Query 022283
Match_columns 299
No_of_seqs 380 out of 2426
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 09:25:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022283hhsearch_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 1.2E-44 2.5E-49 331.1 9.5 171 70-245 76-249 (279)
2 PRK00241 nudC NADH pyrophospha 100.0 4.3E-40 9.4E-45 302.5 16.1 171 71-246 66-237 (256)
3 KOG3084 NADH pyrophosphatase I 100.0 2E-38 4.4E-43 291.1 3.1 244 1-271 67-336 (345)
4 cd04511 Nudix_Hydrolase_4 Memb 99.9 4.6E-27 1E-31 194.0 12.6 128 129-256 1-128 (130)
5 COG1051 ADP-ribose pyrophospha 99.9 2.5E-21 5.4E-26 163.9 13.2 120 134-253 3-128 (145)
6 cd04681 Nudix_Hydrolase_22 Mem 99.8 9.8E-21 2.1E-25 155.3 11.8 118 145-262 6-130 (130)
7 PLN02325 nudix hydrolase 99.8 1.5E-20 3.2E-25 158.7 11.9 125 135-261 3-137 (144)
8 cd04679 Nudix_Hydrolase_20 Mem 99.8 8.5E-20 1.8E-24 149.0 12.1 106 140-245 1-113 (125)
9 cd03675 Nudix_Hydrolase_2 Cont 99.8 8.6E-20 1.9E-24 150.6 11.7 120 143-263 2-129 (134)
10 PRK15434 GDP-mannose mannosyl 99.8 8.2E-20 1.8E-24 157.0 11.6 115 139-253 15-143 (159)
11 cd03430 GDPMH GDP-mannose glyc 99.8 8.6E-20 1.9E-24 153.9 11.5 111 139-249 10-134 (144)
12 cd03429 NADH_pyrophosphatase N 99.8 7E-20 1.5E-24 151.8 10.6 122 143-265 2-128 (131)
13 cd04684 Nudix_Hydrolase_25 Con 99.8 9E-20 2E-24 148.2 10.6 114 143-257 2-126 (128)
14 cd03427 MTH1 MutT homolog-1 (M 99.8 2E-19 4.4E-24 148.7 11.9 120 143-263 3-126 (137)
15 cd04683 Nudix_Hydrolase_24 Mem 99.8 3.6E-19 7.8E-24 144.0 11.4 104 143-246 2-113 (120)
16 cd04673 Nudix_Hydrolase_15 Mem 99.8 4.4E-19 9.6E-24 143.2 11.0 106 143-248 2-115 (122)
17 cd04696 Nudix_Hydrolase_37 Mem 99.8 5.9E-19 1.3E-23 144.2 11.8 105 140-246 1-113 (125)
18 cd04678 Nudix_Hydrolase_19 Mem 99.8 6.7E-19 1.5E-23 144.3 11.8 108 140-247 1-117 (129)
19 cd04691 Nudix_Hydrolase_32 Mem 99.8 6.6E-19 1.4E-23 143.0 11.6 101 144-245 3-106 (117)
20 cd03673 Ap6A_hydrolase Diadeno 99.8 3.9E-19 8.4E-24 145.1 9.9 107 152-262 16-130 (131)
21 cd04671 Nudix_Hydrolase_13 Mem 99.8 9.2E-19 2E-23 143.8 12.1 102 143-245 3-108 (123)
22 cd04680 Nudix_Hydrolase_21 Mem 99.8 7.8E-19 1.7E-23 141.5 11.3 108 147-259 7-118 (120)
23 cd04672 Nudix_Hydrolase_14 Mem 99.8 1.3E-18 2.7E-23 142.0 12.2 109 140-253 1-116 (123)
24 cd04669 Nudix_Hydrolase_11 Mem 99.8 2E-18 4.4E-23 140.9 12.8 101 145-248 5-115 (121)
25 PRK15472 nucleoside triphospha 99.8 1.6E-18 3.4E-23 144.8 12.4 108 141-248 4-126 (141)
26 cd04700 DR1025_like DR1025 fro 99.8 1.2E-18 2.7E-23 146.3 11.5 111 135-245 7-123 (142)
27 PRK09438 nudB dihydroneopterin 99.8 8.8E-19 1.9E-23 147.5 10.0 125 137-264 4-145 (148)
28 cd04687 Nudix_Hydrolase_28 Mem 99.8 3.1E-18 6.7E-23 140.5 12.3 106 142-248 2-122 (128)
29 cd04682 Nudix_Hydrolase_23 Mem 99.8 1.5E-18 3.3E-23 141.3 9.2 110 143-252 3-119 (122)
30 cd03674 Nudix_Hydrolase_1 Memb 99.8 8.8E-18 1.9E-22 140.2 12.4 115 144-262 6-137 (138)
31 PRK10546 pyrimidine (deoxy)nuc 99.7 2.1E-17 4.6E-22 136.3 13.5 121 142-264 5-128 (135)
32 cd04677 Nudix_Hydrolase_18 Mem 99.7 1.6E-17 3.5E-22 136.2 12.0 103 140-245 6-120 (132)
33 cd04690 Nudix_Hydrolase_31 Mem 99.7 9.8E-18 2.1E-22 135.0 10.4 102 143-248 3-111 (118)
34 cd03671 Ap4A_hydrolase_plant_l 99.7 1.7E-17 3.7E-22 139.8 12.1 116 142-261 4-143 (147)
35 cd04664 Nudix_Hydrolase_7 Memb 99.7 7.8E-18 1.7E-22 138.1 9.1 114 141-256 2-126 (129)
36 cd04699 Nudix_Hydrolase_39 Mem 99.7 5.2E-18 1.1E-22 138.0 7.8 110 142-253 2-118 (129)
37 cd03424 ADPRase_NUDT5 ADP-ribo 99.7 2E-17 4.2E-22 137.0 11.4 106 140-245 2-113 (137)
38 PRK05379 bifunctional nicotina 99.7 2.2E-17 4.8E-22 157.8 12.9 127 136-262 198-338 (340)
39 cd04676 Nudix_Hydrolase_17 Mem 99.7 5.7E-17 1.2E-21 131.3 13.1 107 141-252 2-120 (129)
40 cd04688 Nudix_Hydrolase_29 Mem 99.7 4.1E-17 9E-22 133.3 12.1 103 144-249 4-120 (126)
41 cd04670 Nudix_Hydrolase_12 Mem 99.7 1.8E-17 3.9E-22 135.6 9.9 102 145-247 7-113 (127)
42 cd04674 Nudix_Hydrolase_16 Mem 99.7 9.9E-17 2.2E-21 131.4 13.9 112 139-252 2-116 (118)
43 cd03672 Dcp2p mRNA decapping e 99.7 3.6E-17 7.9E-22 138.3 11.5 102 142-246 2-110 (145)
44 PRK10776 nucleoside triphospha 99.7 7.8E-17 1.7E-21 130.9 12.9 114 143-259 7-124 (129)
45 cd04689 Nudix_Hydrolase_30 Mem 99.7 2.4E-17 5.2E-22 134.5 9.9 101 142-245 2-112 (125)
46 cd04667 Nudix_Hydrolase_10 Mem 99.7 3.8E-17 8.3E-22 131.1 10.0 101 145-253 4-105 (112)
47 cd03425 MutT_pyrophosphohydrol 99.7 1.4E-16 3.1E-21 127.6 12.1 109 143-254 4-115 (124)
48 cd03428 Ap4A_hydrolase_human_l 99.7 4.7E-17 1E-21 133.2 9.4 103 153-260 18-127 (130)
49 TIGR00586 mutt mutator mutT pr 99.7 3.6E-16 7.8E-21 127.3 13.3 110 143-255 7-119 (128)
50 cd04661 MRP_L46 Mitochondrial 99.7 6.7E-17 1.5E-21 134.2 9.0 95 150-245 11-118 (132)
51 PRK00714 RNA pyrophosphohydrol 99.7 1.7E-16 3.7E-21 135.6 11.4 120 141-264 8-150 (156)
52 cd04695 Nudix_Hydrolase_36 Mem 99.7 1.4E-16 3.1E-21 131.5 10.0 111 147-259 9-125 (131)
53 cd04693 Nudix_Hydrolase_34 Mem 99.7 1.1E-16 2.4E-21 131.1 8.2 102 143-245 3-111 (127)
54 cd03426 CoAse Coenzyme A pyrop 99.7 1.5E-16 3.2E-21 135.9 9.3 95 152-246 16-117 (157)
55 cd04697 Nudix_Hydrolase_38 Mem 99.7 1.7E-16 3.6E-21 130.4 9.1 101 144-245 4-110 (126)
56 cd04666 Nudix_Hydrolase_9 Memb 99.7 4.1E-16 8.9E-21 128.0 9.6 97 152-252 15-119 (122)
57 PF00293 NUDIX: NUDIX domain; 99.7 1.5E-16 3.2E-21 129.5 6.8 120 141-261 2-132 (134)
58 PRK15393 NUDIX hydrolase YfcD; 99.7 6E-16 1.3E-20 135.3 11.0 123 144-267 41-170 (180)
59 cd04686 Nudix_Hydrolase_27 Mem 99.6 9.3E-16 2E-20 126.9 9.9 101 143-246 2-118 (131)
60 cd02885 IPP_Isomerase Isopente 99.6 8.7E-16 1.9E-20 132.1 8.1 105 141-245 30-146 (165)
61 cd04692 Nudix_Hydrolase_33 Mem 99.6 1.5E-15 3.1E-20 127.5 8.7 103 143-245 5-125 (144)
62 PRK11762 nudE adenosine nucleo 99.6 8.3E-15 1.8E-19 128.5 13.7 107 139-245 46-157 (185)
63 cd04665 Nudix_Hydrolase_8 Memb 99.6 6.8E-15 1.5E-19 120.5 11.9 98 144-245 3-103 (118)
64 cd02883 Nudix_Hydrolase Nudix 99.6 9.3E-15 2E-19 115.9 11.0 102 144-246 3-111 (123)
65 cd04694 Nudix_Hydrolase_35 Mem 99.6 9.3E-15 2E-19 123.4 10.2 103 143-245 3-129 (143)
66 PRK03759 isopentenyl-diphospha 99.6 9.7E-15 2.1E-19 128.0 8.9 104 141-245 34-150 (184)
67 PRK10729 nudF ADP-ribose pyrop 99.5 1.2E-13 2.6E-18 123.1 13.0 109 137-245 46-169 (202)
68 PRK08999 hypothetical protein; 99.5 6.9E-14 1.5E-18 131.6 12.0 110 142-254 7-119 (312)
69 cd04685 Nudix_Hydrolase_26 Mem 99.5 4.2E-14 9.1E-19 117.9 9.2 102 145-246 5-122 (133)
70 TIGR00052 nudix-type nucleosid 99.5 7.2E-14 1.6E-18 122.9 10.0 109 137-245 41-163 (185)
71 TIGR02150 IPP_isom_1 isopenten 99.5 4E-14 8.6E-19 121.2 8.1 99 144-245 31-140 (158)
72 PRK10707 putative NUDIX hydrol 99.5 1.9E-13 4.2E-18 120.7 11.0 106 141-246 32-145 (190)
73 TIGR02705 nudix_YtkD nucleosid 99.5 5.5E-13 1.2E-17 114.2 12.9 99 140-245 24-125 (156)
74 cd04662 Nudix_Hydrolase_5 Memb 99.5 5.6E-13 1.2E-17 110.3 11.4 90 152-241 15-126 (126)
75 cd03670 ADPRase_NUDT9 ADP-ribo 99.5 1E-12 2.3E-17 115.5 12.9 105 153-263 50-184 (186)
76 cd03676 Nudix_hydrolase_3 Memb 99.4 8.2E-13 1.8E-17 115.1 9.3 94 152-245 48-156 (180)
77 PRK15009 GDP-mannose pyrophosp 99.4 4.2E-12 9.2E-17 112.3 11.2 109 136-245 41-164 (191)
78 cd04663 Nudix_Hydrolase_6 Memb 99.3 1.3E-11 2.8E-16 102.3 11.8 90 153-246 15-115 (126)
79 PLN02709 nudix hydrolase 99.3 5.6E-12 1.2E-16 113.5 9.5 94 152-245 51-153 (222)
80 COG0494 MutT NTP pyrophosphohy 99.2 1.5E-10 3.2E-15 93.4 11.7 95 152-248 24-135 (161)
81 PLN02552 isopentenyl-diphospha 99.2 7.8E-11 1.7E-15 108.0 9.9 123 143-265 59-227 (247)
82 PLN03143 nudix hydrolase; Prov 99.1 2.5E-10 5.4E-15 106.9 11.0 109 137-245 125-263 (291)
83 cd03431 DNA_Glycosylase_C DNA 99.1 9.7E-10 2.1E-14 87.6 11.3 103 143-254 5-110 (118)
84 KOG2839 Diadenosine and diphos 99.1 1.7E-10 3.7E-15 96.4 5.0 119 142-263 10-140 (145)
85 PLN02791 Nudix hydrolase homol 98.9 2.1E-09 4.6E-14 111.8 8.9 105 141-245 32-156 (770)
86 KOG3041 Nucleoside diphosphate 98.9 8.4E-09 1.8E-13 90.3 10.1 105 141-245 75-192 (225)
87 PF14803 Nudix_N_2: Nudix N-te 98.8 1.6E-09 3.5E-14 69.4 1.8 34 105-138 1-34 (34)
88 KOG3069 Peroxisomal NUDIX hydr 98.8 1.6E-08 3.4E-13 90.9 6.7 114 132-245 34-161 (246)
89 PF14815 NUDIX_4: NUDIX domain 98.7 5.9E-08 1.3E-12 78.1 7.8 105 144-254 1-108 (114)
90 PF09297 zf-NADH-PPase: NADH p 98.6 1.4E-08 3E-13 64.3 1.8 32 102-137 1-32 (32)
91 COG4119 Predicted NTP pyrophos 98.6 1.1E-07 2.4E-12 78.0 6.1 100 165-267 35-153 (161)
92 KOG0648 Predicted NUDIX hydrol 98.5 1.8E-07 3.9E-12 87.1 5.3 115 139-253 113-237 (295)
93 COG1443 Idi Isopentenyldiphosp 98.0 5.2E-06 1.1E-10 71.8 4.6 99 146-245 39-151 (185)
94 PLN02839 nudix hydrolase 98.0 4.2E-05 9.1E-10 73.6 11.3 94 152-245 218-325 (372)
95 smart00661 RPOL9 RNA polymeras 97.5 0.00022 4.8E-09 49.4 4.8 42 105-148 1-42 (52)
96 KOG2937 Decapping enzyme compl 97.2 6.9E-05 1.5E-09 70.6 -0.6 108 133-244 74-189 (348)
97 KOG4195 Transient receptor pot 97.2 0.0024 5.3E-08 57.3 8.8 40 153-195 140-179 (275)
98 PRK00432 30S ribosomal protein 97.1 0.00041 9E-09 48.3 2.6 33 102-139 18-50 (50)
99 PRK10880 adenine DNA glycosyla 97.0 0.0035 7.6E-08 60.6 9.1 110 144-267 234-346 (350)
100 COG1998 RPS31 Ribosomal protei 96.9 0.00057 1.2E-08 47.1 2.2 35 101-139 16-50 (51)
101 COG4112 Predicted phosphoester 96.9 0.0064 1.4E-07 52.3 8.4 101 145-245 65-185 (203)
102 PF13240 zinc_ribbon_2: zinc-r 95.8 0.0039 8.4E-08 36.4 0.9 22 106-135 1-22 (23)
103 PF02150 RNA_POL_M_15KD: RNA p 95.2 0.0081 1.8E-07 38.7 0.9 31 104-137 1-31 (35)
104 PF13248 zf-ribbon_3: zinc-rib 95.0 0.012 2.5E-07 35.3 1.0 24 104-135 2-25 (26)
105 PF07754 DUF1610: Domain of un 94.7 0.023 4.9E-07 33.6 1.8 24 107-134 1-24 (24)
106 PF13869 NUDIX_2: Nucleotide h 94.7 0.18 3.8E-06 44.6 8.2 40 153-196 59-98 (188)
107 PF10571 UPF0547: Uncharacteri 93.8 0.035 7.5E-07 33.4 1.3 24 105-136 1-24 (26)
108 PRK13910 DNA glycosylase MutY; 93.6 0.33 7.1E-06 45.8 8.2 85 144-256 189-275 (289)
109 PF06677 Auto_anti-p27: Sjogre 93.5 0.056 1.2E-06 36.1 2.0 34 95-133 8-41 (41)
110 PRK00420 hypothetical protein; 93.2 0.08 1.7E-06 43.0 2.9 32 99-135 18-49 (112)
111 TIGR00686 phnA alkylphosphonat 92.6 0.064 1.4E-06 43.1 1.6 51 105-160 3-63 (109)
112 COG1645 Uncharacterized Zn-fin 92.6 0.08 1.7E-06 44.1 2.2 28 104-137 28-55 (131)
113 KOG4548 Mitochondrial ribosoma 91.8 0.49 1.1E-05 43.5 6.4 93 152-245 139-245 (263)
114 PF12773 DZR: Double zinc ribb 91.8 0.088 1.9E-06 36.0 1.3 32 102-138 10-41 (50)
115 KOG4432 Uncharacterized NUDIX 91.5 0.4 8.7E-06 45.2 5.6 74 168-241 81-159 (405)
116 COG1594 RPB9 DNA-directed RNA 91.4 0.24 5.1E-06 40.3 3.6 35 104-140 2-36 (113)
117 PRK00398 rpoP DNA-directed RNA 91.1 0.2 4.2E-06 33.9 2.4 28 106-137 5-32 (46)
118 PF07282 OrfB_Zn_ribbon: Putat 91.1 0.19 4.1E-06 36.7 2.5 30 103-136 27-56 (69)
119 PF06044 DRP: Dam-replacing fa 90.9 0.098 2.1E-06 47.8 1.0 39 99-137 26-64 (254)
120 KOG1689 mRNA cleavage factor I 90.8 0.38 8.1E-06 41.8 4.4 39 152-194 84-122 (221)
121 PF09296 NUDIX-like: NADH pyro 90.7 0.085 1.8E-06 40.5 0.4 31 70-100 67-98 (98)
122 PF13453 zf-TFIIB: Transcripti 90.6 0.21 4.6E-06 32.9 2.2 31 106-138 1-31 (41)
123 PRK10220 hypothetical protein; 90.6 0.19 4.1E-06 40.5 2.2 52 104-160 3-64 (111)
124 PHA00626 hypothetical protein 90.6 0.21 4.5E-06 35.5 2.2 33 105-137 1-34 (59)
125 TIGR01384 TFS_arch transcripti 89.7 0.21 4.5E-06 39.5 1.9 29 105-139 1-29 (104)
126 PF08274 PhnA_Zn_Ribbon: PhnA 89.5 0.21 4.5E-06 31.1 1.3 27 105-136 3-29 (30)
127 TIGR02098 MJ0042_CXXC MJ0042 f 89.3 0.29 6.3E-06 31.5 2.0 32 106-137 4-36 (38)
128 KOG0142 Isopentenyl pyrophosph 89.0 0.26 5.7E-06 43.9 2.1 97 147-245 59-181 (225)
129 PF09538 FYDLN_acid: Protein o 88.7 0.24 5.1E-06 40.0 1.5 32 103-139 8-39 (108)
130 PRK00464 nrdR transcriptional 88.4 0.32 7E-06 41.7 2.2 31 106-136 2-38 (154)
131 PF09862 DUF2089: Protein of u 88.3 0.32 6.9E-06 39.6 2.0 22 107-136 1-22 (113)
132 PF03119 DNA_ligase_ZBD: NAD-d 87.3 0.24 5.1E-06 30.3 0.6 22 106-131 1-22 (28)
133 COG1996 RPC10 DNA-directed RNA 87.0 0.36 7.9E-06 33.4 1.4 31 106-140 8-38 (49)
134 PF13717 zinc_ribbon_4: zinc-r 86.9 0.5 1.1E-05 30.5 2.0 32 106-137 4-36 (36)
135 PF08271 TF_Zn_Ribbon: TFIIB z 86.3 0.45 9.7E-06 31.7 1.5 28 106-136 2-29 (43)
136 COG2824 PhnA Uncharacterized Z 86.2 0.57 1.2E-05 37.6 2.3 52 104-160 3-65 (112)
137 smart00659 RPOLCX RNA polymera 86.2 1 2.2E-05 30.4 3.3 26 106-136 4-29 (44)
138 COG4640 Predicted membrane pro 86.2 0.35 7.5E-06 47.2 1.3 25 104-136 1-25 (465)
139 PF14353 CpXC: CpXC protein 86.2 0.96 2.1E-05 37.1 3.8 49 106-157 3-66 (128)
140 PF13719 zinc_ribbon_5: zinc-r 86.1 0.49 1.1E-05 30.7 1.6 32 106-137 4-36 (37)
141 COG1194 MutY A/G-specific DNA 86.0 2.1 4.6E-05 41.3 6.5 93 143-254 238-332 (342)
142 COG1096 Predicted RNA-binding 85.8 0.44 9.5E-06 42.0 1.6 29 103-137 148-176 (188)
143 KOG2906 RNA polymerase III sub 85.7 0.56 1.2E-05 37.1 2.0 31 105-137 2-32 (105)
144 TIGR02300 FYDLN_acid conserved 85.7 0.49 1.1E-05 39.2 1.7 32 102-138 7-38 (129)
145 PF12760 Zn_Tnp_IS1595: Transp 85.3 1.2 2.7E-05 30.0 3.3 38 93-134 8-45 (46)
146 PF07295 DUF1451: Protein of u 85.1 0.44 9.6E-06 40.5 1.3 33 104-140 112-144 (146)
147 PF08772 NOB1_Zn_bind: Nin one 84.6 0.37 7.9E-06 36.2 0.5 43 126-172 24-69 (73)
148 PF09889 DUF2116: Uncharacteri 84.4 0.24 5.2E-06 35.7 -0.5 26 103-136 2-28 (59)
149 COG3677 Transposase and inacti 84.3 1.2 2.7E-05 37.0 3.6 46 92-137 18-64 (129)
150 PF14205 Cys_rich_KTR: Cystein 84.2 1.3 2.8E-05 31.3 3.1 33 105-137 5-39 (55)
151 TIGR01206 lysW lysine biosynth 83.9 0.87 1.9E-05 32.2 2.2 30 106-137 4-33 (54)
152 COG1571 Predicted DNA-binding 83.9 0.41 8.9E-06 47.3 0.6 37 95-136 341-377 (421)
153 PRK11032 hypothetical protein; 83.8 0.53 1.1E-05 40.7 1.2 32 104-139 124-155 (160)
154 PRK12286 rpmF 50S ribosomal pr 83.5 0.7 1.5E-05 33.0 1.6 23 102-133 25-47 (57)
155 smart00834 CxxC_CXXC_SSSS Puta 83.5 0.61 1.3E-05 30.2 1.2 28 106-134 7-34 (41)
156 COG1997 RPL43A Ribosomal prote 82.9 0.85 1.8E-05 35.4 1.9 37 96-136 27-63 (89)
157 PF12773 DZR: Double zinc ribb 82.8 0.85 1.8E-05 31.0 1.7 25 101-133 26-50 (50)
158 PF03604 DNA_RNApol_7kD: DNA d 82.2 0.76 1.7E-05 29.0 1.2 25 107-136 3-27 (32)
159 PRK14559 putative protein seri 82.2 0.71 1.5E-05 48.2 1.6 35 102-136 13-51 (645)
160 PRK13844 recombination protein 81.8 0.55 1.2E-05 42.0 0.6 95 85-193 38-134 (200)
161 TIGR01031 rpmF_bact ribosomal 81.8 0.85 1.8E-05 32.3 1.4 22 103-133 25-46 (55)
162 PF09723 Zn-ribbon_8: Zinc rib 81.8 0.71 1.5E-05 30.7 1.0 28 106-134 7-34 (42)
163 KOG4432 Uncharacterized NUDIX 81.2 3.5 7.6E-05 39.0 5.7 78 168-245 286-374 (405)
164 PRK11827 hypothetical protein; 81.1 1.2 2.7E-05 32.1 2.1 32 102-138 6-37 (60)
165 COG1779 C4-type Zn-finger prot 81.1 3.1 6.7E-05 37.1 5.0 89 103-195 13-124 (201)
166 TIGR01084 mutY A/G-specific ad 80.4 3.4 7.3E-05 38.7 5.4 24 149-172 236-260 (275)
167 TIGR00244 transcriptional regu 80.0 1.6 3.5E-05 37.1 2.8 45 106-150 2-54 (147)
168 PF13824 zf-Mss51: Zinc-finger 79.7 1.2 2.6E-05 31.7 1.6 25 106-137 1-25 (55)
169 PRK14890 putative Zn-ribbon RN 78.9 2 4.4E-05 30.9 2.6 28 104-135 7-34 (59)
170 COG4260 Membrane protease subu 78.7 0.94 2E-05 42.6 1.0 30 103-135 314-343 (345)
171 PF04216 FdhE: Protein involve 78.6 0.92 2E-05 42.6 1.0 34 104-137 172-208 (290)
172 COG1327 Predicted transcriptio 78.0 1.7 3.8E-05 37.1 2.4 32 105-136 1-38 (156)
173 TIGR00615 recR recombination p 77.5 0.92 2E-05 40.4 0.6 91 89-193 38-130 (195)
174 PF10083 DUF2321: Uncharacteri 77.1 0.33 7.1E-06 41.6 -2.2 22 102-134 26-47 (158)
175 PF08792 A2L_zn_ribbon: A2L zi 77.0 2 4.4E-05 27.2 1.9 29 104-136 3-31 (33)
176 PHA02942 putative transposase; 76.6 2 4.3E-05 42.1 2.8 30 103-137 324-353 (383)
177 COG2888 Predicted Zn-ribbon RN 76.3 2 4.3E-05 30.9 1.9 27 104-134 9-35 (61)
178 PRK00076 recR recombination pr 76.1 0.93 2E-05 40.4 0.2 94 86-193 35-130 (196)
179 PF01783 Ribosomal_L32p: Ribos 75.5 1.4 3.1E-05 31.2 1.1 21 104-133 26-46 (56)
180 PRK10445 endonuclease VIII; Pr 75.5 1.6 3.5E-05 40.5 1.7 31 101-133 232-262 (263)
181 PRK12495 hypothetical protein; 74.8 1.9 4.1E-05 39.0 1.8 33 99-137 37-69 (226)
182 PF14446 Prok-RING_1: Prokaryo 74.6 2.1 4.6E-05 30.3 1.7 28 104-137 5-32 (54)
183 COG0353 RecR Recombinational D 74.5 1.2 2.6E-05 39.6 0.5 99 80-194 32-132 (198)
184 smart00778 Prim_Zn_Ribbon Zinc 74.2 2.8 6.1E-05 27.3 2.1 32 103-134 2-33 (37)
185 TIGR01562 FdhE formate dehydro 73.8 2.2 4.7E-05 40.7 2.1 35 103-137 183-221 (305)
186 PF11023 DUF2614: Protein of u 73.4 1.4 3.1E-05 35.7 0.7 27 105-137 70-96 (114)
187 KOG3507 DNA-directed RNA polym 73.0 1.8 4E-05 31.0 1.0 26 106-136 22-47 (62)
188 PF12677 DUF3797: Domain of un 72.9 2.3 4.9E-05 29.4 1.4 40 94-134 3-46 (49)
189 PRK14892 putative transcriptio 72.8 2.4 5.2E-05 33.7 1.8 34 102-136 19-52 (99)
190 KOG2907 RNA polymerase I trans 72.4 1.2 2.6E-05 36.1 0.0 31 103-137 6-36 (116)
191 COG1656 Uncharacterized conser 72.4 1.9 4.1E-05 37.3 1.2 40 100-139 92-143 (165)
192 COG5349 Uncharacterized protei 72.3 3.1 6.8E-05 34.2 2.4 42 104-148 21-67 (126)
193 PF01599 Ribosomal_S27: Riboso 71.8 1.8 3.9E-05 29.8 0.8 29 102-134 16-46 (47)
194 TIGR03655 anti_R_Lar restricti 71.6 3.4 7.4E-05 28.7 2.2 31 105-135 2-35 (53)
195 TIGR03831 YgiT_finger YgiT-typ 71.3 3.5 7.5E-05 27.1 2.1 14 125-138 31-44 (46)
196 cd04476 RPA1_DBD_C RPA1_DBD_C: 71.1 6.7 0.00015 33.4 4.4 46 104-154 34-81 (166)
197 TIGR00577 fpg formamidopyrimid 71.1 2.4 5.2E-05 39.5 1.7 30 102-133 243-272 (272)
198 PF06827 zf-FPG_IleRS: Zinc fi 70.7 2.2 4.7E-05 26.0 0.9 27 106-134 3-29 (30)
199 TIGR02605 CxxC_CxxC_SSSS putat 70.7 2.4 5.2E-05 29.0 1.2 29 106-135 7-35 (52)
200 KOG4313 Thiamine pyrophosphoki 70.6 7.2 0.00016 36.1 4.6 45 153-197 149-196 (306)
201 PRK01103 formamidopyrimidine/5 70.3 2.6 5.7E-05 39.2 1.8 30 103-134 244-273 (274)
202 PRK14810 formamidopyrimidine-D 70.3 2.6 5.5E-05 39.3 1.7 30 102-133 242-271 (272)
203 COG4031 Predicted metal-bindin 70.1 14 0.00029 32.9 6.0 68 106-197 2-69 (227)
204 PRK13945 formamidopyrimidine-D 70.0 2.7 5.8E-05 39.4 1.8 28 104-133 254-281 (282)
205 PRK14714 DNA polymerase II lar 69.9 2.4 5.1E-05 47.2 1.5 10 105-114 668-677 (1337)
206 PRK12380 hydrogenase nickel in 69.4 2 4.2E-05 34.9 0.6 31 99-135 65-95 (113)
207 PRK05978 hypothetical protein; 69.0 3 6.5E-05 35.6 1.7 37 100-139 29-65 (148)
208 PRK14811 formamidopyrimidine-D 69.0 2.9 6.2E-05 39.0 1.8 32 102-135 233-264 (269)
209 COG0675 Transposase and inacti 68.9 3.4 7.3E-05 38.3 2.2 30 99-137 304-333 (364)
210 PF14354 Lar_restr_allev: Rest 68.4 4.1 8.8E-05 28.8 2.1 31 104-134 3-37 (61)
211 PF09855 DUF2082: Nucleic-acid 68.4 4.9 0.00011 29.4 2.5 12 126-137 36-47 (64)
212 PF09538 FYDLN_acid: Protein o 67.4 2.2 4.7E-05 34.5 0.5 23 122-144 5-28 (108)
213 PF01780 Ribosomal_L37ae: Ribo 67.2 2.5 5.3E-05 33.1 0.7 34 99-136 30-63 (90)
214 PF01927 Mut7-C: Mut7-C RNAse 67.2 4 8.7E-05 34.4 2.1 36 104-139 91-137 (147)
215 PRK04179 rpl37e 50S ribosomal 67.1 2.7 5.9E-05 30.5 0.9 25 103-134 16-40 (62)
216 COG3809 Uncharacterized protei 67.1 3.7 8.1E-05 31.3 1.7 28 105-134 2-29 (88)
217 PF08273 Prim_Zn_Ribbon: Zinc- 67.0 3.6 7.8E-05 27.3 1.4 31 104-134 3-34 (40)
218 PRK03988 translation initiatio 66.7 3.7 8E-05 34.6 1.8 43 93-136 91-133 (138)
219 smart00531 TFIIE Transcription 66.5 2.2 4.9E-05 36.0 0.5 35 104-138 99-135 (147)
220 PF04606 Ogr_Delta: Ogr/Delta- 66.4 4.5 9.8E-05 27.4 1.9 32 106-137 1-38 (47)
221 PRK09710 lar restriction allev 66.0 4.3 9.3E-05 29.7 1.8 33 102-135 4-36 (64)
222 smart00647 IBR In Between Ring 65.6 8.6 0.00019 26.8 3.3 35 100-136 14-50 (64)
223 PRK14559 putative protein seri 65.6 3.4 7.3E-05 43.3 1.6 12 179-190 130-141 (645)
224 TIGR00100 hypA hydrogenase nic 65.6 2.6 5.7E-05 34.2 0.7 30 100-135 66-95 (115)
225 PRK02935 hypothetical protein; 65.5 3.5 7.5E-05 33.1 1.3 27 105-137 71-97 (110)
226 PRK09678 DNA-binding transcrip 65.2 5.6 0.00012 29.8 2.3 33 105-137 2-40 (72)
227 PF11781 RRN7: RNA polymerase 64.7 4.1 8.8E-05 26.3 1.3 31 100-135 3-34 (36)
228 PF01485 IBR: IBR domain; Int 64.6 4.9 0.00011 28.1 1.9 33 100-136 14-50 (64)
229 PRK03564 formate dehydrogenase 64.4 5.1 0.00011 38.2 2.4 35 103-137 186-223 (309)
230 COG0266 Nei Formamidopyrimidin 63.5 4.2 9.1E-05 38.1 1.7 33 100-134 241-273 (273)
231 PRK03681 hypA hydrogenase nick 63.3 3.2 7E-05 33.6 0.8 32 99-135 65-96 (114)
232 smart00653 eIF2B_5 domain pres 63.2 4.5 9.8E-05 32.7 1.6 41 93-134 69-109 (110)
233 PTZ00255 60S ribosomal protein 63.1 5.6 0.00012 31.1 2.1 37 96-136 28-64 (90)
234 PF09986 DUF2225: Uncharacteri 63.0 4.3 9.3E-05 36.5 1.6 15 103-117 4-18 (214)
235 TIGR00311 aIF-2beta translatio 62.8 4.7 0.0001 33.7 1.7 42 94-136 87-128 (133)
236 PF04981 NMD3: NMD3 family ; 62.4 34 0.00074 31.1 7.4 24 107-137 1-24 (236)
237 TIGR00340 zpr1_rel ZPR1-relate 62.3 4.5 9.8E-05 35.0 1.5 31 107-137 1-39 (163)
238 PRK09521 exosome complex RNA-b 62.0 5.9 0.00013 34.8 2.3 31 104-139 149-179 (189)
239 PRK04023 DNA polymerase II lar 61.7 4.6 9.9E-05 44.0 1.8 24 102-135 624-647 (1121)
240 COG3364 Zn-ribbon containing p 61.6 2.9 6.2E-05 33.4 0.2 29 106-138 4-32 (112)
241 PF08646 Rep_fac-A_C: Replicat 61.4 13 0.00029 30.8 4.3 43 104-151 18-63 (146)
242 PF10058 DUF2296: Predicted in 61.1 5.9 0.00013 27.9 1.7 30 106-135 24-53 (54)
243 PRK13130 H/ACA RNA-protein com 60.8 4 8.6E-05 29.1 0.8 25 103-137 4-28 (56)
244 KOG3799 Rab3 effector RIM1 and 59.7 3.6 7.7E-05 34.6 0.4 14 104-117 89-102 (169)
245 PRK00564 hypA hydrogenase nick 59.7 4.2 9.1E-05 33.1 0.9 31 101-136 68-98 (117)
246 PRK08402 replication factor A; 59.5 12 0.00026 36.4 4.1 50 103-157 211-261 (355)
247 COG3877 Uncharacterized protei 59.4 6.2 0.00013 31.8 1.7 26 104-137 6-31 (122)
248 PRK01110 rpmF 50S ribosomal pr 59.1 5.1 0.00011 28.9 1.1 20 104-133 27-46 (60)
249 PRK15103 paraquat-inducible me 59.1 6.6 0.00014 39.0 2.3 34 105-140 11-44 (419)
250 PF01396 zf-C4_Topoisom: Topoi 59.0 11 0.00024 24.5 2.7 31 105-137 2-35 (39)
251 PRK12366 replication factor A; 59.0 9.9 0.00021 39.8 3.7 41 104-151 532-572 (637)
252 COG1326 Uncharacterized archae 58.8 9.6 0.00021 33.9 3.0 34 103-136 5-40 (201)
253 COG2126 RPL37A Ribosomal prote 58.8 4.3 9.3E-05 29.1 0.7 28 102-136 14-41 (61)
254 PRK08665 ribonucleotide-diphos 58.7 5.2 0.00011 42.7 1.6 25 105-135 725-749 (752)
255 TIGR00155 pqiA_fam integral me 58.5 7.2 0.00016 38.5 2.4 33 106-140 15-47 (403)
256 PF12647 RNHCP: RNHCP domain; 58.3 20 0.00044 28.1 4.4 28 105-134 5-32 (92)
257 PRK00423 tfb transcription ini 57.9 6.4 0.00014 37.4 1.9 32 102-136 9-40 (310)
258 PF01155 HypA: Hydrogenase exp 57.8 2.4 5.2E-05 34.3 -0.9 30 101-136 67-96 (113)
259 TIGR00373 conserved hypothetic 57.5 3.4 7.4E-05 35.4 -0.0 30 103-135 108-137 (158)
260 TIGR00310 ZPR1_znf ZPR1 zinc f 57.3 5.6 0.00012 35.3 1.3 31 107-137 3-41 (192)
261 PRK07218 replication factor A; 56.9 14 0.0003 36.8 4.1 40 103-153 296-335 (423)
262 PF09526 DUF2387: Probable met 56.5 7 0.00015 29.2 1.5 36 106-141 10-45 (71)
263 PRK06266 transcription initiat 56.2 3.5 7.5E-05 36.1 -0.2 31 103-136 116-146 (178)
264 PRK12336 translation initiatio 56.1 6.6 0.00014 35.0 1.6 42 94-136 88-129 (201)
265 KOG1710 MYND Zn-finger and ank 55.5 2.9 6.2E-05 39.7 -0.9 43 85-137 300-342 (396)
266 COG0333 RpmF Ribosomal protein 55.3 7.6 0.00016 27.8 1.4 23 103-134 26-48 (57)
267 PRK03976 rpl37ae 50S ribosomal 55.2 8.3 0.00018 30.1 1.8 37 96-136 28-64 (90)
268 PRK04023 DNA polymerase II lar 55.2 6.9 0.00015 42.7 1.8 17 99-115 633-649 (1121)
269 PF03487 IL13: Interleukin-13; 55.0 11 0.00025 24.9 2.1 26 168-193 11-36 (43)
270 PRK14873 primosome assembly pr 54.5 7.2 0.00016 41.1 1.8 26 106-135 394-419 (665)
271 COG1545 Predicted nucleic-acid 54.1 5.8 0.00013 33.3 0.9 26 102-135 27-52 (140)
272 PF01873 eIF-5_eIF-2B: Domain 53.9 8.7 0.00019 31.8 1.8 42 94-136 83-124 (125)
273 TIGR00595 priA primosomal prot 53.8 7.4 0.00016 39.5 1.7 26 107-136 225-250 (505)
274 PF09845 DUF2072: Zn-ribbon co 53.7 6.2 0.00014 32.9 0.9 28 106-137 3-30 (131)
275 PF01907 Ribosomal_L37e: Ribos 53.7 3.4 7.4E-05 29.3 -0.5 27 102-135 13-39 (55)
276 PF03833 PolC_DP2: DNA polymer 53.5 4.4 9.5E-05 43.4 0.0 14 103-116 654-667 (900)
277 TIGR02300 FYDLN_acid conserved 53.1 5.8 0.00013 33.0 0.6 23 122-144 5-28 (129)
278 TIGR02443 conserved hypothetic 52.7 9.8 0.00021 27.4 1.7 36 106-141 11-46 (59)
279 COG1592 Rubrerythrin [Energy p 52.2 8.2 0.00018 33.6 1.5 23 106-135 136-158 (166)
280 PTZ00073 60S ribosomal protein 51.8 7.7 0.00017 30.3 1.1 27 101-134 13-39 (91)
281 TIGR01053 LSD1 zinc finger dom 51.2 14 0.00031 23.0 2.1 27 106-136 3-29 (31)
282 PF03811 Zn_Tnp_IS1: InsA N-te 51.0 14 0.0003 23.9 2.0 30 104-133 5-36 (36)
283 TIGR00280 L37a ribosomal prote 50.8 19 0.00042 28.2 3.2 38 95-136 26-63 (91)
284 PF03966 Trm112p: Trm112p-like 50.6 8.9 0.00019 27.9 1.3 13 124-136 51-63 (68)
285 COG3024 Uncharacterized protei 50.5 7.3 0.00016 28.5 0.8 31 103-136 6-37 (65)
286 COG3791 Uncharacterized conser 50.3 15 0.00033 30.4 2.8 15 104-118 69-83 (133)
287 smart00401 ZnF_GATA zinc finge 50.3 12 0.00027 25.9 1.9 33 104-136 3-35 (52)
288 PRK14714 DNA polymerase II lar 50.2 11 0.00024 42.2 2.4 14 103-116 678-691 (1337)
289 TIGR03830 CxxCG_CxxCG_HTH puta 50.0 13 0.00027 29.8 2.2 13 125-137 30-42 (127)
290 KOG2767 Translation initiation 49.9 6.1 0.00013 38.2 0.4 45 96-140 88-132 (400)
291 PF07191 zinc-ribbons_6: zinc- 49.9 9.9 0.00021 28.3 1.4 24 106-135 3-26 (70)
292 COG2835 Uncharacterized conser 49.7 13 0.00028 26.9 1.9 27 105-135 9-35 (60)
293 PF05191 ADK_lid: Adenylate ki 49.4 6.3 0.00014 25.4 0.3 32 106-139 3-34 (36)
294 PF12172 DUF35_N: Rubredoxin-l 49.1 6.8 0.00015 25.0 0.4 9 105-113 12-20 (37)
295 COG3058 FdhE Uncharacterized p 48.9 7.2 0.00016 36.6 0.6 12 104-115 185-196 (308)
296 COG1499 NMD3 NMD protein affec 48.7 13 0.00029 36.1 2.4 30 102-138 4-33 (355)
297 PRK11788 tetratricopeptide rep 48.0 12 0.00026 35.3 2.0 32 101-140 351-382 (389)
298 PRK08332 ribonucleotide-diphos 47.7 10 0.00022 43.9 1.8 27 103-135 1703-1735(1740)
299 COG2995 PqiA Uncharacterized p 47.7 12 0.00025 36.9 1.9 34 103-138 17-50 (418)
300 TIGR00354 polC DNA polymerase, 46.8 8.7 0.00019 41.8 1.0 24 103-136 624-647 (1095)
301 PRK03824 hypA hydrogenase nick 46.6 8.7 0.00019 32.1 0.8 13 103-115 69-81 (135)
302 smart00709 Zpr1 Duplicated dom 46.0 11 0.00025 32.4 1.4 32 106-137 2-40 (160)
303 cd01121 Sms Sms (bacterial rad 45.6 13 0.00028 36.3 1.9 21 106-134 2-22 (372)
304 COG1439 Predicted nucleic acid 45.1 10 0.00022 33.3 1.0 9 107-115 142-150 (177)
305 KOG2691 RNA polymerase II subu 45.0 14 0.0003 29.8 1.6 36 103-138 3-38 (113)
306 COG2051 RPS27A Ribosomal prote 45.0 14 0.0003 27.2 1.5 25 124-148 17-43 (67)
307 PRK00762 hypA hydrogenase nick 44.8 10 0.00022 31.2 0.9 35 99-135 65-101 (124)
308 PF01096 TFIIS_C: Transcriptio 44.1 21 0.00045 23.2 2.1 31 106-136 2-38 (39)
309 PRK06386 replication factor A; 44.0 28 0.00061 33.9 3.9 42 103-155 235-276 (358)
310 PRK05654 acetyl-CoA carboxylas 43.9 7.4 0.00016 36.8 -0.1 17 100-116 42-58 (292)
311 COG4306 Uncharacterized protei 43.7 5.7 0.00012 33.0 -0.8 19 105-134 29-47 (160)
312 PRK11823 DNA repair protein Ra 43.6 13 0.00029 37.0 1.7 22 105-134 8-29 (446)
313 PRK12496 hypothetical protein; 43.5 13 0.00029 32.0 1.5 26 106-137 129-154 (164)
314 COG2093 DNA-directed RNA polym 43.5 19 0.00041 26.2 2.0 41 103-151 3-43 (64)
315 PRK13264 3-hydroxyanthranilate 43.5 10 0.00022 33.3 0.7 34 106-139 122-170 (177)
316 CHL00174 accD acetyl-CoA carbo 43.0 7.6 0.00016 36.8 -0.2 25 107-134 41-65 (296)
317 PF09332 Mcm10: Mcm10 replicat 42.8 8.1 0.00018 37.4 -0.0 33 104-140 285-317 (344)
318 TIGR00515 accD acetyl-CoA carb 42.7 7.6 0.00016 36.6 -0.2 13 102-114 43-55 (285)
319 PF03367 zf-ZPR1: ZPR1 zinc-fi 42.4 11 0.00024 32.4 0.8 32 106-137 3-41 (161)
320 TIGR00416 sms DNA repair prote 42.0 15 0.00032 36.9 1.7 22 105-134 8-29 (454)
321 COG4111 Uncharacterized conser 42.0 1.6E+02 0.0035 27.6 8.2 69 148-223 32-108 (322)
322 PRK05580 primosome assembly pr 41.6 15 0.00032 38.8 1.7 27 106-136 392-418 (679)
323 TIGR00155 pqiA_fam integral me 41.6 17 0.00036 36.0 2.0 29 105-140 216-244 (403)
324 KOG0402 60S ribosomal protein 40.6 14 0.00029 28.6 0.9 30 102-135 34-63 (92)
325 PF01363 FYVE: FYVE zinc finge 40.5 19 0.00041 25.8 1.7 30 102-137 7-36 (69)
326 PF11672 DUF3268: Protein of u 40.2 22 0.00048 28.4 2.1 13 105-117 3-15 (102)
327 COG1198 PriA Primosomal protei 39.4 17 0.00036 38.8 1.6 25 107-135 447-471 (730)
328 PF03884 DUF329: Domain of unk 39.3 13 0.00028 26.6 0.6 25 106-133 4-29 (57)
329 PRK11088 rrmA 23S rRNA methylt 39.2 43 0.00092 30.7 4.2 20 106-131 4-23 (272)
330 smart00532 LIGANc Ligase N fam 39.1 18 0.00038 36.3 1.7 25 103-131 398-422 (441)
331 PF14690 zf-ISL3: zinc-finger 39.0 24 0.00052 23.2 1.9 10 105-114 3-12 (47)
332 PRK07217 replication factor A; 38.9 44 0.00096 32.0 4.3 45 103-158 187-233 (311)
333 COG0777 AccD Acetyl-CoA carbox 38.6 11 0.00023 35.4 0.1 27 105-134 29-55 (294)
334 COG0272 Lig NAD-dependent DNA 38.5 18 0.0004 37.9 1.8 27 103-133 403-432 (667)
335 COG4068 Uncharacterized protei 38.4 17 0.00036 26.2 1.0 25 102-134 6-31 (64)
336 KOG2463 Predicted RNA-binding 38.3 35 0.00075 32.9 3.4 55 106-171 244-301 (376)
337 COG4888 Uncharacterized Zn rib 37.9 23 0.00049 28.3 1.8 32 105-136 23-56 (104)
338 PF14255 Cys_rich_CPXG: Cystei 37.8 59 0.0013 22.7 3.7 28 106-133 2-31 (52)
339 PF04216 FdhE: Protein involve 37.5 6.7 0.00014 36.7 -1.5 26 102-135 195-220 (290)
340 PF13408 Zn_ribbon_recom: Reco 37.5 19 0.00041 24.6 1.2 15 103-117 4-18 (58)
341 PF14319 Zn_Tnp_IS91: Transpos 37.4 18 0.00038 29.2 1.2 25 106-134 44-68 (111)
342 COG4530 Uncharacterized protei 37.1 19 0.00041 29.2 1.3 22 123-144 6-28 (129)
343 PF03833 PolC_DP2: DNA polymer 37.0 11 0.00024 40.4 0.0 28 100-136 663-690 (900)
344 COG1405 SUA7 Transcription ini 37.0 22 0.00047 33.6 1.9 29 105-136 2-30 (285)
345 PF04810 zf-Sec23_Sec24: Sec23 36.9 24 0.00052 23.0 1.6 32 106-137 4-35 (40)
346 KOG3940 Uncharacterized conser 36.7 14 0.0003 35.2 0.5 26 104-135 322-347 (351)
347 smart00064 FYVE Protein presen 36.6 22 0.00047 25.5 1.5 32 99-136 3-36 (68)
348 cd00350 rubredoxin_like Rubred 36.3 19 0.00042 22.4 1.0 22 107-134 4-25 (33)
349 cd00729 rubredoxin_SM Rubredox 35.6 21 0.00045 22.6 1.1 23 106-134 4-26 (34)
350 PF05876 Terminase_GpA: Phage 35.0 26 0.00056 36.1 2.3 51 88-138 184-241 (557)
351 smart00440 ZnF_C2C2 C2C2 Zinc 34.9 45 0.00098 21.8 2.6 31 106-136 2-38 (40)
352 COG0375 HybF Zn finger protein 34.2 21 0.00044 29.2 1.1 28 104-137 70-97 (115)
353 PRK08351 DNA-directed RNA poly 34.0 15 0.00032 26.7 0.2 35 105-149 4-38 (61)
354 KOG4537 Zn-ribbon-containing p 33.9 9.5 0.00021 32.8 -0.9 26 104-134 40-65 (178)
355 COG0846 SIR2 NAD-dependent pro 33.5 27 0.00059 32.3 1.9 19 175-193 162-180 (250)
356 COG3478 Predicted nucleic-acid 33.1 24 0.00053 25.9 1.2 15 125-139 39-53 (68)
357 PRK14973 DNA topoisomerase I; 32.3 24 0.00051 38.8 1.5 36 105-140 636-671 (936)
358 PF06750 DiS_P_DiS: Bacterial 32.2 30 0.00064 26.9 1.7 32 100-135 29-67 (92)
359 PRK00418 DNA gyrase inhibitor; 32.0 28 0.00061 25.3 1.4 28 104-134 6-34 (62)
360 PRK07956 ligA NAD-dependent DN 31.8 26 0.00057 36.9 1.7 24 103-130 403-426 (665)
361 PRK06260 threonine synthase; V 31.6 25 0.00055 34.3 1.4 24 105-134 4-27 (397)
362 COG4469 CoiA Competence protei 31.5 22 0.00048 34.2 1.0 13 105-117 26-38 (342)
363 cd00202 ZnF_GATA Zinc finger D 31.5 19 0.00041 25.2 0.4 31 106-136 1-31 (54)
364 TIGR01562 FdhE formate dehydro 31.4 20 0.00043 34.2 0.7 26 102-135 208-233 (305)
365 PF14206 Cys_rich_CPCC: Cystei 30.9 32 0.00069 26.2 1.6 28 106-136 3-30 (78)
366 KOG1842 FYVE finger-containing 30.7 14 0.00031 36.8 -0.4 36 94-135 168-205 (505)
367 PRK08271 anaerobic ribonucleos 30.6 30 0.00065 36.3 1.8 26 101-134 563-588 (623)
368 TIGR02820 formald_GSH S-(hydro 30.5 19 0.00042 31.7 0.4 28 170-197 134-162 (182)
369 COG1379 PHP family phosphoeste 30.2 16 0.00035 35.2 -0.2 26 106-134 248-273 (403)
370 COG1579 Zn-ribbon protein, pos 30.1 17 0.00037 33.4 0.0 36 103-138 196-233 (239)
371 PF04032 Rpr2: RNAse P Rpr2/Rp 30.1 32 0.00069 25.6 1.5 14 103-116 45-58 (85)
372 COG1066 Sms Predicted ATP-depe 29.6 29 0.00062 34.7 1.4 22 104-133 7-28 (456)
373 TIGR03037 anthran_nbaC 3-hydro 29.4 23 0.00049 30.6 0.6 10 106-115 116-125 (159)
374 PF09082 DUF1922: Domain of un 29.3 28 0.00061 25.8 1.0 15 179-193 41-57 (68)
375 TIGR02827 RNR_anaer_Bdell anae 29.2 29 0.00064 36.0 1.5 25 102-134 530-554 (586)
376 PF13005 zf-IS66: zinc-finger 29.2 25 0.00054 23.3 0.7 14 104-117 2-15 (47)
377 PRK00415 rps27e 30S ribosomal 28.9 32 0.00068 24.8 1.2 24 125-148 10-35 (59)
378 TIGR00575 dnlj DNA ligase, NAD 28.9 31 0.00066 36.3 1.6 26 104-133 392-419 (652)
379 PRK12722 transcriptional activ 28.9 64 0.0014 28.6 3.3 43 90-134 116-162 (187)
380 PRK08173 DNA topoisomerase III 28.9 31 0.00067 37.5 1.7 28 105-138 625-652 (862)
381 PF15616 TerY-C: TerY-C metal 28.8 32 0.0007 28.7 1.4 32 104-137 77-116 (131)
382 PF04828 GFA: Glutathione-depe 28.6 14 0.00031 27.4 -0.7 15 102-116 46-60 (92)
383 COG2023 RPR2 RNase P subunit R 28.5 42 0.00091 27.0 1.9 33 104-136 56-92 (105)
384 PRK14715 DNA polymerase II lar 28.3 29 0.00062 39.3 1.3 25 103-137 673-697 (1627)
385 KOG2463 Predicted RNA-binding 27.7 24 0.00052 34.0 0.5 14 104-117 257-270 (376)
386 PRK06556 vitamin B12-dependent 27.7 32 0.00069 37.8 1.5 32 98-135 918-949 (953)
387 PF10122 Mu-like_Com: Mu-like 27.7 28 0.0006 24.3 0.7 31 105-137 5-35 (51)
388 PF02132 RecR: RecR protein; 27.6 31 0.00068 22.6 0.9 23 93-115 6-28 (41)
389 PF09779 Ima1_N: Ima1 N-termin 27.6 42 0.00091 27.8 1.9 28 107-137 3-31 (131)
390 PF02318 FYVE_2: FYVE-type zin 27.6 43 0.00094 27.0 2.0 29 103-136 53-81 (118)
391 PRK08579 anaerobic ribonucleos 27.5 35 0.00077 35.7 1.8 24 103-134 567-590 (625)
392 PRK15103 paraquat-inducible me 27.3 39 0.00085 33.6 1.9 30 103-140 220-249 (419)
393 COG1867 TRM1 N2,N2-dimethylgua 26.2 36 0.00079 33.3 1.5 37 93-134 229-265 (380)
394 PRK06450 threonine synthase; V 26.2 35 0.00075 32.8 1.3 22 106-134 5-26 (338)
395 COG4307 Uncharacterized protei 26.2 22 0.00048 33.3 0.0 23 105-135 4-26 (349)
396 PF06906 DUF1272: Protein of u 26.1 19 0.0004 25.7 -0.4 14 127-140 42-55 (57)
397 PF00628 PHD: PHD-finger; Int 26.0 59 0.0013 21.6 2.1 23 106-135 1-23 (51)
398 PRK12860 transcriptional activ 25.9 75 0.0016 28.2 3.3 42 90-133 116-161 (189)
399 TIGR03829 YokU_near_AblA uncha 25.9 38 0.00082 26.4 1.2 34 125-163 34-67 (89)
400 COG1885 Uncharacterized protei 25.9 32 0.00069 27.7 0.8 22 178-200 82-103 (115)
401 KOG3475 60S ribosomal protein 25.8 15 0.00033 28.3 -1.0 29 101-136 13-41 (92)
402 PF14369 zf-RING_3: zinc-finge 25.5 42 0.00091 21.4 1.2 26 106-134 4-29 (35)
403 KOG1597 Transcription initiati 25.5 49 0.0011 31.4 2.1 31 106-137 2-32 (308)
404 PHA02998 RNA polymerase subuni 25.2 54 0.0012 28.9 2.2 36 103-138 142-183 (195)
405 COG2260 Predicted Zn-ribbon RN 25.1 40 0.00087 24.2 1.1 13 106-118 19-31 (59)
406 PRK00504 rpmG 50S ribosomal pr 25.0 32 0.00068 23.9 0.6 15 103-117 33-47 (50)
407 KOG3970 Predicted E3 ubiquitin 25.0 71 0.0015 29.3 2.9 49 95-143 38-111 (299)
408 PF05129 Elf1: Transcription e 24.7 47 0.001 25.3 1.5 34 103-136 21-56 (81)
409 PHA02031 putative DnaG-like pr 24.6 21 0.00045 33.4 -0.5 44 93-138 11-55 (266)
410 TIGR00595 priA primosomal prot 24.5 39 0.00084 34.3 1.4 24 103-135 239-262 (505)
411 TIGR03826 YvyF flagellar opero 24.4 25 0.00055 29.6 0.0 24 104-134 3-26 (137)
412 PRK07111 anaerobic ribonucleos 24.4 41 0.00089 35.9 1.6 25 101-134 677-701 (735)
413 KOG3362 Predicted BBOX Zn-fing 24.2 28 0.00062 29.6 0.3 24 102-136 116-139 (156)
414 TIGR00375 conserved hypothetic 24.0 32 0.0007 33.7 0.6 28 104-135 240-267 (374)
415 PRK07591 threonine synthase; V 23.8 41 0.00089 33.3 1.4 23 105-134 19-41 (421)
416 PF14149 YhfH: YhfH-like prote 23.8 11 0.00023 24.7 -1.8 26 103-132 12-37 (37)
417 PF01921 tRNA-synt_1f: tRNA sy 23.7 17 0.00037 35.4 -1.3 63 99-172 169-234 (360)
418 KOG0720 Molecular chaperone (D 23.6 23 0.00049 35.6 -0.5 64 102-176 325-388 (490)
419 PRK08270 anaerobic ribonucleos 23.4 45 0.00098 35.1 1.7 26 101-135 623-648 (656)
420 PF05280 FlhC: Flagellar trans 23.2 36 0.00078 29.8 0.8 44 89-134 115-162 (175)
421 PRK09263 anaerobic ribonucleos 22.9 52 0.0011 35.0 2.0 30 102-135 639-668 (711)
422 KOG0648 Predicted NUDIX hydrol 22.9 1.3E+02 0.0027 28.7 4.3 48 149-198 39-86 (295)
423 PRK03922 hypothetical protein; 22.7 42 0.00091 27.2 1.0 22 178-200 82-103 (113)
424 TIGR03844 cysteate_syn cysteat 22.5 47 0.001 32.7 1.5 21 106-133 4-24 (398)
425 PRK07220 DNA topoisomerase I; 22.4 57 0.0012 34.9 2.2 33 105-137 636-668 (740)
426 cd00065 FYVE FYVE domain; Zinc 21.9 55 0.0012 22.3 1.4 26 105-136 3-28 (57)
427 COG1198 PriA Primosomal protei 21.8 47 0.001 35.5 1.4 24 103-135 461-484 (730)
428 COG1655 Uncharacterized protei 21.7 31 0.00068 31.7 0.1 18 100-117 15-32 (267)
429 PF09151 DUF1936: Domain of un 21.7 70 0.0015 20.1 1.6 9 106-114 3-11 (36)
430 PF04423 Rad50_zn_hook: Rad50 21.6 29 0.00062 24.0 -0.1 11 106-116 22-32 (54)
431 TIGR02487 NrdD anaerobic ribon 21.6 55 0.0012 33.9 1.8 27 101-135 521-547 (579)
432 PRK05580 primosome assembly pr 21.6 51 0.0011 34.8 1.6 24 104-136 408-431 (679)
433 COG4643 Uncharacterized protei 21.6 69 0.0015 31.0 2.3 41 93-133 21-61 (366)
434 PRK14704 anaerobic ribonucleos 21.5 50 0.0011 34.6 1.5 25 101-134 556-580 (618)
435 PF06943 zf-LSD1: LSD1 zinc fi 21.4 67 0.0015 19.1 1.4 24 107-134 1-24 (25)
436 COG4416 Com Mu-like prophage p 21.4 26 0.00056 24.8 -0.4 31 105-137 5-35 (60)
437 PRK00085 recO DNA repair prote 21.3 48 0.001 29.8 1.2 40 93-133 138-177 (247)
438 KOG0909 Peptide:N-glycanase [P 21.2 70 0.0015 32.1 2.3 45 95-139 145-208 (500)
439 PF10005 DUF2248: Uncharacteri 21.1 75 0.0016 30.8 2.5 33 106-146 1-34 (343)
440 PF04161 Arv1: Arv1-like famil 21.1 59 0.0013 29.0 1.7 30 107-136 3-34 (208)
441 PRK06393 rpoE DNA-directed RNA 20.9 80 0.0017 23.1 2.0 37 103-149 4-40 (64)
442 PF04135 Nop10p: Nucleolar RNA 20.9 56 0.0012 23.0 1.2 17 103-119 15-32 (53)
443 PF00320 GATA: GATA zinc finge 20.8 14 0.00031 23.5 -1.7 28 107-134 1-28 (36)
444 PF13597 NRDD: Anaerobic ribon 20.4 47 0.001 34.1 1.1 26 102-136 489-514 (546)
445 PLN00209 ribosomal protein S27 20.2 70 0.0015 24.8 1.7 9 126-134 36-44 (86)
446 PF13821 DUF4187: Domain of un 20.2 43 0.00094 23.6 0.5 27 100-131 23-49 (55)
447 PRK00595 rpmG 50S ribosomal pr 20.1 45 0.00098 23.3 0.6 14 104-117 37-50 (53)
448 COG2995 PqiA Uncharacterized p 20.1 47 0.001 32.8 0.9 14 104-117 38-51 (418)
No 1
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.2e-44 Score=331.13 Aligned_cols=171 Identities=23% Similarity=0.338 Sum_probs=164.2
Q ss_pred cccceeccccccC-CCCCCcchHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEE
Q 022283 70 RASRVCATRSESN-QDATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLI 148 (299)
Q Consensus 70 ~~~~~~~~r~~~~-~~~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv 148 (299)
.++++.++|+++. +|..++.++++|+||++|+++|+|||+||++|... +++++++|++||..+||+++|+|++++
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 5778999999886 99999999999999999999999999999999998 789999999999999999999999999
Q ss_pred eeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEEEEEEEEEecCCCCC
Q 022283 149 EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKLKRPHFS 228 (299)
Q Consensus 149 ~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~~~~f~a~~~~~~~~ 228 (299)
.+++++||.++.+++ +|+|++.+||||+|||+|+|++||++||+||+|++++|+++|+||+++++|++|.+++.++++.
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 8999999999999999999999999999999999999999999999999999999999999988
Q ss_pred CC-CcceeeEEecCCC-CC
Q 022283 229 PG-PESSECRLFALDE-IP 245 (299)
Q Consensus 229 ~~-~E~~~~~W~~~de-L~ 245 (299)
++ .|+.|++||+.+| ++
T Consensus 231 ~d~~Eleda~WFs~~evl~ 249 (279)
T COG2816 231 PDEGELEDARWFSRDEVLP 249 (279)
T ss_pred CCcchhhhccccCHhHHhh
Confidence 88 7999999999999 55
No 2
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=100.00 E-value=4.3e-40 Score=302.46 Aligned_cols=171 Identities=20% Similarity=0.314 Sum_probs=158.2
Q ss_pred ccceeccccccCCCCCCcchHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEee
Q 022283 71 ASRVCATRSESNQDATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEH 150 (299)
Q Consensus 71 ~~~~~~~r~~~~~~~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~ 150 (299)
+.++.+||+++.+++.+++++++|+||.+|+++++|||+||+++... +++.++.|+.||..+||++.++|+++|.+
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 56677888887788999999999999999999999999999999876 67899999999999999999999999999
Q ss_pred CCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEEEEEEEEEecCCCCCCC
Q 022283 151 DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKLKRPHFSPG 230 (299)
Q Consensus 151 ~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~~~~f~a~~~~~~~~~~ 230 (299)
+++|||+|+.+.+ .|.|++|||+||+|||+++||+||++||||+++..++++++++|++++.+|++|.++..++++..+
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 9999999998776 799999999999999999999999999999999999999999999999999999999887776666
Q ss_pred -CcceeeEEecCCCCCC
Q 022283 231 -PESSECRLFALDEIPF 246 (299)
Q Consensus 231 -~E~~~~~W~~~deL~~ 246 (299)
+|+.+++||+++|++.
T Consensus 221 ~~Ei~~a~W~~~del~~ 237 (256)
T PRK00241 221 PKEIADAQWFRYDELPL 237 (256)
T ss_pred cccEEEEEEECHHHCcc
Confidence 7889999999999984
No 3
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=100.00 E-value=2e-38 Score=291.15 Aligned_cols=244 Identities=30% Similarity=0.374 Sum_probs=183.2
Q ss_pred Ccchhhhcccccccc-cceeecccCceeeeeeeeeecCCCCCccccccccccCCcccccccccccccccccccceecccc
Q 022283 1 MLKSVQILGSSSGFL-SLILKKSHNSCYGLSFVAVSTNPLPYSTARRHEIVSKTDSLVSPAFLTRRTRCFRASRVCATRS 79 (299)
Q Consensus 1 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~ 79 (299)
|++|.|+.+|.||++ +++.+..++. ++++++.++.+-. .+.-... .+. +|.+.|+..-
T Consensus 67 ~~~a~~~~~~~sg~~~~~~~~~~~~e-~~v~~~~~~~~e~----------------~l~~~~~-g~~-~F~~~r~~~~-- 125 (345)
T KOG3084|consen 67 MLDAVRIPGWESGLVISQDLTKDRKE-SSVSYIGSSLNES----------------QLTSSLG-GRI-SFVPLRMSMS-- 125 (345)
T ss_pred chhheecccccccceeeehhccCccc-ccceecccchhhh----------------hhcccCC-Cce-eeccchhhcc--
Confidence 789999999999999 6776666655 6666665333322 2222222 222 7777777542
Q ss_pred ccCCCCCCc-chHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecC--CCC--ceeecCCcEEEEEEE-eeC-C
Q 022283 80 ESNQDATSS-HPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICT--VCG--KIAYQNPKMVVGCLI-EHD-K 152 (299)
Q Consensus 80 ~~~~~~~~~-~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~--~Cg--~~~y~~p~~vV~~iv-~~~-~ 152 (299)
+.++++++ ++.+.|+++++|+.+++|||.||+++.+. ++|.+..|. .|. ...||+.+++|++++ +++ .
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 45566665 89999999999999999999999999988 667788888 688 888998887776554 555 4
Q ss_pred EEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecC-CCCEEEEEEEEEecC-CCCCCC
Q 022283 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP-RIGQIYIIFLAKLKR-PHFSPG 230 (299)
Q Consensus 153 kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p-~~~~~~~~f~a~~~~-~~~~~~ 230 (299)
++||.|+.+.+ +|+|++++||+|+|||+||||+||++||+|++|+.+.|+.+|+|| .+.++|+++.+-... +++..+
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 67777766554 899999999999999999999999999999999999999999999 788899888765544 455554
Q ss_pred --CcceeeEEecCCCCCC--------------CCCCCccHHHHHHHHHHHHHcCCce
Q 022283 231 --PESSECRLFALDEIPF--------------DSLAFSSISVTLQLFIDDIRMGKLN 271 (299)
Q Consensus 231 --~E~~~~~W~~~deL~~--------------~~laf~s~~~~l~~~l~~~~~g~~~ 271 (299)
.|++|++||+.+++.. ..+-+|....+..+++..+..+.+.
T Consensus 280 ~dlEleDaqwF~r~ev~~aL~~kg~~Rv~~~~a~i~~P~~~aIA~qLI~~~~~~~~~ 336 (345)
T KOG3084|consen 280 KDLELEDAQWFDREEVKSALTTKGLVRVQIEKALILIPPPFAIAHQLILHWVGFVPN 336 (345)
T ss_pred cchhhhhcccccHHHHHHHHHhcCCccccccCcceecCChhHHHHHHHHHHHccchh
Confidence 4899999999877531 0233444455555666666554443
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=4.6e-27 Score=194.04 Aligned_cols=128 Identities=53% Similarity=1.031 Sum_probs=115.9
Q ss_pred cCCCCceeecCCcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec
Q 022283 129 CTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI 208 (299)
Q Consensus 129 C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~ 208 (299)
||.||+++|++|.++|++++.++++|||++|...+..|.|++|||+||+||++++|++||++||||+++....+++.++.
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 99999999999999999998888999999998776678999999999999999999999999999999988888888888
Q ss_pred CCCCEEEEEEEEEecCCCCCCCCcceeeEEecCCCCCCCCCCCccHHH
Q 022283 209 PRIGQIYIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISV 256 (299)
Q Consensus 209 p~~~~~~~~f~a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~~~ 256 (299)
+..+..+++|.++...+.+..+.|..+++|+++++|++..++|++.+.
T Consensus 81 ~~~~~~~~~f~~~~~~~~~~~~~e~~~~~~~~~~~l~~~~l~~~~~~~ 128 (130)
T cd04511 81 PHISQVYMFYRARLLDLDFAPGPESLEVRLFTEEEIPWDELAFPTVRR 128 (130)
T ss_pred CCceEEEEEEEEEEcCCcccCCcchhceEEECHHHCCchhcccccccc
Confidence 877788899999998776666788889999999999988999987654
No 5
>COG1051 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]
Probab=99.86 E-value=2.5e-21 Score=163.91 Aligned_cols=120 Identities=35% Similarity=0.581 Sum_probs=98.7
Q ss_pred ceeecCCcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCC--
Q 022283 134 KIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI-- 211 (299)
Q Consensus 134 ~~~y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~-- 211 (299)
...|++|.++|.+++..+++|||+||+..|..|.|++|||+||.|||+++||.||++||||+++..++++++++.+..
T Consensus 3 ~~~~~~p~~~v~~~i~~~~~iLLvrR~~~p~~g~WalPGG~ve~GEt~eeaa~REl~EETgL~~~~~~~~~v~~~~~rd~ 82 (145)
T COG1051 3 AMGYRTPLVAVGALIVRNGRILLVRRANEPGAGYWALPGGFVEIGETLEEAARRELKEETGLRVRVLELLAVFDDPGRDP 82 (145)
T ss_pred cccCCCcceeeeEEEEeCCEEEEEEecCCCCCCcEeCCCccCCCCCCHHHHHHHHHHHHhCCcccceeEEEEecCCCCCC
Confidence 456889999999999998999999999998889999999999999999999999999999999999999998887653
Q ss_pred --CEEEEEEEEEecCCCCCCC--CcceeeEEecCCCCCCCCCCCcc
Q 022283 212 --GQIYIIFLAKLKRPHFSPG--PESSECRLFALDEIPFDSLAFSS 253 (299)
Q Consensus 212 --~~~~~~f~a~~~~~~~~~~--~E~~~~~W~~~deL~~~~laf~s 253 (299)
+...++|.+....++.... ++..++.||+.++|+...+....
T Consensus 83 r~~~v~~~~~~~~~~g~~~~~~~~d~~~~~~~~~~~l~~~~~~~~~ 128 (145)
T COG1051 83 RGHHVSFLFFAAEPEGELLAGDGDDAAEVGWFPLDELPELPLPLAF 128 (145)
T ss_pred ceeEEEEEEEEEecCCCcccCChhhHhhcceecHhHcccccccccc
Confidence 3444555555544544433 47888999999999964454433
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=9.8e-21 Score=155.27 Aligned_cols=118 Identities=25% Similarity=0.426 Sum_probs=92.4
Q ss_pred EEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec--CCC----CEEEEEE
Q 022283 145 GCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI--PRI----GQIYIIF 218 (299)
Q Consensus 145 ~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~--p~~----~~~~~~f 218 (299)
++|++.+++|||++|...+..|.|.+|||++|.|||+++||.||++||||+++..+.+++.... +.. +...++|
T Consensus 6 ~~i~~~~~~vLL~~r~~~~~~~~w~~PgG~ve~gEs~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (130)
T cd04681 6 VLILNEDGELLVVRRAREPGKGTLDLPGGFVDPGESAEEALIREIREETGLKVTELSYLFSLPNTYPYGGMEYDTLDLFF 85 (130)
T ss_pred EEEEcCCCcEEEEEecCCCCCCcEeCCceeecCCCCHHHHHHHHHHHHhCCcccceeEEEeecceeeeCCceeEEEEEEE
Confidence 3344556899999998766678999999999999999999999999999999988877765432 111 1233567
Q ss_pred EEEecCCCCCCC-CcceeeEEecCCCCCCCCCCCccHHHHHHHHH
Q 022283 219 LAKLKRPHFSPG-PESSECRLFALDEIPFDSLAFSSISVTLQLFI 262 (299)
Q Consensus 219 ~a~~~~~~~~~~-~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l 262 (299)
.+.+.......+ +|+.+++|+++++|+...+.+++.+.++++|+
T Consensus 86 ~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~~~~~~~~~~ 130 (130)
T cd04681 86 VCQVDDKPIVKAPDDVAELKWVVPQDIELENFAFPSIRQAVERWL 130 (130)
T ss_pred EEEeCCCCCcCChHHhheeEEecHHHCCcccCCcHHHHHHHHhhC
Confidence 787765543333 78899999999999877899998888888764
No 7
>PLN02325 nudix hydrolase
Probab=99.84 E-value=1.5e-20 Score=158.68 Aligned_cols=125 Identities=20% Similarity=0.233 Sum_probs=93.9
Q ss_pred eeecCCcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCC----
Q 022283 135 IAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPR---- 210 (299)
Q Consensus 135 ~~y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~---- 210 (299)
..|+.|.+.|.+++.++++|||+||...+..|.|.+|||+||.|||+++||+||++||||+++...++++.....+
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 3578899999999988899999999876657899999999999999999999999999999998888877644311
Q ss_pred --CCEEEEEEEEEecCCCCC---CC-CcceeeEEecCCCCCCCCCCCccHHHHHHHH
Q 022283 211 --IGQIYIIFLAKLKRPHFS---PG-PESSECRLFALDEIPFDSLAFSSISVTLQLF 261 (299)
Q Consensus 211 --~~~~~~~f~a~~~~~~~~---~~-~E~~~~~W~~~deL~~~~laf~s~~~~l~~~ 261 (299)
.+...++|.+...++... .. +|..+++||++++|+ ...+...+.++..|
T Consensus 83 ~~~~~i~~~f~~~~~~~~~~~~~~e~~e~~~~~W~~~d~Lp--~~~~~p~~~~~~~~ 137 (144)
T PLN02325 83 KPSHYVTVFMRAVLADPSQVPQNLEPEKCYGWDWYEWDNLP--EPLFWPLEKLVGSG 137 (144)
T ss_pred CCcEEEEEEEEEEECCCCCCCCcCCchhcCceEEEChHHCC--hhhhHHHHHHHHcC
Confidence 123456677776554321 12 456789999999999 33344444444443
No 8
>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=99.82 E-value=8.5e-20 Score=149.04 Aligned_cols=106 Identities=26% Similarity=0.363 Sum_probs=84.2
Q ss_pred CcEEEEEEEe-eCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecC----CCCEE
Q 022283 140 PKMVVGCLIE-HDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP----RIGQI 214 (299)
Q Consensus 140 p~~vV~~iv~-~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p----~~~~~ 214 (299)
|++.|++++. .+++|||++|...+..|.|.+|||++|+|||+++||+||++||||+++....+++..... ..+.+
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 4566666654 458999999987665789999999999999999999999999999999888877755432 23455
Q ss_pred EEEEEEEecCCCCC-C-CCcceeeEEecCCCCC
Q 022283 215 YIIFLAKLKRPHFS-P-GPESSECRLFALDEIP 245 (299)
Q Consensus 215 ~~~f~a~~~~~~~~-~-~~E~~~~~W~~~deL~ 245 (299)
.++|.+....+... . .+|..+++|+++++++
T Consensus 81 ~~~f~~~~~~~~~~~~~~~E~~~~~W~~~~~l~ 113 (125)
T cd04679 81 APVYLAENFSGEPRLMEPDKLLELGWFALDALP 113 (125)
T ss_pred EEEEEEeecCCccccCCCccccEEEEeCHHHCC
Confidence 67788887665432 2 3688999999999998
No 9
>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=99.82 E-value=8.6e-20 Score=150.60 Aligned_cols=120 Identities=23% Similarity=0.270 Sum_probs=92.7
Q ss_pred EEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCC----CEEEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI----GQIYIIF 218 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~----~~~~~~f 218 (299)
+|++++.+++++||++|.+. ..+.|.+|||++|+|||+++||.||++||||+++....+++.+.+..+ ...+++|
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 56778888899999999876 468999999999999999999999999999999988777776554322 2344678
Q ss_pred EEEecCCCC--CCCCcceeeEEecCCCCCCCC--CCCccHHHHHHHHHH
Q 022283 219 LAKLKRPHF--SPGPESSECRLFALDEIPFDS--LAFSSISVTLQLFID 263 (299)
Q Consensus 219 ~a~~~~~~~--~~~~E~~~~~W~~~deL~~~~--laf~s~~~~l~~~l~ 263 (299)
.+.+..+.. ..++|+.++.|+++++++... +..+...+.+..|+.
T Consensus 81 ~~~~~~~~~~~~~~~e~~~~~w~~~~el~~~~~~~~~~~~~~~i~~~l~ 129 (134)
T cd03675 81 AAELLEHLPDQPLDSGIVRAHWLTLEEILALAARLRSPLVLRCIEDYLA 129 (134)
T ss_pred EEEECCCCCCCCCCCCceeeEEEeHHHHHhhhhhhcCchHHHHHHHHHh
Confidence 888766543 334788899999999998543 345556666666664
No 10
>PRK15434 GDP-mannose mannosyl hydrolase NudD; Provisional
Probab=99.82 E-value=8.2e-20 Score=156.97 Aligned_cols=115 Identities=16% Similarity=0.249 Sum_probs=86.2
Q ss_pred CCcEEEEEEEee-CCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCcee--eccceeeeec----C--
Q 022283 139 NPKMVVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVE--VQSPFAQLDI----P-- 209 (299)
Q Consensus 139 ~p~~vV~~iv~~-~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~--~~~~~~~~~~----p-- 209 (299)
.|.++|.++|.+ +++|||+||...+..|.|++|||+||+|||+++||+||++||||+++. ..++++.+.. .
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 589999999876667999999999999999999999999999999974 3355543221 1
Q ss_pred ----CCCEEEEEEEEEecCCCCCCC-CcceeeEEecCCCCCCCCCCCcc
Q 022283 210 ----RIGQIYIIFLAKLKRPHFSPG-PESSECRLFALDEIPFDSLAFSS 253 (299)
Q Consensus 210 ----~~~~~~~~f~a~~~~~~~~~~-~E~~~~~W~~~deL~~~~laf~s 253 (299)
..+.++++|.++...+++... +|+.+++|+++++++......+.
T Consensus 95 ~~~~~~~~i~~~f~~~~~~g~~~~~~~E~~~~~W~~~~el~~~~~~~~~ 143 (159)
T PRK15434 95 GTDFTTHYVVLGFRLRVAEEDLLLPDEQHDDYRWLTPDALLASDNVHAN 143 (159)
T ss_pred CCccceEEEEEEEEEEecCCcccCChHHeeEEEEEeHHHhhhccccCHH
Confidence 113455778888877766554 68999999999999854343333
No 11
>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=99.82 E-value=8.6e-20 Score=153.86 Aligned_cols=111 Identities=22% Similarity=0.354 Sum_probs=86.3
Q ss_pred CCcEEEEEEEee-CCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeec--cceeeeec-------
Q 022283 139 NPKMVVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ--SPFAQLDI------- 208 (299)
Q Consensus 139 ~p~~vV~~iv~~-~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~--~~~~~~~~------- 208 (299)
.|.++|.++|.+ +++|||+||...|.+|.|.+|||+||.|||+++||+||++||||+++... ++++....
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 456677777765 58999999987666899999999999999999999999999999998766 66554431
Q ss_pred -CC--CCEEEEEEEEEecCCCCC-CCCcceeeEEecCCCCCCCCC
Q 022283 209 -PR--IGQIYIIFLAKLKRPHFS-PGPESSECRLFALDEIPFDSL 249 (299)
Q Consensus 209 -p~--~~~~~~~f~a~~~~~~~~-~~~E~~~~~W~~~deL~~~~l 249 (299)
+. .+...++|.+....+.+. ..+|..+++|+++++++....
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~ 134 (144)
T cd03430 90 GDDFSTHYVVLGYVLKLSSNELLLPDEQHSEYQWLTSDELLADDD 134 (144)
T ss_pred cCCCccEEEEEEEEEEEcCCcccCCchhccEeEEecHHHHhcCCC
Confidence 11 134567788887766533 447899999999999985433
No 12
>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=99.82 E-value=7e-20 Score=151.79 Aligned_cols=122 Identities=24% Similarity=0.281 Sum_probs=94.2
Q ss_pred EEEEEEee-CCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEEEEEEEEE
Q 022283 143 VVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAK 221 (299)
Q Consensus 143 vV~~iv~~-~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~~~~f~a~ 221 (299)
+|.+.+.+ ++++||++|+..+ .|.|++|||+++.|||+++||.||++||||+++..+.+++...+...+..+++|.+.
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 44444444 4899999998765 789999999999999999999999999999999988888877666667778889998
Q ss_pred ecCCCCCCC-CcceeeEEecCCCCCCC---CCCCccHHHHHHHHHHHH
Q 022283 222 LKRPHFSPG-PESSECRLFALDEIPFD---SLAFSSISVTLQLFIDDI 265 (299)
Q Consensus 222 ~~~~~~~~~-~E~~~~~W~~~deL~~~---~laf~s~~~~l~~~l~~~ 265 (299)
...+++..+ +|+.++.|++++++... ...++......+..++..
T Consensus 81 ~~~~~~~~~~~E~~~~~w~~~~el~~~~~~~~~~~~~~~~~~~~~~~~ 128 (131)
T cd03429 81 ADSGEIVVDDDELEDARWFSRDEVRAAGEGLPELPPPGSIARQLIEAW 128 (131)
T ss_pred EcCCcccCCchhhhccEeecHHHHhhcccCCccCCCcchHHHHHHHHH
Confidence 876655544 78889999999997643 344444444444444443
No 13
>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=9e-20 Score=148.22 Aligned_cols=114 Identities=27% Similarity=0.377 Sum_probs=88.0
Q ss_pred EEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec----CC----CCEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----PR----IGQI 214 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~----p~----~~~~ 214 (299)
.|.+|+.++++|||++|...+.+|.|.+|||+||+|||+++||+||++||||+++....+++...+ +. .+..
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 455667777999999998766579999999999999999999999999999999988887775443 22 1456
Q ss_pred EEEEEEEecCCCC---CCCCcceeeEEecCCCCCCCCCCCccHHHH
Q 022283 215 YIIFLAKLKRPHF---SPGPESSECRLFALDEIPFDSLAFSSISVT 257 (299)
Q Consensus 215 ~~~f~a~~~~~~~---~~~~E~~~~~W~~~deL~~~~laf~s~~~~ 257 (299)
.++|.+....+.. ...+|..+++|+++++++. ....+..+.+
T Consensus 82 ~~~f~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~-~~~~~~~~~a 126 (128)
T cd04684 82 CVFYDARVVGGALPVQEPGEDSHGAAWLPLDEAIE-RLLSPLVLWA 126 (128)
T ss_pred EEEEEEEEecCccccCCCCCCceeeEEECHHHhhc-cCCCHHHHHh
Confidence 6788888876652 3347788999999999984 3334544433
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=2e-19 Score=148.74 Aligned_cols=120 Identities=27% Similarity=0.388 Sum_probs=93.8
Q ss_pred EEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCC----CCEEEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPR----IGQIYIIF 218 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~----~~~~~~~f 218 (299)
+..+++.++++|||++|...+..|.|.+|||+||.|||+++||+||++||||+++....+++...+.. ....+++|
T Consensus 3 ~~~~~i~~~~~vLL~~r~~~~~~~~w~~PgG~ve~gEs~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~f 82 (137)
T cd03427 3 TTLCFIKDPDKVLLLNRKKGPGWGGWNGPGGKVEPGETPEECAIRELKEETGLTIDNLKLVGIIKFPFPGEEERYGVFVF 82 (137)
T ss_pred EEEEEEEECCEEEEEEecCCCCCCeEeCCceeCCCCCCHHHHHHHHHHHhhCeEeecceEEEEEEEEcCCCCcEEEEEEE
Confidence 45566777799999999876557899999999999999999999999999999999888887766533 23455667
Q ss_pred EEEecCCCCCCCCcceeeEEecCCCCCCCCCCCccHHHHHHHHHH
Q 022283 219 LAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLFID 263 (299)
Q Consensus 219 ~a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l~ 263 (299)
.+....+.....+|..+++|+++++++...+ .+....++..+++
T Consensus 83 ~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~-~~~~~~~l~~~~~ 126 (137)
T cd03427 83 LATEFEGEPLKESEEGILDWFDIDDLPLLPM-WPGDREWLPLMLE 126 (137)
T ss_pred EECCcccccCCCCccccceEEcHhhcccccC-CCCcHHHHHHHhC
Confidence 7776665554345667899999999985444 4556777777774
No 15
>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=99.80 E-value=3.6e-19 Score=144.02 Aligned_cols=104 Identities=28% Similarity=0.369 Sum_probs=80.2
Q ss_pred EEEEEEeeCCEEEEEEeecCC-CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCcee--eccceeeeecCC---CCEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVE--VQSPFAQLDIPR---IGQIYI 216 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p-~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~--~~~~~~~~~~p~---~~~~~~ 216 (299)
.|.+++.++++|||+||...+ .+|.|.+|||++|+|||+++||+||++||||+++. .+.+++.+.... .+.+++
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 466777778999999987643 26899999999999999999999999999999987 455565544322 245567
Q ss_pred EEEEEecCCCCC-C-CCcceeeEEecCCCCCC
Q 022283 217 IFLAKLKRPHFS-P-GPESSECRLFALDEIPF 246 (299)
Q Consensus 217 ~f~a~~~~~~~~-~-~~E~~~~~W~~~deL~~ 246 (299)
+|.+....+... . .+|..+++|+++++++.
T Consensus 82 ~f~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~ 113 (120)
T cd04683 82 FFTVRRWSGEPRNCEPDKCAELRWFPLDALPD 113 (120)
T ss_pred EEEEEeecCccccCCCCcEeeEEEEchHHCcc
Confidence 787876555432 2 36788999999999984
No 16
>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=99.80 E-value=4.4e-19 Score=143.17 Aligned_cols=106 Identities=29% Similarity=0.508 Sum_probs=83.5
Q ss_pred EEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCC--------CCEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPR--------IGQI 214 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~--------~~~~ 214 (299)
+|++++.++++|||++|.+.+..+.|.+|||++++|||+++||+||++||||+++....+++...... .+..
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 45556666789999999876657899999999999999999999999999999998877776544321 1234
Q ss_pred EEEEEEEecCCCCCCCCcceeeEEecCCCCCCCC
Q 022283 215 YIIFLAKLKRPHFSPGPESSECRLFALDEIPFDS 248 (299)
Q Consensus 215 ~~~f~a~~~~~~~~~~~E~~~~~W~~~deL~~~~ 248 (299)
++.|.+....++....+|..+++|++++++....
T Consensus 82 ~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~~~ 115 (122)
T cd04673 82 LIDFLCRYLGGEPVAGDDALDARWVPLDELAALS 115 (122)
T ss_pred EEEEEEEeCCCcccCCcccceeEEECHHHHhhCc
Confidence 5667887766665555788899999999998433
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=99.80 E-value=5.9e-19 Score=144.21 Aligned_cols=105 Identities=27% Similarity=0.334 Sum_probs=81.2
Q ss_pred CcEEEEEEEee-CCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec---C----CC
Q 022283 140 PKMVVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI---P----RI 211 (299)
Q Consensus 140 p~~vV~~iv~~-~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~---p----~~ 211 (299)
|.++|.++|.+ +++|||+||.. ..|.|.+|||++++|||+++||+||++||||+++..+.++..... + ..
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 44566666655 78999998764 368999999999999999999999999999999987776554322 1 12
Q ss_pred CEEEEEEEEEecCCCCCCCCcceeeEEecCCCCCC
Q 022283 212 GQIYIIFLAKLKRPHFSPGPESSECRLFALDEIPF 246 (299)
Q Consensus 212 ~~~~~~f~a~~~~~~~~~~~E~~~~~W~~~deL~~ 246 (299)
+..++.|.+....+++..++|..+++|++++++..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~ 113 (125)
T cd04696 79 HFVLFDFFARTDGTEVTPNEEIVEWEWVTPEEALD 113 (125)
T ss_pred EEEEEEEEEEecCCcccCCcccceeEEECHHHHhc
Confidence 34456677877655566668899999999999983
No 18
>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=99.79 E-value=6.7e-19 Score=144.33 Aligned_cols=108 Identities=29% Similarity=0.398 Sum_probs=84.7
Q ss_pred CcEEEEEEEee-CCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec----CCCCEE
Q 022283 140 PKMVVGCLIEH-DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----PRIGQI 214 (299)
Q Consensus 140 p~~vV~~iv~~-~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~----p~~~~~ 214 (299)
|.++|.+++.+ +++|||++|...+..|.|.+|||+|++|||+++||+||++||||+++....+++.... ...+..
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 56677777665 4899999998755578999999999999999999999999999999988777664432 223456
Q ss_pred EEEEEEEecCCCCCC---C-CcceeeEEecCCCCCCC
Q 022283 215 YIIFLAKLKRPHFSP---G-PESSECRLFALDEIPFD 247 (299)
Q Consensus 215 ~~~f~a~~~~~~~~~---~-~E~~~~~W~~~deL~~~ 247 (299)
.++|.+....++... . +|..+++|+++++++..
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~ 117 (129)
T cd04678 81 TIFVKAEVDDGEAEPNKMEPEKCEGWEWFDWEELPSV 117 (129)
T ss_pred EEEEEEEeCCCCcccCCCCCceeCceEEeCHHHCCCc
Confidence 677888877654322 2 56778999999999954
No 19
>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=99.79 E-value=6.6e-19 Score=142.96 Aligned_cols=101 Identities=25% Similarity=0.337 Sum_probs=79.3
Q ss_pred EEEEEeeCCEEEEEEeecCC--CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCC-CEEEEEEEE
Q 022283 144 VGCLIEHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI-GQIYIIFLA 220 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p--~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~-~~~~~~f~a 220 (299)
|++++.++++|||+||...+ .+|.|++|||++|+|||+++||+||++||||+++....++..+..+.. ...+++|.+
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 33444456999999997653 478999999999999999999999999999999876776666555433 345567777
Q ss_pred EecCCCCCCCCcceeeEEecCCCCC
Q 022283 221 KLKRPHFSPGPESSECRLFALDEIP 245 (299)
Q Consensus 221 ~~~~~~~~~~~E~~~~~W~~~deL~ 245 (299)
....+.+.. +|..+++|+++++++
T Consensus 83 ~~~~~~~~~-~E~~~~~W~~~~~l~ 106 (117)
T cd04691 83 TFWQGEIPA-QEAAEVHWMTANDIV 106 (117)
T ss_pred EEecCCCCc-ccccccEEcCHHHcc
Confidence 766665433 788899999999998
No 20
>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=99.79 E-value=3.9e-19 Score=145.05 Aligned_cols=107 Identities=28% Similarity=0.402 Sum_probs=87.4
Q ss_pred CEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCC------CCEEEEEEEEEecCC
Q 022283 152 KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPR------IGQIYIIFLAKLKRP 225 (299)
Q Consensus 152 ~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~------~~~~~~~f~a~~~~~ 225 (299)
++|||++|.+ .+.|.+|||++++|||+++||.||++||||+++..+..++.+.+++ .+..+.+|.+....+
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 7999999874 3789999999999999999999999999999999888777655433 234566788877666
Q ss_pred CCC--CCCcceeeEEecCCCCCCCCCCCccHHHHHHHHH
Q 022283 226 HFS--PGPESSECRLFALDEIPFDSLAFSSISVTLQLFI 262 (299)
Q Consensus 226 ~~~--~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l 262 (299)
+.. ..+|..+++|++++++. ..+.++..+.++..++
T Consensus 93 ~~~~~~~~E~~~~~W~~~~el~-~~~~~~~~~~~l~~~~ 130 (131)
T cd03673 93 EFTPQPDEEVDEVRWLPPDEAR-DRLSYPNDRELLRAAL 130 (131)
T ss_pred CcccCCCCcEEEEEEcCHHHHH-HHcCCHhHHHHHHHhh
Confidence 555 35788899999999998 4567888888887765
No 21
>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=99.79 E-value=9.2e-19 Score=143.82 Aligned_cols=102 Identities=25% Similarity=0.403 Sum_probs=82.1
Q ss_pred EEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEEEEEEEEEe
Q 022283 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKL 222 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~~~~f~a~~ 222 (299)
+.+++++.+++|||++|.+.+..+.|.+|||+||.|||+++||+||++||||+++....++.....+ .+..+++|.++.
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 3344455678999999987666789999999999999999999999999999999888877655433 456678898988
Q ss_pred cCCCCCC----CCcceeeEEecCCCCC
Q 022283 223 KRPHFSP----GPESSECRLFALDEIP 245 (299)
Q Consensus 223 ~~~~~~~----~~E~~~~~W~~~deL~ 245 (299)
.++.+.. +.|+.+++|+++++++
T Consensus 82 ~~g~~~~~~~~~~e~~~~~W~~~~el~ 108 (123)
T cd04671 82 TGGDLKTEKEADSESLQARWYSNKDLP 108 (123)
T ss_pred eCCeEccCCCCCcceEEEEEECHHHCC
Confidence 7765332 2567799999999996
No 22
>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=7.8e-19 Score=141.50 Aligned_cols=108 Identities=27% Similarity=0.355 Sum_probs=83.3
Q ss_pred EEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCcee-eccceeeeecCC--CCEEEEEEEEEec
Q 022283 147 LIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVE-VQSPFAQLDIPR--IGQIYIIFLAKLK 223 (299)
Q Consensus 147 iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~-~~~~~~~~~~p~--~~~~~~~f~a~~~ 223 (299)
+++.+++|||++|+.. +.|.+|||++++|||+++||+||++||||+.+. ....++.+.... ....+++|.+...
T Consensus 7 i~~~~~~vLL~~r~~~---~~w~~PgG~ve~gEt~~~aa~REl~EEtG~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~ 83 (120)
T cd04680 7 VTDADGRVLLVRHTYG---PGWYLPGGGLERGETFAEAARRELLEELGIRLAVVAELLGVYYHSASGSWDHVIVFRARAD 83 (120)
T ss_pred EECCCCeEEEEEECCC---CcEeCCCCcCCCCCCHHHHHHHHHHHHHCCccccccceEEEEecCCCCCceEEEEEEeccc
Confidence 3455689999998743 489999999999999999999999999999998 888777665533 3456678888877
Q ss_pred CCC-CCCCCcceeeEEecCCCCCCCCCCCccHHHHHH
Q 022283 224 RPH-FSPGPESSECRLFALDEIPFDSLAFSSISVTLQ 259 (299)
Q Consensus 224 ~~~-~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~ 259 (299)
.+. ...++|..+++||++++++. ...+..+..+.
T Consensus 84 ~~~~~~~~~E~~~~~w~~~~~l~~--~~~~~~~~~~~ 118 (120)
T cd04680 84 TQPVIRPSHEISEARFFPPDALPE--PTTPATRRRIA 118 (120)
T ss_pred CCCccCCcccEEEEEEECHHHCcc--cCChHHHHHhh
Confidence 655 33447889999999999993 33344444443
No 23
>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=1.3e-18 Score=142.01 Aligned_cols=109 Identities=38% Similarity=0.564 Sum_probs=85.4
Q ss_pred CcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecC---C----CC
Q 022283 140 PKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP---R----IG 212 (299)
Q Consensus 140 p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p---~----~~ 212 (299)
|.+.|.++|.++++|||++|+. .|.|.+|||+|++|||+++||+||++||||+.+...++++..... . .+
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 4567777777779999999874 689999999999999999999999999999999777766654321 1 12
Q ss_pred EEEEEEEEEecCCCCCCCCcceeeEEecCCCCCCCCCCCcc
Q 022283 213 QIYIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSS 253 (299)
Q Consensus 213 ~~~~~f~a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s 253 (299)
..+++|.+....+.+...+|..+++|+++++++ .+.++.
T Consensus 78 ~~~~~f~~~~~~~~~~~~~E~~~~~W~~~~el~--~l~~~~ 116 (123)
T cd04672 78 VYKLFFLCEILGGEFKPNIETSEVGFFALDDLP--PLSEKR 116 (123)
T ss_pred EEEEEEEEEecCCcccCCCceeeeEEECHHHCc--ccccCC
Confidence 344678888776665556888999999999998 455544
No 24
>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=99.78 E-value=2e-18 Score=140.89 Aligned_cols=101 Identities=26% Similarity=0.315 Sum_probs=78.6
Q ss_pred EEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEEEEEEEEEecC
Q 022283 145 GCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKLKR 224 (299)
Q Consensus 145 ~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~~~~f~a~~~~ 224 (299)
++|++++++|||++|.... .+.|.+|||+||.|||+++||+||++||||+++.....++.+..+ +...++|.+...+
T Consensus 5 ~ii~~~~~~vLL~~r~~~~-~~~w~lPGG~ve~gEs~~~a~~REl~EEtGl~~~~~~~~~~~~~~--~~~~~~f~~~~~~ 81 (121)
T cd04669 5 IVIINDQGEILLIRRIKPG-KTYYVFPGGGIEEGETPEEAAKREALEELGLDVRVEEIFLIVNQN--GRTEHYFLARVIS 81 (121)
T ss_pred EEEEeCCCEEEEEEEecCC-CCcEECCceeccCCCCHHHHHHHHHHHhhCeeEeeeeEEEEEeeC--CcEEEEEEEEEEC
Confidence 3445555899999987543 688999999999999999999999999999999887777776653 4456788888776
Q ss_pred CCCCC----------CCcceeeEEecCCCCCCCC
Q 022283 225 PHFSP----------GPESSECRLFALDEIPFDS 248 (299)
Q Consensus 225 ~~~~~----------~~E~~~~~W~~~deL~~~~ 248 (299)
+++.. +.+..+++|+++++|+...
T Consensus 82 g~~~~~~~~e~~~~~~~~~~~~~Wv~~~el~~l~ 115 (121)
T cd04669 82 GKLGLGVGEEFERQSDDNQYHPVWVDLDQLETIP 115 (121)
T ss_pred CeecCCCchhhcccCCCCceEEEEEEHHHcccCC
Confidence 55322 1234568999999999433
No 25
>PRK15472 nucleoside triphosphatase NudI; Provisional
Probab=99.78 E-value=1.6e-18 Score=144.79 Aligned_cols=108 Identities=23% Similarity=0.276 Sum_probs=77.5
Q ss_pred cEEEEEEEeeCCEEEEEEeecCC--CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccce-----e---eeecCC
Q 022283 141 KMVVGCLIEHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPF-----A---QLDIPR 210 (299)
Q Consensus 141 ~~vV~~iv~~~~kILL~rr~~~p--~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~-----~---~~~~p~ 210 (299)
..++++++.++++|||+||+..+ .+|.|++|||++|+|||+++||.||++||||+++...... . ...++.
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 45677778788999999987543 3699999999999999999999999999999987543211 0 111222
Q ss_pred CC--EEE---EEEEEEecCCCCCCCCcceeeEEecCCCCCCCC
Q 022283 211 IG--QIY---IIFLAKLKRPHFSPGPESSECRLFALDEIPFDS 248 (299)
Q Consensus 211 ~~--~~~---~~f~a~~~~~~~~~~~E~~~~~W~~~deL~~~~ 248 (299)
.. ..+ ++|.+....+++..++|+.+++|+++++++...
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~l~ 126 (141)
T PRK15472 84 GRKEEIYMIYLIFDCVSANRDVKINEEFQDYAWVKPEDLVHYD 126 (141)
T ss_pred CCceeEEEEEEEEEeecCCCcccCChhhheEEEccHHHhcccc
Confidence 11 222 334454445555666889999999999999433
No 26
>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=99.78 E-value=1.2e-18 Score=146.29 Aligned_cols=111 Identities=23% Similarity=0.297 Sum_probs=86.9
Q ss_pred eeecCCcEEEEEEEe-eCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCC-
Q 022283 135 IAYQNPKMVVGCLIE-HDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG- 212 (299)
Q Consensus 135 ~~y~~p~~vV~~iv~-~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~- 212 (299)
.+|+....+|++++. .++++||++|...+..|.|++|||+|++|||+++||+||++||||+++....+++.+......
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 456777777776665 467999999876666799999999999999999999999999999999888877765432222
Q ss_pred --EEEEEEEEEecCCC--CCCCCcceeeEEecCCCCC
Q 022283 213 --QIYIIFLAKLKRPH--FSPGPESSECRLFALDEIP 245 (299)
Q Consensus 213 --~~~~~f~a~~~~~~--~~~~~E~~~~~W~~~deL~ 245 (299)
...++|.+....+. +...+|+.+++||+++++.
T Consensus 87 ~~~~~~~f~~~~~~~~~~~~~~~E~~~~~w~~~~el~ 123 (142)
T cd04700 87 VLVLRHVWLAEPEGQTLAPKFTDEIAEASFFSREDVA 123 (142)
T ss_pred cEEEEEEEEEEecCCccccCCCCCEEEEEEECHHHhh
Confidence 23467888875543 2334789999999999988
No 27
>PRK09438 nudB dihydroneopterin triphosphate pyrophosphatase; Provisional
Probab=99.78 E-value=8.8e-19 Score=147.49 Aligned_cols=125 Identities=21% Similarity=0.193 Sum_probs=88.8
Q ss_pred ecCCcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCce--eeccceee--------e
Q 022283 137 YQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADV--EVQSPFAQ--------L 206 (299)
Q Consensus 137 y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v--~~~~~~~~--------~ 206 (299)
|..+..+++++++.+++|||++|... ++.|++|||++|+|||+++||+||++||||+++ ....++.. +
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 33445555566667889999988643 588999999999999999999999999999998 43333210 0
Q ss_pred e-----cC--CCCEEEEEEEEEecCCCCCCCCcceeeEEecCCCCCCCCCCCccHHHHHHHHHHH
Q 022283 207 D-----IP--RIGQIYIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLFIDD 264 (299)
Q Consensus 207 ~-----~p--~~~~~~~~f~a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l~~ 264 (299)
+ ++ ..+...++|.+....+.....+|..+++|++++++.. ....++.+.+++.++..
T Consensus 82 ~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~E~~~~~W~~~~e~~~-~~~~~~~~~~l~~~~~~ 145 (148)
T PRK09438 82 PHWRHRYAPGVTRNTEHWFCLALPHERPVVLTEHLAYQWLDAREAAA-LTKSWSNAEAIEQLVIR 145 (148)
T ss_pred hhhhhccccccCCceeEEEEEecCCCCccccCcccceeeCCHHHHHH-HhcChhHHHHHHHHHHH
Confidence 0 01 1234567788876544222225889999999999984 34567778888877654
No 28
>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=99.77 E-value=3.1e-18 Score=140.51 Aligned_cols=106 Identities=26% Similarity=0.300 Sum_probs=80.5
Q ss_pred EEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec----------CCC
Q 022283 142 MVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----------PRI 211 (299)
Q Consensus 142 ~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~----------p~~ 211 (299)
+.+.+|+.++++|||++|... ..+.|.+|||+||+|||+++||.||++||||+++...+++....+ ...
T Consensus 2 ~~a~~iv~~~~~vLl~~r~~~-~~~~~~lPGG~ve~gEt~~~aa~RE~~EEtGl~v~~~~~~~~~~~~~~~~~~~~~~~~ 80 (128)
T cd04687 2 NSAKAVIIKNDKILLIKHHDD-GGVWYILPGGGQEPGETLEDAAHRECKEEIGIDVEIGPLLFVREYIGHNPTSELPGHF 80 (128)
T ss_pred cEEEEEEEECCEEEEEEEEcC-CCCeEECCCcccCCCCCHHHHHHHHHHHHHCCccccCcEEEEEEEeccCccccCCCce
Confidence 456667778899999998754 357899999999999999999999999999999977665443322 123
Q ss_pred CEEEEEEEEEecCCCC-----CCCCcceeeEEecCCCCCCCC
Q 022283 212 GQIYIIFLAKLKRPHF-----SPGPESSECRLFALDEIPFDS 248 (299)
Q Consensus 212 ~~~~~~f~a~~~~~~~-----~~~~E~~~~~W~~~deL~~~~ 248 (299)
+..+++|.+....+.. ..+++..+++|+++++++...
T Consensus 81 ~~i~~~f~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~l~~~~ 122 (128)
T cd04687 81 HQVELMFECKIKSGTPAKTPSKPDPNQIGVEWLKLKELGDIP 122 (128)
T ss_pred eEEEEEEEEEECCCCcccccCCCCCCEEeeEEEcHHHhCccc
Confidence 4566788888876542 234455689999999998433
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=1.5e-18 Score=141.32 Aligned_cols=110 Identities=26% Similarity=0.291 Sum_probs=82.1
Q ss_pred EEEEEEeeCCEEEEEEeecCC---CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeecc--ceeeeecCCCCEEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEP---SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQS--PFAQLDIPRIGQIYII 217 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p---~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~--~~~~~~~p~~~~~~~~ 217 (299)
++++++.++++|||++|...| .+|.|.+|||+|+.||++++||.||++||||+++.... +...+..+.....+++
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 344555666999999998653 26999999999999999999999999999999986433 2333333334567788
Q ss_pred EEEEecCCC-C-CCCCcceeeEEecCCCCCCCCCCCc
Q 022283 218 FLAKLKRPH-F-SPGPESSECRLFALDEIPFDSLAFS 252 (299)
Q Consensus 218 f~a~~~~~~-~-~~~~E~~~~~W~~~deL~~~~laf~ 252 (299)
|.+...... . ...+|+.+++|++++++.......|
T Consensus 83 f~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~~~~ 119 (122)
T cd04682 83 FVVPLTAREDAILFGDEGQALRLMTVEEFLAHEDAIP 119 (122)
T ss_pred EEEEEecCCCccccCchhheeecccHHHHhhccccCc
Confidence 888876553 2 3348889999999999975544433
No 30
>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=99.76 E-value=8.8e-18 Score=140.16 Aligned_cols=115 Identities=25% Similarity=0.355 Sum_probs=81.9
Q ss_pred EEEEEeeC-CEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeecccee------eee---cCC---
Q 022283 144 VGCLIEHD-KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFA------QLD---IPR--- 210 (299)
Q Consensus 144 V~~iv~~~-~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~------~~~---~p~--- 210 (299)
.+++++++ ++|||++|+. .|.|.+|||++|+|||+++||.||++||||++++.+...+ ... .+.
T Consensus 6 ~~~v~~~~~~~vLLv~r~~---~~~w~lPgG~ve~gE~~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (138)
T cd03674 6 SAFVVNPDRGKVLLTHHRK---LGSWLQPGGHIDPDESLLEAALRELREETGIELLGLRPLSVLVDLDVHPIDGHPKRGV 82 (138)
T ss_pred EEEEEeCCCCeEEEEEEcC---CCcEECCceecCCCCCHHHHHHHHHHHHHCCCcccceeccccccceeEeecCCCCCCC
Confidence 33444554 8999999864 5789999999999999999999999999999886655432 111 111
Q ss_pred --CCEEEEEEEEEecCCCCC--CCCcceeeEEecCCCCCCCCCCCccHHHHHHHHH
Q 022283 211 --IGQIYIIFLAKLKRPHFS--PGPESSECRLFALDEIPFDSLAFSSISVTLQLFI 262 (299)
Q Consensus 211 --~~~~~~~f~a~~~~~~~~--~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l 262 (299)
.....++|.+....++.. ..+|..+++|++++++....+ .+..+.++++.+
T Consensus 83 ~~~~~~~~~y~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~-~~~~~~~i~~~~ 137 (138)
T cd03674 83 PGHLHLDLRFLAVAPADDVAPPKSDESDAVRWFPLDELASLEL-PEDVRRLVEKAL 137 (138)
T ss_pred CCcEEEEEEEEEEccCccccCCCCCcccccEEEcHHHhhhccC-CHHHHHHHHHHh
Confidence 112446788887665544 347889999999999964333 455566666554
No 31
>PRK10546 pyrimidine (deoxy)nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=99.75 E-value=2.1e-17 Score=136.26 Aligned_cols=121 Identities=26% Similarity=0.261 Sum_probs=88.7
Q ss_pred EEEEEEEeeCCEEEEEEeecCC-CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCE--EEEEE
Q 022283 142 MVVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQ--IYIIF 218 (299)
Q Consensus 142 ~vV~~iv~~~~kILL~rr~~~p-~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~--~~~~f 218 (299)
.++.+|+.++++|||.+|.... ..|+|++|||++|+||++++|+.||++||||+++....+++...+.+.+. .+++|
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 3455666778999999987543 36899999999999999999999999999999998777776665544443 34556
Q ss_pred EEEecCCCCCCCCcceeeEEecCCCCCCCCCCCccHHHHHHHHHHH
Q 022283 219 LAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLFIDD 264 (299)
Q Consensus 219 ~a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l~~ 264 (299)
.+....+++. ..|..+++|+++++++...+ .+..+.+++.|++.
T Consensus 85 ~~~~~~~~~~-~~e~~~~~W~~~~el~~~~~-~~~~~~~l~~~~~~ 128 (135)
T PRK10546 85 HVPDFHGELQ-AHEHQALVWCTPEEALRYPL-APADIPLLEAFMAL 128 (135)
T ss_pred EEEEecCccc-ccccceeEEcCHHHcccCCC-CcCcHHHHHHHHHh
Confidence 6665444332 24567889999999984444 34456677666654
No 32
>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=99.74 E-value=1.6e-17 Score=136.18 Aligned_cols=103 Identities=32% Similarity=0.470 Sum_probs=74.1
Q ss_pred CcEEEEEEE-eeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec------CCCC
Q 022283 140 PKMVVGCLI-EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI------PRIG 212 (299)
Q Consensus 140 p~~vV~~iv-~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~------p~~~ 212 (299)
+.+.+.+++ +.+++|||++|.. .+.|.+|||+|++|||+++||.||++||||+++.....++.+.. +...
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 344454444 5558999998874 37899999999999999999999999999999987776654321 1111
Q ss_pred ----EEEEEEEEEecCCCCC-CCCcceeeEEecCCCCC
Q 022283 213 ----QIYIIFLAKLKRPHFS-PGPESSECRLFALDEIP 245 (299)
Q Consensus 213 ----~~~~~f~a~~~~~~~~-~~~E~~~~~W~~~deL~ 245 (299)
..+++|.+....+.+. ..+|..+++||++++++
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~e~~ 120 (132)
T cd04677 83 DEQYIVTLYYVTKVFGGKLVPDGDETLELKFFSLDELP 120 (132)
T ss_pred cEEEEEEEEEEEeccCCcccCCCCceeeEEEEChhHCc
Confidence 2234455544444433 34788899999999998
No 33
>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=99.74 E-value=9.8e-18 Score=135.04 Aligned_cols=102 Identities=24% Similarity=0.378 Sum_probs=79.3
Q ss_pred EEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceee--ccceeeeecCC-----CCEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEV--QSPFAQLDIPR-----IGQIY 215 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~--~~~~~~~~~p~-----~~~~~ 215 (299)
+++++++.++++||+||+. .+.|.+|||++++||++++||+||++||||+++.. +..++.+..+. .....
T Consensus 3 ~~~~v~~~~~~vLl~~r~~---~~~w~~PgG~ve~~Es~~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (118)
T cd04690 3 AAALILVRDGRVLLVRKRG---TDVFYLPGGKIEAGETPLQALIRELSEELGLDLDPDSLEYLGTFRAPAANEPGVDVRA 79 (118)
T ss_pred EEEEEEecCCeEEEEEECC---CCcEECCCCccCCCCCHHHHHHHHHHHHHCCccChhheEEEEEEecccccCCCcEEEE
Confidence 4455667778999998863 57899999999999999999999999999999877 77766655421 12455
Q ss_pred EEEEEEecCCCCCCCCcceeeEEecCCCCCCCC
Q 022283 216 IIFLAKLKRPHFSPGPESSECRLFALDEIPFDS 248 (299)
Q Consensus 216 ~~f~a~~~~~~~~~~~E~~~~~W~~~deL~~~~ 248 (299)
++|.+.... .+...+|..+++|+++++++...
T Consensus 80 ~~f~~~~~~-~~~~~~e~~~~~W~~~~e~~~~~ 111 (118)
T cd04690 80 TVYVAELTG-EPVPAAEIEEIRWVDYDDPADDR 111 (118)
T ss_pred EEEEEcccC-CcCCCchhhccEEecHHHccccc
Confidence 778887655 44455788999999999986433
No 34
>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=99.74 E-value=1.7e-17 Score=139.82 Aligned_cols=116 Identities=28% Similarity=0.461 Sum_probs=82.2
Q ss_pred EEEEEE-EeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeee------ecC-----
Q 022283 142 MVVGCL-IEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQL------DIP----- 209 (299)
Q Consensus 142 ~vV~~i-v~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~------~~p----- 209 (299)
++|+++ ++.+++|||+||...+ +.|.+|||++|+||++.+||.||++||||+++....+++.. ..+
T Consensus 4 ~~v~~ii~~~~~~vLL~~r~~~~--~~W~~PgG~~e~gE~~~~aA~REv~EEtGl~~~~~~~l~~~~~~~~y~~~~~~~~ 81 (147)
T cd03671 4 PNVGVVLFNEDGKVFVGRRIDTP--GAWQFPQGGIDEGEDPEQAALRELEEETGLDPDSVEIIAEIPDWLRYDLPPELKL 81 (147)
T ss_pred ceEEEEEEeCCCEEEEEEEcCCC--CCEECCcCCCCCCcCHHHHHHHHHHHHHCCCcCceEEEEEcCCeeEeeChhhhhc
Confidence 344444 4567899999998765 89999999999999999999999999999998776665542 211
Q ss_pred ------CCCEEEEEEEEEecC--CCC--CC--CCcceeeEEecCCCCCCCCCCCccHHHHHHHH
Q 022283 210 ------RIGQIYIIFLAKLKR--PHF--SP--GPESSECRLFALDEIPFDSLAFSSISVTLQLF 261 (299)
Q Consensus 210 ------~~~~~~~~f~a~~~~--~~~--~~--~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~ 261 (299)
+.+...++|.+.+.. ..+ .. ++|+.+++|+++++++ .+..+....++...
T Consensus 82 ~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~E~~~~~W~~~~el~--~~~~~~~~~~~~~~ 143 (147)
T cd03671 82 KIWGGRYRGQEQKWFLFRFTGDDSEIDLNAPEHPEFDEWRWVPLEELP--DLIVPFKRPVYEAV 143 (147)
T ss_pred cccCCcCCCEEEEEEEEEecCCCccccCCCCCCCCEeeEEeCCHHHHH--HhchhhhHHHHHHH
Confidence 113344566666554 232 33 3689999999999999 44444444444443
No 35
>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=99.74 E-value=7.8e-18 Score=138.15 Aligned_cols=114 Identities=23% Similarity=0.179 Sum_probs=84.2
Q ss_pred cEEEEEEEee--CCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeee------cCC--
Q 022283 141 KMVVGCLIEH--DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD------IPR-- 210 (299)
Q Consensus 141 ~~vV~~iv~~--~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~------~p~-- 210 (299)
+.+.+++.+. +++|||+||... .+|.|.+|||+++.|||+++||.||++||||+++....++.... +..
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 4455555566 789999999876 47899999999999999999999999999999986555544322 221
Q ss_pred CCEEEEEEEEEecCCC-CCCCCcceeeEEecCCCCCCCCCCCccHHH
Q 022283 211 IGQIYIIFLAKLKRPH-FSPGPESSECRLFALDEIPFDSLAFSSISV 256 (299)
Q Consensus 211 ~~~~~~~f~a~~~~~~-~~~~~E~~~~~W~~~deL~~~~laf~s~~~ 256 (299)
.+...++|.+...... ...++|+.++.|+++++++ ..+.++..+.
T Consensus 81 ~~~~~~~f~~~~~~~~~~~~~~E~~~~~W~~~~e~~-~~~~~~~~~~ 126 (129)
T cd04664 81 RVWTEHPFAFHLPSDAVVTLDWEHDAFEWVPPEEAA-ALLLWESNRR 126 (129)
T ss_pred eEEEEeEEEEEcCCCCcccCCccccccEecCHHHHH-HHHcChhhhh
Confidence 2245577888876654 3345788899999999997 3444555443
No 36
>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=99.74 E-value=5.2e-18 Score=138.02 Aligned_cols=110 Identities=27% Similarity=0.411 Sum_probs=80.2
Q ss_pred EEEEEEEeeC-CEEEEEEeecCC--CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeecccee-eeecCCC---CEE
Q 022283 142 MVVGCLIEHD-KKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFA-QLDIPRI---GQI 214 (299)
Q Consensus 142 ~vV~~iv~~~-~kILL~rr~~~p--~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~-~~~~p~~---~~~ 214 (299)
++|.++|.++ ++|||+||...+ .+|.|++|||++++|||+++||+||++||||+++....++. ....... ...
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 3455566555 899999998765 27899999999999999999999999999999998777643 2222222 344
Q ss_pred EEEEEEEecCCCCCCCCcceeeEEecCCCCCCCCCCCcc
Q 022283 215 YIIFLAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSS 253 (299)
Q Consensus 215 ~~~f~a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s 253 (299)
+++|.+....+....++|..+++|++++++. .+.++.
T Consensus 82 ~~~~~~~~~~~~~~~~~e~~~~~w~~~~el~--~~~~~~ 118 (129)
T cd04699 82 YLVFVCEALSGAVKLSDEHEEYAWVTLEELA--ILKADI 118 (129)
T ss_pred EEEEEeeecCCcccCChhheEEEEecHHHhh--hhhccc
Confidence 4667765554433345788899999999986 444443
No 37
>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=99.74 E-value=2e-17 Score=136.97 Aligned_cols=106 Identities=27% Similarity=0.252 Sum_probs=81.8
Q ss_pred CcEEEEEEEeeCCEEEEEEeecCCC-CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecC--CCCEEEE
Q 022283 140 PKMVVGCLIEHDKKILLCKRKIEPS-YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP--RIGQIYI 216 (299)
Q Consensus 140 p~~vV~~iv~~~~kILL~rr~~~p~-~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p--~~~~~~~ 216 (299)
+..+++++++.++++||++|.+.+. ++.|.+|||++|.||++++||+||++||||+++..+.+++.+... ..+..+.
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 4556666667779999998876553 578999999999999999999999999999999877777655432 2234566
Q ss_pred EEEEEecCCC--CCC-CCcceeeEEecCCCCC
Q 022283 217 IFLAKLKRPH--FSP-GPESSECRLFALDEIP 245 (299)
Q Consensus 217 ~f~a~~~~~~--~~~-~~E~~~~~W~~~deL~ 245 (299)
+|.+...... ... ++|+.+++|++++++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~ 113 (137)
T cd03424 82 LFLAEDLSPGEEGLLDEGEDIEVVLVPLDEAL 113 (137)
T ss_pred EEEEEcccccccCCCCCCCeeEEEEecHHHHH
Confidence 7777776543 223 3788999999999987
No 38
>PRK05379 bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional
Probab=99.73 E-value=2.2e-17 Score=157.78 Aligned_cols=127 Identities=24% Similarity=0.400 Sum_probs=96.7
Q ss_pred eecCCcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceee------eecC
Q 022283 136 AYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQ------LDIP 209 (299)
Q Consensus 136 ~y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~------~~~p 209 (299)
-|+.+.++|.+|+.++++|||++|...|..|.|.+|||+||+|||+++||+||++||||+++....+.+. +..|
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 3666778888888888999999998877789999999999999999999999999999999865544332 2233
Q ss_pred C----CCEEEEEEEEEecCCC---CCCCCcceeeEEecCCCCCCC-CCCCccHHHHHHHHH
Q 022283 210 R----IGQIYIIFLAKLKRPH---FSPGPESSECRLFALDEIPFD-SLAFSSISVTLQLFI 262 (299)
Q Consensus 210 ~----~~~~~~~f~a~~~~~~---~~~~~E~~~~~W~~~deL~~~-~laf~s~~~~l~~~l 262 (299)
. .+...++|.+....++ +..++|..+++|+++++++.. ...+.+...+|+.|+
T Consensus 278 ~r~~~~~~i~~~f~~~~~~~~~~~~~~~de~~~~~W~~~~el~~~~~~~~~dh~~ii~~~~ 338 (340)
T PRK05379 278 GRSLRGRTITHAFLFEFPAGELPRVKGGDDADKARWVPLAELLAMRDRMFEDHFQIITHFL 338 (340)
T ss_pred CCCCCCcEEEEEEEEEecCCccCccCCCCceeeEEEEEHHHhhhhhhhhhhHHHHHHHHHh
Confidence 2 2355677877766443 345578899999999999842 234566677777665
No 39
>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=131.27 Aligned_cols=107 Identities=31% Similarity=0.459 Sum_probs=78.4
Q ss_pred cEEEEEEE-eeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeee-------cCCC-
Q 022283 141 KMVVGCLI-EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD-------IPRI- 211 (299)
Q Consensus 141 ~~vV~~iv-~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~-------~p~~- 211 (299)
.+.|.+++ ++++++||++|.. .|.|.+|||+++.||++++||.||++||||+++....+++.+. ++..
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 4458999999874 3889999999999999999999999999999987766543221 1221
Q ss_pred --CEEEEEEEEEecCCCC-CCCCcceeeEEecCCCCCCCCCCCc
Q 022283 212 --GQIYIIFLAKLKRPHF-SPGPESSECRLFALDEIPFDSLAFS 252 (299)
Q Consensus 212 --~~~~~~f~a~~~~~~~-~~~~E~~~~~W~~~deL~~~~laf~ 252 (299)
+...++|.+....+.. ...+|..+++|+++++++ .+.++
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~~w~~~~el~--~~~~~ 120 (129)
T cd04676 79 VRQYLDITFRCRVVGGELRVGDDESLDVAWFDPDGLP--PLLMH 120 (129)
T ss_pred cEEEEEEEEEEEeeCCeecCCCCceeEEEEEChhhCc--cccCC
Confidence 2344667776665543 344788899999999999 44444
No 40
>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=99.73 E-value=4.1e-17 Score=133.30 Aligned_cols=103 Identities=25% Similarity=0.302 Sum_probs=80.4
Q ss_pred EEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec----CC--CCEEEEE
Q 022283 144 VGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----PR--IGQIYII 217 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~----p~--~~~~~~~ 217 (299)
|.+++.++++|||+|+.. .+.|.+|||+||+||++++||.||++||||+++....+++.... .. .+...++
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 445555677999998764 57899999999999999999999999999999988887765432 11 2345678
Q ss_pred EEEEecCCCCC--------CCCcceeeEEecCCCCCCCCC
Q 022283 218 FLAKLKRPHFS--------PGPESSECRLFALDEIPFDSL 249 (299)
Q Consensus 218 f~a~~~~~~~~--------~~~E~~~~~W~~~deL~~~~l 249 (299)
|.+....+... .++|..+++|++++++....+
T Consensus 81 f~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~~~ 120 (126)
T cd04688 81 YLVTLLDESLYQQDIEILEEEGEKIVFRWIPIDELKEIKL 120 (126)
T ss_pred EEEEeCCCcccccccceeccCCCEEEEEEeeHHHcccCcc
Confidence 88888766532 236788999999999985444
No 41
>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=1.8e-17 Score=135.64 Aligned_cols=102 Identities=25% Similarity=0.433 Sum_probs=73.4
Q ss_pred EEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec-CC-CCEEEEEEEEEe
Q 022283 145 GCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI-PR-IGQIYIIFLAKL 222 (299)
Q Consensus 145 ~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~-p~-~~~~~~~f~a~~ 222 (299)
++|++.+++|||++|+.. ..|.|.+|||++|.|||+++||.||++||||+++....+++...+ +. .+...++|.+.+
T Consensus 7 ~~v~~~~~~vLl~~r~~~-~~~~w~~PGG~ve~gEt~~~aa~RE~~EE~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (127)
T cd04670 7 GLVLNEKNEVLVVQERNK-TPNGWKLPGGLVDPGEDIFDGAVREVLEETGIDTEFVSVVGFRHAHPGAFGKSDLYFICRL 85 (127)
T ss_pred EEEEcCCCeEEEEEccCC-CCCcEECCCccCCCCCCHHHHHHHHHHHHHCCCcceeEEEEEEecCCCCcCceeEEEEEEE
Confidence 344455689999988754 478999999999999999999999999999999977776654332 11 122223455544
Q ss_pred cC--CCCCC-CCcceeeEEecCCCCCCC
Q 022283 223 KR--PHFSP-GPESSECRLFALDEIPFD 247 (299)
Q Consensus 223 ~~--~~~~~-~~E~~~~~W~~~deL~~~ 247 (299)
.. ..+.. .+|..+++|+++++++..
T Consensus 86 ~~~~~~~~~~~~E~~~~~w~~~~el~~~ 113 (127)
T cd04670 86 KPLSFDINFDTSEIAAAKWMPLEEYISQ 113 (127)
T ss_pred ccCcCcCCCChhhhheeEEEcHHHHhcc
Confidence 32 22333 367888999999999743
No 42
>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=9.9e-17 Score=131.38 Aligned_cols=112 Identities=28% Similarity=0.426 Sum_probs=80.8
Q ss_pred CCcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceee--ccceeeeecCCCCEEEE
Q 022283 139 NPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEV--QSPFAQLDIPRIGQIYI 216 (299)
Q Consensus 139 ~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~--~~~~~~~~~p~~~~~~~ 216 (299)
||.+++++++..++++||++|...+..|.|.+|||+||+|||+++||.||++||+|+++.. +..+..+..+....+++
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 6777887777666678888887766679999999999999999999999999999999863 44555666676667777
Q ss_pred EEEEEecCCCCCC-CCcceeeEEecCCCCCCCCCCCc
Q 022283 217 IFLAKLKRPHFSP-GPESSECRLFALDEIPFDSLAFS 252 (299)
Q Consensus 217 ~f~a~~~~~~~~~-~~E~~~~~W~~~deL~~~~laf~ 252 (299)
+|.+....+.... ..+.+...|+.....+ .++|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~--~~~~~ 116 (118)
T cd04674 82 GLLPERRAADLPPFEPTDETTERAVVTAPS--ELAFP 116 (118)
T ss_pred EEEeccccccCCCCCCCcceeeEEEccCCc--ccccc
Confidence 7877766554322 2333344455555555 34443
No 43
>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=99.72 E-value=3.6e-17 Score=138.28 Aligned_cols=102 Identities=24% Similarity=0.275 Sum_probs=70.5
Q ss_pred EEEEEEEee--CCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec-CCCCEEEEEE
Q 022283 142 MVVGCLIEH--DKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI-PRIGQIYIIF 218 (299)
Q Consensus 142 ~vV~~iv~~--~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~-p~~~~~~~~f 218 (299)
+++++++.+ +++|||+||.. .+.|++|||++|+|||+++||+||++||||+++........+.. ...+..+.+|
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 355555544 36999999863 35899999999999999999999999999999876432122211 1223344455
Q ss_pred EEEecCCC----CCCCCcceeeEEecCCCCCC
Q 022283 219 LAKLKRPH----FSPGPESSECRLFALDEIPF 246 (299)
Q Consensus 219 ~a~~~~~~----~~~~~E~~~~~W~~~deL~~ 246 (299)
.+....+. ....+|+.+++|+++++++.
T Consensus 79 ~~~~~~~~~~~~~~~~~E~~~~~Wv~~~el~~ 110 (145)
T cd03672 79 IVPGVPEDTPFEPKTRKEISKIEWFDIKDLPT 110 (145)
T ss_pred EEecCCCCcccCcCChhhhheEEEeeHHHhhh
Confidence 55433221 12236899999999999984
No 44
>PRK10776 nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=99.72 E-value=7.8e-17 Score=130.88 Aligned_cols=114 Identities=21% Similarity=0.321 Sum_probs=81.5
Q ss_pred EEEEEEeeCCEEEEEEeecCCC-CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCE--EEEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPS-YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQ--IYIIFL 219 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~-~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~--~~~~f~ 219 (299)
++++|++.+++|||.||+..+. .|+|++|||++++||++++||.||++||+|+++.....++...+.+++. .+.+|.
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 3334444567999999987654 6899999999999999999999999999999987766666655544443 345566
Q ss_pred EEecCCCCCCCCcceeeEEecCCCCCCCCCCCccH-HHHHH
Q 022283 220 AKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSI-SVTLQ 259 (299)
Q Consensus 220 a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~-~~~l~ 259 (299)
+....+.. ...|..+.+|+++++++. +.++.. +++++
T Consensus 87 ~~~~~~~~-~~~e~~~~~W~~~~~l~~--~~~p~~~~~~~~ 124 (129)
T PRK10776 87 VESWEGEP-WGKEGQPGRWVSQVALNA--DEFPPANEPIIA 124 (129)
T ss_pred EEEECCcc-CCccCCccEEecHHHCcc--CCCCcccHHHHH
Confidence 65443332 235677889999999994 445443 33443
No 45
>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=99.72 E-value=2.4e-17 Score=134.54 Aligned_cols=101 Identities=18% Similarity=0.198 Sum_probs=77.7
Q ss_pred EEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec--C--C--CCEEE
Q 022283 142 MVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI--P--R--IGQIY 215 (299)
Q Consensus 142 ~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~--p--~--~~~~~ 215 (299)
..|.+++.++++|||+++.. .+.|.+|||++|+|||+++||.||++||||+++....+++.... . . .+..+
T Consensus 2 ~~~~~vi~~~~~vLlv~~~~---~~~~~lPGG~ve~gEt~~~aa~REl~EEtGl~~~~~~~l~~~~~~~~~~~~~~~~~~ 78 (125)
T cd04689 2 LRARAIVRAGNKVLLARVIG---QPHYFLPGGHVEPGETAENALRRELQEELGVAVSDGRFLGAIENQWHEKGVRTHEIN 78 (125)
T ss_pred eEEEEEEEeCCEEEEEEecC---CCCEECCCCcCCCCCCHHHHHHHHHHHHhCceeeccEEEEEEeeeeccCCceEEEEE
Confidence 35666777889999999863 57899999999999999999999999999999988877765432 1 1 12345
Q ss_pred EEEEEEecCCC----CCCCCcceeeEEecCCCCC
Q 022283 216 IIFLAKLKRPH----FSPGPESSECRLFALDEIP 245 (299)
Q Consensus 216 ~~f~a~~~~~~----~~~~~E~~~~~W~~~deL~ 245 (299)
++|.+....+. ...++|+.+++|++++++.
T Consensus 79 ~~f~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~ 112 (125)
T cd04689 79 HIFAVESSWLASDGPPQADEDHLSFSWVPVSDLS 112 (125)
T ss_pred EEEEEEcccccccCCccCccceEEEEEccHHHcc
Confidence 67777765432 2234678899999999987
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=3.8e-17 Score=131.11 Aligned_cols=101 Identities=25% Similarity=0.351 Sum_probs=78.9
Q ss_pred EEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEEEEEEEEEecC
Q 022283 145 GCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYIIFLAKLKR 224 (299)
Q Consensus 145 ~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~~~~f~a~~~~ 224 (299)
++|+.++++|||++|. .|.|++|||++++||++++||.||++||||+++..+..++.+.. ....+++|.+.+..
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 38899999999999999999999999999999877777665543 34455678887665
Q ss_pred CC-CCCCCcceeeEEecCCCCCCCCCCCcc
Q 022283 225 PH-FSPGPESSECRLFALDEIPFDSLAFSS 253 (299)
Q Consensus 225 ~~-~~~~~E~~~~~W~~~deL~~~~laf~s 253 (299)
+. ..+.+|..+++|++++++. ++..+.
T Consensus 78 ~~~~~~~~e~~~~~W~~~~el~--~~~~~~ 105 (112)
T cd04667 78 SAQPKPSNEIADCRWLSLDALG--DLNASA 105 (112)
T ss_pred cCCCCCchheeEEEEecHHHhh--hcccch
Confidence 43 3345788899999999998 444444
No 47
>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=99.71 E-value=1.4e-16 Score=127.64 Aligned_cols=109 Identities=28% Similarity=0.409 Sum_probs=83.1
Q ss_pred EEEEEEeeCCEEEEEEeecCC-CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCC--CEEEEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIFL 219 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p-~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~--~~~~~~f~ 219 (299)
++++++++++++||++|+..+ ..|+|.+|||+++.||+++++|.||++||+|+++....+++...+.++ +..+.+|.
T Consensus 4 ~~~~i~~~~~~~Ll~~r~~~~~~~g~w~~p~G~~~~~e~~~~~a~Re~~EE~g~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (124)
T cd03425 4 VAAIIIDDDGRILIAQRPAGKHLGGLWEFPGGKVEPGETPEQALVRELREELGIEVEVGELLATVEHDYPDKRVTLHVFL 83 (124)
T ss_pred EEEEEECCCCEEEEEEeCCCCCCCCeEeCCCcccCCCCCHHHHHHHHHHHhhCcEEeccceEEEEEeeCCCCeEEEEEEE
Confidence 344444555899999998665 479999999999999999999999999999999988777776655443 45567777
Q ss_pred EEecCCCCCCCCcceeeEEecCCCCCCCCCCCccH
Q 022283 220 AKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSI 254 (299)
Q Consensus 220 a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~ 254 (299)
+....+... ..|..++.|++++++. .++++..
T Consensus 84 ~~~~~~~~~-~~e~~~~~W~~~~el~--~~~~~~~ 115 (124)
T cd03425 84 VELWSGEPQ-LLEHQELRWVPPEELD--DLDFPPA 115 (124)
T ss_pred EeeeCCCcc-cccCceEEEeeHHHcc--cCCCCcc
Confidence 766544332 4567789999999998 4555543
No 48
>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=99.71 E-value=4.7e-17 Score=133.19 Aligned_cols=103 Identities=26% Similarity=0.363 Sum_probs=79.5
Q ss_pred EEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeecccee----eeecC--CCCEEEEEEEEEecCC-
Q 022283 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFA----QLDIP--RIGQIYIIFLAKLKRP- 225 (299)
Q Consensus 153 kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~----~~~~p--~~~~~~~~f~a~~~~~- 225 (299)
++||++|+. +.|.+|||++++|||+++||.||++||||+++....+++ ...+. ..+..+++|.+.+..+
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 799999873 889999999999999999999999999999998777642 22222 2345667788887633
Q ss_pred CCCCCCcceeeEEecCCCCCCCCCCCccHHHHHHH
Q 022283 226 HFSPGPESSECRLFALDEIPFDSLAFSSISVTLQL 260 (299)
Q Consensus 226 ~~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~ 260 (299)
.+..++|..+++|++++++. ..+.++..+.++++
T Consensus 94 ~~~~~~E~~~~~W~~~~e~~-~~~~~~~~~~~~~~ 127 (130)
T cd03428 94 EVKLSEEHQDYRWLPYEEAL-KLLTYEDLKAVLDK 127 (130)
T ss_pred ccccccceeeEEeecHHHHH-HHcCchhHHHHHHH
Confidence 34555789999999999998 45556776666554
No 49
>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=3.6e-16 Score=127.29 Aligned_cols=110 Identities=15% Similarity=0.113 Sum_probs=80.4
Q ss_pred EEEEEEeeCCEEEEEEeecCCC-CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCC--EEEEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPS-YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIFL 219 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~-~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~--~~~~~f~ 219 (299)
++++|+.+++++||.+|...+. .|+|++|||.+|.||++++|+.||+.||||+++.....++...+.+.+ ..+.+|.
T Consensus 7 ~~~ii~~~~~~vLl~~R~~~~~~~g~w~~Pgg~ve~ge~~~~~~~RE~~EE~g~~~~~~~~~~~~~h~~~~~~~~~~~~~ 86 (128)
T TIGR00586 7 AVGIIRNENGEIIITRRADGHMFAKLLEFPGGKEEGGETPEQAVVRELEEEIGIPQHFSEFEKLEYEFYPRHITLWFWLL 86 (128)
T ss_pred EEEEEECCCCEEEEEEEeCCCCCCCeEECCCcccCCCCCHHHHHHHHHHHHHCCcceeeeEEEEEEEECCCcEEEEEEEE
Confidence 3444445667999999976543 789999999999999999999999999999998776666554443333 3445666
Q ss_pred EEecCCCCCCCCcceeeEEecCCCCCCCCCCCccHH
Q 022283 220 AKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSIS 255 (299)
Q Consensus 220 a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~~ 255 (299)
+...++.. ...+..+.+|+++++++ .++++...
T Consensus 87 ~~~~~~~~-~~~~~~~~~W~~~~~l~--~~~~p~~~ 119 (128)
T TIGR00586 87 ERWEGGPP-GKEGQPEEWWVLVGLLA--DDFFPAAN 119 (128)
T ss_pred EEEcCCCc-CcccccccEEeCHHHCC--ccCCCCCC
Confidence 66654432 23455678999999999 56676543
No 50
>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=99.69 E-value=6.7e-17 Score=134.15 Aligned_cols=95 Identities=24% Similarity=0.411 Sum_probs=74.0
Q ss_pred eCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeecc----ceeeeec--CC-------CCEEEE
Q 022283 150 HDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQS----PFAQLDI--PR-------IGQIYI 216 (299)
Q Consensus 150 ~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~----~~~~~~~--p~-------~~~~~~ 216 (299)
+++++||+++... ..|.|+||+|+||+|||+++||.||++||||+++.... ..+.+.+ +. .+...+
T Consensus 11 ~~~~~Llvk~~~~-~~g~W~fPgG~ve~gEt~~eaa~REl~EEtGl~v~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (132)
T cd04661 11 DDTLVLLVQQKVG-SQNHWILPQGKREEGETLRQTAERTLKELCGNNLKAKFYGNAPVGFYKYKYPKAVRNEGIVGAKVF 89 (132)
T ss_pred cCcEEEEEEeecC-CCCeeECCcccccCCCCHHHHHHHHHHHhhCCCceEEEEEecCcEEEEEecCcccccccCcccEEE
Confidence 4678999998753 36899999999999999999999999999999876421 1122222 21 124567
Q ss_pred EEEEEecCCCCCCCCcceeeEEecCCCCC
Q 022283 217 IFLAKLKRPHFSPGPESSECRLFALDEIP 245 (299)
Q Consensus 217 ~f~a~~~~~~~~~~~E~~~~~W~~~deL~ 245 (299)
+|.+...++++...+|+.+++|+++++++
T Consensus 90 ~f~~~~~~g~~~~~~e~~~~~W~~~~el~ 118 (132)
T cd04661 90 FFKARYMSGQFELSQNQVDFKWLAKEELQ 118 (132)
T ss_pred EEEEEEecCccccCCCcceeEecCHHHHH
Confidence 88999888877666889999999999998
No 51
>PRK00714 RNA pyrophosphohydrolase; Reviewed
Probab=99.69 E-value=1.7e-16 Score=135.60 Aligned_cols=120 Identities=20% Similarity=0.250 Sum_probs=84.1
Q ss_pred cEEEEE-EEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeee------cC----
Q 022283 141 KMVVGC-LIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD------IP---- 209 (299)
Q Consensus 141 ~~vV~~-iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~------~p---- 209 (299)
.++|.+ |++.+++|||+||... ++.|++|||++++||++++||.||++||||+++..+.+++... .|
T Consensus 8 ~~~v~~~i~~~~g~vLL~~r~~~--~~~w~~P~G~~~~gE~~~~aa~REl~EEtG~~~~~~~~~~~~~~~~~y~~~~~~~ 85 (156)
T PRK00714 8 RPNVGIILLNRQGQVFWGRRIGQ--GHSWQFPQGGIDPGETPEQAMYRELYEEVGLRPEDVEILAETRDWLRYDLPKRLV 85 (156)
T ss_pred CCeEEEEEEecCCEEEEEEEcCC--CCeEECCcccCCCCcCHHHHHHHHHHHHhCCCccceEEEEEcCCeEEecCcHHHh
Confidence 334444 4456789999999753 4889999999999999999999999999999987766655431 11
Q ss_pred ------CCCEEEEEEEEEecCC--CCCC----CCcceeeEEecCCCCCCCCCCCccHHHHHHHHHHH
Q 022283 210 ------RIGQIYIIFLAKLKRP--HFSP----GPESSECRLFALDEIPFDSLAFSSISVTLQLFIDD 264 (299)
Q Consensus 210 ------~~~~~~~~f~a~~~~~--~~~~----~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l~~ 264 (299)
+.+...++|.+....+ .+.. ++|+.+++|+++++++ +...+..+.++++.++.
T Consensus 86 ~~~~~~~~~~~~~~fl~~~~~~~~~~~l~~~~~~E~~~~~W~~~del~--~~~~~~~r~~~~~~~~~ 150 (156)
T PRK00714 86 RRSKGVYRGQKQKWFLLRLTGDDSEINLNTTSHPEFDAWRWVSYWYPL--DQVVPFKRDVYRRVLKE 150 (156)
T ss_pred hccCCcccCcEEEEEEEEecCCCccccCCCCCCCCeeeeEeCCHHHHH--HhchhhhHHHHHHHHHH
Confidence 1122456777776432 2222 2688999999999998 33344445566555543
No 52
>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=99.69 E-value=1.4e-16 Score=131.47 Aligned_cols=111 Identities=22% Similarity=0.246 Sum_probs=79.6
Q ss_pred EEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeecccee----eeecCCCC-EEEEEEEEE
Q 022283 147 LIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFA----QLDIPRIG-QIYIIFLAK 221 (299)
Q Consensus 147 iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~----~~~~p~~~-~~~~~f~a~ 221 (299)
.+..+++|||++|... ..|.|.+|||++|+|||+++||.||++||||+++..+.... .+..+... ....+|.+.
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 47899999999999999999999999999999987553221 12222211 233457776
Q ss_pred ecCCC-CCCCCcceeeEEecCCCCCCCCCCCccHHHHHH
Q 022283 222 LKRPH-FSPGPESSECRLFALDEIPFDSLAFSSISVTLQ 259 (299)
Q Consensus 222 ~~~~~-~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~ 259 (299)
...+. ...++|..+++|++++++. .....+..+.++.
T Consensus 88 ~~~~~~~~~~~E~~~~~W~~~~e~~-~~~~~~~~~~~~~ 125 (131)
T cd04695 88 VPPHQEVVLNHEHTEYRWCSFAEAL-ELAPFPGQRALYD 125 (131)
T ss_pred ecCCCccccCchhcccEecCHHHHH-HhcCChhHHHHHH
Confidence 65433 4445789999999999998 3455666555443
No 53
>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=99.68 E-value=1.1e-16 Score=131.09 Aligned_cols=102 Identities=25% Similarity=0.382 Sum_probs=72.8
Q ss_pred EEEEEEeeCCEEEEEEeecCC--CCCceeec-eEEeeCCCCHHHHHHHHHHHHhCCceeecc--ceeeeecCC-CCEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQS--PFAQLDIPR-IGQIYI 216 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p--~~g~w~lP-gG~VE~GEs~eeAa~REv~EEtGl~v~~~~--~~~~~~~p~-~~~~~~ 216 (299)
+.+++++.+++|||++|+... .+|.|++| ||++|+||++ +||+||++||||+++.... .+..+..+. ....++
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 344556667899999988543 36899998 8999999999 9999999999999986433 334443332 233344
Q ss_pred EEEEEecCCCCCCC-CcceeeEEecCCCCC
Q 022283 217 IFLAKLKRPHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 217 ~f~a~~~~~~~~~~-~E~~~~~W~~~deL~ 245 (299)
+|.+....+....+ +|+.+++|++++|+.
T Consensus 82 ~~~~~~~~~~~~~~~~E~~~~~w~~~~el~ 111 (127)
T cd04693 82 LFYADVEIGKLILQKEEVDEVKFVSKDEID 111 (127)
T ss_pred EEEecCcccccccCHHHhhhEEEeCHHHHH
Confidence 45444434444444 788999999999886
No 54
>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=99.68 E-value=1.5e-16 Score=135.90 Aligned_cols=95 Identities=22% Similarity=0.231 Sum_probs=74.9
Q ss_pred CEEEEEEeecCC--CCCceeeceEEeeCC-CCHHHHHHHHHHHHhCCceeeccceeeeec--CCCCEEEEEEEEEecCC-
Q 022283 152 KKILLCKRKIEP--SYGLWTLPAGYMEIG-ESAAEGAIRETWEEARADVEVQSPFAQLDI--PRIGQIYIIFLAKLKRP- 225 (299)
Q Consensus 152 ~kILL~rr~~~p--~~g~w~lPgG~VE~G-Es~eeAa~REv~EEtGl~v~~~~~~~~~~~--p~~~~~~~~f~a~~~~~- 225 (299)
++|||+||.... .+|.|++|||++|+| ||+++||+||++||||+++..+.+++.... ......+..|.+.....
T Consensus 16 ~~vLL~~R~~~~~~~~g~w~lPGG~ve~gdEs~~eaa~REl~EEtGl~~~~~~~l~~~~~~~~~~~~~v~~~~~~~~~~~ 95 (157)
T cd03426 16 LRVLLTKRASHLRSHPGQVAFPGGKVDPGDEDPVATALREAEEEIGLPPDSVEVLGRLPPYYTRSGFVVTPVVGLVPPPL 95 (157)
T ss_pred eEEEEEEcccccccCCCcEECCCCCcCCCcCCHHHHHHHHHHHHhCCCccceEEEEECCCccccCCCEEEEEEEEECCCC
Confidence 689999998753 378999999999999 999999999999999999988877776542 12234455666766553
Q ss_pred CCCCC-CcceeeEEecCCCCCC
Q 022283 226 HFSPG-PESSECRLFALDEIPF 246 (299)
Q Consensus 226 ~~~~~-~E~~~~~W~~~deL~~ 246 (299)
.+.++ +|+.+++|++++++..
T Consensus 96 ~~~~~~~E~~~~~W~~~~el~~ 117 (157)
T cd03426 96 PLVLNPDEVAEVFEVPLSFLLD 117 (157)
T ss_pred CCCCCHHHhheeEEEcHHHHhC
Confidence 34455 5889999999999984
No 55
>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=99.68 E-value=1.7e-16 Score=130.37 Aligned_cols=101 Identities=21% Similarity=0.227 Sum_probs=77.6
Q ss_pred EEEEEeeCCEEEEEEeecCC--CCCceee-ceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCC--CEEEEEE
Q 022283 144 VGCLIEHDKKILLCKRKIEP--SYGLWTL-PAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIF 218 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p--~~g~w~l-PgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~--~~~~~~f 218 (299)
.+++++.+++|||++|...+ .+|+|++ |||++++||++++||+||++||||+++..+..++.+.+... .....+|
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 34556677999999987543 3789999 69999999999999999999999999987777766655332 2334567
Q ss_pred EEEecCCCCCCC-CcceeeEEecCCCCC
Q 022283 219 LAKLKRPHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 219 ~a~~~~~~~~~~-~E~~~~~W~~~deL~ 245 (299)
.+... .++.++ +|..+++|++++++.
T Consensus 84 ~~~~~-~~~~~~~~E~~~~~w~~~~el~ 110 (126)
T cd04697 84 SCVYD-GPLKLQEEEVEEITWLSINEIL 110 (126)
T ss_pred EEEEC-CCCCCCHhHhhheEEcCHHHHH
Confidence 77664 334444 788899999999886
No 56
>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=4.1e-16 Score=128.03 Aligned_cols=97 Identities=24% Similarity=0.356 Sum_probs=73.7
Q ss_pred CEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeec-cceeeeecCCC------CEEEEEEEEEecC
Q 022283 152 KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ-SPFAQLDIPRI------GQIYIIFLAKLKR 224 (299)
Q Consensus 152 ~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~-~~~~~~~~p~~------~~~~~~f~a~~~~ 224 (299)
++|||+++.+ .+.|.+|||+||.|||+++||+||++||||+++... .+++.+.+... +...++|.+....
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 6899999863 388999999999999999999999999999998777 77777665332 3445667777654
Q ss_pred CCCC-CCCcceeeEEecCCCCCCCCCCCc
Q 022283 225 PHFS-PGPESSECRLFALDEIPFDSLAFS 252 (299)
Q Consensus 225 ~~~~-~~~E~~~~~W~~~deL~~~~laf~ 252 (299)
.... +..+..+++|++++++. ..+.++
T Consensus 92 ~~~~~~~~e~~~~~W~~~~ea~-~~~~~~ 119 (122)
T cd04666 92 ELDEWPEMHQRKRKWFSPEEAA-LLVEEP 119 (122)
T ss_pred cccCCcccCceEEEEecHHHHH-HhcCCh
Confidence 3322 33567789999999985 344444
No 57
>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=99.66 E-value=1.5e-16 Score=129.45 Aligned_cols=120 Identities=35% Similarity=0.471 Sum_probs=85.0
Q ss_pred cEEEEEEEee-CCEEEEEEeecCC--CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec--CCC---C
Q 022283 141 KMVVGCLIEH-DKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI--PRI---G 212 (299)
Q Consensus 141 ~~vV~~iv~~-~~kILL~rr~~~p--~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~--p~~---~ 212 (299)
+.+|.+++.+ +++|||++|.+.+ ..+.|.+|||++++|||+++||+||+.||||+++..........+ +.. +
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 3456666654 4599999999875 368999999999999999999999999999999976666654443 222 2
Q ss_pred EEEEEEEEEecCCC--CCCC-CcceeeEEecCCCCCCCCCCCccHHHHHHHH
Q 022283 213 QIYIIFLAKLKRPH--FSPG-PESSECRLFALDEIPFDSLAFSSISVTLQLF 261 (299)
Q Consensus 213 ~~~~~f~a~~~~~~--~~~~-~E~~~~~W~~~deL~~~~laf~s~~~~l~~~ 261 (299)
...++|.+....+. ...+ .|..++.|++++++.. .........++..+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~-~~~~~~~~~~i~~~ 132 (134)
T PF00293_consen 82 EIVIFFIAELPSEQSEIQPQDEEISEVKWVPPDELLE-LLLNGRIRKIIPWL 132 (134)
T ss_dssp EEEEEEEEEEEEEESECHTTTTTEEEEEEEEHHHHHH-HHHTTHHHHHHHHH
T ss_pred EEEEEEEEEEeCCccccCCCCccEEEEEEEEHHHhhh-chhCcchhhhhccc
Confidence 45666776665443 2233 5899999999999873 22233333344443
No 58
>PRK15393 NUDIX hydrolase YfcD; Provisional
Probab=99.66 E-value=6e-16 Score=135.31 Aligned_cols=123 Identities=20% Similarity=0.138 Sum_probs=85.6
Q ss_pred EEEEEeeCCEEEEEEeecCCC--CCce-eeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCC--CEEEEEE
Q 022283 144 VGCLIEHDKKILLCKRKIEPS--YGLW-TLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIF 218 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p~--~g~w-~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~--~~~~~~f 218 (299)
.++|++.+++|||.+|..... +|.| .+|||+|++|||+++||+||++||||+.+....+++.+..... .....+|
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 334445568999998874332 4666 5899999999999999999999999999776666655433222 2233456
Q ss_pred EEEecCCCCCCC-CcceeeEEecCCCCCCCCCCC-ccHHHHHHHHHHHHHc
Q 022283 219 LAKLKRPHFSPG-PESSECRLFALDEIPFDSLAF-SSISVTLQLFIDDIRM 267 (299)
Q Consensus 219 ~a~~~~~~~~~~-~E~~~~~W~~~deL~~~~laf-~s~~~~l~~~l~~~~~ 267 (299)
.+.. .+...++ +|+.+++|+++++++.....| +.....+..++.+..+
T Consensus 121 ~~~~-~~~~~~~~~E~~~~~W~~~~el~~~~~~~~~~~~~~l~~~l~~~~~ 170 (180)
T PRK15393 121 SCVS-HGPFALQEEEVSEVCWMTPEEITARCDEFTPDSLKALALWLTRNAK 170 (180)
T ss_pred EEEe-CCCCCCChHHeeEEEECCHHHHhhhhhhcCccHHHHHHHHHHhhcc
Confidence 6654 3444444 788999999999998432133 5667788888776543
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=99.64 E-value=9.3e-16 Score=126.93 Aligned_cols=101 Identities=28% Similarity=0.297 Sum_probs=72.1
Q ss_pred EEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCce-eeccceeeee----cCCC-----C
Q 022283 143 VVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADV-EVQSPFAQLD----IPRI-----G 212 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v-~~~~~~~~~~----~p~~-----~ 212 (299)
.|.+||.++++|||+++.+ .+.|.+|||+||+|||+++||+||++||||+++ .....++.+. +... +
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 3566777789999999864 368999999999999999999999999999987 4455555432 1111 2
Q ss_pred EEEEEEEEEecCCC--CCCC-Ccc---eeeEEecCCCCCC
Q 022283 213 QIYIIFLAKLKRPH--FSPG-PES---SECRLFALDEIPF 246 (299)
Q Consensus 213 ~~~~~f~a~~~~~~--~~~~-~E~---~~~~W~~~deL~~ 246 (299)
...++|.+.+.... ...+ .|. .+++|++++++..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~W~~~~ea~~ 118 (131)
T cd04686 79 MISYYYLCEVDAELGAQQLEDYEAELGMKPIWINIHEAIE 118 (131)
T ss_pred EEEEEEEEEEcCCcCCcccchhhHhcCCCcEEecHHHHHH
Confidence 33467888776543 2222 222 2589999999873
No 60
>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=99.62 E-value=8.7e-16 Score=132.11 Aligned_cols=105 Identities=22% Similarity=0.303 Sum_probs=76.6
Q ss_pred cEEEEE-EEeeCCEEEEEEeecCC--CCCceeec-eEEeeCCCCHHHHHHHHHHHHhCCceeeccce-eeeec--CC---
Q 022283 141 KMVVGC-LIEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQSPF-AQLDI--PR--- 210 (299)
Q Consensus 141 ~~vV~~-iv~~~~kILL~rr~~~p--~~g~w~lP-gG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~-~~~~~--p~--- 210 (299)
..+|++ |++.+++|||+||+... .+|.|.+| ||++|+|||+++||+||++||||+.+....++ ....+ ++
T Consensus 30 ~~~v~v~i~~~~~~iLl~kR~~~~~~~Pg~w~~~~gG~ie~GEt~~eaa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~ 109 (165)
T cd02885 30 HRAFSVFLFNSKGRLLLQRRALSKYTFPGLWTNTCCSHPLPGEGVKDAAQRRLREELGITGDLLELVLPRFRYRAPDDGG 109 (165)
T ss_pred eeEEEEEEEcCCCcEEEEeccCCCccCCCcccccccCCCCCCCCHHHHHHHHHHHHhCCCccchhhccceEEEEEEcCCC
Confidence 344444 45666899999988643 27999997 89999999999999999999999999877665 33222 11
Q ss_pred --CCEEEEEEEEEecCCCCCCCCcceeeEEecCCCCC
Q 022283 211 --IGQIYIIFLAKLKRPHFSPGPESSECRLFALDEIP 245 (299)
Q Consensus 211 --~~~~~~~f~a~~~~~~~~~~~E~~~~~W~~~deL~ 245 (299)
.+...++|.+....+.....+|+.+++|++++++.
T Consensus 110 ~~~~~i~~~f~~~~~~~~~~~~~Ev~~~~w~~~~el~ 146 (165)
T cd02885 110 LVEHEIDHVFFARADVTLIPNPDEVSEYRWVSLEDLK 146 (165)
T ss_pred ceeeEEEEEEEEEeCCCCCCCccceeEEEEECHHHHH
Confidence 12344667777654433333788999999999987
No 61
>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=99.62 E-value=1.5e-15 Score=127.53 Aligned_cols=103 Identities=31% Similarity=0.405 Sum_probs=73.9
Q ss_pred EEEEEEeeC---CEEEEEEeecCC--CCCceee-ceEEeeCCCCHHHHHHHHHHHHhCCcee--eccceeeeecCC----
Q 022283 143 VVGCLIEHD---KKILLCKRKIEP--SYGLWTL-PAGYMEIGESAAEGAIRETWEEARADVE--VQSPFAQLDIPR---- 210 (299)
Q Consensus 143 vV~~iv~~~---~kILL~rr~~~p--~~g~w~l-PgG~VE~GEs~eeAa~REv~EEtGl~v~--~~~~~~~~~~p~---- 210 (299)
+.+.|++.+ ++|||++|+... .+|.|++ |||+||+|||+++||+||++||||+.+. .+..++.+....
T Consensus 5 v~~~v~~~~~~~~~vLl~~R~~~~~~~pg~W~~~~gG~ve~gEt~~~aa~REl~EEtGl~~~~~~l~~~~~~~~~~~~~~ 84 (144)
T cd04692 5 FHCWIITKDEGKGYVLLQKRSANKKTYPGLWDISSAGHILAGETPLEDGIRELEEELGLDVSADDLIPLGTFKIEYDHIG 84 (144)
T ss_pred EEEEEEEccCCCCEEEEEecCCCCCCCCCccccccCcccCCCCCHHHHHHHHHHHHhCCCCChHHeEEeeEEEEeccccC
Confidence 334445555 899999998642 3689999 5999999999999999999999999874 344444433211
Q ss_pred ---CCEEEEEEEEEecC--CCCCCC-CcceeeEEecCCCCC
Q 022283 211 ---IGQIYIIFLAKLKR--PHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 211 ---~~~~~~~f~a~~~~--~~~~~~-~E~~~~~W~~~deL~ 245 (299)
......+|.+.... +.+.++ +|+.+++|++++++.
T Consensus 85 ~~~~~~~~~~f~~~~~~~~~~~~~~~~E~~~~~W~~~~el~ 125 (144)
T cd04692 85 KLIDREFHHVYLYELKVPLEEFTLQKEEVAGVVLIPLDEFA 125 (144)
T ss_pred CCccceEEEEEEEeccCChhhcCCChhHhheEEEECHHHHH
Confidence 12355677777654 334444 788999999998876
No 62
>PRK11762 nudE adenosine nucleotide hydrolase NudE; Provisional
Probab=99.62 E-value=8.3e-15 Score=128.49 Aligned_cols=107 Identities=23% Similarity=0.265 Sum_probs=79.2
Q ss_pred CCcEEEEEEEeeCCEEEEEEeecCCC-CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec-C-CCCEEE
Q 022283 139 NPKMVVGCLIEHDKKILLCKRKIEPS-YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI-P-RIGQIY 215 (299)
Q Consensus 139 ~p~~vV~~iv~~~~kILL~rr~~~p~-~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~-p-~~~~~~ 215 (299)
++..++++.+.+++++||+|+.+.+. .+.|++|||.+|+||++++||+||++||||+++..+.+++.+.. + .....+
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 33444444456778999999987653 56799999999999999999999999999999999888876543 2 223556
Q ss_pred EEEEEEecCCC-CCCC-CcceeeEEecCCCCC
Q 022283 216 IIFLAKLKRPH-FSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 216 ~~f~a~~~~~~-~~~~-~E~~~~~W~~~deL~ 245 (299)
++|.+....+. ...+ .|..++.|+++++++
T Consensus 126 ~~f~a~~~~~~~~~~~e~E~i~~~~~~~~e~~ 157 (185)
T PRK11762 126 NIVLAEDLYPERLEGDEPEPLEVVRWPLADLD 157 (185)
T ss_pred EEEEEEccccccCCCCCCceeEEEEEcHHHHH
Confidence 67777654332 2222 555678999999875
No 63
>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=99.61 E-value=6.8e-15 Score=120.47 Aligned_cols=98 Identities=24% Similarity=0.311 Sum_probs=79.3
Q ss_pred EEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCC--CEEEEEEEEE
Q 022283 144 VGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRI--GQIYIIFLAK 221 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~--~~~~~~f~a~ 221 (299)
|.+++.+++++||+++. .+.|.+|||++|+||++++||+||++||+|+++..+.+++.+..+.. .....+|.+.
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 44555667999999986 35799999999999999999999999999999988888887765443 4556778888
Q ss_pred ecCCC-CCCCCcceeeEEecCCCCC
Q 022283 222 LKRPH-FSPGPESSECRLFALDEIP 245 (299)
Q Consensus 222 ~~~~~-~~~~~E~~~~~W~~~deL~ 245 (299)
..... ..++.|+....|++.+...
T Consensus 79 ~~~~~~~~~~~E~~~~~~~~~~~~~ 103 (118)
T cd04665 79 SAQLEEKASYLETDGPVLFKNEPEE 103 (118)
T ss_pred EEecccccccccccCcEEeccCCcc
Confidence 77654 4467899999999976553
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=99.60 E-value=9.3e-15 Score=115.90 Aligned_cols=102 Identities=38% Similarity=0.582 Sum_probs=78.4
Q ss_pred EEEEEeeC-CEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec--C--CCCEEEEEE
Q 022283 144 VGCLIEHD-KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI--P--RIGQIYIIF 218 (299)
Q Consensus 144 V~~iv~~~-~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~--p--~~~~~~~~f 218 (299)
+++++.++ +++||++|... ..|.|.+|+|+++.||++.++|.||+.||+|+.+........... + .....+.+|
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 45555454 89999999865 479999999999999999999999999999999865554444333 2 234566778
Q ss_pred EEEecCCCC--CCCCcceeeEEecCCCCCC
Q 022283 219 LAKLKRPHF--SPGPESSECRLFALDEIPF 246 (299)
Q Consensus 219 ~a~~~~~~~--~~~~E~~~~~W~~~deL~~ 246 (299)
.+....+.. ....|..+.+|++++++..
T Consensus 82 ~~~~~~~~~~~~~~~e~~~~~w~~~~~l~~ 111 (123)
T cd02883 82 LARLVGGEPTLLPPDEISEVRWVTLDELPA 111 (123)
T ss_pred EEEeCCCCcCCCCCCccceEEEEcHHHCcc
Confidence 888766544 3347778899999999983
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=99.58 E-value=9.3e-15 Score=123.42 Aligned_cols=103 Identities=24% Similarity=0.342 Sum_probs=71.8
Q ss_pred EEEEE-EeeCCEEEEEEeecCC--CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeec----cceeeeec--CC---
Q 022283 143 VVGCL-IEHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ----SPFAQLDI--PR--- 210 (299)
Q Consensus 143 vV~~i-v~~~~kILL~rr~~~p--~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~----~~~~~~~~--p~--- 210 (299)
+|.+| ++.+++|||+||...+ .+|.|++|||++++||++++||+||++||+|+.+... ++++.... +.
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 5567899999998653 3789999999999999999999999999999998754 44443321 21
Q ss_pred -----CCEEEEEEEEEecCC------CCCCC-CcceeeEEecCCCCC
Q 022283 211 -----IGQIYIIFLAKLKRP------HFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 211 -----~~~~~~~f~a~~~~~------~~~~~-~E~~~~~W~~~deL~ 245 (299)
.+...++|.+..... .+.++ +|+.+++|++++++.
T Consensus 83 ~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~Ev~~~~Wv~~~~a~ 129 (143)
T cd04694 83 RGLPKRHHIVVYILVKSSETHQQLQARLQPDPNEVSAAAWLDKSLAK 129 (143)
T ss_pred CCcccceeEEEEEEEEeccccccccccccCChhhccceEeeCHHHHH
Confidence 122333333333221 12343 789999999998875
No 66
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=99.56 E-value=9.7e-15 Score=127.96 Aligned_cols=104 Identities=19% Similarity=0.411 Sum_probs=74.4
Q ss_pred cEEEEEEE-eeCCEEEEEEeecCC--CCCceeec-eEEeeCCCCHHHHHHHHHHHHhCCceeeccc-eeeeec----CC-
Q 022283 141 KMVVGCLI-EHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQSP-FAQLDI----PR- 210 (299)
Q Consensus 141 ~~vV~~iv-~~~~kILL~rr~~~p--~~g~w~lP-gG~VE~GEs~eeAa~REv~EEtGl~v~~~~~-~~~~~~----p~- 210 (299)
..+|.+++ +.+++|||+||+... .+|.|.+| ||++++|||+++||+||++||||+++..+.. ++.+.+ +.
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 34444444 556899999986432 26788886 8999999999999999999999999875432 333221 11
Q ss_pred --CCEEEEEEEEEecCCCCCCC-CcceeeEEecCCCCC
Q 022283 211 --IGQIYIIFLAKLKRPHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 211 --~~~~~~~f~a~~~~~~~~~~-~E~~~~~W~~~deL~ 245 (299)
.+..+.+|.+...+ .+.++ +|+.+++|++++++.
T Consensus 114 ~~~~~~~~vf~~~~~~-~~~~~~~Ev~~~~W~~~~el~ 150 (184)
T PRK03759 114 IVENEVCPVFAARVTS-ALQPNPDEVMDYQWVDPADLL 150 (184)
T ss_pred ceeeEEEEEEEEEECC-CCCCChhHeeeEEEECHHHHH
Confidence 12345678887653 44555 788999999999986
No 67
>PRK10729 nudF ADP-ribose pyrophosphatase NudF; Provisional
Probab=99.53 E-value=1.2e-13 Score=123.13 Aligned_cols=109 Identities=19% Similarity=0.192 Sum_probs=81.6
Q ss_pred ecCCcEEEEEEEee-CCEEEEEEeecCCCC------CceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeee-c
Q 022283 137 YQNPKMVVGCLIEH-DKKILLCKRKIEPSY------GLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD-I 208 (299)
Q Consensus 137 y~~p~~vV~~iv~~-~~kILL~rr~~~p~~------g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~-~ 208 (299)
+.++..++++.++. +++|||+++.+.+.. -.|++|+|.+|+||++++||+||+.||||+.+..+.++..+. .
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 46677766666655 579999999987642 369999999999999999999999999999998877765433 3
Q ss_pred C-CCCEEEEEEEEEecCC---C--CCCC-CcceeeEEecCCCCC
Q 022283 209 P-RIGQIYIIFLAKLKRP---H--FSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 209 p-~~~~~~~~f~a~~~~~---~--~~~~-~E~~~~~W~~~deL~ 245 (299)
| ..+..+++|.|+.... . ...+ +|..++.|++++++.
T Consensus 126 pg~~~e~~~~fla~~~~~~~~~~~~~~de~E~i~v~~~~~~e~~ 169 (202)
T PRK10729 126 PGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAY 169 (202)
T ss_pred CCcCceEEEEEEEEEcchhcccCCCCCCCCCceEEEEEcHHHHH
Confidence 3 3456778888885221 1 1223 555678999999875
No 68
>PRK08999 hypothetical protein; Provisional
Probab=99.53 E-value=6.9e-14 Score=131.58 Aligned_cols=110 Identities=24% Similarity=0.320 Sum_probs=80.2
Q ss_pred EEEEEEEeeCCEEEEEEeecCC-CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCC--EEEEEE
Q 022283 142 MVVGCLIEHDKKILLCKRKIEP-SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIF 218 (299)
Q Consensus 142 ~vV~~iv~~~~kILL~rr~~~p-~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~--~~~~~f 218 (299)
.++++|++.+++|||.||.... ..|+|++|||++|+||++++|+.||++||+|+++.....+....+.+++ ..+.+|
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 3344444556899999987543 3799999999999999999999999999999998776666665554443 445566
Q ss_pred EEEecCCCCCCCCcceeeEEecCCCCCCCCCCCccH
Q 022283 219 LAKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSI 254 (299)
Q Consensus 219 ~a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~ 254 (299)
.+....+.. ...|..+++|+++++++ ++.++..
T Consensus 87 ~~~~~~~~~-~~~e~~~~~Wv~~~el~--~~~~~~~ 119 (312)
T PRK08999 87 RVTAWQGEP-HGREGQPLAWVAPDELA--VYPFPPA 119 (312)
T ss_pred EEEEecCcc-cCccCCccEEecHHHcc--cCCCCcc
Confidence 665544432 23566788999999998 4555543
No 69
>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=99.52 E-value=4.2e-14 Score=117.89 Aligned_cols=102 Identities=25% Similarity=0.289 Sum_probs=73.2
Q ss_pred EEEEeeCCEEEEEEeecCC--CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCce-eeccceee----eecC--CCCEEE
Q 022283 145 GCLIEHDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADV-EVQSPFAQ----LDIP--RIGQIY 215 (299)
Q Consensus 145 ~~iv~~~~kILL~rr~~~p--~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v-~~~~~~~~----~~~p--~~~~~~ 215 (299)
+++++.+++|||+++.... ..+.|.+|||+|+.||++++||.||++||||+++ .....+.. +.+. ..+...
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 3455678999999987542 4679999999999999999999999999999998 54444332 2222 223456
Q ss_pred EEEEEEecCCCCC-----CC--CcceeeEEecCCCCCC
Q 022283 216 IIFLAKLKRPHFS-----PG--PESSECRLFALDEIPF 246 (299)
Q Consensus 216 ~~f~a~~~~~~~~-----~~--~E~~~~~W~~~deL~~ 246 (299)
++|.++....++. .. .+..+++|+++++|..
T Consensus 85 ~~f~~~~~~~~~~~~~~~~~E~~~~~~~~W~~~~el~~ 122 (133)
T cd04685 85 RFFLARTPRTEPSPAGWTALERRSILGWRWWTRAELAA 122 (133)
T ss_pred EEEEEEcCCccccCCCCChhhhhhcccccCCCHHHHhh
Confidence 7788877643321 11 2355789999999984
No 70
>TIGR00052 nudix-type nucleoside diphosphatase, YffH/AdpP family.
Probab=99.51 E-value=7.2e-14 Score=122.89 Aligned_cols=109 Identities=21% Similarity=0.260 Sum_probs=80.3
Q ss_pred ecCCcEEEEEEEee-CCEEEEEEeecCCC------CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec-
Q 022283 137 YQNPKMVVGCLIEH-DKKILLCKRKIEPS------YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI- 208 (299)
Q Consensus 137 y~~p~~vV~~iv~~-~~kILL~rr~~~p~------~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~- 208 (299)
+.++..+++++++. ++++||+++.+.+. ...|++|||++|+||++++||+||++||||+++..+..++.+..
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 35566555555544 57999999887542 46799999999999999999999999999999988877765432
Q ss_pred C-CCCEEEEEEEEEecCCC---C-C-CCCcceeeEEecCCCCC
Q 022283 209 P-RIGQIYIIFLAKLKRPH---F-S-PGPESSECRLFALDEIP 245 (299)
Q Consensus 209 p-~~~~~~~~f~a~~~~~~---~-~-~~~E~~~~~W~~~deL~ 245 (299)
+ ..+..+++|.++...+. . . .++|..+..|++++++.
T Consensus 121 ~g~~~~~~~~f~a~~~~~~~~~~~~~~~~E~ie~~~~~~~e~~ 163 (185)
T TIGR00052 121 PGGVTELIHLFIAEVDDNQAAGIGGGADEEEIEVLHLVFSQAL 163 (185)
T ss_pred CCCCcEEEEEEEEEEchhhcCCCCCCCCccceEEEEeCHHHHH
Confidence 3 23467788899865432 1 1 23455678899988875
No 71
>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=99.51 E-value=4e-14 Score=121.17 Aligned_cols=99 Identities=23% Similarity=0.328 Sum_probs=71.3
Q ss_pred EEEEEeeCCEEEEEEeecCC--CCCceeec-eEEeeCCCCHHHHHHHHHHHHhCCceeecc--ceeeee----cCC-CCE
Q 022283 144 VGCLIEHDKKILLCKRKIEP--SYGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQS--PFAQLD----IPR-IGQ 213 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p--~~g~w~lP-gG~VE~GEs~eeAa~REv~EEtGl~v~~~~--~~~~~~----~p~-~~~ 213 (299)
.++|++.+++|||+||+... .+|.|++| ||+++.|| .+||+||++|||||++...+ .+.... .+. ...
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 33444567899999987632 37999998 89999999 49999999999999987654 222111 121 134
Q ss_pred EEEEEEEEecCCCCCCC-CcceeeEEecCCCCC
Q 022283 214 IYIIFLAKLKRPHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 214 ~~~~f~a~~~~~~~~~~-~E~~~~~W~~~deL~ 245 (299)
...+|.+.... .+.++ +|+.+++|++++|++
T Consensus 109 ~~~~f~~~~~~-~~~~~~~Ev~~~~W~~~~el~ 140 (158)
T TIGR02150 109 LCPVFFARAPV-PLNPNPEEVAEYRWVSLEELK 140 (158)
T ss_pred EEEEEEEecCC-cccCChhHeeeEEEeCHHHHH
Confidence 45667776654 34555 699999999999987
No 72
>PRK10707 putative NUDIX hydrolase; Provisional
Probab=99.49 E-value=1.9e-13 Score=120.70 Aligned_cols=106 Identities=18% Similarity=0.180 Sum_probs=75.6
Q ss_pred cEEEEEEEee-CCEEEEEEeecCC--CCCceeeceEEeeCC-CCHHHHHHHHHHHHhCCceeeccceeeeec--CCCCEE
Q 022283 141 KMVVGCLIEH-DKKILLCKRKIEP--SYGLWTLPAGYMEIG-ESAAEGAIRETWEEARADVEVQSPFAQLDI--PRIGQI 214 (299)
Q Consensus 141 ~~vV~~iv~~-~~kILL~rr~~~p--~~g~w~lPgG~VE~G-Es~eeAa~REv~EEtGl~v~~~~~~~~~~~--p~~~~~ 214 (299)
+++++.++.+ ++.|||.+|.... ..|.|+||||.+|+| |++++||+||++||||+++..+.+++.... ...+..
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 3333334433 4589999977543 268999999999985 689999999999999999998888887542 233444
Q ss_pred EEEEEEEecCC-CCCCC-CcceeeEEecCCCCCC
Q 022283 215 YIIFLAKLKRP-HFSPG-PESSECRLFALDEIPF 246 (299)
Q Consensus 215 ~~~f~a~~~~~-~~~~~-~E~~~~~W~~~deL~~ 246 (299)
+..|.+.+... ...++ +|..++.|++++++..
T Consensus 112 ~~~~v~~~~~~~~~~~d~~Ev~~v~~vpl~e~~~ 145 (190)
T PRK10707 112 VTPVVGIIPPDLPYRANEDEVAAVFEMPLAEALH 145 (190)
T ss_pred EEEEEEEECCCCCCCCChhhhheEEEEeHHHHhC
Confidence 44454444332 24445 7888999999999873
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=99.48 E-value=5.5e-13 Score=114.24 Aligned_cols=99 Identities=26% Similarity=0.346 Sum_probs=73.8
Q ss_pred CcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecC--CCCEEEEE
Q 022283 140 PKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIP--RIGQIYII 217 (299)
Q Consensus 140 p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p--~~~~~~~~ 217 (299)
|..++ +|...++++||+++.. ..|++|||++|+|||+++||.||++||||+.+..+.+++.+... .....+.+
T Consensus 24 ~~~V~-ii~~~~~~~LL~~~~~----~~~elPgG~vE~gEt~~eaA~REl~EETG~~~~~~~~lg~~~~~~~~~~~~~~v 98 (156)
T TIGR02705 24 PNHVL-VIPRYKDQWLLTEHKR----RGLEFPGGKVEPGETSKEAAIREVMEETGAIVKELHYIGQYEVEGESTDFVKDV 98 (156)
T ss_pred CCEEE-EEEEECCEEEEEEEcC----CcEECCceecCCCCCHHHHHHHHHHHHhCcEeeeeEEEEEEEecCCCcEEEEEE
Confidence 44443 3444566999998763 34999999999999999999999999999999999999876543 23466688
Q ss_pred EEEEecCCCCCCCCcceeeE-EecCCCCC
Q 022283 218 FLAKLKRPHFSPGPESSECR-LFALDEIP 245 (299)
Q Consensus 218 f~a~~~~~~~~~~~E~~~~~-W~~~deL~ 245 (299)
|.|+....+ ..+|..+.. ++++++++
T Consensus 99 f~A~~~~~~--~~~e~~E~~~~~~~~~~~ 125 (156)
T TIGR02705 99 YFAEVSALE--SKDDYLETKGPVLLQEIP 125 (156)
T ss_pred EEEEEeccc--cCCCceeeEeEEEHHHHH
Confidence 889887443 224544544 68877775
No 74
>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=99.46 E-value=5.6e-13 Score=110.27 Aligned_cols=90 Identities=21% Similarity=0.200 Sum_probs=61.8
Q ss_pred CEEEEEEeecC----CCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeec-cceeeeecCC---------------C
Q 022283 152 KKILLCKRKIE----PSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ-SPFAQLDIPR---------------I 211 (299)
Q Consensus 152 ~kILL~rr~~~----p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~-~~~~~~~~p~---------------~ 211 (299)
.+|||++|... +..+.|++|||+++.||++++||+||++||||+++... ..+..+..+. .
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 46999987432 34688999999999999999999999999999987521 1111121111 1
Q ss_pred CEEEEEEEEEecCCCCCC--CCcceeeEEecC
Q 022283 212 GQIYIIFLAKLKRPHFSP--GPESSECRLFAL 241 (299)
Q Consensus 212 ~~~~~~f~a~~~~~~~~~--~~E~~~~~W~~~ 241 (299)
....++|.++..+++... .+|..+++||++
T Consensus 95 ~~~~~~f~~~~~~~~~~~~~~~e~~~~~w~~~ 126 (126)
T cd04662 95 DIKSNTFEMEWPKGSGKMRKFPEVDRAGWFDI 126 (126)
T ss_pred HeEEEEEEEEccCCCCccccCCccceeEeecC
Confidence 233355666665554443 588899999984
No 75
>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=99.45 E-value=1e-12 Score=115.55 Aligned_cols=105 Identities=21% Similarity=0.241 Sum_probs=70.9
Q ss_pred EEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeecc----------------ceeee----ecCCC-
Q 022283 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQS----------------PFAQL----DIPRI- 211 (299)
Q Consensus 153 kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~----------------~~~~~----~~p~~- 211 (299)
++||++|+ ..|.|.+|||+||+||++++||.||++||||+.+..+. .+.++ ..|..
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 78888885 36899999999999999999999999999977542220 12222 22221
Q ss_pred ---CEEEEEEEEEecCC------CCCCCCcceeeEEecCCCCCCCCCCCccHHHHHHHHHH
Q 022283 212 ---GQIYIIFLAKLKRP------HFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLFID 263 (299)
Q Consensus 212 ---~~~~~~f~a~~~~~------~~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l~ 263 (299)
....+.|......+ .+...+|..+++||++++++ .+.++. ..+|+++++
T Consensus 127 d~~w~~Tva~~f~~~~~~~~~~~~~~a~dda~~a~W~~v~~l~--~L~~dH-~~Il~~a~~ 184 (186)
T cd03670 127 DNAWMETVAVNFHDEDGNDVENLPLEAGDDAGSVRWQDIDSKL--PLYANH-SQFLKKVAE 184 (186)
T ss_pred CcceEEEEEEEEEecCcccccccccCCCCchheeEEEEccccc--ccccCH-HHHHHHHHH
Confidence 11334443333222 23345788899999999998 676655 567777664
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=99.41 E-value=8.2e-13 Score=115.09 Aligned_cols=94 Identities=22% Similarity=0.294 Sum_probs=69.3
Q ss_pred CEEEEEEeecCCC--CCce-eeceEEeeCCCCHHHHHHHHHHHHhCCceeecc---ceeeee--c--CC---CCEEEEEE
Q 022283 152 KKILLCKRKIEPS--YGLW-TLPAGYMEIGESAAEGAIRETWEEARADVEVQS---PFAQLD--I--PR---IGQIYIIF 218 (299)
Q Consensus 152 ~kILL~rr~~~p~--~g~w-~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~---~~~~~~--~--p~---~~~~~~~f 218 (299)
++|++.||+.... +|+| .+|||++++||++++||+||++||||+++..+. +++... . .. .+...++|
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 7899999987543 7999 599999999999999999999999999987533 333211 1 11 22455667
Q ss_pred EEEecCCC-CCCC-CcceeeEEecCCCCC
Q 022283 219 LAKLKRPH-FSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 219 ~a~~~~~~-~~~~-~E~~~~~W~~~deL~ 245 (299)
.+.+.... +.++ +|+.++.|++++|+.
T Consensus 128 ~~~~~~~~~~~~~~~Ev~~~~~~~~~el~ 156 (180)
T cd03676 128 DLELPPDFIPAPQDGEVESFRLLTIDEVL 156 (180)
T ss_pred EEEcCCCCeeCCCCCcEeEEEEECHHHHH
Confidence 77654332 3344 789999999999975
No 77
>PRK15009 GDP-mannose pyrophosphatase NudK; Provisional
Probab=99.37 E-value=4.2e-12 Score=112.26 Aligned_cols=109 Identities=16% Similarity=0.143 Sum_probs=79.0
Q ss_pred eecCCcEEEEEEEee-CCEEEEEEeecCCC-------CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeee-
Q 022283 136 AYQNPKMVVGCLIEH-DKKILLCKRKIEPS-------YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQL- 206 (299)
Q Consensus 136 ~y~~p~~vV~~iv~~-~~kILL~rr~~~p~-------~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~- 206 (299)
.+.++..+++++++. +++|||+++.+.+. .-.|++|||.+|+| ++++||+||+.||||+.+..+..++.+
T Consensus 41 vv~~~~~v~Vl~~~~~~~~vvLvrQyR~~v~~~~~~~~~~lElPAG~vd~~-~p~~aA~REL~EETGy~a~~~~~l~~~~ 119 (191)
T PRK15009 41 VYDRGNGATILLYNAKKKTVVLIRQFRVATWVNGNESGQLIETCAGLLDND-EPEVCIRKEAIEETGYEVGEVRKLFELY 119 (191)
T ss_pred EEEECCEEEEEEEECCCCEEEEEEcccccccccCCCCceEEEEeccccCCC-CHHHHHHHHHHHhhCCccceEEEeeEEE
Confidence 345566555555554 67999999998773 23599999999975 699999999999999999888777643
Q ss_pred ecCC-CCEEEEEEEEEecCC-CC---C-CCCcceeeEEecCCCCC
Q 022283 207 DIPR-IGQIYIIFLAKLKRP-HF---S-PGPESSECRLFALDEIP 245 (299)
Q Consensus 207 ~~p~-~~~~~~~f~a~~~~~-~~---~-~~~E~~~~~W~~~deL~ 245 (299)
+.|. .+..++.|.|+.... .. . ..+|..++.|++++++.
T Consensus 120 ~spG~s~e~~~lf~a~~~~~~~~~~~~~de~E~iev~~~~~~e~~ 164 (191)
T PRK15009 120 MSPGGVTELIHFFIAEYSDSQRANAGGGVEDEDIEVLELPFSQAL 164 (191)
T ss_pred cCCcccCcEEEEEEEEECchhcccCCCCCCCceEEEEEEcHHHHH
Confidence 3332 346678888886421 11 1 13566789999999975
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=99.34 E-value=1.3e-11 Score=102.28 Aligned_cols=90 Identities=16% Similarity=0.169 Sum_probs=56.4
Q ss_pred EEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccc-eeeeecCC--CCEEEEEEEEEecCC--C-
Q 022283 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSP-FAQLDIPR--IGQIYIIFLAKLKRP--H- 226 (299)
Q Consensus 153 kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~-~~~~~~p~--~~~~~~~f~a~~~~~--~- 226 (299)
+||+.|.. .+.|.+|||.+|+||++++||+||++||||+++..... .......+ .+..++.+.+..... .
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 66666543 24599999999999999999999999999999733222 22221111 233444444444211 1
Q ss_pred ---CCCCCccee--eEEecCCCCCC
Q 022283 227 ---FSPGPESSE--CRLFALDEIPF 246 (299)
Q Consensus 227 ---~~~~~E~~~--~~W~~~deL~~ 246 (299)
....+|... +.|+++++++.
T Consensus 91 ~~~~~~~~E~~~i~~~Wv~l~~~~~ 115 (126)
T cd04663 91 WVHFVQDDGGHEFRFFWVDLASCLD 115 (126)
T ss_pred ccCcccCCCCceEEEEEEccccccc
Confidence 112234444 45999999974
No 79
>PLN02709 nudix hydrolase
Probab=99.33 E-value=5.6e-12 Score=113.54 Aligned_cols=94 Identities=21% Similarity=0.194 Sum_probs=71.5
Q ss_pred CEEEEEEeecCC--CCCceeeceEEeeCC-CCHHHHHHHHHHHHhCCceeeccceeeeec--CCCCEEEEEEEEEecC--
Q 022283 152 KKILLCKRKIEP--SYGLWTLPAGYMEIG-ESAAEGAIRETWEEARADVEVQSPFAQLDI--PRIGQIYIIFLAKLKR-- 224 (299)
Q Consensus 152 ~kILL~rr~~~p--~~g~w~lPgG~VE~G-Es~eeAa~REv~EEtGl~v~~~~~~~~~~~--p~~~~~~~~f~a~~~~-- 224 (299)
.+|||++|+... ..|.|+||||++|+| +++.+||+||++||+||....+..++..+. ...+..+.-|.+.+..
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 389999998753 479999999999997 579999999999999999988887775442 2233444456655543
Q ss_pred -CCCCCC-CcceeeEEecCCCCC
Q 022283 225 -PHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 225 -~~~~~~-~E~~~~~W~~~deL~ 245 (299)
..+.++ +|++++.|++++++.
T Consensus 131 ~~~~~~np~EV~~vf~vPL~~ll 153 (222)
T PLN02709 131 AFKPLPNPAEVEEIFDVPLEMFL 153 (222)
T ss_pred CccccCChhhhheeEEecHHHHh
Confidence 123355 799999999998875
No 80
>COG0494 MutT NTP pyrophosphohydrolases including oxidative damage repair enzymes [DNA replication, recombination, and repair / General function prediction only]
Probab=99.22 E-value=1.5e-10 Score=93.39 Aligned_cols=95 Identities=26% Similarity=0.369 Sum_probs=63.8
Q ss_pred CEEEEEEeecCCCCCceeeceEEeeCCCCHHH-HHHHHHHHHhCCcee--eccceeeeecCCCC------EEE-EEEEEE
Q 022283 152 KKILLCKRKIEPSYGLWTLPAGYMEIGESAAE-GAIRETWEEARADVE--VQSPFAQLDIPRIG------QIY-IIFLAK 221 (299)
Q Consensus 152 ~kILL~rr~~~p~~g~w~lPgG~VE~GEs~ee-Aa~REv~EEtGl~v~--~~~~~~~~~~p~~~------~~~-~~f~a~ 221 (299)
+++|+.++.... +.|.+|||.||+||++.+ ||+||++||||+++. ....++.+...... ... ..+...
T Consensus 24 ~~vl~~~~~~~~--~~~~~PgG~ve~~e~~~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 (161)
T COG0494 24 GEVLLAQRRDDG--GLWELPGGKVEPGEELPEEAAARELEEETGLRVKDERLELLGEFPPSPGDGSSVGGREHRVFFVAE 101 (161)
T ss_pred CEEeEEEccccC--CceecCCcccCCCCchHHHHHHHHHHHHhCCeeeeecceeeeeccCcccCcccccceEEEEEEeee
Confidence 789998887542 689999999999999888 999999999999998 55555554432211 111 112222
Q ss_pred ec---CCCCCC----CCcceeeEEecCCCCCCCC
Q 022283 222 LK---RPHFSP----GPESSECRLFALDEIPFDS 248 (299)
Q Consensus 222 ~~---~~~~~~----~~E~~~~~W~~~deL~~~~ 248 (299)
.. ...... ..|..+..|++.+++....
T Consensus 102 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~ 135 (161)
T COG0494 102 VDDSLAVAIEGLSAPSEELEDLEWVPLDELAALV 135 (161)
T ss_pred ccccccccccccCCCcchhhceeeeeHHHccccc
Confidence 11 111111 2467889999999987433
No 81
>PLN02552 isopentenyl-diphosphate delta-isomerase
Probab=99.20 E-value=7.8e-11 Score=107.98 Aligned_cols=123 Identities=13% Similarity=0.135 Sum_probs=76.9
Q ss_pred EEEEEEeeCCEEEEEEeecCCC--CCceeec-eEEeeCCCC-----------------HHHHHHHHHHHHhCCceee---
Q 022283 143 VVGCLIEHDKKILLCKRKIEPS--YGLWTLP-AGYMEIGES-----------------AAEGAIRETWEEARADVEV--- 199 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~--~g~w~lP-gG~VE~GEs-----------------~eeAa~REv~EEtGl~v~~--- 199 (299)
+-++|.+.+++|||.||+.... +|+|+.. +|++..||+ ..+||+||++||+||++..
T Consensus 59 ~~v~i~n~~g~lLLQkRs~~K~~~Pg~Wd~s~~GHp~~ge~~~e~~~e~~~~~~~~~~~~eAA~REL~EElGI~~~~~~~ 138 (247)
T PLN02552 59 FSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLYGQDPNEVDRESELIDGNVLGVKNAAQRKLLHELGIPAEDVPV 138 (247)
T ss_pred EEEEEEcCCCeEEEEEecCCCCCCCcceecccCCccccccccccccccccccccchhhHHHHHHhHHHHHhCCCcccccc
Confidence 3334456678999999987542 7999666 355444422 6789999999999999653
Q ss_pred --ccceeeeec--CC-------C----CEEEEEEEEEe-cCCCCCCC-CcceeeEEecCCCCCCC---C---CCCccHHH
Q 022283 200 --QSPFAQLDI--PR-------I----GQIYIIFLAKL-KRPHFSPG-PESSECRLFALDEIPFD---S---LAFSSISV 256 (299)
Q Consensus 200 --~~~~~~~~~--p~-------~----~~~~~~f~a~~-~~~~~~~~-~E~~~~~W~~~deL~~~---~---laf~s~~~ 256 (299)
+.+++.+.+ +. . +....+|.... ..+.+.++ +|+.+++|+++++++.. . ..-|..+.
T Consensus 139 ~~l~~~~~~~y~~~~~~~~~~~~~~~E~e~~~v~~~~~~~~~~l~lq~eEV~~~~wvs~~el~~~~~~~~~~~~tpw~~~ 218 (247)
T PLN02552 139 DQFTFLTRLHYKAADDVTHGPDGKWGEHELDYLLFIRPVRDVKVNPNPDEVADVKYVNREELKEMMRKESGLKLSPWFRL 218 (247)
T ss_pred ccceeeeEEEEecccccccccCCCccceEEEEEEEEEecCCCcccCCHHHhheEEEEeHHHHHHHHhhcCCcccCHHHHH
Confidence 344443222 11 1 22333333332 23356766 88999999999998732 1 12344566
Q ss_pred HHHHHHHHH
Q 022283 257 TLQLFIDDI 265 (299)
Q Consensus 257 ~l~~~l~~~ 265 (299)
++.+++..|
T Consensus 219 ~~~~~l~~w 227 (247)
T PLN02552 219 IVDNFLMKW 227 (247)
T ss_pred HHHHHHHHH
Confidence 666777664
No 82
>PLN03143 nudix hydrolase; Provisional
Probab=99.15 E-value=2.5e-10 Score=106.88 Aligned_cols=109 Identities=17% Similarity=0.195 Sum_probs=69.8
Q ss_pred ecCCcE-EEEEEEeeCCE--EEEEEeecCCC-CCceeeceEEeeCC-CCHHHHHHHHHHHHhCCceeec--cce------
Q 022283 137 YQNPKM-VVGCLIEHDKK--ILLCKRKIEPS-YGLWTLPAGYMEIG-ESAAEGAIRETWEEARADVEVQ--SPF------ 203 (299)
Q Consensus 137 y~~p~~-vV~~iv~~~~k--ILL~rr~~~p~-~g~w~lPgG~VE~G-Es~eeAa~REv~EEtGl~v~~~--~~~------ 203 (299)
+.++.. +|.++++.+++ +||++|.+.+. .-.|++|||.+|++ |++++||+||++||||+.+... ..+
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 444444 44444454444 99999998764 44699999999974 8999999999999999986422 222
Q ss_pred ----eeeecCCC-CEEEEEEEEEecCC---------C---CCCCCcceeeEEecCCCCC
Q 022283 204 ----AQLDIPRI-GQIYIIFLAKLKRP---------H---FSPGPESSECRLFALDEIP 245 (299)
Q Consensus 204 ----~~~~~p~~-~~~~~~f~a~~~~~---------~---~~~~~E~~~~~W~~~deL~ 245 (299)
..++.|.. +..+.+|.+..... . .....|..++.|++++++-
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 23333322 23445566543211 0 1122566688999999975
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=99.11 E-value=9.7e-10 Score=87.59 Aligned_cols=103 Identities=21% Similarity=0.322 Sum_probs=74.3
Q ss_pred EEEEEEeeCCEEEEEEeecCCC-CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCC--EEEEEEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPS-YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIG--QIYIIFL 219 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~-~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~--~~~~~f~ 219 (299)
.+.+++.+++++||.||..... .|+|+||+|.++.+|+.+++..||+.||.++ ....++...+.+++ ..+.+|.
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 4455566678999999976543 8999999999999999999999999999765 22334455555555 3456677
Q ss_pred EEecCCCCCCCCcceeeEEecCCCCCCCCCCCccH
Q 022283 220 AKLKRPHFSPGPESSECRLFALDEIPFDSLAFSSI 254 (299)
Q Consensus 220 a~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~ 254 (299)
+....+. .+..+.+|+++++++ .++++..
T Consensus 82 ~~~~~~~----~~~~~~~W~~~eel~--~~~~p~~ 110 (118)
T cd03431 82 ARLEGDL----LAPDEGRWVPLEELD--EYALPTV 110 (118)
T ss_pred EEEeCCC----cCccccEEccHHHHh--hCCCCHH
Confidence 7665432 244578999999998 5666653
No 84
>KOG2839 consensus Diadenosine and diphosphoinositol polyphosphate phosphohydrolase [Signal transduction mechanisms]
Probab=99.06 E-value=1.7e-10 Score=96.37 Aligned_cols=119 Identities=22% Similarity=0.368 Sum_probs=74.7
Q ss_pred EEEEEEEe--eCC--EEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeee-c-CCCCEEE
Q 022283 142 MVVGCLIE--HDK--KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLD-I-PRIGQIY 215 (299)
Q Consensus 142 ~vV~~iv~--~~~--kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~-~-p~~~~~~ 215 (299)
.+++||.. +++ +|||+..++. +..|.+|+|++|+||+..+||.||++||.|+.-.....++... . +..+...
T Consensus 10 ~vagCi~~r~~~~~ieVLlvsSs~~--~~~wi~PKGGwE~dE~~~eAA~REt~EEAGv~G~l~~~~~g~~~~~~~~~~~~ 87 (145)
T KOG2839|consen 10 LVAGCICYRSDKEKIEVLLVSSSKK--PHRWIVPKGGWEPDESVEEAALRETWEEAGVKGKLGRLLGGFEDFLSKKHRTK 87 (145)
T ss_pred EEEEeeeeeecCcceEEEEEecCCC--CCCccCCCCCCCCCCCHHHHHHHHHHHHhCceeeeeccccchhhccChhhccc
Confidence 44555542 333 8999987754 3569999999999999999999999999999988888555432 2 1111111
Q ss_pred ---EEEEEEecC-CCCCCC--CcceeeEEecCCCCCCCCCCCccHHHHHHHHHH
Q 022283 216 ---IIFLAKLKR-PHFSPG--PESSECRLFALDEIPFDSLAFSSISVTLQLFID 263 (299)
Q Consensus 216 ---~~f~a~~~~-~~~~~~--~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l~ 263 (299)
+.|...... -+..++ .|..+.+|+.++|.-. ...+.-+...+..+++
T Consensus 88 ~k~~~~~l~v~e~le~wp~~~~~~r~r~W~~ledA~~-~~~~~~m~~al~e~~~ 140 (145)
T KOG2839|consen 88 PKGVMYVLAVTEELEDWPESEHEFREREWLKLEDAIE-LCQHKWMKAALEEFLQ 140 (145)
T ss_pred ccceeehhhhhhhcccChhhhcccceeEEeeHHHHHH-HHhhHHHHHHHHHHHH
Confidence 223222221 122333 4477899999998651 2334444444444443
No 85
>PLN02791 Nudix hydrolase homolog
Probab=98.94 E-value=2.1e-09 Score=111.78 Aligned_cols=105 Identities=20% Similarity=0.254 Sum_probs=73.1
Q ss_pred cEEEEEEE-ee-CCEEEEEEeecCCC--CCceee-ceEEeeCCCCHHHHHHHHHHHHhCCceee--ccceeee--e---c
Q 022283 141 KMVVGCLI-EH-DKKILLCKRKIEPS--YGLWTL-PAGYMEIGESAAEGAIRETWEEARADVEV--QSPFAQL--D---I 208 (299)
Q Consensus 141 ~~vV~~iv-~~-~~kILL~rr~~~p~--~g~w~l-PgG~VE~GEs~eeAa~REv~EEtGl~v~~--~~~~~~~--~---~ 208 (299)
..++.+++ +. +++|||+||+.... +|+|++ +||+++.||+.++||+||+.||+||.+.. +.+++.+ . .
T Consensus 32 HrAvhVwIfn~~~gelLLQkRS~~K~~~PG~WDiS~gGHv~aGEs~~eAA~REL~EELGI~l~~~~l~~l~~~~~~~~~~ 111 (770)
T PLN02791 32 HRAVHVWIYSESTQELLLQRRADCKDSWPGQWDISSAGHISAGDTSLLSAQRELEEELGIILPKDAFELLFVFLQECVIN 111 (770)
T ss_pred eEEEEEEEEECCCCeEEEEEecCCCCCCCCcccCcCCCCCCCCCCHHHHHHHHHHHHhCCCCChhheeeeeeEEEEeecc
Confidence 34444444 43 58999999986543 899999 69999999999999999999999998643 3333332 1 1
Q ss_pred C--C-CCEEEEEEEEEecCC----CCCCC-CcceeeEEecCCCCC
Q 022283 209 P--R-IGQIYIIFLAKLKRP----HFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 209 p--~-~~~~~~~f~a~~~~~----~~~~~-~E~~~~~W~~~deL~ 245 (299)
. . .+....+|.+..... ++.++ +|+.+++|++.+|+.
T Consensus 112 ~g~~~e~E~~~VYlv~~~~~~p~~~~~lq~eEV~~v~wvsl~El~ 156 (770)
T PLN02791 112 DGKFINNEYNDVYLVTTLDPIPLEAFTLQESEVSAVKYMSIEEYK 156 (770)
T ss_pred CCCcceeeEEEEEEEEECCCCCcccCCCChhhhheeEEEcHHHHH
Confidence 1 1 123445566554322 34566 899999999999975
No 86
>KOG3041 consensus Nucleoside diphosphate-sugar hydrolase of the MutT (NUDIX) family [Replication, recombination and repair]
Probab=98.91 E-value=8.4e-09 Score=90.31 Aligned_cols=105 Identities=25% Similarity=0.222 Sum_probs=69.3
Q ss_pred cEEEEEEEeeCC--EEEEEEeecCCCCCc-eeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccce-eeeecC---CCCE
Q 022283 141 KMVVGCLIEHDK--KILLCKRKIEPSYGL-WTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPF-AQLDIP---RIGQ 213 (299)
Q Consensus 141 ~~vV~~iv~~~~--kILL~rr~~~p~~g~-w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~-~~~~~p---~~~~ 213 (299)
.+++.+++..++ .|+|+++-+.|-++. .++|+|-+|.||++++||+||++||||+.-+....- ..+..| +.+.
T Consensus 75 gVaIl~il~~dG~~~ivL~kQfRpP~Gk~ciElPAGLiD~ge~~~~aAiREl~EEtGy~gkv~~~s~~~f~DPGltn~~~ 154 (225)
T KOG3041|consen 75 GVAILAILESDGKPYIVLVKQFRPPTGKICIELPAGLIDDGEDFEGAAIRELEEETGYKGKVDMVSPTVFLDPGLTNCNL 154 (225)
T ss_pred eEEEEEEEecCCcEEEEEEEeecCCCCcEEEEcccccccCCCchHHHHHHHHHHHhCccceeeeccccEEcCCCCCCCce
Confidence 455556666555 689999998885443 899999999999999999999999999984332211 112222 3345
Q ss_pred EEEEEEEEecCCC-CC----C-CCcceeeEEecCCCCC
Q 022283 214 IYIIFLAKLKRPH-FS----P-GPESSECRLFALDEIP 245 (299)
Q Consensus 214 ~~~~f~a~~~~~~-~~----~-~~E~~~~~W~~~deL~ 245 (299)
.++.+..+....+ .+ + +.|..++.-++..+|.
T Consensus 155 ~iv~v~idg~~pEnqrp~q~ledgEfIev~~i~~~~L~ 192 (225)
T KOG3041|consen 155 CIVVVDIDGDVPENQRPVQQLEDGEFIEVFLIPLSELW 192 (225)
T ss_pred EEEEEEecCCCccccCccccCCCCceEEEEEeeHHHHH
Confidence 5566655544332 11 2 3666677777766665
No 87
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=98.82 E-value=1.6e-09 Score=69.41 Aligned_cols=34 Identities=41% Similarity=1.094 Sum_probs=22.6
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
+|||.||++++.++++||+..|.+|++||+++|.
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 6999999999999999999999999999999984
No 88
>KOG3069 consensus Peroxisomal NUDIX hydrolase [Replication, recombination and repair]
Probab=98.76 E-value=1.6e-08 Score=90.87 Aligned_cols=114 Identities=24% Similarity=0.235 Sum_probs=76.9
Q ss_pred CCceeecCCcEEEEE-EEee---CCEEEEEEeecCCC--CCceeeceEEeeCCC-CHHHHHHHHHHHHhCCceeecccee
Q 022283 132 CGKIAYQNPKMVVGC-LIEH---DKKILLCKRKIEPS--YGLWTLPAGYMEIGE-SAAEGAIRETWEEARADVEVQSPFA 204 (299)
Q Consensus 132 Cg~~~y~~p~~vV~~-iv~~---~~kILL~rr~~~p~--~g~w~lPgG~VE~GE-s~eeAa~REv~EEtGl~v~~~~~~~ 204 (299)
|....++++..+|.+ ++.. +-+|||.||.+.-. .|.-+||||.+|+.+ |-+++|.||.+||+|++...+.+++
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 334444666655544 3333 24799999987533 789999999999664 7788999999999999987777766
Q ss_pred eeec---CC-CC-EEEEEEEEEecC-CCCCCC-CcceeeEEecCCCCC
Q 022283 205 QLDI---PR-IG-QIYIIFLAKLKR-PHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 205 ~~~~---p~-~~-~~~~~f~a~~~~-~~~~~~-~E~~~~~W~~~deL~ 245 (299)
..+- +. .. .-+++|.....- ....++ +|+.++.|++++++-
T Consensus 114 ~l~~~~~r~~~~v~p~v~~l~~~~~l~~~~ln~gEv~~~F~VPL~~ll 161 (246)
T KOG3069|consen 114 ALPPFVLRSGWSVFPVVGFLSDKKILPSLRLNSGEVESAFWVPLTDLL 161 (246)
T ss_pred hccceeeccCcccceeEEEEecccccccccCCchheeeeeeeeHHHHh
Confidence 4431 11 11 223445443321 224455 899999999999986
No 89
>PF14815 NUDIX_4: NUDIX domain; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A.
Probab=98.70 E-value=5.9e-08 Score=78.08 Aligned_cols=105 Identities=17% Similarity=0.198 Sum_probs=65.7
Q ss_pred EEEEEeeCCEEEEEEeecCCC-CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEE--EEEEEE
Q 022283 144 VGCLIEHDKKILLCKRKIEPS-YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQI--YIIFLA 220 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p~-~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~--~~~f~a 220 (299)
|.++++++|++||.||..... .|+|+||.-.++ +++..+.+.+.+.+..|+.+.....++...+.+.|.. +.+|.+
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 456778899999999997654 899999997776 3444666666677888998888888888888777744 466777
Q ss_pred EecCCCCCCCCcceeeEEecCCCCCCCCCCCccH
Q 022283 221 KLKRPHFSPGPESSECRLFALDEIPFDSLAFSSI 254 (299)
Q Consensus 221 ~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~ 254 (299)
.+...... +..+.+|++++++. .+++|..
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 77655322 34678999999998 6777764
No 90
>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=98.63 E-value=1.4e-08 Score=64.29 Aligned_cols=32 Identities=31% Similarity=0.643 Sum_probs=22.8
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
++++||++||+++... ++++.++|++||..+|
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 4789999999999887 6799999999999887
No 91
>COG4119 Predicted NTP pyrophosphohydrolase [DNA replication, recombination, and repair / General function prediction only]
Probab=98.58 E-value=1.1e-07 Score=78.01 Aligned_cols=100 Identities=20% Similarity=0.199 Sum_probs=65.3
Q ss_pred CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceee-ccceeeeecCCCCEEEEEE----------------EEEecC--C
Q 022283 165 YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEV-QSPFAQLDIPRIGQIYIIF----------------LAKLKR--P 225 (299)
Q Consensus 165 ~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~-~~~~~~~~~p~~~~~~~~f----------------~a~~~~--~ 225 (299)
.|-|++|.|.+..||+++.||+||.-||+||.|+- ...++.+.-+.. .+...| ..+... +
T Consensus 35 ~GAWSIPKGey~~gEdp~~AArREf~EE~Gi~vdGP~~~lG~~kQ~GG-KvVta~~veae~Dva~~rSntFe~eWPprSG 113 (161)
T COG4119 35 DGAWSIPKGEYTGGEDPWLAARREFSEEIGICVDGPRIDLGSLKQSGG-KVVTAFGVEAELDVADARSNTFELEWPPRSG 113 (161)
T ss_pred CCcccccccccCCCcCHHHHHHHHhhhhhceeecCchhhhhhhccCCC-cEEEEEeeeeeeehhhhhcceeeeecCCCCC
Confidence 68899999999999999999999999999999843 233444333322 222333 222221 1
Q ss_pred CCCCCCcceeeEEecCCCCCCCCCCCccHHHHHHHHHHHHHc
Q 022283 226 HFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLFIDDIRM 267 (299)
Q Consensus 226 ~~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l~~~~~ 267 (299)
....-+|++.+.||++.+.. .-.....+.+|.++.+....
T Consensus 114 ~M~~FPEVDRagWF~l~eAr--~Kil~gQRpfldrL~a~~~a 153 (161)
T COG4119 114 KMRKFPEVDRAGWFPLAEAR--TKILKGQRPFLDRLMAHAVA 153 (161)
T ss_pred ccccCcccccccceecHHHH--hHHhhccchHHHHHHHHhcc
Confidence 12233788999999999876 22234446666666655443
No 92
>KOG0648 consensus Predicted NUDIX hydrolase FGF-2 and related proteins [Signal transduction mechanisms]
Probab=98.47 E-value=1.8e-07 Score=87.11 Aligned_cols=115 Identities=23% Similarity=0.321 Sum_probs=76.9
Q ss_pred CCcEEEEEEEe-eCCEEEEEEeecCC--CCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceee---eecCCC-
Q 022283 139 NPKMVVGCLIE-HDKKILLCKRKIEP--SYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQ---LDIPRI- 211 (299)
Q Consensus 139 ~p~~vV~~iv~-~~~kILL~rr~~~p--~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~---~~~p~~- 211 (299)
...+.|++.|. .+++||+++..... ..|.|-+|+|.|++||++.++|+||++||||++..-...+.. ....+.
T Consensus 113 sh~vgvg~~V~n~~~eVlVv~e~d~~~~~~~~wK~ptG~v~~~e~i~~gavrEvkeetgid~ef~eVla~r~~H~~~~~~ 192 (295)
T KOG0648|consen 113 SHRVGVGAFVLNKKKEVLVVQEKDGAVKIRGGWKLPTGRVEEGEDIWHGAVREVKEETGIDTEFVEVLAFRRAHNATFGL 192 (295)
T ss_pred hhheeeeeeEecCCceeEEEEecccceeecccccccceEecccccchhhhhhhhHHHhCcchhhhhHHHHHhhhcchhhc
Confidence 33466666554 44699999865433 278999999999999999999999999999997654444321 111211
Q ss_pred CEEEEEEEEEecCC--CCCCC-CcceeeEEecCCCCCCCCCCCcc
Q 022283 212 GQIYIIFLAKLKRP--HFSPG-PESSECRLFALDEIPFDSLAFSS 253 (299)
Q Consensus 212 ~~~~~~f~a~~~~~--~~~~~-~E~~~~~W~~~deL~~~~laf~s 253 (299)
....++|.+.+... ++... .|+..+.|++.++........+.
T Consensus 193 ~ksd~f~~c~L~p~s~~i~~~~~ei~~~~Wmp~~e~v~qp~~~~~ 237 (295)
T KOG0648|consen 193 IKSDMFFTCELRPRSLDITKCKREIEAAAWMPIEEYVSQPLVHPK 237 (295)
T ss_pred ccccceeEEEeeccccccchhHHHHHHHhcccHHHhhcccccccc
Confidence 12335566665432 23333 67788899999987755554444
No 93
>COG1443 Idi Isopentenyldiphosphate isomerase [Lipid metabolism]
Probab=98.05 E-value=5.2e-06 Score=71.77 Aligned_cols=99 Identities=19% Similarity=0.301 Sum_probs=71.3
Q ss_pred EEEeeCCEEEEEEeecCCC--CCceeec-eEEeeCCCCHHHHHHHHHHHHhCCceeecc---ceeeeec--CCC-----C
Q 022283 146 CLIEHDKKILLCKRKIEPS--YGLWTLP-AGYMEIGESAAEGAIRETWEEARADVEVQS---PFAQLDI--PRI-----G 212 (299)
Q Consensus 146 ~iv~~~~kILL~rr~~~p~--~g~w~lP-gG~VE~GEs~eeAa~REv~EEtGl~v~~~~---~~~~~~~--p~~-----~ 212 (299)
.|.+.+|++||.||+.... +|.|+-- .|+--+||+.++|++|-+.+|+||++.... ++.-+.+ +.. +
T Consensus 39 ~lFne~g~LLltrRA~~K~twP~vWTNSvCsHP~~~es~~~A~~rRl~~ELGie~~~~d~~~il~rf~YrA~~~~~~~E~ 118 (185)
T COG1443 39 FLFNERGQLLLTRRALSKKTWPGVWTNSVCSHPLPGESNEDAARRRLAYELGIEPDQYDKLEILPRFRYRAADPDGIVEN 118 (185)
T ss_pred eEECCCCceeeehhhhhcccCcccccccccCCCcCCCchHHHHHHHHHHHhCCCCcccCccccccceEEeccCCCCccee
Confidence 3456679999999986543 7888765 788889999999999999999999987322 2222221 221 2
Q ss_pred EEEEEEEEEecCCCCCCC-CcceeeEEecCCCCC
Q 022283 213 QIYIIFLAKLKRPHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 213 ~~~~~f~a~~~~~~~~~~-~E~~~~~W~~~deL~ 245 (299)
.+..++.++... .+.++ +|+.+.+|++++++-
T Consensus 119 Eic~V~~~~~~~-~~~~npdEV~~~~wv~~e~l~ 151 (185)
T COG1443 119 EICPVLAARLDS-ALDPNPDEVMDYRWVSPEDLK 151 (185)
T ss_pred eeeeEEEEeecC-CCCCChHHhhheeccCHHHHH
Confidence 344556666655 45555 899999999999986
No 94
>PLN02839 nudix hydrolase
Probab=98.04 E-value=4.2e-05 Score=73.62 Aligned_cols=94 Identities=18% Similarity=0.188 Sum_probs=64.8
Q ss_pred CEEEEEEeecCCC--CCceeec-eEEeeCCCCHHHHHHHHHHHHhCCcee---eccceeeeecC------CCCEEEEEEE
Q 022283 152 KKILLCKRKIEPS--YGLWTLP-AGYMEIGESAAEGAIRETWEEARADVE---VQSPFAQLDIP------RIGQIYIIFL 219 (299)
Q Consensus 152 ~kILL~rr~~~p~--~g~w~lP-gG~VE~GEs~eeAa~REv~EEtGl~v~---~~~~~~~~~~p------~~~~~~~~f~ 219 (299)
.++.+.||+.... +|+|+.. ||.+..||++.++++||.+||.||... .....|...+- ......++|-
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 4678888875432 7998765 899999999999999999999999753 23333333221 1112233466
Q ss_pred EEecCCC-CCC-CCcceeeEEecCCCCC
Q 022283 220 AKLKRPH-FSP-GPESSECRLFALDEIP 245 (299)
Q Consensus 220 a~~~~~~-~~~-~~E~~~~~W~~~deL~ 245 (299)
.++..+- +.+ |+|++++.+++++|+.
T Consensus 298 LeLP~df~P~~qDGEVe~F~Lm~v~EV~ 325 (372)
T PLN02839 298 LELPQDFVPKNQDGEVESFKLIPVAQVA 325 (372)
T ss_pred eecCCccccCCCccceeEEEEecHHHHH
Confidence 6655543 233 4899999999999975
No 95
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=97.47 E-value=0.00022 Score=49.44 Aligned_cols=42 Identities=31% Similarity=0.525 Sum_probs=30.9
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEE
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLI 148 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv 148 (299)
+|||.||.-+.... ++...+..|+.||+..+.++..++.-.+
T Consensus 1 ~FCp~Cg~~l~~~~--~~~~~~~vC~~Cg~~~~~~~~~~~~~~~ 42 (52)
T smart00661 1 KFCPKCGNMLIPKE--GKEKRRFVCRKCGYEEPIEQKYVYKEKL 42 (52)
T ss_pred CCCCCCCCcccccc--CCCCCEEECCcCCCeEECCCcEEEEEEe
Confidence 59999999876652 1223488999999999998885554333
No 96
>KOG2937 consensus Decapping enzyme complex, predicted pyrophosphatase DCP2 [RNA processing and modification]
Probab=97.19 E-value=6.9e-05 Score=70.62 Aligned_cols=108 Identities=24% Similarity=0.266 Sum_probs=75.3
Q ss_pred CceeecCCcEEEEEEEeeC--CEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeec--cceeeeec
Q 022283 133 GKIAYQNPKMVVGCLIEHD--KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQ--SPFAQLDI 208 (299)
Q Consensus 133 g~~~y~~p~~vV~~iv~~~--~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~--~~~~~~~~ 208 (299)
.+.-|..+.|+.++++.+. .++||++.-. ...|.+|-|++..+|+..+++.|||.||||.++... ...+ .+.
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 4566788888888887654 5899988653 334999999999999999999999999999998432 1222 222
Q ss_pred CCCCEEEEEEEEEecCCC----CCCCCcceeeEEecCCCC
Q 022283 209 PRIGQIYIIFLAKLKRPH----FSPGPESSECRLFALDEI 244 (299)
Q Consensus 209 p~~~~~~~~f~a~~~~~~----~~~~~E~~~~~W~~~deL 244 (299)
...+.+...|..-..+.+ +....|++.+.|+.++++
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 223344444443222211 334488899999999999
No 97
>KOG4195 consensus Transient receptor potential-related channel 7 [Inorganic ion transport and metabolism]
Probab=97.15 E-value=0.0024 Score=57.31 Aligned_cols=40 Identities=33% Similarity=0.531 Sum_probs=34.1
Q ss_pred EEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCC
Q 022283 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARA 195 (299)
Q Consensus 153 kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl 195 (299)
+++.++|. ..|.|.+|||-||+||-+-.+++||+.||.==
T Consensus 140 e~vavkr~---d~~~WAiPGGmvdpGE~vs~tLkRef~eEa~n 179 (275)
T KOG4195|consen 140 EFVAVKRP---DNGEWAIPGGMVDPGEKVSATLKREFGEEAMN 179 (275)
T ss_pred EEEEEecC---CCCcccCCCCcCCchhhhhHHHHHHHHHHHHH
Confidence 45666665 47899999999999999999999999999643
No 98
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=97.08 E-value=0.00041 Score=48.32 Aligned_cols=33 Identities=30% Similarity=0.578 Sum_probs=25.3
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecC
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (299)
+.++|||+||+. .+. ....+..|..||+..|.+
T Consensus 18 ~~~~fCP~Cg~~-~m~----~~~~r~~C~~Cgyt~~~~ 50 (50)
T PRK00432 18 RKNKFCPRCGSG-FMA----EHLDRWHCGKCGYTEFKK 50 (50)
T ss_pred EccCcCcCCCcc-hhe----ccCCcEECCCcCCEEecC
Confidence 467899999996 333 234689999999999853
No 99
>PRK10880 adenine DNA glycosylase; Provisional
Probab=97.01 E-value=0.0035 Score=60.56 Aligned_cols=110 Identities=12% Similarity=0.121 Sum_probs=62.1
Q ss_pred EEEEEeeCCEEEEEEeecCCC-CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEE--EEEEEE
Q 022283 144 VGCLIEHDKKILLCKRKIEPS-YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQI--YIIFLA 220 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p~-~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~--~~~f~a 220 (299)
..+++.+++++||.||..... .|+|+||.. +. . + ..++..|+.|+.......++...+.+.|.. +..|.+
T Consensus 234 ~~~~~~~~~~~~l~~r~~~gl~~gl~~fP~~--~~---~-~-~~~~~~~~~~~~~~~~~~~~~~~H~fTH~~~~~~~~~~ 306 (350)
T PRK10880 234 YFLLLQHGDEVWLEQRPPSGLWGGLFCFPQF--AD---E-E-ELRQWLAQRGIAADNLTQLTAFRHTFSHFHLDIVPMWL 306 (350)
T ss_pred EEEEEEECCEEEEEECCccChhhccccCCCC--cc---h-h-hHHHHHHhcCCchhhhcccCceEEEEeeEEEEEEEEEE
Confidence 334556788999999986543 899999962 21 1 1 245566788876432222334444444433 334555
Q ss_pred EecCCCCCCCCcceeeEEecCCCCCCCCCCCccHHHHHHHHHHHHHc
Q 022283 221 KLKRPHFSPGPESSECRLFALDEIPFDSLAFSSISVTLQLFIDDIRM 267 (299)
Q Consensus 221 ~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~~~~l~~~l~~~~~ 267 (299)
.......... ..+..|++++++. .+++|+.. +++++....
T Consensus 307 ~~~~~~~~~~--~~~~~w~~~~~~~--~~~~p~~~---~k~l~~~~~ 346 (350)
T PRK10880 307 PVSSFTGCMD--EGNGLWYNLAQPP--SVGLAAPV---ERLLQQLRT 346 (350)
T ss_pred EccccccccC--CcCCeEechHHhc--ccCCcHHH---HHHHHHhcc
Confidence 4432211111 1234799999998 68888743 455544443
No 100
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=96.95 E-value=0.00057 Score=47.06 Aligned_cols=35 Identities=29% Similarity=0.562 Sum_probs=27.9
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecC
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (299)
.+.++|||+||.-..+. +...|..|-.||.+.|.+
T Consensus 16 ~rk~~~CPrCG~gvfmA----~H~dR~~CGkCgyTe~~~ 50 (51)
T COG1998 16 KRKNRFCPRCGPGVFMA----DHKDRWACGKCGYTEFKK 50 (51)
T ss_pred EEccccCCCCCCcchhh----hcCceeEeccccceEeec
Confidence 46789999999776665 345599999999998864
No 101
>COG4112 Predicted phosphoesterase (MutT family) [General function prediction only]
Probab=96.86 E-value=0.0064 Score=52.27 Aligned_cols=101 Identities=22% Similarity=0.246 Sum_probs=68.2
Q ss_pred EEEEeeCCEEEEEEeecCCC----CCceeec-eEEeeCCC---CHHHH----HHHHHHHHhCCc---eeeccceeeeecC
Q 022283 145 GCLIEHDKKILLCKRKIEPS----YGLWTLP-AGYMEIGE---SAAEG----AIRETWEEARAD---VEVQSPFAQLDIP 209 (299)
Q Consensus 145 ~~iv~~~~kILL~rr~~~p~----~g~w~lP-gG~VE~GE---s~eeA----a~REv~EEtGl~---v~~~~~~~~~~~p 209 (299)
.|++.++++||+-.|-.... .+.+++- ||++..++ +.++. +.||+.||+++. ...+.++|.....
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 45677888999999876543 4677775 89998665 33332 679999999998 4556677765432
Q ss_pred CC--C-E-EEEEEEEEecCCCCCCC-CcceeeEEecCCCCC
Q 022283 210 RI--G-Q-IYIIFLAKLKRPHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 210 ~~--~-~-~~~~f~a~~~~~~~~~~-~E~~~~~W~~~deL~ 245 (299)
.. + . +-+.|..+....++... .+.-+..|+..++|.
T Consensus 145 ~neVgkVHiG~lf~~~~k~ndvevKEkd~~~~kwik~~ele 185 (203)
T COG4112 145 TNEVGKVHIGALFLGRGKFNDVEVKEKDLFEWKWIKLEELE 185 (203)
T ss_pred CcccceEEEEEEEEeeccccceeeeecceeeeeeeeHHHHH
Confidence 21 1 2 22456666655444443 556678999999987
No 102
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.83 E-value=0.0039 Score=36.43 Aligned_cols=22 Identities=27% Similarity=0.936 Sum_probs=17.2
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
|||.||+++... ...|+.||..
T Consensus 1 ~Cp~CG~~~~~~--------~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD--------AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc--------CcchhhhCCc
Confidence 799999997432 5679999963
No 103
>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=95.20 E-value=0.0081 Score=38.69 Aligned_cols=31 Identities=29% Similarity=0.563 Sum_probs=20.4
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.+|||.||.-|..... ..... .|..|++.+-
T Consensus 1 m~FCp~C~nlL~p~~~--~~~~~-~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGNLLYPKED--KEKRV-ACRTCGYEEP 31 (35)
T ss_dssp --BETTTTSBEEEEEE--TTTTE-EESSSS-EEE
T ss_pred CeeCCCCCccceEcCC--CccCc-CCCCCCCccC
Confidence 3799999999987632 22233 8999998653
No 104
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=94.96 E-value=0.012 Score=35.31 Aligned_cols=24 Identities=29% Similarity=0.718 Sum_probs=18.0
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.++||.||+.+.. ..+.|+.||..
T Consensus 2 ~~~Cp~Cg~~~~~--------~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDP--------DAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCc--------ccccChhhCCC
Confidence 4689999996432 26899999963
No 105
>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=94.73 E-value=0.023 Score=33.55 Aligned_cols=24 Identities=29% Similarity=0.671 Sum_probs=20.3
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
|..||..+..+ +......||+||+
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 78899998776 5578999999995
No 106
>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=94.72 E-value=0.18 Score=44.64 Aligned_cols=40 Identities=28% Similarity=0.444 Sum_probs=29.8
Q ss_pred EEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCc
Q 022283 153 KILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARAD 196 (299)
Q Consensus 153 kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~ 196 (299)
.|||.|.. ...|.+|||.+.+||+.++...|.+.+-.|..
T Consensus 59 HvLLLq~~----~~~fkLPGg~l~~gE~e~~gLkrkL~~~l~~~ 98 (188)
T PF13869_consen 59 HVLLLQIG----NTFFKLPGGRLRPGEDEIEGLKRKLTEKLSPE 98 (188)
T ss_dssp EEEEEEET----TTEEE-SEEE--TT--HHHHHHHHHHHHHB-S
T ss_pred EEEEEecc----CccccCCccEeCCCCChhHHHHHHHHHHcCCC
Confidence 68888854 45899999999999999999999999999875
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=93.83 E-value=0.035 Score=33.40 Aligned_cols=24 Identities=25% Similarity=0.599 Sum_probs=18.6
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
+.||.||+.... ....||.||+.+
T Consensus 1 K~CP~C~~~V~~--------~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPE--------SAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchh--------hcCcCCCCCCCC
Confidence 469999998643 367899999754
No 108
>PRK13910 DNA glycosylase MutY; Provisional
Probab=93.62 E-value=0.33 Score=45.83 Aligned_cols=85 Identities=15% Similarity=0.235 Sum_probs=46.9
Q ss_pred EEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCE--EEEEEEEE
Q 022283 144 VGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQ--IYIIFLAK 221 (299)
Q Consensus 144 V~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~--~~~~f~a~ 221 (299)
..+++.+++++||.||...-..|+|+||.. +. +.+.... ..+...+.+.|. .+.+|.+.
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 334455678999998853223899999962 21 0111111 123333333332 23445554
Q ss_pred ecCCCCCCCCcceeeEEecCCCCCCCCCCCccHHH
Q 022283 222 LKRPHFSPGPESSECRLFALDEIPFDSLAFSSISV 256 (299)
Q Consensus 222 ~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~~~ 256 (299)
.... ..+.+|++++++. .+++|....
T Consensus 250 ~~~~-------~~~~~w~~~~~~~--~~~~p~~~~ 275 (289)
T PRK13910 250 IKDL-------KNPIRFYSLKDLE--TLPISSMTL 275 (289)
T ss_pred eccC-------CccceEecHHHhh--hcCCcHHHH
Confidence 4211 1345899999998 688887543
No 109
>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=93.47 E-value=0.056 Score=36.07 Aligned_cols=34 Identities=21% Similarity=0.454 Sum_probs=26.9
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
.-|.+|.--..+||.||.|+... ......|+.|+
T Consensus 8 ~LL~G~~ML~~~Cp~C~~PL~~~-----k~g~~~Cv~C~ 41 (41)
T PF06677_consen 8 YLLQGWTMLDEHCPDCGTPLMRD-----KDGKIYCVSCG 41 (41)
T ss_pred HHHHhHhHhcCccCCCCCeeEEe-----cCCCEECCCCC
Confidence 55778999999999999998663 22357999996
No 110
>PRK00420 hypothetical protein; Validated
Probab=93.18 E-value=0.08 Score=43.05 Aligned_cols=32 Identities=25% Similarity=0.491 Sum_probs=24.1
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
+|..-...||.||.++... .....+||.||..
T Consensus 18 Ga~ml~~~CP~Cg~pLf~l-----k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 18 GAKMLSKHCPVCGLPLFEL-----KDGEVVCPVHGKV 49 (112)
T ss_pred HHHHccCCCCCCCCcceec-----CCCceECCCCCCe
Confidence 5555679999999998652 1236899999963
No 111
>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=92.64 E-value=0.064 Score=43.07 Aligned_cols=51 Identities=20% Similarity=0.328 Sum_probs=34.2
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcE----------EEEEEEeeCCEEEEEEee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKM----------VVGCLIEHDKKILLCKRK 160 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~----------vV~~iv~~~~kILL~rr~ 160 (299)
.-||+|++...+. ++.-..||.|++.+-+.-.. +.+.++.+++.|.|++--
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 4699999997764 45679999999988654311 111223456778888743
No 112
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=92.62 E-value=0.08 Score=44.09 Aligned_cols=28 Identities=25% Similarity=0.618 Sum_probs=21.8
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
..+||.||.|+-.+ ++ .-+||.||+..+
T Consensus 28 ~~hCp~Cg~PLF~K----dG--~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCGTPLFRK----DG--EVFCPVCGYREV 55 (131)
T ss_pred HhhCcccCCcceee----CC--eEECCCCCceEE
Confidence 35899999998775 33 679999997444
No 113
>KOG4548 consensus Mitochondrial ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=91.80 E-value=0.49 Score=43.52 Aligned_cols=93 Identities=18% Similarity=0.243 Sum_probs=60.4
Q ss_pred CEEEEEEeecCCCCCceeeceEEe-eCCCCHHHHHHHHHHHHhCCceeec----cceeeeecCC---------CCEEEEE
Q 022283 152 KKILLCKRKIEPSYGLWTLPAGYM-EIGESAAEGAIRETWEEARADVEVQ----SPFAQLDIPR---------IGQIYII 217 (299)
Q Consensus 152 ~kILL~rr~~~p~~g~w~lPgG~V-E~GEs~eeAa~REv~EEtGl~v~~~----~~~~~~~~p~---------~~~~~~~ 217 (299)
.=+||+++... ..+.|.||-+-. +.++++...|.|++++-.|=..... ..++...... .....++
T Consensus 139 ~LyLLV~~k~g-~~s~w~fP~~~~s~~~~~lr~~ae~~Lk~~~ge~~~t~fvgnaP~g~~~~q~pr~~~~e~~~~sk~ff 217 (263)
T KOG4548|consen 139 KLYLLVKRKFG-KSSVWIFPNRQFSSSEKTLRGHAERDLKVLSGENKSTWFVGNAPFGHTPLQSPREMTTEEPVSSKVFF 217 (263)
T ss_pred eEEEEEeeccC-ccceeeCCCcccCCccchHHHHHHHHHHHHhcchhhhheeccCccccccccCcccccccccccceeEE
Confidence 34677775533 367899999999 9999999999999999888654321 1233222111 1233455
Q ss_pred EEEEecCCCCCCCCcceeeEEecCCCCC
Q 022283 218 FLAKLKRPHFSPGPESSECRLFALDEIP 245 (299)
Q Consensus 218 f~a~~~~~~~~~~~E~~~~~W~~~deL~ 245 (299)
|.+.+..+...-..-..|..|++.++|.
T Consensus 218 ~k~~lv~~~~~kn~n~edfvWvTkdel~ 245 (263)
T KOG4548|consen 218 FKASLVANSNQKNQNKEDFVWVTKDELG 245 (263)
T ss_pred eeeeeccccchhcccccceEEechHHHh
Confidence 6666655543222334569999999997
No 114
>PF12773 DZR: Double zinc ribbon
Probab=91.80 E-value=0.088 Score=36.02 Aligned_cols=32 Identities=25% Similarity=0.589 Sum_probs=23.7
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
...+||+.||.++.. .......|+.||....+
T Consensus 10 ~~~~fC~~CG~~l~~-----~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPP-----PDQSKKICPNCGAENPP 41 (50)
T ss_pred ccccCChhhcCChhh-----ccCCCCCCcCCcCCCcC
Confidence 457899999999872 23456889999986543
No 115
>KOG4432 consensus Uncharacterized NUDIX family hydrolase [General function prediction only]
Probab=91.48 E-value=0.4 Score=45.19 Aligned_cols=74 Identities=19% Similarity=0.187 Sum_probs=52.2
Q ss_pred eeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeec----CCCCEEEEEEEEEecCCC-CCCCCcceeeEEecC
Q 022283 168 WTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDI----PRIGQIYIIFLAKLKRPH-FSPGPESSECRLFAL 241 (299)
Q Consensus 168 w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~----p~~~~~~~~f~a~~~~~~-~~~~~E~~~~~W~~~ 241 (299)
.++-||-|+.+-|+.|-|..|+.||.|.+|....+.-++.+ ....+.|+.|.|++.+.. +.....+..-+..++
T Consensus 81 ielc~g~idke~s~~eia~eev~eecgy~v~~d~l~hv~~~~~g~~~s~sa~~l~y~ei~es~kis~gggv~~~~~~~~ 159 (405)
T KOG4432|consen 81 IELCAGLIDKELSPREIASEEVAEECGYRVDPDDLIHVITFVVGAHQSGSAQHLYYAEIDESMKISEGGGVITKVYYPV 159 (405)
T ss_pred eeeeccccccccCHHHHhHHHHHHHhCCcCChhHceEEEEEEeccccCccchheeeeecchhhccccCCceeeEEEEee
Confidence 56779999999999999999999999999977666554443 234567888888876542 433333333344443
No 116
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=91.38 E-value=0.24 Score=40.33 Aligned_cols=35 Identities=23% Similarity=0.521 Sum_probs=27.0
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
++|||.||+-|..+.. +.+....|+.||...=...
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 6899999999988743 2345999999997765443
No 117
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.08 E-value=0.2 Score=33.93 Aligned_cols=28 Identities=25% Similarity=0.553 Sum_probs=20.9
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
-|+.||..+... +......||.||....
T Consensus 5 ~C~~CG~~~~~~----~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 5 KCARCGREVELD----EYGTGVRCPYCGYRIL 32 (46)
T ss_pred ECCCCCCEEEEC----CCCCceECCCCCCeEE
Confidence 499999997664 2333789999997554
No 118
>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=91.08 E-value=0.19 Score=36.67 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=24.8
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
+.+-||.||...... ..+....|+.||...
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 788999999998773 356789999999874
No 119
>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=90.90 E-value=0.098 Score=47.83 Aligned_cols=39 Identities=15% Similarity=0.325 Sum_probs=16.9
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.|...+.|||.||+.-......+.----+.|+.|+..+-
T Consensus 26 ~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 26 DWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp HHHHHH---TTT--SS-EE--------EEE-TTT--EEE
T ss_pred HHHHHCCcCCCCCChhHhhccCCCccceeECCCCchHHh
Confidence 699999999999999333322222223478999986654
No 120
>KOG1689 consensus mRNA cleavage factor I subunit [RNA processing and modification]
Probab=90.78 E-value=0.38 Score=41.84 Aligned_cols=39 Identities=28% Similarity=0.395 Sum_probs=33.8
Q ss_pred CEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhC
Q 022283 152 KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEAR 194 (299)
Q Consensus 152 ~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtG 194 (299)
-.|||.+-. .-.+.+|||.+++||+-.+.+.|-+-|-+|
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 478877632 457999999999999999999999999999
No 121
>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=90.69 E-value=0.085 Score=40.53 Aligned_cols=31 Identities=6% Similarity=-0.082 Sum_probs=21.9
Q ss_pred cccceecccccc-CCCCCCcchHHHHHHHHhh
Q 022283 70 RASRVCATRSES-NQDATSSHPSSAAVHSAGN 100 (299)
Q Consensus 70 ~~~~~~~~r~~~-~~~~~~~~~~~~a~~l~~w 100 (299)
...++.+||+++ .+++.+++++++|+||++|
T Consensus 67 ~~~~~~~LR~~~~~l~~~~~~l~a~A~~ll~W 98 (98)
T PF09296_consen 67 EGFEFVDLRQLGGQLPEEDAGLAARARQLLDW 98 (98)
T ss_dssp ----EE-GGGGT-TS-HHHHHHHHHHHHHHH-
T ss_pred ccccchhHHHHHHcCCHHHHHHHHHHHHHhcC
Confidence 456788889875 6899999999999999999
No 122
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=90.60 E-value=0.21 Score=32.94 Aligned_cols=31 Identities=23% Similarity=0.542 Sum_probs=24.6
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
.||+|+..|..... .+.....|++|+-..+.
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 59999999887754 44677889999987764
No 123
>PRK10220 hypothetical protein; Provisional
Probab=90.60 E-value=0.19 Score=40.48 Aligned_cols=52 Identities=17% Similarity=0.337 Sum_probs=34.8
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEE----------EEEEEeeCCEEEEEEee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMV----------VGCLIEHDKKILLCKRK 160 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~v----------V~~iv~~~~kILL~rr~ 160 (299)
..-||+|++...+. ++.-..||.|++.+-+.-... .+.++.+++.|.|++--
T Consensus 3 lP~CP~C~seytY~-----d~~~~vCpeC~hEW~~~~~~~~~~~~~vkDsnG~~L~dGDsV~viKDL 64 (111)
T PRK10220 3 LPHCPKCNSEYTYE-----DNGMYICPECAHEWNDAEPAQESDELIVKDANGNLLADGDSVTIVKDL 64 (111)
T ss_pred CCcCCCCCCcceEc-----CCCeEECCcccCcCCccccccccCCceEEcCCCCCccCCCEEEEEeec
Confidence 45799999997764 456799999999887654211 11122356678887743
No 124
>PHA00626 hypothetical protein
Probab=90.58 E-value=0.21 Score=35.52 Aligned_cols=33 Identities=18% Similarity=0.283 Sum_probs=20.8
Q ss_pred CCCcCCCCCCcccccC-CCCcceeecCCCCceee
Q 022283 105 SFCQWCGGQTKHEVPH-GEEKMRAICTVCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~-~~~~~~~~C~~Cg~~~y 137 (299)
..||.||+....+.-- ..-..+..|++||+.+-
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 3699999974443100 01135679999998764
No 125
>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=89.71 E-value=0.21 Score=39.53 Aligned_cols=29 Identities=24% Similarity=0.583 Sum_probs=22.6
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeecC
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (299)
+|||.||..|... +....|+.|++.....
T Consensus 1 ~fC~~Cg~~l~~~------~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 1 KFCPKCGSLMTPK------NGVYVCPSCGYEKEKK 29 (104)
T ss_pred CCCcccCcccccC------CCeEECcCCCCccccc
Confidence 4999999999653 2378999999876543
No 126
>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=89.50 E-value=0.21 Score=31.08 Aligned_cols=27 Identities=26% Similarity=0.604 Sum_probs=14.8
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.-||.||+..... ++...+|+.|+...
T Consensus 3 p~Cp~C~se~~y~-----D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYE-----DGELLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE------SSSEEETTTTEEE
T ss_pred CCCCCCCCcceec-----cCCEEeCCcccccC
Confidence 4699999997763 56789999999753
No 127
>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=89.31 E-value=0.29 Score=31.51 Aligned_cols=32 Identities=22% Similarity=0.461 Sum_probs=21.5
Q ss_pred CCcCCCCCCcccc-cCCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEV-PHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~-~~~~~~~~~~C~~Cg~~~y 137 (299)
-||.||+...... ..++.+....|+.||...+
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 4999999754431 0112345789999998776
No 128
>KOG0142 consensus Isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=88.95 E-value=0.26 Score=43.90 Aligned_cols=97 Identities=28% Similarity=0.369 Sum_probs=59.1
Q ss_pred EEeeCCEEEEEEeecCCC--CCceee---------ceEEee-CCCCHHHHHHHHHHHHhCCceeecc-----ceeeeec-
Q 022283 147 LIEHDKKILLCKRKIEPS--YGLWTL---------PAGYME-IGESAAEGAIRETWEEARADVEVQS-----PFAQLDI- 208 (299)
Q Consensus 147 iv~~~~kILL~rr~~~p~--~g~w~l---------PgG~VE-~GEs~eeAa~REv~EEtGl~v~~~~-----~~~~~~~- 208 (299)
+.+.++++||.+|+.... ++.|+- |+.--+ .+.-+..||.|-+.-|+||..+.+. ++.-+.+
T Consensus 59 lFns~~~lLlQqRS~~KitFP~~~TNtccSHPL~~~~el~~~d~lGVr~AAqRkL~~ELGIp~e~v~pee~~~ltrihYk 138 (225)
T KOG0142|consen 59 LFNSKNELLLQQRSDEKITFPGLWTNTCCSHPLYNPGELEENDALGVRRAAQRKLKAELGIPLEEVPPEEFNFLTRIHYK 138 (225)
T ss_pred EecCcchHHHhhhccccccccchhhhhhhcCcCCChhhhccCchHHHHHHHHHHHHHhhCCCccccCHHHcccceeeeee
Confidence 345678999999886432 555542 222211 1235678999999999999875443 4443322
Q ss_pred -C------CCCEEEEEEEEEecCCCCCCC-CcceeeEEecCCCCC
Q 022283 209 -P------RIGQIYIIFLAKLKRPHFSPG-PESSECRLFALDEIP 245 (299)
Q Consensus 209 -p------~~~~~~~~f~a~~~~~~~~~~-~E~~~~~W~~~deL~ 245 (299)
+ ....-++.|... .-.+.++ +|+.+++|++.+||.
T Consensus 139 A~sdg~wGEhEiDYiL~~~~--~~~~nPnpnEv~e~ryvs~eelk 181 (225)
T KOG0142|consen 139 APSDGIWGEHEIDYILFLVK--DVTLNPNPNEVSEIRYVSREELK 181 (225)
T ss_pred cCCCCCcccceeeEEEEEec--cCCCCCChhhhhHhheecHHHHH
Confidence 1 111233444332 2235565 899999999999985
No 129
>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=88.67 E-value=0.24 Score=40.05 Aligned_cols=32 Identities=22% Similarity=0.420 Sum_probs=21.9
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeecC
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (299)
+-|-||.||++..-. .....+||.||..+-+.
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 457888888886543 22456788888776554
No 130
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=88.41 E-value=0.32 Score=41.73 Aligned_cols=31 Identities=29% Similarity=0.689 Sum_probs=18.8
Q ss_pred CCcCCCCCCcccc-----cCCC-CcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEV-----PHGE-EKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~-----~~~~-~~~~~~C~~Cg~~~ 136 (299)
-||.||++-.... .+|. -..++.|+.||..+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5999998752221 1111 12348999999765
No 131
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=88.25 E-value=0.32 Score=39.61 Aligned_cols=22 Identities=36% Similarity=0.859 Sum_probs=18.4
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
||.||+++... +..|++|+...
T Consensus 1 CPvCg~~l~vt--------~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVT--------RLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEE--------EEEcCCCCCEE
Confidence 99999998765 68999998543
No 132
>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=87.33 E-value=0.24 Score=30.26 Aligned_cols=22 Identities=27% Similarity=0.594 Sum_probs=12.2
Q ss_pred CCcCCCCCCcccccCCCCcceeecCC
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTV 131 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~ 131 (299)
+||.||+++... +++...+|++
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 699999998865 4556777763
No 133
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=87.02 E-value=0.36 Score=33.44 Aligned_cols=31 Identities=23% Similarity=0.549 Sum_probs=22.9
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
-|..||+..+.. .......||.||+...-.+
T Consensus 8 ~C~~Cg~~~~~~----~~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 8 KCARCGREVELD----QETRGIRCPYCGSRILVKE 38 (49)
T ss_pred EhhhcCCeeehh----hccCceeCCCCCcEEEEec
Confidence 399999998533 3456789999998776433
No 134
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.89 E-value=0.5 Score=30.46 Aligned_cols=32 Identities=16% Similarity=0.468 Sum_probs=22.3
Q ss_pred CCcCCCCCCccccc-CCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVP-HGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~-~~~~~~~~~C~~Cg~~~y 137 (299)
-||.|++....... ..+.+....|+.||..++
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 49999998644310 114567899999998764
No 135
>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=86.26 E-value=0.45 Score=31.69 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=18.4
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.||.||+..... . ....-.+|+.||.+.
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 234456999999764
No 136
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=86.20 E-value=0.57 Score=37.60 Aligned_cols=52 Identities=21% Similarity=0.365 Sum_probs=35.3
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcE-----------EEEEEEeeCCEEEEEEee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKM-----------VVGCLIEHDKKILLCKRK 160 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~-----------vV~~iv~~~~kILL~rr~ 160 (299)
..-||.|++...+. ++....||.|++.+-++-.. +.+.++.+++.|.|++--
T Consensus 3 lp~cp~c~sEytYe-----d~~~~~cpec~~ew~~~~~~~~~~~~~~v~DsnGn~L~dGDsV~lIKDL 65 (112)
T COG2824 3 LPPCPKCNSEYTYE-----DGGQLICPECAHEWNENEAAEEADEALIVKDSNGNLLADGDSVTLIKDL 65 (112)
T ss_pred CCCCCccCCceEEe-----cCceEeCchhccccccccccccccCceEEEcCCCcEeccCCeEEEEEee
Confidence 45799999997764 44589999999988754321 112334456777777643
No 137
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.18 E-value=1 Score=30.42 Aligned_cols=26 Identities=27% Similarity=0.578 Sum_probs=20.1
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
-|+.||...... ......|+.||...
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCceE
Confidence 399999997764 34568999999754
No 138
>COG4640 Predicted membrane protein [Function unknown]
Probab=86.17 E-value=0.35 Score=47.17 Aligned_cols=25 Identities=36% Similarity=0.881 Sum_probs=16.7
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
++||+.||+.-.. + ...|+.||...
T Consensus 1 M~fC~kcG~qk~E------d--~~qC~qCG~~~ 25 (465)
T COG4640 1 MKFCPKCGSQKAE------D--DVQCTQCGHKF 25 (465)
T ss_pred CCccccccccccc------c--cccccccCCcC
Confidence 5899999955211 1 23499999654
No 139
>PF14353 CpXC: CpXC protein
Probab=86.16 E-value=0.96 Score=37.06 Aligned_cols=49 Identities=20% Similarity=0.427 Sum_probs=29.8
Q ss_pred CCcCCCCCCccccc---C------------CCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEE
Q 022283 106 FCQWCGGQTKHEVP---H------------GEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLC 157 (299)
Q Consensus 106 fC~~CG~~~~~~~~---~------------~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~ 157 (299)
-||.||++...... + ...-....||+||.......... .++.+.++++.
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~l---Y~D~~~~~~i~ 66 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLL---YHDPEKKFMIY 66 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEE---EEcCCCCEEEE
Confidence 59999998754411 0 11235789999999887544332 23445555554
No 140
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.07 E-value=0.49 Score=30.65 Aligned_cols=32 Identities=16% Similarity=0.332 Sum_probs=22.5
Q ss_pred CCcCCCCCCccccc-CCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVP-HGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~-~~~~~~~~~C~~Cg~~~y 137 (299)
-||.|++....... ..+.+.+..|+.|+..+.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 49999999654311 114567899999998764
No 141
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=85.97 E-value=2.1 Score=41.26 Aligned_cols=93 Identities=18% Similarity=0.199 Sum_probs=54.0
Q ss_pred EEEEEEeeCCEEEEEEeecCCC-CCceeeceEEeeCCCCHHHHHHHHHHHHhCCceeeccceeeeecCCCCEEEEE-EEE
Q 022283 143 VVGCLIEHDKKILLCKRKIEPS-YGLWTLPAGYMEIGESAAEGAIRETWEEARADVEVQSPFAQLDIPRIGQIYII-FLA 220 (299)
Q Consensus 143 vV~~iv~~~~kILL~rr~~~p~-~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~~~~~~~~~p~~~~~~~~-f~a 220 (299)
.+.+++.++++++|.+|...+. .|+|.+|....+. .. .+...+.|+.. +.++.+.+.+.+..... |.+
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 4445556778999999887654 7999999864433 22 22223334443 33454444454433322 333
Q ss_pred EecCCCCCCCCcceeeEEecCCCCCCCCCCCccH
Q 022283 221 KLKRPHFSPGPESSECRLFALDEIPFDSLAFSSI 254 (299)
Q Consensus 221 ~~~~~~~~~~~E~~~~~W~~~deL~~~~laf~s~ 254 (299)
.... .+. +..|++++++. .++++..
T Consensus 308 ~~~~------~~~-~~~w~~~~~~~--~~~l~~p 332 (342)
T COG1194 308 SASL------VLS-DGRWYNLSDLE--SIGLPAP 332 (342)
T ss_pred eccc------CCC-Cceeccccccc--cccccHH
Confidence 3221 222 78999999998 5666654
No 142
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=85.78 E-value=0.44 Score=42.02 Aligned_cols=29 Identities=17% Similarity=0.370 Sum_probs=23.7
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
-+-.|++||++|... +....||.||.+.-
T Consensus 148 I~A~CsrC~~~L~~~------~~~l~Cp~Cg~tEk 176 (188)
T COG1096 148 IYARCSRCRAPLVKK------GNMLKCPNCGNTEK 176 (188)
T ss_pred EEEEccCCCcceEEc------CcEEECCCCCCEEe
Confidence 456899999999774 56899999998764
No 143
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=85.72 E-value=0.56 Score=37.11 Aligned_cols=31 Identities=32% Similarity=0.549 Sum_probs=23.5
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.|||.||.-|... .|+.-.+..|..|++++-
T Consensus 2 ~FCP~Cgn~Live--~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 2 LFCPTCGNMLIVE--SGESCNRFSCRTCPYVFP 32 (105)
T ss_pred cccCCCCCEEEEe--cCCeEeeEEcCCCCceee
Confidence 6999999998765 233457899999986653
No 144
>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=85.69 E-value=0.49 Score=39.22 Aligned_cols=32 Identities=13% Similarity=0.094 Sum_probs=23.2
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
-+-+-||.||++..-. .....+||.||..+-+
T Consensus 7 GtKr~Cp~cg~kFYDL-----nk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 7 GTKRICPNTGSKFYDL-----NRRPAVSPYTGEQFPP 38 (129)
T ss_pred CccccCCCcCcccccc-----CCCCccCCCcCCccCc
Confidence 3567899999997554 2456789999987543
No 145
>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=85.26 E-value=1.2 Score=30.03 Aligned_cols=38 Identities=18% Similarity=0.358 Sum_probs=26.5
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 93 AAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
..+.-++|-.. ..||.||+.-...+ ....+..|.+|+.
T Consensus 8 ~~l~~~RW~~g-~~CP~Cg~~~~~~~---~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 8 EYLEEIRWPDG-FVCPHCGSTKHYRL---KTRGRYRCKACRK 45 (46)
T ss_pred HHHHHhcCCCC-CCCCCCCCeeeEEe---CCCCeEECCCCCC
Confidence 44556678777 44999999833332 3357889999975
No 146
>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=85.13 E-value=0.44 Score=40.51 Aligned_cols=33 Identities=18% Similarity=0.509 Sum_probs=26.5
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
.-.|-.||..+.... .+.-..||.||...|.|-
T Consensus 112 ~l~C~~Cg~~~~~~~----~~~l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 112 TLVCENCGHEVELTH----PERLPPCPKCGHTEFTRQ 144 (146)
T ss_pred eEecccCCCEEEecC----CCcCCCCCCCCCCeeeeC
Confidence 457999999988873 346789999999999653
No 147
>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=84.61 E-value=0.37 Score=36.24 Aligned_cols=43 Identities=26% Similarity=0.350 Sum_probs=5.9
Q ss_pred eeecCCCCceeecCCcEEEEEEEeeCCEEEE--EEeecCCC-CCceeece
Q 022283 126 RAICTVCGKIAYQNPKMVVGCLIEHDKKILL--CKRKIEPS-YGLWTLPA 172 (299)
Q Consensus 126 ~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL--~rr~~~p~-~g~w~lPg 172 (299)
+..||.||..- -.-|.+.++.+|++-+ .++..... +-.|++|.
T Consensus 24 k~FCp~CGn~T----L~rvsvsv~~~G~~~~~~~~~~~~n~RG~~ySlPk 69 (73)
T PF08772_consen 24 KQFCPKCGNAT----LKRVSVSVDEDGKIKLHLKKNFQWNLRGTKYSLPK 69 (73)
T ss_dssp --S-SSS--S------EEEE-B--SS---B--------------------
T ss_pred ceeCcccCCCc----ceEEEEEECCCCCEEEEecCCceeccCCCCccCCC
Confidence 45566665431 2223344555554433 33322222 33588883
No 148
>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=84.38 E-value=0.24 Score=35.69 Aligned_cols=26 Identities=19% Similarity=0.561 Sum_probs=19.2
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecC-CCCcee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICT-VCGKIA 136 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~~~ 136 (299)
.|++|+.||.+.... ...|. .|+..+
T Consensus 2 ~HkHC~~CG~~Ip~~--------~~fCS~~C~~~~ 28 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPD--------ESFCSPKCREEY 28 (59)
T ss_pred CCCcCCcCCCcCCcc--------hhhhCHHHHHHH
Confidence 589999999996542 46885 687544
No 149
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=84.35 E-value=1.2 Score=36.97 Aligned_cols=46 Identities=15% Similarity=0.248 Sum_probs=31.2
Q ss_pred HHHHHHHhhhhcCCCCcCCCCCCcccc-cCCCCcceeecCCCCceee
Q 022283 92 SAAVHSAGNVLKISFCQWCGGQTKHEV-PHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 92 ~~a~~l~~w~~~~~fC~~CG~~~~~~~-~~~~~~~~~~C~~Cg~~~y 137 (299)
+.|..-..|+....+||.|++....+. ....+..+..|++|+...-
T Consensus 18 ~~~~~~~~~~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 18 ADAAYAIRMQITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred HHHHHHHhhhcccCcCCCCCccceeeECCccccccccccCCcCccee
Confidence 344445578888999999999982221 1112357889999997653
No 150
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=84.19 E-value=1.3 Score=31.32 Aligned_cols=33 Identities=18% Similarity=0.579 Sum_probs=21.9
Q ss_pred CCCcCCCCCCcccccCCC--CcceeecCCCCceee
Q 022283 105 SFCQWCGGQTKHEVPHGE--EKMRAICTVCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~--~~~~~~C~~Cg~~~y 137 (299)
-+||.||.++..++-.+. .....+||.|....-
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~Etl 39 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETL 39 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEE
Confidence 479999999865532111 224578999987653
No 151
>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=83.95 E-value=0.87 Score=32.22 Aligned_cols=30 Identities=30% Similarity=0.498 Sum_probs=22.8
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
-||.||+.+... ....+....|+.||....
T Consensus 4 ~CP~CG~~iev~--~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 4 ECPDCGAEIELE--NPELGELVICDECGAELE 33 (54)
T ss_pred CCCCCCCEEecC--CCccCCEEeCCCCCCEEE
Confidence 699999987654 224467789999997765
No 152
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=83.86 E-value=0.41 Score=47.25 Aligned_cols=37 Identities=30% Similarity=0.548 Sum_probs=28.9
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
..|..|...+.-||.||..|+.. | .+ -..|+.||...
T Consensus 341 ~~l~~~~~~~p~Cp~Cg~~m~S~---G-~~-g~rC~kCg~~~ 377 (421)
T COG1571 341 LKLARYERVNPVCPRCGGRMKSA---G-RN-GFRCKKCGTRA 377 (421)
T ss_pred EEeeeeEEcCCCCCccCCchhhc---C-CC-CcccccccccC
Confidence 34556778888999999999876 2 22 78999999764
No 153
>PRK11032 hypothetical protein; Provisional
Probab=83.81 E-value=0.53 Score=40.67 Aligned_cols=32 Identities=19% Similarity=0.482 Sum_probs=26.5
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceeecC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (299)
.--|-+||..+.... .+.-..||.||...|.|
T Consensus 124 ~LvC~~Cg~~~~~~~----p~~i~pCp~C~~~~F~R 155 (160)
T PRK11032 124 NLVCEKCHHHLAFYT----PEVLPLCPKCGHDQFQR 155 (160)
T ss_pred eEEecCCCCEEEecC----CCcCCCCCCCCCCeeee
Confidence 456999999998874 35678999999999965
No 154
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=83.52 E-value=0.7 Score=33.03 Aligned_cols=23 Identities=26% Similarity=0.693 Sum_probs=18.3
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
.....||.||+..... ..|+.||
T Consensus 25 ~~l~~C~~CG~~~~~H---------~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKLPH---------RVCPSCG 47 (57)
T ss_pred CcceECCCCCCccCCe---------EECCCCC
Confidence 3457899999996553 6899999
No 155
>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=83.46 E-value=0.61 Score=30.21 Aligned_cols=28 Identities=25% Similarity=0.464 Sum_probs=19.9
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.|+.||+..+......+ +....||.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 59999998765433222 45678999997
No 156
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.88 E-value=0.85 Score=35.36 Aligned_cols=37 Identities=19% Similarity=0.326 Sum_probs=25.8
Q ss_pred HHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 96 HSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 96 ~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.+..=++.---||.||.+...+ .+-..+.|..||+.+
T Consensus 27 ~ie~~~~~~~~Cp~C~~~~VkR----~a~GIW~C~kCg~~f 63 (89)
T COG1997 27 EIEAQQRAKHVCPFCGRTTVKR----IATGIWKCRKCGAKF 63 (89)
T ss_pred HHHHHHhcCCcCCCCCCcceee----eccCeEEcCCCCCee
Confidence 3333444556799999997666 344578999999764
No 157
>PF12773 DZR: Double zinc ribbon
Probab=82.84 E-value=0.85 Score=31.03 Aligned_cols=25 Identities=24% Similarity=0.623 Sum_probs=19.0
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
.....+|+.||+.+.. ...+|+.||
T Consensus 26 ~~~~~~C~~Cg~~~~~--------~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPP--------NAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcC--------CcCccCccc
Confidence 3456899999998543 357899997
No 158
>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=82.21 E-value=0.76 Score=28.97 Aligned_cols=25 Identities=24% Similarity=0.581 Sum_probs=17.6
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
|+.||+..... ......|+.||...
T Consensus 3 C~~Cg~~~~~~-----~~~~irC~~CG~RI 27 (32)
T PF03604_consen 3 CGECGAEVELK-----PGDPIRCPECGHRI 27 (32)
T ss_dssp ESSSSSSE-BS-----TSSTSSBSSSS-SE
T ss_pred CCcCCCeeEcC-----CCCcEECCcCCCeE
Confidence 89999998754 23457999999753
No 159
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.19 E-value=0.71 Score=48.24 Aligned_cols=35 Identities=31% Similarity=0.579 Sum_probs=17.9
Q ss_pred hcCCCCcCCCCCCccc-cc---CCCCcceeecCCCCcee
Q 022283 102 LKISFCQWCGGQTKHE-VP---HGEEKMRAICTVCGKIA 136 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~-~~---~~~~~~~~~C~~Cg~~~ 136 (299)
...+||+.||.++... .+ .......+.|+.||...
T Consensus 13 ~~akFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 13 NNNRFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CCCccccccCCCCCCCcCCCCCCCCCcccccccccCCcc
Confidence 3566777777775421 00 00112346777777543
No 160
>PRK13844 recombination protein RecR; Provisional
Probab=81.79 E-value=0.55 Score=41.97 Aligned_cols=95 Identities=15% Similarity=0.223 Sum_probs=63.0
Q ss_pred CCCcchHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEEEeecCCC
Q 022283 85 ATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPS 164 (299)
Q Consensus 85 ~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr~~~p~ 164 (299)
.+....-.-|.+|..-..+.++|+.||.-++. -.|+-|.-.. .+-...|||..-..++-+.+... .
T Consensus 38 ~~~~~~~~la~~i~~~~~~i~~C~~C~~lte~----------~~C~IC~d~~---Rd~~~iCVVE~~~Dv~aiE~t~~-y 103 (200)
T PRK13844 38 KSPETAIAIANSLLDATANIKKCVYCQALTED----------DVCNICSNTN---RDDTKLCIIESMLDMIAIEEAGI-Y 103 (200)
T ss_pred CCHHHHHHHHHHHHHHHHhCCcCCCCCCCCCC----------CCCCCCCCCC---CCCCEEEEECCHHHHHHHHhhCc-c
Confidence 33333445567777788899999999988643 2477775433 34445566665545555554433 3
Q ss_pred CCceeeceEEee--CCCCHHHHHHHHHHHHh
Q 022283 165 YGLWTLPAGYME--IGESAAEGAIRETWEEA 193 (299)
Q Consensus 165 ~g~w~lPgG~VE--~GEs~eeAa~REv~EEt 193 (299)
.|.|-+.+|.+. .|..+++--..++.+-.
T Consensus 104 ~G~YhVL~G~ispl~gi~p~~l~i~~L~~Ri 134 (200)
T PRK13844 104 RGKYFVLNGRISPLDGIGPSELKLDILQQII 134 (200)
T ss_pred ceEEEEccCccCccCCCChhhcCHHHHHHHH
Confidence 799999999998 45677777677776654
No 161
>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=81.79 E-value=0.85 Score=32.32 Aligned_cols=22 Identities=27% Similarity=0.801 Sum_probs=17.5
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
....|+.||+..... .+|+.||
T Consensus 25 ~l~~C~~cG~~~~~H---------~vc~~cG 46 (55)
T TIGR01031 25 TLVVCPNCGEFKLPH---------RVCPSCG 46 (55)
T ss_pred cceECCCCCCcccCe---------eECCccC
Confidence 446799999986543 7899999
No 162
>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=81.78 E-value=0.71 Score=30.71 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=21.2
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.|..||+..+......+ .....||.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 48999988766655444 56789999997
No 163
>KOG4432 consensus Uncharacterized NUDIX family hydrolase [General function prediction only]
Probab=81.24 E-value=3.5 Score=39.05 Aligned_cols=78 Identities=23% Similarity=0.227 Sum_probs=48.5
Q ss_pred eeeceEEeeCCCCHHHHHHHHHHHHhCCceeec--cceeeeec--CCCCEEEEEEEEEecCCC-------CCCCCcceee
Q 022283 168 WTLPAGYMEIGESAAEGAIRETWEEARADVEVQ--SPFAQLDI--PRIGQIYIIFLAKLKRPH-------FSPGPESSEC 236 (299)
Q Consensus 168 w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~~~--~~~~~~~~--p~~~~~~~~f~a~~~~~~-------~~~~~E~~~~ 236 (299)
.+|.+|.|+..-|..+-|.||..||.|.++..- +.+..+-. ...+.....|.+++.+.. ....+|..+.
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 567789999889999999999999999998543 33333321 112233344556554432 1122455556
Q ss_pred EEecCCCCC
Q 022283 237 RLFALDEIP 245 (299)
Q Consensus 237 ~W~~~deL~ 245 (299)
.-+++++++
T Consensus 366 v~lsle~a~ 374 (405)
T KOG4432|consen 366 VRLSLEDAP 374 (405)
T ss_pred EEechhhhh
Confidence 666777766
No 164
>PRK11827 hypothetical protein; Provisional
Probab=81.14 E-value=1.2 Score=32.13 Aligned_cols=32 Identities=31% Similarity=0.616 Sum_probs=23.6
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
...--||.|.+++... .+.....|..|+ ..||
T Consensus 6 LeILaCP~ckg~L~~~----~~~~~Lic~~~~-laYP 37 (60)
T PRK11827 6 LEIIACPVCNGKLWYN----QEKQELICKLDN-LAFP 37 (60)
T ss_pred HhheECCCCCCcCeEc----CCCCeEECCccC-eecc
Confidence 3445799999999875 345578999998 4554
No 165
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=81.08 E-value=3.1 Score=37.11 Aligned_cols=89 Identities=19% Similarity=0.275 Sum_probs=51.2
Q ss_pred cCCCCcCCCCCCcccccCC----CC---cceeecCCCCceeec-------CCcEEEEEEEe-eCCEEEEEEeecCCCCCc
Q 022283 103 KISFCQWCGGQTKHEVPHG----EE---KMRAICTVCGKIAYQ-------NPKMVVGCLIE-HDKKILLCKRKIEPSYGL 167 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~----~~---~~~~~C~~Cg~~~y~-------~p~~vV~~iv~-~~~kILL~rr~~~p~~g~ 167 (299)
..--||.||+.+....... -+ ..-..|..||+.+.. .|.-+..-+-. ++-+.+++|.. .+.
T Consensus 13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~eP~r~~lkve~~edL~~~V~RS~----s~~ 88 (201)
T COG1779 13 TRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEEREPRRYTLKVESEEDLSARVVRSK----SAT 88 (201)
T ss_pred eeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeecccCCCeEEEEEeCCHHHhhhheeecC----Ccc
Confidence 3457999999765442100 01 134689999987752 34222222212 23466677654 455
Q ss_pred eeec--eEEeeCCC------CHHHHHHHHHHHHhCC
Q 022283 168 WTLP--AGYMEIGE------SAAEGAIRETWEEARA 195 (299)
Q Consensus 168 w~lP--gG~VE~GE------s~eeAa~REv~EEtGl 195 (299)
..+| |=.++||. |-.|.+++-+.|++..
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 6676 44555654 4467777778888776
No 166
>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=80.45 E-value=3.4 Score=38.73 Aligned_cols=24 Identities=29% Similarity=0.440 Sum_probs=19.1
Q ss_pred eeCCEEEEEEeecCCC-CCceeece
Q 022283 149 EHDKKILLCKRKIEPS-YGLWTLPA 172 (299)
Q Consensus 149 ~~~~kILL~rr~~~p~-~g~w~lPg 172 (299)
..++++||.+|..... .|+|+||.
T Consensus 236 ~~~~~~~~~~r~~~~~~~gl~~~p~ 260 (275)
T TIGR01084 236 NYDGEVLLEQRPEKGLWGGLYCFPQ 260 (275)
T ss_pred eCCCeEEEEeCCCCchhhccccCCC
Confidence 4478999999976543 89999996
No 167
>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=79.97 E-value=1.6 Score=37.10 Aligned_cols=45 Identities=13% Similarity=0.437 Sum_probs=25.2
Q ss_pred CCcCCCCCCcccc---cCCC--C-cceeecCCCCcee--ecCCcEEEEEEEee
Q 022283 106 FCQWCGGQTKHEV---PHGE--E-KMRAICTVCGKIA--YQNPKMVVGCLIEH 150 (299)
Q Consensus 106 fC~~CG~~~~~~~---~~~~--~-~~~~~C~~Cg~~~--y~~p~~vV~~iv~~ 150 (299)
.||.||+.-...+ +..+ . ..|+.|..||..+ |-+.-.....||-.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~ViKk 54 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQ 54 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccccEEEcC
Confidence 6999999743322 1111 1 2568999999654 54444333334433
No 168
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=79.68 E-value=1.2 Score=31.66 Aligned_cols=25 Identities=20% Similarity=0.494 Sum_probs=19.6
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
+||.|++... +.....||.||...|
T Consensus 1 ~Cpv~~~~~~-------~~v~~~Cp~cGipth 25 (55)
T PF13824_consen 1 LCPVCKKDLP-------AHVNFECPDCGIPTH 25 (55)
T ss_pred CCCCCccccc-------cccCCcCCCCCCcCc
Confidence 6999999752 245689999998877
No 169
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=78.85 E-value=2 Score=30.86 Aligned_cols=28 Identities=25% Similarity=0.682 Sum_probs=20.6
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
-..|..||..+... +...++.||+||..
T Consensus 7 ~~~CtSCg~~i~~~----~~~~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPR----EKAVKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCC----CccCEeeCCCCCCe
Confidence 34688888887655 45678888888865
No 170
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=78.67 E-value=0.94 Score=42.55 Aligned_cols=30 Identities=30% Similarity=0.731 Sum_probs=22.7
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
+.+||+.||.-+.... +.+....||.||..
T Consensus 314 k~nfc~ncG~~~t~~~---~ng~a~fcp~cgq~ 343 (345)
T COG4260 314 KLNFCLNCGCGTTADF---DNGKAKFCPECGQG 343 (345)
T ss_pred ccccccccCcccccCC---ccchhhhChhhcCC
Confidence 5679999995544433 56788999999853
No 171
>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=78.62 E-value=0.92 Score=42.55 Aligned_cols=34 Identities=26% Similarity=0.537 Sum_probs=16.4
Q ss_pred CCCCcCCCCCCcccccCCC---CcceeecCCCCceee
Q 022283 104 ISFCQWCGGQTKHEVPHGE---EKMRAICTVCGKIAY 137 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~---~~~~~~C~~Cg~~~y 137 (299)
..|||.||++-......++ +....+|.-|+..+-
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~ 208 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR 208 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee
Confidence 4799999999554443333 346678988887653
No 172
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=77.97 E-value=1.7 Score=37.06 Aligned_cols=32 Identities=28% Similarity=0.653 Sum_probs=20.5
Q ss_pred CCCcCCCCCCcccc---cCCC---CcceeecCCCCcee
Q 022283 105 SFCQWCGGQTKHEV---PHGE---EKMRAICTVCGKIA 136 (299)
Q Consensus 105 ~fC~~CG~~~~~~~---~~~~---~~~~~~C~~Cg~~~ 136 (299)
.+||.||+.-...+ +..+ -..|+.|+.||..+
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 37999998843332 1111 13678999999765
No 173
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.53 E-value=0.92 Score=40.42 Aligned_cols=91 Identities=16% Similarity=0.312 Sum_probs=60.9
Q ss_pred chHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEEEeecCCCCCce
Q 022283 89 HPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLW 168 (299)
Q Consensus 89 ~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w 168 (299)
....-|.+|..-..+.++|+.||.-++. -.|+-|.-. +.+-...|||.+-.-++-+.+... ..|.|
T Consensus 38 ~~~~la~ai~~~~~~i~~C~~C~~lse~----------~~C~IC~d~---~Rd~~~iCVVE~~~Dv~aiE~~~~-y~G~Y 103 (195)
T TIGR00615 38 EVLRLAQALLEAKENLRTCSVCGAISDQ----------EVCNICSDE---RRDNSVICVVEDPKDVFALEKTKE-FRGRY 103 (195)
T ss_pred HHHHHHHHHHHHHHcCCcCCCCCCCCCC----------CcCCCCCCC---CCCCCEEEEECCHHHHHHHHhhCc-cceEE
Confidence 3445566777788899999999987532 247777643 334445666766555555555433 37999
Q ss_pred eeceEEeeC--CCCHHHHHHHHHHHHh
Q 022283 169 TLPAGYMEI--GESAAEGAIRETWEEA 193 (299)
Q Consensus 169 ~lPgG~VE~--GEs~eeAa~REv~EEt 193 (299)
-+.+|.+.| |..+++--..++.+-+
T Consensus 104 hVL~G~iSPldgigp~~l~i~~L~~Ri 130 (195)
T TIGR00615 104 HVLGGHISPLDGIGPEDLTIAALLKRL 130 (195)
T ss_pred EEccCccCccCCCChhhcCHHHHHHHH
Confidence 999999985 5567776666666654
No 174
>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=77.07 E-value=0.33 Score=41.57 Aligned_cols=22 Identities=36% Similarity=0.925 Sum_probs=17.8
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.+..||.+||+++... ||+|+.
T Consensus 26 ~~~~fC~kCG~~tI~~-----------Cp~C~~ 47 (158)
T PF10083_consen 26 LREKFCSKCGAKTITS-----------CPNCST 47 (158)
T ss_pred HHHHHHHHhhHHHHHH-----------CcCCCC
Confidence 4568999999998654 999984
No 175
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=76.99 E-value=2 Score=27.20 Aligned_cols=29 Identities=28% Similarity=0.629 Sum_probs=21.8
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.+-|+.||+...... ......|..||..+
T Consensus 3 ~~~C~~C~~~~i~~~----~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNK----EDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEe----cCCeEEcccCCcEe
Confidence 457999999987731 23468999999765
No 176
>PHA02942 putative transposase; Provisional
Probab=76.65 E-value=2 Score=42.09 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=22.6
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
+.+.||.||..... .......|+.||+..-
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 67899999998642 1234689999998763
No 177
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=76.30 E-value=2 Score=30.94 Aligned_cols=27 Identities=26% Similarity=0.657 Sum_probs=20.0
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
...|..||..+... +....+.||+||.
T Consensus 9 ~~~CtSCg~~i~p~----e~~v~F~CPnCGe 35 (61)
T COG2888 9 PPVCTSCGREIAPG----ETAVKFPCPNCGE 35 (61)
T ss_pred CceeccCCCEeccC----CceeEeeCCCCCc
Confidence 45788888886554 6677888888884
No 178
>PRK00076 recR recombination protein RecR; Reviewed
Probab=76.12 E-value=0.93 Score=40.44 Aligned_cols=94 Identities=22% Similarity=0.355 Sum_probs=62.0
Q ss_pred CCcchHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEEEeecCCCC
Q 022283 86 TSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSY 165 (299)
Q Consensus 86 ~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr~~~p~~ 165 (299)
+......-|.+|..-..+.++|+.||.-++. -.|+-|.-. ..+-.+.|||..-..++...+... ..
T Consensus 35 ~~~~~~~la~~i~~~~~~i~~C~~C~~lse~----------~~C~IC~d~---~Rd~~~icVVE~~~Dv~aiE~s~~-y~ 100 (196)
T PRK00076 35 DREDVLRLAQALEEAKEKIKHCSVCGNLTEQ----------DPCEICSDP---RRDQSLICVVESPADVLAIERTGE-YR 100 (196)
T ss_pred CHHHHHHHHHHHHHHHHcCCcCCCCCCcCCC----------CcCCCCCCC---CCCCCEEEEECCHHHHHHHHhhCc-Cc
Confidence 3334445567777788899999999988643 247777543 334455667766555665555433 37
Q ss_pred CceeeceEEeeC--CCCHHHHHHHHHHHHh
Q 022283 166 GLWTLPAGYMEI--GESAAEGAIRETWEEA 193 (299)
Q Consensus 166 g~w~lPgG~VE~--GEs~eeAa~REv~EEt 193 (299)
|.|-+.+|.+.+ |-.+++--..++.+-.
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 5556665556665555
No 179
>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=75.54 E-value=1.4 Score=31.16 Aligned_cols=21 Identities=29% Similarity=0.825 Sum_probs=16.2
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
...||.||..... ...|+.||
T Consensus 26 l~~c~~cg~~~~~---------H~vc~~cG 46 (56)
T PF01783_consen 26 LVKCPNCGEPKLP---------HRVCPSCG 46 (56)
T ss_dssp EEESSSSSSEEST---------TSBCTTTB
T ss_pred eeeeccCCCEecc---------cEeeCCCC
Confidence 4689999977433 36899998
No 180
>PRK10445 endonuclease VIII; Provisional
Probab=75.50 E-value=1.6 Score=40.50 Aligned_cols=31 Identities=19% Similarity=0.380 Sum_probs=23.8
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
.+.-+-||+||.++..... .+.....||.|.
T Consensus 232 ~r~g~~Cp~Cg~~I~~~~~--~gR~t~~CP~CQ 262 (263)
T PRK10445 232 HRDGEACERCGGIIEKTTL--SSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCCCEeEEEEE--CCCCcEECCCCc
Confidence 3345889999999877655 346788999996
No 181
>PRK12495 hypothetical protein; Provisional
Probab=74.77 E-value=1.9 Score=39.04 Aligned_cols=33 Identities=18% Similarity=0.499 Sum_probs=24.1
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.......+|+.||.++-.. ....+|+.|+..+-
T Consensus 37 gatmsa~hC~~CG~PIpa~------pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 37 GATMTNAHCDECGDPIFRH------DGQEFCPTCQQPVT 69 (226)
T ss_pred hcccchhhcccccCcccCC------CCeeECCCCCCccc
Confidence 3445678999999997632 23678999996654
No 182
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=74.60 E-value=2.1 Score=30.28 Aligned_cols=28 Identities=25% Similarity=0.463 Sum_probs=21.2
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
-.-|+.||.++... .-..+|+.||..+-
T Consensus 5 ~~~C~~Cg~~~~~~------dDiVvCp~CgapyH 32 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG------DDIVVCPECGAPYH 32 (54)
T ss_pred CccChhhCCcccCC------CCEEECCCCCCccc
Confidence 45699999997543 34789999997653
No 183
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=74.48 E-value=1.2 Score=39.60 Aligned_cols=99 Identities=20% Similarity=0.327 Sum_probs=63.7
Q ss_pred ccCCCCCCcchHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEEEe
Q 022283 80 ESNQDATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKR 159 (299)
Q Consensus 80 ~~~~~~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr 159 (299)
|+..+..+. -.-|.+|..-..+.++|+.||.-+... .|.-|.-..- +-.+.+||.....++...+
T Consensus 32 LL~~~~~~~--~~la~al~~a~~~i~~C~~C~~~te~d----------~C~ICsd~~R---d~~~icVVe~p~Dv~a~E~ 96 (198)
T COG0353 32 LLQRDREDV--ERLAKALLEAKENIKHCSVCGNLTESD----------PCDICSDESR---DKSQLCVVEEPKDVLALEK 96 (198)
T ss_pred HHccCHHHH--HHHHHHHHHHHhcCccccccCCcCCCC----------cCcCcCCccc---CCceEEEEcchHHHHHHHH
Confidence 334444433 445667777889999999999886432 5777764333 3346666766544554444
Q ss_pred ecCCCCCceeeceEEeeC--CCCHHHHHHHHHHHHhC
Q 022283 160 KIEPSYGLWTLPAGYMEI--GESAAEGAIRETWEEAR 194 (299)
Q Consensus 160 ~~~p~~g~w~lPgG~VE~--GEs~eeAa~REv~EEtG 194 (299)
... ..|.|-+.+|.+.| |-.+++--..++.+-.+
T Consensus 97 ~~~-f~G~YhVL~G~lspl~gigpe~l~i~~L~~Rl~ 132 (198)
T COG0353 97 TGE-FRGLYHVLGGLLSPLDGIGPEDLNIDELLQRLA 132 (198)
T ss_pred hcc-cCeeEEEecCccCcccCCCcccccHHHHHHHHh
Confidence 433 37999999999984 44677766676666544
No 184
>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=74.16 E-value=2.8 Score=27.30 Aligned_cols=32 Identities=25% Similarity=0.665 Sum_probs=22.2
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
++.=||.||..-..+..+.++.-..+|..|+.
T Consensus 2 ~~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 2 RHGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 35679999998666654433445678988863
No 185
>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=73.81 E-value=2.2 Score=40.67 Aligned_cols=35 Identities=14% Similarity=0.326 Sum_probs=23.5
Q ss_pred cCCCCcCCCCCCccccc-C---CCCcceeecCCCCceee
Q 022283 103 KISFCQWCGGQTKHEVP-H---GEEKMRAICTVCGKIAY 137 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~-~---~~~~~~~~C~~Cg~~~y 137 (299)
...|||.||+.-..... . .++....+|.-|+..+-
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~ 221 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWH 221 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccc
Confidence 46699999999543211 1 14556779999987664
No 186
>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=73.44 E-value=1.4 Score=35.66 Aligned_cols=27 Identities=30% Similarity=0.409 Sum_probs=20.7
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
--||.||+++... |..-.|..|+...-
T Consensus 70 V~CP~C~K~TKmL------Gr~D~CM~C~~pLT 96 (114)
T PF11023_consen 70 VECPNCGKQTKML------GRVDACMHCKEPLT 96 (114)
T ss_pred eECCCCCChHhhh------chhhccCcCCCcCc
Confidence 3499999999775 44568999987654
No 187
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=73.00 E-value=1.8 Score=31.04 Aligned_cols=26 Identities=23% Similarity=0.492 Sum_probs=21.1
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
-|+-||++.... .+....|..||+..
T Consensus 22 iCgdC~~en~lk-----~~D~irCReCG~RI 47 (62)
T KOG3507|consen 22 ICGDCGQENTLK-----RGDVIRCRECGYRI 47 (62)
T ss_pred Eecccccccccc-----CCCcEehhhcchHH
Confidence 599999998775 45678999999753
No 188
>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=72.85 E-value=2.3 Score=29.38 Aligned_cols=40 Identities=23% Similarity=0.397 Sum_probs=23.5
Q ss_pred HHHHHhhhhcCCCCcCCCCCCccc----ccCCCCcceeecCCCCc
Q 022283 94 AVHSAGNVLKISFCQWCGGQTKHE----VPHGEEKMRAICTVCGK 134 (299)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~----~~~~~~~~~~~C~~Cg~ 134 (299)
|++.+.-...+-+||.||..-.-. ....|+-.++.| .||+
T Consensus 3 ~~~~~~L~~kY~~Cp~CGN~~vGngEG~liV~edtfkRtC-kCGf 46 (49)
T PF12677_consen 3 AWKTLKLSNKYCKCPKCGNDKVGNGEGTLIVEEDTFKRTC-KCGF 46 (49)
T ss_pred hhhhcchhhhhccCcccCCcEeecCcceEEEeccceeeee-cccc
Confidence 344555566788999999874222 111244466777 4665
No 189
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=72.84 E-value=2.4 Score=33.71 Aligned_cols=34 Identities=24% Similarity=0.358 Sum_probs=22.5
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.+.--||.||...... +-+.+.....|+.||...
T Consensus 19 pt~f~CP~Cge~~v~v-~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISV-KIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeee-ecCCCcceEECCCCCCcc
Confidence 4567899999654332 112345678999999754
No 190
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=72.38 E-value=1.2 Score=36.09 Aligned_cols=31 Identities=19% Similarity=0.498 Sum_probs=24.6
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
...||+.||+-+... ...+...|..|+..+-
T Consensus 6 ~~~FC~~CG~ll~~~----~~~~~~~C~~Ck~~~~ 36 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEP----SAQSTVLCIRCKIEYP 36 (116)
T ss_pred Ccchhhhhhhhcccc----cccCceEeccccccCC
Confidence 567999999998765 4566777999997654
No 191
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=72.36 E-value=1.9 Score=37.33 Aligned_cols=40 Identities=23% Similarity=0.463 Sum_probs=25.3
Q ss_pred hhhc-CCCCcCCCCCCcccccC-----------CCCcceeecCCCCceeecC
Q 022283 100 NVLK-ISFCQWCGGQTKHEVPH-----------GEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 100 w~~~-~~fC~~CG~~~~~~~~~-----------~~~~~~~~C~~Cg~~~y~~ 139 (299)
|... +.-||.|+.++....-+ .....-..|+.||..+++-
T Consensus 92 ~~~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~G 143 (165)
T COG1656 92 RLFPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKG 143 (165)
T ss_pred hcccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCc
Confidence 3334 78899999998665100 0011124599999998863
No 192
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.28 E-value=3.1 Score=34.22 Aligned_cols=42 Identities=24% Similarity=0.405 Sum_probs=25.6
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceee-cC----CcEEEEEEE
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY-QN----PKMVVGCLI 148 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y-~~----p~~vV~~iv 148 (299)
.--||+||.---.+ +=-..+..|..||..+- .+ |...|+.|+
T Consensus 21 ~grCP~CGeGrLF~---gFLK~~p~C~aCG~dyg~~~a~DgPa~fvI~Iv 67 (126)
T COG5349 21 RGRCPRCGEGRLFR---GFLKVVPACEACGLDYGFADADDGPAYFVILIV 67 (126)
T ss_pred cCCCCCCCCchhhh---hhcccCchhhhccccccCCcccCCCcEEEEEee
Confidence 45799999873221 22346789999997653 22 444454444
No 193
>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=71.75 E-value=1.8 Score=29.76 Aligned_cols=29 Identities=31% Similarity=0.510 Sum_probs=20.8
Q ss_pred hcCCCCc--CCCCCCcccccCCCCcceeecCCCCc
Q 022283 102 LKISFCQ--WCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 102 ~~~~fC~--~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
+..+.|| .||.-.-+. +-..|..|..||.
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 3568999 999987555 3345899999986
No 194
>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=71.64 E-value=3.4 Score=28.70 Aligned_cols=31 Identities=23% Similarity=0.448 Sum_probs=18.0
Q ss_pred CCCcCCCCCCcccc---cCCCCcceeecCCCCce
Q 022283 105 SFCQWCGGQTKHEV---PHGEEKMRAICTVCGKI 135 (299)
Q Consensus 105 ~fC~~CG~~~~~~~---~~~~~~~~~~C~~Cg~~ 135 (299)
+=||.||+.-.... .+.+......|..||..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 45999999866221 11122223369999865
No 195
>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=71.35 E-value=3.5 Score=27.08 Aligned_cols=14 Identities=21% Similarity=0.579 Sum_probs=10.4
Q ss_pred ceeecCCCCceeec
Q 022283 125 MRAICTVCGKIAYQ 138 (299)
Q Consensus 125 ~~~~C~~Cg~~~y~ 138 (299)
....|+.||...|.
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 45678999888774
No 196
>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=71.10 E-value=6.7 Score=33.39 Aligned_cols=46 Identities=13% Similarity=0.268 Sum_probs=31.0
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCcee-ecCCcEEEEEEEeeC-CEE
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA-YQNPKMVVGCLIEHD-KKI 154 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~-y~~p~~vV~~iv~~~-~kI 154 (299)
+.-||.|.+++... ......|+.|+... -+.++..+-+.+.++ +.+
T Consensus 34 Y~aC~~C~kkv~~~-----~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~ 81 (166)
T cd04476 34 YPACPGCNKKVVEE-----GNGTYRCEKCNKSVPNPEYRYILSLNVADHTGEA 81 (166)
T ss_pred EccccccCcccEeC-----CCCcEECCCCCCcCCCccEEEEEEEEEEeCCCCE
Confidence 56899999997653 12578999999876 455565555555443 443
No 197
>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=71.06 E-value=2.4 Score=39.47 Aligned_cols=30 Identities=20% Similarity=0.376 Sum_probs=22.6
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
+.-+-||+||++....... +.....||.|.
T Consensus 243 r~g~pC~~Cg~~I~~~~~~--gR~t~~CP~CQ 272 (272)
T TIGR00577 243 RKGEPCRRCGTPIEKIKVG--GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCCCeeEEEEEC--CCCCEECCCCC
Confidence 3446899999998766553 46778999995
No 198
>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=70.71 E-value=2.2 Score=26.04 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=16.3
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-|++||..+..... .+.....|+.|..
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 49999999766543 3466789999964
No 199
>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=70.68 E-value=2.4 Score=29.04 Aligned_cols=29 Identities=24% Similarity=0.443 Sum_probs=19.4
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.|..||...+......+ .....||.||..
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSD-DPLATCPECGGE 35 (52)
T ss_pred EeCCCCCEeEEEEecCC-CCCCCCCCCCCC
Confidence 59999997665433222 344679999973
No 200
>KOG4313 consensus Thiamine pyrophosphokinase [Nucleotide transport and metabolism]
Probab=70.58 E-value=7.2 Score=36.08 Aligned_cols=45 Identities=29% Similarity=0.209 Sum_probs=35.8
Q ss_pred EEEEEEeecCC--CCCceee-ceEEeeCCCCHHHHHHHHHHHHhCCce
Q 022283 153 KILLCKRKIEP--SYGLWTL-PAGYMEIGESAAEGAIRETWEEARADV 197 (299)
Q Consensus 153 kILL~rr~~~p--~~g~w~l-PgG~VE~GEs~eeAa~REv~EEtGl~v 197 (299)
.|.+-||+.-. .+|+|+- .||.+-.|-.+.++|+.|..||+++..
T Consensus 149 ~iWvprRS~TKqTWP~~lDN~vaGGl~~g~gI~eT~iKE~~EEAnl~~ 196 (306)
T KOG4313|consen 149 CIWVPRRSNTKQTWPGKLDNMVAGGLSVGFGIKETAIKEAAEEANLPS 196 (306)
T ss_pred EEEecccCCccccCcchhhhhhccccccCchHHHHHHHHHHHhcCCch
Confidence 56666666422 2677764 599999999999999999999999986
No 201
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=70.30 E-value=2.6 Score=39.22 Aligned_cols=30 Identities=20% Similarity=0.439 Sum_probs=22.5
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.-+-||+||++...... .+.....||.|..
T Consensus 244 ~g~pC~~Cg~~I~~~~~--~gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQ--GGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEEEE--CCCCcEECcCCCC
Confidence 34579999999876554 3467789999974
No 202
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=70.27 E-value=2.6 Score=39.34 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=23.1
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
+.-+-||+||++...... .+.....||.|.
T Consensus 242 R~g~pCprCG~~I~~~~~--~gR~t~~CP~CQ 271 (272)
T PRK14810 242 RTGEPCLNCKTPIRRVVV--AGRSSHYCPHCQ 271 (272)
T ss_pred CCCCcCCCCCCeeEEEEE--CCCccEECcCCc
Confidence 345789999999876655 346778999997
No 203
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=70.10 E-value=14 Score=32.90 Aligned_cols=68 Identities=18% Similarity=0.378 Sum_probs=36.3
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHH
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGA 185 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa 185 (299)
-| +||.++.. ...|+.||.. ..++.-+-..+-+++..--. ....-++|- +-+|+- -
T Consensus 2 ~C-rCG~~l~~---------p~~Cl~Cg~~-----~av~~~vy~~~~r~~v~~vg---e~D~~t~~~---~gDedg---~ 57 (227)
T COG4031 2 IC-RCGAELSS---------PAFCLNCGRR-----HAVGCGVYVSESRVFVRIVG---ERDFETFSI---RGDEDG---S 57 (227)
T ss_pred cc-ccCCcccc---------cchhcccCCc-----ceeEeeeeccccEEEEEEec---cccceeecc---cCCCcc---h
Confidence 48 99999743 2689999976 33333333344454433111 133445554 334443 4
Q ss_pred HHHHHHHhCCce
Q 022283 186 IRETWEEARADV 197 (299)
Q Consensus 186 ~REv~EEtGl~v 197 (299)
+|-+.|-++-.+
T Consensus 58 lRNl~erlae~i 69 (227)
T COG4031 58 LRNLYERLAERI 69 (227)
T ss_pred HHHHHHHHHHHH
Confidence 566666665443
No 204
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=69.98 E-value=2.7 Score=39.38 Aligned_cols=28 Identities=18% Similarity=0.361 Sum_probs=21.9
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
-+-|++||++...... .+.....||.|.
T Consensus 254 g~pC~~Cg~~I~~~~~--~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKL--AGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEE--CCCccEECCCCc
Confidence 4689999999876654 346778999996
No 205
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=69.88 E-value=2.4 Score=47.18 Aligned_cols=10 Identities=40% Similarity=0.859 Sum_probs=6.3
Q ss_pred CCCcCCCCCC
Q 022283 105 SFCQWCGGQT 114 (299)
Q Consensus 105 ~fC~~CG~~~ 114 (299)
+.||.||+.+
T Consensus 668 rkCPkCG~~t 677 (1337)
T PRK14714 668 RRCPSCGTET 677 (1337)
T ss_pred EECCCCCCcc
Confidence 5666666653
No 206
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=69.36 E-value=2 Score=34.87 Aligned_cols=31 Identities=16% Similarity=0.243 Sum_probs=20.0
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.+...--+|..||...... .....||.||..
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~------~~~~~CP~Cgs~ 95 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIH------QHDAQCPHCHGE 95 (113)
T ss_pred EeeCcEEEcccCCCEEecC------CcCccCcCCCCC
Confidence 3445566899999765432 234559999854
No 207
>PRK05978 hypothetical protein; Provisional
Probab=69.01 E-value=3 Score=35.57 Aligned_cols=37 Identities=19% Similarity=0.180 Sum_probs=25.4
Q ss_pred hhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecC
Q 022283 100 NVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (299)
|.--..-||+||+---.+ +--..+..|+.||..+-..
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 445567899999984332 1234677899999876543
No 208
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=68.98 E-value=2.9 Score=38.96 Aligned_cols=32 Identities=19% Similarity=0.390 Sum_probs=23.7
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
+.-+-||+||++....... +.....||.|...
T Consensus 233 R~g~pC~~Cg~~I~~~~~~--gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 233 REGQPCPRCGTPIEKIVVG--GRGTHFCPQCQPL 264 (269)
T ss_pred CCcCCCCcCCCeeEEEEEC--CCCcEECCCCcCC
Confidence 3446799999998766543 4677899999853
No 209
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=68.94 E-value=3.4 Score=38.27 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=23.0
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.|..+.+-||.||. + .+....|+.||+.+-
T Consensus 304 ~~~~tS~~C~~cg~-~--------~~r~~~C~~cg~~~~ 333 (364)
T COG0675 304 PPYYTSKTCPCCGH-L--------SGRLFKCPRCGFVHD 333 (364)
T ss_pred CCCCCcccccccCC-c--------cceeEECCCCCCeeh
Confidence 35677899999999 1 134689999998765
No 210
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=68.44 E-value=4.1 Score=28.78 Aligned_cols=31 Identities=23% Similarity=0.450 Sum_probs=19.2
Q ss_pred CCCCcCCCCCCcccccCCCC--c--ceeecCCCCc
Q 022283 104 ISFCQWCGGQTKHEVPHGEE--K--MRAICTVCGK 134 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~--~--~~~~C~~Cg~ 134 (299)
.+=||-||.+.......... + ....|..||.
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 35699999886554321111 1 4567999987
No 211
>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=68.44 E-value=4.9 Score=29.41 Aligned_cols=12 Identities=33% Similarity=0.844 Sum_probs=8.0
Q ss_pred eeecCCCCceee
Q 022283 126 RAICTVCGKIAY 137 (299)
Q Consensus 126 ~~~C~~Cg~~~y 137 (299)
...|++||+..+
T Consensus 36 ~v~C~~CGYTE~ 47 (64)
T PF09855_consen 36 TVSCTNCGYTEF 47 (64)
T ss_pred EEECCCCCCEEE
Confidence 356777877654
No 212
>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=67.42 E-value=2.2 Score=34.48 Aligned_cols=23 Identities=30% Similarity=0.558 Sum_probs=17.7
Q ss_pred CCcceeecCCCCceee-cCCcEEE
Q 022283 122 EEKMRAICTVCGKIAY-QNPKMVV 144 (299)
Q Consensus 122 ~~~~~~~C~~Cg~~~y-~~p~~vV 144 (299)
+-|.++.|++||..+| .|-.++|
T Consensus 5 elGtKR~Cp~CG~kFYDLnk~Piv 28 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDLNKDPIV 28 (108)
T ss_pred ccCCcccCCCCcchhccCCCCCcc
Confidence 4578999999999999 3445544
No 213
>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=67.18 E-value=2.5 Score=33.08 Aligned_cols=34 Identities=24% Similarity=0.372 Sum_probs=23.6
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.-+...-.||.||+....+. +--.+.|..|+...
T Consensus 30 ~~q~~ky~Cp~Cgk~~vkR~----a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 30 ISQHAKYTCPFCGKTSVKRV----ATGIWKCKKCGKKF 63 (90)
T ss_dssp HHHHS-BEESSSSSSEEEEE----ETTEEEETTTTEEE
T ss_pred HHHhCCCcCCCCCCceeEEe----eeEEeecCCCCCEE
Confidence 34455668999999976553 33458999999654
No 214
>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=67.16 E-value=4 Score=34.40 Aligned_cols=36 Identities=25% Similarity=0.433 Sum_probs=25.2
Q ss_pred CCCCcCCCCCCcccccCC-----------CCcceeecCCCCceeecC
Q 022283 104 ISFCQWCGGQTKHEVPHG-----------EEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~-----------~~~~~~~C~~Cg~~~y~~ 139 (299)
+.-|+.|++++.....+. ....-..|+.||.++++-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~G 137 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEG 137 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEeccc
Confidence 789999999986652110 011357899999999863
No 215
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=67.09 E-value=2.7 Score=30.46 Aligned_cols=25 Identities=24% Similarity=0.643 Sum_probs=20.1
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
+|..|.+||...... ....|.+||+
T Consensus 16 tHt~CrRCG~~syh~-------qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRHSYNV-------RKKYCAACGF 40 (62)
T ss_pred ccchhcccCcccccc-------cccchhhcCC
Confidence 788999999995433 4678999997
No 216
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.06 E-value=3.7 Score=31.27 Aligned_cols=28 Identities=21% Similarity=0.425 Sum_probs=21.1
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.-||.||-.+.+..- .+...-.||.|+-
T Consensus 2 llCP~C~v~l~~~~r--s~vEiD~CPrCrG 29 (88)
T COG3809 2 LLCPICGVELVMSVR--SGVEIDYCPRCRG 29 (88)
T ss_pred cccCcCCceeeeeee--cCceeeeCCcccc
Confidence 469999999987643 3455678999973
No 217
>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=67.01 E-value=3.6 Score=27.27 Aligned_cols=31 Identities=26% Similarity=0.644 Sum_probs=16.7
Q ss_pred CCCCcCCCCCCccc-ccCCCCcceeecCCCCc
Q 022283 104 ISFCQWCGGQTKHE-VPHGEEKMRAICTVCGK 134 (299)
Q Consensus 104 ~~fC~~CG~~~~~~-~~~~~~~~~~~C~~Cg~ 134 (299)
+.=||.||..-..+ ..+.++.-..+|..|+.
T Consensus 3 h~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCCCCCcCccccccCcCcccCCCEECCCCCC
Confidence 34599999997776 44334456789999943
No 218
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=66.69 E-value=3.7 Score=34.60 Aligned_cols=43 Identities=16% Similarity=0.306 Sum_probs=30.8
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 93 AAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
-...|-++...+--|+.||+|=....-. ..-.-..|..||...
T Consensus 91 i~~~L~~yI~~yVlC~~C~spdT~l~k~-~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 91 INEKIDRYVKEYVICPECGSPDTKLIKE-GRIWVLKCEACGAET 133 (138)
T ss_pred HHHHHHHHHHhcEECCCCCCCCcEEEEc-CCeEEEEcccCCCCC
Confidence 3456778889999999999993322221 344678999999754
No 219
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=66.50 E-value=2.2 Score=35.97 Aligned_cols=35 Identities=14% Similarity=0.194 Sum_probs=21.1
Q ss_pred CCCCcCCCCCCccccc--CCCCcceeecCCCCceeec
Q 022283 104 ISFCQWCGGQTKHEVP--HGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~--~~~~~~~~~C~~Cg~~~y~ 138 (299)
+=.||.||........ ..+....+.||.||.....
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 0011223999999976643
No 220
>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=66.43 E-value=4.5 Score=27.44 Aligned_cols=32 Identities=22% Similarity=0.535 Sum_probs=19.6
Q ss_pred CCcCCCCCCccccc----CCCCcceeecCC--CCceee
Q 022283 106 FCQWCGGQTKHEVP----HGEEKMRAICTV--CGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~----~~~~~~~~~C~~--Cg~~~y 137 (299)
+||.||++...+.. ..-...-..|.+ ||..+-
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEE
Confidence 69999999765521 111234456766 887654
No 221
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=65.95 E-value=4.3 Score=29.69 Aligned_cols=33 Identities=21% Similarity=0.407 Sum_probs=23.3
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
...+=||.||......... ..-.+..|..|+..
T Consensus 4 d~lKPCPFCG~~~~~v~~~-~g~~~v~C~~CgA~ 36 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAI-SGYYRAKCNGCESR 36 (64)
T ss_pred ccccCCCCCCCceeEEEec-CceEEEEcCCCCcC
Confidence 3457799999996555432 34566899999864
No 222
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=65.63 E-value=8.6 Score=26.81 Aligned_cols=35 Identities=20% Similarity=0.352 Sum_probs=24.1
Q ss_pred hhhcCCCCc--CCCCCCcccccCCCCcceeecCCCCcee
Q 022283 100 NVLKISFCQ--WCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 100 w~~~~~fC~--~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
-+.+.++|| .|+....... +.+.....|+.|+...
T Consensus 14 ~~~~~~~CP~~~C~~~~~~~~--~~~~~~v~C~~C~~~f 50 (64)
T smart00647 14 SNPDLKWCPAPDCSAAIIVTE--EEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCccCCCCCCCcceEEecC--CCCCCeeECCCCCCeE
Confidence 346789999 9988865531 1245678899888543
No 223
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=65.62 E-value=3.4 Score=43.30 Aligned_cols=12 Identities=17% Similarity=0.086 Sum_probs=7.1
Q ss_pred CCHHHHHHHHHH
Q 022283 179 ESAAEGAIRETW 190 (299)
Q Consensus 179 Es~eeAa~REv~ 190 (299)
.|+.+++.-++.
T Consensus 130 ~s~~~~~~~~~~ 141 (645)
T PRK14559 130 PSPLEALLEQLE 141 (645)
T ss_pred cCHHHHHHHHhh
Confidence 377777655543
No 224
>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=65.59 E-value=2.6 Score=34.18 Aligned_cols=30 Identities=20% Similarity=0.271 Sum_probs=18.6
Q ss_pred hhhcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 100 NVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
+....-+|..||...... .....||.||..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~------~~~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPE------IDLYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecC------CcCccCcCCcCC
Confidence 444566888888664332 224568888854
No 225
>PRK02935 hypothetical protein; Provisional
Probab=65.55 E-value=3.5 Score=33.12 Aligned_cols=27 Identities=22% Similarity=0.368 Sum_probs=21.4
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
--||.|+++++.. |..-.|..|+...-
T Consensus 71 V~CP~C~K~TKmL------GrvD~CM~C~~PLT 97 (110)
T PRK02935 71 VICPSCEKPTKML------GRVDACMHCNQPLT 97 (110)
T ss_pred eECCCCCchhhhc------cceeecCcCCCcCC
Confidence 4799999999875 55678999987543
No 226
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=65.18 E-value=5.6 Score=29.79 Aligned_cols=33 Identities=12% Similarity=0.337 Sum_probs=21.7
Q ss_pred CCCcCCCCCCccc----ccCCCCcceeecC--CCCceee
Q 022283 105 SFCQWCGGQTKHE----VPHGEEKMRAICT--VCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~----~~~~~~~~~~~C~--~Cg~~~y 137 (299)
.+||.||++...+ ..++-.+....|. .||..+-
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 5899999996433 1222344667888 7997654
No 227
>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=64.73 E-value=4.1 Score=26.30 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=20.3
Q ss_pred hhhcC-CCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 100 NVLKI-SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 100 w~~~~-~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
|.+.. .-|+.||+..... .....+|..||..
T Consensus 3 ~~~~~~~~C~~C~~~~~~~-----~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 3 WMRGPNEPCPVCGSRWFYS-----DDGFYYCDRCGHQ 34 (36)
T ss_pred ccccCCCcCCCCCCeEeEc-----cCCEEEhhhCceE
Confidence 44443 2499999993332 2347899999865
No 228
>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=64.62 E-value=4.9 Score=28.07 Aligned_cols=33 Identities=18% Similarity=0.408 Sum_probs=15.6
Q ss_pred hhhcCCCCcC--CCCCCcccccCCCCcce--eecCCCCcee
Q 022283 100 NVLKISFCQW--CGGQTKHEVPHGEEKMR--AICTVCGKIA 136 (299)
Q Consensus 100 w~~~~~fC~~--CG~~~~~~~~~~~~~~~--~~C~~Cg~~~ 136 (299)
-....++||. |+...... ++... ..|+.|+...
T Consensus 14 ~~~~~~~Cp~~~C~~~~~~~----~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 14 SDPNIRWCPNPDCEYIIEKD----DGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp S---CC--TTSST---ECS-----SSTTS--CCTTSCCSEE
T ss_pred CCCCccCCCCCCCcccEEec----CCCCCCeeECCCCCCcC
Confidence 3445579988 99997655 22223 7899988653
No 229
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=64.43 E-value=5.1 Score=38.24 Aligned_cols=35 Identities=20% Similarity=0.366 Sum_probs=23.0
Q ss_pred cCCCCcCCCCCCcccc--c-CCCCcceeecCCCCceee
Q 022283 103 KISFCQWCGGQTKHEV--P-HGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~--~-~~~~~~~~~C~~Cg~~~y 137 (299)
...+||.||+.-.... . ..++....+|.-|+..+.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~ 223 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWH 223 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccc
Confidence 4689999999953321 1 123456678988887654
No 230
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=63.53 E-value=4.2 Score=38.12 Aligned_cols=33 Identities=21% Similarity=0.330 Sum_probs=25.7
Q ss_pred hhhcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 100 NVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
..+.-.-|++||++.+.... .+.....||.|..
T Consensus 241 YgR~GepC~~CGt~I~k~~~--~gR~t~~CP~CQ~ 273 (273)
T COG0266 241 YGRAGEPCRRCGTPIEKIKL--GGRSTFYCPVCQK 273 (273)
T ss_pred ecCCCCCCCccCCEeEEEEE--cCCcCEeCCCCCC
Confidence 44577899999999877655 3566889999973
No 231
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=63.27 E-value=3.2 Score=33.64 Aligned_cols=32 Identities=13% Similarity=0.203 Sum_probs=19.8
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 99 GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.+....-+|..||...... ......||.||..
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~ 96 (114)
T PRK03681 65 EEQEAECWCETCQQYVTLL-----TQRVRRCPQCHGD 96 (114)
T ss_pred EeeCcEEEcccCCCeeecC-----CccCCcCcCcCCC
Confidence 4445567899999764332 1223569999854
No 232
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=63.18 E-value=4.5 Score=32.72 Aligned_cols=41 Identities=15% Similarity=0.332 Sum_probs=29.7
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 93 AAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-...|.++...+--|+.||+|=....-+ ..-.-..|..||.
T Consensus 69 i~~~l~~yI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa 109 (110)
T smart00653 69 LQDLLRRYIKEYVLCPECGSPDTELIKE-NRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHHhcEECCCCCCCCcEEEEe-CCeEEEEccccCC
Confidence 3456778899999999999993322222 3556788999995
No 233
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=63.12 E-value=5.6 Score=31.08 Aligned_cols=37 Identities=19% Similarity=0.334 Sum_probs=25.0
Q ss_pred HHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 96 HSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 96 ~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.+..-+..--.||.||.....+ .+-..+.|..|+...
T Consensus 28 kie~~q~a~y~CpfCgk~~vkR----~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 28 KIEISQHAKYFCPFCGKHAVKR----QAVGIWRCKGCKKTV 64 (90)
T ss_pred HHHHHHhCCccCCCCCCCceee----eeeEEEEcCCCCCEE
Confidence 3334455667899999875444 344568999998754
No 234
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=63.03 E-value=4.3 Score=36.51 Aligned_cols=15 Identities=33% Similarity=0.587 Sum_probs=10.5
Q ss_pred cCCCCcCCCCCCccc
Q 022283 103 KISFCQWCGGQTKHE 117 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~ 117 (299)
+..-||.||+.....
T Consensus 4 k~~~CPvC~~~F~~~ 18 (214)
T PF09986_consen 4 KKITCPVCGKEFKTK 18 (214)
T ss_pred CceECCCCCCeeeee
Confidence 345699999986544
No 235
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=62.81 E-value=4.7 Score=33.74 Aligned_cols=42 Identities=19% Similarity=0.317 Sum_probs=29.5
Q ss_pred HHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 94 AVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
...|.++...+--|+.||+|=....-+ +...-..|..||...
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 456778889999999999993332221 234457999999653
No 236
>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=62.36 E-value=34 Score=31.05 Aligned_cols=24 Identities=21% Similarity=0.656 Sum_probs=17.6
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
|+.||.+.... ....|++|-...+
T Consensus 1 C~~CG~~~~~~-------~~~lC~~C~~~~~ 24 (236)
T PF04981_consen 1 CPRCGREIEPL-------IDGLCPDCYLKRF 24 (236)
T ss_pred CCCCCCCCCCc-------ccccChHHhcccC
Confidence 99999987654 2248999966555
No 237
>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=62.25 E-value=4.5 Score=35.02 Aligned_cols=31 Identities=35% Similarity=0.716 Sum_probs=18.2
Q ss_pred CcCCCCCC-ccc-----ccC-CC-CcceeecCCCCceee
Q 022283 107 CQWCGGQT-KHE-----VPH-GE-EKMRAICTVCGKIAY 137 (299)
Q Consensus 107 C~~CG~~~-~~~-----~~~-~~-~~~~~~C~~Cg~~~y 137 (299)
||.||++. ... +|. ++ --....|++||+.+-
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchh
Confidence 99999873 221 110 00 013578999998764
No 238
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=61.99 E-value=5.9 Score=34.75 Aligned_cols=31 Identities=19% Similarity=0.518 Sum_probs=23.8
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceeecC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (299)
+..|+.||.+|.+. ......|+.||......
T Consensus 149 ~a~~~~~g~~~~~~-----~~~~~~c~~~~~~e~rk 179 (189)
T PRK09521 149 YAMCSRCRTPLVKK-----GENELKCPNCGNIETRK 179 (189)
T ss_pred EEEccccCCceEEC-----CCCEEECCCCCCEEeec
Confidence 45799999999775 22468999999876644
No 239
>PRK04023 DNA polymerase II large subunit; Validated
Probab=61.72 E-value=4.6 Score=44.04 Aligned_cols=24 Identities=29% Similarity=0.620 Sum_probs=18.2
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
...+||+.||..+. ...||.||..
T Consensus 624 Vg~RfCpsCG~~t~----------~frCP~CG~~ 647 (1121)
T PRK04023 624 IGRRKCPSCGKETF----------YRRCPFCGTH 647 (1121)
T ss_pred ccCccCCCCCCcCC----------cccCCCCCCC
Confidence 45789999999852 3578888865
No 240
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=61.56 E-value=2.9 Score=33.41 Aligned_cols=29 Identities=28% Similarity=0.642 Sum_probs=22.3
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
-|-+||+-... |+.....-||.||...|.
T Consensus 4 ~CtrCG~vf~~----g~~~il~GCp~CG~nkF~ 32 (112)
T COG3364 4 QCTRCGEVFDD----GSEEILSGCPKCGCNKFL 32 (112)
T ss_pred eeccccccccc----ccHHHHccCccccchheE
Confidence 49999998643 356677889999987773
No 241
>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=61.38 E-value=13 Score=30.84 Aligned_cols=43 Identities=14% Similarity=0.269 Sum_probs=26.1
Q ss_pred CCCCc--CCCCCCcccccCCCCcceeecCCCCcee-ecCCcEEEEEEEeeC
Q 022283 104 ISFCQ--WCGGQTKHEVPHGEEKMRAICTVCGKIA-YQNPKMVVGCLIEHD 151 (299)
Q Consensus 104 ~~fC~--~CG~~~~~~~~~~~~~~~~~C~~Cg~~~-y~~p~~vV~~iv~~~ 151 (299)
+.=|| .|++++... +.....|+.|+... -+.++..+-+.+.++
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 22468999999775 455555665555554
No 242
>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=61.10 E-value=5.9 Score=27.91 Aligned_cols=30 Identities=20% Similarity=0.480 Sum_probs=21.7
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
-|++|.+...............+|+.||..
T Consensus 24 IC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 24 ICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred ECcccchhhcccccccCCceEEEcCCCCCc
Confidence 599999886665333345678999999863
No 243
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=60.77 E-value=4 Score=29.11 Aligned_cols=25 Identities=44% Similarity=0.801 Sum_probs=18.5
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
..+.|+.||.-+- ...||.||....
T Consensus 4 ~mr~C~~CgvYTL----------k~~CP~CG~~t~ 28 (56)
T PRK13130 4 KIRKCPKCGVYTL----------KEICPVCGGKTK 28 (56)
T ss_pred cceECCCCCCEEc----------cccCcCCCCCCC
Confidence 5788999998753 357999986543
No 244
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=59.71 E-value=3.6 Score=34.57 Aligned_cols=14 Identities=36% Similarity=0.968 Sum_probs=6.5
Q ss_pred CCCCcCCCCCCccc
Q 022283 104 ISFCQWCGGQTKHE 117 (299)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (299)
.+||.+||.+...+
T Consensus 89 ~r~CARCGGrv~lr 102 (169)
T KOG3799|consen 89 TRFCARCGGRVSLR 102 (169)
T ss_pred hhHHHhcCCeeeec
Confidence 34455555544433
No 245
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=59.70 E-value=4.2 Score=33.11 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=18.8
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
....-+|..||...... ......||.||...
T Consensus 68 vp~~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 68 EKVELECKDCSHVFKPN-----ALDYGVCEKCHSKN 98 (117)
T ss_pred cCCEEEhhhCCCccccC-----CccCCcCcCCCCCc
Confidence 33456899999664432 11233599999543
No 246
>PRK08402 replication factor A; Reviewed
Probab=59.50 E-value=12 Score=36.42 Aligned_cols=50 Identities=12% Similarity=0.186 Sum_probs=31.4
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeC-CEEEEE
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHD-KKILLC 157 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~-~kILL~ 157 (299)
-+.-||.|.+++... ++.....|+.||.. .|..+..+.+.+.++ |.+-+.
T Consensus 211 ~y~aCp~CnKkv~~~----~~~~~~~Ce~~~~v-~p~~ryil~~~l~D~TG~~~vt 261 (355)
T PRK08402 211 VYDACPECRRKVDYD----PATDTWICPEHGEV-EPIKITILDFGLDDGTGYIRVT 261 (355)
T ss_pred eEecCCCCCeEEEEe----cCCCCEeCCCCCCc-CcceeEEEEEEEEcCCCcEEEE
Confidence 467899999997633 23346789999952 334455555555544 555444
No 247
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.44 E-value=6.2 Score=31.80 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=19.9
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
..-||.||.++... ...|+.|+...-
T Consensus 6 ~~~cPvcg~~~iVT--------eL~c~~~etTVr 31 (122)
T COG3877 6 INRCPVCGRKLIVT--------ELKCSNCETTVR 31 (122)
T ss_pred CCCCCcccccceeE--------EEecCCCCceEe
Confidence 45699999997654 578999986544
No 248
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=59.14 E-value=5.1 Score=28.89 Aligned_cols=20 Identities=15% Similarity=0.114 Sum_probs=15.7
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
...|+.||...... ..|+ ||
T Consensus 27 ~~~c~~cg~~~~pH---------~vc~-cG 46 (60)
T PRK01110 27 LSVDKTTGEYHLPH---------HVSP-KG 46 (60)
T ss_pred eeEcCCCCceeccc---------eecC-Cc
Confidence 46799999986554 6799 98
No 249
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=59.05 E-value=6.6 Score=38.98 Aligned_cols=34 Identities=21% Similarity=0.298 Sum_probs=24.5
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
.=|+.||.-..... -+.+.+..|+.||..-|.+.
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 44999998754332 24566889999999888543
No 250
>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=58.97 E-value=11 Score=24.53 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=21.3
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCC---CCceee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTV---CGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~---Cg~~~y 137 (299)
.-||.||+.|..+.- ..+.-..|.. |.+...
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 469999999887742 3445567864 776654
No 251
>PRK12366 replication factor A; Reviewed
Probab=58.96 E-value=9.9 Score=39.80 Aligned_cols=41 Identities=17% Similarity=0.514 Sum_probs=27.7
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHD 151 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~ 151 (299)
+.-||.|.+++.. .....+|+.||.. -|.....+-+.+.++
T Consensus 532 y~aCp~CnkKv~~------~~g~~~C~~c~~~-~p~~~~~l~~~i~D~ 572 (637)
T PRK12366 532 LYLCPNCRKRVEE------VDGEYICEFCGEV-EPNELLMLNFTLDDG 572 (637)
T ss_pred EecccccCeEeEc------CCCcEECCCCCCC-CCcEEEEEEEEEEcC
Confidence 5679999998753 2346899999988 444445555555544
No 252
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=58.83 E-value=9.6 Score=33.92 Aligned_cols=34 Identities=18% Similarity=0.409 Sum_probs=20.1
Q ss_pred cCCCCcCCCCCCcc--cccCCCCcceeecCCCCcee
Q 022283 103 KISFCQWCGGQTKH--EVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 103 ~~~fC~~CG~~~~~--~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.+-.||.||..-.. .+-..-...-..|..||.++
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 35689999944221 11110112467999999887
No 253
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=58.79 E-value=4.3 Score=29.12 Aligned_cols=28 Identities=25% Similarity=0.550 Sum_probs=21.9
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.+|.-|-+||...... ...+|..||+..
T Consensus 14 ~tH~~CRRCGr~syhv-------~k~~CaaCGfgr 41 (61)
T COG2126 14 KTHIRCRRCGRRSYHV-------RKKYCAACGFGR 41 (61)
T ss_pred cceehhhhccchheee-------ccceecccCCCC
Confidence 6788899999996443 367999999763
No 254
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=58.69 E-value=5.2 Score=42.69 Aligned_cols=25 Identities=32% Similarity=0.724 Sum_probs=18.6
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
..||.||..+... +.-..|.+||+.
T Consensus 725 ~~Cp~Cg~~l~~~------~GC~~C~~CG~s 749 (752)
T PRK08665 725 GACPECGSILEHE------EGCVVCHSCGYS 749 (752)
T ss_pred CCCCCCCcccEEC------CCCCcCCCCCCC
Confidence 4799999876553 235799999974
No 255
>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=58.49 E-value=7.2 Score=38.52 Aligned_cols=33 Identities=21% Similarity=0.353 Sum_probs=24.4
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
=|+.||.-.... .-+.+.+..|+.||..-|.+.
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 224567889999999888543
No 256
>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=58.27 E-value=20 Score=28.10 Aligned_cols=28 Identities=21% Similarity=0.385 Sum_probs=20.3
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
--|..||......-. ....+.+||.|=+
T Consensus 5 F~C~~CG~~V~p~~~--g~~~RNHCP~CL~ 32 (92)
T PF12647_consen 5 FTCVHCGLTVSPLAA--GSAHRNHCPSCLS 32 (92)
T ss_pred cCccccCCCcccCCC--CCCccCcCccccc
Confidence 469999998765422 3458999999954
No 257
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=57.92 E-value=6.4 Score=37.36 Aligned_cols=32 Identities=22% Similarity=0.457 Sum_probs=20.6
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.....||.||+.. .. .+ ....-.+|.+||.+.
T Consensus 9 ~~~~~Cp~Cg~~~-iv-~d-~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGSDK-LI-YD-YERGEIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCCCC-ee-EE-CCCCeEeecccCCcc
Confidence 3456899999842 21 11 334568999999643
No 258
>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=57.83 E-value=2.4 Score=34.29 Aligned_cols=30 Identities=23% Similarity=0.515 Sum_probs=17.5
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
....-+|..||...... .....||.||...
T Consensus 67 ~p~~~~C~~Cg~~~~~~------~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPD------EFDFSCPRCGSPD 96 (113)
T ss_dssp E--EEEETTTS-EEECH------HCCHH-SSSSSS-
T ss_pred cCCcEECCCCCCEEecC------CCCCCCcCCcCCC
Confidence 33456899999987554 2336799998654
No 259
>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=57.48 E-value=3.4 Score=35.43 Aligned_cols=30 Identities=13% Similarity=0.299 Sum_probs=20.1
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.+=+||.||.+..... .-..-+.||.||..
T Consensus 108 ~~Y~Cp~c~~r~tf~e---A~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNE---AMELNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHH---HHHcCCcCCCCCCE
Confidence 3446999998864431 11245899999975
No 260
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=57.28 E-value=5.6 Score=35.33 Aligned_cols=31 Identities=26% Similarity=0.625 Sum_probs=19.0
Q ss_pred CcCCCCCCcccccCCC-----C---cceeecCCCCceee
Q 022283 107 CQWCGGQTKHEVPHGE-----E---KMRAICTVCGKIAY 137 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~-----~---~~~~~C~~Cg~~~y 137 (299)
||.||+....+...-+ + .....|++||+.+.
T Consensus 3 Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 3 CPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred CCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccc
Confidence 9999977433321101 0 13678999998764
No 261
>PRK07218 replication factor A; Provisional
Probab=56.85 E-value=14 Score=36.84 Aligned_cols=40 Identities=15% Similarity=0.401 Sum_probs=30.1
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCE
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKK 153 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~k 153 (299)
-.+-||.|+..+.. ..|+.||.+ -+..+..+-++++++..
T Consensus 296 li~rCP~C~r~v~~----------~~C~~hG~v-e~~~dlrik~vLDDGtg 335 (423)
T PRK07218 296 LIERCPECGRVIQK----------GQCRSHGAV-EGEDDLRIKAILDDGTG 335 (423)
T ss_pred ceecCcCccccccC----------CcCCCCCCc-CCeeeeEEEEEEECCCC
Confidence 34689999999732 479999966 55667788888888743
No 262
>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=56.52 E-value=7 Score=29.17 Aligned_cols=36 Identities=17% Similarity=0.261 Sum_probs=25.4
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeecCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPK 141 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~ 141 (299)
-||.|++--.......++....-|-.||+..-..+.
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 499999885444322345678899999988776555
No 263
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=56.24 E-value=3.5 Score=36.13 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=20.3
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.+=+||.||.+..... .-..-+.||.||..-
T Consensus 116 ~~Y~Cp~C~~rytf~e---A~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDE---AMEYGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHH---HhhcCCcCCCCCCCC
Confidence 3556999998864431 112458999999643
No 264
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=56.05 E-value=6.6 Score=35.05 Aligned_cols=42 Identities=19% Similarity=0.346 Sum_probs=29.6
Q ss_pred HHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 94 AVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
...|.++...+--|+.||+|=....-. +.-.-..|..||...
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 455667888999999999993332222 344567999999654
No 265
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=55.53 E-value=2.9 Score=39.67 Aligned_cols=43 Identities=21% Similarity=0.475 Sum_probs=29.7
Q ss_pred CCCcchHHHHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 85 ATSSHPSSAAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 85 ~~~~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
++.+....+|.-=..|...-+||..||.+- -..+|..|..+.|
T Consensus 300 P~A~~vl~qAi~Gqr~~~d~~fCstCG~~g----------a~KrCs~CKav~Y 342 (396)
T KOG1710|consen 300 PSAYEVLVQAIFGQRIAADCQFCSTCGHPG----------AKKRCSQCKAVAY 342 (396)
T ss_pred CcHHHHHHHHHcCceeEEecccccccCCCC----------ccchhhhhHHHHH
Confidence 334455566666668999999999999983 2456777764444
No 266
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=55.27 E-value=7.6 Score=27.79 Aligned_cols=23 Identities=30% Similarity=0.765 Sum_probs=17.7
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
....|+.||.-.... .+|+.||+
T Consensus 26 ~~~~c~~cG~~~l~H---------rvc~~cg~ 48 (57)
T COG0333 26 TLSVCPNCGEYKLPH---------RVCLKCGY 48 (57)
T ss_pred cceeccCCCCcccCc---------eEcCCCCC
Confidence 357899999985443 68999994
No 267
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=55.16 E-value=8.3 Score=30.14 Aligned_cols=37 Identities=16% Similarity=0.258 Sum_probs=24.6
Q ss_pred HHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 96 HSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 96 ~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.+..-+..--.||.||+....+ .+-..+.|..|+...
T Consensus 28 kie~~q~a~y~CpfCgk~~vkR----~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 28 DIEEKMRAKHVCPVCGRPKVKR----VGTGIWECRKCGAKF 64 (90)
T ss_pred HHHHHHhcCccCCCCCCCceEE----EEEEEEEcCCCCCEE
Confidence 3333445566899999876555 344568899998654
No 268
>PRK04023 DNA polymerase II large subunit; Validated
Probab=55.16 E-value=6.9 Score=42.73 Aligned_cols=17 Identities=29% Similarity=0.659 Sum_probs=12.4
Q ss_pred hhhhcCCCCcCCCCCCc
Q 022283 99 GNVLKISFCQWCGGQTK 115 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~ 115 (299)
++.....+||.||+.+.
T Consensus 633 G~~t~~frCP~CG~~Te 649 (1121)
T PRK04023 633 GKETFYRRCPFCGTHTE 649 (1121)
T ss_pred CCcCCcccCCCCCCCCC
Confidence 44456789999998853
No 269
>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=54.95 E-value=11 Score=24.89 Aligned_cols=26 Identities=27% Similarity=0.284 Sum_probs=12.1
Q ss_pred eeeceEEeeCCCCHHHHHHHHHHHHh
Q 022283 168 WTLPAGYMEIGESAAEGAIRETWEEA 193 (299)
Q Consensus 168 w~lPgG~VE~GEs~eeAa~REv~EEt 193 (299)
..+.||...+|--+...+.||+-||.
T Consensus 11 ltClggLasPgPvp~~~alkELIeEL 36 (43)
T PF03487_consen 11 LTCLGGLASPGPVPSSTALKELIEEL 36 (43)
T ss_dssp ------------S-HHHHHHHHHHHH
T ss_pred HHHhcccCCCCCCCchHHHHHHHHHH
Confidence 35668999999999999999999995
No 270
>PRK14873 primosome assembly protein PriA; Provisional
Probab=54.46 E-value=7.2 Score=41.06 Aligned_cols=26 Identities=23% Similarity=0.552 Sum_probs=14.3
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
-|++|+.+|..+ .......|..||+.
T Consensus 394 ~C~~C~~~L~~h----~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 394 RCRHCTGPLGLP----SAGGTPRCRWCGRA 419 (665)
T ss_pred ECCCCCCceeEe----cCCCeeECCCCcCC
Confidence 366666666654 22335566666654
No 271
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=54.09 E-value=5.8 Score=33.32 Aligned_cols=26 Identities=35% Similarity=0.586 Sum_probs=18.4
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
-.-..|++||+-..+- +..|+.|+..
T Consensus 27 l~g~kC~~CG~v~~PP--------r~~Cp~C~~~ 52 (140)
T COG1545 27 LLGTKCKKCGRVYFPP--------RAYCPKCGSE 52 (140)
T ss_pred EEEEEcCCCCeEEcCC--------cccCCCCCCC
Confidence 3456799999885442 5788888865
No 272
>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=53.91 E-value=8.7 Score=31.76 Aligned_cols=42 Identities=14% Similarity=0.298 Sum_probs=30.9
Q ss_pred HHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 94 AVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 94 a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
...|.++...+--|+.||+|=...... ...+...|..||...
T Consensus 83 ~~~L~~fI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 83 QDLLDKFIKEYVLCPECGSPDTELIKE-GRLIFLKCKACGASR 124 (125)
T ss_dssp HHHHHHHHCHHSSCTSTSSSSEEEEEE-TTCCEEEETTTSCEE
T ss_pred HHHHHHHHHHEEEcCCCCCCccEEEEc-CCEEEEEecccCCcC
Confidence 456777889999999999993322222 466788999999753
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=53.84 E-value=7.4 Score=39.49 Aligned_cols=26 Identities=19% Similarity=0.470 Sum_probs=17.2
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
||.|+.+|..+ .......|..||+..
T Consensus 225 C~~C~~~l~~h----~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 225 CPNCDVSLTYH----KKEGKLRCHYCGYQE 250 (505)
T ss_pred CCCCCCceEEe----cCCCeEEcCCCcCcC
Confidence 88888888776 234466677776543
No 274
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=53.75 E-value=6.2 Score=32.92 Aligned_cols=28 Identities=25% Similarity=0.656 Sum_probs=21.5
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
-|-+||+.... |......-||.||...|
T Consensus 3 ~Ct~Cg~~f~d----gs~eil~GCP~CGg~kF 30 (131)
T PF09845_consen 3 QCTKCGRVFED----GSKEILSGCPECGGNKF 30 (131)
T ss_pred ccCcCCCCcCC----CcHHHHccCcccCCcce
Confidence 49999998654 35567788999997766
No 275
>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=53.67 E-value=3.4 Score=29.28 Aligned_cols=27 Identities=26% Similarity=0.706 Sum_probs=19.0
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.+|..|.+||...... ....|..||+.
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 4678899999985443 35789999953
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=53.45 E-value=4.4 Score=43.39 Aligned_cols=14 Identities=29% Similarity=0.396 Sum_probs=0.0
Q ss_pred cCCCCcCCCCCCcc
Q 022283 103 KISFCQWCGGQTKH 116 (299)
Q Consensus 103 ~~~fC~~CG~~~~~ 116 (299)
..+.||.||..+..
T Consensus 654 ~~r~Cp~Cg~~t~~ 667 (900)
T PF03833_consen 654 GRRRCPKCGKETFY 667 (900)
T ss_dssp --------------
T ss_pred ecccCcccCCcchh
Confidence 46778888877533
No 277
>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=53.08 E-value=5.8 Score=32.96 Aligned_cols=23 Identities=26% Similarity=0.449 Sum_probs=17.2
Q ss_pred CCcceeecCCCCceeec-CCcEEE
Q 022283 122 EEKMRAICTVCGKIAYQ-NPKMVV 144 (299)
Q Consensus 122 ~~~~~~~C~~Cg~~~y~-~p~~vV 144 (299)
+-|.++.|++||..+|- |-.++|
T Consensus 5 elGtKr~Cp~cg~kFYDLnk~p~v 28 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDLNRRPAV 28 (129)
T ss_pred hhCccccCCCcCccccccCCCCcc
Confidence 45788999999999993 444444
No 278
>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=52.66 E-value=9.8 Score=27.40 Aligned_cols=36 Identities=19% Similarity=0.341 Sum_probs=23.8
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeecCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPK 141 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~ 141 (299)
-||.|++-=.......++....-|-.||+..-..+.
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~~ 46 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQEQQKDQ 46 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCccccCCc
Confidence 599999874443322244567889999987765443
No 279
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=52.24 E-value=8.2 Score=33.56 Aligned_cols=23 Identities=26% Similarity=0.795 Sum_probs=17.4
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
-|+.||-.... ...-.||.||..
T Consensus 136 vC~vCGy~~~g-------e~P~~CPiCga~ 158 (166)
T COG1592 136 VCPVCGYTHEG-------EAPEVCPICGAP 158 (166)
T ss_pred EcCCCCCcccC-------CCCCcCCCCCCh
Confidence 69999998654 334689999954
No 280
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=51.85 E-value=7.7 Score=30.26 Aligned_cols=27 Identities=26% Similarity=0.669 Sum_probs=21.1
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
..+|..|.+||...... ....|.+||+
T Consensus 13 ~ktHtlCrRCG~~syH~-------qK~~CasCGy 39 (91)
T PTZ00073 13 GKTHTLCRRCGKRSFHV-------QKKRCASCGY 39 (91)
T ss_pred CcCcchhcccCcccccc-------ccccchhcCC
Confidence 36789999999995443 3578999997
No 281
>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=51.20 E-value=14 Score=23.00 Aligned_cols=27 Identities=15% Similarity=0.391 Sum_probs=20.7
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
-|+.|+..+..- .+-....|+.|..+.
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 599999998664 455678999997653
No 282
>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=50.98 E-value=14 Score=23.87 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=19.3
Q ss_pred CCCCcCCCCCC-ccccc-CCCCcceeecCCCC
Q 022283 104 ISFCQWCGGQT-KHEVP-HGEEKMRAICTVCG 133 (299)
Q Consensus 104 ~~fC~~CG~~~-~~~~~-~~~~~~~~~C~~Cg 133 (299)
.-.||.|++.. ..+.- ...+..+..|.+|.
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCcCC
Confidence 45799999997 33311 11345788888883
No 283
>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=50.78 E-value=19 Score=28.16 Aligned_cols=38 Identities=18% Similarity=0.290 Sum_probs=25.2
Q ss_pred HHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 95 VHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 95 ~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
..+..-+...-.||.||..-..+ .+-..+.|..|+...
T Consensus 26 ~kie~~q~a~y~CpfCgk~~vkR----~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 26 KKIEIQQKAKYVCPFCGKKTVKR----GSTGIWTCRKCGAKF 63 (91)
T ss_pred HHHHHHHhcCccCCCCCCCceEE----EeeEEEEcCCCCCEE
Confidence 33444455667899999775444 344568899998654
No 284
>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=50.59 E-value=8.9 Score=27.93 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=10.3
Q ss_pred cceeecCCCCcee
Q 022283 124 KMRAICTVCGKIA 136 (299)
Q Consensus 124 ~~~~~C~~Cg~~~ 136 (299)
....+|+.||..+
T Consensus 51 eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 51 EGELICPECGREY 63 (68)
T ss_dssp TTEEEETTTTEEE
T ss_pred CCEEEcCCCCCEE
Confidence 3579999999765
No 285
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.53 E-value=7.3 Score=28.47 Aligned_cols=31 Identities=26% Similarity=0.492 Sum_probs=19.8
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecC-CCCcee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICT-VCGKIA 136 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~~~ 136 (299)
...-||.||++..-.. +...|..|. .|..+.
T Consensus 6 ~~v~CP~Cgkpv~w~~---~s~frPFCSkRCklID 37 (65)
T COG3024 6 ITVPCPTCGKPVVWGE---ESPFRPFCSKRCKLID 37 (65)
T ss_pred ccccCCCCCCcccccc---cCCcCcchhHhhhhcc
Confidence 3457999999976532 345667776 475443
No 286
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=50.31 E-value=15 Score=30.36 Aligned_cols=15 Identities=27% Similarity=0.508 Sum_probs=11.9
Q ss_pred CCCCcCCCCCCcccc
Q 022283 104 ISFCQWCGGQTKHEV 118 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~ 118 (299)
+.||+.||++|....
T Consensus 69 r~FC~~CGs~l~~~~ 83 (133)
T COG3791 69 RGFCPTCGSPLFWRG 83 (133)
T ss_pred CeecccCCCceEEec
Confidence 449999999987653
No 287
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=50.31 E-value=12 Score=25.90 Aligned_cols=33 Identities=21% Similarity=0.457 Sum_probs=23.4
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
-+.|..||.......-.+..+....|..||..+
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 467999998866554344455578999999654
No 288
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=50.20 E-value=11 Score=42.19 Aligned_cols=14 Identities=29% Similarity=0.473 Sum_probs=10.6
Q ss_pred cCCCCcCCCCCCcc
Q 022283 103 KISFCQWCGGQTKH 116 (299)
Q Consensus 103 ~~~fC~~CG~~~~~ 116 (299)
...|||.||+++..
T Consensus 678 ~~~fCP~CGs~te~ 691 (1337)
T PRK14714 678 YENRCPDCGTHTEP 691 (1337)
T ss_pred ccccCcccCCcCCC
Confidence 34599999999743
No 289
>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=50.05 E-value=13 Score=29.84 Aligned_cols=13 Identities=23% Similarity=0.498 Sum_probs=8.3
Q ss_pred ceeecCCCCceee
Q 022283 125 MRAICTVCGKIAY 137 (299)
Q Consensus 125 ~~~~C~~Cg~~~y 137 (299)
...+|+.||...|
T Consensus 30 ~~~~C~~CGe~~~ 42 (127)
T TIGR03830 30 PGWYCPACGEELL 42 (127)
T ss_pred eeeECCCCCCEEE
Confidence 3456777776655
No 290
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=49.94 E-value=6.1 Score=38.20 Aligned_cols=45 Identities=16% Similarity=0.330 Sum_probs=33.7
Q ss_pred HHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 96 HSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 96 ~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
-|.+|-+.|--||.|+.|-...+...+......|..||+..-...
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 355788999999999999544444335567889999998776544
No 291
>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=49.85 E-value=9.9 Score=28.34 Aligned_cols=24 Identities=21% Similarity=0.426 Sum_probs=12.3
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.||.|+++|... +...+|..|+..
T Consensus 3 ~CP~C~~~L~~~------~~~~~C~~C~~~ 26 (70)
T PF07191_consen 3 TCPKCQQELEWQ------GGHYHCEACQKD 26 (70)
T ss_dssp B-SSS-SBEEEE------TTEEEETTT--E
T ss_pred cCCCCCCccEEe------CCEEECcccccc
Confidence 578888876554 245666666653
No 292
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=49.67 E-value=13 Score=26.89 Aligned_cols=27 Identities=33% Similarity=0.597 Sum_probs=21.2
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
--||.|-+++... +.+...+|+.|+..
T Consensus 9 LaCP~~kg~L~~~----~~~~~L~c~~~~~a 35 (60)
T COG2835 9 LACPVCKGPLVYD----EEKQELICPRCKLA 35 (60)
T ss_pred eeccCcCCcceEe----ccCCEEEecccCce
Confidence 3599999998776 55668999999843
No 293
>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=49.39 E-value=6.3 Score=25.39 Aligned_cols=32 Identities=28% Similarity=0.578 Sum_probs=17.4
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeecC
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~ 139 (299)
.|+.||+....... .-.....|..||-..+.+
T Consensus 3 ~C~~Cg~~Yh~~~~--pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 3 ICPKCGRIYHIEFN--PPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EETTTTEEEETTTB----SSTTBCTTTTEBEBEE
T ss_pred CcCCCCCccccccC--CCCCCCccCCCCCeeEeC
Confidence 57888877543321 112335777787655543
No 294
>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=49.06 E-value=6.8 Score=24.95 Aligned_cols=9 Identities=33% Similarity=0.756 Sum_probs=3.0
Q ss_pred CCCcCCCCC
Q 022283 105 SFCQWCGGQ 113 (299)
Q Consensus 105 ~fC~~CG~~ 113 (299)
+.|..||..
T Consensus 12 ~rC~~Cg~~ 20 (37)
T PF12172_consen 12 QRCRDCGRV 20 (37)
T ss_dssp EE-TTT--E
T ss_pred EEcCCCCCE
Confidence 345555554
No 295
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=48.88 E-value=7.2 Score=36.64 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=9.1
Q ss_pred CCCCcCCCCCCc
Q 022283 104 ISFCQWCGGQTK 115 (299)
Q Consensus 104 ~~fC~~CG~~~~ 115 (299)
-.|||.||++-.
T Consensus 185 ~~~CPvCGS~Pv 196 (308)
T COG3058 185 RQYCPVCGSMPV 196 (308)
T ss_pred cccCCCcCCCCc
Confidence 458999998843
No 296
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=48.67 E-value=13 Score=36.14 Aligned_cols=30 Identities=17% Similarity=0.395 Sum_probs=21.9
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
....+|+.||.+.... ....|++|-...++
T Consensus 4 ~~~~~C~~CGr~~~~~-------~~~lC~dC~~~~~~ 33 (355)
T COG1499 4 ASTILCVRCGRSVDPL-------IDGLCGDCYVETTP 33 (355)
T ss_pred CcccEeccCCCcCchh-------hccccHHHHhccCc
Confidence 3568999999997532 35689999776554
No 297
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=48.04 E-value=12 Score=35.33 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=23.3
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
...-..|..||... ..|...||.||....-.|
T Consensus 351 ~~p~~~c~~cg~~~--------~~~~~~c~~c~~~~~~~~ 382 (389)
T PRK11788 351 RKPRYRCRNCGFTA--------RTLYWHCPSCKAWETIKP 382 (389)
T ss_pred CCCCEECCCCCCCC--------ccceeECcCCCCccCcCC
Confidence 34456699999985 346889999997665444
No 298
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=47.73 E-value=10 Score=43.94 Aligned_cols=27 Identities=30% Similarity=0.626 Sum_probs=20.3
Q ss_pred cCCCCcCCCCC------CcccccCCCCcceeecCCCCce
Q 022283 103 KISFCQWCGGQ------TKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 103 ~~~fC~~CG~~------~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
...+||.||.+ +.. .+.-..|+.||+.
T Consensus 1703 ~~~~cp~c~~~~~~~~~~~~------~~gc~~c~~cg~s 1735 (1740)
T PRK08332 1703 GVVYCPVCYEKEGKLVELRM------ESGCATCPVCGWS 1735 (1740)
T ss_pred ccCCCCCCCCCCCcceeeEe------cCCceeCCCCCCc
Confidence 66789999999 333 2346799999974
No 299
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=47.70 E-value=12 Score=36.91 Aligned_cols=34 Identities=18% Similarity=0.388 Sum_probs=24.6
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
...-||.||-....- .-+.+....||.||..-+.
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 456799999885443 2366788899999987764
No 300
>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=46.80 E-value=8.7 Score=41.77 Aligned_cols=24 Identities=33% Similarity=0.811 Sum_probs=19.0
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
..+.||.||..+. ...||.||...
T Consensus 624 ~~RKCPkCG~yTl----------k~rCP~CG~~T 647 (1095)
T TIGR00354 624 AIRKCPQCGKESF----------WLKCPVCGELT 647 (1095)
T ss_pred EEEECCCCCcccc----------cccCCCCCCcc
Confidence 3689999999863 35799999764
No 301
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.65 E-value=8.7 Score=32.07 Aligned_cols=13 Identities=23% Similarity=0.603 Sum_probs=8.9
Q ss_pred cCCCCcCCCCCCc
Q 022283 103 KISFCQWCGGQTK 115 (299)
Q Consensus 103 ~~~fC~~CG~~~~ 115 (299)
..-.|+.||....
T Consensus 69 ~~~~C~~CG~~~~ 81 (135)
T PRK03824 69 AVLKCRNCGNEWS 81 (135)
T ss_pred eEEECCCCCCEEe
Confidence 4457999996643
No 302
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=45.99 E-value=11 Score=32.40 Aligned_cols=32 Identities=31% Similarity=0.570 Sum_probs=18.9
Q ss_pred CCcCCCCCCccc-----ccC-CC-CcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHE-----VPH-GE-EKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~-----~~~-~~-~~~~~~C~~Cg~~~y 137 (299)
-||.||+....+ +|. ++ -.....|++||+..-
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 40 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNN 40 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccc
Confidence 599999875422 110 00 013578999997654
No 303
>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=45.56 E-value=13 Score=36.33 Aligned_cols=21 Identities=33% Similarity=0.770 Sum_probs=15.6
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.|..||... ..|...||.|+.
T Consensus 2 ~c~~cg~~~--------~~~~g~cp~c~~ 22 (372)
T cd01121 2 VCSECGYVS--------PKWLGKCPECGE 22 (372)
T ss_pred CCCCCCCCC--------CCccEECcCCCC
Confidence 588998884 346778999973
No 304
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=45.09 E-value=10 Score=33.27 Aligned_cols=9 Identities=22% Similarity=0.497 Sum_probs=5.4
Q ss_pred CcCCCCCCc
Q 022283 107 CQWCGGQTK 115 (299)
Q Consensus 107 C~~CG~~~~ 115 (299)
|-.|+....
T Consensus 142 C~GC~~~f~ 150 (177)
T COG1439 142 CHGCKRIFP 150 (177)
T ss_pred EecCceecC
Confidence 666666655
No 305
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=45.03 E-value=14 Score=29.85 Aligned_cols=36 Identities=17% Similarity=0.390 Sum_probs=22.8
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
.++||.-|..-+.++...-+......|.+|..+.++
T Consensus 3 ~~rfC~eCNNmLYPkEDked~~L~laCrnCd~ve~A 38 (113)
T KOG2691|consen 3 GIRFCRECNNMLYPKEDKEDRILLLACRNCDYVEEA 38 (113)
T ss_pred ccchhhhhhccccccccccccEEEEEecCCcceEec
Confidence 567777777777666433344556667777766654
No 306
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=44.99 E-value=14 Score=27.25 Aligned_cols=25 Identities=36% Similarity=0.778 Sum_probs=17.0
Q ss_pred cceeecCCCCcee--ecCCcEEEEEEE
Q 022283 124 KMRAICTVCGKIA--YQNPKMVVGCLI 148 (299)
Q Consensus 124 ~~~~~C~~Cg~~~--y~~p~~vV~~iv 148 (299)
..+-.|++|+... |.++...|.+++
T Consensus 17 Fl~VkCpdC~N~q~vFshast~V~C~~ 43 (67)
T COG2051 17 FLRVKCPDCGNEQVVFSHASTVVTCLI 43 (67)
T ss_pred EEEEECCCCCCEEEEeccCceEEEecc
Confidence 4566788888654 677777776655
No 307
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.78 E-value=10 Score=31.15 Aligned_cols=35 Identities=20% Similarity=0.317 Sum_probs=19.1
Q ss_pred hhhhcCCCCcCCCCCCcccccCCCCcc--eeecCCCCce
Q 022283 99 GNVLKISFCQWCGGQTKHEVPHGEEKM--RAICTVCGKI 135 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~~~~~~~~~~~~~--~~~C~~Cg~~ 135 (299)
.+....-+| .||......... .... ...||.||-.
T Consensus 65 ~~vp~~~~C-~Cg~~~~~~~~~-~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 65 EMIPVEIEC-ECGYEGVVDEDE-IDHYAAVIECPVCGNK 101 (124)
T ss_pred EecCeeEEe-eCcCcccccccc-hhccccCCcCcCCCCC
Confidence 455566789 999764332000 0111 2569999843
No 308
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=44.07 E-value=21 Score=23.23 Aligned_cols=31 Identities=19% Similarity=0.377 Sum_probs=15.4
Q ss_pred CCcCCCCCCcccc-----cCC-CCcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEV-----PHG-EEKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~-----~~~-~~~~~~~C~~Cg~~~ 136 (299)
-||.||+.-.... ..+ ..-.-..|.+||..+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 3999999743221 111 112446788898753
No 309
>PRK06386 replication factor A; Reviewed
Probab=43.96 E-value=28 Score=33.91 Aligned_cols=42 Identities=12% Similarity=0.163 Sum_probs=28.8
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEE
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKIL 155 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kIL 155 (299)
-.+-||.|+..+.. ..|+.||. .=+..+..+-++++++...+
T Consensus 235 li~rCP~C~R~l~~----------g~C~~HG~-v~~~~dlr~k~vLDDGtg~~ 276 (358)
T PRK06386 235 IFTKCSVCNKIIED----------GVCKDHPD-APVYLDIFGYFTISDGTGFV 276 (358)
T ss_pred eEecCcCCCeEccC----------CcCCCCCC-CCCeeEEEEEEEEECCCCeE
Confidence 35789999998752 38999996 33445566656777775443
No 310
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=43.90 E-value=7.4 Score=36.82 Aligned_cols=17 Identities=18% Similarity=0.474 Sum_probs=9.7
Q ss_pred hhhcCCCCcCCCCCCcc
Q 022283 100 NVLKISFCQWCGGQTKH 116 (299)
Q Consensus 100 w~~~~~fC~~CG~~~~~ 116 (299)
+..+..-||.||.....
T Consensus 42 l~~~~~vc~~c~~h~rl 58 (292)
T PRK05654 42 LEANLNVCPKCGHHMRI 58 (292)
T ss_pred HHhcCCCCCCCCCCeeC
Confidence 33445667777766543
No 311
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.66 E-value=5.7 Score=33.00 Aligned_cols=19 Identities=37% Similarity=1.013 Sum_probs=14.9
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.||+.||..+.. .||.|..
T Consensus 29 afcskcgeati~-----------qcp~csa 47 (160)
T COG4306 29 AFCSKCGEATIT-----------QCPICSA 47 (160)
T ss_pred HHHhhhchHHHh-----------cCCccCC
Confidence 499999999755 4888864
No 312
>PRK11823 DNA repair protein RadA; Provisional
Probab=43.63 E-value=13 Score=37.03 Aligned_cols=22 Identities=36% Similarity=0.832 Sum_probs=16.7
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-.|..||... ..|..+||+|+.
T Consensus 8 y~C~~Cg~~~--------~~~~g~Cp~C~~ 29 (446)
T PRK11823 8 YVCQECGAES--------PKWLGRCPECGA 29 (446)
T ss_pred EECCcCCCCC--------cccCeeCcCCCC
Confidence 3599999884 346789999973
No 313
>PRK12496 hypothetical protein; Provisional
Probab=43.52 E-value=13 Score=31.97 Aligned_cols=26 Identities=19% Similarity=0.598 Sum_probs=17.0
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.|+.||...... ...-.||.||....
T Consensus 129 ~C~gC~~~~~~~------~~~~~C~~CG~~~~ 154 (164)
T PRK12496 129 VCKGCKKKYPED------YPDDVCEICGSPVK 154 (164)
T ss_pred ECCCCCccccCC------CCCCcCCCCCChhh
Confidence 399999775332 12347999997644
No 314
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=43.51 E-value=19 Score=26.25 Aligned_cols=41 Identities=22% Similarity=0.411 Sum_probs=26.2
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeC
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHD 151 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~ 151 (299)
..+-|-+|..-+.. ....||.||-..+..--....+|++.+
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 34568888766533 246799999887765555555555443
No 315
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=43.49 E-value=10 Score=33.34 Aligned_cols=34 Identities=15% Similarity=0.384 Sum_probs=23.0
Q ss_pred CCcCCCCCCccccc---------------CCCCcceeecCCCCceeecC
Q 022283 106 FCQWCGGQTKHEVP---------------HGEEKMRAICTVCGKIAYQN 139 (299)
Q Consensus 106 fC~~CG~~~~~~~~---------------~~~~~~~~~C~~Cg~~~y~~ 139 (299)
||+.|+..+..... =..+...+.|..||.++..+
T Consensus 122 yc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 122 YCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred ECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCcCCcccCcc
Confidence 89999888643310 00234678999999988765
No 316
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=42.96 E-value=7.6 Score=36.84 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=11.0
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
||.||+.+..+.. ...-.+||.||+
T Consensus 41 c~~C~~~~~~~~l---~~~~~vcp~c~~ 65 (296)
T CHL00174 41 CENCYGLNYKKFL---KSKMNICEQCGY 65 (296)
T ss_pred CCCccchhhHHHH---HHcCCCCCCCCC
Confidence 5555555433311 112345555554
No 317
>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=42.77 E-value=8.1 Score=37.41 Aligned_cols=33 Identities=24% Similarity=0.533 Sum_probs=13.6
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
|--|+.||..+... +.-....|+.||...|.+.
T Consensus 285 FFkC~~C~~Rt~sl----~r~P~~~C~~Cg~~~wer~ 317 (344)
T PF09332_consen 285 FFKCKDCGNRTISL----ERLPKKHCSNCGSSKWERT 317 (344)
T ss_dssp EEE-T-TS-EEEES----SSS--S--TTT-S---EEE
T ss_pred eEECCCCCCeeeec----ccCCCCCCCcCCcCceeeh
Confidence 44588888876543 3455578888887766543
No 318
>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=42.73 E-value=7.6 Score=36.63 Aligned_cols=13 Identities=15% Similarity=0.521 Sum_probs=5.8
Q ss_pred hcCCCCcCCCCCC
Q 022283 102 LKISFCQWCGGQT 114 (299)
Q Consensus 102 ~~~~fC~~CG~~~ 114 (299)
.++.-||.||...
T Consensus 43 ~~~~vc~~c~~h~ 55 (285)
T TIGR00515 43 RNLEVCPKCDHHM 55 (285)
T ss_pred hhCCCCCCCCCcC
Confidence 3344444444443
No 319
>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=42.36 E-value=11 Score=32.41 Aligned_cols=32 Identities=28% Similarity=0.517 Sum_probs=16.2
Q ss_pred CCcCCCCCCcccc-----cCC-C-CcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEV-----PHG-E-EKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~-----~~~-~-~~~~~~C~~Cg~~~y 137 (299)
-||.||+....+. |.= + -.....|++||+...
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 5999999864431 100 0 013468999998764
No 320
>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=42.01 E-value=15 Score=36.87 Aligned_cols=22 Identities=32% Similarity=0.829 Sum_probs=16.8
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-.|..||... ..|..+||.|+.
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 346789999973
No 321
>COG4111 Uncharacterized conserved protein [General function prediction only]
Probab=41.98 E-value=1.6e+02 Score=27.57 Aligned_cols=69 Identities=12% Similarity=0.231 Sum_probs=39.9
Q ss_pred EeeC-CEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHH-HHHHhCCceeeccceeeee---c---CCCCEEEEEEE
Q 022283 148 IEHD-KKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRE-TWEEARADVEVQSPFAQLD---I---PRIGQIYIIFL 219 (299)
Q Consensus 148 v~~~-~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~RE-v~EEtGl~v~~~~~~~~~~---~---p~~~~~~~~f~ 219 (299)
|+++ -.||-+++. . .+|.|-.|+.---.|+-.|+ |.+.|+..+.-+.-+.++. . .....+.+.|+
T Consensus 32 v~~~~p~VLtV~q~----~---aLP~GPfep~hrslq~glr~wV~~qT~~plGYiEQLYTF~Dr~R~~~~g~rvisv~YL 104 (322)
T COG4111 32 VTDGGPRVLTVRQG----A---ALPSGPFEPAHRSLQAGLRAWVEKQTSQPLGYIEQLYTFADRDRRNEGGMRVISVSYL 104 (322)
T ss_pred EcCCCceEEEeccc----c---cCCCCCCchHHHHHHHHHHHHHHHHhcCccchHHhhhhhccccccCcCCceEEEEEEe
Confidence 3444 466666543 1 29999999886555555555 6667888876554332221 1 12345667788
Q ss_pred EEec
Q 022283 220 AKLK 223 (299)
Q Consensus 220 a~~~ 223 (299)
+-..
T Consensus 105 gLtr 108 (322)
T COG4111 105 GLTR 108 (322)
T ss_pred eecc
Confidence 7543
No 322
>PRK05580 primosome assembly protein PriA; Validated
Probab=41.62 E-value=15 Score=38.78 Aligned_cols=27 Identities=22% Similarity=0.457 Sum_probs=16.2
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
-||.|+.++..+ .......|..||+..
T Consensus 392 ~C~~C~~~l~~h----~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 392 ECPHCDASLTLH----RFQRRLRCHHCGYQE 418 (679)
T ss_pred CCCCCCCceeEE----CCCCeEECCCCcCCC
Confidence 377777776655 234456677777553
No 323
>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=41.61 E-value=17 Score=35.98 Aligned_cols=29 Identities=17% Similarity=0.424 Sum_probs=21.0
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
.-|+.||.... .+.+..||.||..-|.+.
T Consensus 216 ~~C~~Cd~~~~-------~~~~a~CpRC~~~L~~~~ 244 (403)
T TIGR00155 216 RSCSACHTTIL-------PAQEPVCPRCSTPLYVRR 244 (403)
T ss_pred CcCCCCCCccC-------CCCCcCCcCCCCcccCCC
Confidence 44999999642 234678999999877543
No 324
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=40.55 E-value=14 Score=28.56 Aligned_cols=30 Identities=23% Similarity=0.458 Sum_probs=20.9
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
..--.|+.||+.+.-+ ..-..+.|..|..+
T Consensus 34 haky~CsfCGK~~vKR----~AvGiW~C~~C~kv 63 (92)
T KOG0402|consen 34 HAKYTCSFCGKKTVKR----KAVGIWKCGSCKKV 63 (92)
T ss_pred hhhhhhhhcchhhhhh----hceeEEecCCccce
Confidence 3445799999997666 34456788888753
No 325
>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=40.47 E-value=19 Score=25.83 Aligned_cols=30 Identities=27% Similarity=0.578 Sum_probs=15.2
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.....|..|+++.... ..+..|..||.+.=
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 3478999999998543 46889999997543
No 326
>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=40.20 E-value=22 Score=28.40 Aligned_cols=13 Identities=31% Similarity=0.951 Sum_probs=10.5
Q ss_pred CCCcCCCCCCccc
Q 022283 105 SFCQWCGGQTKHE 117 (299)
Q Consensus 105 ~fC~~CG~~~~~~ 117 (299)
..||.||.+....
T Consensus 3 ~~CpYCg~~~~l~ 15 (102)
T PF11672_consen 3 IICPYCGGPAELV 15 (102)
T ss_pred cccCCCCCeeEEc
Confidence 4799999997665
No 327
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=39.38 E-value=17 Score=38.81 Aligned_cols=25 Identities=20% Similarity=0.490 Sum_probs=10.8
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
||.|..++..+ .......|..||+.
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 44444444443 22334455555443
No 328
>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=39.26 E-value=13 Score=26.61 Aligned_cols=25 Identities=28% Similarity=0.731 Sum_probs=12.3
Q ss_pred CCcCCCCCCcccccCCCCcceeecCC-CC
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTV-CG 133 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~-Cg 133 (299)
-||.||++..... +...+..|.. |.
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 5999999987642 4456777763 53
No 329
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=39.17 E-value=43 Score=30.72 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=14.7
Q ss_pred CCcCCCCCCcccccCCCCcceeecCC
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTV 131 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~ 131 (299)
-||.|++++... .....|++
T Consensus 4 ~CP~C~~~l~~~------~~~~~C~~ 23 (272)
T PRK11088 4 QCPLCHQPLTLE------ENSWICPQ 23 (272)
T ss_pred cCCCCCcchhcC------CCEEEcCC
Confidence 499999998543 23588876
No 330
>smart00532 LIGANc Ligase N family.
Probab=39.07 E-value=18 Score=36.29 Aligned_cols=25 Identities=24% Similarity=0.511 Sum_probs=18.4
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCC
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTV 131 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~ 131 (299)
.-.+||.||+++... +++...+|++
T Consensus 398 ~P~~CP~C~s~l~~~----~~~~~~~C~n 422 (441)
T smart00532 398 MPTHCPSCGSELVRE----EGEVDIRCPN 422 (441)
T ss_pred CCCCCCCCCCEeEec----CCceEEEeCC
Confidence 468999999998654 3456677874
No 331
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=38.96 E-value=24 Score=23.25 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=6.9
Q ss_pred CCCcCCCCCC
Q 022283 105 SFCQWCGGQT 114 (299)
Q Consensus 105 ~fC~~CG~~~ 114 (299)
..||.||+..
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 3577777775
No 332
>PRK07217 replication factor A; Reviewed
Probab=38.91 E-value=44 Score=31.95 Aligned_cols=45 Identities=13% Similarity=0.277 Sum_probs=33.2
Q ss_pred cCCCCcC--CCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEEE
Q 022283 103 KISFCQW--CGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCK 158 (299)
Q Consensus 103 ~~~fC~~--CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~r 158 (299)
-.+-||. |+..+.. -.|+.||.+.. ..+..+-++++++...+-+.
T Consensus 187 lI~rCP~~~C~Rvl~~----------g~C~~HG~ve~-~~DLrik~vlDDGt~~~~~~ 233 (311)
T PRK07217 187 LIKRCPEEDCTRVLQN----------GRCSEHGKVEG-EFDLRIKGVLDDGEEVQEVI 233 (311)
T ss_pred CeecCCccccCccccC----------CCCCCCCCcCC-ceeeEEEEEEECCCCeEEEE
Confidence 4578999 9998732 37999996554 77888888888876554443
No 333
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=38.63 E-value=11 Score=35.45 Aligned_cols=27 Identities=26% Similarity=0.584 Sum_probs=17.6
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.-||.||.-+..... .....+||.|++
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 458888887765521 234678888874
No 334
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=38.47 E-value=18 Score=37.93 Aligned_cols=27 Identities=30% Similarity=0.589 Sum_probs=21.9
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCC---CC
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTV---CG 133 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~---Cg 133 (299)
.-.+||.||+++... +++...+|++ |.
T Consensus 403 ~P~~CP~C~s~l~r~----~~e~~~rC~n~~~C~ 432 (667)
T COG0272 403 FPTHCPVCGSELVRE----EGEVVIRCTNGLNCP 432 (667)
T ss_pred CCCCCCCCCCeeEec----cCceeEecCCCCCCh
Confidence 567999999998774 5678889986 75
No 335
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=38.39 E-value=17 Score=26.24 Aligned_cols=25 Identities=24% Similarity=0.760 Sum_probs=17.5
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecC-CCCc
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICT-VCGK 134 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~ 134 (299)
..|++|+.||++..+. -..|+ .|+.
T Consensus 6 ~PH~HC~VCg~aIp~d--------e~~CSe~C~e 31 (64)
T COG4068 6 VPHRHCVVCGKAIPPD--------EQVCSEECGE 31 (64)
T ss_pred CCCccccccCCcCCCc--------cchHHHHHHH
Confidence 3589999999996432 25676 4773
No 336
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=38.32 E-value=35 Score=32.95 Aligned_cols=55 Identities=22% Similarity=0.286 Sum_probs=29.7
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEE--EEEEeecCCC-CCceeec
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKI--LLCKRKIEPS-YGLWTLP 171 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kI--LL~rr~~~p~-~g~w~lP 171 (299)
-|-.|=+-+ .+-.+..|++||..- -.-++|-|..+|.+ -+-.|..+.. +-.|++|
T Consensus 244 RCh~Cfsit-------~~m~k~FCp~CG~~T----L~K~aVsv~~dG~~~~h~k~r~~~n~RG~~YSlp 301 (376)
T KOG2463|consen 244 RCHGCFSIT-------SEMPKDFCPSCGHKT----LTKCAVSVDEDGNGQTHFKKRFQWNNRGLQYSLP 301 (376)
T ss_pred EeeeeeEec-------CccchhcccccCCCe----eeEEEEEecCCCceeEEeecccccccCcceeecC
Confidence 466665554 234578999999762 23333445555433 3333433322 3459887
No 337
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=37.94 E-value=23 Score=28.29 Aligned_cols=32 Identities=22% Similarity=0.409 Sum_probs=17.1
Q ss_pred CCCcCCCCCCcccc--cCCCCcceeecCCCCcee
Q 022283 105 SFCQWCGGQTKHEV--PHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 105 ~fC~~CG~~~~~~~--~~~~~~~~~~C~~Cg~~~ 136 (299)
--||.||+...... .-....--..|..||..+
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 35777877754410 011234456777777554
No 338
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=37.77 E-value=59 Score=22.74 Aligned_cols=28 Identities=25% Similarity=0.679 Sum_probs=17.8
Q ss_pred CCcCCCCCCcccccC--CCCcceeecCCCC
Q 022283 106 FCQWCGGQTKHEVPH--GEEKMRAICTVCG 133 (299)
Q Consensus 106 fC~~CG~~~~~~~~~--~~~~~~~~C~~Cg 133 (299)
.||.||.+....+.. ++....-.|+.|-
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC 31 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCC 31 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcC
Confidence 599999998766432 2223445677765
No 339
>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=37.53 E-value=6.7 Score=36.74 Aligned_cols=26 Identities=27% Similarity=0.752 Sum_probs=14.4
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.++-+|+.||+.=.. .|..|+.||..
T Consensus 195 ~R~L~Cs~C~t~W~~--------~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRF--------VRIKCPYCGNT 220 (290)
T ss_dssp EEEEEETTT--EEE----------TTS-TTT---
T ss_pred cEEEEcCCCCCeeee--------cCCCCcCCCCC
Confidence 478899999988433 46789999864
No 340
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=37.52 E-value=19 Score=24.62 Aligned_cols=15 Identities=20% Similarity=0.592 Sum_probs=10.2
Q ss_pred cCCCCcCCCCCCccc
Q 022283 103 KISFCQWCGGQTKHE 117 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~ 117 (299)
..-+|+.||+++...
T Consensus 4 g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRR 18 (58)
T ss_pred CcEEcccCCcEeEEE
Confidence 445788888887554
No 341
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=37.37 E-value=18 Score=29.19 Aligned_cols=25 Identities=24% Similarity=0.440 Sum_probs=14.5
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.|+.||....... .-+ .+.||.||.
T Consensus 44 ~C~~Cg~~~~~~~---SCk-~R~CP~C~~ 68 (111)
T PF14319_consen 44 RCEDCGHEKIVYN---SCK-NRHCPSCQA 68 (111)
T ss_pred ecCCCCceEEecC---ccc-CcCCCCCCC
Confidence 5777777753331 233 347777774
No 342
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.08 E-value=19 Score=29.24 Aligned_cols=22 Identities=27% Similarity=0.232 Sum_probs=14.1
Q ss_pred CcceeecCCCCceee-cCCcEEE
Q 022283 123 EKMRAICTVCGKIAY-QNPKMVV 144 (299)
Q Consensus 123 ~~~~~~C~~Cg~~~y-~~p~~vV 144 (299)
-|.++.||.||..+| .|.+++|
T Consensus 6 LGtKridPetg~KFYDLNrdPiV 28 (129)
T COG4530 6 LGTKRIDPETGKKFYDLNRDPIV 28 (129)
T ss_pred ccccccCccccchhhccCCCccc
Confidence 355677788877777 3555544
No 343
>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=37.04 E-value=11 Score=40.42 Aligned_cols=28 Identities=25% Similarity=0.497 Sum_probs=0.0
Q ss_pred hhhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 100 NVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
-..-...||.||++|... ..|+.|+...
T Consensus 663 ~~t~~~~Cp~CG~~T~~~---------~~Cp~C~~~~ 690 (900)
T PF03833_consen 663 KETFYNRCPECGSHTEPV---------YVCPDCGIEV 690 (900)
T ss_dssp -------------------------------------
T ss_pred CcchhhcCcccCCccccc---------eecccccccc
Confidence 344567899999998654 5677776554
No 344
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=36.96 E-value=22 Score=33.58 Aligned_cols=29 Identities=24% Similarity=0.546 Sum_probs=19.5
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.-||.||...... +......+|.+||.+.
T Consensus 2 ~~CpeCg~~~~~~---d~~~ge~VC~~CG~Vi 30 (285)
T COG1405 2 MSCPECGSTNIIT---DYERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCCcccee---eccCCeEEeccCCEEe
Confidence 3599999993322 1234568999999654
No 345
>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=36.93 E-value=24 Score=22.99 Aligned_cols=32 Identities=19% Similarity=0.378 Sum_probs=18.8
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.|.+|++=+-....-.+++....|+-|+....
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTKNP 35 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--EEE
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCCcCC
Confidence 58899988766544445678899999998654
No 346
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.70 E-value=14 Score=35.20 Aligned_cols=26 Identities=15% Similarity=0.323 Sum_probs=18.6
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
+++||.||.+.... .+.+.|+.|+..
T Consensus 322 ~~~Cp~cg~r~~~~------~~ak~~~~c~~r 347 (351)
T KOG3940|consen 322 YVQCPHCGRRFNEQ------AAAKHIPKCVNR 347 (351)
T ss_pred cccCccccccchHH------HHHhhccccccc
Confidence 68899998885432 467788888754
No 347
>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 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=36.29 E-value=19 Score=22.40 Aligned_cols=22 Identities=36% Similarity=0.810 Sum_probs=14.0
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
|+.||-..... ..-..||.||.
T Consensus 4 C~~CGy~y~~~------~~~~~CP~Cg~ 25 (33)
T cd00350 4 CPVCGYIYDGE------EAPWVCPVCGA 25 (33)
T ss_pred CCCCCCEECCC------cCCCcCcCCCC
Confidence 78888664332 23457888875
No 349
>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=35.65 E-value=21 Score=22.56 Aligned_cols=23 Identities=30% Similarity=0.782 Sum_probs=14.4
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-|..||...... ..-..||.||.
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 388888664322 12348888885
No 350
>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=35.03 E-value=26 Score=36.07 Aligned_cols=51 Identities=18% Similarity=0.279 Sum_probs=33.2
Q ss_pred cchHHHHHHHHhhhhcCCCCcCCCCCCcccc-----cC--CCCcceeecCCCCceeec
Q 022283 88 SHPSSAAVHSAGNVLKISFCQWCGGQTKHEV-----PH--GEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 88 ~~~~~~a~~l~~w~~~~~fC~~CG~~~~~~~-----~~--~~~~~~~~C~~Cg~~~y~ 138 (299)
.+-..++.+-.+-..=+--||.||....... +. ....-+..|+.||.....
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 3344556666555555778999999876541 11 134467899999976654
No 351
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=34.94 E-value=45 Score=21.78 Aligned_cols=31 Identities=26% Similarity=0.486 Sum_probs=16.8
Q ss_pred CCcCCCCCCcccc-----cCCC-CcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEV-----PHGE-EKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~-----~~~~-~~~~~~C~~Cg~~~ 136 (299)
-||.||+.-.... ..++ --.-..|.+||+..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 4899998743211 1111 12346788888653
No 352
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=34.17 E-value=21 Score=29.24 Aligned_cols=28 Identities=29% Similarity=0.694 Sum_probs=18.5
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
.-.|..|++..... .+...||.||-..+
T Consensus 70 ~~~C~~C~~~~~~e------~~~~~CP~C~s~~~ 97 (115)
T COG0375 70 ECWCLDCGQEVELE------ELDYRCPKCGSINL 97 (115)
T ss_pred EEEeccCCCeecch------hheeECCCCCCCce
Confidence 44688888876543 34455999986554
No 353
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=34.03 E-value=15 Score=26.67 Aligned_cols=35 Identities=23% Similarity=0.468 Sum_probs=19.7
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEe
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIE 149 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~ 149 (299)
+=|-.|..-+.. ..||.||...+..--...++|++
T Consensus 4 kAC~~C~~i~~~----------~~CP~Cgs~~~T~~W~G~viI~d 38 (61)
T PRK08351 4 KACRHCHYITTE----------DRCPVCGSRDLSDEWFDLVIIID 38 (61)
T ss_pred hhhhhCCcccCC----------CcCCCCcCCccccccccEEEEeC
Confidence 457788666421 25999998775433333333343
No 354
>KOG4537 consensus Zn-ribbon-containing protein implicated in mitosis [Cell cycle control, cell division, chromosome partitioning; Defense mechanisms]
Probab=33.93 E-value=9.5 Score=32.76 Aligned_cols=26 Identities=15% Similarity=0.385 Sum_probs=18.6
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
--+||.||+-+.. +....++|-.|..
T Consensus 40 de~Cp~C~~Ilm~-----dr~~~~~CVsC~~ 65 (178)
T KOG4537|consen 40 DEICPKCEKILMR-----DRDNPMFCVSCIN 65 (178)
T ss_pred hhhcchHHHHHHh-----hccCceEEEeeec
Confidence 4599999998543 4556778887754
No 355
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=33.48 E-value=27 Score=32.31 Aligned_cols=19 Identities=21% Similarity=0.256 Sum_probs=10.5
Q ss_pred eeCCCCHHHHHHHHHHHHh
Q 022283 175 MEIGESAAEGAIRETWEEA 193 (299)
Q Consensus 175 VE~GEs~eeAa~REv~EEt 193 (299)
|-.||.+-+.+.++..+++
T Consensus 162 V~fGE~lp~~~~~~~~~~~ 180 (250)
T COG0846 162 VWFGEPLPASFLDEALEAL 180 (250)
T ss_pred EEeCCCCCHHHHHHHHHHh
Confidence 4455655554455566665
No 356
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.11 E-value=24 Score=25.88 Aligned_cols=15 Identities=20% Similarity=0.627 Sum_probs=10.4
Q ss_pred ceeecCCCCceeecC
Q 022283 125 MRAICTVCGKIAYQN 139 (299)
Q Consensus 125 ~~~~C~~Cg~~~y~~ 139 (299)
....|..||+..|=.
T Consensus 39 ~~itCk~CgYtEfY~ 53 (68)
T COG3478 39 IVITCKNCGYTEFYS 53 (68)
T ss_pred EEEEeccCCchhhee
Confidence 456788888876633
No 357
>PRK14973 DNA topoisomerase I; Provisional
Probab=32.33 E-value=24 Score=38.78 Aligned_cols=36 Identities=14% Similarity=0.284 Sum_probs=25.6
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
.-||.||.+.....-.|..++-.-||.|.++.+...
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 479999997555444455666677999988777444
No 358
>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=32.17 E-value=30 Score=26.94 Aligned_cols=32 Identities=25% Similarity=0.530 Sum_probs=22.1
Q ss_pred hhhcCCCCcCCCCCCcccccCCCCc-------ceeecCCCCce
Q 022283 100 NVLKISFCQWCGGQTKHEVPHGEEK-------MRAICTVCGKI 135 (299)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~-------~~~~C~~Cg~~ 135 (299)
+.....+|+.|++++... |-- .+-+|..|+..
T Consensus 29 i~~~rS~C~~C~~~L~~~----~lIPi~S~l~lrGrCr~C~~~ 67 (92)
T PF06750_consen 29 IIFPRSHCPHCGHPLSWW----DLIPILSYLLLRGRCRYCGAP 67 (92)
T ss_pred ccCCCCcCcCCCCcCccc----ccchHHHHHHhCCCCcccCCC
Confidence 334568999999998665 211 45678888754
No 359
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=32.00 E-value=28 Score=25.33 Aligned_cols=28 Identities=21% Similarity=0.495 Sum_probs=18.4
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecC-CCCc
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICT-VCGK 134 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~-~Cg~ 134 (299)
..-||.||+++.... +...+..|. .|..
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 467999999975431 345667776 3653
No 360
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=31.85 E-value=26 Score=36.93 Aligned_cols=24 Identities=25% Similarity=0.469 Sum_probs=18.0
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecC
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICT 130 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~ 130 (299)
.-.+||.||+++... +++...+|+
T Consensus 403 ~P~~CP~Cgs~l~~~----~~~~~~~C~ 426 (665)
T PRK07956 403 MPTHCPVCGSELVRV----EGEAVLRCT 426 (665)
T ss_pred CCCCCCCCCCEeEec----CCCeEEECC
Confidence 346999999998654 455677886
No 361
>PRK06260 threonine synthase; Validated
Probab=31.57 E-value=25 Score=34.33 Aligned_cols=24 Identities=25% Similarity=0.612 Sum_probs=16.3
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-.|..||..... ......||.||-
T Consensus 4 ~~C~~cg~~~~~------~~~~~~Cp~cg~ 27 (397)
T PRK06260 4 LKCIECGKEYDP------DEIIYTCPECGG 27 (397)
T ss_pred EEECCCCCCCCC------CCccccCCCCCC
Confidence 369999988543 234567998974
No 362
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=31.50 E-value=22 Score=34.20 Aligned_cols=13 Identities=38% Similarity=0.744 Sum_probs=11.5
Q ss_pred CCCcCCCCCCccc
Q 022283 105 SFCQWCGGQTKHE 117 (299)
Q Consensus 105 ~fC~~CG~~~~~~ 117 (299)
-|||.||+++..+
T Consensus 26 ffCPaC~~~l~lK 38 (342)
T COG4469 26 FFCPACGSQLILK 38 (342)
T ss_pred cccCCCCCeeeee
Confidence 4999999998776
No 363
>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=31.50 E-value=19 Score=25.24 Aligned_cols=31 Identities=26% Similarity=0.509 Sum_probs=21.3
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.|..||.......-.+..+....|..||..+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~ 31 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHH
Confidence 4889998765554434445678899998544
No 364
>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=31.45 E-value=20 Score=34.16 Aligned_cols=26 Identities=23% Similarity=0.577 Sum_probs=20.1
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
.++-+|+.|++.=.. .|..|+.||..
T Consensus 208 ~RyL~CslC~teW~~--------~R~~C~~Cg~~ 233 (305)
T TIGR01562 208 LRYLSCSLCATEWHY--------VRVKCSHCEES 233 (305)
T ss_pred ceEEEcCCCCCcccc--------cCccCCCCCCC
Confidence 468899999988433 47899999963
No 365
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=30.93 E-value=32 Score=26.18 Aligned_cols=28 Identities=36% Similarity=0.466 Sum_probs=19.0
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.||-||..|.... ..+.--.|+-|++..
T Consensus 3 ~CPCCg~~Tl~~~---~~~~ydIC~VC~WEd 30 (78)
T PF14206_consen 3 PCPCCGYYTLEER---GEGTYDICPVCFWED 30 (78)
T ss_pred cCCCCCcEEeccC---CCcCceECCCCCccc
Confidence 5899999876542 122366899888754
No 366
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=30.70 E-value=14 Score=36.81 Aligned_cols=36 Identities=19% Similarity=0.508 Sum_probs=26.5
Q ss_pred HHHHHhhhhc--CCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 94 AVHSAGNVLK--ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 94 a~~l~~w~~~--~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
-++...|... -.|||-|+.+.... ..+.+|.-||.+
T Consensus 168 EqsvVpW~DDs~V~~CP~Ca~~F~l~------rRrHHCRLCG~V 205 (505)
T KOG1842|consen 168 EQSVVPWLDDSSVQFCPECANSFGLT------RRRHHCRLCGRV 205 (505)
T ss_pred HhccccccCCCcccccccccchhhhH------HHhhhhhhcchH
Confidence 3455678764 78999999998665 456788888753
No 367
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.60 E-value=30 Score=36.25 Aligned_cols=26 Identities=27% Similarity=0.712 Sum_probs=19.0
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
......|+.||... .+....||.||.
T Consensus 563 n~~~~iC~~CG~~~--------~g~~~~CP~CGs 588 (623)
T PRK08271 563 NVKITICNDCHHID--------KRTGKRCPICGS 588 (623)
T ss_pred CCCCccCCCCCCcC--------CCCCcCCcCCCC
Confidence 34678999999752 233478999996
No 368
>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=30.48 E-value=19 Score=31.72 Aligned_cols=28 Identities=18% Similarity=0.289 Sum_probs=16.9
Q ss_pred eceEEeeCCCCHHH-HHHHHHHHHhCCce
Q 022283 170 LPAGYMEIGESAAE-GAIRETWEEARADV 197 (299)
Q Consensus 170 lPgG~VE~GEs~ee-Aa~REv~EEtGl~v 197 (299)
+..-.+|.|-++|. --+|--..|+|++.
T Consensus 134 ft~s~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (182)
T TIGR02820 134 FVSSIIETGTDPERMDGIRARLRELGLEP 162 (182)
T ss_pred EEeeccccCCChHHhHHHHHHHHHcCCCc
Confidence 44566777777653 23455556778765
No 369
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=30.15 E-value=16 Score=35.23 Aligned_cols=26 Identities=27% Similarity=0.557 Sum_probs=19.1
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-|.+|........ ....+..||.||-
T Consensus 248 AC~rC~t~y~le~---A~~~~wrCpkCGg 273 (403)
T COG1379 248 ACSRCYTRYSLEE---AKSLRWRCPKCGG 273 (403)
T ss_pred HHHHhhhccCcch---hhhhcccCccccc
Confidence 5999998765531 3456789999996
No 370
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=30.08 E-value=17 Score=33.40 Aligned_cols=36 Identities=19% Similarity=0.437 Sum_probs=23.6
Q ss_pred cCCCCcCCCCCCcccccC--CCCcceeecCCCCceeec
Q 022283 103 KISFCQWCGGQTKHEVPH--GEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~--~~~~~~~~C~~Cg~~~y~ 138 (299)
..+-|+.|+-.+...... -.......||.||.+.|-
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 467899998876443210 013456789999988773
No 371
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=30.07 E-value=32 Score=25.60 Aligned_cols=14 Identities=29% Similarity=0.601 Sum_probs=5.3
Q ss_pred cCCCCcCCCCCCcc
Q 022283 103 KISFCQWCGGQTKH 116 (299)
Q Consensus 103 ~~~fC~~CG~~~~~ 116 (299)
...||..||..+.+
T Consensus 45 kr~~Ck~C~~~liP 58 (85)
T PF04032_consen 45 KRTICKKCGSLLIP 58 (85)
T ss_dssp CCTB-TTT--B--C
T ss_pred hcccccCCCCEEeC
Confidence 34567777666544
No 372
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=29.65 E-value=29 Score=34.68 Aligned_cols=22 Identities=36% Similarity=0.730 Sum_probs=16.6
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
.-.|..||... ..|.-.||+||
T Consensus 7 ~f~C~~CG~~s--------~KW~GkCp~Cg 28 (456)
T COG1066 7 AFVCQECGYVS--------PKWLGKCPACG 28 (456)
T ss_pred EEEcccCCCCC--------ccccccCCCCC
Confidence 34699999872 35677899998
No 373
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=29.36 E-value=23 Score=30.61 Aligned_cols=10 Identities=40% Similarity=1.102 Sum_probs=7.1
Q ss_pred CCcCCCCCCc
Q 022283 106 FCQWCGGQTK 115 (299)
Q Consensus 106 fC~~CG~~~~ 115 (299)
||+.|+..+.
T Consensus 116 yc~~c~~~~~ 125 (159)
T TIGR03037 116 FCPQCGHKLH 125 (159)
T ss_pred ECCCCCCeEE
Confidence 7888877654
No 374
>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=29.30 E-value=28 Score=25.78 Aligned_cols=15 Identities=40% Similarity=0.490 Sum_probs=8.4
Q ss_pred CCHHHH--HHHHHHHHh
Q 022283 179 ESAAEG--AIRETWEEA 193 (299)
Q Consensus 179 Es~eeA--a~REv~EEt 193 (299)
|+.+|| ++|+++||.
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 567788774
No 375
>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=29.20 E-value=29 Score=36.03 Aligned_cols=25 Identities=32% Similarity=0.801 Sum_probs=18.3
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
..+..|+.||.. .++....||.||.
T Consensus 530 ~~~siC~~CGy~--------~g~~~~~CP~CGs 554 (586)
T TIGR02827 530 IKITICNDCHHI--------DKRTLHRCPVCGS 554 (586)
T ss_pred CCCeecCCCCCc--------CCCcCCcCcCCCC
Confidence 357889999983 2233478999996
No 376
>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=29.19 E-value=25 Score=23.29 Aligned_cols=14 Identities=36% Similarity=0.643 Sum_probs=10.8
Q ss_pred CCCCcCCCCCCccc
Q 022283 104 ISFCQWCGGQTKHE 117 (299)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (299)
-.+|+.||+.|...
T Consensus 2 ~~~C~~Cg~~l~~i 15 (47)
T PF13005_consen 2 PRACPDCGGELKEI 15 (47)
T ss_pred CCcCCCCCceeeEC
Confidence 36899999998743
No 377
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=28.93 E-value=32 Score=24.82 Aligned_cols=24 Identities=29% Similarity=0.818 Sum_probs=12.9
Q ss_pred ceeecCCCCcee--ecCCcEEEEEEE
Q 022283 125 MRAICTVCGKIA--YQNPKMVVGCLI 148 (299)
Q Consensus 125 ~~~~C~~Cg~~~--y~~p~~vV~~iv 148 (299)
.+-.|++|+.+. |.+...+|.+.+
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~ 35 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLV 35 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcc
Confidence 445677776543 555555554433
No 378
>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=28.87 E-value=31 Score=36.33 Aligned_cols=26 Identities=27% Similarity=0.537 Sum_probs=18.7
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecC--CCC
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICT--VCG 133 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~--~Cg 133 (299)
-.+||.||+++... +++...+|+ .|.
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 46999999998654 445667786 463
No 379
>PRK12722 transcriptional activator FlhC; Provisional
Probab=28.87 E-value=64 Score=28.63 Aligned_cols=43 Identities=21% Similarity=0.360 Sum_probs=32.0
Q ss_pred hHHHHHHHHhhhhc----CCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 90 PSSAAVHSAGNVLK----ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 90 ~~~~a~~l~~w~~~----~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-+.+|..|+++... ..-|..||+....... +-.....|+-|.-
T Consensus 116 s~tRAw~LvRf~~s~~L~l~~C~~Cgg~fv~~~~--e~~~~f~CplC~~ 162 (187)
T PRK12722 116 SLTRAWTLVRFVDSGMLQLSSCNCCGGHFVTHAH--DPVGSFVCGLCQP 162 (187)
T ss_pred cHHHHHHHHHHHhcCcEeeccCCCCCCCeecccc--ccCCCCcCCCCCC
Confidence 36789999888765 5669999999764422 3456789999976
No 380
>PRK08173 DNA topoisomerase III; Validated
Probab=28.85 E-value=31 Score=37.52 Aligned_cols=28 Identities=36% Similarity=0.616 Sum_probs=20.3
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
.-||.||+.+. ..+....|.+|++..+.
T Consensus 625 ~~CP~Cg~~~~------~~~~~~~Cs~C~f~~~~ 652 (862)
T PRK08173 625 TPCPNCGGVVK------ENYRRFACTKCDFSISK 652 (862)
T ss_pred ccCCccccccc------ccCceeEcCCCCcccch
Confidence 35999998752 23445899999987753
No 381
>PF15616 TerY-C: TerY-C metal binding domain
Probab=28.76 E-value=32 Score=28.73 Aligned_cols=32 Identities=22% Similarity=0.440 Sum_probs=18.5
Q ss_pred CCCCcCCCCCCccc--------ccCCCCcceeecCCCCceee
Q 022283 104 ISFCQWCGGQTKHE--------VPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 104 ~~fC~~CG~~~~~~--------~~~~~~~~~~~C~~Cg~~~y 137 (299)
..=||.||..+... ... +.....||-||....
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 47899999985332 122 223566666665543
No 382
>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=28.57 E-value=14 Score=27.38 Aligned_cols=15 Identities=27% Similarity=0.600 Sum_probs=10.2
Q ss_pred hcCCCCcCCCCCCcc
Q 022283 102 LKISFCQWCGGQTKH 116 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~ 116 (299)
....||+.||+++..
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 355899999999864
No 383
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=28.48 E-value=42 Score=27.00 Aligned_cols=33 Identities=18% Similarity=0.380 Sum_probs=21.0
Q ss_pred CCCCcCCCCCCccccc----CCCCcceeecCCCCcee
Q 022283 104 ISFCQWCGGQTKHEVP----HGEEKMRAICTVCGKIA 136 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~----~~~~~~~~~C~~Cg~~~ 136 (299)
-.||..|.+.|.+-.. ...+.....|..||+..
T Consensus 56 R~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 56 RTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIR 92 (105)
T ss_pred HHhccccCcccccCcceEEEEcCCeEEEEecCCCcEE
Confidence 4699999998654310 00233667888888765
No 384
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=28.27 E-value=29 Score=39.35 Aligned_cols=25 Identities=24% Similarity=0.534 Sum_probs=18.8
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
..+-||.||+.+. ...||.||...-
T Consensus 673 ~~~~Cp~Cg~~~~----------~~~Cp~CG~~~~ 697 (1627)
T PRK14715 673 AFFKCPKCGKVGL----------YHVCPFCGTRVE 697 (1627)
T ss_pred EeeeCCCCCCccc----------cccCcccCCccc
Confidence 3578999999853 357999997643
No 385
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=27.72 E-value=24 Score=34.01 Aligned_cols=14 Identities=36% Similarity=0.783 Sum_probs=11.2
Q ss_pred CCCCcCCCCCCccc
Q 022283 104 ISFCQWCGGQTKHE 117 (299)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (299)
-.|||.||..|-.+
T Consensus 257 k~FCp~CG~~TL~K 270 (376)
T KOG2463|consen 257 KDFCPSCGHKTLTK 270 (376)
T ss_pred hhcccccCCCeeeE
Confidence 57999999996443
No 386
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=27.71 E-value=32 Score=37.83 Aligned_cols=32 Identities=22% Similarity=0.570 Sum_probs=24.3
Q ss_pred HhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 98 AGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 98 ~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
......-.-|+.||+.|.. .|.-.+|.+||..
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 4455667779999988754 3678999999964
No 387
>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=27.68 E-value=28 Score=24.34 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=20.7
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
--|+.|++-+...- +-...--.||.|+...-
T Consensus 5 iRC~~CnklLa~~g--~~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 5 IRCGHCNKLLAKAG--EVIELEIKCPRCKTINH 35 (51)
T ss_pred eeccchhHHHhhhc--CccEEEEECCCCCccce
Confidence 45999998876531 12345678999987654
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=27.63 E-value=31 Score=22.58 Aligned_cols=23 Identities=26% Similarity=0.447 Sum_probs=14.9
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCc
Q 022283 93 AAVHSAGNVLKISFCQWCGGQTK 115 (299)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~ 115 (299)
-|.+|..-..+.+||..||.-+.
T Consensus 6 La~al~~~~~~i~~C~~C~nlse 28 (41)
T PF02132_consen 6 LADALKEAKENIKFCSICGNLSE 28 (41)
T ss_dssp HHHHHHHHHHH-EE-SSS--EES
T ss_pred HHHHHHHHHHcCCccCCCCCcCC
Confidence 46677778889999999998754
No 389
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=27.63 E-value=42 Score=27.80 Aligned_cols=28 Identities=21% Similarity=0.570 Sum_probs=20.4
Q ss_pred CcCCCCCCcccccCCCCcce-eecCCCCceee
Q 022283 107 CQWCGGQTKHEVPHGEEKMR-AICTVCGKIAY 137 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~-~~C~~Cg~~~y 137 (299)
|-.||+.+.... ++..+ +.|+.|+...+
T Consensus 3 C~fC~~~s~~~~---~~~~~~w~C~~C~q~N~ 31 (131)
T PF09779_consen 3 CWFCGQNSKVPY---DNRNSNWTCPHCEQYNG 31 (131)
T ss_pred eccCCCCCCCCC---CCCCCeeECCCCCCccC
Confidence 778998875542 33444 99999998776
No 390
>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=27.59 E-value=43 Score=27.01 Aligned_cols=29 Identities=17% Similarity=0.394 Sum_probs=18.3
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
..+.|..|+.++.... .....|.+|+...
T Consensus 53 ~~~~C~~C~~~fg~l~-----~~~~~C~~C~~~V 81 (118)
T PF02318_consen 53 GERHCARCGKPFGFLF-----NRGRVCVDCKHRV 81 (118)
T ss_dssp CCSB-TTTS-BCSCTS-----TTCEEETTTTEEE
T ss_pred CCcchhhhCCcccccC-----CCCCcCCcCCccc
Confidence 5679999999986542 2347788777543
No 391
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.52 E-value=35 Score=35.72 Aligned_cols=24 Identities=33% Similarity=0.826 Sum_probs=18.2
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
...+|+.||... .+....||.||.
T Consensus 567 ~~~~C~~CG~~~--------~g~~~~CP~CGs 590 (625)
T PRK08579 567 AITVCNKCGRST--------TGLYTRCPRCGS 590 (625)
T ss_pred CCccCCCCCCcc--------CCCCCcCcCCCC
Confidence 478999999853 123578999996
No 392
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=27.30 E-value=39 Score=33.58 Aligned_cols=30 Identities=17% Similarity=0.466 Sum_probs=21.1
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCC
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNP 140 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p 140 (299)
...-|+.||.-.. +.+..||.||..-|.+.
T Consensus 220 ~l~~C~~Cd~l~~--------~~~a~CpRC~~~L~~~~ 249 (419)
T PRK15103 220 GLRSCSCCTAILP--------ADQPVCPRCHTKGYVRR 249 (419)
T ss_pred CCCcCCCCCCCCC--------CCCCCCCCCCCcCcCCC
Confidence 4556999998631 23458999999877544
No 393
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=26.21 E-value=36 Score=33.33 Aligned_cols=37 Identities=24% Similarity=0.399 Sum_probs=23.6
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 93 AAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
+|-.+..-.--..||+.||..... .......||.||.
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 445555555566899999932221 2345678999995
No 394
>PRK06450 threonine synthase; Validated
Probab=26.21 E-value=35 Score=32.76 Aligned_cols=22 Identities=27% Similarity=0.733 Sum_probs=15.1
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.|.+||+.... .....|+.||-
T Consensus 5 ~C~~Cg~~~~~-------~~~~~C~~cg~ 26 (338)
T PRK06450 5 VCMKCGKERES-------IYEIRCKKCGG 26 (338)
T ss_pred EECCcCCcCCC-------cccccCCcCCC
Confidence 69999988522 22467998974
No 395
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.20 E-value=22 Score=33.32 Aligned_cols=23 Identities=30% Similarity=0.778 Sum_probs=16.9
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
-+|+.||+++... ...|..||..
T Consensus 4 FhC~~CgQ~v~Fe--------N~~C~~Cg~~ 26 (349)
T COG4307 4 FHCPNCGQRVAFE--------NSACLSCGSA 26 (349)
T ss_pred ccCCCCCCeeeec--------chHHHhhhhH
Confidence 4799999996542 3579999854
No 396
>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=26.07 E-value=19 Score=25.72 Aligned_cols=14 Identities=29% Similarity=0.819 Sum_probs=8.8
Q ss_pred eecCCCCceeecCC
Q 022283 127 AICTVCGKIAYQNP 140 (299)
Q Consensus 127 ~~C~~Cg~~~y~~p 140 (299)
.+||+||-..-++|
T Consensus 42 ~~CPNCgGelv~RP 55 (57)
T PF06906_consen 42 GVCPNCGGELVRRP 55 (57)
T ss_pred CcCcCCCCccccCC
Confidence 46777776655555
No 397
>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=26.02 E-value=59 Score=21.64 Aligned_cols=23 Identities=22% Similarity=0.744 Sum_probs=17.2
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
||+.||+.. +++....|..|+..
T Consensus 1 ~C~vC~~~~-------~~~~~i~C~~C~~~ 23 (51)
T PF00628_consen 1 YCPVCGQSD-------DDGDMIQCDSCNRW 23 (51)
T ss_dssp EBTTTTSSC-------TTSSEEEBSTTSCE
T ss_pred eCcCCCCcC-------CCCCeEEcCCCChh
Confidence 689999931 45678899999843
No 398
>PRK12860 transcriptional activator FlhC; Provisional
Probab=25.93 E-value=75 Score=28.22 Aligned_cols=42 Identities=17% Similarity=0.334 Sum_probs=31.7
Q ss_pred hHHHHHHHHhhhhc----CCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 90 PSSAAVHSAGNVLK----ISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 90 ~~~~a~~l~~w~~~----~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
-+.+|..|+++... ..-|..||+....... +......|+-|.
T Consensus 116 s~tRAw~LvRf~~s~~L~l~~C~~Cgg~fv~~~~--e~~~~f~CplC~ 161 (189)
T PRK12860 116 DLTRAWTLVRFFDAGMLQLARCCRCGGKFVTHAH--DLRHNFVCGLCQ 161 (189)
T ss_pred cHHHHHHHHHHhcCCCeeeccCCCCCCCeecccc--ccCCCCcCCCCC
Confidence 36789999888774 5679999999764422 445678999997
No 399
>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=25.87 E-value=38 Score=26.43 Aligned_cols=34 Identities=24% Similarity=0.413 Sum_probs=19.5
Q ss_pred ceeecCCCCceeecCCcEEEEEEEeeCCEEEEEEeecCC
Q 022283 125 MRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEP 163 (299)
Q Consensus 125 ~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr~~~p 163 (299)
....|++||..++..-. +-.=+++++|+..+.-|
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 56789999988773220 00114566777655433
No 400
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.86 E-value=32 Score=27.67 Aligned_cols=22 Identities=18% Similarity=0.042 Sum_probs=15.5
Q ss_pred CCCHHHHHHHHHHHHhCCceeec
Q 022283 178 GESAAEGAIRETWEEARADVEVQ 200 (299)
Q Consensus 178 GEs~eeAa~REv~EEtGl~v~~~ 200 (299)
-||+|.| .|-.+-|.|-..+++
T Consensus 82 aes~EHA-~RIAK~eIGk~L~~i 103 (115)
T COG1885 82 AESDEHA-ERIAKAEIGKALKDI 103 (115)
T ss_pred CCCHHHH-HHHHHHHHhhHhhcC
Confidence 4777765 677888888766544
No 401
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=25.78 E-value=15 Score=28.30 Aligned_cols=29 Identities=28% Similarity=0.688 Sum_probs=20.7
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
..++.-|-+||..-... ....|..||+..
T Consensus 13 nkshtlC~RCG~~syH~-------QKstC~~CGYpa 41 (92)
T KOG3475|consen 13 NKSHTLCRRCGRRSYHI-------QKSTCSSCGYPA 41 (92)
T ss_pred ccchHHHHHhCchhhhh-------hcccccccCCcc
Confidence 46678899999985433 356799998543
No 402
>PF14369 zf-RING_3: zinc-finger
Probab=25.55 E-value=42 Score=21.37 Aligned_cols=26 Identities=15% Similarity=0.519 Sum_probs=15.9
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
||-.|.......... ++ ...||.|+-
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 788898886654221 11 125999974
No 403
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=25.46 E-value=49 Score=31.41 Aligned_cols=31 Identities=16% Similarity=0.470 Sum_probs=20.7
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
+|+.|..... ....+.......|+.||.+.-
T Consensus 2 ~c~~C~~~~~-~~V~d~~~gdtvC~~CGlVl~ 32 (308)
T KOG1597|consen 2 TCPDCKRHPE-NLVEDHSAGDTVCSECGLVLE 32 (308)
T ss_pred CCCCCCCCCC-CeeeeccCCceecccCCeeec
Confidence 6888888876 222234445679999997553
No 404
>PHA02998 RNA polymerase subunit; Provisional
Probab=25.21 E-value=54 Score=28.93 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=20.5
Q ss_pred cCCCCcCCCCCCccc-----ccCCCC-cceeecCCCCceeec
Q 022283 103 KISFCQWCGGQTKHE-----VPHGEE-KMRAICTVCGKIAYQ 138 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~-----~~~~~~-~~~~~C~~Cg~~~y~ 138 (299)
...-||.||+.-... ...++. -.-..|..||..+-|
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 456799999873221 112121 133478999976654
No 405
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=25.06 E-value=40 Score=24.23 Aligned_cols=13 Identities=46% Similarity=0.825 Sum_probs=9.7
Q ss_pred CCcCCCCCCcccc
Q 022283 106 FCQWCGGQTKHEV 118 (299)
Q Consensus 106 fC~~CG~~~~~~~ 118 (299)
-||.||..+....
T Consensus 19 ~Cp~CG~~t~~~~ 31 (59)
T COG2260 19 KCPVCGGDTKVPH 31 (59)
T ss_pred cCCCCCCccccCC
Confidence 6888888876653
No 406
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=25.00 E-value=32 Score=23.92 Aligned_cols=15 Identities=33% Similarity=0.716 Sum_probs=11.7
Q ss_pred cCCCCcCCCCCCccc
Q 022283 103 KISFCQWCGGQTKHE 117 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~ 117 (299)
-.+|||.|+..+...
T Consensus 33 lkKycp~c~khtlhk 47 (50)
T PRK00504 33 LKKFCPRCNKHTLHK 47 (50)
T ss_pred EECcCCCCCCeEeee
Confidence 358999999987654
No 407
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.96 E-value=71 Score=29.31 Aligned_cols=49 Identities=12% Similarity=0.326 Sum_probs=31.3
Q ss_pred HHHHhhhhcCCC---CcCCCCCCccc----------------------ccCCCCcceeecCCCCceeecCCcEE
Q 022283 95 VHSAGNVLKISF---CQWCGGQTKHE----------------------VPHGEEKMRAICTVCGKIAYQNPKMV 143 (299)
Q Consensus 95 ~~l~~w~~~~~f---C~~CG~~~~~~----------------------~~~~~~~~~~~C~~Cg~~~y~~p~~v 143 (299)
+..+.|.++..| |.-|+.++... .|...+-...+||.|....||+...+
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 567789888766 66777777543 11112223367888988888876543
No 408
>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=24.71 E-value=47 Score=25.29 Aligned_cols=34 Identities=24% Similarity=0.472 Sum_probs=13.4
Q ss_pred cCCCCcCCCCCCccc--ccCCCCcceeecCCCCcee
Q 022283 103 KISFCQWCGGQTKHE--VPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~--~~~~~~~~~~~C~~Cg~~~ 136 (299)
+.--||.||+..... +.-.++.-...|..||..+
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 455689998552221 1111334567888887654
No 409
>PHA02031 putative DnaG-like primase
Probab=24.65 E-value=21 Score=33.40 Aligned_cols=44 Identities=23% Similarity=0.436 Sum_probs=29.5
Q ss_pred HHHHHH-hhhhcCCCCcCCCCCCcccccCCCCcceeecCCCCceeec
Q 022283 93 AAVHSA-GNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQ 138 (299)
Q Consensus 93 ~a~~l~-~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~ 138 (299)
+|..|+ +=..++++| ||......+..+.+.|..+|..|+...+.
T Consensus 11 ~~q~l~~g~~~r~~~~--~~~~~~~~~~~~~~~w~ayc~rc~~~~~~ 55 (266)
T PHA02031 11 QAQRLAVGQTGRFRHC--CGGGAAMTLYNNPDRWVAYCYRCKEGGKV 55 (266)
T ss_pred HHHHHhccccceeeec--cCCCceeEEecCcchHHHHHHhhcccchh
Confidence 444443 233456666 77776666666678899999999985553
No 410
>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=24.51 E-value=39 Score=34.32 Aligned_cols=24 Identities=29% Similarity=0.638 Sum_probs=16.6
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
..-.|.+||..... ...||.||..
T Consensus 239 ~~l~Ch~Cg~~~~~---------~~~Cp~C~s~ 262 (505)
T TIGR00595 239 GKLRCHYCGYQEPI---------PKTCPQCGSE 262 (505)
T ss_pred CeEEcCCCcCcCCC---------CCCCCCCCCC
Confidence 34568899987533 3579999864
No 411
>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=24.37 E-value=25 Score=29.57 Aligned_cols=24 Identities=25% Similarity=0.612 Sum_probs=17.7
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
.+-|+.||+..... .+..|++|..
T Consensus 3 l~nC~~CgklF~~~-------~~~iCp~C~~ 26 (137)
T TIGR03826 3 LANCPKCGRLFVKT-------GRDVCPSCYE 26 (137)
T ss_pred Cccccccchhhhhc-------CCccCHHHhH
Confidence 46799999986542 3468999974
No 412
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.36 E-value=41 Score=35.93 Aligned_cols=25 Identities=24% Similarity=0.570 Sum_probs=17.8
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
......|+.||... +....||.||.
T Consensus 677 n~~~~~C~~CG~~~---------~~~~~CP~CG~ 701 (735)
T PRK07111 677 NHPVDRCPVCGYLG---------VIEDKCPKCGS 701 (735)
T ss_pred CCCCeecCCCCCCC---------CcCccCcCCCC
Confidence 34567899999432 22478999996
No 413
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=24.20 E-value=28 Score=29.55 Aligned_cols=24 Identities=29% Similarity=0.659 Sum_probs=15.5
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
---.||..||-.- .-.|..||..+
T Consensus 116 P~r~fCaVCG~~S-----------~ysC~~CG~ky 139 (156)
T KOG3362|consen 116 PLRKFCAVCGYDS-----------KYSCVNCGTKY 139 (156)
T ss_pred CcchhhhhcCCCc-----------hhHHHhcCCce
Confidence 3457999999432 23578888554
No 414
>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=23.95 E-value=32 Score=33.72 Aligned_cols=28 Identities=32% Similarity=0.596 Sum_probs=19.6
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
..+|.+|+..+.... .......|| ||..
T Consensus 240 ~~~c~~C~~~~~~~~---~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 240 QTACEACGEPAVSED---AETACANCP-CGGR 267 (374)
T ss_pred hhhhcccCCcCCchh---hhhcCCCCC-CCCc
Confidence 458999999987652 122347899 9964
No 415
>PRK07591 threonine synthase; Validated
Probab=23.83 E-value=41 Score=33.26 Aligned_cols=23 Identities=22% Similarity=0.541 Sum_probs=15.6
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
-.|..||+.... + .. ..|+.||-
T Consensus 19 l~C~~Cg~~~~~-----~-~~-~~C~~cg~ 41 (421)
T PRK07591 19 LKCRECGAEYPL-----G-PI-HVCEECFG 41 (421)
T ss_pred EEeCCCCCcCCC-----C-CC-ccCCCCCC
Confidence 479999988532 1 22 77988973
No 416
>PF14149 YhfH: YhfH-like protein
Probab=23.82 E-value=11 Score=24.67 Aligned_cols=26 Identities=23% Similarity=0.511 Sum_probs=16.1
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCC
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVC 132 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~C 132 (299)
..+-|+.||+.+... ..-....|..|
T Consensus 12 p~K~C~~CG~~i~EQ----~E~Y~n~C~~C 37 (37)
T PF14149_consen 12 PPKKCTECGKEIEEQ----AECYGNECDRC 37 (37)
T ss_pred CCcccHHHHHHHHHH----HHHHhCcCCCC
Confidence 467899999987554 22334455554
No 417
>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=23.69 E-value=17 Score=35.40 Aligned_cols=63 Identities=16% Similarity=0.161 Sum_probs=30.0
Q ss_pred hhhhcCCCCcCCCCC-Ccccc--cCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEEEeecCCCCCceeece
Q 022283 99 GNVLKISFCQWCGGQ-TKHEV--PHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPA 172 (299)
Q Consensus 99 ~w~~~~~fC~~CG~~-~~~~~--~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPg 172 (299)
.|.--.-+|+.||.- +.... ..+.......|+.||+..- +-..+++.=|.=|-.++ ..|...+
T Consensus 169 ~y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~---------~~i~~g~gKL~WkvDW~--mRW~~lg 234 (360)
T PF01921_consen 169 TYSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGE---------VDITGGNGKLQWKVDWP--MRWAALG 234 (360)
T ss_dssp T--SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---E---------EETTTT-EEE-HHHHHH--HHHHHTT
T ss_pred CeeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEE---------EecCCCcccccCCCcCh--hhhhhcC
Confidence 455667899999993 22221 1234667789999997654 11234444455455443 5566654
No 418
>KOG0720 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=23.64 E-value=23 Score=35.62 Aligned_cols=64 Identities=17% Similarity=0.263 Sum_probs=37.6
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEeeCCEEEEEEeecCCCCCceeeceEEee
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIEHDKKILLCKRKIEPSYGLWTLPAGYME 176 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~~~~kILL~rr~~~p~~g~w~lPgG~VE 176 (299)
.+..||..||.........-.-..++.|..||..|=. .+|.|+..++...-..-.|.+--|.|-
T Consensus 325 ~ntI~CskC~n~H~r~~T~rs~s~AR~C~~C~~~H~A-----------Kdgdiw~Ek~hlgl~~tyy~c~DgkVY 388 (490)
T KOG0720|consen 325 RNTIFCSKCGNTHFRVLTSRSPSQARWCAECGVKHPA-----------KDGDIWAEKSHLGLTPTYYACMDGKVY 388 (490)
T ss_pred HhheehhhhcCcceeeeecCChhhhHHHHHhCccCcc-----------ccCCEeeeehhccccceeeeecCCceE
Confidence 4678999999985444332244567899999976542 235555555442211334555555553
No 419
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.40 E-value=45 Score=35.13 Aligned_cols=26 Identities=23% Similarity=0.463 Sum_probs=19.1
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
......|+.||... +....||.||..
T Consensus 623 n~~~~~C~~CG~~~---------g~~~~CP~CG~~ 648 (656)
T PRK08270 623 TPTFSICPKHGYLS---------GEHEFCPKCGEE 648 (656)
T ss_pred CCCCcccCCCCCcC---------CCCCCCcCCcCc
Confidence 44678999999631 235789999954
No 420
>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=23.17 E-value=36 Score=29.77 Aligned_cols=44 Identities=18% Similarity=0.362 Sum_probs=21.7
Q ss_pred chHHHHHHHHhhhhc----CCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 89 HPSSAAVHSAGNVLK----ISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 89 ~~~~~a~~l~~w~~~----~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
--+.+|..|++.... ...|..||........ +-.....|+-|.-
T Consensus 115 Ls~tRAW~L~R~~~sg~l~l~~C~~C~~~fv~~~~--~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 115 LSLTRAWTLARFFDSGMLQLAPCRRCGGHFVTHAH--DPRHSFVCPFCQP 162 (175)
T ss_dssp S-HHHHHHHHHHHHTTSEEEEE-TTT--EEEEESS----SS----TT---
T ss_pred ccHHHHHHHHHHHhcCCccccCCCCCCCCeECcCC--CCCcCcCCCCCCC
Confidence 346788888877664 6789999999765422 3345678888873
No 421
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.86 E-value=52 Score=35.03 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=19.0
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
....+|+.||..=+... .+....||.||..
T Consensus 639 ~~~~~C~~CG~~Ge~~~----~~~~~~CP~CG~~ 668 (711)
T PRK09263 639 TPIDECYECGFTGEFEC----TEKGFTCPKCGNH 668 (711)
T ss_pred CCCcccCCCCCCccccC----CCCCCcCcCCCCC
Confidence 46789999997422211 1122689999963
No 422
>KOG0648 consensus Predicted NUDIX hydrolase FGF-2 and related proteins [Signal transduction mechanisms]
Probab=22.86 E-value=1.3e+02 Score=28.70 Aligned_cols=48 Identities=21% Similarity=0.131 Sum_probs=37.5
Q ss_pred eeCCEEEEEEeecCCCCCceeeceEEeeCCCCHHHHHHHHHHHHhCCcee
Q 022283 149 EHDKKILLCKRKIEPSYGLWTLPAGYMEIGESAAEGAIRETWEEARADVE 198 (299)
Q Consensus 149 ~~~~kILL~rr~~~p~~g~w~lPgG~VE~GEs~eeAa~REv~EEtGl~v~ 198 (299)
...+..+++...+.... .|.. .|.++.++++.+++.|+|.|++|....
T Consensus 39 ~~~d~~~f~~~l~~Sl~-~W~~-~Gr~~iwl~l~~~~~~lV~~a~~~gf~ 86 (295)
T KOG0648|consen 39 EPMDEKLFIEELRASLQ-KWYL-QGRKGIWLKLPEELARLVEEAAKYGFD 86 (295)
T ss_pred CCCCHHHHHHHHHHHHH-HHHH-ccCcccceechHHHHhHHHHHHhcCcE
Confidence 45566666654443224 7998 999999999999999999999998654
No 423
>PRK03922 hypothetical protein; Provisional
Probab=22.66 E-value=42 Score=27.19 Aligned_cols=22 Identities=18% Similarity=0.051 Sum_probs=15.3
Q ss_pred CCCHHHHHHHHHHHHhCCceeec
Q 022283 178 GESAAEGAIRETWEEARADVEVQ 200 (299)
Q Consensus 178 GEs~eeAa~REv~EEtGl~v~~~ 200 (299)
-||.|.| .|-.+-|.|-..+++
T Consensus 82 Aes~EHA-~RIAK~eIG~aL~dv 103 (113)
T PRK03922 82 AESEEHA-SRIAKSEIGKALRDI 103 (113)
T ss_pred cCCHHHH-HHHHHHHHhhHHhcC
Confidence 3666664 678888888776554
No 424
>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=22.49 E-value=47 Score=32.70 Aligned_cols=21 Identities=19% Similarity=0.412 Sum_probs=15.2
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
.|++||+... . + ....|+.|+
T Consensus 4 ~C~~Cg~~~~-~----~--~~~~C~~c~ 24 (398)
T TIGR03844 4 RCPGCGEVLP-D----H--YTLSCPLDC 24 (398)
T ss_pred EeCCCCCccC-C----c--cccCCCCCC
Confidence 6999998863 1 1 257899886
No 425
>PRK07220 DNA topoisomerase I; Validated
Probab=22.39 E-value=57 Score=34.86 Aligned_cols=33 Identities=18% Similarity=0.356 Sum_probs=15.5
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
..||.||.++....-.+...+-..||.|.+..+
T Consensus 636 ~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~~~~ 668 (740)
T PRK07220 636 KVCEAHGLNHIRIINGGKRPWDLGCPQCNFIEW 668 (740)
T ss_pred CCCCCCCCceEEEEecCCccceeeCCCCCCccc
Confidence 468888764332211111112346777765443
No 426
>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=21.94 E-value=55 Score=22.31 Aligned_cols=26 Identities=35% Similarity=0.678 Sum_probs=17.6
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
+.|..|++++... ..+..|..||.+.
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 3467788887653
No 427
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=21.81 E-value=47 Score=35.46 Aligned_cols=24 Identities=29% Similarity=0.679 Sum_probs=16.2
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
..-.|..||..- . ....||+||..
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 455788888872 1 23578988854
No 428
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.72 E-value=31 Score=31.65 Aligned_cols=18 Identities=28% Similarity=0.313 Sum_probs=12.6
Q ss_pred hhhcCCCCcCCCCCCccc
Q 022283 100 NVLKISFCQWCGGQTKHE 117 (299)
Q Consensus 100 w~~~~~fC~~CG~~~~~~ 117 (299)
+....--||.|+......
T Consensus 15 f~kk~ieCPvC~tkFkke 32 (267)
T COG1655 15 FYKKTIECPVCNTKFKKE 32 (267)
T ss_pred HhhceeccCcccchhhhh
Confidence 334556799999987544
No 429
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=21.68 E-value=70 Score=20.08 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=5.0
Q ss_pred CCcCCCCCC
Q 022283 106 FCQWCGGQT 114 (299)
Q Consensus 106 fC~~CG~~~ 114 (299)
.||.||--.
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 477777653
No 430
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=21.65 E-value=29 Score=23.97 Aligned_cols=11 Identities=27% Similarity=0.797 Sum_probs=6.0
Q ss_pred CCcCCCCCCcc
Q 022283 106 FCQWCGGQTKH 116 (299)
Q Consensus 106 fC~~CG~~~~~ 116 (299)
-||.||.++..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999999754
No 431
>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=21.64 E-value=55 Score=33.93 Aligned_cols=27 Identities=26% Similarity=0.602 Sum_probs=18.2
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCce
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKI 135 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~ 135 (299)
......|..||..- ......||.||..
T Consensus 521 n~~~~~C~~CG~~g--------~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 521 NPPVDVCEDCGYTG--------EGLNDKCPKCGSH 547 (579)
T ss_pred ccCCccCCCCCCCC--------CCCCCcCcCCCCc
Confidence 34578899999631 1123689999964
No 432
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.59 E-value=51 Score=34.78 Aligned_cols=24 Identities=29% Similarity=0.598 Sum_probs=16.2
Q ss_pred CCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 104 ISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 104 ~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.-.|..||..... ...||.||...
T Consensus 408 ~l~Ch~Cg~~~~~---------~~~Cp~Cg~~~ 431 (679)
T PRK05580 408 RLRCHHCGYQEPI---------PKACPECGSTD 431 (679)
T ss_pred eEECCCCcCCCCC---------CCCCCCCcCCe
Confidence 3468899987432 24699998654
No 433
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.55 E-value=69 Score=31.04 Aligned_cols=41 Identities=22% Similarity=0.443 Sum_probs=29.1
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 93 AAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
.|..+-.-+..+.-||.||++-..++++.++...+.|--|+
T Consensus 21 ~aL~~~~~~~~~~~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 21 EALAIPGLKPGGHPCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred HHHhcccccCCCCCCCccCCccccccCCccCCccEEEEeec
Confidence 34445445555569999999988887665556677888777
No 434
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.51 E-value=50 Score=34.59 Aligned_cols=25 Identities=20% Similarity=0.560 Sum_probs=17.8
Q ss_pred hhcCCCCcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 101 VLKISFCQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 101 ~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
......|+.||..- +....||.||.
T Consensus 556 n~~~~~C~~CGy~g---------~~~~~CP~CG~ 580 (618)
T PRK14704 556 NHPVDRCKCCSYHG---------VIGNECPSCGN 580 (618)
T ss_pred CCCCeecCCCCCCC---------CcCccCcCCCC
Confidence 44678899999631 12368999995
No 435
>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=21.41 E-value=67 Score=19.09 Aligned_cols=24 Identities=17% Similarity=0.355 Sum_probs=15.7
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
|+.|...+..- .+-..-.|..|..
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 77888887654 2344567877764
No 436
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=21.40 E-value=26 Score=24.84 Aligned_cols=31 Identities=16% Similarity=0.424 Sum_probs=22.4
Q ss_pred CCCcCCCCCCcccccCCCCcceeecCCCCceee
Q 022283 105 SFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAY 137 (299)
Q Consensus 105 ~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y 137 (299)
--|..|++-+... ++.+.....||.|..+.+
T Consensus 5 iRC~~CnKlLa~a--~~~~yle~KCPrCK~vN~ 35 (60)
T COG4416 5 IRCAKCNKLLAEA--EGQAYLEKKCPRCKEVNE 35 (60)
T ss_pred eehHHHhHHHHhc--ccceeeeecCCccceeee
Confidence 4588898887554 334567789999987765
No 437
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=21.32 E-value=48 Score=29.77 Aligned_cols=40 Identities=25% Similarity=0.565 Sum_probs=25.6
Q ss_pred HHHHHHhhhhcCCCCcCCCCCCcccccCCCCcceeecCCCC
Q 022283 93 AAVHSAGNVLKISFCQWCGGQTKHEVPHGEEKMRAICTVCG 133 (299)
Q Consensus 93 ~a~~l~~w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg 133 (299)
+..+..+|.-....|..||++....... .......|..|+
T Consensus 138 ~lL~~~G~~p~l~~C~~Cg~~~~~~~f~-~~~gg~~c~~c~ 177 (247)
T PRK00085 138 RLLAELGYGLDLDHCAVCGAPGDHRYFS-PKEGGAVCSECG 177 (247)
T ss_pred HHHHHcCCccchhhHhcCCCCCCceEEe-cccCCccccccc
Confidence 3445567777888999999985521110 123356899897
No 438
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=21.20 E-value=70 Score=32.09 Aligned_cols=45 Identities=24% Similarity=0.478 Sum_probs=27.9
Q ss_pred HHHHhhhhcC-------CCCcCCCCCCcccc---cCCCCc--------ceeecCCCCcee-ecC
Q 022283 95 VHSAGNVLKI-------SFCQWCGGQTKHEV---PHGEEK--------MRAICTVCGKIA-YQN 139 (299)
Q Consensus 95 ~~l~~w~~~~-------~fC~~CG~~~~~~~---~~~~~~--------~~~~C~~Cg~~~-y~~ 139 (299)
++|++|..+- .-|+.||..+.... ++.+.+ ....|..||... ||+
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 4799998764 56999999983221 111111 346899998643 444
No 439
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=21.12 E-value=75 Score=30.83 Aligned_cols=33 Identities=21% Similarity=0.488 Sum_probs=20.9
Q ss_pred CCcCCCCCCcccccCCCCcceeecCCCCcee-ecCCcEEEEE
Q 022283 106 FCQWCGGQTKHEVPHGEEKMRAICTVCGKIA-YQNPKMVVGC 146 (299)
Q Consensus 106 fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~-y~~p~~vV~~ 146 (299)
-|+.||+.+... ...|..||... |......+.+
T Consensus 1 ~C~~Cg~~v~Fe--------Nt~C~~Cg~~LGf~p~~~~~~a 34 (343)
T PF10005_consen 1 SCPNCGQPVFFE--------NTRCLSCGSALGFDPDRREMVA 34 (343)
T ss_pred CCCCCCCcceeC--------CCccccCCccccCCCCCCcEEe
Confidence 399999997553 35799998755 5433333333
No 440
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=21.12 E-value=59 Score=28.99 Aligned_cols=30 Identities=30% Similarity=0.530 Sum_probs=19.8
Q ss_pred CcCCCCCCcc--cccCCCCcceeecCCCCcee
Q 022283 107 CQWCGGQTKH--EVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 107 C~~CG~~~~~--~~~~~~~~~~~~C~~Cg~~~ 136 (299)
|-.||.+... +....+...-..|++||...
T Consensus 3 CIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~va 34 (208)
T PF04161_consen 3 CIECGHPVKSLYRQYSPGNIRLTKCPNCGKVA 34 (208)
T ss_pred eccCCCcchhhhhccCCCcEEEeeccccCCcc
Confidence 8899999532 22222334556999999765
No 441
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=20.95 E-value=80 Score=23.13 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=21.0
Q ss_pred cCCCCcCCCCCCcccccCCCCcceeecCCCCceeecCCcEEEEEEEe
Q 022283 103 KISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIAYQNPKMVVGCLIE 149 (299)
Q Consensus 103 ~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~y~~p~~vV~~iv~ 149 (299)
.++=|-.|..-+. ...||.||...+..---.+++|++
T Consensus 4 ~~~AC~~C~~i~~----------~~~Cp~Cgs~~~S~~w~G~v~i~d 40 (64)
T PRK06393 4 QYRACKKCKRLTP----------EKTCPVHGDEKTTTEWFGFLIITE 40 (64)
T ss_pred hhhhHhhCCcccC----------CCcCCCCCCCcCCcCcceEEEEEC
Confidence 3566888876652 127999998754333333334443
No 442
>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=20.86 E-value=56 Score=23.00 Aligned_cols=17 Identities=35% Similarity=0.776 Sum_probs=12.7
Q ss_pred cCC-CCcCCCCCCccccc
Q 022283 103 KIS-FCQWCGGQTKHEVP 119 (299)
Q Consensus 103 ~~~-fC~~CG~~~~~~~~ 119 (299)
+.+ -||.||.++....|
T Consensus 15 TLk~~cp~cG~~T~~ahP 32 (53)
T PF04135_consen 15 TLKDKCPPCGGPTESAHP 32 (53)
T ss_dssp ESSSBBTTTSSBSEESSS
T ss_pred eCCCccCCCCCCCcCCcC
Confidence 344 79999999877643
No 443
>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=20.84 E-value=14 Score=23.51 Aligned_cols=28 Identities=29% Similarity=0.747 Sum_probs=13.6
Q ss_pred CcCCCCCCcccccCCCCcceeecCCCCc
Q 022283 107 CQWCGGQTKHEVPHGEEKMRAICTVCGK 134 (299)
Q Consensus 107 C~~CG~~~~~~~~~~~~~~~~~C~~Cg~ 134 (299)
|..||..-....-.+..+....|..||.
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 6778877544432233455557888874
No 444
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=20.40 E-value=47 Score=34.14 Aligned_cols=26 Identities=27% Similarity=0.538 Sum_probs=11.8
Q ss_pred hcCCCCcCCCCCCcccccCCCCcceeecCCCCcee
Q 022283 102 LKISFCQWCGGQTKHEVPHGEEKMRAICTVCGKIA 136 (299)
Q Consensus 102 ~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~Cg~~~ 136 (299)
.....|+.||... ++ ...||.||...
T Consensus 489 ~~~~~C~~CG~~~--------~~-~~~CP~CGs~~ 514 (546)
T PF13597_consen 489 PPIDICPDCGYIG--------GE-GDKCPKCGSEN 514 (546)
T ss_dssp --EEEETTT---S-----------EEE-CCC----
T ss_pred cCcccccCCCcCC--------CC-CCCCCCCCCcc
Confidence 3567899999752 23 67899999765
No 445
>PLN00209 ribosomal protein S27; Provisional
Probab=20.19 E-value=70 Score=24.78 Aligned_cols=9 Identities=22% Similarity=0.482 Sum_probs=4.3
Q ss_pred eeecCCCCc
Q 022283 126 RAICTVCGK 134 (299)
Q Consensus 126 ~~~C~~Cg~ 134 (299)
.-.|++|+.
T Consensus 36 ~VkCp~C~n 44 (86)
T PLN00209 36 DVKCQGCFN 44 (86)
T ss_pred EEECCCCCC
Confidence 334555554
No 446
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.17 E-value=43 Score=23.60 Aligned_cols=27 Identities=26% Similarity=0.662 Sum_probs=19.1
Q ss_pred hhhcCCCCcCCCCCCcccccCCCCcceeecCC
Q 022283 100 NVLKISFCQWCGGQTKHEVPHGEEKMRAICTV 131 (299)
Q Consensus 100 w~~~~~fC~~CG~~~~~~~~~~~~~~~~~C~~ 131 (299)
-...+.||=.||...... ......||.
T Consensus 23 LR~~~~YC~~Cg~~Y~d~-----~dL~~~CPG 49 (55)
T PF13821_consen 23 LREEHNYCFWCGTKYDDE-----EDLERNCPG 49 (55)
T ss_pred HHhhCceeeeeCCccCCH-----HHHHhCCCC
Confidence 445799999999996442 345567874
No 447
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=20.08 E-value=45 Score=23.35 Aligned_cols=14 Identities=7% Similarity=-0.002 Sum_probs=10.9
Q ss_pred CCCCcCCCCCCccc
Q 022283 104 ISFCQWCGGQTKHE 117 (299)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (299)
.+|||.|+..+...
T Consensus 37 kKycp~~~khtlhk 50 (53)
T PRK00595 37 KKYDPVLRKHVLHK 50 (53)
T ss_pred ECcCCCCCCEEeEE
Confidence 47999999886543
No 448
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=20.05 E-value=47 Score=32.82 Aligned_cols=14 Identities=21% Similarity=0.700 Sum_probs=11.4
Q ss_pred CCCCcCCCCCCccc
Q 022283 104 ISFCQWCGGQTKHE 117 (299)
Q Consensus 104 ~~fC~~CG~~~~~~ 117 (299)
.-|||+||+.+...
T Consensus 38 ~A~CPRC~~~l~~~ 51 (418)
T COG2995 38 SAYCPRCGHTLTRG 51 (418)
T ss_pred cccCCCCCCccccC
Confidence 35999999998664
Done!