... -|.++..+-+.+.+
T Consensus 34 Y~aC~~C~kkv~~~-----~~~~~~C~~C~~~~~~~~~ry~l~~~i~D 76 (166)
T cd04476 34 YPACPGCNKKVVEE-----GNGTYRCEKCNKSVPNPEYRYILSLNVAD 76 (166)
T ss_pred EccccccCcccEeC-----CCCcEECCCCCCcCCCccEEEEEEEEEEe
Confidence 57899999997543 22568999999876 45555555555544
No 194
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=74.04 E-value=1.9 Score=25.86 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=16.3
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
-|++||..+..... .+.....|+.|..
T Consensus 3 ~C~rC~~~~~~~~~--~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGI--NGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEE--TTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEe--cCCCCeECcCCcC
Confidence 59999999866543 3456789999964
No 195
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=73.92 E-value=1.1 Score=34.55 Aligned_cols=36 Identities=22% Similarity=0.361 Sum_probs=24.0
Q ss_pred HHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 96 HSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 96 ~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.+..=....-.||.||+....+. +--.+.|..|+..
T Consensus 27 kie~~q~~ky~Cp~Cgk~~vkR~----a~GIW~C~~C~~~ 62 (90)
T PF01780_consen 27 KIEISQHAKYTCPFCGKTSVKRV----ATGIWKCKKCGKK 62 (90)
T ss_dssp HHHHHHHS-BEESSSSSSEEEEE----ETTEEEETTTTEE
T ss_pred HHHHHHhCCCcCCCCCCceeEEe----eeEEeecCCCCCE
Confidence 33334455668999999976552 3335899999854
No 196
>KOG4313 consensus Thiamine pyrophosphokinase [Nucleotide transport and metabolism]
Probab=73.91 E-value=6.5 Score=35.84 Aligned_cols=90 Identities=20% Similarity=0.107 Sum_probs=56.5
Q ss_pred eEEEEEeccCC--CCCceee-eeEEeeCCCCHHHHHHHHHHHHhCCcc---ccceeeEEEE--------eCCCCEEEEEE
Q 023914 153 KILLCKRKIEP--SYGLWTL-PAGYMEIGESAAEGAIRETWEEARADV---EVQSPFAQLD--------IPRIGQIYIIF 218 (275)
Q Consensus 153 ~iLL~rr~~~p--~~g~w~l-PgG~vE~GEs~eeAa~REl~EEtGl~v---~~~~~~~~~~--------~~~~~~~~~~f 218 (275)
++.+.||+... ++|+|+- .||.+..|-...++++.|..||+.+.. .++..-|... +-++... .+|
T Consensus 149 ~iWvprRS~TKqTWP~~lDN~vaGGl~~g~gI~eT~iKE~~EEAnl~~~~~~Nlv~~G~VSy~~~esr~~~~pe~q-YVf 227 (306)
T KOG4313|consen 149 CIWVPRRSNTKQTWPGKLDNMVAGGLSVGFGIKETAIKEAAEEANLPSDLVKNLVSAGCVSYYKFESRQGLFPETQ-YVF 227 (306)
T ss_pred EEEecccCCccccCcchhhhhhccccccCchHHHHHHHHHHHhcCCchhhHhcceecceeEEEeeehhhccCccce-EEE
Confidence 67788887543 5788874 499999999999999999999999976 2232222222 2223332 335
Q ss_pred EEEEcCCCC-CC-CCCceeEEEecCCC
Q 023914 219 LAKLKRPHF-SP-GPESSECRLFALDE 243 (275)
Q Consensus 219 ~a~~~~~e~-~~-~~E~~d~~W~~~de 243 (275)
-..+...-+ ++ +.|.+....++..|
T Consensus 228 DL~l~~d~iP~~nDGEV~~F~Lltl~~ 254 (306)
T KOG4313|consen 228 DLELPLDFIPQNNDGEVQAFELLTLKD 254 (306)
T ss_pred eccCchhhcCCCCCCceeeEeeecHHH
Confidence 444433222 22 36777776766655
No 197
>PRK10445 endonuclease VIII; Provisional
Probab=73.54 E-value=2 Score=39.31 Aligned_cols=29 Identities=21% Similarity=0.449 Sum_probs=22.6
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
.-+-||+||++....... +.....||.|.
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~--gR~t~~CP~CQ 262 (263)
T PRK10445 234 DGEACERCGGIIEKTTLS--SRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCEeEEEEEC--CCCcEECCCCc
Confidence 458899999998776553 45678999996
No 198
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=73.49 E-value=2.6 Score=32.98 Aligned_cols=33 Identities=24% Similarity=0.392 Sum_probs=21.6
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
+.-.||.||+..... +-+.+.....|+.||...
T Consensus 20 t~f~CP~Cge~~v~v-~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKVSISV-KIKKNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCeEeee-ecCCCcceEECCCCCCcc
Confidence 446799999654332 222345568999999764
No 199
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=73.31 E-value=3.9 Score=26.22 Aligned_cols=32 Identities=25% Similarity=0.665 Sum_probs=21.6
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
++.=||.||+.-..+..+-++.-.++|..|+.
T Consensus 2 ~~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 2 RHGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 35679999998766644323334578998863
No 200
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=73.24 E-value=1.2 Score=35.60 Aligned_cols=32 Identities=19% Similarity=0.467 Sum_probs=25.0
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
...||+.||.-+... ...+...|..|+..+-+
T Consensus 6 ~~~FC~~CG~ll~~~----~~~~~~~C~~Ck~~~~v 37 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEP----SAQSTVLCIRCKIEYPV 37 (116)
T ss_pred Ccchhhhhhhhcccc----cccCceEeccccccCCH
Confidence 568999999998665 56677789999976543
No 201
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=73.23 E-value=2.1 Score=28.87 Aligned_cols=29 Identities=24% Similarity=0.443 Sum_probs=19.6
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.|..||...+......+ .....||.||..
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSD-DPLATCPECGGE 35 (52)
T ss_pred EeCCCCCEeEEEEecCC-CCCCCCCCCCCC
Confidence 59999997665533222 344679999974
No 202
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=72.95 E-value=2.4 Score=27.47 Aligned_cols=14 Identities=21% Similarity=0.579 Sum_probs=10.4
Q ss_pred ceeecCCCCCcccc
Q 023914 125 MRAICTVCGKIAYQ 138 (275)
Q Consensus 125 ~~~~C~~Cg~~~y~ 138 (275)
..++|+.||...|.
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 45679999987764
No 203
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=72.84 E-value=2.6 Score=29.41 Aligned_cols=28 Identities=25% Similarity=0.463 Sum_probs=21.2
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
..-|+.||.++... ....+|+.||..+-
T Consensus 5 ~~~C~~Cg~~~~~~------dDiVvCp~CgapyH 32 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG------DDIVVCPECGAPYH 32 (54)
T ss_pred CccChhhCCcccCC------CCEEECCCCCCccc
Confidence 35699999997433 35689999997764
No 204
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=71.89 E-value=2.6 Score=27.48 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=16.0
Q ss_pred CCCCcCCCCCCccc-ccCCCccceeecCCCC
Q 023914 104 ISFCQWCGGQTKHE-VPHGEEKMRAICTVCG 133 (275)
Q Consensus 104 ~~fC~~CG~~~~~~-~~~~~~~~~~~C~~Cg 133 (275)
+.=||.||+.-..+ ..+.++.-.++|..|+
T Consensus 3 h~pCP~CGG~DrFri~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 3 HGPCPICGGKDRFRIFDDKDGRGTWICRQCG 33 (40)
T ss_dssp EE--TTTT-TTTEEEETT----S-EEETTTT
T ss_pred CCCCCCCcCccccccCcCcccCCCEECCCCC
Confidence 34599999997766 3332334567999994
No 205
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=71.45 E-value=2.6 Score=38.45 Aligned_cols=31 Identities=19% Similarity=0.372 Sum_probs=23.0
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
.|..+.+-||.||. + .+....|+.||+.+-.
T Consensus 304 ~~~~tS~~C~~cg~-~--------~~r~~~C~~cg~~~~r 334 (364)
T COG0675 304 PPYYTSKTCPCCGH-L--------SGRLFKCPRCGFVHDR 334 (364)
T ss_pred CCCCCcccccccCC-c--------cceeEECCCCCCeehh
Confidence 36677799999999 1 1345799999987553
No 206
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=71.43 E-value=24 Score=31.51 Aligned_cols=25 Identities=20% Similarity=0.642 Sum_probs=17.9
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
||.||.+.... ....|+.|-...++
T Consensus 1 C~~CG~~~~~~-------~~~lC~~C~~~~~~ 25 (236)
T PF04981_consen 1 CPRCGREIEPL-------IDGLCPDCYLKRFD 25 (236)
T ss_pred CCCCCCCCCCc-------ccccChHHhcccCC
Confidence 99999987543 22489999766663
No 207
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=71.17 E-value=5.4 Score=30.72 Aligned_cols=37 Identities=19% Similarity=0.318 Sum_probs=25.3
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..+..=....-.||.||+..... .+--.+.|..|+..
T Consensus 27 ~kie~~q~a~y~CpfCgk~~vkR----~a~GIW~C~~C~~~ 63 (90)
T PTZ00255 27 KKIEISQHAKYFCPFCGKHAVKR----QAVGIWRCKGCKKT 63 (90)
T ss_pred HHHHHHHhCCccCCCCCCCceee----eeeEEEEcCCCCCE
Confidence 34444455667899999876554 33446899999865
No 208
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=71.08 E-value=9.1 Score=29.59 Aligned_cols=54 Identities=19% Similarity=0.333 Sum_probs=32.0
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccC--Cc---------E-EEEEEEeeCCeEEEEEec
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN--PK---------M-VVGCLIEHDKKILLCKRK 160 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~--p~---------~-~V~viI~~~~~iLL~rr~ 160 (275)
--|..||......-. ....+.+||.|=+..-.. |. + -+.+.+..+++..|++|=
T Consensus 5 F~C~~CG~~V~p~~~--g~~~RNHCP~CL~S~Hvd~~pGDRas~C~g~M~Pi~v~~~~~g~w~iiHrC 70 (92)
T PF12647_consen 5 FTCVHCGLTVSPLAA--GSAHRNHCPSCLSSLHVDIVPGDRASDCGGRMEPIAVWVRRDGEWMIIHRC 70 (92)
T ss_pred cCccccCCCcccCCC--CCCccCcCcccccccccCCCCCCccccCCCeeeEEEEEEEcCCCEEEEEec
Confidence 469999998755422 345788999996543322 11 1 133444555666666654
No 209
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.02 E-value=2.2 Score=46.66 Aligned_cols=19 Identities=16% Similarity=0.179 Sum_probs=10.0
Q ss_pred cccccccccccceeeccee
Q 023914 56 LVSPAFLTRRTRCFRASRV 74 (275)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~ 74 (275)
.++|.....+...+...|+
T Consensus 595 ~~s~~~ir~ra~trIG~Rm 613 (1337)
T PRK14714 595 ELAPFKVRERAPTRIGNRM 613 (1337)
T ss_pred hhCCcEEeccCcceeeccc
Confidence 3555555555555555553
No 210
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=69.85 E-value=1.9 Score=31.92 Aligned_cols=15 Identities=33% Similarity=0.780 Sum_probs=6.0
Q ss_pred hcCCCCcCCCCCCcc
Q 023914 102 LKISFCQWCGGQTKH 116 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~ 116 (275)
..-.|||.||..+-.
T Consensus 22 ~~k~FCp~CGn~TL~ 36 (73)
T PF08772_consen 22 MTKQFCPKCGNATLK 36 (73)
T ss_dssp SS--S-SSS--S--E
T ss_pred CCceeCcccCCCcce
Confidence 345899999999643
No 211
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=69.55 E-value=2.9 Score=28.78 Aligned_cols=31 Identities=19% Similarity=0.449 Sum_probs=14.6
Q ss_pred hhcCCCCcC--CCCCCcccccCCCccce--eecCCCCCc
Q 023914 101 VLKISFCQW--CGGQTKHEVPHGEEKMR--AICTVCGKI 135 (275)
Q Consensus 101 ~~~~~fC~~--CG~~~~~~~~~~~~~~~--~~C~~Cg~~ 135 (275)
....++||. |+...... ++... ..|+.|+..
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~----~~~~~~~~~C~~C~~~ 49 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKD----DGCNSPIVTCPSCGTE 49 (64)
T ss_dssp ---CC--TTSST---ECS-----SSTTS--CCTTSCCSE
T ss_pred CCCccCCCCCCCcccEEec----CCCCCCeeECCCCCCc
Confidence 344579988 99997665 22233 789988864
No 212
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=69.22 E-value=2.7 Score=43.35 Aligned_cols=12 Identities=17% Similarity=0.086 Sum_probs=7.2
Q ss_pred CCHHHHHHHHHH
Q 023914 179 ESAAEGAIRETW 190 (275)
Q Consensus 179 Es~eeAa~REl~ 190 (275)
.|+.+++.-++.
T Consensus 130 ~s~~~~~~~~~~ 141 (645)
T PRK14559 130 PSPLEALLEQLE 141 (645)
T ss_pred cCHHHHHHHHhh
Confidence 477777655443
No 213
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=68.88 E-value=3 Score=38.47 Aligned_cols=28 Identities=18% Similarity=0.351 Sum_probs=21.6
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
-+-||+||++....... +.....||.|.
T Consensus 254 g~pC~~Cg~~I~~~~~~--gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLA--GRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEEC--CCccEECCCCc
Confidence 46899999998766542 45678999996
No 214
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=68.65 E-value=3.2 Score=31.99 Aligned_cols=37 Identities=16% Similarity=0.280 Sum_probs=25.0
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..+..=....-.||.||+....+ .+--.+.|..|+..
T Consensus 27 ~kie~~q~a~y~CpfCgk~~vkR----~a~GIW~C~~C~~~ 63 (90)
T PRK03976 27 ADIEEKMRAKHVCPVCGRPKVKR----VGTGIWECRKCGAK 63 (90)
T ss_pred HHHHHHHhcCccCCCCCCCceEE----EEEEEEEcCCCCCE
Confidence 33444455566899999886555 33446899999864
No 215
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=68.45 E-value=17 Score=31.88 Aligned_cols=20 Identities=35% Similarity=0.984 Sum_probs=15.4
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
-| +||.++..- ..|+.||..
T Consensus 2 ~C-rCG~~l~~p---------~~Cl~Cg~~ 21 (227)
T COG4031 2 IC-RCGAELSSP---------AFCLNCGRR 21 (227)
T ss_pred cc-ccCCccccc---------chhcccCCc
Confidence 48 999997332 589999976
No 216
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=68.39 E-value=2.8 Score=26.65 Aligned_cols=31 Identities=19% Similarity=0.355 Sum_probs=20.1
Q ss_pred hhhcC-CCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 100 NVLKI-SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 100 w~~~~-~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
|.+.. .-|+.||+..-.. ++| ..+|..||+.
T Consensus 3 ~~~~~~~~C~~C~~~~~~~----~dG-~~yC~~cG~~ 34 (36)
T PF11781_consen 3 WMRGPNEPCPVCGSRWFYS----DDG-FYYCDRCGHQ 34 (36)
T ss_pred ccccCCCcCCCCCCeEeEc----cCC-EEEhhhCceE
Confidence 44443 3599999993222 233 5899999975
No 217
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.35 E-value=3 Score=38.27 Aligned_cols=28 Identities=18% Similarity=0.391 Sum_probs=21.5
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
-+-||+||.+....... +.....||.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~--gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVG--GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEEC--CCCCEECCCCC
Confidence 46899999998776543 45678999994
No 218
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=68.19 E-value=3.6 Score=38.55 Aligned_cols=35 Identities=14% Similarity=0.326 Sum_probs=22.1
Q ss_pred cCCCCcCCCCCCccccc-C---CCccceeecCCCCCccc
Q 023914 103 KISFCQWCGGQTKHEVP-H---GEEKMRAICTVCGKIAY 137 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~-~---~~~~~~~~C~~Cg~~~y 137 (275)
...|||.||+.-..... . .++....+|.-|+...-
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~ 221 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWH 221 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccc
Confidence 35699999999644322 1 13445568888886643
No 219
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=68.13 E-value=3.1 Score=38.21 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=23.0
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
+.-+-||+||++....... +.....||.|..
T Consensus 242 R~g~pCprCG~~I~~~~~~--gR~t~~CP~CQ~ 272 (272)
T PRK14810 242 RTGEPCLNCKTPIRRVVVA--GRSSHYCPHCQK 272 (272)
T ss_pred CCCCcCCCCCCeeEEEEEC--CCccEECcCCcC
Confidence 3457899999998766543 456789999963
No 220
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=67.85 E-value=3.3 Score=36.70 Aligned_cols=15 Identities=27% Similarity=0.676 Sum_probs=11.1
Q ss_pred ceeecCCCCCccccC
Q 023914 125 MRAICTVCGKIAYQN 139 (275)
Q Consensus 125 ~~~~C~~Cg~~~y~~ 139 (275)
...+||+||+..+.+
T Consensus 47 ~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 47 EVWVCPHCGYAAFEE 61 (214)
T ss_pred eEEECCCCCCccccc
Confidence 347899999877765
No 221
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=67.76 E-value=3.3 Score=37.99 Aligned_cols=29 Identities=21% Similarity=0.433 Sum_probs=21.8
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.+-||+||++....... +.....||.|..
T Consensus 245 g~pC~~Cg~~I~~~~~~--gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQG--GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEEC--CCCcEECcCCCC
Confidence 46799999998765442 456789999974
No 222
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=67.39 E-value=2.2 Score=34.01 Aligned_cols=28 Identities=18% Similarity=0.344 Sum_probs=17.6
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.-.-+|..||+..... .....||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~------~~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIH------QHDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecC------CcCccCcCCCCC
Confidence 3345899999765432 233459999844
No 223
>PRK12495 hypothetical protein; Provisional
Probab=67.13 E-value=3.8 Score=36.60 Aligned_cols=33 Identities=15% Similarity=0.449 Sum_probs=23.8
Q ss_pred hhhcCCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 100 NVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
......+|+.||.++-.. . ...+|+.|+...-.
T Consensus 38 atmsa~hC~~CG~PIpa~--p----G~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 38 ATMTNAHCDECGDPIFRH--D----GQEFCPTCQQPVTE 70 (226)
T ss_pred cccchhhcccccCcccCC--C----CeeECCCCCCcccc
Confidence 355678999999998532 1 24689999976543
No 224
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=67.03 E-value=6.7 Score=30.26 Aligned_cols=38 Identities=18% Similarity=0.311 Sum_probs=25.6
Q ss_pred HHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 94 AVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
...+..-....-.||.||+....+ .+--.+.|..|+..
T Consensus 25 v~kie~~q~a~y~CpfCgk~~vkR----~a~GIW~C~~C~~~ 62 (91)
T TIGR00280 25 VKKIEIQQKAKYVCPFCGKKTVKR----GSTGIWTCRKCGAK 62 (91)
T ss_pred HHHHHHHHhcCccCCCCCCCceEE----EeeEEEEcCCCCCE
Confidence 344444455667899999876554 34446899999864
No 225
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=66.59 E-value=3.5 Score=37.80 Aligned_cols=31 Identities=19% Similarity=0.426 Sum_probs=23.0
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.-+-||+||.+....... +.....|+.|...
T Consensus 234 ~g~pC~~Cg~~I~~~~~~--gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVVG--GRGTHFCPQCQPL 264 (269)
T ss_pred CcCCCCcCCCeeEEEEEC--CCCcEECCCCcCC
Confidence 346799999998766543 4567899999753
No 226
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=66.20 E-value=4.7 Score=29.05 Aligned_cols=9 Identities=33% Similarity=0.911 Sum_probs=7.0
Q ss_pred CCcCCCCCC
Q 023914 106 FCQWCGGQT 114 (275)
Q Consensus 106 fC~~CG~~~ 114 (275)
-||+||...
T Consensus 2 ~C~KCg~~~ 10 (64)
T PF09855_consen 2 KCPKCGNEE 10 (64)
T ss_pred CCCCCCCcc
Confidence 489998875
No 227
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=65.82 E-value=6.9 Score=26.89 Aligned_cols=33 Identities=21% Similarity=0.387 Sum_probs=22.5
Q ss_pred hhcCCCCc--CCCCCCcccccCCCccceeecCCCCCc
Q 023914 101 VLKISFCQ--WCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 101 ~~~~~fC~--~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
+.+.++|| .|+....... +.+.....|+.|+..
T Consensus 15 ~~~~~~CP~~~C~~~~~~~~--~~~~~~v~C~~C~~~ 49 (64)
T smart00647 15 NPDLKWCPAPDCSAAIIVTE--EEGCNRVTCPKCGFS 49 (64)
T ss_pred CCCccCCCCCCCcceEEecC--CCCCCeeECCCCCCe
Confidence 45789999 9988765531 124456789888754
No 228
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=65.56 E-value=5.8 Score=34.78 Aligned_cols=34 Identities=18% Similarity=0.431 Sum_probs=20.1
Q ss_pred cCCCCcCCCCCCccc--ccCCCccceeecCCCCCcc
Q 023914 103 KISFCQWCGGQTKHE--VPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~--~~~~~~~~~~~C~~Cg~~~ 136 (275)
.+-.||.||..-..+ ....-...-..|..||.++
T Consensus 5 iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEe
Confidence 356899999443211 1110112357899999877
No 229
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=65.48 E-value=2.3 Score=35.33 Aligned_cols=35 Identities=14% Similarity=0.194 Sum_probs=20.9
Q ss_pred CCCCcCCCCCCccccc--CCCccceeecCCCCCcccc
Q 023914 104 ISFCQWCGGQTKHEVP--HGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~--~~~~~~~~~C~~Cg~~~y~ 138 (275)
+-.||.||.......- ..+......||.||.....
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 4459999988654210 0011123899999976543
No 230
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=65.34 E-value=2.7 Score=33.54 Aligned_cols=30 Identities=13% Similarity=0.215 Sum_probs=17.7
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..-.-+|..||...... ......||.||..
T Consensus 67 ~p~~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQYVTLL-----TQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCCeeecC-----CccCCcCcCcCCC
Confidence 33446899998654332 1122569999854
No 231
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=65.27 E-value=3.3 Score=33.12 Aligned_cols=29 Identities=31% Similarity=0.486 Sum_probs=21.1
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
-||.||+.+..- |..-.|..|+...--.|
T Consensus 71 ~CP~C~K~TKmL------Gr~D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 71 ECPNCGKQTKML------GRVDACMHCKEPLTLDP 99 (114)
T ss_pred ECCCCCChHhhh------chhhccCcCCCcCccCc
Confidence 499999998765 23358999997655443
No 232
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=65.11 E-value=9.7 Score=31.20 Aligned_cols=43 Identities=14% Similarity=0.269 Sum_probs=26.1
Q ss_pred CCCCc--CCCCCCcccccCCCccceeecCCCCCcc-ccCCcEEEEEEEeeC
Q 023914 104 ISFCQ--WCGGQTKHEVPHGEEKMRAICTVCGKIA-YQNPKMVVGCLIEHD 151 (275)
Q Consensus 104 ~~fC~--~CG~~~~~~~~~~~~~~~~~C~~Cg~~~-y~~p~~~V~viI~~~ 151 (275)
+.=|| .|++++... +.....|+.|+... -|.++..+-+.+.++
T Consensus 18 Y~aC~~~~C~kKv~~~-----~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~ 63 (146)
T PF08646_consen 18 YPACPNEKCNKKVTEN-----GDGSYRCEKCNKTVENPKYRYRLSLKISDG 63 (146)
T ss_dssp EEE-TSTTTS-B-EEE-----TTTEEEETTTTEEESS-EEEEEEEEEEEET
T ss_pred ECCCCCccCCCEeecC-----CCcEEECCCCCCcCCCeeEEEEEEEEEEeC
Confidence 45699 999997654 22358999999774 555666665555554
No 233
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=65.03 E-value=4.1 Score=33.18 Aligned_cols=41 Identities=15% Similarity=0.306 Sum_probs=30.5
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
-.|.++...+--|+.||++-...... ...+-..|.+||...
T Consensus 84 ~~L~~fI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 84 DLLDKFIKEYVLCPECGSPDTELIKE-GRLIFLKCKACGASR 124 (125)
T ss_dssp HHHHHHHCHHSSCTSTSSSSEEEEEE-TTCCEEEETTTSCEE
T ss_pred HHHHHHHHHEEEcCCCCCCccEEEEc-CCEEEEEecccCCcC
Confidence 45677888999999999995443332 455778999999753
No 234
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=64.37 E-value=5.5 Score=29.39 Aligned_cols=32 Identities=13% Similarity=0.354 Sum_probs=20.2
Q ss_pred CCCcCCCCCCccc----ccCCCccceeecC--CCCCcc
Q 023914 105 SFCQWCGGQTKHE----VPHGEEKMRAICT--VCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~----~~~~~~~~~~~C~--~Cg~~~ 136 (275)
.+||.||++.... ..++-.+....|. .||+.+
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATF 39 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEE
Confidence 5899999997433 1112233456787 798754
No 235
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=64.34 E-value=5.5 Score=38.96 Aligned_cols=34 Identities=21% Similarity=0.298 Sum_probs=24.3
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
.=|+.||.-..... .+.+.+..|+.||..-|.+.
T Consensus 11 ~~C~~Cd~l~~~~~--l~~g~~a~CpRCg~~L~~~~ 44 (419)
T PRK15103 11 ILCPQCDMLVALPR--LEHGQKAACPRCGTTLTVRW 44 (419)
T ss_pred ccCCCCCceeecCC--CCCCCeeECCCCCCCCcCCC
Confidence 44999998754432 23556789999999887643
No 236
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=64.34 E-value=1.9 Score=40.32 Aligned_cols=44 Identities=20% Similarity=0.462 Sum_probs=31.7
Q ss_pred CCCCccHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 84 DATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 84 ~~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
+|..+..+..|+-=..|..+-.||..||++- -..+|..|..+.|
T Consensus 299 ~P~A~~vl~qAi~Gqr~~~d~~fCstCG~~g----------a~KrCs~CKav~Y 342 (396)
T KOG1710|consen 299 RPSAYEVLVQAIFGQRIAADCQFCSTCGHPG----------AKKRCSQCKAVAY 342 (396)
T ss_pred CCcHHHHHHHHHcCceeEEecccccccCCCC----------ccchhhhhHHHHH
Confidence 4455566777777788999999999999983 2346776664444
No 237
>PRK04023 DNA polymerase II large subunit; Validated
Probab=64.14 E-value=4 Score=43.87 Aligned_cols=13 Identities=31% Similarity=0.641 Sum_probs=10.2
Q ss_pred hcCCCCcCCCCCC
Q 023914 102 LKISFCQWCGGQT 114 (275)
Q Consensus 102 ~~~~fC~~CG~~~ 114 (275)
...+||+.||..+
T Consensus 624 Vg~RfCpsCG~~t 636 (1121)
T PRK04023 624 IGRRKCPSCGKET 636 (1121)
T ss_pred ccCccCCCCCCcC
Confidence 3468999999885
No 238
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=64.11 E-value=5.9 Score=38.53 Aligned_cols=33 Identities=21% Similarity=0.353 Sum_probs=24.2
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
-|+.||.-.... ..+.+.+..|+.||..-|.+.
T Consensus 15 ~C~~Cd~l~~~~--~l~~g~~a~CpRCg~~L~~~~ 47 (403)
T TIGR00155 15 LCSQCDMLVALP--RIESGQKAACPRCGTTLTVGW 47 (403)
T ss_pred eCCCCCCccccc--CCCCCCeeECCCCCCCCcCCC
Confidence 499999886443 224566789999999887643
No 239
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=63.92 E-value=6.9 Score=24.88 Aligned_cols=29 Identities=17% Similarity=0.351 Sum_probs=18.7
Q ss_pred CCCCcCCCCCC-cccc-cCCCccceeecCCC
Q 023914 104 ISFCQWCGGQT-KHEV-PHGEEKMRAICTVC 132 (275)
Q Consensus 104 ~~fC~~CG~~~-~~~~-~~~~~~~~~~C~~C 132 (275)
.-.||+|++.. .... ....+..+..|.+|
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 35799999987 3321 11234567889888
No 240
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=63.66 E-value=5 Score=26.80 Aligned_cols=31 Identities=23% Similarity=0.582 Sum_probs=18.3
Q ss_pred CCcCCCCCCcccccC----CCccceeecCC--CCCcc
Q 023914 106 FCQWCGGQTKHEVPH----GEEKMRAICTV--CGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~~----~~~~~~~~C~~--Cg~~~ 136 (275)
+||.||++....... .-.+.-.+|.+ ||+..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 699999998654221 11223346765 88654
No 241
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=63.64 E-value=4.6 Score=34.88 Aligned_cols=30 Identities=20% Similarity=0.526 Sum_probs=22.7
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
+..|+.||.+|... ......|+.||+....
T Consensus 149 ~a~~~~~g~~~~~~-----~~~~~~c~~~~~~e~r 178 (189)
T PRK09521 149 YAMCSRCRTPLVKK-----GENELKCPNCGNIETR 178 (189)
T ss_pred EEEccccCCceEEC-----CCCEEECCCCCCEEee
Confidence 45799999999775 2245899999976653
No 242
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.57 E-value=1.9 Score=35.25 Aligned_cols=20 Identities=35% Similarity=0.933 Sum_probs=14.8
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.||++||..+.. .||.|...
T Consensus 29 afcskcgeati~-----------qcp~csas 48 (160)
T COG4306 29 AFCSKCGEATIT-----------QCPICSAS 48 (160)
T ss_pred HHHhhhchHHHh-----------cCCccCCc
Confidence 499999998744 47777654
No 243
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=63.09 E-value=3.1 Score=33.24 Aligned_cols=28 Identities=21% Similarity=0.286 Sum_probs=16.5
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.-.-+|..||...... .....||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~------~~~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPE------IDLYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecC------CcCccCcCCcCC
Confidence 3345788888654332 123568888754
No 244
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=63.05 E-value=5.4 Score=33.09 Aligned_cols=44 Identities=16% Similarity=0.276 Sum_probs=31.5
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 93 AAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
-...|.++...+--|+.||++-...... ..-+-..|.+||...-
T Consensus 91 i~~~L~~yI~~yVlC~~C~spdT~l~k~-~r~~~l~C~ACGa~~~ 134 (138)
T PRK03988 91 INEKIDRYVKEYVICPECGSPDTKLIKE-GRIWVLKCEACGAETP 134 (138)
T ss_pred HHHHHHHHHHhcEECCCCCCCCcEEEEc-CCeEEEEcccCCCCCc
Confidence 3456778889999999999995443332 2345789999997643
No 245
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=62.62 E-value=4.7 Score=29.64 Aligned_cols=36 Identities=17% Similarity=0.261 Sum_probs=25.0
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCccccCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPK 141 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~ 141 (275)
-||+|++--....-..++...+-|-+||+..-..+.
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 599999885544332245567899999987765554
No 246
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=62.61 E-value=3.5 Score=28.93 Aligned_cols=26 Identities=42% Similarity=0.744 Sum_probs=18.3
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
.+.+.|+.||.-+- ...|+.||....
T Consensus 3 s~mr~C~~CgvYTL----------k~~CP~CG~~t~ 28 (56)
T PRK13130 3 SKIRKCPKCGVYTL----------KEICPVCGGKTK 28 (56)
T ss_pred ccceECCCCCCEEc----------cccCcCCCCCCC
Confidence 35678999988763 247888986543
No 247
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=62.60 E-value=2.8 Score=32.99 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=22.3
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
-|-+||+..... +.....-|+.||...|.
T Consensus 4 ~CtrCG~vf~~g----~~~il~GCp~CG~nkF~ 32 (112)
T COG3364 4 QCTRCGEVFDDG----SEEILSGCPKCGCNKFL 32 (112)
T ss_pred eecccccccccc----cHHHHccCccccchheE
Confidence 499999986443 56677889999987774
No 248
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=62.47 E-value=3.9 Score=29.25 Aligned_cols=25 Identities=24% Similarity=0.643 Sum_probs=19.4
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.|..|.+||...-.. ....|.+||+
T Consensus 16 tHt~CrRCG~~syh~-------qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRHSYNV-------RKKYCAACGF 40 (62)
T ss_pred ccchhcccCcccccc-------cccchhhcCC
Confidence 688999999985332 3568999997
No 249
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=61.86 E-value=8.3 Score=24.77 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=20.2
Q ss_pred CCCcCCCCCCcccccCCCccceeecCC---CCCccc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTV---CGKIAY 137 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~---Cg~~~y 137 (275)
..||.||+.|..+.- ..+.-..|.+ |.+...
T Consensus 2 ~~CP~Cg~~lv~r~~--k~g~F~~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRG--KKGKFLGCSNYPECKYTEP 35 (39)
T ss_pred cCCCCCCceeEEEEC--CCCCEEECCCCCCcCCeEe
Confidence 469999999877632 3344457764 665543
No 250
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=61.12 E-value=3.7 Score=37.92 Aligned_cols=16 Identities=19% Similarity=0.557 Sum_probs=11.3
Q ss_pred CCCCcCCCCCCccccc
Q 023914 104 ISFCQWCGGQTKHEVP 119 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~ 119 (275)
..|||.||++-+..+.
T Consensus 185 ~~~CPvCGS~PvaSmV 200 (308)
T COG3058 185 RQYCPVCGSMPVASMV 200 (308)
T ss_pred cccCCCcCCCCcceee
Confidence 3599999998654433
No 251
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=60.91 E-value=5.7 Score=37.08 Aligned_cols=32 Identities=22% Similarity=0.453 Sum_probs=19.8
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.....||.||+..... . ...--.+|..||.+.
T Consensus 9 ~~~~~Cp~Cg~~~iv~-d--~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGSDKLIY-D--YERGEIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCCCCeeE-E--CCCCeEeecccCCcc
Confidence 3457899999842211 1 122237999999754
No 252
>PRK08402 replication factor A; Reviewed
Probab=60.50 E-value=11 Score=36.07 Aligned_cols=49 Identities=12% Similarity=0.193 Sum_probs=30.0
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeC-CeEEE
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHD-KKILL 156 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~-~~iLL 156 (275)
-+.-||.|.+++... ++...+.|+.||.+ -|..+..+-+.+.++ +.+.+
T Consensus 211 ~y~aCp~CnKkv~~~----~~~~~~~Ce~~~~v-~p~~ryil~~~l~D~TG~~~v 260 (355)
T PRK08402 211 VYDACPECRRKVDYD----PATDTWICPEHGEV-EPIKITILDFGLDDGTGYIRV 260 (355)
T ss_pred eEecCCCCCeEEEEe----cCCCCEeCCCCCCc-CcceeEEEEEEEEcCCCcEEE
Confidence 468899999997643 23345799999963 333344454555443 44443
No 253
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.47 E-value=7.9 Score=41.70 Aligned_cols=40 Identities=28% Similarity=0.551 Sum_probs=20.9
Q ss_pred hhhhcCCCCcCCCCCCccc--ccC-CCccceeecCCCCCcccc
Q 023914 99 GNVLKISFCQWCGGQTKHE--VPH-GEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~--~~~-~~~~~~~~C~~Cg~~~y~ 138 (275)
++.....+||.||+.+... ++. +.......|++||+..-+
T Consensus 633 G~~t~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 633 GKETFYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred CCcCCcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 3334668999999985332 211 111122346666655443
No 254
>PRK12366 replication factor A; Reviewed
Probab=60.43 E-value=10 Score=39.12 Aligned_cols=41 Identities=17% Similarity=0.514 Sum_probs=27.2
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHD 151 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~ 151 (275)
+.-||.|.+++... .-.++|+.||.. -|.....+-+.+.++
T Consensus 532 y~aCp~CnkKv~~~------~g~~~C~~c~~~-~p~~~~~l~~~i~D~ 572 (637)
T PRK12366 532 LYLCPNCRKRVEEV------DGEYICEFCGEV-EPNELLMLNFTLDDG 572 (637)
T ss_pred EecccccCeEeEcC------CCcEECCCCCCC-CCcEEEEEEEEEEcC
Confidence 57899999987432 235799999988 444444444555443
No 255
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=60.42 E-value=15 Score=34.60 Aligned_cols=35 Identities=20% Similarity=0.356 Sum_probs=21.8
Q ss_pred cCCCCcCCCCCCcccc--cCC-CccceeecCCCCCccc
Q 023914 103 KISFCQWCGGQTKHEV--PHG-EEKMRAICTVCGKIAY 137 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~--~~~-~~~~~~~C~~Cg~~~y 137 (275)
...+||.||+.-.... ..+ +|....+|.-|+....
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~ 223 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWH 223 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccc
Confidence 4589999999954331 122 3344558888876543
No 256
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.36 E-value=5.1 Score=30.11 Aligned_cols=27 Identities=22% Similarity=0.454 Sum_probs=20.4
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
.-||.||-.+++..- .+-..-.||.|+
T Consensus 2 llCP~C~v~l~~~~r--s~vEiD~CPrCr 28 (88)
T COG3809 2 LLCPICGVELVMSVR--SGVEIDYCPRCR 28 (88)
T ss_pred cccCcCCceeeeeee--cCceeeeCCccc
Confidence 469999999987643 344567899997
No 257
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=60.24 E-value=6.8 Score=27.20 Aligned_cols=31 Identities=19% Similarity=0.442 Sum_probs=20.7
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.-|++|.+..-......-.....+|+.||..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 3599998776554222235568899999863
No 258
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.09 E-value=4 Score=32.75 Aligned_cols=27 Identities=19% Similarity=0.290 Sum_probs=16.3
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.-+|..||...... ......||.||..
T Consensus 71 ~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~ 97 (117)
T PRK00564 71 ELECKDCSHVFKPN-----ALDYGVCEKCHSK 97 (117)
T ss_pred EEEhhhCCCccccC-----CccCCcCcCCCCC
Confidence 35799999664332 1122359999854
No 259
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=59.91 E-value=5.3 Score=42.00 Aligned_cols=25 Identities=36% Similarity=0.792 Sum_probs=18.5
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..||.||..+... +| -..|.+||+.
T Consensus 725 ~~Cp~Cg~~l~~~----~G--C~~C~~CG~s 749 (752)
T PRK08665 725 GACPECGSILEHE----EG--CVVCHSCGYS 749 (752)
T ss_pred CCCCCCCcccEEC----CC--CCcCCCCCCC
Confidence 4799999876554 22 4599999975
No 260
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=59.76 E-value=4.2 Score=32.31 Aligned_cols=23 Identities=30% Similarity=0.595 Sum_probs=17.4
Q ss_pred CccceeecCCCCCcccc-CCcEEE
Q 023914 122 EEKMRAICTVCGKIAYQ-NPKMVV 144 (275)
Q Consensus 122 ~~~~~~~C~~Cg~~~y~-~p~~~V 144 (275)
+-|.+|+|++||..+|- |-.|+|
T Consensus 5 elGtKR~Cp~CG~kFYDLnk~Piv 28 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDLNKDPIV 28 (108)
T ss_pred ccCCcccCCCCcchhccCCCCCcc
Confidence 45789999999999995 444443
No 261
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.52 E-value=6.2 Score=40.92 Aligned_cols=24 Identities=13% Similarity=0.223 Sum_probs=12.3
Q ss_pred eEEEEEeccCC-CCCceeeeeEEeeC
Q 023914 153 KILLCKRKIEP-SYGLWTLPAGYMEI 177 (275)
Q Consensus 153 ~iLL~rr~~~p-~~g~w~lPgG~vE~ 177 (275)
.||+..+...| ..|.+.+. |-++.
T Consensus 473 ~IlVGTqgaepm~~g~~~lV-~ilda 497 (665)
T PRK14873 473 ALVVATPGAEPRVEGGYGAA-LLLDA 497 (665)
T ss_pred CEEEECCCCcccccCCceEE-EEEcc
Confidence 47777764333 13455554 45553
No 262
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=59.12 E-value=7 Score=31.12 Aligned_cols=40 Identities=15% Similarity=0.350 Sum_probs=29.5
Q ss_pred HHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 94 AVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
...|.++...+--|+.||+|-.....+ ..-.-..|.+||.
T Consensus 70 ~~~l~~yI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa 109 (110)
T smart00653 70 QDLLRRYIKEYVLCPECGSPDTELIKE-NRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHhcEECCCCCCCCcEEEEe-CCeEEEEccccCC
Confidence 356778899999999999995443332 3445778999995
No 263
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=58.68 E-value=5.9 Score=36.59 Aligned_cols=33 Identities=21% Similarity=0.324 Sum_probs=24.9
Q ss_pred hhhcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 100 NVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
..+.-..|++||++.+..... +.....||.|..
T Consensus 241 YgR~GepC~~CGt~I~k~~~~--gR~t~~CP~CQ~ 273 (273)
T COG0266 241 YGRAGEPCRRCGTPIEKIKLG--GRSTFYCPVCQK 273 (273)
T ss_pred ecCCCCCCCccCCEeEEEEEc--CCcCEeCCCCCC
Confidence 345668899999998776553 456789999963
No 264
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=58.63 E-value=8 Score=26.47 Aligned_cols=33 Identities=21% Similarity=0.457 Sum_probs=23.2
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
-+.|..||.......-.+..+....|.+||..+
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 467999998766554444455578999999544
No 265
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=57.90 E-value=6.4 Score=28.56 Aligned_cols=24 Identities=38% Similarity=0.861 Sum_probs=13.2
Q ss_pred ceeecCCCCCc--cccCCcEEEEEEE
Q 023914 125 MRAICTVCGKI--AYQNPKMVVGCLI 148 (275)
Q Consensus 125 ~~~~C~~Cg~~--~y~~p~~~V~viI 148 (275)
.+-.|++|+++ .|.++...|.+++
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~ 43 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLI 43 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecc
Confidence 34566666653 4556655555443
No 266
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=57.66 E-value=5.8 Score=28.15 Aligned_cols=21 Identities=14% Similarity=0.075 Sum_probs=15.8
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
...|+.||.....+ ++|+ ||+
T Consensus 27 ~~~c~~cg~~~~pH---------~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGEYHLPH---------HVSP-KGY 47 (60)
T ss_pred eeEcCCCCceeccc---------eecC-Ccc
Confidence 46799999986443 6799 993
No 267
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=57.52 E-value=8.2 Score=32.91 Aligned_cols=30 Identities=33% Similarity=0.660 Sum_probs=18.1
Q ss_pred CcCCCCCCccc------ccCCCcc---ceeecCCCCCccc
Q 023914 107 CQWCGGQTKHE------VPHGEEK---MRAICTVCGKIAY 137 (275)
Q Consensus 107 C~~CG~~~~~~------~~~~~~~---~~~~C~~Cg~~~y 137 (275)
||.||++.... +|. =+. ....|++||+..-
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~-F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPY-FGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCC-cceEEEEEEECCCCCCchh
Confidence 99999873221 111 111 3578999997653
No 268
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=57.44 E-value=7.5 Score=32.03 Aligned_cols=42 Identities=19% Similarity=0.317 Sum_probs=29.8
Q ss_pred HHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 94 AVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
...|.++...+--|+.||+|-...... ..-.-..|.+||...
T Consensus 87 ~~~L~~yI~~yVlC~~C~sPdT~l~k~-~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 87 NERIEDYVRKYVICRECNRPDTRIIKE-GRVSLLKCEACGAKA 128 (133)
T ss_pred HHHHHHHHhheEECCCCCCCCcEEEEe-CCeEEEecccCCCCC
Confidence 356778899999999999995443332 223456999999754
No 269
>PRK02935 hypothetical protein; Provisional
Probab=57.41 E-value=7.6 Score=30.75 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=21.7
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
--||.|++++..- |..-.|..|+...--.
T Consensus 71 V~CP~C~K~TKmL------GrvD~CM~C~~PLTLd 99 (110)
T PRK02935 71 VICPSCEKPTKML------GRVDACMHCNQPLTLD 99 (110)
T ss_pred eECCCCCchhhhc------cceeecCcCCCcCCcC
Confidence 3699999998775 3456899999765443
No 270
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=57.35 E-value=7.1 Score=27.51 Aligned_cols=22 Identities=32% Similarity=0.798 Sum_probs=17.1
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
...|+.||.-.... ++|..||+
T Consensus 27 ~~~c~~cG~~~l~H---------rvc~~cg~ 48 (57)
T COG0333 27 LSVCPNCGEYKLPH---------RVCLKCGY 48 (57)
T ss_pred ceeccCCCCcccCc---------eEcCCCCC
Confidence 57899999985333 68999994
No 271
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=57.25 E-value=8.1 Score=27.40 Aligned_cols=35 Identities=20% Similarity=0.337 Sum_probs=23.2
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
-||+|++--...+...++....-|..||+..-..+
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~ 45 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQEQQKD 45 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCccccCC
Confidence 59999987544433223445688999998765443
No 272
>PRK07218 replication factor A; Provisional
Probab=56.99 E-value=15 Score=35.97 Aligned_cols=47 Identities=13% Similarity=0.295 Sum_probs=32.8
Q ss_pred HHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeCCe
Q 023914 96 HSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKK 153 (275)
Q Consensus 96 ~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~ 153 (275)
.+..=..-.+-||.|+..+.. ..|+.||.+ -|.....+-++++++..
T Consensus 289 ~i~~gsgli~rCP~C~r~v~~----------~~C~~hG~v-e~~~dlrik~vLDDGtg 335 (423)
T PRK07218 289 SVRDGSGLIERCPECGRVIQK----------GQCRSHGAV-EGEDDLRIKAILDDGTG 335 (423)
T ss_pred EeccCCcceecCcCccccccC----------CcCCCCCCc-CCeeeeEEEEEEECCCC
Confidence 333333445789999999732 489999976 55667777778887753
No 273
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.50 E-value=7.4 Score=38.91 Aligned_cols=24 Identities=21% Similarity=0.535 Sum_probs=14.3
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCC
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
||.|+.++..+ .......|..||+
T Consensus 225 C~~C~~~l~~h----~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 225 CPNCDVSLTYH----KKEGKLRCHYCGY 248 (505)
T ss_pred CCCCCCceEEe----cCCCeEEcCCCcC
Confidence 88888887765 2233445555543
No 274
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=55.06 E-value=10 Score=28.84 Aligned_cols=36 Identities=19% Similarity=0.322 Sum_probs=24.1
Q ss_pred HHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 96 HSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 96 ~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.+..=...--.|+.||+.+..+ ..--.+.|..|..+
T Consensus 28 kiei~Qhaky~CsfCGK~~vKR----~AvGiW~C~~C~kv 63 (92)
T KOG0402|consen 28 KIEIQQHAKYTCSFCGKKTVKR----KAVGIWKCGSCKKV 63 (92)
T ss_pred HHHHHHhhhhhhhhcchhhhhh----hceeEEecCCccce
Confidence 3333334445799999998776 34456889988753
No 275
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=54.33 E-value=3.9 Score=34.55 Aligned_cols=30 Identities=13% Similarity=0.303 Sum_probs=20.0
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.+=+||.||.+.....- -..-+.||.||..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA---~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEA---MELNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHHH---HHcCCcCCCCCCE
Confidence 34459999988654311 1235899999975
No 276
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=54.17 E-value=4.2 Score=42.91 Aligned_cols=11 Identities=36% Similarity=0.703 Sum_probs=0.0
Q ss_pred CCCCcCCCCCC
Q 023914 104 ISFCQWCGGQT 114 (275)
Q Consensus 104 ~~fC~~CG~~~ 114 (275)
.+.||.||..+
T Consensus 655 ~r~Cp~Cg~~t 665 (900)
T PF03833_consen 655 RRRCPKCGKET 665 (900)
T ss_dssp -----------
T ss_pred cccCcccCCcc
Confidence 46777777765
No 277
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=54.16 E-value=2.8 Score=33.33 Aligned_cols=26 Identities=23% Similarity=0.616 Sum_probs=16.0
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
-+|..||...... .....||.||...
T Consensus 71 ~~C~~Cg~~~~~~------~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 71 ARCRDCGHEFEPD------EFDFSCPRCGSPD 96 (113)
T ss_dssp EEETTTS-EEECH------HCCHH-SSSSSS-
T ss_pred EECCCCCCEEecC------CCCCCCcCCcCCC
Confidence 5799999886554 2236799998654
No 278
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.99 E-value=9.6 Score=42.01 Aligned_cols=15 Identities=20% Similarity=0.078 Sum_probs=7.4
Q ss_pred CCCcccccccccccc
Q 023914 38 PLPYSTARRHEIVSK 52 (275)
Q Consensus 38 ~~~~~~~~~~~~~~~ 52 (275)
|.-++.-|+-|--+|
T Consensus 606 ~trIG~RmGRPeKs~ 620 (1337)
T PRK14714 606 PTRIGNRMGRPEKSK 620 (1337)
T ss_pred cceeecccCCccccc
Confidence 334555555554444
No 279
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=53.96 E-value=5.9 Score=28.00 Aligned_cols=29 Identities=24% Similarity=0.509 Sum_probs=21.6
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
..|.-|-+||...-.. ...+|.+||+..-
T Consensus 14 ~tH~~CRRCGr~syhv-------~k~~CaaCGfgrs 42 (61)
T COG2126 14 KTHIRCRRCGRRSYHV-------RKKYCAACGFGRS 42 (61)
T ss_pred cceehhhhccchheee-------ccceecccCCCCc
Confidence 5678899999986433 3568999997643
No 280
>PF03487 IL13: Interleukin-13; InterPro: IPR020470 Interleukin-13 (IL-13) is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses []. It inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related.; PDB: 3G6D_A 3L5W_J 3BPO_A 1GA3_A 1IK0_A 3L5X_A 3L5Y_A 1IJZ_A 3LB6_B.
Probab=53.73 E-value=12 Score=24.35 Aligned_cols=26 Identities=27% Similarity=0.284 Sum_probs=12.1
Q ss_pred eeeeeEEeeCCCCHHHHHHHHHHHHh
Q 023914 168 WTLPAGYMEIGESAAEGAIRETWEEA 193 (275)
Q Consensus 168 w~lPgG~vE~GEs~eeAa~REl~EEt 193 (275)
..+.||...+|--+...+.||+-||+
T Consensus 11 ltClggLasPgPvp~~~alkELIeEL 36 (43)
T PF03487_consen 11 LTCLGGLASPGPVPSSTALKELIEEL 36 (43)
T ss_dssp ------------S-HHHHHHHHHHHH
T ss_pred HHHhcccCCCCCCCchHHHHHHHHHH
Confidence 34668888999999999999999996
No 281
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.57 E-value=4.2 Score=35.10 Aligned_cols=30 Identities=20% Similarity=0.478 Sum_probs=20.1
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
+=+||.||.+.....- -..-+.|+.||...
T Consensus 117 ~Y~Cp~C~~rytf~eA---~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA---MEYGFRCPQCGEML 146 (178)
T ss_pred EEECCCCCcEEeHHHH---hhcCCcCCCCCCCC
Confidence 4569999988754411 12358999999653
No 282
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=52.65 E-value=8 Score=30.37 Aligned_cols=32 Identities=22% Similarity=0.417 Sum_probs=18.0
Q ss_pred CCCcCCCCCCccccc--CCCccceeecCCCCCcc
Q 023914 105 SFCQWCGGQTKHEVP--HGEEKMRAICTVCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~--~~~~~~~~~C~~Cg~~~ 136 (275)
--||+||+.....+. -....--..|..||..+
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 358888888755111 01223346788888554
No 283
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=52.63 E-value=11 Score=29.61 Aligned_cols=29 Identities=24% Similarity=0.630 Sum_probs=18.2
Q ss_pred CCCcCCCCCCcccc-------cCCCccceeecCCCC
Q 023914 105 SFCQWCGGQTKHEV-------PHGEEKMRAICTVCG 133 (275)
Q Consensus 105 ~fC~~CG~~~~~~~-------~~~~~~~~~~C~~Cg 133 (275)
..||.||.+..... ..++......|+.|+
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~ 38 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCD 38 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCceeEECCCCC
Confidence 57999999976652 011233446777776
No 284
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=52.51 E-value=5.7 Score=37.82 Aligned_cols=45 Identities=16% Similarity=0.330 Sum_probs=33.4
Q ss_pred HHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 96 HSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 96 ~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
-|.+|.+.|--||.|+.|-...+...+......|.+||+..-...
T Consensus 88 lLdgFIkKFVlC~~C~NPETel~itk~q~i~~~CkACG~r~~~d~ 132 (400)
T KOG2767|consen 88 LLDGFIKKFVLCPSCENPETELIITKKQTISLKCKACGFRSDMDL 132 (400)
T ss_pred HHHHHHHHheeCcCCCCCceeEEecccchhhhHHHHcCCcccccc
Confidence 456789999999999999544444335567789999998765443
No 285
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=51.86 E-value=9.7 Score=30.05 Aligned_cols=14 Identities=21% Similarity=0.484 Sum_probs=9.0
Q ss_pred ceeecCCCCCcccc
Q 023914 125 MRAICTVCGKIAYQ 138 (275)
Q Consensus 125 ~~~~C~~Cg~~~y~ 138 (275)
..++|+.||...|.
T Consensus 30 ~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 30 PGWYCPACGEELLD 43 (127)
T ss_pred eeeECCCCCCEEEc
Confidence 34677777776553
No 286
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=51.62 E-value=11 Score=35.04 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=23.1
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
....-.|.+||... ..|...||+|+....-.|
T Consensus 351 ~~p~~~c~~cg~~~--------~~~~~~c~~c~~~~~~~~ 382 (389)
T PRK11788 351 RKPRYRCRNCGFTA--------RTLYWHCPSCKAWETIKP 382 (389)
T ss_pred CCCCEECCCCCCCC--------ccceeECcCCCCccCcCC
Confidence 33445799999985 357889999997655444
No 287
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=51.61 E-value=7.2 Score=33.71 Aligned_cols=11 Identities=36% Similarity=0.966 Sum_probs=5.1
Q ss_pred CCCCcCCCCCC
Q 023914 104 ISFCQWCGGQT 114 (275)
Q Consensus 104 ~~fC~~CG~~~ 114 (275)
..|||.||+++
T Consensus 153 ~~~Cp~CG~~~ 163 (177)
T COG1439 153 KDFCPICGSPL 163 (177)
T ss_pred CCcCCCCCCce
Confidence 34444444443
No 288
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=51.59 E-value=9.7 Score=36.61 Aligned_cols=21 Identities=33% Similarity=0.770 Sum_probs=16.4
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.|..||... .+|..+||+|+.
T Consensus 2 ~c~~cg~~~--------~~~~g~cp~c~~ 22 (372)
T cd01121 2 VCSECGYVS--------PKWLGKCPECGE 22 (372)
T ss_pred CCCCCCCCC--------CCccEECcCCCC
Confidence 599999884 457789999983
No 289
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=51.44 E-value=4 Score=28.52 Aligned_cols=27 Identities=26% Similarity=0.706 Sum_probs=18.4
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..|..|.+||...-.. ....|.+||+.
T Consensus 13 ktH~~CrRCG~~syH~-------qK~~CasCGyp 39 (55)
T PF01907_consen 13 KTHTLCRRCGRRSYHI-------QKKTCASCGYP 39 (55)
T ss_dssp -SEEE-TTTSSEEEET-------TTTEETTTBTT
T ss_pred ccEeeecccCCeeeec-------CCCcccccCCC
Confidence 4678899999985333 34689999954
No 290
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=51.24 E-value=10 Score=33.37 Aligned_cols=42 Identities=19% Similarity=0.346 Sum_probs=29.9
Q ss_pred HHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 94 AVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
...|.++...+--|+.||++-...... ..-.-..|.+||...
T Consensus 88 ~~~l~~yi~~yV~C~~C~~pdT~l~k~-~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 88 QAAIDAYVDEYVICSECGLPDTRLVKE-DRVLMLRCDACGAHR 129 (201)
T ss_pred HHHHHHHHHheEECCCCCCCCcEEEEc-CCeEEEEcccCCCCc
Confidence 345677888999999999995443332 234567999999654
No 291
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=50.52 E-value=9.7 Score=32.62 Aligned_cols=23 Identities=26% Similarity=0.795 Sum_probs=17.1
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
-|+.||-.... ....+||.||..
T Consensus 136 vC~vCGy~~~g-------e~P~~CPiCga~ 158 (166)
T COG1592 136 VCPVCGYTHEG-------EAPEVCPICGAP 158 (166)
T ss_pred EcCCCCCcccC-------CCCCcCCCCCCh
Confidence 79999998644 233589999954
No 292
>PRK11823 DNA repair protein RadA; Provisional
Probab=49.91 E-value=9.9 Score=37.38 Aligned_cols=22 Identities=36% Similarity=0.832 Sum_probs=17.3
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
-.|..||... .+|-.+||+|+.
T Consensus 8 y~C~~Cg~~~--------~~~~g~Cp~C~~ 29 (446)
T PRK11823 8 YVCQECGAES--------PKWLGRCPECGA 29 (446)
T ss_pred EECCcCCCCC--------cccCeeCcCCCC
Confidence 3599999984 457789999983
No 293
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=49.82 E-value=14 Score=22.76 Aligned_cols=27 Identities=15% Similarity=0.391 Sum_probs=20.2
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.|+.|+..+..- .+-...+|..|..+.
T Consensus 3 ~C~~C~t~L~yP----~gA~~vrCs~C~~vt 29 (31)
T TIGR01053 3 VCGGCRTLLMYP----RGASSVRCALCQTVN 29 (31)
T ss_pred CcCCCCcEeecC----CCCCeEECCCCCeEe
Confidence 599999998554 455678899997653
No 294
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=49.21 E-value=8.3 Score=31.71 Aligned_cols=29 Identities=24% Similarity=0.580 Sum_probs=21.4
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
-|-+||+..... ......-||.||...|.
T Consensus 3 ~Ct~Cg~~f~dg----s~eil~GCP~CGg~kF~ 31 (131)
T PF09845_consen 3 QCTKCGRVFEDG----SKEILSGCPECGGNKFQ 31 (131)
T ss_pred ccCcCCCCcCCC----cHHHHccCcccCCcceE
Confidence 489999986443 54567889999976663
No 295
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=49.20 E-value=9.3 Score=33.44 Aligned_cols=31 Identities=26% Similarity=0.625 Sum_probs=18.8
Q ss_pred CcCCCCCCcccccCCC-----cc---ceeecCCCCCccc
Q 023914 107 CQWCGGQTKHEVPHGE-----EK---MRAICTVCGKIAY 137 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~-----~~---~~~~C~~Cg~~~y 137 (275)
||.||+.........+ +. ....|++||+.+-
T Consensus 3 Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 3 CPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred CCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccc
Confidence 9999977543221111 11 3578999997653
No 296
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=49.14 E-value=13 Score=26.51 Aligned_cols=29 Identities=38% Similarity=0.680 Sum_probs=22.0
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
--||.|-+++... +.+...+|+.|+. .||
T Consensus 9 LaCP~~kg~L~~~----~~~~~L~c~~~~~-aYp 37 (60)
T COG2835 9 LACPVCKGPLVYD----EEKQELICPRCKL-AYP 37 (60)
T ss_pred eeccCcCCcceEe----ccCCEEEecccCc-eee
Confidence 3599999998776 5566789999984 444
No 297
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=49.11 E-value=14 Score=35.42 Aligned_cols=30 Identities=17% Similarity=0.382 Sum_probs=21.9
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
...+|+.||.+... .....|++|-...++.
T Consensus 5 ~~~~C~~CGr~~~~-------~~~~lC~dC~~~~~~~ 34 (355)
T COG1499 5 STILCVRCGRSVDP-------LIDGLCGDCYVETTPL 34 (355)
T ss_pred cccEeccCCCcCch-------hhccccHHHHhccCcc
Confidence 46899999999742 2345799998776653
No 298
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=48.67 E-value=20 Score=29.22 Aligned_cols=13 Identities=31% Similarity=0.731 Sum_probs=10.9
Q ss_pred CCCcCCCCCCccc
Q 023914 105 SFCQWCGGQTKHE 117 (275)
Q Consensus 105 ~fC~~CG~~~~~~ 117 (275)
.||+.||.++-..
T Consensus 70 ~FC~~CGs~l~~~ 82 (133)
T COG3791 70 GFCPTCGSPLFWR 82 (133)
T ss_pred eecccCCCceEEe
Confidence 3999999998665
No 299
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=48.40 E-value=11 Score=31.95 Aligned_cols=30 Identities=30% Similarity=0.622 Sum_probs=18.6
Q ss_pred CCcCCCCCCccc-----ccCCCcc---ceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHE-----VPHGEEK---MRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~-----~~~~~~~---~~~~C~~Cg~~~ 136 (275)
-||.||+..... +|. -+. ....|++||+..
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~-F~evii~sf~C~~CGyk~ 39 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPY-FREVIIMSFECEHCGYRN 39 (160)
T ss_pred cCCCCCCCCEEEEEEecCCC-cceEEEEEEECCCCCCcc
Confidence 599999775422 111 111 357899999754
No 300
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=48.13 E-value=11 Score=37.20 Aligned_cols=22 Identities=32% Similarity=0.829 Sum_probs=17.4
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
-.|..||... .+|..+||+|+.
T Consensus 8 y~C~~Cg~~~--------~~~~g~Cp~C~~ 29 (454)
T TIGR00416 8 FVCQHCGADS--------PKWQGKCPACHA 29 (454)
T ss_pred EECCcCCCCC--------ccccEECcCCCC
Confidence 4699999884 457789999983
No 301
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.94 E-value=11 Score=29.97 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=19.5
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
..-||-||.++... ..+|+.|+...-
T Consensus 6 ~~~cPvcg~~~iVT--------eL~c~~~etTVr 31 (122)
T COG3877 6 INRCPVCGRKLIVT--------ELKCSNCETTVR 31 (122)
T ss_pred CCCCCcccccceeE--------EEecCCCCceEe
Confidence 35699999998665 468999986543
No 302
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=47.86 E-value=3.2 Score=38.31 Aligned_cols=26 Identities=27% Similarity=0.712 Sum_probs=13.5
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.++.+|+.||+.=. -.|..|+.||..
T Consensus 195 ~R~L~Cs~C~t~W~--------~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 195 KRYLHCSLCGTEWR--------FVRIKCPYCGNT 220 (290)
T ss_dssp EEEEEETTT--EEE----------TTS-TTT---
T ss_pred cEEEEcCCCCCeee--------ecCCCCcCCCCC
Confidence 47788999988732 235679999864
No 303
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=47.72 E-value=6.2 Score=37.63 Aligned_cols=32 Identities=25% Similarity=0.549 Sum_probs=12.1
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
|--|+.||.++... +.-....|.+||...|.+
T Consensus 285 FFkC~~C~~Rt~sl----~r~P~~~C~~Cg~~~wer 316 (344)
T PF09332_consen 285 FFKCKDCGNRTISL----ERLPKKHCSNCGSSKWER 316 (344)
T ss_dssp EEE-T-TS-EEEES----SSS--S--TTT-S---EE
T ss_pred eEECCCCCCeeeec----ccCCCCCCCcCCcCceee
Confidence 34477777776543 233446777777766654
No 304
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=47.60 E-value=13 Score=36.16 Aligned_cols=29 Identities=17% Similarity=0.424 Sum_probs=21.0
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
.-|+.||.... .+.+.+|+.||..-|.+.
T Consensus 216 ~~C~~Cd~~~~-------~~~~a~CpRC~~~L~~~~ 244 (403)
T TIGR00155 216 RSCSACHTTIL-------PAQEPVCPRCSTPLYVRR 244 (403)
T ss_pred CcCCCCCCccC-------CCCCcCCcCCCCcccCCC
Confidence 45999999641 234578999999887653
No 305
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=47.50 E-value=9.2 Score=31.64 Aligned_cols=24 Identities=33% Similarity=0.582 Sum_probs=15.9
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
-..|+.||+-.-. .+..|+.|+..
T Consensus 29 g~kC~~CG~v~~P--------Pr~~Cp~C~~~ 52 (140)
T COG1545 29 GTKCKKCGRVYFP--------PRAYCPKCGSE 52 (140)
T ss_pred EEEcCCCCeEEcC--------CcccCCCCCCC
Confidence 4578888877422 25678888765
No 306
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=46.81 E-value=9.1 Score=33.13 Aligned_cols=35 Identities=14% Similarity=0.388 Sum_probs=23.7
Q ss_pred CCcCCCCCCcccccC---------------CCccceeecCCCCCccccCC
Q 023914 106 FCQWCGGQTKHEVPH---------------GEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 106 fC~~CG~~~~~~~~~---------------~~~~~~~~C~~Cg~~~y~~p 140 (275)
||+.|+..+...... ......+.|.+||.++..+.
T Consensus 122 yc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~CG~v~~~~~ 171 (177)
T PRK13264 122 YCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDNCGTVHPGKA 171 (177)
T ss_pred ECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCcCCcccCccC
Confidence 999998876422110 02346789999999988763
No 307
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=46.65 E-value=11 Score=29.05 Aligned_cols=26 Identities=27% Similarity=0.737 Sum_probs=20.0
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
..|..|-+||...-.. ....|.+||+
T Consensus 14 ktHtlCrRCG~~syH~-------qK~~CasCGy 39 (91)
T PTZ00073 14 KTHTLCRRCGKRSFHV-------QKKRCASCGY 39 (91)
T ss_pred cCcchhcccCcccccc-------ccccchhcCC
Confidence 5788999999985333 3468999997
No 308
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.63 E-value=8.5 Score=31.63 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=8.1
Q ss_pred CCCCcCCCCCCc
Q 023914 104 ISFCQWCGGQTK 115 (275)
Q Consensus 104 ~~fC~~CG~~~~ 115 (275)
.-.|+.||....
T Consensus 70 ~~~C~~CG~~~~ 81 (135)
T PRK03824 70 VLKCRNCGNEWS 81 (135)
T ss_pred EEECCCCCCEEe
Confidence 347888886643
No 309
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=46.55 E-value=9.9 Score=27.16 Aligned_cols=36 Identities=25% Similarity=0.466 Sum_probs=20.6
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEee
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEH 150 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~ 150 (275)
+=|-.|.--+. + ..||.||...+..--...++|++.
T Consensus 4 kAC~~C~~i~~-------~---~~CP~Cgs~~~T~~W~G~viI~dP 39 (61)
T PRK08351 4 KACRHCHYITT-------E---DRCPVCGSRDLSDEWFDLVIIIDV 39 (61)
T ss_pred hhhhhCCcccC-------C---CcCCCCcCCccccccccEEEEeCC
Confidence 45778866641 1 269999987754433333344443
No 310
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=46.38 E-value=18 Score=23.53 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=7.7
Q ss_pred CCCcCCCCCC
Q 023914 105 SFCQWCGGQT 114 (275)
Q Consensus 105 ~fC~~CG~~~ 114 (275)
..||.||+..
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 4688888776
No 311
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=45.71 E-value=11 Score=27.70 Aligned_cols=23 Identities=22% Similarity=0.500 Sum_probs=12.4
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.||.|.++|... +...+|..|+.
T Consensus 3 ~CP~C~~~L~~~------~~~~~C~~C~~ 25 (70)
T PF07191_consen 3 TCPKCQQELEWQ------GGHYHCEACQK 25 (70)
T ss_dssp B-SSS-SBEEEE------TTEEEETTT--
T ss_pred cCCCCCCccEEe------CCEEECccccc
Confidence 588888887554 13466777765
No 312
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=45.43 E-value=9.6 Score=40.90 Aligned_cols=23 Identities=35% Similarity=0.852 Sum_probs=18.2
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.+.||.||..+- ...|+.||...
T Consensus 625 ~RKCPkCG~yTl----------k~rCP~CG~~T 647 (1095)
T TIGR00354 625 IRKCPQCGKESF----------WLKCPVCGELT 647 (1095)
T ss_pred EEECCCCCcccc----------cccCCCCCCcc
Confidence 589999999862 35899999764
No 313
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=44.92 E-value=13 Score=42.59 Aligned_cols=27 Identities=30% Similarity=0.626 Sum_probs=19.7
Q ss_pred cCCCCcCCCCC------CcccccCCCccceeecCCCCCc
Q 023914 103 KISFCQWCGGQ------TKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 103 ~~~fC~~CG~~------~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
...+||-||.+ +... +--..|+.||+.
T Consensus 1703 ~~~~cp~c~~~~~~~~~~~~~------~gc~~c~~cg~s 1735 (1740)
T PRK08332 1703 GVVYCPVCYEKEGKLVELRME------SGCATCPVCGWS 1735 (1740)
T ss_pred ccCCCCCCCCCCCcceeeEec------CCceeCCCCCCc
Confidence 56789999999 3332 234699999985
No 314
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=44.69 E-value=6.6 Score=24.91 Aligned_cols=32 Identities=28% Similarity=0.572 Sum_probs=17.2
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCccccC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (275)
.|+.||+.......+ ....-.|..||-..+.|
T Consensus 3 ~C~~Cg~~Yh~~~~p--P~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNP--PKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EETTTTEEEETTTB----SSTTBCTTTTEBEBEE
T ss_pred CcCCCCCccccccCC--CCCCCccCCCCCeeEeC
Confidence 578888775443221 22334677777655443
No 315
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=43.93 E-value=7.5 Score=36.32 Aligned_cols=27 Identities=26% Similarity=0.548 Sum_probs=11.8
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.-||.||+.+-.... ...-.+|+.||+
T Consensus 39 ~kc~~C~~~~~~~~l---~~~~~vcp~c~~ 65 (296)
T CHL00174 39 VQCENCYGLNYKKFL---KSKMNICEQCGY 65 (296)
T ss_pred eECCCccchhhHHHH---HHcCCCCCCCCC
Confidence 345555555433311 122345555554
No 316
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=43.91 E-value=20 Score=35.21 Aligned_cols=45 Identities=24% Similarity=0.469 Sum_probs=28.3
Q ss_pred HHHHhhhhcC-------CCCcCCCCCCcccc---cCCCcc--------ceeecCCCCCc-cccC
Q 023914 95 VHSAGNVLKI-------SFCQWCGGQTKHEV---PHGEEK--------MRAICTVCGKI-AYQN 139 (275)
Q Consensus 95 ~~l~~w~~~~-------~fC~~CG~~~~~~~---~~~~~~--------~~~~C~~Cg~~-~y~~ 139 (275)
++|++|.++. .-|++||+.+.... ++.+.+ ...+|..||.. .|||
T Consensus 145 leLL~WFKq~FF~WvN~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPR 208 (500)
T KOG0909|consen 145 LELLNWFKQDFFKWVNNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPR 208 (500)
T ss_pred HHHHHHHHHhhheecCCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCcc
Confidence 4699997765 56999999984210 111111 34689999965 3554
No 317
>smart00532 LIGANc Ligase N family.
Probab=43.83 E-value=14 Score=36.44 Aligned_cols=27 Identities=26% Similarity=0.595 Sum_probs=19.8
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCC--CC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTV--CG 133 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~--Cg 133 (275)
.-.+||.||+++... +++...+|++ |.
T Consensus 398 ~P~~CP~C~s~l~~~----~~~~~~~C~n~~C~ 426 (441)
T smart00532 398 MPTHCPSCGSELVRE----EGEVDIRCPNPLCP 426 (441)
T ss_pred CCCCCCCCCCEeEec----CCceEEEeCCCCCH
Confidence 458999999999764 3456678874 64
No 318
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.79 E-value=12 Score=27.01 Aligned_cols=29 Identities=28% Similarity=0.554 Sum_probs=19.6
Q ss_pred CCCCcCCCCCCcccccCCCccceeecC-CCCCc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICT-VCGKI 135 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~~ 135 (275)
..-||.||++..-.. +...+..|. .|..+
T Consensus 7 ~v~CP~Cgkpv~w~~---~s~frPFCSkRCklI 36 (65)
T COG3024 7 TVPCPTCGKPVVWGE---ESPFRPFCSKRCKLI 36 (65)
T ss_pred cccCCCCCCcccccc---cCCcCcchhHhhhhc
Confidence 457999999976541 345677776 46544
No 319
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=43.75 E-value=14 Score=26.51 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=9.2
Q ss_pred ceeecCCCCCcc
Q 023914 125 MRAICTVCGKIA 136 (275)
Q Consensus 125 ~~~~C~~Cg~~~ 136 (275)
-..+|+.||+.+
T Consensus 52 g~L~Cp~c~r~Y 63 (68)
T PF03966_consen 52 GELICPECGREY 63 (68)
T ss_dssp TEEEETTTTEEE
T ss_pred CEEEcCCCCCEE
Confidence 358999999654
No 320
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=43.61 E-value=16 Score=36.98 Aligned_cols=51 Identities=18% Similarity=0.280 Sum_probs=34.2
Q ss_pred ccHHHHHHHHHhhhhcCCCCcCCCCCCccccc-----C--CCccceeecCCCCCcccc
Q 023914 88 SHPSSAAVHSAGNVLKISFCQWCGGQTKHEVP-----H--GEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 88 ~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~-----~--~~~~~~~~C~~Cg~~~y~ 138 (275)
.+-+.++++-.+-.+=+--||+||+....... . ....-+..|+.||.....
T Consensus 184 ~~~I~~~~~~sdqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 184 TSRIERLYEESDQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred CCHHHHHHHhCCceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 34456666666666667789999998765411 1 123467899999977664
No 321
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=43.61 E-value=13 Score=25.02 Aligned_cols=15 Identities=20% Similarity=0.592 Sum_probs=10.8
Q ss_pred cCCCCcCCCCCCccc
Q 023914 103 KISFCQWCGGQTKHE 117 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~ 117 (275)
..-+|+.||+++...
T Consensus 4 g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRR 18 (58)
T ss_pred CcEEcccCCcEeEEE
Confidence 446788888887654
No 322
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=43.54 E-value=9.4 Score=32.38 Aligned_cols=32 Identities=22% Similarity=0.427 Sum_probs=15.9
Q ss_pred CCcCCCCCCcccccC----CCcc---ceeecCCCCCccc
Q 023914 106 FCQWCGGQTKHEVPH----GEEK---MRAICTVCGKIAY 137 (275)
Q Consensus 106 fC~~CG~~~~~~~~~----~~~~---~~~~C~~Cg~~~y 137 (275)
-||.||+....++.. .-+. ....|++||+..-
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN 41 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence 599999986543110 0011 3468999997653
No 323
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=43.53 E-value=15 Score=26.10 Aligned_cols=25 Identities=32% Similarity=0.643 Sum_probs=11.5
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCC
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
||.|+......- .......|..||.
T Consensus 14 Cp~C~n~q~vFs---ha~t~V~C~~Cg~ 38 (59)
T PRK00415 14 CPDCGNEQVVFS---HASTVVRCLVCGK 38 (59)
T ss_pred CCCCCCeEEEEe---cCCcEEECcccCC
Confidence 555555543331 2333445555554
No 324
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=43.11 E-value=14 Score=38.10 Aligned_cols=28 Identities=29% Similarity=0.564 Sum_probs=22.7
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCC---CCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTV---CGK 134 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~---Cg~ 134 (275)
--.+||.||+++... +++...+|++ |..
T Consensus 403 ~P~~CP~C~s~l~r~----~~e~~~rC~n~~~C~a 433 (667)
T COG0272 403 FPTHCPVCGSELVRE----EGEVVIRCTNGLNCPA 433 (667)
T ss_pred CCCCCCCCCCeeEec----cCceeEecCCCCCChH
Confidence 568999999999774 5778889986 864
No 325
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=43.00 E-value=8.5 Score=35.61 Aligned_cols=27 Identities=26% Similarity=0.584 Sum_probs=19.0
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.-||.||+-+-.... +....+|++|++
T Consensus 29 ~KCp~c~~~~y~~eL---~~n~~vcp~c~~ 55 (294)
T COG0777 29 TKCPSCGEMLYRKEL---ESNLKVCPKCGH 55 (294)
T ss_pred eECCCccceeeHHHH---HhhhhcccccCc
Confidence 579999988755522 334678999985
No 326
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=42.88 E-value=8.1 Score=36.01 Aligned_cols=16 Identities=19% Similarity=0.549 Sum_probs=9.3
Q ss_pred hhhcCCCCcCCCCCCc
Q 023914 100 NVLKISFCQWCGGQTK 115 (275)
Q Consensus 100 w~~~~~fC~~CG~~~~ 115 (275)
+..+..-||.||....
T Consensus 42 l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 42 LEANLNVCPKCGHHMR 57 (292)
T ss_pred HHhcCCCCCCCCCCee
Confidence 4444566666666654
No 327
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.56 E-value=11 Score=30.49 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=16.7
Q ss_pred hhhcCCCCcCCCCCCcccccCCCccc--eeecCCCCCc
Q 023914 100 NVLKISFCQWCGGQTKHEVPHGEEKM--RAICTVCGKI 135 (275)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~--~~~C~~Cg~~ 135 (275)
+..-.-+| .||......... .... ...||.||..
T Consensus 66 ~vp~~~~C-~Cg~~~~~~~~~-~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 66 MIPVEIEC-ECGYEGVVDEDE-IDHYAAVIECPVCGNK 101 (124)
T ss_pred ecCeeEEe-eCcCcccccccc-hhccccCCcCcCCCCC
Confidence 33344678 888664332000 0111 2468888843
No 328
>PRK05580 primosome assembly protein PriA; Validated
Probab=42.12 E-value=16 Score=37.95 Aligned_cols=26 Identities=23% Similarity=0.474 Sum_probs=14.4
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
-||.|+.++..+ .......|..||+.
T Consensus 392 ~C~~C~~~l~~h----~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 392 ECPHCDASLTLH----RFQRRLRCHHCGYQ 417 (679)
T ss_pred CCCCCCCceeEE----CCCCeEECCCCcCC
Confidence 377777776654 22334556555544
No 329
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=41.92 E-value=11 Score=35.27 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=19.3
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.++-+|+.|++.=. -.|..|+.||..
T Consensus 208 ~RyL~CslC~teW~--------~~R~~C~~Cg~~ 233 (305)
T TIGR01562 208 LRYLSCSLCATEWH--------YVRVKCSHCEES 233 (305)
T ss_pred ceEEEcCCCCCccc--------ccCccCCCCCCC
Confidence 46788999988732 246789999864
No 330
>KOG4537 consensus Zn-ribbon-containing protein implicated in mitosis [Cell cycle control, cell division, chromosome partitioning; Defense mechanisms]
Probab=41.83 E-value=9.1 Score=32.42 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 90 PSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 90 ~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.+-+.+.+++ .+||.||+-+-. +....++|-.|...
T Consensus 31 ylLrGytmLd-----e~Cp~C~~Ilm~-----dr~~~~~CVsC~~~ 66 (178)
T KOG4537|consen 31 YLLRGYTMLD-----EICPKCEKILMR-----DRDNPMFCVSCIND 66 (178)
T ss_pred HHHhhhHHhh-----hhcchHHHHHHh-----hccCceEEEeeecc
Confidence 3445555554 599999998633 34566788888543
No 331
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=41.74 E-value=8.7 Score=35.67 Aligned_cols=14 Identities=14% Similarity=0.439 Sum_probs=6.2
Q ss_pred hhcCCCCcCCCCCC
Q 023914 101 VLKISFCQWCGGQT 114 (275)
Q Consensus 101 ~~~~~fC~~CG~~~ 114 (275)
..++.-||.||...
T Consensus 42 ~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 42 ERNLEVCPKCDHHM 55 (285)
T ss_pred HhhCCCCCCCCCcC
Confidence 33344444444443
No 332
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=41.29 E-value=16 Score=38.29 Aligned_cols=25 Identities=20% Similarity=0.490 Sum_probs=11.3
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
||.|...+..+ .......|..||+.
T Consensus 447 Cp~Cd~~lt~H----~~~~~L~CH~Cg~~ 471 (730)
T COG1198 447 CPNCDSPLTLH----KATGQLRCHYCGYQ 471 (730)
T ss_pred CCCCCcceEEe----cCCCeeEeCCCCCC
Confidence 44455554444 22334455555543
No 333
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.23 E-value=10 Score=35.47 Aligned_cols=25 Identities=16% Similarity=0.368 Sum_probs=15.4
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
+++||+||.+... -.+.+.|+.|+.
T Consensus 322 ~~~Cp~cg~r~~~------~~~ak~~~~c~~ 346 (351)
T KOG3940|consen 322 YVQCPHCGRRFNE------QAAAKHIPKCVN 346 (351)
T ss_pred cccCccccccchH------HHHHhhcccccc
Confidence 5777777777432 235566777764
No 334
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=41.17 E-value=11 Score=26.51 Aligned_cols=25 Identities=28% Similarity=0.729 Sum_probs=12.7
Q ss_pred CCcCCCCCCcccccCCCccceeecC-CCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICT-VCG 133 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg 133 (275)
-||.||++..... +...+..|. .|.
T Consensus 4 ~CP~C~k~~~~~~---~n~~rPFCS~RCk 29 (57)
T PF03884_consen 4 KCPICGKPVEWSP---ENPFRPFCSERCK 29 (57)
T ss_dssp E-TTT--EEE-SS---SSS--SSSSHHHH
T ss_pred cCCCCCCeecccC---CCCcCCcccHhhc
Confidence 5999999987641 456777886 364
No 335
>PRK06386 replication factor A; Reviewed
Probab=40.83 E-value=40 Score=32.40 Aligned_cols=43 Identities=12% Similarity=0.149 Sum_probs=28.7
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeCCeEEE
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILL 156 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~iLL 156 (275)
-.+-||.|+..++. ..|+.||. .=+.....+-++++++...+-
T Consensus 235 li~rCP~C~R~l~~----------g~C~~HG~-v~~~~dlr~k~vLDDGtg~~~ 277 (358)
T PRK06386 235 IFTKCSVCNKIIED----------GVCKDHPD-APVYLDIFGYFTISDGTGFVT 277 (358)
T ss_pred eEecCcCCCeEccC----------CcCCCCCC-CCCeeEEEEEEEEECCCCeEE
Confidence 35789999998742 38999997 333445555567777654443
No 336
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK12722 transcriptional activator FlhC; Provisional
Probab=40.66 E-value=33 Score=29.92 Aligned_cols=42 Identities=21% Similarity=0.366 Sum_probs=31.5
Q ss_pred HHHHHHHHhhhhc----CCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 91 SSAAVHSAGNVLK----ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 91 ~~~a~~l~~w~~~----~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
+.+|..|..+... ..-|..||+....... +......|+-|.-
T Consensus 117 ~tRAw~LvRf~~s~~L~l~~C~~Cgg~fv~~~~--e~~~~f~CplC~~ 162 (187)
T PRK12722 117 LTRAWTLVRFVDSGMLQLSSCNCCGGHFVTHAH--DPVGSFVCGLCQP 162 (187)
T ss_pred HHHHHHHHHHHhcCcEeeccCCCCCCCeecccc--ccCCCCcCCCCCC
Confidence 7799999988655 4679999999765422 3445789999975
No 338
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=40.63 E-value=16 Score=23.49 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=18.1
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.|.+|++=+-....-.+++..+.|+-|+...
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--EE
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCCcC
Confidence 5889998876654444567789999998754
No 339
>PRK07217 replication factor A; Reviewed
Probab=40.49 E-value=47 Score=31.28 Aligned_cols=48 Identities=13% Similarity=0.225 Sum_probs=34.4
Q ss_pred hhhcCCCCcC--CCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeCCeEEEEE
Q 023914 100 NVLKISFCQW--CGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCK 158 (275)
Q Consensus 100 w~~~~~fC~~--CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~iLL~r 158 (275)
=..-.+-||. |+..++. -.|+.||.+.. ..+..+-++++++...+-+.
T Consensus 184 GsglI~rCP~~~C~Rvl~~----------g~C~~HG~ve~-~~DLrik~vlDDGt~~~~~~ 233 (311)
T PRK07217 184 GSGLIKRCPEEDCTRVLQN----------GRCSEHGKVEG-EFDLRIKGVLDDGEEVQEVI 233 (311)
T ss_pred CCCCeecCCccccCccccC----------CCCCCCCCcCC-ceeeEEEEEEECCCCeEEEE
Confidence 3444588999 9998722 37999996654 66778888888876555444
No 340
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=40.08 E-value=20 Score=34.83 Aligned_cols=34 Identities=18% Similarity=0.388 Sum_probs=23.9
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
...-||.||-....- .-+.+....||.||+..+.
T Consensus 17 ~~~~C~eCd~~~~~P--~l~~~q~A~CPRC~~~l~~ 50 (418)
T COG2995 17 HLILCPECDMLVSLP--RLDSGQSAYCPRCGHTLTR 50 (418)
T ss_pred ceecCCCCCceeccc--cCCCCCcccCCCCCCcccc
Confidence 346799998886443 3356777889999876654
No 341
>PRK12496 hypothetical protein; Provisional
Probab=39.82 E-value=18 Score=30.67 Aligned_cols=27 Identities=19% Similarity=0.594 Sum_probs=17.1
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
.|+.||...... ...-.|+.||.....
T Consensus 129 ~C~gC~~~~~~~------~~~~~C~~CG~~~~r 155 (164)
T PRK12496 129 VCKGCKKKYPED------YPDDVCEICGSPVKR 155 (164)
T ss_pred ECCCCCccccCC------CCCCcCCCCCChhhh
Confidence 399999775322 123479999976543
No 342
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=39.61 E-value=18 Score=25.63 Aligned_cols=30 Identities=27% Similarity=0.578 Sum_probs=15.1
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
.....|..|+++.... ..+.+|..||.+.=
T Consensus 7 ~~~~~C~~C~~~F~~~------~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 7 SEASNCMICGKKFSLF------RRRHHCRNCGRVVC 36 (69)
T ss_dssp GG-SB-TTT--B-BSS------S-EEE-TTT--EEE
T ss_pred CCCCcCcCcCCcCCCc------eeeEccCCCCCEEC
Confidence 4478999999998443 45789999997543
No 343
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=39.50 E-value=16 Score=28.98 Aligned_cols=27 Identities=22% Similarity=0.327 Sum_probs=17.0
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
-.|+.||....... .-+. +.||.||..
T Consensus 43 ~~C~~Cg~~~~~~~---SCk~-R~CP~C~~~ 69 (111)
T PF14319_consen 43 YRCEDCGHEKIVYN---SCKN-RHCPSCQAK 69 (111)
T ss_pred eecCCCCceEEecC---cccC-cCCCCCCCh
Confidence 36888888764442 2333 488888853
No 344
>PRK14973 DNA topoisomerase I; Provisional
Probab=38.71 E-value=18 Score=39.13 Aligned_cols=36 Identities=14% Similarity=0.284 Sum_probs=26.7
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
.-||.||.+.......|..|+-.-||.|.+..+...
T Consensus 636 ~~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~~~~~~~ 671 (936)
T PRK14973 636 EVCPIHHLNHVRLIRKGARPWDIGCPLCSHIESNTE 671 (936)
T ss_pred CCCCCCCCCceEEeecCCCcccccCccccchhhccc
Confidence 479999998666555666777778999988776443
No 345
>PF15616 TerY-C: TerY-C metal binding domain
Probab=38.62 E-value=16 Score=30.01 Aligned_cols=32 Identities=22% Similarity=0.440 Sum_probs=20.0
Q ss_pred CCCCcCCCCCCccc--------ccCCCccceeecCCCCCccc
Q 023914 104 ISFCQWCGGQTKHE--------VPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 104 ~~fC~~CG~~~~~~--------~~~~~~~~~~~C~~Cg~~~y 137 (275)
..=||.||...... +.. +.....||-||....
T Consensus 77 ~PgCP~CGn~~~fa~C~CGkl~Ci~--g~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVCGCGKLFCID--GEGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCCcChhcEEEecCCCEEEeC--CCCCEECCCCCCeee
Confidence 37899999985332 222 233567777776543
No 346
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=38.56 E-value=7.6 Score=38.12 Aligned_cols=35 Identities=20% Similarity=0.537 Sum_probs=24.9
Q ss_pred HHHHhhh--hcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 95 VHSAGNV--LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 95 ~~l~~w~--~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.+...|. +.-.|||-|+.+.... ..+.+|.-||.+
T Consensus 169 qsvVpW~DDs~V~~CP~Ca~~F~l~------rRrHHCRLCG~V 205 (505)
T KOG1842|consen 169 QSVVPWLDDSSVQFCPECANSFGLT------RRRHHCRLCGRV 205 (505)
T ss_pred hccccccCCCcccccccccchhhhH------HHhhhhhhcchH
Confidence 3456785 4479999999997654 345678877754
No 347
>PRK08173 DNA topoisomerase III; Validated
Probab=38.50 E-value=18 Score=38.63 Aligned_cols=28 Identities=32% Similarity=0.592 Sum_probs=20.3
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
.-||.||+.+ . ..+..+.|.+|++..+.
T Consensus 625 ~~CP~Cg~~~--~----~~~~~~~Cs~C~f~~~~ 652 (862)
T PRK08173 625 TPCPNCGGVV--K----ENYRRFACTKCDFSISK 652 (862)
T ss_pred ccCCcccccc--c----ccCceeEcCCCCcccch
Confidence 3599999875 2 23445899999987764
No 348
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=38.41 E-value=15 Score=34.76 Aligned_cols=13 Identities=38% Similarity=0.744 Sum_probs=11.3
Q ss_pred CCCcCCCCCCccc
Q 023914 105 SFCQWCGGQTKHE 117 (275)
Q Consensus 105 ~fC~~CG~~~~~~ 117 (275)
-|||.||+++..+
T Consensus 26 ffCPaC~~~l~lK 38 (342)
T COG4469 26 FFCPACGSQLILK 38 (342)
T ss_pred cccCCCCCeeeee
Confidence 4999999998766
No 349
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=38.38 E-value=13 Score=25.62 Aligned_cols=31 Identities=26% Similarity=0.509 Sum_probs=20.6
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.|..||.......-.+..+....|.+||...
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~ 31 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHH
Confidence 4889998765544333335567899999543
No 350
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=38.24 E-value=20 Score=25.70 Aligned_cols=41 Identities=22% Similarity=0.411 Sum_probs=25.8
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHD 151 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~ 151 (275)
..+-|-+|..-+.. ....||.||...+..--...++|++.+
T Consensus 3 ~~kAC~~Ck~l~~~--------d~e~CP~Cgs~~~te~W~G~~iIidpe 43 (64)
T COG2093 3 TEKACKNCKRLTPE--------DTEICPVCGSTDLTEEWFGLLIIIDPE 43 (64)
T ss_pred hhHHHhhccccCCC--------CCccCCCCCCcccchhhccEEEEEcCc
Confidence 34668888766522 245799999887765444555555543
No 351
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=38.21 E-value=38 Score=32.23 Aligned_cols=56 Identities=21% Similarity=0.285 Sum_probs=30.7
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeCCe--EEEEEeccCC-CCCceeee
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKK--ILLCKRKIEP-SYGLWTLP 171 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~~~--iLL~rr~~~p-~~g~w~lP 171 (275)
--|..|=+-+ .+-.+-.|++||.-. ..-++|-|..+|. .-+-.|..+. .+-.|++|
T Consensus 243 LRCh~Cfsit-------~~m~k~FCp~CG~~T----L~K~aVsv~~dG~~~~h~k~r~~~n~RG~~YSlp 301 (376)
T KOG2463|consen 243 LRCHGCFSIT-------SEMPKDFCPSCGHKT----LTKCAVSVDEDGNGQTHFKKRFQWNNRGLQYSLP 301 (376)
T ss_pred eEeeeeeEec-------CccchhcccccCCCe----eeEEEEEecCCCceeEEeecccccccCcceeecC
Confidence 3466665544 234567999999872 2333444555543 3344344432 24468887
No 352
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=38.20 E-value=14 Score=30.22 Aligned_cols=23 Identities=26% Similarity=0.449 Sum_probs=16.9
Q ss_pred CccceeecCCCCCcccc-CCcEEE
Q 023914 122 EEKMRAICTVCGKIAYQ-NPKMVV 144 (275)
Q Consensus 122 ~~~~~~~C~~Cg~~~y~-~p~~~V 144 (275)
+-|.++.|++||..+|- |-.|+|
T Consensus 5 elGtKr~Cp~cg~kFYDLnk~p~v 28 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDLNRRPAV 28 (129)
T ss_pred hhCccccCCCcCccccccCCCCcc
Confidence 45788999999999995 334433
No 353
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=37.37 E-value=20 Score=37.18 Aligned_cols=23 Identities=26% Similarity=0.510 Sum_probs=17.9
Q ss_pred CCCCcCCCCCCcccccCCCccceeecC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICT 130 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~ 130 (275)
-.+||.||+++... +++...+|+
T Consensus 404 P~~CP~Cgs~l~~~----~~~~~~~C~ 426 (665)
T PRK07956 404 PTHCPVCGSELVRV----EGEAVLRCT 426 (665)
T ss_pred CCCCCCCCCEeEec----CCCeEEECC
Confidence 46999999999764 455677886
No 354
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=36.60 E-value=22 Score=28.13 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=20.6
Q ss_pred CCCcCCCCCCcccccC----CCccceeecCCCCCcc
Q 023914 105 SFCQWCGGQTKHEVPH----GEEKMRAICTVCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~----~~~~~~~~C~~Cg~~~ 136 (275)
.||.+|.+.+..-... -.+.....|..||+..
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIR 92 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEE
Confidence 6999999976432110 0233667899999764
No 355
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=36.10 E-value=21 Score=25.27 Aligned_cols=14 Identities=50% Similarity=0.947 Sum_probs=10.1
Q ss_pred CCcCCCCCCccccc
Q 023914 106 FCQWCGGQTKHEVP 119 (275)
Q Consensus 106 fC~~CG~~~~~~~~ 119 (275)
-||.||+.+....|
T Consensus 19 ~Cp~CG~~t~~~~P 32 (59)
T COG2260 19 KCPVCGGDTKVPHP 32 (59)
T ss_pred cCCCCCCccccCCC
Confidence 68888888766543
No 356
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=36.06 E-value=11 Score=34.21 Aligned_cols=36 Identities=19% Similarity=0.437 Sum_probs=23.4
Q ss_pred cCCCCcCCCCCCcccccC--CCccceeecCCCCCcccc
Q 023914 103 KISFCQWCGGQTKHEVPH--GEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~--~~~~~~~~C~~Cg~~~y~ 138 (275)
...-|+.|+-.+...... -.+....+||.||++.|-
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy~ 233 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILYY 233 (239)
T ss_pred cCCcccCCeeeecHHHHHHHhcCCCCccCCccchHHHh
Confidence 457899998776432110 023456899999998774
No 357
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=35.97 E-value=12 Score=39.64 Aligned_cols=19 Identities=26% Similarity=0.445 Sum_probs=0.0
Q ss_pred hhhhcCCCCcCCCCCCccc
Q 023914 99 GNVLKISFCQWCGGQTKHE 117 (275)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~ 117 (275)
.-..-...||.||+.|...
T Consensus 662 g~~t~~~~Cp~CG~~T~~~ 680 (900)
T PF03833_consen 662 GKETFYNRCPECGSHTEPV 680 (900)
T ss_dssp -------------------
T ss_pred CCcchhhcCcccCCccccc
Confidence 3344567899999997554
No 358
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.82 E-value=19 Score=24.88 Aligned_cols=29 Identities=21% Similarity=0.616 Sum_probs=18.3
Q ss_pred CCcCCCCCCcccccCC--CccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHG--EEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~--~~~~~~~C~~Cg~ 134 (275)
.||.||+......... +....-.|+.|-+
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~ 32 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCR 32 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCC
Confidence 5999999987654332 2233456777653
No 359
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=35.52 E-value=24 Score=25.33 Aligned_cols=28 Identities=21% Similarity=0.495 Sum_probs=18.7
Q ss_pred CCCCcCCCCCCcccccCCCccceeecC-CCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICT-VCGK 134 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~ 134 (275)
..-||.||+++.-.. +...+..|. .|..
T Consensus 6 ~v~CP~C~k~~~w~~---~~~~rPFCS~RCk~ 34 (62)
T PRK00418 6 TVNCPTCGKPVEWGE---ISPFRPFCSKRCQL 34 (62)
T ss_pred cccCCCCCCcccccC---CCCcCCcccHHHHh
Confidence 457999999975431 345677886 4654
No 360
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=35.19 E-value=56 Score=29.43 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=14.8
Q ss_pred CCcCCCCCCcccccCCCccceeecCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTV 131 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~ 131 (275)
-||.|++++... ....+|.+
T Consensus 4 ~CP~C~~~l~~~------~~~~~C~~ 23 (272)
T PRK11088 4 QCPLCHQPLTLE------ENSWICPQ 23 (272)
T ss_pred cCCCCCcchhcC------CCEEEcCC
Confidence 499999998543 23578977
No 361
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=35.08 E-value=29 Score=28.32 Aligned_cols=29 Identities=21% Similarity=0.520 Sum_probs=20.8
Q ss_pred CcCCCCCCcccccCCCccce-eecCCCCCcccc
Q 023914 107 CQWCGGQTKHEVPHGEEKMR-AICTVCGKIAYQ 138 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~-~~C~~Cg~~~y~ 138 (275)
|-.||+.+.... .+..+ +.|+.|+...+-
T Consensus 3 C~fC~~~s~~~~---~~~~~~w~C~~C~q~N~f 32 (131)
T PF09779_consen 3 CWFCGQNSKVPY---DNRNSNWTCPHCEQYNGF 32 (131)
T ss_pred eccCCCCCCCCC---CCCCCeeECCCCCCccCc
Confidence 788999875542 34444 999999977663
No 362
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=34.98 E-value=21 Score=28.74 Aligned_cols=27 Identities=30% Similarity=0.753 Sum_probs=17.4
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
-.|..|++..... .+...||.||-..+
T Consensus 71 ~~C~~C~~~~~~e------~~~~~CP~C~s~~~ 97 (115)
T COG0375 71 CWCLDCGQEVELE------ELDYRCPKCGSINL 97 (115)
T ss_pred EEeccCCCeecch------hheeECCCCCCCce
Confidence 4688888776543 24455888885544
No 363
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=34.46 E-value=18 Score=23.57 Aligned_cols=14 Identities=36% Similarity=0.643 Sum_probs=11.0
Q ss_pred CCCCcCCCCCCccc
Q 023914 104 ISFCQWCGGQTKHE 117 (275)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (275)
-++||.||+.|...
T Consensus 2 ~~~C~~Cg~~l~~i 15 (47)
T PF13005_consen 2 PRACPDCGGELKEI 15 (47)
T ss_pred CCcCCCCCceeeEC
Confidence 36899999998643
No 364
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=33.68 E-value=20 Score=24.65 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=20.4
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
--|+.|++-+..... -...--.|+.|+...-
T Consensus 5 iRC~~CnklLa~~g~--~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGE--VIELEIKCPRCKTINH 35 (51)
T ss_pred eeccchhHHHhhhcC--ccEEEEECCCCCccce
Confidence 469999988755311 1234568999997654
No 365
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=33.20 E-value=29 Score=31.60 Aligned_cols=30 Identities=13% Similarity=0.187 Sum_probs=16.9
Q ss_pred EeeCCCCHHHHHHHHHHHHhCCccccceeeE
Q 023914 174 YMEIGESAAEGAIRETWEEARADVEVQSPFA 204 (275)
Q Consensus 174 ~vE~GEs~eeAa~REl~EEtGl~v~~~~~~~ 204 (275)
-|-.||.+-+...++..+++ -+.+.+-.+|
T Consensus 161 VV~fGE~lp~~~~~~~~~~~-~~~d~liviG 190 (250)
T COG0846 161 VVWFGEPLPASFLDEALEAL-KEADLLIVIG 190 (250)
T ss_pred EEEeCCCCCHHHHHHHHHHh-ccCCEEEEEC
Confidence 35567766666666677776 3444433333
No 366
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=33.19 E-value=16 Score=31.73 Aligned_cols=28 Identities=18% Similarity=0.289 Sum_probs=15.9
Q ss_pred eeeEEeeCCCCHHH-HHHHHHHHHhCCcc
Q 023914 170 LPAGYMEIGESAAE-GAIRETWEEARADV 197 (275)
Q Consensus 170 lPgG~vE~GEs~ee-Aa~REl~EEtGl~v 197 (275)
+..-..|.|..+|. --+|--..|+|++.
T Consensus 134 ft~s~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (182)
T TIGR02820 134 FVSSIIETGTDPERMDGIRARLRELGLEP 162 (182)
T ss_pred EEeeccccCCChHHhHHHHHHHHHcCCCc
Confidence 34555677766653 23344455778764
No 367
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.12 E-value=17 Score=32.84 Aligned_cols=17 Identities=29% Similarity=0.391 Sum_probs=12.1
Q ss_pred hhcCCCCcCCCCCCccc
Q 023914 101 VLKISFCQWCGGQTKHE 117 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~ 117 (275)
....--||.|+...+..
T Consensus 16 ~kk~ieCPvC~tkFkke 32 (267)
T COG1655 16 YKKTIECPVCNTKFKKE 32 (267)
T ss_pred hhceeccCcccchhhhh
Confidence 34446799999887654
No 368
>PHA02998 RNA polymerase subunit; Provisional
Probab=32.80 E-value=37 Score=29.50 Aligned_cols=36 Identities=19% Similarity=0.344 Sum_probs=21.0
Q ss_pred cCCCCcCCCCCCccc----ccCCCcc--ceeecCCCCCcccc
Q 023914 103 KISFCQWCGGQTKHE----VPHGEEK--MRAICTVCGKIAYQ 138 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~----~~~~~~~--~~~~C~~Cg~~~y~ 138 (275)
...-||.||+.-... .-..|++ .-..|..||+..-|
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 346799999874321 1111222 23489999987655
No 369
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=32.69 E-value=17 Score=34.42 Aligned_cols=13 Identities=38% Similarity=0.812 Sum_probs=10.5
Q ss_pred CCCCcCCCCCCcc
Q 023914 104 ISFCQWCGGQTKH 116 (275)
Q Consensus 104 ~~fC~~CG~~~~~ 116 (275)
-.|||.||+.+-.
T Consensus 257 k~FCp~CG~~TL~ 269 (376)
T KOG2463|consen 257 KDFCPSCGHKTLT 269 (376)
T ss_pred hhcccccCCCeee
Confidence 4799999999633
No 370
>COG4111 Uncharacterized conserved protein [General function prediction only]
Probab=32.26 E-value=1.4e+02 Score=27.61 Aligned_cols=97 Identities=11% Similarity=0.142 Sum_probs=51.2
Q ss_pred EEEEEee-CCeEEEEEeccCCCCCceeeeeEEeeCCCCHHHHHHHH-HHHHhCCccccceeeEEEE---eC---CCCEEE
Q 023914 144 VGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRE-TWEEARADVEVQSPFAQLD---IP---RIGQIY 215 (275)
Q Consensus 144 V~viI~~-~~~iLL~rr~~~p~~g~w~lPgG~vE~GEs~eeAa~RE-l~EEtGl~v~~~~~~~~~~---~~---~~~~~~ 215 (275)
|++.|++ +-+||-+++.. .+|.|-.|+.-...|+-.|+ |.+.|+..+..++-+.++. .. ..+.+.
T Consensus 28 VvvAv~~~~p~VLtV~q~~-------aLP~GPfep~hrslq~glr~wV~~qT~~plGYiEQLYTF~Dr~R~~~~g~rvis 100 (322)
T COG4111 28 VVVAVTDGGPRVLTVRQGA-------ALPSGPFEPAHRSLQAGLRAWVEKQTSQPLGYIEQLYTFADRDRRNEGGMRVIS 100 (322)
T ss_pred EEEEEcCCCceEEEecccc-------cCCCCCCchHHHHHHHHHHHHHHHHhcCccchHHhhhhhccccccCcCCceEEE
Confidence 3333444 45677666441 28989888876555555555 5666888765554333332 11 234677
Q ss_pred EEEEEEEcCCCCCCCC---CceeEEEecCCCCCCC
Q 023914 216 IIFLAKLKRPHFSPGP---ESSECRLFALDEIPFD 247 (275)
Q Consensus 216 ~~f~a~~~~~e~~~~~---E~~d~~W~~~deL~~~ 247 (275)
+.|++-.....-.... =...+.+|++++....
T Consensus 101 v~YLgLtr~~~~~~~~~a~W~~wy~yfPWED~R~g 135 (322)
T COG4111 101 VSYLGLTREAADSIHAGAHWADWYGYFPWEDHRTG 135 (322)
T ss_pred EEEeeecchhcccCCccccccchhccCCHhhhccC
Confidence 7887765432211111 1122445677776543
No 371
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=31.72 E-value=32 Score=21.40 Aligned_cols=12 Identities=25% Similarity=0.955 Sum_probs=4.3
Q ss_pred eecCCCCCcccc
Q 023914 127 AICTVCGKIAYQ 138 (275)
Q Consensus 127 ~~C~~Cg~~~y~ 138 (275)
.+|.+||...||
T Consensus 12 ~rC~~Cg~~~~p 23 (37)
T PF12172_consen 12 QRCRDCGRVQFP 23 (37)
T ss_dssp EE-TTT--EEES
T ss_pred EEcCCCCCEecC
Confidence 345555555443
No 372
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=31.71 E-value=32 Score=25.74 Aligned_cols=29 Identities=34% Similarity=0.409 Sum_probs=19.8
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
.||-||..+-.... ++.--+|+-|++..-
T Consensus 3 ~CPCCg~~Tl~~~~---~~~ydIC~VC~WEdD 31 (78)
T PF14206_consen 3 PCPCCGYYTLEERG---EGTYDICPVCFWEDD 31 (78)
T ss_pred cCCCCCcEEeccCC---CcCceECCCCCcccC
Confidence 59999999755421 223568999987654
No 373
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=31.63 E-value=14 Score=25.99 Aligned_cols=14 Identities=29% Similarity=0.819 Sum_probs=7.8
Q ss_pred eecCCCCCccccCC
Q 023914 127 AICTVCGKIAYQNP 140 (275)
Q Consensus 127 ~~C~~Cg~~~y~~p 140 (275)
.+||+||-..-+||
T Consensus 42 ~~CPNCgGelv~RP 55 (57)
T PF06906_consen 42 GVCPNCGGELVRRP 55 (57)
T ss_pred CcCcCCCCccccCC
Confidence 35666665555544
No 374
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.37 E-value=26 Score=28.09 Aligned_cols=22 Identities=27% Similarity=0.270 Sum_probs=14.1
Q ss_pred ccceeecCCCCCcccc-CCcEEE
Q 023914 123 EKMRAICTVCGKIAYQ-NPKMVV 144 (275)
Q Consensus 123 ~~~~~~C~~Cg~~~y~-~p~~~V 144 (275)
-|.++.||.||+-+|. |..|+|
T Consensus 6 LGtKridPetg~KFYDLNrdPiV 28 (129)
T COG4530 6 LGTKRIDPETGKKFYDLNRDPIV 28 (129)
T ss_pred ccccccCccccchhhccCCCccc
Confidence 3566778888877774 444544
No 375
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.31 E-value=26 Score=21.45 Aligned_cols=23 Identities=35% Similarity=0.777 Sum_probs=14.0
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
-|+.||-..... ..-..||.||.
T Consensus 3 ~C~~CGy~y~~~------~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGE------EAPWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCC------cCCCcCcCCCC
Confidence 378888664322 13357888875
No 376
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=31.23 E-value=46 Score=24.01 Aligned_cols=39 Identities=21% Similarity=0.281 Sum_probs=22.3
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCccccCCcEEEEEEEeeC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHD 151 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~~V~viI~~~ 151 (275)
.++-|-.|..-+. + ..||.||...+..---.++++++.+
T Consensus 4 ~~~AC~~C~~i~~-------~---~~Cp~Cgs~~~S~~w~G~v~i~dPe 42 (64)
T PRK06393 4 QYRACKKCKRLTP-------E---KTCPVHGDEKTTTEWFGFLIITEPE 42 (64)
T ss_pred hhhhHhhCCcccC-------C---CcCCCCCCCcCCcCcceEEEEECCc
Confidence 3566888876651 1 2799999875443333344444433
No 377
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=31.02 E-value=28 Score=24.29 Aligned_cols=26 Identities=23% Similarity=0.514 Sum_probs=11.3
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
||.|+......- .....-.|..||..
T Consensus 10 Cp~C~~~q~vFS---ha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 10 CPGCYNIQTVFS---HAQTVVKCVVCGTV 35 (55)
T ss_dssp -TTT-SEEEEET---T-SS-EE-SSSTSE
T ss_pred CCCCCCeeEEEe---cCCeEEEcccCCCE
Confidence 666666654431 23445566666643
No 378
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=30.97 E-value=22 Score=24.35 Aligned_cols=14 Identities=36% Similarity=0.817 Sum_probs=11.2
Q ss_pred CCCCcCCCCCCccc
Q 023914 104 ISFCQWCGGQTKHE 117 (275)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (275)
.+|||.|+..+...
T Consensus 34 kKycp~c~khtlhk 47 (50)
T PRK00504 34 KKFCPRCNKHTLHK 47 (50)
T ss_pred ECcCCCCCCeEeee
Confidence 48999999987554
No 379
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=30.69 E-value=29 Score=35.98 Aligned_cols=26 Identities=27% Similarity=0.537 Sum_probs=19.1
Q ss_pred CCCCcCCCCCCcccccCCCccceeecC--CCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICT--VCG 133 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~--~Cg 133 (275)
-.+||.||++++.. +++...+|+ .|.
T Consensus 392 P~~CP~C~s~l~~~----~~~~~~~C~n~~C~ 419 (652)
T TIGR00575 392 PTHCPSCGSPLVKI----EEEAVIRCPNLNCP 419 (652)
T ss_pred CCCCCCCCCEeEec----CCcEEEEECCCCCH
Confidence 46999999998664 455667886 464
No 380
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=30.67 E-value=16 Score=30.89 Aligned_cols=41 Identities=20% Similarity=0.412 Sum_probs=29.5
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
--+......+.-|+.||++-...... +.-+...|.+||...
T Consensus 96 ~~i~~yi~~yv~C~~c~s~dt~l~~~-~R~~~l~c~acGa~~ 136 (151)
T COG1601 96 NEIERYIAEYVKCKECGSPDTELIKE-ERLLFLKCEACGAIR 136 (151)
T ss_pred HHHHHHHHheeEeccCCCCchhhhhh-hhhHhhHHHHhCCcc
Confidence 34566778889999999996554333 344677999999653
No 381
>PLN00209 ribosomal protein S27; Provisional
Probab=30.43 E-value=34 Score=26.10 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=12.5
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCC
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
||.|+......- .......|..||.
T Consensus 39 Cp~C~n~q~VFS---hA~t~V~C~~Cg~ 63 (86)
T PLN00209 39 CQGCFNITTVFS---HSQTVVVCGSCQT 63 (86)
T ss_pred CCCCCCeeEEEe---cCceEEEccccCC
Confidence 666665544431 2334455655554
No 382
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.36 E-value=17 Score=33.54 Aligned_cols=25 Identities=28% Similarity=0.650 Sum_probs=18.3
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.-.|+.||+++... ...|.+||...
T Consensus 3 ~FhC~~CgQ~v~Fe--------N~~C~~Cg~~L 27 (349)
T COG4307 3 DFHCPNCGQRVAFE--------NSACLSCGSAL 27 (349)
T ss_pred cccCCCCCCeeeec--------chHHHhhhhHh
Confidence 35799999997443 36799998644
No 383
>PRK06260 threonine synthase; Validated
Probab=30.19 E-value=27 Score=33.57 Aligned_cols=24 Identities=25% Similarity=0.612 Sum_probs=15.5
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
-.|..||...... .....|+.||.
T Consensus 4 ~~C~~cg~~~~~~------~~~~~Cp~cg~ 27 (397)
T PRK06260 4 LKCIECGKEYDPD------EIIYTCPECGG 27 (397)
T ss_pred EEECCCCCCCCCC------CccccCCCCCC
Confidence 3588888885322 23467888873
No 384
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=29.45 E-value=29 Score=34.14 Aligned_cols=21 Identities=38% Similarity=0.778 Sum_probs=16.7
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
-.|..||..- .+|.-+|++||
T Consensus 8 f~C~~CG~~s--------~KW~GkCp~Cg 28 (456)
T COG1066 8 FVCQECGYVS--------PKWLGKCPACG 28 (456)
T ss_pred EEcccCCCCC--------ccccccCCCCC
Confidence 4699999873 45777899998
No 385
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=29.34 E-value=29 Score=24.61 Aligned_cols=24 Identities=25% Similarity=0.767 Sum_probs=17.1
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecC-CCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICT-VCGK 134 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~ 134 (275)
.|++|+-||++.... -..|. .|+.
T Consensus 7 PH~HC~VCg~aIp~d--------e~~CSe~C~e 31 (64)
T COG4068 7 PHRHCVVCGKAIPPD--------EQVCSEECGE 31 (64)
T ss_pred CCccccccCCcCCCc--------cchHHHHHHH
Confidence 589999999995332 25776 4774
No 386
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=29.30 E-value=29 Score=35.51 Aligned_cols=26 Identities=31% Similarity=0.742 Sum_probs=19.0
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
...+..|+.||.. .++....||.||.
T Consensus 529 n~~~siC~~CGy~--------~g~~~~~CP~CGs 554 (586)
T TIGR02827 529 NIKITICNDCHHI--------DKRTLHRCPVCGS 554 (586)
T ss_pred CCCCeecCCCCCc--------CCCcCCcCcCCCC
Confidence 4457899999983 2334579999996
No 387
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=29.28 E-value=38 Score=25.92 Aligned_cols=37 Identities=22% Similarity=0.322 Sum_probs=22.6
Q ss_pred hhhcCCCCcCCCCCCcccccCC---CccceeecCCCCCcc
Q 023914 100 NVLKISFCQWCGGQTKHEVPHG---EEKMRAICTVCGKIA 136 (275)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~---~~~~~~~C~~Cg~~~ 136 (275)
+.....+|+.|++++....... ---.+-+|..|+...
T Consensus 29 i~~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I 68 (92)
T PF06750_consen 29 IIFPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPI 68 (92)
T ss_pred ccCCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCC
Confidence 3445689999999986541100 001356788888643
No 388
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=29.17 E-value=30 Score=22.30 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=15.3
Q ss_pred HHHHHHHhhhhcCCCCcCCCCCCc
Q 023914 92 SAAVHSAGNVLKISFCQWCGGQTK 115 (275)
Q Consensus 92 ~~a~~l~~w~~~~~fC~~CG~~~~ 115 (275)
.-|.+|..-..+.+||..||.-+.
T Consensus 5 ~La~al~~~~~~i~~C~~C~nlse 28 (41)
T PF02132_consen 5 QLADALKEAKENIKFCSICGNLSE 28 (41)
T ss_dssp HHHHHHHHHHHH-EE-SSS--EES
T ss_pred HHHHHHHHHHHcCCccCCCCCcCC
Confidence 446677778888999999998753
No 389
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=29.02 E-value=38 Score=25.78 Aligned_cols=25 Identities=20% Similarity=0.445 Sum_probs=12.9
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCC
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
||.|+......- .......|..||.
T Consensus 38 Cp~C~n~q~VFS---hA~t~V~C~~Cg~ 62 (85)
T PTZ00083 38 CPGCSQITTVFS---HAQTVVLCGGCSS 62 (85)
T ss_pred CCCCCCeeEEEe---cCceEEEccccCC
Confidence 666666654431 2334455666654
No 390
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.87 E-value=29 Score=34.67 Aligned_cols=24 Identities=29% Similarity=0.638 Sum_probs=17.2
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
+.-.|++||..... ...|+.||..
T Consensus 239 ~~l~Ch~Cg~~~~~---------~~~Cp~C~s~ 262 (505)
T TIGR00595 239 GKLRCHYCGYQEPI---------PKTCPQCGSE 262 (505)
T ss_pred CeEEcCCCcCcCCC---------CCCCCCCCCC
Confidence 34679999987533 2589999863
No 391
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=28.77 E-value=32 Score=37.26 Aligned_cols=32 Identities=22% Similarity=0.570 Sum_probs=24.2
Q ss_pred HhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 98 AGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 98 ~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.....+-.-|+.||..+.. .|.-.+|..||..
T Consensus 918 ~~~~~~~~~c~~c~~~~~~------~g~c~~c~~cg~t 949 (953)
T PRK06556 918 LGEAADAPLCPTCGTKMVR------NGSCYVCEGCGST 949 (953)
T ss_pred hcccccCCcCCCccCeeeE------CCceEeccCCCCC
Confidence 3455666789999988744 4678999999964
No 392
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=28.68 E-value=19 Score=29.84 Aligned_cols=25 Identities=24% Similarity=0.603 Sum_probs=18.3
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
..+-|+.||+..... .+.+|++|..
T Consensus 2 ~l~nC~~CgklF~~~-------~~~iCp~C~~ 26 (137)
T TIGR03826 2 ELANCPKCGRLFVKT-------GRDVCPSCYE 26 (137)
T ss_pred CCccccccchhhhhc-------CCccCHHHhH
Confidence 346899999986442 2468999984
No 393
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=28.66 E-value=34 Score=21.22 Aligned_cols=23 Identities=30% Similarity=0.782 Sum_probs=14.2
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
-|..||...... ..-..||.||.
T Consensus 4 ~C~~CG~i~~g~------~~p~~CP~Cg~ 26 (34)
T cd00729 4 VCPVCGYIHEGE------EAPEKCPICGA 26 (34)
T ss_pred ECCCCCCEeECC------cCCCcCcCCCC
Confidence 488888664322 12247888885
No 394
>PRK12860 transcriptional activator FlhC; Provisional
Probab=28.53 E-value=73 Score=27.89 Aligned_cols=41 Identities=17% Similarity=0.348 Sum_probs=31.3
Q ss_pred HHHHHHHHhhhhc----CCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 91 SSAAVHSAGNVLK----ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 91 ~~~a~~l~~w~~~----~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
+.+|..|..+... ..-|..||+....... +......|+-|.
T Consensus 117 ~tRAw~LvRf~~s~~L~l~~C~~Cgg~fv~~~~--e~~~~f~CplC~ 161 (189)
T PRK12860 117 LTRAWTLVRFFDAGMLQLARCCRCGGKFVTHAH--DLRHNFVCGLCQ 161 (189)
T ss_pred HHHHHHHHHHhcCCCeeeccCCCCCCCeecccc--ccCCCCcCCCCC
Confidence 7799999988664 4679999999765422 445678999997
No 395
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.48 E-value=27 Score=27.62 Aligned_cols=22 Identities=18% Similarity=0.042 Sum_probs=15.2
Q ss_pred CCCHHHHHHHHHHHHhCCccccc
Q 023914 178 GESAAEGAIRETWEEARADVEVQ 200 (275)
Q Consensus 178 GEs~eeAa~REl~EEtGl~v~~~ 200 (275)
-||.|.| .|-.+-|.|-..+++
T Consensus 82 aes~EHA-~RIAK~eIGk~L~~i 103 (115)
T COG1885 82 AESDEHA-ERIAKAEIGKALKDI 103 (115)
T ss_pred CCCHHHH-HHHHHHHHhhHhhcC
Confidence 4677665 488888988665544
No 396
>PRK06450 threonine synthase; Validated
Probab=28.39 E-value=30 Score=32.72 Aligned_cols=22 Identities=27% Similarity=0.733 Sum_probs=14.4
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.|.+||+.... .....|+.||-
T Consensus 5 ~C~~Cg~~~~~-------~~~~~C~~cg~ 26 (338)
T PRK06450 5 VCMKCGKERES-------IYEIRCKKCGG 26 (338)
T ss_pred EECCcCCcCCC-------cccccCCcCCC
Confidence 68888887521 22467888863
No 397
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.38 E-value=35 Score=35.25 Aligned_cols=27 Identities=26% Similarity=0.652 Sum_probs=19.5
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
......|+.||... .+....||.||..
T Consensus 563 n~~~~iC~~CG~~~--------~g~~~~CP~CGs~ 589 (623)
T PRK08271 563 NVKITICNDCHHID--------KRTGKRCPICGSE 589 (623)
T ss_pred CCCCccCCCCCCcC--------CCCCcCCcCCCCc
Confidence 45678999999762 2234789999963
No 398
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=28.30 E-value=39 Score=26.86 Aligned_cols=28 Identities=18% Similarity=0.360 Sum_probs=17.0
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..+.|..|+.++... ......|..|...
T Consensus 53 ~~~~C~~C~~~fg~l-----~~~~~~C~~C~~~ 80 (118)
T PF02318_consen 53 GERHCARCGKPFGFL-----FNRGRVCVDCKHR 80 (118)
T ss_dssp CCSB-TTTS-BCSCT-----STTCEEETTTTEE
T ss_pred CCcchhhhCCccccc-----CCCCCcCCcCCcc
Confidence 567999999997654 2233667776643
No 399
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=28.28 E-value=32 Score=23.84 Aligned_cols=14 Identities=43% Similarity=0.871 Sum_probs=11.7
Q ss_pred CCcCCCCCCccccc
Q 023914 106 FCQWCGGQTKHEVP 119 (275)
Q Consensus 106 fC~~CG~~~~~~~~ 119 (275)
-||.||+++...+|
T Consensus 19 ~cp~cG~~T~~ahP 32 (53)
T PF04135_consen 19 KCPPCGGPTESAHP 32 (53)
T ss_dssp BBTTTSSBSEESSS
T ss_pred ccCCCCCCCcCCcC
Confidence 89999999977654
No 400
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=28.17 E-value=32 Score=33.25 Aligned_cols=37 Identities=24% Similarity=0.399 Sum_probs=23.7
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 93 AAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
+|-.+.+-..-..||+.||..... .......|+.||.
T Consensus 229 ~ad~~~e~~g~~~~c~~cg~~~~~-----~~~~~~~c~~Cg~ 265 (380)
T COG1867 229 RADKLLENLGYIYHCSRCGEIVGS-----FREVDEKCPHCGG 265 (380)
T ss_pred hHHHHHHhcCcEEEcccccceecc-----cccccccCCcccc
Confidence 445555555556899999933222 2345678999996
No 401
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.98 E-value=39 Score=31.81 Aligned_cols=25 Identities=24% Similarity=0.678 Sum_probs=18.1
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.++-+|+.|++.=. -.|..|+.||.
T Consensus 210 ~RyL~CslC~teW~--------~~R~~C~~Cg~ 234 (309)
T PRK03564 210 LRYLHCNLCESEWH--------VVRVKCSNCEQ 234 (309)
T ss_pred ceEEEcCCCCCccc--------ccCccCCCCCC
Confidence 46788999988732 23678888885
No 402
>PF14369 zf-RING_3: zinc-finger
Probab=27.98 E-value=36 Score=21.37 Aligned_cols=26 Identities=15% Similarity=0.519 Sum_probs=15.6
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
||-.|.......... ++ ...||.|+.
T Consensus 4 wCh~C~~~V~~~~~~-~~--~~~CP~C~~ 29 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSP-DS--DVACPRCHG 29 (35)
T ss_pred eCccCCCEeEeCcCC-CC--CcCCcCCCC
Confidence 788898876554221 11 125998873
No 403
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=27.98 E-value=33 Score=27.34 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=7.3
Q ss_pred eecCCCCCccccC
Q 023914 127 AICTVCGKIAYQN 139 (275)
Q Consensus 127 ~~C~~Cg~~~y~~ 139 (275)
+.|..|+...||+
T Consensus 5 rfC~eCNNmLYPk 17 (113)
T KOG2691|consen 5 RFCRECNNMLYPK 17 (113)
T ss_pred chhhhhhcccccc
Confidence 3455555555555
No 404
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=27.72 E-value=10 Score=23.82 Aligned_cols=28 Identities=29% Similarity=0.747 Sum_probs=13.6
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCC
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
|..||..-....-.+..+....|.+||.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 6778777544333233445558988874
No 405
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=27.64 E-value=12 Score=24.29 Aligned_cols=28 Identities=25% Similarity=0.585 Sum_probs=12.7
Q ss_pred CCCcCCCCCCccc--ccCCCccceeecCCCC
Q 023914 105 SFCQWCGGQTKHE--VPHGEEKMRAICTVCG 133 (275)
Q Consensus 105 ~fC~~CG~~~~~~--~~~~~~~~~~~C~~Cg 133 (275)
++|+.||.+-... +..|.+ ....|..|=
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~-~~~IC~~Cv 31 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPN-GAYICDECV 31 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES--SEEEEHHHH
T ss_pred CCccCCCCCHHHHhceecCCC-CcEECHHHH
Confidence 5788998885432 222221 366777663
No 406
>PRK07220 DNA topoisomerase I; Validated
Probab=27.58 E-value=42 Score=35.29 Aligned_cols=35 Identities=20% Similarity=0.325 Sum_probs=18.7
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCcccc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (275)
...||.||..+......+...+-..|+.|.+..+.
T Consensus 635 ~~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~~~~~ 669 (740)
T PRK07220 635 DKVCEAHGLNHIRIINGGKRPWDLGCPQCNFIEWQ 669 (740)
T ss_pred CCCCCCCCCceEEEEecCCccceeeCCCCCCcccc
Confidence 35799998654332111111224578888765443
No 407
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=27.32 E-value=37 Score=31.58 Aligned_cols=29 Identities=24% Similarity=0.507 Sum_probs=18.7
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
.-||.||+....... ..-..+|..||-+.
T Consensus 2 ~~CpeCg~~~~~~d~---~~ge~VC~~CG~Vi 30 (285)
T COG1405 2 MSCPECGSTNIITDY---ERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCCccceeec---cCCeEEeccCCEEe
Confidence 459999999433211 22347999999543
No 408
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=26.97 E-value=49 Score=32.41 Aligned_cols=30 Identities=17% Similarity=0.472 Sum_probs=21.0
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCccccCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
+..-|+.||.-. .+ .+..|+.||..-|.+.
T Consensus 220 ~l~~C~~Cd~l~-------~~-~~a~CpRC~~~L~~~~ 249 (419)
T PRK15103 220 GLRSCSCCTAIL-------PA-DQPVCPRCHTKGYVRR 249 (419)
T ss_pred CCCcCCCCCCCC-------CC-CCCCCCCCCCcCcCCC
Confidence 345699999863 11 2348999999887654
No 409
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=26.94 E-value=30 Score=26.57 Aligned_cols=34 Identities=24% Similarity=0.413 Sum_probs=19.8
Q ss_pred ceeecCCCCCccccCCcEEEEEEEeeCCeEEEEEeccCC
Q 023914 125 MRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEP 163 (275)
Q Consensus 125 ~~~~C~~Cg~~~y~~p~~~V~viI~~~~~iLL~rr~~~p 163 (275)
....|++||..++..-. +-.-+++++|+..+.-|
T Consensus 34 Pa~~C~~CGe~y~~dev-----~~eIE~~l~l~~~~~~p 67 (89)
T TIGR03829 34 PSISCSHCGMEYQDDTT-----VKEIEDQLLLVDTKKLP 67 (89)
T ss_pred CcccccCCCcEeecHHH-----HHHHHhhhEEeecccCC
Confidence 45789999987764310 01124567777665443
No 410
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=26.92 E-value=17 Score=34.96 Aligned_cols=38 Identities=18% Similarity=0.319 Sum_probs=17.9
Q ss_pred hhhcCCCCcCCCCCCccc--cc-CCCccceeecCCCCCccc
Q 023914 100 NVLKISFCQWCGGQTKHE--VP-HGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 100 w~~~~~fC~~CG~~~~~~--~~-~~~~~~~~~C~~Cg~~~y 137 (275)
|.--.-+|+.||.-.... .. ...+.....|+.||+..-
T Consensus 170 y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~ 210 (360)
T PF01921_consen 170 YSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGE 210 (360)
T ss_dssp --SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---E
T ss_pred eeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEE
Confidence 444457899999942221 11 124556789999997643
No 411
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=26.85 E-value=47 Score=21.76 Aligned_cols=24 Identities=21% Similarity=0.682 Sum_probs=17.3
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
||+.||+.. +++....|..|+..+
T Consensus 1 ~C~vC~~~~-------~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 1 YCPVCGQSD-------DDGDMIQCDSCNRWY 24 (51)
T ss_dssp EBTTTTSSC-------TTSSEEEBSTTSCEE
T ss_pred eCcCCCCcC-------CCCCeEEcCCCChhh
Confidence 688999931 455678999998543
No 412
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=26.72 E-value=15 Score=26.88 Aligned_cols=15 Identities=27% Similarity=0.600 Sum_probs=10.0
Q ss_pred hcCCCCcCCCCCCcc
Q 023914 102 LKISFCQWCGGQTKH 116 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~ 116 (275)
....||+.||.++-.
T Consensus 46 ~~r~FC~~CGs~l~~ 60 (92)
T PF04828_consen 46 VERYFCPTCGSPLFS 60 (92)
T ss_dssp CEEEEETTT--EEEE
T ss_pred CcCcccCCCCCeeec
Confidence 345899999999854
No 413
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=26.65 E-value=53 Score=31.34 Aligned_cols=28 Identities=29% Similarity=0.591 Sum_probs=19.3
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCccccCCc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPK 141 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~ 141 (275)
-|+.||+.+-.. ...|.+||...=-.|.
T Consensus 1 ~C~~Cg~~v~Fe--------Nt~C~~Cg~~LGf~p~ 28 (343)
T PF10005_consen 1 SCPNCGQPVFFE--------NTRCLSCGSALGFDPD 28 (343)
T ss_pred CCCCCCCcceeC--------CCccccCCccccCCCC
Confidence 399999997443 3589999976543333
No 414
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=26.50 E-value=36 Score=25.51 Aligned_cols=33 Identities=21% Similarity=0.454 Sum_probs=12.0
Q ss_pred CCCCcCCCCCCccc--ccCCCccceeecCCCCCcc
Q 023914 104 ISFCQWCGGQTKHE--VPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 104 ~~fC~~CG~~~~~~--~~~~~~~~~~~C~~Cg~~~ 136 (275)
.--||.||+..... +.--.+.-...|..||..+
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 34689998553222 1111223346788887543
No 415
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=26.46 E-value=47 Score=22.30 Aligned_cols=26 Identities=35% Similarity=0.678 Sum_probs=17.8
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
+.|..|+.++... ..+..|..||.+.
T Consensus 3 ~~C~~C~~~F~~~------~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTLT------RRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccCC------ccccccCcCcCCc
Confidence 5688888876553 2456788888663
No 416
>PRK03922 hypothetical protein; Provisional
Probab=26.30 E-value=34 Score=27.33 Aligned_cols=22 Identities=18% Similarity=0.051 Sum_probs=15.3
Q ss_pred CCCHHHHHHHHHHHHhCCccccc
Q 023914 178 GESAAEGAIRETWEEARADVEVQ 200 (275)
Q Consensus 178 GEs~eeAa~REl~EEtGl~v~~~ 200 (275)
-|+.|.| .|-.+-|.|-..+++
T Consensus 82 Aes~EHA-~RIAK~eIG~aL~dv 103 (113)
T PRK03922 82 AESEEHA-SRIAKSEIGKALRDI 103 (113)
T ss_pred cCCHHHH-HHHHHHHHhhHHhcC
Confidence 3666665 488888999766554
No 417
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.00 E-value=37 Score=35.76 Aligned_cols=25 Identities=24% Similarity=0.570 Sum_probs=18.1
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.....+|+.||-.. +....||.||.
T Consensus 677 n~~~~~C~~CG~~~---------~~~~~CP~CG~ 701 (735)
T PRK07111 677 NHPVDRCPVCGYLG---------VIEDKCPKCGS 701 (735)
T ss_pred CCCCeecCCCCCCC---------CcCccCcCCCC
Confidence 45568899999432 23379999996
No 418
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.99 E-value=34 Score=35.93 Aligned_cols=24 Identities=29% Similarity=0.679 Sum_probs=16.7
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
+...|.+||..- . ....|++||..
T Consensus 461 ~~L~CH~Cg~~~-~--------~p~~Cp~Cgs~ 484 (730)
T COG1198 461 GQLRCHYCGYQE-P--------IPQSCPECGSE 484 (730)
T ss_pred CeeEeCCCCCCC-C--------CCCCCCCCCCC
Confidence 456789999882 1 23579999854
No 419
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.55 E-value=41 Score=34.75 Aligned_cols=26 Identities=31% Similarity=0.733 Sum_probs=18.8
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.....+|+.||... .+....||.||.
T Consensus 565 np~~~~C~~CG~~~--------~g~~~~CP~CGs 590 (625)
T PRK08579 565 TPAITVCNKCGRST--------TGLYTRCPRCGS 590 (625)
T ss_pred CCCCccCCCCCCcc--------CCCCCcCcCCCC
Confidence 34478999999853 123468999996
No 420
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=25.50 E-value=46 Score=19.72 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=9.2
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
+.|..||.+. .+++...|..|++..
T Consensus 1 ~~C~~C~~~~-------~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 1 FRCDACGKPI-------DGGWFYRCSECDFDL 25 (30)
T ss_dssp ---TTTS-----------S--EEE-TTT----
T ss_pred CcCCcCCCcC-------CCCceEECccCCCcc
Confidence 3588898884 224678999998753
No 421
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=25.50 E-value=20 Score=34.09 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=18.9
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.-|.+|+....... ....++.|+.||-
T Consensus 247 TAC~rC~t~y~le~---A~~~~wrCpkCGg 273 (403)
T COG1379 247 TACSRCYTRYSLEE---AKSLRWRCPKCGG 273 (403)
T ss_pred HHHHHhhhccCcch---hhhhcccCccccc
Confidence 35999997765541 2345789999996
No 422
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.22 E-value=40 Score=35.02 Aligned_cols=26 Identities=23% Similarity=0.463 Sum_probs=19.2
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.....+|+.||... +....||.||..
T Consensus 623 n~~~~~C~~CG~~~---------g~~~~CP~CG~~ 648 (656)
T PRK08270 623 TPTFSICPKHGYLS---------GEHEFCPKCGEE 648 (656)
T ss_pred CCCCcccCCCCCcC---------CCCCCCcCCcCc
Confidence 55678999999631 234799999954
No 423
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=25.22 E-value=33 Score=38.32 Aligned_cols=20 Identities=30% Similarity=0.768 Sum_probs=0.0
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
.+-||.||+.+-.. .|+.||
T Consensus 674 ~~~Cp~Cg~~~~~~----------~Cp~CG 693 (1627)
T PRK14715 674 FFKCPKCGKVGLYH----------VCPFCG 693 (1627)
T ss_pred eeeCCCCCCccccc----------cCcccC
No 424
>KOG0720 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=25.16 E-value=22 Score=35.22 Aligned_cols=35 Identities=20% Similarity=0.432 Sum_probs=25.1
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
++..||.+||..-......-....++.|..||..|
T Consensus 325 ~ntI~CskC~n~H~r~~T~rs~s~AR~C~~C~~~H 359 (490)
T KOG0720|consen 325 RNTIFCSKCGNTHFRVLTSRSPSQARWCAECGVKH 359 (490)
T ss_pred HhheehhhhcCcceeeeecCChhhhHHHHHhCccC
Confidence 56789999999865544333445678999999654
No 425
>PRK05580 primosome assembly protein PriA; Validated
Probab=25.10 E-value=39 Score=35.09 Aligned_cols=23 Identities=30% Similarity=0.628 Sum_probs=16.3
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
...|+.||..... ...|+.||..
T Consensus 408 ~l~Ch~Cg~~~~~---------~~~Cp~Cg~~ 430 (679)
T PRK05580 408 RLRCHHCGYQEPI---------PKACPECGST 430 (679)
T ss_pred eEECCCCcCCCCC---------CCCCCCCcCC
Confidence 3469999987432 2579999865
No 426
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=25.05 E-value=60 Score=22.03 Aligned_cols=22 Identities=14% Similarity=-0.053 Sum_probs=15.7
Q ss_pred HHHHhhhhcCCCCcCCCCCCcc
Q 023914 95 VHSAGNVLKISFCQWCGGQTKH 116 (275)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~ 116 (275)
..+.+|...+..||.||.++..
T Consensus 26 ~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 26 RAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred HHHHHHHHHCCCCCCCcCCCCh
Confidence 3455565667899999998743
No 427
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=24.92 E-value=36 Score=33.00 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=15.4
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
-.|++||+... . + ....|+.|+
T Consensus 3 l~C~~Cg~~~~-~----~--~~~~C~~c~ 24 (398)
T TIGR03844 3 LRCPGCGEVLP-D----H--YTLSCPLDC 24 (398)
T ss_pred EEeCCCCCccC-C----c--cccCCCCCC
Confidence 36999998863 2 1 247898876
No 428
>PF15025 DUF4524: Domain of unknown function (DUF4524)
Probab=24.86 E-value=62 Score=27.18 Aligned_cols=82 Identities=10% Similarity=0.069 Sum_probs=49.4
Q ss_pred cccccccccceeecceeecccccccCCCCCccHHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 58 SPAFLTRRTRCFRASRVCATRSESNQDATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 58 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
.|.-..+.+.+...|-....|+. -.+.+++.+.+--||.|...+... .+.++.........|
T Consensus 40 hplq~~~~~RQrT~Fa~S~~r~~-------------v~~aL~fRN~fa~~Pyl~~~li~~-----~rk~~~~~~~~~~~W 101 (148)
T PF15025_consen 40 HPLQQPERIRQRTRFATSRYREQ-------------VLAALEFRNRFATRPYLPESLIPS-----ERKKRIFIDISEVAW 101 (148)
T ss_pred CcCCCcceeeehhHHHHHhHHHH-------------HHHHHHHhhhcCCCCccchHhChh-----hceeeeeecceeeeC
Confidence 34444555566666655555543 244456777777788888887554 233445556677778
Q ss_pred cCCcEEEEEEEeeCCeEEEE
Q 023914 138 QNPKMVVGCLIEHDKKILLC 157 (275)
Q Consensus 138 ~~p~~~V~viI~~~~~iLL~ 157 (275)
|.++....+....+|.|=+.
T Consensus 102 P~~~~~~~~~~~~~G~v~i~ 121 (148)
T PF15025_consen 102 PSSSSDDSVIRDQDGSVEIS 121 (148)
T ss_pred CCccCCCcEEECCCCeEEEE
Confidence 88776665555555555443
No 429
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.81 E-value=51 Score=32.25 Aligned_cols=34 Identities=21% Similarity=0.267 Sum_probs=28.1
Q ss_pred hh-hhcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 99 GN-VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 99 ~w-~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
+| ..+.+-||.|+-..+.. +|-.+++|..||...
T Consensus 362 kwl~~N~krCP~C~v~IEr~----eGCnKM~C~~c~~~f 396 (445)
T KOG1814|consen 362 KWLESNSKRCPKCKVVIERS----EGCNKMHCTKCGTYF 396 (445)
T ss_pred HHHHhcCCCCCcccceeecC----CCccceeeccccccc
Confidence 78 45679999999998776 678899999999763
No 430
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=24.24 E-value=27 Score=29.20 Aligned_cols=31 Identities=23% Similarity=0.433 Sum_probs=18.4
Q ss_pred CCCCcCCCCCCcccccC-C--CccceeecCCCCC
Q 023914 104 ISFCQWCGGQTKHEVPH-G--EEKMRAICTVCGK 134 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~-~--~~~~~~~C~~Cg~ 134 (275)
.--||+||+.-...... | .-+--++|.+|..
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~e 138 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKE 138 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCC
Confidence 46899999986543221 0 1123467888864
No 431
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.07 E-value=42 Score=34.63 Aligned_cols=25 Identities=20% Similarity=0.564 Sum_probs=18.1
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
.....+|+.||.. ++....||.||.
T Consensus 556 n~~~~~C~~CGy~---------g~~~~~CP~CG~ 580 (618)
T PRK14704 556 NHPVDRCKCCSYH---------GVIGNECPSCGN 580 (618)
T ss_pred CCCCeecCCCCCC---------CCcCccCcCCCC
Confidence 4557899999963 122378999995
No 432
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=24.03 E-value=34 Score=23.61 Aligned_cols=14 Identities=7% Similarity=-0.002 Sum_probs=10.8
Q ss_pred CCCCcCCCCCCccc
Q 023914 104 ISFCQWCGGQTKHE 117 (275)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (275)
.+|||.|+..+...
T Consensus 37 kKycp~~~khtlhk 50 (53)
T PRK00595 37 KKYDPVLRKHVLHK 50 (53)
T ss_pred ECcCCCCCCEEeEE
Confidence 48999999886543
No 433
>PRK01343 zinc-binding protein; Provisional
Probab=23.95 E-value=48 Score=23.35 Aligned_cols=25 Identities=20% Similarity=0.571 Sum_probs=16.3
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecC-CCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICT-VCGK 134 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~ 134 (275)
..+-||.||++... ..+..|. .|..
T Consensus 8 p~~~CP~C~k~~~~-------~~rPFCS~RC~~ 33 (57)
T PRK01343 8 PTRPCPECGKPSTR-------EAYPFCSERCRD 33 (57)
T ss_pred CCCcCCCCCCcCcC-------CCCcccCHHHhh
Confidence 45789999988532 3566776 3653
No 434
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.94 E-value=49 Score=34.70 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=19.5
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
.....+|+.||..=+... .+....||.||..
T Consensus 638 n~~~~~C~~CG~~Ge~~~----~~~~~~CP~CG~~ 668 (711)
T PRK09263 638 NTPIDECYECGFTGEFEC----TEKGFTCPKCGNH 668 (711)
T ss_pred CCCCcccCCCCCCccccC----CCCCCcCcCCCCC
Confidence 355789999997422211 1122689999964
No 435
>PRK07591 threonine synthase; Validated
Probab=23.66 E-value=43 Score=32.60 Aligned_cols=22 Identities=23% Similarity=0.582 Sum_probs=15.2
Q ss_pred CCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
-.|..||+..... .. ..|+.||
T Consensus 19 l~C~~Cg~~~~~~------~~-~~C~~cg 40 (421)
T PRK07591 19 LKCRECGAEYPLG------PI-HVCEECF 40 (421)
T ss_pred EEeCCCCCcCCCC------CC-ccCCCCC
Confidence 4788999885322 22 7788887
No 436
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=23.46 E-value=67 Score=18.81 Aligned_cols=24 Identities=17% Similarity=0.355 Sum_probs=15.5
Q ss_pred CcCCCCCCcccccCCCccceeecCCCCC
Q 023914 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
|+.|...+..- .+-....|..|..
T Consensus 1 C~~Cr~~L~yp----~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYP----RGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcC----CCCCCeECCccCc
Confidence 77787776443 3445567888864
No 437
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=23.46 E-value=46 Score=28.68 Aligned_cols=41 Identities=20% Similarity=0.405 Sum_probs=21.6
Q ss_pred HHHHHHHHhhhhc----CCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 91 SSAAVHSAGNVLK----ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 91 ~~~a~~l~~w~~~----~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
+.+|..|.++... ...|..||+....... +......|+-|.
T Consensus 117 ~tRAW~L~R~~~sg~l~l~~C~~C~~~fv~~~~--~~~~~~~Cp~C~ 161 (175)
T PF05280_consen 117 LTRAWTLARFFDSGMLQLAPCRRCGGHFVTHAH--DPRHSFVCPFCQ 161 (175)
T ss_dssp HHHHHHHHHHHHTTSEEEEE-TTT--EEEEESS----SS----TT--
T ss_pred HHHHHHHHHHHhcCCccccCCCCCCCCeECcCC--CCCcCcCCCCCC
Confidence 7788888877654 5789999999766422 334567898887
No 438
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=23.17 E-value=47 Score=29.45 Aligned_cols=11 Identities=64% Similarity=1.244 Sum_probs=7.7
Q ss_pred ceeecCCCCCc
Q 023914 125 MRAICTVCGKI 135 (275)
Q Consensus 125 ~~~~C~~Cg~~ 135 (275)
...+|..|+..
T Consensus 117 ~~~~C~~C~~~ 127 (225)
T cd01411 117 YRIYCTVCGKT 127 (225)
T ss_pred CeeEeCCCCCc
Confidence 45688888754
No 439
>PF14149 YhfH: YhfH-like protein
Probab=22.89 E-value=10 Score=24.37 Aligned_cols=14 Identities=21% Similarity=0.544 Sum_probs=10.3
Q ss_pred CCCCcCCCCCCccc
Q 023914 104 ISFCQWCGGQTKHE 117 (275)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (275)
.+-|+.||+.+...
T Consensus 13 ~K~C~~CG~~i~EQ 26 (37)
T PF14149_consen 13 PKKCTECGKEIEEQ 26 (37)
T ss_pred CcccHHHHHHHHHH
Confidence 57888898886443
No 440
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=22.88 E-value=1.2e+02 Score=26.75 Aligned_cols=48 Identities=15% Similarity=0.251 Sum_probs=31.4
Q ss_pred HHHHHHhh-hhcCCCCcC---CCCCCccc---ccCCCccceeecCCCCCccccCC
Q 023914 93 AAVHSAGN-VLKISFCQW---CGGQTKHE---VPHGEEKMRAICTVCGKIAYQNP 140 (275)
Q Consensus 93 ~a~~l~~w-~~~~~fC~~---CG~~~~~~---~~~~~~~~~~~C~~Cg~~~y~~p 140 (275)
-+.++.+| +..+-.||+ ||+++-.. -.+|..-.+..||+|..+++|+.
T Consensus 94 l~~M~eKy~~~dFG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~dvY~P~s 148 (216)
T KOG3092|consen 94 LAAMLEKYKNGDFGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCEDVYIPKS 148 (216)
T ss_pred HHHHHHHHhcCCCCcCCcccccCCccccccccCCCCcceEEEeCCCccccccccc
Confidence 34455566 456889998 45554322 11234557789999999999876
No 441
>PF09505 Dimeth_Pyl: Dimethylamine methyltransferase (Dimeth_PyL); InterPro: IPR012653 This family consists of dimethylamine methyltransferases from the genus Methanosarcina. It is found in three nearly identical copies in each of Methanosarcina acetivorans, Methanosarcina barkeri, and Methanosarcina mazei. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrrolysine residue in these species (along with trimethylamine methyltransferase and monomethylamine methyltransferase). It demethylates dimethylamine, leaving monomethylamine, and methylates the prosthetic group of the small corrinoid protein MtbC. The methyl group is then transferred by methylcorrinoid:coenzyme M methyltransferase to coenzyme M. Note that the pyrrolysine residue is variously translated as K or X, or as a stop codon that truncates the sequence.; GO: 0008168 methyltransferase activity, 0015948 methanogenesis
Probab=22.82 E-value=45 Score=31.79 Aligned_cols=24 Identities=29% Similarity=0.184 Sum_probs=19.8
Q ss_pred EeeCCCCHHHHHHHHHHHHhCCcc
Q 023914 174 YMEIGESAAEGAIRETWEEARADV 197 (275)
Q Consensus 174 ~vE~GEs~eeAa~REl~EEtGl~v 197 (275)
.|+..+-..+.+.||++||+++-+
T Consensus 408 ~V~~~dLsDe~~MrelReeL~IG~ 431 (466)
T PF09505_consen 408 GVEPMDLSDEYVMRELREELNIGV 431 (466)
T ss_pred CCChhhcccHHHHHHHHHhcCcce
Confidence 467777788999999999999753
No 442
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.65 E-value=65 Score=30.77 Aligned_cols=43 Identities=21% Similarity=0.393 Sum_probs=30.1
Q ss_pred HHHHHHHHhhhhcCCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 91 SSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 91 ~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
+..|..+..-+..+.-||.||++-..+.++.++.-.+.|.-|+
T Consensus 19 il~aL~~~~~~~~~~~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 19 ILEALAIPGLKPGGHPCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred HHHHHhcccccCCCCCCCccCCccccccCCccCCccEEEEeec
Confidence 4455556656666669999999987776554444567888887
No 443
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=22.64 E-value=38 Score=23.47 Aligned_cols=14 Identities=21% Similarity=0.648 Sum_probs=11.0
Q ss_pred CCCCcCCCCCCccc
Q 023914 104 ISFCQWCGGQTKHE 117 (275)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (275)
.+|||.|+..+...
T Consensus 38 kKycp~~~khtlhk 51 (54)
T TIGR01023 38 RKYCPVCRKHVLHK 51 (54)
T ss_pred ECcCCCCCCeEeEE
Confidence 48999999887543
No 444
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=22.57 E-value=55 Score=22.72 Aligned_cols=35 Identities=20% Similarity=0.462 Sum_probs=22.3
Q ss_pred HHHHHHHhh-hhcCCCCcCCCCCCcccccCCCccceeecCC
Q 023914 92 SAAVHSAGN-VLKISFCQWCGGQTKHEVPHGEEKMRAICTV 131 (275)
Q Consensus 92 ~~a~~l~~w-~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~ 131 (275)
.+-..|..+ ...|.||-.||...... ......||.
T Consensus 14 e~L~~l~~YLR~~~~YC~~Cg~~Y~d~-----~dL~~~CPG 49 (55)
T PF13821_consen 14 ERLDKLLSYLREEHNYCFWCGTKYDDE-----EDLERNCPG 49 (55)
T ss_pred HHHHHHHHHHHhhCceeeeeCCccCCH-----HHHHhCCCC
Confidence 344444455 45699999999996443 334567774
No 445
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.32 E-value=1e+02 Score=27.95 Aligned_cols=49 Identities=12% Similarity=0.326 Sum_probs=30.9
Q ss_pred HHHHhhhhcCCC---CcCCCCCCccc----------------------ccCCCccceeecCCCCCccccCCcEE
Q 023914 95 VHSAGNVLKISF---CQWCGGQTKHE----------------------VPHGEEKMRAICTVCGKIAYQNPKMV 143 (275)
Q Consensus 95 ~~l~~w~~~~~f---C~~CG~~~~~~----------------------~~~~~~~~~~~C~~Cg~~~y~~p~~~ 143 (275)
...+.|.++..| |.-||.++... .|...+.-..+|+.|.-+.||+...+
T Consensus 38 QSYLqWL~DsDY~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~Nlv 111 (299)
T KOG3970|consen 38 QSYLQWLQDSDYNPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLV 111 (299)
T ss_pred HHHHHHHhhcCCCCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCcccc
Confidence 456789888766 66667776432 11112223468999999999876543
No 446
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.19 E-value=50 Score=34.36 Aligned_cols=27 Identities=26% Similarity=0.561 Sum_probs=15.5
Q ss_pred CCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
-|++|+.++..+ .......|..||+..
T Consensus 394 ~C~~C~~~L~~h----~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 394 RCRHCTGPLGLP----SAGGTPRCRWCGRAA 420 (665)
T ss_pred ECCCCCCceeEe----cCCCeeECCCCcCCC
Confidence 366677776654 233456666666543
No 447
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=22.05 E-value=36 Score=23.32 Aligned_cols=14 Identities=29% Similarity=0.714 Sum_probs=11.0
Q ss_pred CCCCcCCCCCCccc
Q 023914 104 ISFCQWCGGQTKHE 117 (275)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (275)
.+|||.|++.+...
T Consensus 34 kKycp~~~khtlhk 47 (50)
T COG0267 34 KKYCPVCRKHTLHK 47 (50)
T ss_pred EecCcccccEEEEe
Confidence 58999999887544
No 448
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=22.04 E-value=37 Score=24.80 Aligned_cols=15 Identities=40% Similarity=0.490 Sum_probs=8.1
Q ss_pred CCHHHH--HHHHHHHHh
Q 023914 179 ESAAEG--AIRETWEEA 193 (275)
Q Consensus 179 Es~eeA--a~REl~EEt 193 (275)
|+.+|| ++|++.||.
T Consensus 41 ~~~~eA~eiVrklQ~e~ 57 (68)
T PF09082_consen 41 ENAEEASEIVRKLQEEK 57 (68)
T ss_dssp SSHHHHHHHHHHHSS--
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 455554 567787774
No 449
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=21.98 E-value=47 Score=32.34 Aligned_cols=14 Identities=21% Similarity=0.700 Sum_probs=11.3
Q ss_pred CCCCcCCCCCCccc
Q 023914 104 ISFCQWCGGQTKHE 117 (275)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (275)
.-|||+||+.+...
T Consensus 38 ~A~CPRC~~~l~~~ 51 (418)
T COG2995 38 SAYCPRCGHTLTRG 51 (418)
T ss_pred cccCCCCCCccccC
Confidence 35999999998654
No 450
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=21.55 E-value=20 Score=25.00 Aligned_cols=32 Identities=16% Similarity=0.404 Sum_probs=22.0
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
.--|..|++-+... ++.+-....||.|..+.+
T Consensus 4 tiRC~~CnKlLa~a--~~~~yle~KCPrCK~vN~ 35 (60)
T COG4416 4 TIRCAKCNKLLAEA--EGQAYLEKKCPRCKEVNE 35 (60)
T ss_pred eeehHHHhHHHHhc--ccceeeeecCCccceeee
Confidence 34588898887555 334556778999986654
No 451
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.50 E-value=59 Score=30.17 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=16.8
Q ss_pred HHHHH-HHhhhhc--------------CCCCcCCCCCCcc
Q 023914 92 SAAVH-SAGNVLK--------------ISFCQWCGGQTKH 116 (275)
Q Consensus 92 ~~a~~-l~~w~~~--------------~~fC~~CG~~~~~ 116 (275)
.+++. +..|+.. -.-||.||.+-..
T Consensus 212 ~k~r~~l~sw~~~l~~ap~~sss~~t~~~~C~~Cg~~Pti 251 (298)
T KOG2879|consen 212 RKLRRVLKSWKLDLDRAPKFSSSTGTSDTECPVCGEPPTI 251 (298)
T ss_pred HHHHHHHHhhcccccCCCCcccccccCCceeeccCCCCCC
Confidence 34555 6677766 3569999998544
No 452
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.40 E-value=55 Score=28.53 Aligned_cols=32 Identities=22% Similarity=0.429 Sum_probs=19.6
Q ss_pred CCCCcCCCCCCcccccC-----CCcc-----ceeecCCCCCc
Q 023914 104 ISFCQWCGGQTKHEVPH-----GEEK-----MRAICTVCGKI 135 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~-----~~~~-----~~~~C~~Cg~~ 135 (275)
.+.|+.||......+.. ..++ ....|..|+..
T Consensus 17 ~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~t 58 (203)
T COG4332 17 AKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYT 58 (203)
T ss_pred hhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCc
Confidence 37899999987655310 0011 23678888864
No 453
>PHA02031 putative DnaG-like primase
Probab=21.16 E-value=26 Score=32.24 Aligned_cols=46 Identities=20% Similarity=0.304 Sum_probs=29.8
Q ss_pred HHHHHHHHHh-hhhcCCCCcCCCCCCcccccCCCccceeecCCCCCccc
Q 023914 90 PSSAAVHSAG-NVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (275)
Q Consensus 90 ~~~~a~~l~~-w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (275)
++-+|..|.- =.+++++| ||......+-...+.|..+|..|+..-+
T Consensus 8 wl~~~q~l~~g~~~r~~~~--~~~~~~~~~~~~~~~w~ayc~rc~~~~~ 54 (266)
T PHA02031 8 WLRQAQRLAVGQTGRFRHC--CGGGAAMTLYNNPDRWVAYCYRCKEGGK 54 (266)
T ss_pred HHHHHHHHhccccceeeec--cCCCceeEEecCcchHHHHHHhhcccch
Confidence 3445555553 24455666 7777666555556789999999997544
No 454
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=20.90 E-value=59 Score=33.16 Aligned_cols=27 Identities=26% Similarity=0.602 Sum_probs=18.5
Q ss_pred hhcCCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
......|..||..- ......||.||..
T Consensus 521 n~~~~~C~~CG~~g--------~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 521 NPPVDVCEDCGYTG--------EGLNDKCPKCGSH 547 (579)
T ss_pred ccCCccCCCCCCCC--------CCCCCcCcCCCCc
Confidence 45578999999631 1122689999964
No 455
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=20.76 E-value=51 Score=25.59 Aligned_cols=21 Identities=33% Similarity=0.877 Sum_probs=15.1
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (275)
..+.|..||.++.. ..|..|.
T Consensus 79 ~~~~C~~CG~pss~----------~iC~~C~ 99 (104)
T TIGR00269 79 DLRRCERCGEPTSG----------RICKACK 99 (104)
T ss_pred cCCcCCcCcCcCCc----------cccHhhh
Confidence 34789999998632 3687774
No 456
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=20.56 E-value=63 Score=28.60 Aligned_cols=31 Identities=23% Similarity=0.479 Sum_probs=19.1
Q ss_pred cCCCCcCCCCCCcccccCCCccceeecCCCCC
Q 023914 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (275)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (275)
+.+-||.||+.-....+. .+-....|..|.-
T Consensus 217 k~r~CPsC~k~Wqlk~~i-~d~fhfkcd~crl 247 (256)
T COG5595 217 KYRCCPSCGKDWQLKNPI-FDTFHFKCDTCRL 247 (256)
T ss_pred ccCCCCcccccceeccch-hhheeeeccccee
Confidence 456788888876555333 2345567777753
No 457
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=20.25 E-value=42 Score=32.46 Aligned_cols=28 Identities=32% Similarity=0.596 Sum_probs=19.3
Q ss_pred CCCCcCCCCCCcccccCCCccceeecCCCCCc
Q 023914 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (275)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (275)
..+|-+|+..+.... .......|| ||..
T Consensus 240 ~~~c~~C~~~~~~~~---~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 240 QTACEACGEPAVSED---AETACANCP-CGGR 267 (374)
T ss_pred hhhhcccCCcCCchh---hhhcCCCCC-CCCc
Confidence 358999999886552 122347899 9964
No 458
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=20.22 E-value=24 Score=27.40 Aligned_cols=35 Identities=20% Similarity=0.352 Sum_probs=22.5
Q ss_pred hcCCCCcCCCCCCcccccCCCccceeecCCCCCcc
Q 023914 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (275)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (275)
++..+|.+||..-.........-.++.|..|+..+
T Consensus 3 ~n~i~C~~C~~~H~r~~t~r~~~~AR~C~~C~~~H 37 (94)
T PF14901_consen 3 SNTIRCDKCGGKHKRIETDRPPSAARYCQDCKIRH 37 (94)
T ss_pred cceeechhhCCeeeeEEecCchhhhHhHHHhhhhc
Confidence 34578999998865543333334567888887544
No 459
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=20.12 E-value=53 Score=25.78 Aligned_cols=20 Identities=20% Similarity=0.121 Sum_probs=12.6
Q ss_pred CCCHHHHHHHHHHHHhCCccc
Q 023914 178 GESAAEGAIRETWEEARADVE 198 (275)
Q Consensus 178 GEs~eeAa~REl~EEtGl~v~ 198 (275)
-||.|.| .|-.+-|.|-..+
T Consensus 80 Aes~EHA-~RIAKs~iGkaL~ 99 (102)
T PF04475_consen 80 AESEEHA-ERIAKSEIGKALR 99 (102)
T ss_pred cCCHHHH-HHHHHHHHhHHhc
Confidence 3666665 4777777775544
Done!